Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 756 of 770
Found at i:239663980 original size:31 final size:31
Alignment explanation
Indices: 239663916--239663980 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
239663906 AAGGCACTAA
* *
239663916 GTGTGCATGCTGGAAAAATATGACACTATGT
1 GTGTGCAAGCTGGAAAAATATGACACTAGGT
* *
239663947 GTGTGCAAGCTGGAAAAATATGGCACTGGGT
1 GTGTGCAAGCTGGAAAAATATGACACTAGGT
239663978 GTG
1 GTG
239663981 CGAGCTCGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.26
Consensus pattern (31 bp):
GTGTGCAAGCTGGAAAAATATGACACTAGGT
Found at i:239667555 original size:19 final size:19
Alignment explanation
Indices: 239667515--239667555 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
239667505 TAGCTGTATA
*
239667515 ATTATTATTTTAATAAATT
1 ATTATTATTTTAATAAAGT
239667534 ATTATTACTTTTAAT-AAGT
1 ATTATTA-TTTTAATAAAGT
239667553 ATT
1 ATT
239667556 GATAAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTATTATTTTAATAAAGT
Found at i:239668703 original size:20 final size:20
Alignment explanation
Indices: 239668678--239668726 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
239668668 ATGTTAGTCC
* *
239668678 CATGAATAGTGGGGTCAACT
1 CATGAATAGTGGAGTCAAAT
*
239668698 CATGAACAGTGGAGTCAAAT
1 CATGAATAGTGGAGTCAAAT
239668718 CATGAATAG
1 CATGAATAG
239668727 CTATAACATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (20 bp):
CATGAATAGTGGAGTCAAAT
Found at i:239674772 original size:40 final size:40
Alignment explanation
Indices: 239674706--239674872 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
239674696 AAATTGAATG
* * *
239674706 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
239674745 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
239674785 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
239674825 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
239674865 ATATCCGG
1 ATATCCGG
239674873 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:239682999 original size:40 final size:39
Alignment explanation
Indices: 239682947--239683159 Score: 200
Period size: 40 Copynumber: 5.4 Consensus size: 39
239682937 CGATTGTCTT
* * *
239682947 GGGACATT-GCCCGGTTATAGTGATTCGCACAATTGCCTTC
1 GGGAC-TTAGCCCGGTT-TAGTAACTCGCACAAATGCCTTC
* * *
239682987 GAGAATTAGCCCGGATTTAGTAACTCGCACGAATGCCTTC
1 GGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGCCTTC
* *
239683027 GGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGCCTTC
* *
239683067 -GGACTTAACCCGGTTTTGGTAACT-GCACAAATGCCTTC
1 GGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGCCTTC
* * * *
239683105 GGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGCCTTC
1 GGGACTTAG-CCCGG-TTTAGTAAC-TCGCACAAATGCCTTC
239683146 GGGACTTAGCCCGG
1 GGGACTTAGCCCGG
239683160 ACACCATTCG
Statistics
Matches: 147, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
38 14 0.10
39 43 0.29
40 63 0.43
41 26 0.18
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (39 bp):
GGGACTTAGCCCGGTTTAGTAACTCGCACAAATGCCTTC
Found at i:239683082 original size:39 final size:40
Alignment explanation
Indices: 239682971--239683160 Score: 222
Period size: 40 Copynumber: 4.8 Consensus size: 40
239682961 TTATAGTGAT
* * * *
239682971 TCGCACAATTGCCTTCGAGAATTAGCCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
239683011 TCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* *
239683051 TCGCACAAATGCCTTC-GGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
239683090 T-GCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
239683129 TTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 -TCGCACAAATGCCTTCGGGACTTAACCCGGA
239683161 CACCATTCGA
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 14 0.11
39 42 0.32
40 49 0.38
41 25 0.19
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
Found at i:239683144 original size:79 final size:79
Alignment explanation
Indices: 239682981--239683160 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 79
239682971 TCGCACAATT
* * * * *
239682981 GCCTTCGAGAATTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTG
1 GCCTTCG-GACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTA
* *
239683046 GTAACTCGCACAAAT
65 GTAACTAGCACAAAA
* * * *
239683061 GCCTTCGGACTTAACCCGGTTTTGGTAACT-GCACAAATGCCTTCGGGAATTGACCCGGATTTAG
1 GCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAG
*
239683125 TCACTTAGCACAAAA
66 TAAC-TAGCACAAAA
239683140 GCCTTCGGGACTTAGCCCGGA
1 GCCTTC-GGACTTAGCCCGGA
239683161 CACCATTCGA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 32 0.38
79 33 0.39
80 19 0.23
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAG
TAACTAGCACAAAA
Found at i:239687656 original size:46 final size:44
Alignment explanation
Indices: 239687552--239687659 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
239687542 TGTCTTTGAC
** * * *
239687552 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
239687596 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
239687642 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
239687660 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:239693795 original size:46 final size:44
Alignment explanation
Indices: 239693691--239693798 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
239693681 TGTCTTTGAC
** * * *
239693691 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
239693735 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
239693781 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
239693799 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:239699912 original size:46 final size:44
Alignment explanation
Indices: 239699808--239699915 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
239699798 TGTCTTTGAC
** * * *
239699808 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
239699852 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
239699898 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
239699916 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:239706903 original size:40 final size:40
Alignment explanation
Indices: 239706803--239707056 Score: 326
Period size: 40 Copynumber: 6.5 Consensus size: 40
239706793 TGGATGATAA
* * *
239706803 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
239706843 -CGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
239706881 CTGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
239706921 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
239706960 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
239707000 CTGGGCTAAGTCCCAAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
239707039 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
239707057 TACTTGGTTG
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
37 1 0.01
38 43 0.23
39 54 0.28
40 93 0.49
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:239706947 original size:79 final size:80
Alignment explanation
Indices: 239706803--239707056 Score: 326
Period size: 79 Copynumber: 3.2 Consensus size: 80
239706793 TGGATGATAA
* * *
239706803 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T-CGGGC-AAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTT
239706865 GTGCG-AGTTACTATAT
65 GTGCGAAG-TACTATAT
* *
239706881 CTGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
239706945 TGCGAAGTACTATAT
66 TGCGAAGTACTATAT
* * *
239706960 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACTGGGCTAAGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
239707025 AGC--AGTAGCTATAT
66 TGCGAAGTA-CTATAT
**
239707039 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
239707057 TACTTGGTTG
Statistics
Matches: 157, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
77 1 0.01
78 51 0.32
79 85 0.54
80 20 0.13
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAAGTACTATAT
Found at i:239707013 original size:119 final size:117
Alignment explanation
Indices: 239706803--239707056 Score: 347
Period size: 119 Copynumber: 2.2 Consensus size: 117
239706793 TGGATGATAA
*
239706803 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCGGGCAAGTCCCGAAGGCATTTGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTAGTTCGGGCAAGTCCCGAAGGCATTTGTG
* * *
239706868 CGAGTTACTATATCTGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTA-CTATAT
66 CGAGTTACTATAACTGGGCTAAGTCCCAAAGGCATTGGAGC-AG-TAGCTATAT
*
239706921 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAAGT-ACTA-TATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGC-AAGTGACTAGT-T-CGGGC-AAGTCCCGAAGGCATT
*
239706983 TGTGCGAGTTACTATAACTGGGCTAAGTCCCAAAGGCATTTGAGCAGTAGCTATAT
62 TGTGCGAGTTACTATAACTGGGCTAAGTCCCAAAGGCATTGGAGCAGTAGCTATAT
**
239707039 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
239707057 TACTTGGTTG
Statistics
Matches: 122, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
116 1 0.01
117 28 0.23
118 36 0.30
119 57 0.47
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (117 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTAGTTCGGGCAAGTCCCGAAGGCATTTGTG
CGAGTTACTATAACTGGGCTAAGTCCCAAAGGCATTGGAGCAGTAGCTATAT
Found at i:239710558 original size:40 final size:40
Alignment explanation
Indices: 239710454--239710581 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
239710444 CGGAATATAA
** *
239710454 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
* * * *
239710494 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
*** * * *
239710534 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
239710574 CCGGATAT
1 CCGGATAT
239710582 CATTCAATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:239713070 original size:22 final size:22
Alignment explanation
Indices: 239713042--239713086 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
239713032 CGCTCGATGA
239713042 CCATCGGTTTGGGGGTGAAAGG
1 CCATCGGTTTGGGGGTGAAAGG
239713064 CCATCGGTTTGGGGGTGAAAGG
1 CCATCGGTTTGGGGGTGAAAGG
239713086 C
1 C
239713087 GGTGCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.44, T:0.22
Consensus pattern (22 bp):
CCATCGGTTTGGGGGTGAAAGG
Found at i:239720492 original size:20 final size:20
Alignment explanation
Indices: 239720465--239720511 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
239720455 TAAATATAAG
*
239720465 ATAATAAAC-AAATAAAAAC
1 ATAATAAACAAAAGAAAAAC
239720484 ATGAATAAACTAAAAGAAAAAC
1 AT-AATAAAC-AAAAGAAAAAC
239720506 ATAATA
1 ATAATA
239720512 CATGCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 7 0.29
21 4 0.17
22 11 0.46
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.17
Consensus pattern (20 bp):
ATAATAAACAAAAGAAAAAC
Found at i:239722236 original size:41 final size:40
Alignment explanation
Indices: 239722183--239722352 Score: 161
Period size: 41 Copynumber: 4.2 Consensus size: 40
239722173 AGTCCGACTC
*
239722183 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
* * *
239722222 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG-
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA
* * *
239722262 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A
239722307 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
239722346 TTTAGAC
1 -TTAGAC
239722353 CCCGATTAGC
Statistics
Matches: 107, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
39 5 0.05
40 18 0.17
41 51 0.48
42 19 0.18
43 10 0.09
44 1 0.01
45 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
Found at i:239730582 original size:41 final size:40
Alignment explanation
Indices: 239730529--239730698 Score: 161
Period size: 41 Copynumber: 4.2 Consensus size: 40
239730519 AGTCCGACTC
*
239730529 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
* * *
239730568 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG-
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA
* * *
239730608 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A
239730653 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
239730692 TTTAGAC
1 -TTAGAC
239730699 CCCGATTAGC
Statistics
Matches: 107, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
39 5 0.05
40 18 0.17
41 51 0.48
42 19 0.18
43 10 0.09
44 1 0.01
45 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
Found at i:239738857 original size:27 final size:28
Alignment explanation
Indices: 239738801--239738870 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
239738791 AAATTTGTAC
239738801 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
239738829 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
239738856 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
239738871 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:239738881 original size:27 final size:27
Alignment explanation
Indices: 239738801--239738882 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
239738791 AAATTTGTAC
* *
239738801 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
239738829 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
239738856 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
239738883 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:239747009 original size:27 final size:28
Alignment explanation
Indices: 239746953--239747022 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
239746943 AAATTTGTAC
239746953 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
239746981 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
239747008 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
239747023 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:239747033 original size:27 final size:27
Alignment explanation
Indices: 239746953--239747034 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
239746943 AAATTTGTAC
* *
239746953 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
239746981 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
239747008 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
239747035 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:239750070 original size:40 final size:40
Alignment explanation
Indices: 239750003--239750150 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 40
239749993 TTTAACCACA
* * **
239750003 AGCACAATTG-CTTCGGGTCTTAACCCGGATTTGGTAACT
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAATAACT
* *
239750042 TGCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACT
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAATAACT
* *
239750082 CGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAATCACT
1 AGCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATAACT
* * *
239750122 AGCATAAATGCCTTCGGGACTTAGCCCGG
1 AGCACAATTGCCTTCGGGTCTTAGCCCGG
239750151 GATCATTCAA
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
39 11 0.12
40 81 0.86
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAATAACT
Found at i:239758108 original size:39 final size:36
Alignment explanation
Indices: 239758018--239758162 Score: 121
Period size: 39 Copynumber: 3.8 Consensus size: 36
239758008 TTTAACCACA
* *
239758018 AGCACAATTGCCTTCGGGTCTTAACCCGGAT-TGGTAACT
1 AGCACAA-TGCCTTC-GGTCTTAGCCCGGATAT--AAACT
*
239758057 TGCACAATTGCCTTCGGGTCTTAGCCCGGATATACAACT
1 AGCACAA-TGCCTTC-GGTCTTAGCCCGGATATA-AACT
* *
239758096 CGCACGAATGCCTTCGGTCATAGCCCGGATATAATCACT
1 AGCAC-AATGCCTTCGGTCTTAGCCCGGATATAA--ACT
* *
239758135 AGCATAAATGCCTTCGGACTTAGCCCGG
1 AGCA-CAATGCCTTCGGTCTTAGCCCGG
239758163 GTATCATTCA
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
37 1 0.01
38 17 0.19
39 70 0.77
40 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (36 bp):
AGCACAATGCCTTCGGTCTTAGCCCGGATATAAACT
Found at i:239760060 original size:25 final size:25
Alignment explanation
Indices: 239760026--239760076 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
239760016 AAATTAAAAT
239760026 AAGCTATCATATTATTATGTTCATC
1 AAGCTATCATATTATTATGTTCATC
239760051 AAGCTATCATATTATTATGTTCATC
1 AAGCTATCATATTATTATGTTCATC
239760076 A
1 A
239760077 CCGAAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (25 bp):
AAGCTATCATATTATTATGTTCATC
Found at i:239761310 original size:53 final size:54
Alignment explanation
Indices: 239761247--239761452 Score: 240
Period size: 53 Copynumber: 3.9 Consensus size: 54
239761237 TTGGTAAGAT
* * *
239761247 AAGGATATCATGTAAGACCATGCCAAGGCAT-GCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGC
* * *
239761300 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGGC
* * * * *
239761355 AAAGG-TCCCATGTAAGACCATG-AAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGC
* * *
239761407 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTC
239761453 AAAAAGGAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
51 4 0.03
52 22 0.17
53 48 0.36
54 31 0.23
55 23 0.17
56 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGC
Found at i:239767083 original size:15 final size:14
Alignment explanation
Indices: 239767065--239767103 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
239767055 AACCTAACCC
239767065 AAAAAAAAACAAAGA
1 AAAAAAAAACAAA-A
*
239767080 AAAAAAAAAGAAAA
1 AAAAAAAAACAAAA
*
239767094 AGAAAAAAAC
1 AAAAAAAAAC
239767104 CTACCCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:239767085 original size:17 final size:17
Alignment explanation
Indices: 239767065--239767102 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
239767055 AACCTAACCC
*
239767065 AAAAAAAA-ACAAAGAA
1 AAAAAAAAGAAAAAGAA
239767081 AAAAAAAAGAAAAAGAA
1 AAAAAAAAGAAAAAGAA
239767098 AAAAA
1 AAAAA
239767103 CCTACCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAGAA
Found at i:239767099 original size:11 final size:11
Alignment explanation
Indices: 239767067--239767100 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
239767057 CCTAACCCAA
239767067 AAAAAAACAAAG
1 AAAAAAA-AAAG
239767079 AAAAAAAAAAG
1 AAAAAAAAAAG
239767090 AAAAAGAAAAA
1 AAAAA-AAAAA
239767101 AACCTACCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:239767115 original size:16 final size:17
Alignment explanation
Indices: 239767096--239767127 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
239767086 AAAGAAAAAG
239767096 AAAAAAACCT-ACCCCA
1 AAAAAAACCTAACCCCA
239767112 AAAAAAACCTAACCCC
1 AAAAAAACCTAACCCC
239767128 CCCCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.38, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAACCTAACCCCA
Found at i:239767176 original size:22 final size:24
Alignment explanation
Indices: 239767135--239767181 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
239767125 CCCCCCCAAA
239767135 AAAAAAAGAAGAAAAGAAAAACCT
1 AAAAAAAGAAGAAAAGAAAAACCT
*
239767159 AAAAAAA-AAGATAA-AAAAACCT
1 AAAAAAAGAAGAAAAGAAAAACCT
239767181 A
1 A
239767182 GCCACCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 7 0.32
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (24 bp):
AAAAAAAGAAGAAAAGAAAAACCT
Found at i:239767781 original size:41 final size:39
Alignment explanation
Indices: 239767650--239767788 Score: 99
Period size: 39 Copynumber: 3.5 Consensus size: 39
239767640 TTTTTTTAGG
* * *
239767650 TATT-TTATATATATTATGTATATATATTTTTTAATGCCA
1 TATTGTTATATATATTATATATATATA-TTTTAAATACCA
* * *
239767689 T-TAGTTATATAT-TTCTTATGTATATATTCTTAAATA-C-
1 TATTGTTATATATATT-ATATATATATATT-TTAAATACCA
*
239767726 TATTATATACATATATATATATATATATATATTTTAAATACCA
1 TATTGT-T--ATATATAT-TATATATATATATTTTAAATACCA
239767769 TATTGTGTATATATTATTAT
1 TATTGT-TATATA-TATTAT
239767789 TACAAATTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
37 1 0.01
38 8 0.11
39 23 0.30
41 21 0.28
42 16 0.21
43 7 0.09
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (39 bp):
TATTGTTATATATATTATATATATATATTTTAAATACCA
Found at i:239769742 original size:12 final size:12
Alignment explanation
Indices: 239769722--239769757 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
239769712 ATTCATTTAA
239769722 CATTCATGCATT
1 CATTCATGCATT
*
239769734 CATTTATGCATT
1 CATTCATGCATT
*
239769746 CATTCATTCATT
1 CATTCATGCATT
239769758 GCATATTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:239776749 original size:67 final size:65
Alignment explanation
Indices: 239776653--239777047 Score: 282
Period size: 67 Copynumber: 6.1 Consensus size: 65
239776643 GTTTTTCAAA
* * *
239776653 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTT
1 ATCAACTCATATTGCGAGAGATGAGTTGAGCCTC--GGCACGCTGAGGTATTTTTAATTTTTGTT
239776718 TT
64 TT
* *
239776720 ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGTT
1 ATCAACTCATATTGCGAGAGATGAGTTGAGCCTC--GGCACGCTGAGGTATTTTTAATTTTTGTT
*
239776785 TCAAA
64 T---T
* *
239776790 ATCAACTCATATTGCGAGA-AGTGAGTTGAG-CTCGGCACGCTGAGGTATTTTTAGTTTATGTTT
1 ATCAACTCATATTGCGAGAGA-TGAGTTGAGCCTCGGCACGCTGAGGTATTTTTAATTTTTGTTT
239776853 T
65 T
** * * * * * **
239776854 AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT-------TTTA---ATTTTT-GTTTTT-CA
1 --ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCACGCTGAGGTATTTTTAATTTTTGTT
**
239776907 AA
64 TT
* * *
239776909 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGCACGCTGAGGTATTTTCAATTTTTGTGTT
1 ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCACGCTGAGGTATTTTTAA-TTTT-TGTT
239776974 TT
64 TT
* * * * *
239776976 AATTTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGA-GTA-ATTTAATTTCTG
1 -A-TCAACTCATATTGCGAGAGATGAGTTGAGCCTC-GG-CACGCTGAGGTATTTTTAATTTTTG
239777039 TTTT
62 TTTT
*
239777043 GTCAA
1 ATCAA
239777048 GAATCAACTC
Statistics
Matches: 258, Mismatches: 44, Indels: 54
0.72 0.12 0.15
Matches are distributed among these distances:
53 29 0.11
56 5 0.02
57 6 0.02
60 4 0.02
63 5 0.02
65 7 0.03
66 26 0.10
67 93 0.36
68 4 0.02
69 39 0.15
70 33 0.13
71 7 0.03
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (65 bp):
ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCACGCTGAGGTATTTTTAATTTTTGTTTT
Found at i:239776880 original size:66 final size:68
Alignment explanation
Indices: 239776632--239776888 Score: 315
Period size: 67 Copynumber: 3.8 Consensus size: 68
239776622 GAGTTAAGCC
* *
239776632 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCT
239776697 GAGGTAT
62 GAGGTAT
* * * *
239776704 TTTCAATTTTTGTTTT--ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAG
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAG
239776767 GTAT
65 GTAT
* *
239776771 TTTTAATTTTTGTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAG-CTC-GGCACGCTGAG
1 TTTTAATTTTTGTTT-TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAG
239776834 GTAT
65 GTAT
* * ** *
239776838 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
239776889 TTTAATTTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
66 28 0.17
67 87 0.54
69 3 0.02
70 28 0.17
71 4 0.02
72 11 0.07
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (68 bp):
TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGG
TAT
Found at i:239776936 original size:189 final size:192
Alignment explanation
Indices: 239776720--239777149 Score: 529
Period size: 193 Copynumber: 2.2 Consensus size: 192
239776710 TTTTTGTTTT
* * *
239776720 ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT-
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC--GACACGCTGAGGTATTTTCAATTTTTGTG
* * *
239776784 TTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAG-CTC-GG-CACGCTGAGGTATTTTTAGTT
64 TTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGATGA-GTA-ATTTAATT
** **
239776846 TATG-TTT-T-A-AATTGACTCATATTGCGAGAGGTGAGTT-AAGCCTTTTAATTT-TTGTTTTT
127 TATGTTTTGTAAGAATCAACTCATATTGCGAGA-GTGAGTTGAA--CTTTTAATTTCTACTTTTT
239776905 CAAA
189 CAAA
* *
239776909 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGCACGCTGAGGTATTTTCAATTTTTGTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGACACGCTGAGGTATTTTCAATTTTTGTGTT
** * * * *
239776974 TTAATTTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGTAATTTAATTTCTG
66 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGATGAGTAATTTAATTTATG
*
239777039 TTTTGTCAAGAATCAACTCATATTGCGAGAGTGGGTTGAACTTTTAATTTCTACTTTTTCAAA
131 TTTTGT-AAGAATCAACTCATATTGCGAGAGTGAGTTGAACTTTTAATTTCTACTTTTTCAAA
*
239777102 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GACACGCTGAGGT
239777150 TTTAGTTTTT
Statistics
Matches: 209, Mismatches: 20, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
187 25 0.12
188 31 0.15
189 44 0.21
190 8 0.04
191 8 0.04
192 10 0.05
193 50 0.24
194 33 0.16
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (192 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGACACGCTGAGGTATTTTCAATTTTTGTGTT
CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGATGAGTAATTTAATTTATG
TTTTGTAAGAATCAACTCATATTGCGAGAGTGAGTTGAACTTTTAATTTCTACTTTTTCAAA
Found at i:239776961 original size:254 final size:255
Alignment explanation
Indices: 239776465--239777077 Score: 967
Period size: 256 Copynumber: 2.4 Consensus size: 255
239776455 TTTCAAGGAA
*
239776465 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTG-
239776530 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
65 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
239776595 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
130 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
239776660 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA-TTTT-TGTTTT
195 CATATTGCTAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
239776720 -ATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
239776784 TTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAG-CTC-GG-CACGCTGAGGTATTTTTAGTT
66 TTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTA---TT--TT
239776846 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAT
126 TA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAT
239776911 CAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGCACGCTGAGGTATTTTCAATTTTTGTGTTT
190 CAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTTTGTGTTT
239776975 T
255 T
* * * * *
239776976 AATTTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGA-GTA-ATTTAATTTCTG
1 AA-TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-T-
* *
239777039 TTTTGTCAAGAATCAACTCATATTGCGAG-AGTGGGTTGA
63 TGTT-TCAA-AATCAACTCATATTGCGAGAAGTGAGTTGA
239777078 ACTTTTAATT
Statistics
Matches: 336, Mismatches: 8, Indels: 24
0.91 0.02 0.07
Matches are distributed among these distances:
250 12 0.04
251 2 0.01
252 3 0.01
253 39 0.12
254 83 0.25
255 8 0.02
256 108 0.32
257 5 0.01
258 44 0.13
259 13 0.04
260 19 0.06
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (255 bp):
AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
TTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGTT
TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTC
ATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
Found at i:239777035 original size:69 final size:68
Alignment explanation
Indices: 239776889--239777077 Score: 222
Period size: 69 Copynumber: 2.7 Consensus size: 68
239776879 AGTTAAGCCT
* *
239776889 TTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGCACGCTGAG
1 TTTAATTTTTGTTTTT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACGATGAG
*
239776954 GTAT
65 GTAA
* *
239776958 TTTCAATTTTTGTGTTTT-AATTTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
1 TTT-AATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-CACGAT
239777022 GA-GTAA
62 GAGGTAA
* *
239777028 TTTAATTTCTGTTTTGTCAAGAATCAACTCATATTGCGAGA-GTGGGTTGA
1 TTTAATTTTTGTTTT-T-AA-AATCAACTCATATTGCGAGAGGTGAGTTGA
239777078 ACTTTTAATT
Statistics
Matches: 103, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
68 3 0.03
69 45 0.44
70 17 0.17
71 20 0.19
72 18 0.17
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (68 bp):
TTTAATTTTTGTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACGATGAGG
TAA
Found at i:239777110 original size:52 final size:54
Alignment explanation
Indices: 239777028--239777130 Score: 158
Period size: 53 Copynumber: 1.9 Consensus size: 54
239777018 CGATGAGTAA
* *
239777028 TTTAATTTCTGTTTTGTCAAGAATCAACTCATATTGCGAGA-GTGGGTTGAACT
1 TTTAATTTCTCTTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAACT
239777081 TTTAATTTCTACTTTT-TCAA-AATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTAATTTCT-CTTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGA
239777131 GCCTCGGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 20 0.43
53 22 0.48
54 4 0.09
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (54 bp):
TTTAATTTCTCTTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAACT
Found at i:239777206 original size:307 final size:319
Alignment explanation
Indices: 239776783--239777475 Score: 1083
Period size: 307 Copynumber: 2.2 Consensus size: 319
239776773 TTAATTTTTG
*
239776783 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAG-CTC-GGCACGCTGAGGTATTTTTAGTT
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGG---TTTTAG-T
239776846 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAT
62 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTCAAAAT
239776911 CAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGCACGCTGAGGTATTTTCAA-TTTTTGTGTT
126 CAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTTTTGTGTT
239776974 TTAATTT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGA-GTAATTT-AATTT
191 TTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTT
*
239777036 CTG-TT-TTG-TCAAGAATCAACTCATATTGCGAGA-GTGGGTTGAA-CTTTTAATTTCTACTT
256 CTGTTTATTGTTCAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTACTT
239777095 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTTTTAG-T-T-
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTTTTAGTTATG
*
239777157 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTTTCAAAATCAACT
66 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTCAAAATCAACT
239777222 CATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTTTTGTGTTTTAAT
131 CATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTTTTGTGTTTTAAT
* * *
239777287 TTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTT
196 TTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTG--
239777352 TTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTA
259 -----TTTA--TTGTTCAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTA
239777417 CTT
317 CTT
*
239777420 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGT
239777476 AATTTCAATT
Statistics
Matches: 352, Mismatches: 7, Indels: 30
0.90 0.02 0.08
Matches are distributed among these distances:
306 42 0.12
307 70 0.20
308 18 0.05
309 42 0.12
310 6 0.02
311 14 0.04
312 36 0.10
313 3 0.01
314 12 0.03
319 2 0.01
322 3 0.01
323 25 0.07
324 9 0.03
325 57 0.16
326 13 0.04
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (319 bp):
TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTTTTAGTTATG
TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTCAAAATCAACT
CATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTTTTGTGTTTTAAT
TTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTT
TATTGTTCAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTACTT
Found at i:239777561 original size:76 final size:73
Alignment explanation
Indices: 239777424--239777563 Score: 208
Period size: 74 Copynumber: 1.9 Consensus size: 73
239777414 CTACTTTTTC
* *
239777424 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCCGAGGTAATTTCAATTTCT
239777489 GTTGTCAA
66 GTTGTCAA
* * *
239777497 AAAATCAACTCGTATTGGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATT
1 AAAATCAACTCATATT-GCGAGAGGCGAGTTGAGCCTCAGG--ACACGCCGAGGTAATTTCAATT
239777562 TC
63 TC
239777564 CGTTTTTCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
73 15 0.25
74 22 0.37
76 22 0.37
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCCGAGGTAATTTCAATTTCT
GTTGTCAA
Found at i:239777796 original size:164 final size:162
Alignment explanation
Indices: 239777424--239777897 Score: 642
Period size: 165 Copynumber: 2.9 Consensus size: 162
239777414 CTACTTTTTC
239777424 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * * *
239777489 GTTGTCAAAAAATCAACTCGTATTGGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAT
66 GTT-TC-AAAAATCAACTCGTATT-GCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTAT
* *
239777554 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAAA
128 TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAA
*
239777589 AAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTCAGGACACGCTAAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
239777653 GTTTC-AAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACG-TGAGGTATTTT
66 GTTTCAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTT
*
239777716 C-ATTTCCATTTTTCAATTTCTGCATTTCAAAAAAAA
131 CAATTTCCGTTTTTCAATTTCTGCATTTC-----AAA
*
239777752 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTTAATTTCAATTT-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG-TAATTTCAATTTC
* * ** *
239777816 TGTTTTCAAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTTCA-A--ACACGTTGAGGTA
65 TG-TTTCAAAAA-TCAACTCGTATTGCGAGAGGTGAGTTGAGCC-TCAGATCACACGCTGAGGTA
*
239777878 -TTTCAATTTCTGTTTTTCAA
127 TTTTCAATTTCCGTTTTTCAA
239777898 AAAATCAACT
Statistics
Matches: 280, Mismatches: 16, Indels: 25
0.87 0.05 0.08
Matches are distributed among these distances:
158 24 0.09
159 11 0.04
160 28 0.10
161 16 0.06
163 38 0.14
164 50 0.18
165 58 0.21
166 24 0.09
167 28 0.10
168 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (162 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTCAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTT
CAATTTCCGTTTTTCAATTTCTGCATTTCAAA
Found at i:239777834 original size:73 final size:73
Alignment explanation
Indices: 239777750--239777936 Score: 229
Period size: 73 Copynumber: 2.6 Consensus size: 73
239777740 TTTCAAAAAA
*
239777750 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTTAATTTCAATT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGG-T-ATTTCAATT
239777815 T-TG-TTTTC
64 TCTGTTTTTC
* * * ** *
239777823 AAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTTC-AAACACGTTGAGGTATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-TCGGGACACGCTGAGGTATTTCAATTT
239777887 CTGTTTTTC
65 CTGTTTTTC
* * *
239777896 AAAAAATCAACTCACATTGC-AGATGTGAGTTGAACCTCGGG
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG
239777937 TTACATGTCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
71 12 0.13
72 16 0.17
73 65 0.68
74 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTCAATTTC
TGTTTTTC
Found at i:239778056 original size:87 final size:87
Alignment explanation
Indices: 239777878--239778099 Score: 214
Period size: 81 Copynumber: 2.6 Consensus size: 87
239777868 CGTTGAGGTA
* * * * *
239777878 TTTCAATTTCTGTTTTTCAAAAAATCAACTCACATTGC-AGATGTGAGTTGAACCTCGGGTTACA
1 TTTCAA-TTCTG-TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACA
239777942 TGTCGACGGTATTTTAAAATCTGTT
64 TGTCGAC-GTATTTTAAAATCTGTT
* *
239777967 TTTCAAATTCTGTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGCTCACGT
1 TTTC-AATTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACAT
**
239778030 G-CTGAC-TATTTTCAATTTCTGTT
65 GTC-GACGTATTTT-AAAATCTGTT
*
239778053 TTT---TT-T-TTTTCAAAAAATTC-ACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTCAATTCTGTTTTCAAAAAA-TCAACTCATATTGCGAGAAGTGAGTTGAGC
239778100 TTTTAATTCT
Statistics
Matches: 117, Mismatches: 10, Indels: 20
0.80 0.07 0.14
Matches are distributed among these distances:
80 5 0.04
81 32 0.27
82 4 0.03
85 6 0.05
86 12 0.10
87 27 0.23
88 20 0.17
89 9 0.08
90 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (87 bp):
TTTCAATTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATG
TCGACGTATTTTAAAATCTGTT
Found at i:239778121 original size:28 final size:29
Alignment explanation
Indices: 239778081--239778136 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
239778071 TCACTCATAT
239778081 TGCGAGAGGTGAGTTGAG-CTTTTAATTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTC
*
239778109 TGCGAGAGTTGAGTTGAGTCTTTTAATT
1 TGCGAGAGGTGAGTTGAGTCTTTTAATT
239778137 TCTGTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.39
Consensus pattern (29 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTC
Found at i:239782124 original size:40 final size:40
Alignment explanation
Indices: 239782080--239782189 Score: 125
Period size: 40 Copynumber: 2.7 Consensus size: 40
239782070 ACTATGTTTG
* *
239782080 GCACTTAGTGTGCGTTTTGAGATAGCTTTGGCTATATATA
1 GCACTTAGTGTGCGTATTGAGATAGCTTCGGCTATATATA
* *
239782120 GCACTTAGTGTGCG-AGTTG-GAATAGCTTCGGCTATATGTG
1 GCACTTAGTGTGCGTA-TTGAG-ATAGCTTCGGCTATATATA
* *
239782160 GCACTAAGTGTACGATATTGAGATAGCTTC
1 GCACTTAGTGTGCG-TATTGAGATAGCTTC
239782190 AGCTTAATGT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
39 1 0.02
40 45 0.76
41 11 0.19
42 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (40 bp):
GCACTTAGTGTGCGTATTGAGATAGCTTCGGCTATATATA
Found at i:239782200 original size:41 final size:44
Alignment explanation
Indices: 239782141--239782237 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 44
239782131 GCGAGTTGGA
* *
239782141 ATAGCTTCGGC-TATA-TG-TGGCACTAAGTGTACGATATTGAG
1 ATAGCTTCAGCTTATAGTGATGGCACTAAGTGTACGATATCGAG
* * **
239782182 ATAGCTTCAGCTTA-ATGTGATGGCATTAAGTGTGCGATATCGTT
1 ATAGCTTCAGCTTATA-GTGATGGCACTAAGTGTACGATATCGAG
239782226 ATAGCTTCAGCT
1 ATAGCTTCAGCT
239782238 AATCATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
41 11 0.24
42 2 0.04
43 2 0.04
44 31 0.67
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (44 bp):
ATAGCTTCAGCTTATAGTGATGGCACTAAGTGTACGATATCGAG
Found at i:239788419 original size:39 final size:39
Alignment explanation
Indices: 239788342--239788526 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
239788332 GCTACTCGTT
* * *
239788342 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
*
239788382 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
*
239788421 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
239788461 CAAATGCCTTCGGATCTTAGTCCAGATATAGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
239788502 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
239788527 CATCATTCGA
Statistics
Matches: 129, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 36 0.28
40 82 0.64
41 11 0.09
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:239794703 original size:22 final size:23
Alignment explanation
Indices: 239794675--239794720 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
239794665 TGTTTTGTTG
239794675 GGAATGGAGGTTGTGG-ACAGCC
1 GGAATGGAGGTTGTGGAACAGCC
239794697 GGAATGGAGGTTGTGGAACAGCC
1 GGAATGGAGGTTGTGGAACAGCC
239794720 G
1 G
239794721 TATTAGTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.24, C:0.13, G:0.46, T:0.17
Consensus pattern (23 bp):
GGAATGGAGGTTGTGGAACAGCC
Found at i:239796457 original size:27 final size:31
Alignment explanation
Indices: 239796427--239796499 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
239796417 TGTCTTGAAT
*
239796427 TTGTTAGATATT-AATTA-TGT-TTC-AAGC
1 TTGTTAGATATTGAATTATTATGTTCTAAGC
239796454 TTGTTAGATATTGAATTATTATGTTCTAAGC
1 TTGTTAGATATTGAATTATTATGTTCTAAGC
*
239796485 TTGTTGGATATTGAA
1 TTGTTAGATATTGAA
239796500 ATGATTGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 12 0.30
28 5 0.12
29 2 0.05
30 3 0.08
31 18 0.45
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (31 bp):
TTGTTAGATATTGAATTATTATGTTCTAAGC
Found at i:239796478 original size:31 final size:31
Alignment explanation
Indices: 239796409--239796499 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
239796399 TGGATTCTGA
* *
239796409 AATTATTATGTCTTGAA-TTTGTTAGATATT-
1 AATTATTATGT-TTCAAGCTTGTTAGATATTG
239796439 -A--ATTATGTTTCAAGCTTGTTAGATATTG
1 AATTATTATGTTTCAAGCTTGTTAGATATTG
*
239796467 AATTATTATG-TTCTAAGCTTGTTGGATATTG
1 AATTATTATGTTTC-AAGCTTGTTAGATATTG
239796498 AA
1 AA
239796500 ATGATTGACA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
26 4 0.08
27 19 0.37
29 2 0.04
30 3 0.06
31 24 0.46
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.48
Consensus pattern (31 bp):
AATTATTATGTTTCAAGCTTGTTAGATATTG
Found at i:239797929 original size:19 final size:20
Alignment explanation
Indices: 239797905--239797946 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
239797895 CAAACACCAA
239797905 AAAAGTAAATCA-TTTCCAG
1 AAAAGTAAATCATTTTCCAG
239797924 AAAAGTAAATCATTTTCCAG
1 AAAAGTAAATCATTTTCCAG
239797944 AAA
1 AAA
239797947 TCATTTCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAGTAAATCATTTTCCAG
Found at i:239801666 original size:37 final size:37
Alignment explanation
Indices: 239801624--239801704 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
239801614 CGGGGTTTTA
* *
239801624 ACCCGGATAAAATCTCCACACGTGGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
*
239801661 ACCCGGACAGAATCTCCACACGTAGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
239801698 ACCCGGA
1 ACCCGGA
239801705 ATATATTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.21
Consensus pattern (37 bp):
ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
Found at i:239801963 original size:48 final size:48
Alignment explanation
Indices: 239801863--239801987 Score: 180
Period size: 48 Copynumber: 2.6 Consensus size: 48
239801853 TATTGCACAA
* * *
239801863 TAGCCATTCGGCTTTACCAAATATACAT-CCTCATACATATTTCATAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCATAT
* *
239801910 TAGCCATTTGGCTTTACCACATATACATATCTCATACATGTCTCATAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCATAT
* *
239801958 TAGCCATTCGGCTTTACCACACATATATAT
1 TAGCCATTCGGCTTTACCACATATACATAT
239801988 ATTTACCTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
47 26 0.38
48 43 0.62
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCATAT
Found at i:239805850 original size:38 final size:39
Alignment explanation
Indices: 239805795--239806134 Score: 351
Period size: 38 Copynumber: 8.7 Consensus size: 39
239805785 CACATCACCG
* *
239805795 GCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACG
1 GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACACA
* * * *
239805834 GCACGAA-ACCCTTCGGGATTTAGCCCGGATACATCACTA
1 GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACAC-A
* *
239805873 GCACGAATG--CTTCAGGACTTAGCCCGGATATAACACC
1 GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACACA
239805910 GCACGAATAG-CCTTCGGGACTTAGCCCGGATAT--CACTA
1 GCACGAAT-GCCCTTCGGGACTTAGCCCGGATATAACAC-A
* *
239805948 GCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACCG
1 GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACA-CA
* * *
239805988 GCACGAATGCCCTTCGGGACTTAGCCTGGATACATCACTA
1 GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACAC-A
* *
239806028 GCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACTA
1 GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACAC-A
* * *
239806068 ACACGATTG-CCTTCGGG-CTTAGCCCGGAATTAGTAACTC-
1 GCACGAATGCCCTTCGGGACTTAGCCCGG-A-TA-TAACACA
239806107 GCAC-AATTG-CCTTCGGGACTTAGCCCGG
1 GCACGAA-TGCCCTTCGGGACTTAGCCCGG
239806135 TTATCATCCG
Statistics
Matches: 257, Mismatches: 29, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
37 12 0.05
38 92 0.36
39 57 0.22
40 91 0.35
41 5 0.02
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (39 bp):
GCACGAATGCCCTTCGGGACTTAGCCCGGATATAACACA
Found at i:239805997 original size:115 final size:114
Alignment explanation
Indices: 239805776--239806095 Score: 349
Period size: 115 Copynumber: 2.7 Consensus size: 114
239805766 AGGCACAAAG
* * *
239805776 GCCCGAATACACATCACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACAC-GGCACGA
1 GCCCGGATACA-A-CACC-GCACGAATG-CCTTCGGGACTTAGCCCGGATAT--CACTAGCACGA
** * * *
239805840 AACCCTTCGGGATTTAGCCCGGATACATCACTAGCACGAATG-CTTCAGGACTTA
60 ATGCCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCCTTCAGGACTTA
*
239805894 GCCCGGATATAACACCGCACGAATAGCCTTCGGGACTTAGCCCGGATATCACTAGCACGAATGCT
1 GCCCGGATACAACACCGCACGAAT-GCCTTCGGGACTTAGCCCGGATATCACTAGCACGAATGC-
* * *
239805959 CTTCGGGACTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGACTTA
64 CTTCGGGACTTAGCCCGGATACAACACCAGCACGAATG-CCTTCAGGACTTA
* * * * *
239806011 GCCTGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAACACGATT
1 GCCCGGATACAACAC-CGCACGAATGC-CTTCGGGACTTAGCCCGG--ATATCACTAGCACGAAT
239806076 GCCTTCGGG-CTTAGCCCGGA
62 GCCTTCGGGACTTAGCCCGGA
239806096 ATTAGTAACT
Statistics
Matches: 175, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
113 3 0.02
114 8 0.05
115 63 0.36
116 5 0.03
117 26 0.15
118 46 0.26
119 7 0.04
120 17 0.10
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (114 bp):
GCCCGGATACAACACCGCACGAATGCCTTCGGGACTTAGCCCGGATATCACTAGCACGAATGCCT
TCGGGACTTAGCCCGGATACAACACCAGCACGAATGCCTTCAGGACTTA
Found at i:239806003 original size:40 final size:40
Alignment explanation
Indices: 239805790--239806134 Score: 349
Period size: 40 Copynumber: 8.8 Consensus size: 40
239805780 GAATACACAT
* *
239805790 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* * * * *
239805830 CA-CGGCACGAA-ACCCTTCGGGATTTAGCCCGGATACAT
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* *
239805868 CACTAGCACGAATG--CTTCAGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
239805906 CACC-GCACGAATAG-CCTTCGGGACTTAGCCCGGATAT--
1 CACCAGCACGAAT-GCCCTTCGGGACTTAGCCCGGATATAA
* *
239805943 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* * * *
239805983 CACCGGCACGAATGCCCTTCGGGACTTAGCCTGGATACAT
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* * *
239806023 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
* * *
239806063 CACTAACACGATTG-CCTTCGGG-CTTAGCCCGGAATTAGTAA
1 CACCAGCACGAATGCCCTTCGGGACTTAGCCCGG-A-TA-TAA
*
239806104 C-TC-GCAC-AATTG-CCTTCGGGACTTAGCCCGG
1 CACCAGCACGAA-TGCCCTTCGGGACTTAGCCCGG
239806135 TTATCATCCG
Statistics
Matches: 259, Mismatches: 33, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
37 12 0.05
38 91 0.35
39 58 0.22
40 95 0.37
41 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
Found at i:239808373 original size:37 final size:37
Alignment explanation
Indices: 239808331--239808411 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
239808321 CGGGGTTTTA
* *
239808331 ACCCGGATAAAATCTCCACACGTGGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
*
239808368 ACCCGGACAGAATCTCCACACGTAGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
239808405 ACCCGGA
1 ACCCGGA
239808412 ATATATTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.21
Consensus pattern (37 bp):
ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
Found at i:239808685 original size:48 final size:48
Alignment explanation
Indices: 239808570--239808695 Score: 180
Period size: 48 Copynumber: 2.6 Consensus size: 48
239808560 TATTGCACAA
* ** *
239808570 TAGCCATTCGGCTTTACCAAATATACATCCCTCATACATATTTCATAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCATAT
* *
239808618 TAGCCATTTGGCTTTACCACATATACATATCTCATACATGTCTCATAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCATAT
* *
239808666 TAGCCATTCGGCTTTACCACACATATATAT
1 TAGCCATTCGGCTTTACCACATATACATAT
239808696 ATTTACCTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATCTCATAT
Found at i:239813632 original size:39 final size:39
Alignment explanation
Indices: 239813532--239813632 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
239813522 TATGGTATTT
* * * *
239813532 AAATATATATATATATATATATGTATATAATAGTATTTAA
1 AAATATATACATA-ATATATATATATATAATAGCATTAAA
* * * *
239813572 GAATATATACATAAGAAATATATA-ACTAATGGCATTAAA
1 AAATATATACATAATATATATATATA-TAATAGCATTAAA
239813611 AAATATATACATAATATATATA
1 AAATATATACATAATATATATA
239813633 AAATACCTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.02
39 37 0.76
40 11 0.22
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (39 bp):
AAATATATACATAATATATATATATATAATAGCATTAAA
Found at i:239815028 original size:30 final size:30
Alignment explanation
Indices: 239814992--239815053 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
239814982 TTTTGAAAAA
239814992 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
239815022 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
239815052 CA
1 CA
239815054 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:239815100 original size:87 final size:84
Alignment explanation
Indices: 239814953--239815110 Score: 262
Period size: 87 Copynumber: 1.8 Consensus size: 84
239814943 GACTGGAGGT
239814953 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
239815018 CTCGCAGAAATTAAAAAGC
66 CTCGCAGAAATTAAAAAGC
* *
239815037 TCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAACAGAAATTAAAAGGCTTAACTCA
1 TCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTGAAAAACAGAAATTAAAAGACTCAACTCA
*
239815102 CCTCTCGCA
63 ACTCTCGCA
239815111 ACATGAGTTG
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
84 27 0.40
85 1 0.01
87 40 0.59
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (84 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
CTCGCAGAAATTAAAAAGC
Found at i:239815110 original size:57 final size:55
Alignment explanation
Indices: 239815022--239815145 Score: 178
Period size: 57 Copynumber: 2.2 Consensus size: 55
239815012 TCAACTCTCG
*
239815022 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAA-AA
1 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTG-A--TTTTTGAAACAA
* *
239815079 CAGAAATTAAAAGGCTTAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA
1 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA
*
239815134 CAAAAATTAAAA
1 CAGAAATTAAAA
239815146 TACCTCAGCG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
54 9 0.15
55 13 0.21
56 1 0.02
57 39 0.63
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (55 bp):
CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA
Found at i:239815474 original size:73 final size:72
Alignment explanation
Indices: 239815382--239815571 Score: 267
Period size: 72 Copynumber: 2.6 Consensus size: 72
239815372 ATTAAAAGGT
* * *
239815382 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAAAAATTGAAATTACCTCAT-CGTG
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGAAAAACAAAAATTGAAAATACCTC-TGCGTG
*
239815446 TCCTGAGGC
64 CCCTGAGGC
**
239815455 TCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACACAAAAATTGAAAATACCTCTGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA-ACAAAAATTGAAAATACCTCTGCGTGC
239815519 CCTGAGGC
65 CCTGAGGC
* *
239815527 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAAT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAT
239815572 AAAAAGGCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
71 4 0.04
72 69 0.66
73 31 0.30
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.26
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAAATACCTCTGCGTGCC
CTGAGGC
Found at i:239815527 original size:287 final size:288
Alignment explanation
Indices: 239815035--239815556 Score: 685
Period size: 288 Copynumber: 1.8 Consensus size: 288
239815025 AAATTAAAAA
* * *
239815035 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAACAGAAATTAAAAGGCTTAACT
1 GCTCAACTCACCTCTCGCAATATGAGCTGAA--TTTTTGAAAAAAAGAAATTAAAAGGCTTAACC
*
239815100 CACCTCTCGCAACATGAGTTGATTTTTGAAACAACAAAAATTAAAATACCTCAGCGTGACCTAAG
64 CACCTCTCGCAACATGAGTTGATTCTTGAAACAACAAAAATTAAAATACCTCAGCGTGACCTAAG
** * * * ** * *
239815165 GCTTGACTCACTTCTCACAGTTTGAGTCAAAATTTGAAACATAAACTAAAAATACTTCAGCGCGT
129 GCTCAACTCACCTCTCACAATATGAGTCAAAATTAAAAACAAAAACTAAAAATACCTCA-CGCGT
* * * *
239815230 GGCTTGAGGCTCGACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACATAATAATGAAAAC
193 GCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTCTTTCAAAAACATAATAATGAAAAC
239815295 AGAAATTGAAAATACCTCGGCGTGACCTGAG
258 AGAAATTGAAAATACCTCGGCGTGACCTGAG
239815326 GCTCAACTCACCTCTCGCAATATGAGCTG-A-TTTTGAAAAAGAAGAAATTAAAAGG-TTCAACC
1 GCTCAACTCACCTCTCGCAATATGAGCTGAATTTTTGAAAAA-AAGAAATTAAAAGGCTT-AACC
* * * * * *
239815388 CACCTCTCGCAATATGAGTTGATTCTTGACA-AACAAAAATTGAAATTACCTCATCGTGTCCTGA
64 CACCTCTCGCAACATGAGTTGATTCTTGAAACAACAAAAATT-AAAATACCTCAGCGTGACCTAA
* ** * * *
239815452 GGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTC-TGCG
128 GGCTCAACTCACCTCTCACAATATGAGTCAAAATTAAAA-ACAAAAACTAAAAATACCTCACGCG
239815516 TGCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATT
192 TGCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATT
239815557 TTGAAAAACC
Statistics
Matches: 198, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
287 62 0.31
288 91 0.46
289 16 0.08
290 1 0.01
291 28 0.14
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (288 bp):
GCTCAACTCACCTCTCGCAATATGAGCTGAATTTTTGAAAAAAAGAAATTAAAAGGCTTAACCCA
CCTCTCGCAACATGAGTTGATTCTTGAAACAACAAAAATTAAAATACCTCAGCGTGACCTAAGGC
TCAACTCACCTCTCACAATATGAGTCAAAATTAAAAACAAAAACTAAAAATACCTCACGCGTGCC
CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTCTTTCAAAAACATAATAATGAAAACAGA
AATTGAAAATACCTCGGCGTGACCTGAG
Found at i:239815586 original size:53 final size:53
Alignment explanation
Indices: 239815523--239815719 Score: 169
Period size: 53 Copynumber: 3.5 Consensus size: 53
239815513 GCGTGCCCTG
239815523 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAATAAAA
1 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAATAAAA
* * ** * *** ****
239815576 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTTAGCGTGCCCG
1 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTT-----TGAAAA-ACC--AAAAT-AAAA
* *
239815638 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
1 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAATAAAA
* *
239815691 AGGCTTAACTCACCTCTCGCAATATGAGT
1 AGGCTCAACTCACCTCTAGCAATATGAGT
239815720 CAATTTAAAA
Statistics
Matches: 108, Mismatches: 27, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
53 58 0.54
54 2 0.02
56 2 0.02
57 5 0.05
58 5 0.05
59 3 0.03
61 2 0.02
62 31 0.29
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (53 bp):
AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAATAAAA
Found at i:239815653 original size:62 final size:62
Alignment explanation
Indices: 239815576--239815780 Score: 202
Period size: 62 Copynumber: 3.5 Consensus size: 62
239815566 CAAAATAAAA
*
239815576 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTTAGCGTGCCCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTTAGCGTGCCCG
* * * **
239815638 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA--ACAAAA-A--TTA-------AA
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACTA-AAAATACCTTAGCGTGCCCG
* *
239815691 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACT-AAAATACCTCAGCGTGCCCCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTTAGCGTG-CCCG
*
239815753 AGGCTCAACTCACTTCTCGCAATATGAG
1 AGGCTCAACTCACCTCTCGCAATATGAG
239815781 CTGATTTTGA
Statistics
Matches: 112, Mismatches: 15, Indels: 32
0.70 0.09 0.20
Matches are distributed among these distances:
51 8 0.07
52 6 0.05
53 26 0.23
54 2 0.02
60 3 0.03
62 54 0.48
63 9 0.08
64 4 0.04
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (62 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTTAGCGTGCCCG
Found at i:239815705 original size:115 final size:114
Alignment explanation
Indices: 239815502--239815805 Score: 495
Period size: 115 Copynumber: 2.6 Consensus size: 114
239815492 ACAAAAATTG
239815502 AAAATACCTCT-GCGTGCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAC
1 AAAATACCT-TAGCGTGCCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAC
* *
239815566 CAAAATAAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACT
64 AAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACT
239815617 AAAAATACCTTAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
1 -AAAATACCTTAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
239815682 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACT
65 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACT
* * * *
239815732 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGCTGATTTTG-AAAACA
1 AAAATACCTTAGCGTG-CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
*
239815796 ACAATTAAAA
65 AAAATTAAAA
239815806 ATACATCAAC
Statistics
Matches: 179, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
114 30 0.17
115 132 0.74
116 17 0.09
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (114 bp):
AAAATACCTTAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAA
AAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACT
Found at i:239824116 original size:12 final size:12
Alignment explanation
Indices: 239824094--239824129 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
239824084 TGGGATATGC
*
239824094 AATGAATGAATG
1 AATGCATGAATG
*
239824106 GATGCATGAATG
1 AATGCATGAATG
239824118 AATGCATGAATG
1 AATGCATGAATG
239824130 TCAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:239824116 original size:16 final size:17
Alignment explanation
Indices: 239824090--239824121 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
239824080 AGTATGGGAT
239824090 ATGCAATGAATGAATGG
1 ATGCAATGAATGAATGG
239824107 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
239824122 CATGAATGTC
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:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (17 bp):
ATGCAATGAATGAATGG
Found at i:239826111 original size:2 final size:2
Alignment explanation
Indices: 239826062--239826092 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
239826052 TGGTATTTAA
239826062 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 A
239826093 ATAGTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239826164 original size:39 final size:39
Alignment explanation
Indices: 239826066--239826164 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
239826056 ATTTAAATAT
* * * *
239826066 ATATATATATATATATATATATATATAATAGTATTTAAGA
1 ATATATACATA-ATATATATATATATAATAGCATTAAAAA
* * *
239826106 ATATATACATAAGAAATATATA-ACTAATGGCATTAAAAA
1 ATATATACATAATATATATATATA-TAATAGCATTAAAAA
239826145 ATATATACATAATATATATA
1 ATATATACATAATATATATA
239826165 AAATACCTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 38 0.78
40 10 0.20
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (39 bp):
ATATATACATAATATATATATATATAATAGCATTAAAAA
Found at i:239828111 original size:28 final size:28
Alignment explanation
Indices: 239828067--239828146 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
239828057 CATACATGCT
* * *
239828067 TATGGCCTACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAAGCCCAATCACATCT-A
*
239828095 TATGGCCCATTAAGCCCAAATCACATCTA
1 TATGGCCCACTAAGCCC-AATCACATCTA
*
239828124 TATGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAAGCCCAATCAC
239828147 TTTTATAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 20 0.45
29 23 0.52
30 1 0.02
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAAGCCCAATCACATCTA
Found at i:239828153 original size:28 final size:28
Alignment explanation
Indices: 239828067--239828153 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 28
239828057 CATACATGCT
* * *
239828067 TATGGCCTACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTTA
* * *
239828095 TATGGCCCATTAAGCCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATTTA
*
239828124 TATGGCCCACTAGGCCCAATCACTTTTA
1 TATGGCCCACTAGGCCCAATCACATTTA
239828152 TA
1 TA
239828154 GTCATGCTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.28
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTTA
Found at i:239828380 original size:16 final size:16
Alignment explanation
Indices: 239828359--239828389 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
239828349 CCAAACTTTC
*
239828359 AGCTTTTTGGCATTTT
1 AGCTTTTCGGCATTTT
239828375 AGCTTTTCGGCATTT
1 AGCTTTTCGGCATTT
239828390 CGACTTTTTA
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:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (16 bp):
AGCTTTTCGGCATTTT
Found at i:239831343 original size:29 final size:29
Alignment explanation
Indices: 239831311--239831388 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
239831301 ATACCCTCCG
** *
239831311 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
239831340 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
239831369 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
239831389 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:239839192 original size:29 final size:29
Alignment explanation
Indices: 239839154--239839232 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
239839144 CATACCCTCG
* *
239839154 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
239839183 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
239839212 AGCACGCACACTTAGTGCCAT
1 AGCTCGCACACCCAGTGCCAT
239839233 CTCGTCACCG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCATATATTTCC
Found at i:239843435 original size:86 final size:86
Alignment explanation
Indices: 239843263--239843661 Score: 613
Period size: 86 Copynumber: 4.6 Consensus size: 86
239843253 NNNNNNNNNN
* * ** *
239843263 CCTGTTACCCTACTGTTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCC-CTAACTACTTA
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTG-CTCCACT-ACTACTTA
*
239843327 GGGAGATAAGATCTGTAATTCAA
64 GGGAGATAAGATCTGCAATTCAA
* *
239843350 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTTCTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTACTTAGG
239843415 GAGATAAGATCTGCAATTCAA
66 GAGATAAGATCTGCAATTCAA
* ** *
239843436 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCC-CTACTACTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTG-CTCCACTACTACTTAG
*
239843500 GGAGATAAGATCTGTAATTCAA
65 GGAGATAAGATCTGCAATTCAA
* *
239843522 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTTCTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTACTTAGG
239843587 GAGATAAGATCTGCAATTCAA
66 GAGATAAGATCTGCAATTCAA
*
239843608 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTGCTCCAC
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCAC
239843662 CATTCTTTGG
Statistics
Matches: 286, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
85 3 0.01
86 234 0.82
87 49 0.17
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (86 bp):
CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTACTTAGG
GAGATAAGATCTGCAATTCAA
Found at i:239843457 original size:42 final size:42
Alignment explanation
Indices: 239843308--239843629 Score: 220
Period size: 42 Copynumber: 7.5 Consensus size: 42
239843298 CGTCTTCGAT
* * *
239843308 CTGTTTCCCTAACTACTTAGGGAGATAAGATCTGTAATTCAAC
1 CTGTTACCCT-ACTGCTTAGGGAGATAAGATCTGCAATTCAAC
* * * ** * *
239843351 CTGTTACCCTACTGCTTAGGG-GTTTAAGGTTCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGAG-ATAA-GATCTGC-AATTCAAC
* *
239843395 CTGCT-CCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAAC
1 CTGTTACC-CTACTGCTTAGGGAGATAAGATCTGCAATTCAAC
* * ** * ** * *
239843437 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGAGATAA-GATCTGC-AATTCAAC
* * *
239843481 CTGTTTCCCTACTACTTAGGGAGATAAGATCTGTAATTCAAC
1 CTGTTACCCTACTGCTTAGGGAGATAAGATCTGCAATTCAAC
* * * ** * *
239843523 CTGTTACCCTACTGCTTAGGG-GTTTAAGGTTCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGAG-ATAA-GATCTGC-AATTCAAC
* *
239843567 CTGCT-CCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAAC
1 CTGTTACC-CTACTGCTTAGGGAGATAAGATCTGCAATTCAAC
239843609 CTGTTACCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGG
239843630 GTTTAAGGTT
Statistics
Matches: 202, Mismatches: 63, Indels: 29
0.69 0.21 0.10
Matches are distributed among these distances:
41 2 0.01
42 83 0.41
43 42 0.21
44 73 0.36
45 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.34
Consensus pattern (42 bp):
CTGTTACCCTACTGCTTAGGGAGATAAGATCTGCAATTCAAC
Found at i:239843550 original size:172 final size:173
Alignment explanation
Indices: 239843263--239843655 Score: 734
Period size: 172 Copynumber: 2.3 Consensus size: 173
239843253 NNNNNNNNNN
*
239843263 CCTGTTACCCTACTGTTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTAACTACTTAG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTAACTACTTAG
239843328 GGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
66 GGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
239843393 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAA
131 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAA
239843436 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCCCT-ACTACTTAG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTAACTACTTAG
239843500 GGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
66 GGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
239843565 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAA
131 ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAA
* ** *
239843608 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTG
239843656 CTCCACCATT
Statistics
Matches: 215, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
172 161 0.75
173 54 0.25
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (173 bp):
CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTAACTACTTAG
GGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
ATCTGCTCCACTTCTGCTTAGGGAGATAAGATCTGCAATTCAA
Found at i:239851526 original size:20 final size:20
Alignment explanation
Indices: 239851489--239851526 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
239851479 TGGGATAATT
*
239851489 GACTCATCATTTCTCTCTAG
1 GACTCATCATTTCGCTCTAG
239851509 GACTCCATCATTT-GCTCT
1 GACT-CATCATTTCGCTCT
239851527 TTCATCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (20 bp):
GACTCATCATTTCGCTCTAG
Found at i:239863310 original size:28 final size:28
Alignment explanation
Indices: 239863264--239863332 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
239863254 TTTAAAACCC
*
239863264 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
239863291 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
239863319 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
239863333 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:239864978 original size:20 final size:20
Alignment explanation
Indices: 239864955--239864992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
239864945 CACATCCAAA
*
239864955 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
239864975 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
239864993 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:239871261 original size:28 final size:28
Alignment explanation
Indices: 239871215--239871283 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
239871205 TTTAAAACCC
*
239871215 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
239871242 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
239871270 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
239871284 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:239872933 original size:20 final size:20
Alignment explanation
Indices: 239872910--239872947 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
239872900 CACATCCAAA
*
239872910 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
239872930 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
239872948 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:239879833 original size:28 final size:28
Alignment explanation
Indices: 239879801--239879899 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
239879791 GCAATAAGCC
*
239879801 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
239879829 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
239879857 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
239879886 CGCACACTTAGTGC
1 CGCACACTTAGTGC
239879900 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:239887512 original size:28 final size:28
Alignment explanation
Indices: 239887480--239887578 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
239887470 GCAATAAGCC
*
239887480 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
239887508 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
239887536 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
239887565 CGCACACTTAGTGC
1 CGCACACTTAGTGC
239887579 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:239891517 original size:68 final size:67
Alignment explanation
Indices: 239891445--239891594 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
239891435 CATCATGTGT
* * * *
239891445 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
239891507 ATGTAG
62 ATGTAG
** * *
239891513 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
239891578 AG
66 AG
239891580 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
239891595 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:239891550 original size:64 final size:64
Alignment explanation
Indices: 239891469--239891652 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
239891459 AGACATTATG
* *
239891469 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
239891533 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
239891598 AA
63 AA
* * * *
239891600 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
239891653 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:239891828 original size:35 final size:35
Alignment explanation
Indices: 239891789--239891859 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
239891779 GTTATGTGAA
239891789 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
1 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
239891824 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
1 TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
239891859 T
1 T
239891860 TATAAACAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.08, G:0.34, T:0.32
Consensus pattern (35 bp):
TGATGTGTTCATTAAGTGACCAGGATGTGGTAAGG
Found at i:239895064 original size:30 final size:30
Alignment explanation
Indices: 239895028--239895128 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
239895018 GACAAGATTG
* * *
239895028 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
239895058 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
239895086 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
239895115 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
239895129 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:239895140 original size:29 final size:28
Alignment explanation
Indices: 239895057--239895132 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
239895047 AAAATTGTAC
* *
239895057 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
239895085 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
239895114 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
239895133 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:239902980 original size:29 final size:28
Alignment explanation
Indices: 239902913--239902984 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
239902903 AAAATTGTAC
* * *
239902913 AGCACTAAGTGTGCGAGTTTGATTCTAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
239902941 AGCACTAAGTGTGCGAG-CTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTG--AATATAT
239902970 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
239902985 GATTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 17 0.44
29 20 0.51
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:239913349 original size:40 final size:39
Alignment explanation
Indices: 239913184--239913367 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
239913174 AAATTGAATG
* * *
239913184 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
239913224 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
239913264 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
239913304 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
239913343 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
239913368 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:239913392 original size:80 final size:81
Alignment explanation
Indices: 239913224--239913412 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
239913214 GCTGGAAATT
* * * *
239913224 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
239913289 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
239913305 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
239913368 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
239913384 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
239913413 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:239915356 original size:586 final size:586
Alignment explanation
Indices: 239914264--239915399 Score: 1326
Period size: 586 Copynumber: 1.9 Consensus size: 586
239914254 CATTGATGAG
* * * *
239914264 TCTATTTTCATATGGAAGAAACGAAATGGTCATAGGAGTTACATGTTAAGAGATATTAAAGCTAT
1 TCTACTTTCACATGGAAGAAACGAAACGATCATAGGAGTTACATGTTAAGAGATATTAAAGCTAT
*
239914329 TGTGAGACAGGGCCAGAACGGTTTCTGGGTTCCCTGTCGCAACTTTAAAAATTTACTATAAATTA
66 TGTGAGACAGGGCCAGAACGGTTTCTGGGTTCCCTGTCGCAACTTTAAAAATTCACTATAAATTA
* * *
239914394 TCCAGAAAGAATTAGGAGACATACCTTATATGTACAGATTCCATTTTGAGTCTAGTTTCATTAGA
131 TCCAGAAAGAATTAGAAGACATACCATATATGTACAGATTCCATTTTAAGTCTAGTTTCATTAGA
* ** * *
239914459 AACAAACGGCACCAGCATTAAAGCCCTGTACAGAGAGATATTCAAGTTATACCGCGCGAAGGTCA
196 AACAAACGGCACCAGCATTAAAGCCCTGTACAGAGAGATATCCAAGCCATAACGCGCAAAGGTCA
* * *
239914524 GAGCAGTCGATCCCTGTAACATGGGTGACTTTAACTAATAAACTGTACCAATTGGCCCGACCAAA
261 GAGCAGTCGATCCCTGTAACATGGGAGACTTTAACTAATAAAATGTACCAATTGGCCCAACCAAA
* * * * * *
239914589 AATTCTAGAAATAAATCCATGGATGGATATATGAGTCTAAATTCAGGGAAAATTTACGAAACCAG
326 AATTCTAGAAAAAAATCCATAGATGCATATACGAGTCTAAATTCAGGGAAAAATCACGAAACCAG
* * * **
239914654 TTTCCGAGTTTTGAAACTCGAGATATGATTTTTAAGGCGACAGTGACGCAGTTTTTCCAGCCTGA
391 TTTCCGAGTTGTGAAACTCAAGATATGATTTTTAAGGCGACAGTGACACAGTTTAGCCAGCCTGA
** * * **
239914719 CTGGAAATGTCCAATGGATGGGCAAAACAAGTGAACTTGGCTTGCTAACCCCTCGTGTCCGACAC
456 CTGGAAATGTAAAATGAATGGGCAAAACAAGTGAACTTAGCCCGCTAACCCCTCGTGTCCGACAC
* *
239914784 CGGCGATGGTCTCGGGTTCGGGGTGTTACAAATAGTGAATAAATTGTGTAATCAAACCTTGATTA
521 CGGCGACGGTCTCGGGTACGGGGTGTTACAAATAGTGAATAAATTGTGTAATCAAACCTTGATTA
239914849 A
586 A
* * *** * *
239914850 TCTACTTTCACATGGAAGAAACGAAACGATCCTATGAGTTGTGTGTTAAGAGATATTTAAG-TTT
1 TCTACTTTCACATGGAAGAAACGAAACGATCATAGGAGTTACATGTTAAGAGATATTAAAGCTAT
* * * * * *
239914914 TCGTGAGACAGGGCTAGAACGGTTTCTGGAG-TCCCTTTTC-CTATTTTAGAAATTCATTATAAA
66 T-GTGAGACAGGGCCAGAACGGTTTCTGG-GTTCCC-TGTCGCAACTTTAAAAATTCACTATAAA
* * * * *
239914977 TT-TACCAGAGATAATTATAAGTCATGCCATATATGTACAGATTCC-TTTTCAAGTCTAGTTTC-
128 TTAT-CCAGAAAGAATTAGAAGACATACCATATATGTACAGATTCCATTTT-AAGTCTAGTTTCA
* * * * * * *
239915039 TGTAGAAACAAACGGCATCAGTATTGAATCCCTGTACAGGGAGATATCCAAGCCGTAATGCGCAA
191 T-TAGAAACAAACGGCACCAGCATTAAAGCCCTGTACAGAGAGATATCCAAGCCATAACGCGCAA
* * * *
239915104 AGGTCAGTGTAGTCGATCCCTGTAACATGTGAGACTTTAACTAATAAAATGTACTAATTGGCCCA
255 AGGTCAGAGCAGTCGATCCCTGTAACATGGGAGACTTTAACTAATAAAATGTACCAATTGGCCCA
*** *
239915169 A-CACAAAATTCTAGAAAAAAATTTGTAGATGCATATACGAGTCT-AGTGTCAGGGAAAAATCAC
320 ACCA-AAAATTCTAGAAAAAAATCCATAGATGCATATACGAGTCTAAAT-TCAGGGAAAAATCAC
* ** * *
239915232 GAAA-CTGATTTTTGAGTTGTGGAACTCAAGATATGATTTTTAAGGTGACAGTGACACAG-TTAG
383 GAAACCAG-TTTCCGAGTTGTGAAACTCAAGATATGATTTTTAAGGCGACAGTGACACAGTTTAG
* * * * ** * *
239915295 CCAG-CTGTCTGGAAATTTTTAAAATGAACTGTGC-TAGTAAGTGGA-TTAAGCCCGTTAACCCC
447 CCAGCCTGACTGGAAA--TGTAAAATGAA-TGGGCAAAACAAGTGAACTT-AGCCCGCTAACCCC
*
239915357 TCGTGTCCGACTCCGGCGACGGTCTCGGGTACGGGGTGTTACA
508 TCGTGTCCGACACCGGCGACGGTCTCGGGTACGGGGTGTTACA
239915400 CCATGGGCGA
Statistics
Matches: 455, Mismatches: 82, Indels: 26
0.81 0.15 0.05
Matches are distributed among these distances:
584 10 0.02
585 23 0.05
586 414 0.91
587 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (586 bp):
TCTACTTTCACATGGAAGAAACGAAACGATCATAGGAGTTACATGTTAAGAGATATTAAAGCTAT
TGTGAGACAGGGCCAGAACGGTTTCTGGGTTCCCTGTCGCAACTTTAAAAATTCACTATAAATTA
TCCAGAAAGAATTAGAAGACATACCATATATGTACAGATTCCATTTTAAGTCTAGTTTCATTAGA
AACAAACGGCACCAGCATTAAAGCCCTGTACAGAGAGATATCCAAGCCATAACGCGCAAAGGTCA
GAGCAGTCGATCCCTGTAACATGGGAGACTTTAACTAATAAAATGTACCAATTGGCCCAACCAAA
AATTCTAGAAAAAAATCCATAGATGCATATACGAGTCTAAATTCAGGGAAAAATCACGAAACCAG
TTTCCGAGTTGTGAAACTCAAGATATGATTTTTAAGGCGACAGTGACACAGTTTAGCCAGCCTGA
CTGGAAATGTAAAATGAATGGGCAAAACAAGTGAACTTAGCCCGCTAACCCCTCGTGTCCGACAC
CGGCGACGGTCTCGGGTACGGGGTGTTACAAATAGTGAATAAATTGTGTAATCAAACCTTGATTA
A
Found at i:239918543 original size:78 final size:78
Alignment explanation
Indices: 239918384--239918581 Score: 258
Period size: 78 Copynumber: 2.5 Consensus size: 78
239918374 TTGGAAATAT
239918384 TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCTGGGCTAAGACCCGAAGGCATTT
1 TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCTGGGCTAAGACCCGAAGGCATTT
* * * *
239918449 GCGAGTTGATATA
66 GCAAGTTCACAAA
*
239918462 TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGA-ATATC-GGGCTAAGACCCGAAGGCCTTT
1 TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCTGGGCTAAGACCCGAAGG-CATT
239918525 GTGCAAG-TCACCAAA
65 -TGCAAGTTCA-CAAA
* * * * *
239918540 TCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCGCTATATC
1 TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATC
239918582 CGGTTAAATC
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
76 17 0.16
77 10 0.09
78 74 0.70
79 5 0.05
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (78 bp):
TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCTGGGCTAAGACCCGAAGGCATTT
GCAAGTTCACAAA
Found at i:239918583 original size:40 final size:40
Alignment explanation
Indices: 239918380--239918584 Score: 251
Period size: 38 Copynumber: 5.2 Consensus size: 40
239918370 AACATTGGAA
239918380 ATAT-TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
239918419 ATATATCTGGGCTAAGACCCGAAGGCATT--TGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
239918457 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
239918497 A-ATAT-CGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
239918534 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
239918575 CTATATCCGG
1 ATATATCCGG
239918585 TTAAATCCCG
Statistics
Matches: 141, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
37 2 0.01
38 64 0.45
39 11 0.08
40 64 0.45
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:239922787 original size:47 final size:47
Alignment explanation
Indices: 239922723--239922833 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
239922713 GACATTGAGT
*
239922723 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
239922770 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
239922817 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
239922834 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:239930036 original size:47 final size:47
Alignment explanation
Indices: 239929972--239930082 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
239929962 GACATTGAGT
*
239929972 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
239930019 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
239930066 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
239930083 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:239935167 original size:2 final size:2
Alignment explanation
Indices: 239935160--239935184 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
239935150 CCATGTATCA
239935160 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 A
239935185 CATGATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239940198 original size:40 final size:40
Alignment explanation
Indices: 239940153--239940320 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
239940143 CGGAATATAA
239940153 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * *
239940193 CCGGATAGAAT-ATCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCA-CTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
239940233 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
239940273 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
239940313 CCGGATAT
1 CCGGATAT
239940321 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.02
40 101 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:239940303 original size:80 final size:80
Alignment explanation
Indices: 239940169--239940318 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
239940159 ATAATCACGT
*
239940169 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATATCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTCGCACGAATGCCTTCGGGAT-TTAGC
239940233 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
239940249 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTC-GCACGAA-TGCCTTCGGGATTTAG
239940312 CCCGGAT
64 CCCGGAT
239940319 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:239948891 original size:28 final size:27
Alignment explanation
Indices: 239948835--239948923 Score: 117
Period size: 28 Copynumber: 3.3 Consensus size: 27
239948825 AGCATGGCTG
* * **
239948835 CCAGAACAGATA-TTGTGACAGAGTTA
1 CCAGAACAGATATTTGTGGCATAGCCA
239948861 CCAGATACAGATATTTGTGGCATAGCCA
1 CCAGA-ACAGATATTTGTGGCATAGCCA
239948889 CCAGAAACAGATATTTGTGGCATAGCCA
1 CCAG-AACAGATATTTGTGGCATAGCCA
239948917 CCAGAAC
1 CCAGAAC
239948924 GCTTCTCCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.09
27 10 0.18
28 40 0.71
29 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (27 bp):
CCAGAACAGATATTTGTGGCATAGCCA
Found at i:239960424 original size:28 final size:28
Alignment explanation
Indices: 239960389--239960447 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
239960379 TTGCCTGAAA
239960389 GAATCATTTCAGATAATGCCACGAATCT
1 GAATCATTTCAGATAATGCCACGAATCT
239960417 GAATCATTTCAGATAATGCCACGAATCT
1 GAATCATTTCAGATAATGCCACGAATCT
239960445 GAA
1 GAA
239960448 CAATAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (28 bp):
GAATCATTTCAGATAATGCCACGAATCT
Found at i:239962129 original size:71 final size:71
Alignment explanation
Indices: 239962010--239962148 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
239962000 GTTTTCCAAG
* *
239962010 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTGAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
239962075 GTTTCA
66 GTTTCA
*
239962081 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
239962146 GTT
66 GTT
239962149 GCGAGAAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:239962152 original size:52 final size:51
Alignment explanation
Indices: 239962095--239962193 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 51
239962085 TCAACTCATA
* * * *
239962095 TTGCGAGAGGTGAGTTGAGCCTCAAGACATGTTGAGGTAATTTCAATTTATG
1 TTGCGAGAAGTGAGTTGAACCTCAAG-CACGCTGAGGTAATTTCAATTTATG
**
239962147 TTGCGAGAAGTGAGTTGAACCTGGAGCACGCTGAGGTAATTTCAATT
1 TTGCGAGAAGTGAGTTGAACCTCAAGCACGCTGAGGTAATTTCAATT
239962194 CTATTAAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
51 19 0.46
52 22 0.54
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.30
Consensus pattern (51 bp):
TTGCGAGAAGTGAGTTGAACCTCAAGCACGCTGAGGTAATTTCAATTTATG
Found at i:239962389 original size:135 final size:132
Alignment explanation
Indices: 239962147--239962403 Score: 331
Period size: 135 Copynumber: 1.9 Consensus size: 132
239962137 TCAATTTATG
* * *
239962147 TTGCGAGAAGTGAGTTGAACCTGGAGCACGCTGAGGTAATTTCAATTCTATTAAATCAAAAATCG
1 TTGCGAGAAGTGAGTTGAACCTCGAGCACGCTAAGGTAATTTCAATTCTATT--ATCAAAAATCA
*
239962212 ACTCATATTGCGAGGTGAGTTGAGCTTTTTAGTTTCTATTTTCAATTCCTGTTTTTTTTATCAAC
64 ACTCATATTGCGAGGTGAGTTGAGCTTTTTAATTTCTATTTTCAATT-CTGTTTTTTTTATCAAC
239962277 TCATA
128 TCATA
* * * *
239962282 TTGCGAGAGGTGAGTTGAGCCTTACG-GCACGCTAAGGTATTTTCAATTCTATT-TCAAAAGTCA
1 TTGCGAGAAGTGAGTTGAACC-T-CGAGCACGCTAAGGTAATTTCAATTCTATTATCAAAAATCA
* *
239962345 ATTCATATTGCGAGAGATGAGTTGAG-TCTTTTAATTTCTATTTTCAATTTTGTTTTTTT
64 ACTCATATTGCGAG-G-TGAGTTGAGCT-TTTTAATTTCTATTTTCAATTCTGTTTTTTT
239962404 AATTTTTAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 11
0.84 0.08 0.09
Matches are distributed among these distances:
133 21 0.20
134 11 0.10
135 48 0.45
136 26 0.24
137 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (132 bp):
TTGCGAGAAGTGAGTTGAACCTCGAGCACGCTAAGGTAATTTCAATTCTATTATCAAAAATCAAC
TCATATTGCGAGGTGAGTTGAGCTTTTTAATTTCTATTTTCAATTCTGTTTTTTTTATCAACTCA
TA
Found at i:239963294 original size:16 final size:16
Alignment explanation
Indices: 239963273--239963304 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
239963263 GCCCAATAAC
*
239963273 CTAAACTACCAGCCCA
1 CTAAACTAACAGCCCA
239963289 CTAAACTAACAGCCCA
1 CTAAACTAACAGCCCA
239963305 TTACACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (16 bp):
CTAAACTAACAGCCCA
Found at i:239968027 original size:39 final size:38
Alignment explanation
Indices: 239967960--239968094 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
239967950 ACCAATATGG
* * *
239967960 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
239967999 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
239968037 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
239968078 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
239968095 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:239968360 original size:18 final size:19
Alignment explanation
Indices: 239968334--239968372 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
239968324 TTTCAATTCA
239968334 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
239968353 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
239968371 AT
1 AT
239968373 ATAATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:239969606 original size:5 final size:5
Alignment explanation
Indices: 239969596--239969652 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
239969586 TTACTTATTT
* *
239969596 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
239969644 ATAT- ATATA
1 ATATA ATATA
239969653 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:239969612 original size:12 final size:12
Alignment explanation
Indices: 239969595--239969650 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
239969585 TTTACTTATT
239969595 TATATAATATAA
1 TATATAATATAA
239969607 TATATAATATAATA
1 TATATAATAT-A-A
239969621 TACTATAATATAA
1 TA-TATAATATAA
*
239969634 TA-ATAATTTAA
1 TATATAATATAA
239969645 TATATA
1 TATATA
239969651 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:239969665 original size:26 final size:26
Alignment explanation
Indices: 239969597--239969652 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
239969587 TACTTATTTA
*
239969597 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
239969624 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
239969649 TATA
1 TATA
239969653 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:239971444 original size:6 final size:6
Alignment explanation
Indices: 239971429--239971468 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
239971419 TACTTCATTA
239971429 TTTT-T TTTTAT TTTTAT TTTTATT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTT
239971469 TTGCATCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTAT
Found at i:239971455 original size:13 final size:13
Alignment explanation
Indices: 239971429--239971469 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
239971419 TACTTCATTA
239971429 TTTT-TTTTTA-T
1 TTTTATTTTTATT
239971440 TTTTATTTTTATT
1 TTTTATTTTTATT
239971453 TTTTATTTTTATT
1 TTTTATTTTTATT
239971466 TTTT
1 TTTT
239971470 TGCATCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 4 0.14
12 6 0.21
13 18 0.64
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:239971456 original size:19 final size:19
Alignment explanation
Indices: 239971432--239971468 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
239971422 TTCATTATTT
239971432 TTTTTTATTTTTATTTTTA
1 TTTTTTATTTTTATTTTTA
239971451 TTTTTTATTTTTATTTTT
1 TTTTTTATTTTTATTTTT
239971469 TTGCATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTTATTTTTATTTTTA
Found at i:239974179 original size:18 final size:17
Alignment explanation
Indices: 239974146--239974190 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
239974136 AACCTTTTGG
*
239974146 TTCATATTTCAATCTCAT
1 TTCA-ATTTCAATCTCAA
239974164 TTCAATTTCAATTCTCAA
1 TTCAATTTCAA-TCTCAA
239974182 TTCAATTTC
1 TTCAATTTC
239974191 TCATTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (17 bp):
TTCAATTTCAATCTCAA
Found at i:239974212 original size:31 final size:30
Alignment explanation
Indices: 239974158--239974217 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
239974148 CATATTTCAA
* *
239974158 TCTCATTTCAATTTCAATTCTCAATTCAATT
1 TCTCATTTCAATTCCAATGCTCAA-TCAATT
239974189 TCTCATTTC-ATTCCAATAGCTCAATCAAT
1 TCTCATTTCAATTCCAAT-GCTCAATCAAT
239974218 CAAATTCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (30 bp):
TCTCATTTCAATTCCAATGCTCAATCAATT
Found at i:239974377 original size:38 final size:39
Alignment explanation
Indices: 239974335--239974444 Score: 91
Period size: 38 Copynumber: 2.8 Consensus size: 39
239974325 TCGGATAGTT
* *
239974335 CGAAGCAATATTTGACACCAGTGTCTCATCG-GCCTAGC
1 CGAAGAAATATTTGACACCAGTGTCTCATCGAACCTAGC
* * ** * *
239974373 CGAAGTAAA-GTTGGTAC-CCAGTACCTCATCGAATCTATC
1 CGAAG-AAATATTTG-ACACCAGTGTCTCATCGAACCTAGC
*
239974412 CGAAGAAATATAGTGACACCAGTGTCTCATCGA
1 CGAAGAAATAT-TTGACACCAGTGTCTCATCGA
239974445 CTCGAGGTCG
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
38 23 0.43
39 16 0.30
40 14 0.26
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (39 bp):
CGAAGAAATATTTGACACCAGTGTCTCATCGAACCTAGC
Done.