Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 95 of 427
Found at i:25151791 original size:41 final size:39
Alignment explanation
Indices: 25151624--25151803 Score: 193
Period size: 40 Copynumber: 4.5 Consensus size: 39
25151614 GCTCAATTGT
* *
25151624 CTTCGGGACA-TAGCCCGG-TTATAGTAATTCGCACAATTGC
1 CTTCGGGA-ATTA-CCCGGATT-TAGTAACTCGCACAAATGC
25151664 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGAATTA-CCCGGATTTAGTAACTCGCACAAATGC
* * *
25151704 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGAATT-ACCCGGATTTAGTAACTCGCACAAATGC
* * *
25151744 CTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGAATT-ACCCGGATTTAGTAAC-TCGCACAAATGC
*
25151785 CTTCGGGACTTAGCCCGGA
1 CTTCGGGAATTA-CCCGGA
25151804 CATCATTCGA
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 92 0.75
41 29 0.24
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CTTCGGGAATTACCCGGATTTAGTAACTCGCACAAATGC
Found at i:25153946 original size:23 final size:21
Alignment explanation
Indices: 25153910--25153962 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
25153900 GTGTAAGCTG
25153910 ATAATAATATACAAATGTAATA
1 ATAATAATATACAAATGTAA-A
*
25153932 ATAATATATATACAATTGTAAA
1 ATAATA-ATATACAAATGTAAA
25153954 ATAAATAAT
1 AT-AATAAT
25153963 TAATTACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
ATAATAATATACAAATGTAAA
Found at i:25157279 original size:16 final size:15
Alignment explanation
Indices: 25157254--25157283 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25157244 ATCCATCTCT
25157254 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
25157269 AAAAAAGAAAAAAGA
1 AAAAAA-AAAAAAGA
25157284 TTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:25158709 original size:15 final size:14
Alignment explanation
Indices: 25158674--25158736 Score: 65
Period size: 14 Copynumber: 4.3 Consensus size: 14
25158664 CTTCTATTTC
25158674 AAAAGCAAAAAAA-A
1 AAAAG-AAAAAAAGA
*
25158688 AAGAGAATAAAAAGA
1 AAAAGAA-AAAAAGA
*
25158703 TAAAGAAAAAAGAGAA
1 AAAAGAAAAAA-AG-A
25158719 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
25158733 AAAA
1 AAAA
25158737 TAGAGAGGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.05
14 18 0.44
15 10 0.24
16 11 0.27
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:25158716 original size:24 final size:24
Alignment explanation
Indices: 25158680--25158742 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
25158670 TTTCAAAAGC
*
25158680 AAAA-AAAAAAGAGAATAAAA-AGA
1 AAAAGAAAAAAGAGAA-AAAAGAAA
*
25158703 TAAAGAAAAAAGAGAAAAAAGAAA
1 AAAAGAAAAAAGAGAAAAAAGAAA
25158727 AAAAGAAAAATAGAGA
1 AAAAGAAAAA-AGAGA
25158743 GGCCAAGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.21
24 22 0.65
25 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (24 bp):
AAAAGAAAAAAGAGAAAAAAGAAA
Found at i:25158720 original size:8 final size:8
Alignment explanation
Indices: 25158685--25158736 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
25158675 AAAGCAAAAA
25158685 AAAAAGAG
1 AAAAAGAG
*
25158693 AATAAAAAG
1 AA-AAAGAG
*
25158702 ATAAAGA-
1 AAAAAGAG
25158709 AAAAAGAG
1 AAAAAGAG
25158717 AAAAA-AG
1 AAAAAGAG
*
25158724 AAAAAAAG
1 AAAAAGAG
25158732 AAAAA
1 AAAAA
25158737 TAGAGAGGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 13 0.35
8 18 0.49
9 6 0.16
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAAAGAG
Found at i:25158720 original size:9 final size:9
Alignment explanation
Indices: 25158706--25158742 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
25158696 AAAAAGATAA
25158706 AGAAAAAAG
1 AGAAAAAAG
25158715 AGAAAAAAG
1 AGAAAAAAG
25158724 A-AAAAAAG
1 AGAAAAAAG
*
25158732 A-AAAATAG
1 AGAAAAAAG
25158740 AGA
1 AGA
25158743 GGCCAAGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 15 0.58
9 11 0.42
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:25159875 original size:82 final size:79
Alignment explanation
Indices: 25159685--25159882 Score: 227
Period size: 82 Copynumber: 2.4 Consensus size: 79
25159675 AAATTCAGCT
* * * * * *
25159685 CCTTAATCGCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCTTAAGTAGTAGT
1 CCTTAATCCCCTAAGTAGTAGGGTAACAGGTT-CA----CAGATCTTATCTCCCTAAGCAGTAGC
25159750 GGAGCAGATCGAAGACTCG
61 GGAGCAGATCGAAGACTCG
* *
25159769 CCTTAATCCCCTAAGTAGTAGGGTAATAGGTTCACAGATTTTATCTCCCTAAGCAGTAGCGGAGC
1 CCTTAATCCCCTAAGTAGTAGGGTAACAGGTTCACAGATCTTATCTCCCTAAGCAGTAGCGGAGC
*
25159834 AGATCAATGACGACTCG
66 AGATC---GAAGACTCG
25159851 CCTTAA-CCACCTAAGTAGTAGGGTAACAGGTT
1 CCTTAATCC-CCTAAGTAGTAGGGTAACAGGTT
25159883 AAAGTATAGC
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
79 32 0.32
81 2 0.02
82 36 0.36
83 1 0.01
84 29 0.29
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (79 bp):
CCTTAATCCCCTAAGTAGTAGGGTAACAGGTTCACAGATCTTATCTCCCTAAGCAGTAGCGGAGC
AGATCGAAGACTCG
Found at i:25160255 original size:207 final size:206
Alignment explanation
Indices: 25159888--25160680 Score: 1250
Period size: 207 Copynumber: 3.8 Consensus size: 206
25159878 AGGTTAAAGT
*
25159888 ATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCATTGTG
1 ATAGCAGATCTGGCCTTCAGATGTTTATACTAAAGCAAGATCCAAGATGGTTTGGCATCATTGTG
25159953 CTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCT
66 CTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCT
*
25160018 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGATG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACG
25160083 GATGGCAGACAC
196 GA-GGCAGACAC
* *
25160095 ATAGCAAATCTTGCCTTCAGATGTTTATACTAAAGCAAGATCCAAGATGGTTTGGCATCATTGTG
1 ATAGCAGATCTGGCCTTCAGATGTTTATACTAAAGCAAGATCCAAGATGGTTTGGCATCATTGTG
* *
25160160 CTTACAAGGAACAAATAGAAGACATAGCTAATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCT
66 CTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCT
*
25160225 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGACGTCTCCATATTCGACG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACG
* *
25160290 AAGGGCGGACAC
196 GA-GGCAGACAC
* *
25160302 ATAGCAGATCTGGCCTTTAGATGTTTATACTGAAA-CAAGATCCAAGATGGTTTGGCATCCTTGT
1 ATAGCAGATCTGGCCTTCAGATGTTTATACT-AAAGCAAGATCCAAGATGGTTTGGCATCATTGT
25160366 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
65 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
*
25160431 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGAC
130 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
*
25160496 GGAGGACAGACAT
195 GGAGG-CAGACAC
** * * * * *
25160509 ATAGCAGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGTG
1 ATAGCAGATCTGGCCTTCAGATGTTTATACTAAAGCAAGATCCAAGATGGTTTGGCATCATTGTG
* * * * *
25160573 CATACAAGGAGA-AAATCGAAAACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATC
66 CTTACAAGGA-ACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
* * * * *
25160637 TAAGAAGATTTGGTATCTCTGTATTGTTAGGGAACAAATTGAAG
130 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
25160681 AAGCAAATTT
Statistics
Matches: 543, Mismatches: 39, Indels: 9
0.92 0.07 0.02
Matches are distributed among these distances:
206 126 0.23
207 414 0.76
208 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (206 bp):
ATAGCAGATCTGGCCTTCAGATGTTTATACTAAAGCAAGATCCAAGATGGTTTGGCATCATTGTG
CTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCT
AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACG
GAGGCAGACAC
Found at i:25161047 original size:17 final size:17
Alignment explanation
Indices: 25161006--25161175 Score: 223
Period size: 17 Copynumber: 9.6 Consensus size: 17
25160996 CAATGATATG
*
25161006 CAATCTTAGATGTGATA
1 CAATCTTAGATATGATA
25161023 CGCAATCTTAGATATGATA
1 --CAATCTTAGATATGATA
* *
25161042 CAATCTTAAATATGATTG
1 CAATCTTAGATATGA-TA
25161060 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
* *
25161077 CAATCTTAAATATGATTG
1 CAATCTTAGATATGA-TA
25161095 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
25161112 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
25161129 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
25161147 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
25161166 CAATCTTAGA
1 CAATCTTAGA
25161176 AGATATGATT
Statistics
Matches: 135, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
17 62 0.46
18 45 0.33
19 27 0.20
20 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:25161067 original size:35 final size:35
Alignment explanation
Indices: 25161006--25161175 Score: 243
Period size: 35 Copynumber: 4.8 Consensus size: 35
25160996 CAATGATATG
* *
25161006 CAATCTTAGATGTGATACGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
*
25161042 CAATCTTAAATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
25161077 CAATCTTAAATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
* *
25161112 CAATCTTAGATATGA-TACAATCTTAGATATGATTG
1 CAATCTTAGATATGATTGCAATCTTAGATATGA-TA
*
25161147 CAATCTTAGATATGATATACAATCTTAGA
1 CAATCTTAGATATGAT-TGCAATCTTAGA
25161176 AGATATGATT
Statistics
Matches: 125, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
34 16 0.13
35 83 0.66
36 14 0.11
37 12 0.10
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:25161116 original size:52 final size:52
Alignment explanation
Indices: 25161006--25161175 Score: 243
Period size: 52 Copynumber: 3.2 Consensus size: 52
25160996 CAATGATATG
* * * *
25161006 CAATCTTAGATGTGATACGCAATCTTAGATATGA-TACAATCTTAAATATGATTG
1 CAATCTTAGATATGATA--CAATCTTAGATATGATTGCAATCTTAGATATGA-TA
*
25161060 CAATCTTAGATATGATACAATCTTAAATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATA
25161112 CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATG--ATA
25161166 CAATCTTAGA
1 CAATCTTAGA
25161176 AGATATGATT
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
52 63 0.59
53 15 0.14
54 29 0.27
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (52 bp):
CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:25168851 original size:61 final size:61
Alignment explanation
Indices: 25168653--25168905 Score: 355
Period size: 61 Copynumber: 4.1 Consensus size: 61
25168643 TATTGCACTG
* * * * * *
25168653 AATAACTAAATAACTGTATTACTAGA-TGAATAATTTATTGTTATTGATTTTTTGATACTG
1 AATAACTGAATGACTGTATTACTGGACTGAATAATTGATTGTTATTGATTGTTTGATACTA
* * * *
25168713 AATAACTGAATGACTGTATTACCGGACTGAATAATTTATTGTTTTTTGATTGCTTGATACTA
1 AATAACTGAATGACTGTATTACTGGACTGAATAATTGATTG-TTATTGATTGTTTGATACTA
* *
25168775 AATAATTGAATGACTGTACTACTGGACTGAATAATTGATTGTTATTGATTGTTTGATACTA
1 AATAACTGAATGACTGTATTACTGGACTGAATAATTGATTGTTATTGATTGTTTGATACTA
* **
25168836 AATAACTGAATGACTGTATTAGTGGACTGAATAACAGATTGTTATTGATTGTTTGATACTA
1 AATAACTGAATGACTGTATTACTGGACTGAATAATTGATTGTTATTGATTGTTTGATACTA
25168897 AATAACTGA
1 AATAACTGA
25168906 TTTTTATTGA
Statistics
Matches: 172, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
60 22 0.13
61 97 0.56
62 53 0.31
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (61 bp):
AATAACTGAATGACTGTATTACTGGACTGAATAATTGATTGTTATTGATTGTTTGATACTA
Found at i:25168913 original size:32 final size:32
Alignment explanation
Indices: 25168804--25168915 Score: 108
Period size: 32 Copynumber: 3.6 Consensus size: 32
25168794 TACTGGACTG
*
25168804 AATAATTGATTGTTATTGATTGTTTGATACTA
1 AATAACTGATTGTTATTGATTGTTTGATACTA
* * * *
25168836 AATAACTGAATG--ACTGTATTAG--TG-GACTG
1 AATAACTGATTGTTATTG-ATT-GTTTGATACTA
*
25168865 AATAACAGATTGTTATTGATTGTTTGATACTA
1 AATAACTGATTGTTATTGATTGTTTGATACTA
*
25168897 AATAACTGATTTTTATTGA
1 AATAACTGATTGTTATTGA
25168916 ATAACAATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
29 14 0.23
30 8 0.13
31 8 0.13
32 31 0.51
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (32 bp):
AATAACTGATTGTTATTGATTGTTTGATACTA
Found at i:25172207 original size:27 final size:27
Alignment explanation
Indices: 25172168--25172231 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
25172158 GTTGTTTGTT
* *
25172168 TCTATAGAAACTAGACTCGAATAGGAA
1 TCTATACATACTAGACTCGAATAGGAA
25172195 TCTATACATACTAGACTCGAATAGGAA
1 TCTATACATACTAGACTCGAATAGGAA
25172222 TCTATACATA
1 TCTATACATA
25172232 TATGGAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (27 bp):
TCTATACATACTAGACTCGAATAGGAA
Found at i:25178654 original size:39 final size:38
Alignment explanation
Indices: 25178569--25178754 Score: 214
Period size: 39 Copynumber: 4.7 Consensus size: 38
25178559 ACTACTTGCT
25178569 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAG-CCCGGTTA-A-TAACTCGCA
25178609 CAAATGCCTTCGGGACTTAGCCCGGTTCAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-AATAACTCGCA
*
25178648 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-T-TAATAACTCGCA
* * * * * *
25178688 CAATTGCCTTCGGG-TTTAGCCCAGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCC-G-GTTAATAACTCGCA
*
25178727 AAAATGCCTTCGGGACTTAGCCCGGTTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA
25178755 TCATCCGAAT
Statistics
Matches: 127, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
38 3 0.02
39 62 0.49
40 59 0.46
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTAATAACTCGCA
Found at i:25178672 original size:79 final size:79
Alignment explanation
Indices: 25178570--25178755 Score: 234
Period size: 79 Copynumber: 2.4 Consensus size: 79
25178560 CTACTTGCTC
*
25178570 AAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-G
1 AAATGCCTTCGGGACTTAG-CCCGGTTATAATAACTCGCACAAATGCCTTCGGG-CTTAGCCCAG
* * *
25178633 -GTTCAATAACTCGCAC
64 AATT-AATAACTAGCAA
* * * *
25178649 CAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAATTGCCTTCGGGTTTAGCCCAGAA
1 AAATGCCTTCGGGACTTAGCCCGGTTATAATAACTCGCACAAATGCCTTCGGGCTTAGCCCAGAA
* *
25178714 TTAGTCACTAGCAA
66 TTAATAACTAGCAA
25178728 AAATGCCTTCGGGACTTAGCCCGGTTAT
1 AAATGCCTTCGGGACTTAGCCCGGTTAT
25178756 CATCCGAATA
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 7 0.08
79 82 0.89
80 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
AAATGCCTTCGGGACTTAGCCCGGTTATAATAACTCGCACAAATGCCTTCGGGCTTAGCCCAGAA
TTAATAACTAGCAA
Found at i:25182011 original size:13 final size:13
Alignment explanation
Indices: 25181993--25182019 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25181983 GGCTGAGACA
25181993 CGGGCGTGTGTCT
1 CGGGCGTGTGTCT
25182006 CGGGCGTGTGTCT
1 CGGGCGTGTGTCT
25182019 C
1 C
25182020 AGCCGCATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.26, G:0.44, T:0.30
Consensus pattern (13 bp):
CGGGCGTGTGTCT
Found at i:25182215 original size:26 final size:26
Alignment explanation
Indices: 25182186--25182239 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
25182176 CAAACAGAGA
25182186 GTTACACGGGTTCAGGACA-CGAGCGT
1 GTTACACGGGTTCAGGACACCG-GCGT
*
25182212 GTTACACGGGTTCGGGACACCGGCGT
1 GTTACACGGGTTCAGGACACCGGCGT
25182238 GT
1 GT
25182240 GTGACCACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.19, C:0.24, G:0.37, T:0.20
Consensus pattern (26 bp):
GTTACACGGGTTCAGGACACCGGCGT
Found at i:25185850 original size:33 final size:33
Alignment explanation
Indices: 25185808--25185874 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
25185798 TCGGCCCCTT
25185808 ACACACCATAACAAAATGGTGTAGCTGAAATGA
1 ACACACCATAACAAAATGGTGTAGCTGAAATGA
25185841 ACACACCATAACAAAATGGTGTAGCTGAAATGA
1 ACACACCATAACAAAATGGTGTAGCTGAAATGA
25185874 A
1 A
25185875 AAATACAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (33 bp):
ACACACCATAACAAAATGGTGTAGCTGAAATGA
Found at i:25188507 original size:20 final size:20
Alignment explanation
Indices: 25188473--25188514 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25188463 CACTATTTAA
** *
25188473 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
25188493 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
25188513 AT
1 AT
25188515 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:25191398 original size:29 final size:27
Alignment explanation
Indices: 25191364--25191466 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 27
25191354 TACTCAATCA
*
25191364 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
25191393 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
25191422 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
25191451 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
25191467 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
28 2 0.03
29 61 0.97
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:25193015 original size:22 final size:22
Alignment explanation
Indices: 25192988--25193065 Score: 138
Period size: 22 Copynumber: 3.5 Consensus size: 22
25192978 AAATAGGGTC
25192988 ACACGCCCGTGTAGACATAGGG
1 ACACGCCCGTGTAGACATAGGG
*
25193010 ACACGCCCATGTAGACATAGGG
1 ACACGCCCGTGTAGACATAGGG
25193032 ACACGCCCGTGTAGACATAGGG
1 ACACGCCCGTGTAGACATAGGG
*
25193054 ACACGCTCGTGT
1 ACACGCCCGTGT
25193066 GCCTTTGGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.15
Consensus pattern (22 bp):
ACACGCCCGTGTAGACATAGGG
Found at i:25195922 original size:21 final size:21
Alignment explanation
Indices: 25195896--25195943 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
25195886 TTTCACACAA
25195896 TTACAACCTATTTTAGAACTT
1 TTACAACCTATTTTAGAACTT
25195917 TTACAACCTATTTTAGAACTT
1 TTACAACCTATTTTAGAACTT
25195938 TTACAA
1 TTACAA
25195944 AATGACCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (21 bp):
TTACAACCTATTTTAGAACTT
Found at i:25197603 original size:47 final size:47
Alignment explanation
Indices: 25197538--25197696 Score: 158
Period size: 47 Copynumber: 3.2 Consensus size: 47
25197528 TTACACGGAT
** *
25197538 CACATATCACACTGATGCCATATCCCAAATATGGTCTTATAC-AGTAG
1 CACATATCACACCAATGCCATATCCCAAATATGGTCTTATACGA-AAG
*
25197585 CACATATCACACCAATGCCATATCCCAGATATGGTCTTATACGAAAG
1 CACATATCACACCAATGCCATATCCCAAATATGGTCTTATACGAAAG
* * * * *
25197632 CACATAATCACATCTCTCCGATGCCATAGCCCAACTATTGTCTTATACGGAAAT
1 CACAT-ATCACA-----CCAATGCCATATCCCAAATATGGTCTTATAC-GAAAG
25197686 CACATATCACA
1 CACATATCACA
25197697 TGTTGCCATG
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
47 46 0.49
48 7 0.07
53 32 0.34
54 9 0.10
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (47 bp):
CACATATCACACCAATGCCATATCCCAAATATGGTCTTATACGAAAG
Found at i:25197642 original size:95 final size:97
Alignment explanation
Indices: 25197472--25197679 Score: 212
Period size: 93 Copynumber: 2.1 Consensus size: 97
25197462 ATAGTAAAAT
** * *
25197472 TATGGTCTTGCACATAGTCACATATTACACACCGAAGCCATAGCCCAGCCATGGTCTTACACGGA
1 TATGGTCTTATACATAGTCACATATTACACACCGAAGCCATAGCCCAGACATGGTCTTACACGAA
* *
25197537 TCACATATCACA-CT-GATGCCATATCCCAAA
66 GCACATATCACATCTCGATGCCATAGCCCAAA
* * *
25197567 TATGGTCTTATACAGTAG-CACATA-T-CACACC-AATGCCATATCCCAGATATGGTCTTATACG
1 TATGGTCTTATACA-TAGTCACATATTACACACCGAA-GCCATAGCCCAGACATGGTCTTACACG
*
25197628 AAAGCACATAATCACATCTCTCCGATGCCATAGCCCAAC
64 -AAGCACAT-ATCACA--TCT-CGATGCCATAGCCCAAA
*
25197667 TATTGTCTTATAC
1 TATGGTCTTATAC
25197680 GGAAATCACA
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
92 2 0.02
93 29 0.31
94 7 0.08
95 24 0.26
96 3 0.03
98 2 0.02
100 26 0.28
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (97 bp):
TATGGTCTTATACATAGTCACATATTACACACCGAAGCCATAGCCCAGACATGGTCTTACACGAA
GCACATATCACATCTCGATGCCATAGCCCAAA
Found at i:25201782 original size:46 final size:46
Alignment explanation
Indices: 25201730--25201974 Score: 303
Period size: 46 Copynumber: 5.3 Consensus size: 46
25201720 TTCTGAAATG
* * * *
25201730 AAATGTGTAAGACCATGGTTGAAAGACACCATGGAAACATGATATA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATA
* * *
25201776 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATA
* *
25201822 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-G
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATA
* * * ** * *
25201867 GAATGAATAAAACCATGGTTGAAAGATACCATGGCAATGTAACATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATA
** * *
25201913 AAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATA
25201959 AAATGAGTAAGACCAT
1 AAATGAGTAAGACCAT
25201975 AGTCAAAAGA
Statistics
Matches: 175, Mismatches: 23, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 37 0.21
46 138 0.79
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATA
Found at i:25202016 original size:91 final size:89
Alignment explanation
Indices: 25201737--25202021 Score: 295
Period size: 91 Copynumber: 3.1 Consensus size: 89
25201727 ATGAAATGTG
* * * * *
25201737 TAAGACCATGGTTGAAAGACACCATGGAAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAAAGA
* * **
25201802 TACCATGGCAACAGGATATAAAATGTG
66 TACCATGGC-ACATG-TA-AAGATGAA
* * *
25201829 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAG-GAATGAATAAAACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAAAGA
25201893 TACCATGGCA-ATGTAACATGAAATGAA
66 TACCATGGCACATGTAA-A-G--ATGAA
* * * **
25201920 CAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCATAGTCAAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAAAGA
* * *
25201985 CACTATGGCATCATGTCAAAGATAAA
66 TACCATGGCA-CATGT-AAAGATGAA
25202011 TAAGACCATGG
1 TAAGACCATGG
25202022 ATGGGAGACG
Statistics
Matches: 161, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
87 1 0.01
88 3 0.02
89 2 0.01
90 1 0.01
91 84 0.52
92 62 0.39
93 1 0.01
94 5 0.03
95 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (89 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAAAGA
TACCATGGCACATGTAAAGATGAA
Found at i:25202301 original size:16 final size:17
Alignment explanation
Indices: 25202280--25202312 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25202270 ATGATGGAGC
25202280 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
25202296 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
25202313 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:25210599 original size:48 final size:48
Alignment explanation
Indices: 25210557--25210827 Score: 317
Period size: 48 Copynumber: 5.6 Consensus size: 48
25210547 CATATCGGTG
* ** **
25210557 CCGATGCCATGTCCCAGACATGGTCTTACACTAGTTCACATATCATTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA
* * * *
25210605 CCGATGCCATGTCCTAAACATGGTCTTACACCGGTACACATATCAACA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA
** *
25210653 CTAATGCCATGTCCCAGACATGGTCTTATACTGGCACACATATCAACA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA
*
25210701 CCGATGTCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA
* * * * * * * * **
25210749 CCGATGCCATGTCCTAGACTTGGTTTTACGCTGGCTCTCATCTCGGATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATC-AACA
*
25210798 CCGATCCCATGTCCCAGACATGGTCTTACA
1 CCGATGCCATGTCCCAGACATGGTCTTACA
25210828 TGGGATCTCA
Statistics
Matches: 188, Mismatches: 34, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
48 162 0.86
49 26 0.14
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA
Found at i:25211267 original size:25 final size:25
Alignment explanation
Indices: 25211239--25211289 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
25211229 TATAATTTAC
25211239 AATTTAAGTATGACATTGCATTATT
1 AATTTAAGTATGACATTGCATTATT
25211264 AATTTAAGTATGACATTGCATTATT
1 AATTTAAGTATGACATTGCATTATT
25211289 A
1 A
25211290 TTATTATCAC
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:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (25 bp):
AATTTAAGTATGACATTGCATTATT
Found at i:25220084 original size:72 final size:72
Alignment explanation
Indices: 25219967--25220107 Score: 246
Period size: 72 Copynumber: 2.0 Consensus size: 72
25219957 TCGTGGATTC
* *
25219967 ATTGACCAAGTCTGCTCACTTCATCTCGGTTAGGACAGACATCTCTTTATAGAAATTGGCTAAAC
1 ATTGACCAAATCTGCTCACTTCATCTCGGTTAGGACAGACATCTCTTTACAGAAATTGGCTAAAC
25220032 TCTATTG
66 TCTATTG
* *
25220039 ATTGACCAAATTTGCTCACTTCATCTCGGTTAGGACAGACTTCTCTTTACAGAAATTGGCTAAAC
1 ATTGACCAAATCTGCTCACTTCATCTCGGTTAGGACAGACATCTCTTTACAGAAATTGGCTAAAC
25220104 TCTA
66 TCTA
25220108 CATCACTGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (72 bp):
ATTGACCAAATCTGCTCACTTCATCTCGGTTAGGACAGACATCTCTTTACAGAAATTGGCTAAAC
TCTATTG
Found at i:25223645 original size:10 final size:10
Alignment explanation
Indices: 25223630--25223654 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25223620 AATTGATAGT
25223630 TGAATATGGG
1 TGAATATGGG
25223640 TGAATATGGG
1 TGAATATGGG
25223650 TGAAT
1 TGAAT
25223655 TGATAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (10 bp):
TGAATATGGG
Found at i:25225095 original size:21 final size:20
Alignment explanation
Indices: 25225067--25225106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
25225057 CAAAACTTGT
25225067 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
25225087 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
25225107 AAATCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:25228717 original size:16 final size:16
Alignment explanation
Indices: 25228696--25228726 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25228686 GTAACTGACA
*
25228696 TTAAAAATTAATAATT
1 TTAAAAATAAATAATT
25228712 TTAAAAATAAATAAT
1 TTAAAAATAAATAAT
25228727 AAAATAGATT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAAATAAATAATT
Found at i:25228951 original size:14 final size:15
Alignment explanation
Indices: 25228932--25228960 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25228922 ATCCCACATT
25228932 TTTCATTTTT-TTCC
1 TTTCATTTTTCTTCC
25228946 TTTCATTTTTCTTCC
1 TTTCATTTTTCTTCC
25228961 ACTTAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCATTTTTCTTCC
Found at i:25232243 original size:29 final size:30
Alignment explanation
Indices: 25232194--25232263 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
25232184 ATTTTTTGTA
*
25232194 TTTTACA-ATTTTGCCCATATTTGTTAG-G
1 TTTTACAGTTTTTGCCCATATTTGTTAGAG
* * *
25232222 TTTTACAGTTTTTGCCCCTATTTTTTAGAT
1 TTTTACAGTTTTTGCCCATATTTGTTAGAG
*
25232252 TTTTATAGTTTT
1 TTTTACAGTTTT
25232264 ACCCAGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 7 0.20
29 17 0.49
30 11 0.31
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (30 bp):
TTTTACAGTTTTTGCCCATATTTGTTAGAG
Found at i:25233867 original size:50 final size:50
Alignment explanation
Indices: 25233813--25233916 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
25233803 TATTCATATC
*
25233813 ACAAAGCCTATCAATATAACTCTAGCCTATACATGCCATATACCATATGT
1 ACAAAGCCTATCAAAATAACTCTAGCCTATACATGCCATATACCATATGT
25233863 ACAAAGCCTATCAAAATAACTCTAGCCTATACATGCCATATACCATATGT
1 ACAAAGCCTATCAAAATAACTCTAGCCTATACATGCCATATACCATATGT
25233913 ACAA
1 ACAA
25233917 CTCTCAAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (50 bp):
ACAAAGCCTATCAAAATAACTCTAGCCTATACATGCCATATACCATATGT
Found at i:25238773 original size:49 final size:49
Alignment explanation
Indices: 25238720--25238817 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
25238710 AAATACACAT
* *
25238720 AATTTCAACAAACCCATTTATGGTCGAATATCATAGGGACCTCTAGCAG
1 AATTTCAACAAACCCATATATGGTCGAATATCATAAGGACCTCTAGCAG
25238769 AATTTCAACAAACCCATATATGGTCGAATATCATAAGGACCTCTAGCAG
1 AATTTCAACAAACCCATATATGGTCGAATATCATAAGGACCTCTAGCAG
25238818 CCCAAAACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (49 bp):
AATTTCAACAAACCCATATATGGTCGAATATCATAAGGACCTCTAGCAG
Found at i:25242897 original size:20 final size:20
Alignment explanation
Indices: 25242869--25242914 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
25242859 TACAATCATC
*
25242869 TCCAATTCAAATAACCATTT
1 TCCATTTCAAATAACCATTT
*
25242889 TCCATTTCATATAACCATTT
1 TCCATTTCAAATAACCATTT
*
25242909 TTCATT
1 TCCATT
25242915 CCATACATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (20 bp):
TCCATTTCAAATAACCATTT
Found at i:25242919 original size:20 final size:20
Alignment explanation
Indices: 25242879--25242965 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
25242869 TCCAATTCAA
* *
25242879 ATAACCATTTTCCATTTCAT
1 ATAACCATTTTTCATTCCAT
25242899 ATAACCATTTTTCATTCCAT
1 ATAACCATTTTTCATTCCAT
* * * *
25242919 ACATCTATTTTTCATTTCAT
1 ATAACCATTTTTCATTCCAT
* *
25242939 ACATCCATTTTTCA-TCCA-
1 ATAACCATTTTTCATTCCAT
25242957 ATGAACCAT
1 AT-AACCAT
25242966 AGTGAAATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
18 1 0.02
19 8 0.14
20 47 0.84
ACGTcount: A:0.30, C:0.25, G:0.01, T:0.44
Consensus pattern (20 bp):
ATAACCATTTTTCATTCCAT
Found at i:25242930 original size:21 final size:20
Alignment explanation
Indices: 25242883--25242953 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
25242873 ATTCAAATAA
* * * *
25242883 CCATTTTCCATTTCATATAA
1 CCATTTTTCATTCCATACAT
25242903 CCATTTTTCATTCCATACAT
1 CCATTTTTCATTCCATACAT
* *
25242923 CTATTTTTCATTTCATACAT
1 CCATTTTTCATTCCATACAT
25242943 CCATTTTTCAT
1 CCATTTTTCAT
25242954 CCAATGAACC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (20 bp):
CCATTTTTCATTCCATACAT
Found at i:25246151 original size:13 final size:13
Alignment explanation
Indices: 25246135--25246195 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
25246125 ACCAAATTTT
25246135 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
25246148 TCAAAAGCACTTT
1 TCAAAAGCACTTC
***
25246161 TCCCCAGCACTTC
1 TCAAAAGCACTTC
*
25246174 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
25246187 TTAAAAGCA
1 TCAAAAGCA
25246196 TTGCCAAACT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.36, C:0.30, G:0.08, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:25246195 original size:26 final size:26
Alignment explanation
Indices: 25246131--25246195 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
25246121 TTAAACCAAA
25246131 TTTTTCAAAAGCACTTCTCAAAAGCAC
1 TTTTT-AAAAGCACTTCTCAAAAGCAC
****
25246158 TTTTCCCCAGCACTTCTCAAAAGCAC
1 TTTTTAAAAGCACTTCTCAAAAGCAC
25246184 TTTTTAAAAGCA
1 TTTTTAAAAGCA
25246196 TTGCCAAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTTTAAAAGCACTTCTCAAAAGCAC
Found at i:25248937 original size:2 final size:2
Alignment explanation
Indices: 25248932--25248957 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25248922 TTACTCTCTT
25248932 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
25248958 ATAGTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25252496 original size:2 final size:2
Alignment explanation
Indices: 25252489--25252518 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25252479 TGGATTGCTG
25252489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25252519 TGTTTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25253919 original size:45 final size:45
Alignment explanation
Indices: 25253855--25253970 Score: 162
Period size: 45 Copynumber: 2.6 Consensus size: 45
25253845 GTAGCAGCAG
* * * *
25253855 CAGTAACATTAATAGTATTCAACACACAAAGTG-CTGAATCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGTC-GAATCGGTAA
*
25253900 CAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCGGTAA
*
25253945 CAGTAACAGTAACAGTAGTCGACACA
1 CAGTAACAGTAACAGTATTCGACACA
25253971 TAAGTGCCTG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
45 62 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCGGTAA
Found at i:25255546 original size:5 final size:5
Alignment explanation
Indices: 25255536--25255573 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
25255526 ATAATCAATT
25255536 ATATA ATATA ATATA ATATA ATATA ATATA TATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA -ATATA AT
25255574 CTAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:25257157 original size:46 final size:46
Alignment explanation
Indices: 25257072--25257164 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
25257062 CAAGGCTTAA
*
25257072 TATTCCTGTATTCTCGAGTCCGCAACATATGCAGAAGCTCGGAACC
1 TATTCATGTATTCTCGAGTCCGCAACATATGCAGAAGCTCGGAACC
* * * *
25257118 TATTCATGTATTCTCGAGTTCGCTATATATTCA-AGAGCTCGGAACC
1 TATTCATGTATTCTCGAGTCCGCAACATATGCAGA-AGCTCGGAACC
25257164 T
1 T
25257165 GGGCGAACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (46 bp):
TATTCATGTATTCTCGAGTCCGCAACATATGCAGAAGCTCGGAACC
Found at i:25259965 original size:28 final size:26
Alignment explanation
Indices: 25259888--25260003 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 26
25259878 TAGCATGGCT
* * *
25259888 ACCAGAATAGATATTGTGACAGAGTC
1 ACCAGAACAGATATTGTGGCAGAGCC
*
25259914 ACTAGATACAGATATTGTGGCAGAGCC
1 ACCAGA-ACAGATATTGTGGCAGAGCC
25259941 ACCAGGAACAGATATTTGTGGCAGAGCC
1 ACCA-GAACAGATA-TTGTGGCAGAGCC
* *
25259969 ACTAGATCAGATATTTGTGGCAGAGCC
1 ACCAGAACAGATA-TTGTGGCAGAGCC
25259996 ACCAGAAC
1 ACCAGAAC
25260004 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.06
27 55 0.71
28 18 0.23
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (26 bp):
ACCAGAACAGATATTGTGGCAGAGCC
Found at i:25259972 original size:55 final size:54
Alignment explanation
Indices: 25259888--25260000 Score: 167
Period size: 55 Copynumber: 2.1 Consensus size: 54
25259878 TAGCATGGCT
* *
25259888 ACCA-GAATAGATATTGTGACAGAGTCACTAGATACAGATA-TTGTGGCAGAGCC
1 ACCAGGAACAGATATTGTGACAGAGCCACTAGAT-CAGATATTTGTGGCAGAGCC
*
25259941 ACCAGGAACAGATATTTGTGGCAGAGCCACTAGATCAGATATTTGTGGCAGAGCC
1 ACCAGGAACAGATA-TTGTGACAGAGCCACTAGATCAGATATTTGTGGCAGAGCC
25259996 ACCAG
1 ACCAG
25260001 AACGCTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
53 4 0.07
54 14 0.26
55 36 0.67
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
ACCAGGAACAGATATTGTGACAGAGCCACTAGATCAGATATTTGTGGCAGAGCC
Found at i:25260163 original size:26 final size:26
Alignment explanation
Indices: 25260107--25260166 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
25260097 AAATTAACCC
* *
25260107 TGGGGTATAATGGTAATTTTGCACCT
1 TGGGGTATAATAGTAATTTTGCAACT
*
25260133 AGGGGTATAATAGTAATTTT-CATACT
1 TGGGGTATAATAGTAATTTTGCA-ACT
25260159 TGGGGTAT
1 TGGGGTAT
25260167 TTTAGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (26 bp):
TGGGGTATAATAGTAATTTTGCAACT
Found at i:25262737 original size:8 final size:8
Alignment explanation
Indices: 25262698--25262722 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25262688 ATATAGACTA
25262698 AATAAAAT
1 AATAAAAT
25262706 AATAAAAT
1 AATAAAAT
25262714 AATAAAAT
1 AATAAAAT
25262722 A
1 A
25262723 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:25262772 original size:29 final size:31
Alignment explanation
Indices: 25262700--25262773 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
25262690 ATAGACTAAA
25262700 TAAAATAA-TA-AAATAATAAAATATCTTAT
1 TAAAATAATTATAAATAATAAAATATCTTAT
* *
25262729 TAAAATATTTAATAAATAAT-AATTATC-TAGT
1 TAAAATAATT-ATAAATAATAAAATATCTTA-T
25262760 T-AAATAATTATAAA
1 TAAAATAATTATAAA
25262774 ATATCACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 12 0.32
30 10 0.26
31 9 0.24
32 7 0.18
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (31 bp):
TAAAATAATTATAAATAATAAAATATCTTAT
Found at i:25262776 original size:30 final size:32
Alignment explanation
Indices: 25262707--25262776 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 32
25262697 AAATAAAATA
*
25262707 ATAAAATAATAAAATATCTTATTAAAATATTT
1 ATAAAATAATAAAATATCTTATTAAAATAATT
*
25262739 A-ATAAATAAT-AATTATC-TAGTT-AAATAATT
1 ATA-AAATAATAAAATATCTTA-TTAAAATAATT
25262769 ATAAAATA
1 ATAAAATA
25262777 TCACCAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
30 15 0.45
31 10 0.30
32 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (32 bp):
ATAAAATAATAAAATATCTTATTAAAATAATT
Found at i:25274475 original size:24 final size:23
Alignment explanation
Indices: 25274447--25274499 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
25274437 TTAAGTAATT
25274447 AATATAAATTATTTGTAAA-ATTTA
1 AATATAAATT-TTT-TAAATATTTA
*
25274471 TATAT-AATTTTTTAAATATTTA
1 AATATAAATTTTTTAAATATTTA
25274493 AATATAA
1 AATATAA
25274500 TAATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 12 0.48
23 5 0.20
24 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AATATAAATTTTTTAAATATTTA
Found at i:25274526 original size:23 final size:24
Alignment explanation
Indices: 25274485--25274547 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
25274475 TAATTTTTTA
25274485 AATATTTAAATATAATAATA-AAT
1 AATATTTAAATATAATAATATAAT
* *
25274508 AATATTTAAATA-ATTTAATATTAT
1 AATATTTAAATATA-ATAATATAAT
*
25274532 AATATGTAAATTATAA
1 AATATTTAAA-TATAA
25274548 ATTAATCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 17 0.53
24 11 0.34
25 2 0.06
26 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATTTAAATATAATAATATAAT
Found at i:25275040 original size:30 final size:30
Alignment explanation
Indices: 25274984--25275072 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
25274974 TAAAATTATT
** *
25274984 AAATTTAATTAGTAAATTAT-TTTAATTTA
1 AAATTTAACAAGTAATTTATATTTAATTTA
*
25275013 AAATTTCACAAGTAATTTATATTTAATTTA
1 AAATTTAACAAGTAATTTATATTTAATTTA
*
25275043 AAATTTAACAAATAATTTA-A-TT-ATTTA
1 AAATTTAACAAGTAATTTATATTTAATTTA
25275070 AAA
1 AAA
25275073 GTTATTTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.15
28 2 0.04
29 17 0.32
30 26 0.49
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
AAATTTAACAAGTAATTTATATTTAATTTA
Found at i:25278850 original size:49 final size:49
Alignment explanation
Indices: 25278790--25278891 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
25278780 GGCACTCTAG
*
25278790 ATGGCCGCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCGTGTT
1 ATGGCCCCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCGTGTT
* *
25278839 ATGGCCCCCACAGATCATAATGAATATACTCCAACTTTCCCTTCGTGTT
1 ATGGCCCCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCGTGTT
25278888 ATGG
1 ATGG
25278892 ATTCCTCTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (49 bp):
ATGGCCCCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCGTGTT
Found at i:25282937 original size:18 final size:18
Alignment explanation
Indices: 25282913--25282952 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
25282903 GGCGCGATCT
25282913 ATTTTTTT-AATAATATA
1 ATTTTTTTAAATAATATA
* *
25282930 ATTTTTTTAAATATTATT
1 ATTTTTTTAAATAATATA
25282948 ATTTT
1 ATTTT
25282953 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTTTAAATAATATA
Found at i:25282942 original size:15 final size:16
Alignment explanation
Indices: 25282913--25282959 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
25282903 GGCGCGATCT
25282913 ATTTTTTTAATAATATA
1 ATTTTTTT-ATAATATA
*
25282930 ATTTTTTTA-AATATT
1 ATTTTTTTATAATATA
* *
25282945 ATTATTTTATTATAT
1 ATTTTTTTATAATAT
25282960 TTTAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 13 0.50
16 5 0.19
17 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTTATAATATA
Found at i:25287169 original size:12 final size:12
Alignment explanation
Indices: 25287128--25287194 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
25287118 CCTGAGTGTA
25287128 GCTCCGGCTCTG
1 GCTCCGGCTCTG
*
25287140 GC-CGCCGCTCTG
1 GCTC-CGGCTCTG
* *
25287152 GGTCCGGCACTG
1 GCTCCGGCTCTG
*
25287164 CCTCCGGCTCTG
1 GCTCCGGCTCTG
*
25287176 GCTCTGGCTCTG
1 GCTCCGGCTCTG
25287188 GCTCCGG
1 GCTCCGG
25287195 AGTTGGTGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.95
13 1 0.02
ACGTcount: A:0.01, C:0.42, G:0.34, T:0.22
Consensus pattern (12 bp):
GCTCCGGCTCTG
Found at i:25288797 original size:11 final size:11
Alignment explanation
Indices: 25288783--25288810 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25288773 ACATTATATC
25288783 AAAATTACATT
1 AAAATTACATT
25288794 AAAATTACATT
1 AAAATTACATT
25288805 AAAATT
1 AAAATT
25288811 TCTTACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTACATT
Found at i:25289893 original size:3 final size:3
Alignment explanation
Indices: 25289867--25289934 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
25289857 TAACATATTT
* * * *
25289867 TTC TTC TT- TTCC TCC TTC TCC TTC TTC TTC TTC TTC TTT TTC TTT
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
25289912 TTT TTC TTC TTC TT- TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC T-TC TT
25289935 TGCTGTTGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 45 0.85
4 4 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:25290165 original size:7 final size:8
Alignment explanation
Indices: 25290143--25290168 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
25290133 CCGACTGAAT
25290143 TTTAAAAA
1 TTTAAAAA
25290151 TTTAAAAA
1 TTTAAAAA
25290159 TTTAAAAA
1 TTTAAAAA
25290167 TT
1 TT
25290169 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTAAAAA
Found at i:25290200 original size:16 final size:17
Alignment explanation
Indices: 25290181--25290224 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
25290171 TAAAATATAA
*
25290181 TAAAATAATAATATT-T
1 TAAAAAAATAATATTAT
*
25290197 TAAAAAAATTATATTAT
1 TAAAAAAATAATATTAT
25290214 TAAAAAAATAA
1 TAAAAAAATAA
25290225 GTCGCACCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAAAATAATATTAT
Found at i:25290204 original size:19 final size:19
Alignment explanation
Indices: 25290182--25290224 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
25290172 AAAATATAAT
25290182 AAAATAATAATATT-TTAAA
1 AAAATAAT-ATATTATTAAA
25290201 AAAAT--TATATTATTAAA
1 AAAATAATATATTATTAAA
25290218 AAAATAA
1 AAAATAA
25290225 GTCGCACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
19 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAATATATTATTAAA
Found at i:25290993 original size:12 final size:12
Alignment explanation
Indices: 25290976--25291035 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 12
25290966 TAAGTGTATT
25290976 TAACAAATTTAA
1 TAACAAATTTAA
25290988 TAACAAATTTAACA
1 TAACAAATTT-A-A
*
25291002 TTTCAA-AAATATAA
1 --T-AACAAATTTAA
25291016 TAACAAATTTAA
1 TAACAAATTTAA
25291028 TAACAAAT
1 TAACAAAT
25291036 CATATTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
11 2 0.05
12 26 0.65
13 1 0.03
14 2 0.05
15 1 0.03
16 6 0.15
17 2 0.05
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (12 bp):
TAACAAATTTAA
Found at i:25291052 original size:38 final size:39
Alignment explanation
Indices: 25290976--25291065 Score: 146
Period size: 38 Copynumber: 2.3 Consensus size: 39
25290966 TAAGTGTATT
25290976 TAACAAATTTAATAACAAATTTAACATTTCAAAAATATAA
1 TAACAAATTTAATAACAAA-TTAACATTTCAAAAATATAA
* *
25291016 TAACAAATTTAATAACAAA-TCATATTTCAAAAATATAA
1 TAACAAATTTAATAACAAATTAACATTTCAAAAATATAA
25291054 TAACAAATTTAA
1 TAACAAATTTAA
25291066 CATTTTAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 29 0.60
40 19 0.40
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (39 bp):
TAACAAATTTAATAACAAATTAACATTTCAAAAATATAA
Found at i:25291061 original size:12 final size:12
Alignment explanation
Indices: 25291008--25291061 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
25290998 AACATTTCAA
25291008 AAATATAATAAC
1 AAATATAATAAC
*
25291020 AAATTTAATAAC
1 AAATATAATAAC
*
25291032 AAATCATATTTCAA-
1 AAAT-ATA-AT-AAC
25291046 AAATATAATAAC
1 AAATATAATAAC
25291058 AAAT
1 AAAT
25291062 TTAACATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.06
12 20 0.59
13 5 0.15
14 5 0.15
15 2 0.06
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAATAAC
Found at i:25292876 original size:46 final size:47
Alignment explanation
Indices: 25292787--25292960 Score: 164
Period size: 46 Copynumber: 3.8 Consensus size: 47
25292777 GTATATCTGT
*
25292787 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GAC--ACATCTCGTA
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAG-CTTACGTCTCGTA
* * *
25292833 GCCGATG-CATGTTCTAGACATGTCTTACACTAGCTTACGTCTCGAA
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGTA
* ** * * *
25292879 GCTGA-AACATGTCCCAAACATGTCTTACACTAGCACT-CGTCTCAATA
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGC-TTACGTCTC-GTA
*
25292926 -CGGATGCCATGTCCCAGACATGTCTTACACTAGCT
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCT
25292961 CACACGAGTG
Statistics
Matches: 104, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
44 11 0.11
45 13 0.12
46 52 0.50
47 28 0.27
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGTA
Found at i:25296228 original size:29 final size:29
Alignment explanation
Indices: 25296188--25296243 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
25296178 TTTTAGCGGC
25296188 GTGTTTGTGGGAAAAGCGCCGCTAAAAGT
1 GTGTTTGTGGGAAAAGCGCCGCTAAAAGT
*
25296217 GTGTTTGTGGGAAAAGTGCCGCTAAAA
1 GTGTTTGTGGGAAAAGCGCCGCTAAAA
25296244 ATCATGGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.25
Consensus pattern (29 bp):
GTGTTTGTGGGAAAAGCGCCGCTAAAAGT
Found at i:25296659 original size:21 final size:21
Alignment explanation
Indices: 25296633--25296685 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
25296623 GCTACTGCCT
* *
25296633 CTGCCTCTCTCGCTGTTGTCG
1 CTGCCTCCCTCGCTGCTGTCG
*
25296654 CTGCCTCCCTCGTTGCTGTCG
1 CTGCCTCCCTCGCTGCTGTCG
*
25296675 CTCCCTCCCTC
1 CTGCCTCCCTC
25296686 TCTACTGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.19, T:0.34
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGTCG
Found at i:25297130 original size:13 final size:14
Alignment explanation
Indices: 25297104--25297132 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25297094 ACTAATGAGG
25297104 AATTAAACCATTAT
1 AATTAAACCATTAT
25297118 AATTAAA-CATTAT
1 AATTAAACCATTAT
25297131 AA
1 AA
25297133 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:25298993 original size:137 final size:137
Alignment explanation
Indices: 25298785--25299071 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
25298775 CTATTGGCCT
** *
25298785 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATCAGAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATCACAATAAACTGGGCCTT
25298850 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
25298915 CATATGC
131 CATATGC
*
25298922 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATCACAATAAACTGGGCCTT
25298987 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
25299052 CATATGC
131 CATATGC
25299059 AAGCCCATTTGGG
1 AAGCCCATTTGGG
25299072 GAGACTACTC
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATCACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:25299348 original size:26 final size:26
Alignment explanation
Indices: 25299319--25299371 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
25299309 TCAAACATGC
25299319 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
25299345 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
25299371 A
1 A
25299372 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:25300891 original size:26 final size:26
Alignment explanation
Indices: 25300855--25300990 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
25300845 CATGAAATTC
25300855 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
25300881 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
25300907 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
25300933 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
25300959 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
25300985 TTATCA
1 TTATCA
25300991 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:25303686 original size:12 final size:12
Alignment explanation
Indices: 25303669--25303703 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
25303659 ATCCTCTTTG
25303669 TCAGATTCATCA
1 TCAGATTCATCA
25303681 TCAGATTCATCA
1 TCAGATTCATCA
25303693 TCAGATTCATC
1 TCAGATTCATC
25303704 CCTCGATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (12 bp):
TCAGATTCATCA
Found at i:25305436 original size:9 final size:9
Alignment explanation
Indices: 25305422--25305623 Score: 230
Period size: 9 Copynumber: 22.7 Consensus size: 9
25305412 TAAGTATAAT
25305422 TAAGTTATG
1 TAAGTTATG
25305431 TAAGTTATG
1 TAAGTTATG
* * **
25305440 ATATGATACC
1 -TAAGTTATG
*
25305450 T-ACTTATG
1 TAAGTTATG
25305458 T-A-TTATG
1 TAAGTTATG
25305465 TAAGTTATG
1 TAAGTTATG
25305474 TAAGTTATG
1 TAAGTTATG
*
25305483 TGAGTTATG
1 TAAGTTATG
*
25305492 TGAGTTATG
1 TAAGTTATG
*
25305501 TGAGTTATG
1 TAAGTTATG
25305510 TAAGTTATG
1 TAAGTTATG
*
25305519 TGAGTTATG
1 TAAGTTATG
25305528 TAAGTTATG
1 TAAGTTATG
* *
25305537 TGAGTTATA
1 TAAGTTATG
25305546 TAAGTTATG
1 TAAGTTATG
* *
25305555 TGAGTTATA
1 TAAGTTATG
25305564 TAAGTTATG
1 TAAGTTATG
25305573 TAAGTTATG
1 TAAGTTATG
* *
25305582 TGAGTTATA
1 TAAGTTATG
25305591 TAAGTTATG
1 TAAGTTATG
25305600 TAAGTTATG
1 TAAGTTATG
*
25305609 TGAGTTATG
1 TAAGTTATG
25305618 TAAGTT
1 TAAGTT
25305624 CAATTATATA
Statistics
Matches: 163, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
7 6 0.04
8 5 0.03
9 147 0.90
10 5 0.03
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:25305483 original size:18 final size:18
Alignment explanation
Indices: 25305460--25305623 Score: 256
Period size: 18 Copynumber: 9.1 Consensus size: 18
25305450 TACTTATGTA
*
25305460 TTATGTAAGTTATGTAAG
1 TTATGTGAGTTATGTAAG
*
25305478 TTATGTGAGTTATGTGAG
1 TTATGTGAGTTATGTAAG
25305496 TTATGTGAGTTATGTAAG
1 TTATGTGAGTTATGTAAG
25305514 TTATGTGAGTTATGTAAG
1 TTATGTGAGTTATGTAAG
*
25305532 TTATGTGAGTTATATAAG
1 TTATGTGAGTTATGTAAG
*
25305550 TTATGTGAGTTATATAAG
1 TTATGTGAGTTATGTAAG
* *
25305568 TTATGTAAGTTATGTGAG
1 TTATGTGAGTTATGTAAG
* *
25305586 TTATATAAGTTATGTAAG
1 TTATGTGAGTTATGTAAG
25305604 TTATGTGAGTTATGTAAG
1 TTATGTGAGTTATGTAAG
25305622 TT
1 TT
25305624 CAATTATATA
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 135 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (18 bp):
TTATGTGAGTTATGTAAG
Found at i:25305758 original size:19 final size:19
Alignment explanation
Indices: 25305734--25305836 Score: 70
Period size: 19 Copynumber: 5.3 Consensus size: 19
25305724 TATTTAAATA
25305734 AATTAATCCAAATTATATT
1 AATTAATCCAAATTATATT
* *
25305753 AATTAAAT--AATATTTAAATA
1 AATT-AATCCAA-A-TTATATT
25305773 AATTAATCCAAATTATATT
1 AATTAATCCAAATTATATT
* * *
25305792 AAATAAAT--AATATTTACATA
1 -AATTAATCCAA-A-TTATATT
*
25305812 AATTAATCCAAATTATAAT
1 AATTAATCCAAATTATATT
25305831 AATTAA
1 AATTAA
25305837 AATAACATGT
Statistics
Matches: 63, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
18 4 0.06
19 30 0.48
20 25 0.40
21 4 0.06
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAATCCAAATTATATT
Found at i:25305767 original size:39 final size:39
Alignment explanation
Indices: 25305723--25305837 Score: 203
Period size: 39 Copynumber: 2.9 Consensus size: 39
25305713 AAATTCTTAT
25305723 ATATTTAAATAAATTAATCCAAATTATATTAATTAAATA
1 ATATTTAAATAAATTAATCCAAATTATATTAATTAAATA
*
25305762 ATATTTAAATAAATTAATCCAAATTATATTAAATAAATA
1 ATATTTAAATAAATTAATCCAAATTATATTAATTAAATA
* *
25305801 ATATTTACATAAATTAATCCAAATTATAATAATTAAA
1 ATATTTAAATAAATTAATCCAAATTATATTAATTAAA
25305838 ATAACATGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (39 bp):
ATATTTAAATAAATTAATCCAAATTATATTAATTAAATA
Found at i:25305858 original size:22 final size:23
Alignment explanation
Indices: 25305833--25305879 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
25305823 ATTATAATAA
*
25305833 TTAAAATA-ACATGTCTTTTGCT
1 TTAAAATAGACATGTCTTTTACT
*
25305855 TTAATATAGACATGTCTTTTACT
1 TTAAAATAGACATGTCTTTTACT
25305878 TT
1 TT
25305880 TATTAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.49
Consensus pattern (23 bp):
TTAAAATAGACATGTCTTTTACT
Found at i:25307042 original size:30 final size:31
Alignment explanation
Indices: 25307006--25307073 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
25306996 GGTTTCATAT
*
25307006 CAGTCACTCAAC-TTTTAAAAAA-TAACAAAA
1 CAGTCACT-AACGTTATAAAAAAGTAACAAAA
*
25307036 CAGTCACTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACTAACGTTATAAAAAAGTAACAAAA
25307067 CAGTCAC
1 CAGTCAC
25307074 CGATTAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 17 0.50
31 14 0.41
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.21
Consensus pattern (31 bp):
CAGTCACTAACGTTATAAAAAAGTAACAAAA
Found at i:25307135 original size:21 final size:21
Alignment explanation
Indices: 25307109--25307148 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
25307099 TCACGGGACT
25307109 GCTGATGTGGCAAGTTAACCA
1 GCTGATGTGGCAAGTTAACCA
25307130 GCTGATGTGGCAAGTTAAC
1 GCTGATGTGGCAAGTTAAC
25307149 TTGCCACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACCA
Found at i:25307232 original size:3 final size:3
Alignment explanation
Indices: 25307224--25307268 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
25307214 TTAATAACAG
*
25307224 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
25307269 GATTGTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:25308557 original size:3 final size:3
Alignment explanation
Indices: 25308549--25308608 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
25308539 CTATTTTTTC
* * * *
25308549 TCT TCT TCT TCT TTT TCT TC- TCC TCT TCT TCT TTT TCT TAT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
25308596 TCT TTT TCT TCT T
1 TCT TCT TCT TCT T
25308609 TTTTTCTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:25308566 original size:9 final size:9
Alignment explanation
Indices: 25308543--25308629 Score: 88
Period size: 9 Copynumber: 9.6 Consensus size: 9
25308533 ACATCTCTAT
25308543 TTTTTC-TC
1 TTTTTCTTC
*
25308551 TTCTTCTTC
1 TTTTTCTTC
25308560 TTTTTCTTC
1 TTTTTCTTC
*
25308569 TCCTCTTCTTC
1 T--TTTTCTTC
*
25308580 TTTTTCTTA
1 TTTTTCTTC
*
25308589 TTCTTCTTC
1 TTTTTCTTC
25308598 TTTTTCTTC
1 TTTTTCTTC
25308607 TTTTT-TTC
1 TTTTTCTTC
*
25308615 TTTTTTTTC
1 TTTTTCTTC
25308624 TCTTTT
1 T-TTTT
25308630 TAAACCCTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
8 13 0.20
9 41 0.62
10 4 0.06
11 8 0.12
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:25308621 original size:20 final size:19
Alignment explanation
Indices: 25308554--25308630 Score: 75
Period size: 20 Copynumber: 4.0 Consensus size: 19
25308544 TTTTCTCTTC
** *
25308554 TTCTTCTTTTTCTTCTCCTC
1 TTCTTCTTTTTC-TCTTTTT
* *
25308574 TTCTTCTTTTTCT-TATTC
1 TTCTTCTTTTTCTCTTTTT
25308592 TTCTTCTTTTTCTTCTTTTT
1 TTCTTCTTTTTC-TCTTTTT
*
25308612 TTCTTTTTTTTCTCTTTTT
1 TTCTTCTTTTTCTCTTTTT
25308631 AAACCCTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
18 15 0.30
19 9 0.18
20 26 0.52
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.75
Consensus pattern (19 bp):
TTCTTCTTTTTCTCTTTTT
Found at i:25308622 original size:12 final size:12
Alignment explanation
Indices: 25308551--25308630 Score: 65
Period size: 12 Copynumber: 6.7 Consensus size: 12
25308541 ATTTTTTCTC
*
25308551 TTCTTCTTCTTT
1 TTCTTTTTCTTT
* *
25308563 TTCTTCTCCTCTTC
1 TTCTT-T-TTCTTT
*
25308577 TTCTTTTTCTTA
1 TTCTTTTTCTTT
*
25308589 TTCTTCTTCTTT
1 TTCTTTTTCTTT
*
25308601 TTCTTCTT-TTT
1 TTCTTTTTCTTT
25308612 TTCTTTTT-TTT
1 TTCTTTTTCTTT
*
25308623 CTCTTTTT
1 TTCTTTTT
25308631 AAACCCTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
11 20 0.35
12 27 0.47
13 1 0.02
14 9 0.16
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:25308622 original size:38 final size:38
Alignment explanation
Indices: 25308542--25308624 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
25308532 TACATCTCTA
*
25308542 TTTTTTC-TCTTCTTCTTCTTTTTCTTCTCCTCTTCTT
1 TTTTTTCTTATTCTTCTTCTTTTTCTTCTCCTCTTCTT
* ** *
25308579 CTTTTTCTTATTCTTCTTCTTTTTCTTCTTTTTTTCTT
1 TTTTTTCTTATTCTTCTTCTTTTTCTTCTCCTCTTCTT
25308617 TTTTTTCT
1 TTTTTTCT
25308625 CTTTTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 6 0.15
38 33 0.85
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (38 bp):
TTTTTTCTTATTCTTCTTCTTTTTCTTCTCCTCTTCTT
Found at i:25311937 original size:7 final size:7
Alignment explanation
Indices: 25311929--25312022 Score: 80
Period size: 7 Copynumber: 13.4 Consensus size: 7
25311919 CATAAACTCT
*
25311929 TAACCCT
1 TAACCCC
25311936 TAACCCC
1 TAACCCC
25311943 TAACCCC
1 TAACCCC
25311950 TAACCCC
1 TAACCCC
* *
25311957 TAATCCT
1 TAACCCC
* *
25311964 TATCCCA
1 TAACCCC
25311971 TAACCCC
1 TAACCCC
* *
25311978 TAATCCT
1 TAACCCC
* *
25311985 TATCTCC
1 TAACCCC
25311992 TAACCCC
1 TAACCCC
** *
25311999 TAATTCT
1 TAACCCC
25312006 TAACCCC
1 TAACCCC
25312013 TAACCCC
1 TAACCCC
25312020 TAA
1 TAA
25312023 ATCTTAAACT
Statistics
Matches: 65, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 65 1.00
ACGTcount: A:0.29, C:0.45, G:0.00, T:0.27
Consensus pattern (7 bp):
TAACCCC
Found at i:25311953 original size:21 final size:21
Alignment explanation
Indices: 25311943--25312022 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
25311933 CCTTAACCCC
25311943 TAACCCCTAACCCCTAATCCT
1 TAACCCCTAACCCCTAATCCT
* *
25311964 TATCCCATAACCCCTAATCCT
1 TAACCCCTAACCCCTAATCCT
* * *
25311985 TATCTCCTAACCCCTAATTCT
1 TAACCCCTAACCCCTAATCCT
25312006 TAACCCCTAACCCCTAA
1 TAACCCCTAACCCCTAA
25312023 ATCTTAAACT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.28
Consensus pattern (21 bp):
TAACCCCTAACCCCTAATCCT
Found at i:25312027 original size:21 final size:21
Alignment explanation
Indices: 25311907--25312029 Score: 97
Period size: 21 Copynumber: 5.8 Consensus size: 21
25311897 CCTTAGACTA
* * *
25311907 TAACCCCTAAATCATAAACTCT
1 TAACCCCTAAATC-TTAACCCC
* ** *
25311929 TAACCCTTAACCCCTAACCCC
1 TAACCCCTAAATCTTAACCCC
* *
25311950 TAACCCCT-AATCCTTATCCCA
1 TAACCCCTAAAT-CTTAACCCC
* *
25311971 TAACCCCT-AATCCTTATCTCC
1 TAACCCCTAAAT-CTTAACCCC
*
25311992 TAACCCCTAATTCTTAACCCC
1 TAACCCCTAAATCTTAACCCC
25312013 TAACCCCTAAATCTTAA
1 TAACCCCTAAATCTTAA
25312030 ACTCCAACTA
Statistics
Matches: 80, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.01
21 67 0.84
22 12 0.15
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.28
Consensus pattern (21 bp):
TAACCCCTAAATCTTAACCCC
Found at i:25315729 original size:9 final size:9
Alignment explanation
Indices: 25315715--25315743 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25315705 CTAAGGTGAC
25315715 TTTATTTAT
1 TTTATTTAT
25315724 TTTATTTAT
1 TTTATTTAT
25315733 TTTATTT-T
1 TTTATTTAT
25315741 TTT
1 TTT
25315744 CTTTTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTATTTAT
Found at i:25316433 original size:3 final size:3
Alignment explanation
Indices: 25316425--25316498 Score: 100
Period size: 3 Copynumber: 25.3 Consensus size: 3
25316415 ATCTAAGATG
* *
25316425 TTA TTA TTA CTC TTA TT- TTCA -TA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
25316468 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25316499 CATCTTATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 5 0.08
3 58 0.92
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:25316937 original size:3 final size:3
Alignment explanation
Indices: 25316916--25317130 Score: 52
Period size: 3 Copynumber: 72.0 Consensus size: 3
25316906 TTATTACTTG
* * * *
25316916 TAT TAT TAC TAT TAA TAT TAT TAT TAT TAC T-T TAC TAT T-T TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* * * * *
25316960 T-T AAT GTAT TAC TAA TAT TAC TCT TAT T-T TCAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
* * * * * * ***
25317005 TAC CAT TACT CT-T TAT TGT TAT TGT CAT TAT T-T CTAT TTT TAT CGC
1 TAT TAT TA-T -TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * *
25317051 TAT TAT T-T TAT CAC TAA TAC TAT TAT TAT TA- TATT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
25317095 TAT TACT T-T TAT TAT AAC TAC TAC TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25317131 AGTTTTATAT
Statistics
Matches: 148, Mismatches: 47, Indels: 34
0.65 0.21 0.15
Matches are distributed among these distances:
2 14 0.09
3 121 0.82
4 12 0.08
5 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:25322173 original size:28 final size:28
Alignment explanation
Indices: 25322141--25322209 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
25322131 GCGTAGATCA
25322141 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
25322169 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
25322197 CGATA-TACCCCTA
1 CGAAATTACCCCTA
25322210 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:25330885 original size:2 final size:2
Alignment explanation
Indices: 25330878--25330907 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25330868 TTATTATTTA
25330878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25330908 GTGTAGTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25331175 original size:21 final size:21
Alignment explanation
Indices: 25331136--25331187 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
25331126 AAGTGAATGG
25331136 AATTATATTGAATTGAAAATATA
1 AATTA-ATT-AATTGAAAATATA
*
25331159 CAGTTAATTAATT-AAAATATA
1 -AATTAATTAATTGAAAATATA
25331180 AATTAATT
1 AATTAATT
25331188 GAAAAGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 4 0.15
23 3 0.12
24 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (21 bp):
AATTAATTAATTGAAAATATA
Found at i:25331843 original size:18 final size:18
Alignment explanation
Indices: 25331553--25331847 Score: 177
Period size: 18 Copynumber: 16.1 Consensus size: 18
25331543 AAAGGTATAA
* *
25331553 AATAACTGATTATTACTG
1 AATAATTGATTGTTACTG
* *
25331571 AATAATTGACTGTTACCG
1 AATAATTGATTGTTACTG
*
25331589 AATAATTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
25331607 GATAATAG-TCTGTTACTG
1 AATAATTGAT-TGTTACTG
* *
25331625 AATAATTGAATATTACTG
1 AATAATTGATTGTTACTG
**
25331643 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
*
25331661 AATAATTGATTGTCACTG
1 AATAATTGATTGTTACTG
* * *
25331679 AATAAATGACTATTACTG
1 AATAATTGATTGTTACTG
* * **
25331697 AATACTTAATTACTACTG
1 AATAATTGATTGTTACTG
*
25331715 AAT-ATCTGATT-TTACTA
1 AATAAT-TGATTGTTACTG
*
25331732 AATAATTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
25331750 GATAATCGATCAATTGGTCGATACTG
1 AATAAT---T-GATT-GT---TACTG
* * *
25331776 AATAACT-AGTTATTATTG
1 AATAATTGA-TTGTTACTG
*
25331794 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
25331812 AATAAGTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
25331830 AATAAATAATTGTT-CTG
1 AATAATTGATTGTTACTG
25331847 A
1 A
25331848 TTGTTAATGA
Statistics
Matches: 213, Mismatches: 49, Indels: 31
0.73 0.17 0.11
Matches are distributed among these distances:
17 16 0.08
18 177 0.83
19 1 0.00
21 3 0.01
22 4 0.02
23 3 0.01
26 9 0.04
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:25336263 original size:44 final size:44
Alignment explanation
Indices: 25336203--25336534 Score: 204
Period size: 44 Copynumber: 7.5 Consensus size: 44
25336193 TACAGATCTT
25336203 AACCCCTTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
1 AACCCC-TAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
* * * ** * ** *
25336248 AACCCCTAAGCAGTAGGGTAACAGGTTGAAAATTTACAGATCTTA
1 AACCCCTAAGCAGTAGGGAAACAGATCG-AAGGTGATGGACCTTA
* * * *
25336293 ACCCCCTAAGCAGTAGGGAAATAGATTGAAGGTGATGGGCCTTA
1 AACCCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
** * * * ** * ** *
25336337 AATGCCTAAGCAGTAGGGTAACAG-GCTAAATTTACAGATCTT-
1 AACCCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
* * * *
25336379 ATCACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGGCTTTA
1 AAC-CCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
* * * ** * ** *
25336424 AACCCCTAAGCAGTAGGGTAACAG-GCTAAATTTACAGATCTT-
1 AACCCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
* * ** *
25336466 ATCACCCTAAGCAGTACGGAAACAGATCGAAGGCAATGGGCCTTA
1 AAC-CCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
* *
25336511 AACCCTTAAGCAGTAGGGTAACAG
1 AACCCCTAAGCAGTAGGGAAACAG
25336535 GCTAAATTTA
Statistics
Matches: 200, Mismatches: 80, Indels: 15
0.68 0.27 0.05
Matches are distributed among these distances:
42 3 0.01
43 53 0.26
44 100 0.50
45 44 0.22
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (44 bp):
AACCCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGGACCTTA
Found at i:25336411 original size:87 final size:88
Alignment explanation
Indices: 25336160--25336837 Score: 848
Period size: 87 Copynumber: 7.7 Consensus size: 88
25336150 CACAAGCTTT
* *
25336160 AACCCCTTAAGCAGTAGGGTAATAGGCTG-AATTTACAGATCTTAAC-CCCTTAAGCAGTAGGGA
1 AACCCC-TAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCC-TAAGCAGTAGGGA
* *
25336223 AACAGATCGAAGGTGATGGACCTTA
64 AACAGATCGAAGGCGATGGGCCTTA
* * *
25336248 AACCCCTAAGCAGTAGGGTAACAGGTTGAAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAA
1 AACCCCTAAGCAGTAGGGTAACAGGCTG-AAATTTACAGATCTTATCACCCTAAGCAGTAGGGAA
* * *
25336313 ATAGATTGAAGGTGATGGGCCTTA
65 ACAGATCGAAGGCGATGGGCCTTA
**
25336337 AATGCCTAAGCAGTAGGGTAACAGGCT-AAATTTACAGATCTTATCACCCTAAGCAGTAGGGAAA
1 AACCCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCCTAAGCAGTAGGGAAA
*
25336401 CAGATCGAAGGCGATGGGCTTTA
66 CAGATCGAAGGCGATGGGCCTTA
*
25336424 AACCCCTAAGCAGTAGGGTAACAGGCT-AAATTTACAGATCTTATCACCCTAAGCAGTACGGAAA
1 AACCCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCCTAAGCAGTAGGGAAA
*
25336488 CAGATCGAAGGCAATGGGCCTTA
66 CAGATCGAAGGCGATGGGCCTTA
* * *
25336511 AACCCTTAAGCAGTAGGGTAACAGGCT-AAATTTACAGATCTTGTCTCCCTAAGCAGTAGTGG-A
1 AACCCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCCTAAGCAGTAG-GGAA
* * * * *
25336574 TCAAATCAAAGACGAAGGGCCTTA
65 ACAGATCGAAGGCGATGGGCCTTA
* * * * * * *
25336598 ACCCCCTAAGCAGTAGGGTAACAAGTTGAAAATTTACAGATTTTGTCTCCCTAAGTAGTAGTGG-
1 AACCCCTAAGCAGTAGGGTAACAGGCTG-AAATTTACAGATCTTATCACCCTAAGCAGTAG-GGA
* * * *
25336662 AGCAAATCGAAGACGAAGGGCCTTA
64 AACAGATCGAAGGCGATGGGCCTTA
* * * *
25336687 ACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAA
1 AACCCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCCTAAGCAGTAG-GGAA
*
25336752 ACAGATCGAAGGCAATGGGCCTTA
65 ACAGATCGAAGGCGATGGGCCTTA
* * * * *
25336776 AACCCCTAAGTAGTAGGGCAACAGGCTGAAAATTACATATCTTATCACCCTAAGTAGTAGGG
1 AACCCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCCTAAGCAGTAGGG
25336838 TAATAGGCTG
Statistics
Matches: 529, Mismatches: 54, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
87 253 0.48
88 42 0.08
89 231 0.44
90 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (88 bp):
AACCCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTATCACCCTAAGCAGTAGGGAAA
CAGATCGAAGGCGATGGGCCTTA
Found at i:25336702 original size:44 final size:44
Alignment explanation
Indices: 25336557--25336702 Score: 116
Period size: 44 Copynumber: 3.3 Consensus size: 44
25336547 GATCTTGTCT
* *
25336557 CCCTAAGCAGTAGTGGATCAAATCAAAGACGAAGGGCCTTAACC
1 CCCTAAGCAGTAGTGGAACAAATCGAAGACGAAGGGCCTTAACC
* * * ** *** ** *
25336601 CCCTAAGCAGTAG-GGTAACAAGTTGAAAATTTACA-GATTTTGTCT
1 CCCTAAGCAGTAGTGG-AACAAATCGAAGA-CGA-AGGGCCTTAACC
* *
25336646 CCCTAAGTAGTAGTGGAGCAAATCGAAGACGAAGGGCCTTAACC
1 CCCTAAGCAGTAGTGGAACAAATCGAAGACGAAGGGCCTTAACC
25336690 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
25336703 GGTAACAGGC
Statistics
Matches: 70, Mismatches: 27, Indels: 10
0.65 0.25 0.09
Matches are distributed among these distances:
43 3 0.04
44 38 0.54
45 26 0.37
46 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (44 bp):
CCCTAAGCAGTAGTGGAACAAATCGAAGACGAAGGGCCTTAACC
Found at i:25336865 original size:44 final size:44
Alignment explanation
Indices: 25336779--25336875 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
25336769 GGCCTTAAAC
*
25336779 CCCTAAGTAGTAGGGCAACAGGCTGAAAATTACATATCTTATCA
1 CCCTAAGTAGTAGGGCAACAGGCTGAAAATTACAAATCTTATCA
* * * * *
25336823 CCCTAAGTAGTAGGGTAATAGGCTGGAAATTTCAAA-CTTTATCT
1 CCCTAAGTAGTAGGGCAACAGGCTGAAAATTACAAATC-TTATCA
25336867 CCCTGAAGT
1 CCCT-AAGT
25336876 TGCAGTGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 40 0.89
45 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
CCCTAAGTAGTAGGGCAACAGGCTGAAAATTACAAATCTTATCA
Found at i:25338374 original size:3 final size:3
Alignment explanation
Indices: 25338366--25338411 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
25338356 TTTCATAATA
*
25338366 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT T-T T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25338412 CATCTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:25338850 original size:3 final size:3
Alignment explanation
Indices: 25338829--25338928 Score: 53
Period size: 3 Copynumber: 33.7 Consensus size: 3
25338819 TTATTACTTG
* * * * * *
25338829 TAT TAT TAC TAT TAA TAT TAT TAT TAT TAT TAC T-T TAC TAT TGT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
25338876 T-T AAT GTAT TAC TAA TAT TAC TCT TAT T-T TCAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
*
25338921 TAC TAT TA
1 TAT TAT TA
25338929 CTCTTTATTG
Statistics
Matches: 69, Mismatches: 23, Indels: 10
0.68 0.23 0.10
Matches are distributed among these distances:
2 4 0.06
3 61 0.88
4 4 0.06
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:25339326 original size:13 final size:13
Alignment explanation
Indices: 25339304--25339338 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
25339294 ATTATTATTT
25339304 AAAAAGAAAGAAAG
1 AAAAA-AAAGAAAG
25339318 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
25339331 AAAAAAAA
1 AAAAAAAA
25339339 CAATTCCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:25339326 original size:17 final size:16
Alignment explanation
Indices: 25339304--25339338 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
25339294 ATTATTATTT
25339304 AAAAAGAAAGAAAGAAA
1 AAAAAGAAAGAAA-AAA
25339321 AAAAAGAAAGAAAAAA
1 AAAAAGAAAGAAAAAA
25339337 AA
1 AA
25339339 CAATTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAA
Found at i:25343745 original size:15 final size:18
Alignment explanation
Indices: 25343715--25343750 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25343705 ACATATATGC
25343715 ATATATAAAGGATAAT-G
1 ATATATAAAGGATAATCG
25343732 ATATATAAA-G-TAATCG
1 ATATATAAAGGATAATCG
25343748 ATA
1 ATA
25343751 AGCGTATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (18 bp):
ATATATAAAGGATAATCG
Found at i:25347433 original size:19 final size:19
Alignment explanation
Indices: 25347409--25347452 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
25347399 AGCGTAACAC
25347409 GGCCATGTGGAGGGCTATT
1 GGCCATGTGGAGGGCTATT
25347428 GGCCATGTGGAGGGCTATT
1 GGCCATGTGGAGGGCTATT
25347447 GGCCAT
1 GGCCAT
25347453 ATTTTGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.41, T:0.25
Consensus pattern (19 bp):
GGCCATGTGGAGGGCTATT
Found at i:25348439 original size:2 final size:2
Alignment explanation
Indices: 25348434--25348463 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25348424 ACGCTTAATC
25348434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25348464 GTTTTGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25350462 original size:27 final size:27
Alignment explanation
Indices: 25350424--25350475 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
25350414 AATGCCTTCA
25350424 GGTCCTAGCCCGGATACAGCAACTCCG
1 GGTCCTAGCCCGGATACAGCAACTCCG
* *
25350451 GGTCTTAGCCCGGATATAGCAACTC
1 GGTCCTAGCCCGGATACAGCAACTC
25350476 GCACAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (27 bp):
GGTCCTAGCCCGGATACAGCAACTCCG
Found at i:25350501 original size:67 final size:66
Alignment explanation
Indices: 25350389--25350515 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 66
25350379 TTTTCGGGAT
25350389 TTAGCCGGATATAACAACTCGCACAAATGCCTTCAGGTCCTAGCCCGGATACAGCAACTCCGGGT
1 TTAGCCGGATATAACAACTCGCACAAATGCCTTCAGGTCCTAGCCCGGATACAGCAACTCCGGGT
25350454 C
66 C
* *
25350455 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTC-GAGT-CTAAGCCCGGATATAGCAACTC
1 TTAG-CCGGATATAACAACTCGCACAAATGCCTTCAG-GTCCT-AGCCCGGATACAGCAACTC
25350516 GCACAAATGC
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
66 7 0.12
67 49 0.88
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (66 bp):
TTAGCCGGATATAACAACTCGCACAAATGCCTTCAGGTCCTAGCCCGGATACAGCAACTCCGGGT
C
Found at i:25350512 original size:40 final size:40
Alignment explanation
Indices: 25350449--25350583 Score: 234
Period size: 40 Copynumber: 3.4 Consensus size: 40
25350439 ACAGCAACTC
25350449 CGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTT
1 CGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTT
* *
25350489 CGAGTCTAAGCCCGGATATAGCAACTCGCACAAATGCCTT
1 CGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTT
* *
25350529 TGGGTCTTAGCCCAGATATAGCAACTCGCACAAATGCCTT
1 CGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTT
25350569 CGGGTCTTAGCCCGG
1 CGGGTCTTAGCCCGG
25350584 TTATCATCCG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (40 bp):
CGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTT
Found at i:25354141 original size:42 final size:42
Alignment explanation
Indices: 25354069--25354151 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
25354059 CAAGGTCATG
* * * * *
25354069 TAACTCATTGTTTGGGACCATATAGTCATGTGTGAGGTTGTA
1 TAACTCACTGTTTGGGACCACAGAGCCATGTGCGAGGTTGTA
*
25354111 TAACTCACTGTTTGGGACCACACGA-CCATGTGCGGGGTTGT
1 TAACTCACTGTTTGGGACCACA-GAGCCATGTGCGAGGTTGT
25354152 GTGAGTTACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.33
Consensus pattern (42 bp):
TAACTCACTGTTTGGGACCACAGAGCCATGTGCGAGGTTGTA
Found at i:25354342 original size:29 final size:29
Alignment explanation
Indices: 25354296--25354356 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
25354286 TTGGTTCGAA
* * *
25354296 TGTAGGCCTTTAGTAGGGTCTGTATGATC
1 TGTAGGCCTTCAGCAGGGTCTGTATAATC
*
25354325 TGTAGGCCTTCCGCAGGGTCTGTATAATC
1 TGTAGGCCTTCAGCAGGGTCTGTATAATC
25354354 TGT
1 TGT
25354357 TTTAAGCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (29 bp):
TGTAGGCCTTCAGCAGGGTCTGTATAATC
Found at i:25355142 original size:25 final size:25
Alignment explanation
Indices: 25355105--25355184 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
25355095 TTCTACTATG
** *
25355105 TTCTGTTCGGTTCTGCTTTGTTCTG
1 TTCTGTTTTGTTCTGCTTTGTTCTA
* *
25355130 TT-TAAG-TTTGTTCTACTCTGTTCTA
1 TTCT--GTTTTGTTCTGCTTTGTTCTA
*
25355155 TTCTGTTTTGTTCTGCTTTGGTTTTA
1 TTCTGTTTTGTTCTGCTTT-GTTCTA
25355181 TTCT
1 TTCT
25355185 ATTCTATTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
24 2 0.05
25 29 0.69
26 11 0.26
ACGTcount: A:0.06, C:0.16, G:0.17, T:0.60
Consensus pattern (25 bp):
TTCTGTTTTGTTCTGCTTTGTTCTA
Found at i:25359675 original size:51 final size:51
Alignment explanation
Indices: 25359613--25359798 Score: 273
Period size: 51 Copynumber: 3.6 Consensus size: 51
25359603 TATAGATGCG
* * * *
25359613 AGCATCTGAGCTCGTTGAGCGGTTCGAGTTCATGATGGATGAGATTCATGT
1 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATGATGGATGAGATTCATGT
25359664 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATGATGGATGAGATTCATGT
1 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATGATGGATGAGATTCATGT
*
25359715 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATGATGGATGCGATTCATGT
1 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATGATGGATGAGATTCATGT
** * * * *
25359766 AATATCTGAGCTCGTTGAGAGGTCTGAGTTCAT
1 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCAT
25359799 TATGTGTTAC
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 124 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (51 bp):
AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATGATGGATGAGATTCATGT
Found at i:25361157 original size:29 final size:28
Alignment explanation
Indices: 25361100--25361157 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
25361090 GACATAGGCG
*
25361100 AGGACACGGGCGTGTCTAGGCCGTGTGA
1 AGGACACGGGCATGTCTAGGCCGTGTGA
*
25361128 AGGACACGGGCATGTGCTCGGCCGTGTGA
1 AGGACACGGGCATGT-CTAGGCCGTGTGA
25361157 A
1 A
25361158 AACCTCTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.17
Consensus pattern (28 bp):
AGGACACGGGCATGTCTAGGCCGTGTGA
Done.