Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold332
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: 2744988
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 17
Found at i:2243137 original size:21 final size:21
Alignment explanation
Indices: 2243111--2243153 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2243101 TTAAAGCTTT
*
2243111 GAAAAAATTCAAAGAAAAACTA
1 GAAAAAA-CCAAAGAAAAACTA
*
2243133 GAAAAAACCTAAGAAAAACTA
1 GAAAAAACCAAAGAAAAACTA
2243154 AGAAGGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (21 bp):
GAAAAAACCAAAGAAAAACTA
Found at i:2243851 original size:29 final size:26
Alignment explanation
Indices: 2243803--2243875 Score: 67
Period size: 29 Copynumber: 2.7 Consensus size: 26
2243793 ATTTAAATGG
*
2243803 TCAATT-AAAATTCTAAATGTAATAAAT
1 TCAATTAAAAATT-TAAATGT-AGAAAT
*
2243830 TCAATTAAAAATTTAATTATGTAGGAAT
1 TCAATTAAAAATTTAA--ATGTAGAAAT
*
2243858 TCTAATTAAAAAATTAAA
1 TC-AATTAAAAATTTAAA
2243876 GGAAAAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 10 0.26
28 12 0.31
29 17 0.44
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.37
Consensus pattern (26 bp):
TCAATTAAAAATTTAAATGTAGAAAT
Found at i:2244157 original size:18 final size:19
Alignment explanation
Indices: 2244124--2244159 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2244114 GGATGAAATT
2244124 TTCAAATATAAAATTTTAA
1 TTCAAATATAAAATTTTAA
*
2244143 TTCAAAT-TTAAATTTTA
1 TTCAAATATAAAATTTTA
2244160 TATTTAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCAAATATAAAATTTTAA
Found at i:2246831 original size:24 final size:24
Alignment explanation
Indices: 2246791--2246837 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2246781 TATAATATGA
*
2246791 ATAAATAAATATCTTAAAATATTT
1 ATAAATAAATATATTAAAATATTT
*
2246815 ATAATATAAAT-TATTAATATATT
1 ATAA-ATAAATATATTAAAATATT
2246838 AAAATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAAATAAATATATTAAAATATTT
Found at i:2248290 original size:21 final size:21
Alignment explanation
Indices: 2248266--2248312 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2248256 ATATTGATAT
2248266 ATTAAGTTAATGTATCAATAC
1 ATTAAGTTAATGTATCAATAC
* *
2248287 ATTAAGTTAGTGTATCGATAC
1 ATTAAGTTAATGTATCAATAC
2248308 ATTAA
1 ATTAA
2248313 CATTAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (21 bp):
ATTAAGTTAATGTATCAATAC
Found at i:2248883 original size:33 final size:31
Alignment explanation
Indices: 2248855--2248917 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
2248845 AAGAAAATTC
*
2248855 TAGGAAAAAATCTAGAGAAAAAGAAGAAAAAGT
1 TAGG-AAAAATATAGA-AAAAAGAAGAAAAAGT
2248888 TAGGAAAAATATAGAAAAAAGGAA-AAAAAG
1 TAGGAAAAATATAGAAAAAA-GAAGAAAAAG
2248918 AAAAAGATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 11 0.39
32 13 0.46
33 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.11
Consensus pattern (31 bp):
TAGGAAAAATATAGAAAAAAGAAGAAAAAGT
Found at i:2248912 original size:18 final size:16
Alignment explanation
Indices: 2248889--2248922 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2248879 AGAAAAAGTT
2248889 AGGAAAAATATAGAAAAA
1 AGGAAAAA-A-AGAAAAA
2248907 AGGAAAAAAAGAAAAA
1 AGGAAAAAAAGAAAAA
2248923 GATCTGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AGGAAAAAAAGAAAAA
Found at i:2253387 original size:20 final size:20
Alignment explanation
Indices: 2253364--2253436 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
2253354 ATACCTAGAT
2253364 GTATCGATACATTTTGCTTA
1 GTATCGATACATTTTGCTTA
* *** **
2253384 GTATCGATAC-GTACCCAAA
1 GTATCGATACATTTTGCTTA
2253403 TGTATCGATACATTTTGCTTA
1 -GTATCGATACATTTTGCTTA
*
2253424 GTATCAATACATT
1 GTATCGATACATT
2253437 GTATCGATAC
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 3 0.08
20 32 0.84
21 3 0.08
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTTTGCTTA
Found at i:2253406 original size:40 final size:40
Alignment explanation
Indices: 2253348--2253435 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
2253338 TTAATTGTAC
* *
2253348 CGATACATACCTAGATGTATCGATACATTTTGCTTAGTAT
1 CGATACATACCCAAATGTATCGATACATTTTGCTTAGTAT
*
2253388 CGATACGTACCCAAATGTATCGATACATTTTGCTTAGTAT
1 CGATACATACCCAAATGTATCGATACATTTTGCTTAGTAT
*
2253428 CAATACAT
1 CGATACAT
2253436 TGTATCGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (40 bp):
CGATACATACCCAAATGTATCGATACATTTTGCTTAGTAT
Found at i:2253559 original size:17 final size:17
Alignment explanation
Indices: 2253537--2253574 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2253527 TATCGATCCA
2253537 TCACTGTTCATAACTAT
1 TCACTGTTCATAACTAT
*
2253554 TCACTGTTCATAACTGT
1 TCACTGTTCATAACTAT
2253571 TCAC
1 TCAC
2253575 GTATCACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.39
Consensus pattern (17 bp):
TCACTGTTCATAACTAT
Found at i:2253587 original size:24 final size:24
Alignment explanation
Indices: 2253554--2253603 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2253544 TCATAACTAT
*
2253554 TCACTGTTCATAACTGTTCACGTA
1 TCACTATTCATAACTGTTCACGTA
* *
2253578 TCACTATTCATCACTGTTCATGTA
1 TCACTATTCATAACTGTTCACGTA
2253602 TC
1 TC
2253604 GATACATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (24 bp):
TCACTATTCATAACTGTTCACGTA
Found at i:2253616 original size:13 final size:13
Alignment explanation
Indices: 2253598--2253626 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2253588 TCACTGTTCA
2253598 TGTATCGATACAT
1 TGTATCGATACAT
2253611 TGTATCGATACAT
1 TGTATCGATACAT
2253624 TGT
1 TGT
2253627 GAACAGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2255738 original size:21 final size:21
Alignment explanation
Indices: 2255714--2255772 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2255704 TAATATTCTT
* *
2255714 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
2255735 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
2255756 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
2255773 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:2256426 original size:11 final size:11
Alignment explanation
Indices: 2256410--2256441 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
2256400 TTGATTGTTC
2256410 TTAATTGCATA
1 TTAATTGCATA
2256421 TTAATTGCATA
1 TTAATTGCATA
2256432 TTAATTGCAT
1 TTAATTGCAT
2256442 TTATGGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (11 bp):
TTAATTGCATA
Found at i:2259268 original size:13 final size:13
Alignment explanation
Indices: 2259234--2259288 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
2259224 TCACTGTTCA
*
2259234 TGTATCGATACAG
1 TGTATCGATACAT
* *
2259247 TGAAACGATACAT
1 TGTATCGATACAT
2259260 TGTATCGATACAT
1 TGTATCGATACAT
*
2259273 TGTATCAATACAT
1 TGTATCGATACAT
2259286 TGT
1 TGT
2259289 GAACAGTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2262885 original size:65 final size:63
Alignment explanation
Indices: 2262636--2263016 Score: 229
Period size: 65 Copynumber: 5.9 Consensus size: 63
2262626 ATAATTTTTT
* * *
2262636 AGGCTTGA-CTAATTTCTAGGAAAATAGGTTCGAATTAGAAGGAAAAAGACCTTGA-TTTCATTC
1 AGGCTTGACCT-ATTT-TAGGAAAATAGGTTCGACTTAAAAGTAAAAAGACCTTGACTTT-ATTC
2262699 -
63 A
* * * * * *
2262699 AGGCTTGACCAATTTGTAGGAAAATAGGTTCGACTTAAAAGAAAAAAGAGCTCGACTTTTTTTTA
1 AGGCTTGACCTATTT-TAGGAAAATAGGTTCGACTTAAAAGTAAAAAGACCTTGAC-TTTATTCA
* * ** * * * *
2262764 TGGCTTGACCTACTTTTAGGAAAACATATTTGACTTAAAAGGT-AACACACCCTGACTTTATCTC
1 AGGCTTGACCTA-TTTTAGGAAAATAGGTTCGACTTAAAA-GTAAAAAGACCTTGACTTTAT-TC
2262828 A
63 A
* * * * *
2262829 AGG-TTGAACCTATATTTAGGAAAATAGGCTCGACTTAAAAGTAAAAGGAGCTTGACTTTGTTTT
1 AGGCTTG-ACCTAT-TTTAGGAAAATAGGTTCGACTTAAAAGTAAAAAGACCTTGACTTT-ATTC
*
2262893 G
63 A
* * * * * *
2262894 AGGCTTAACCGATGTTTAGGAAAAT-GAGTTCAACTTAAAA--AGAAAAGATCTCGACTTTATTT
1 AGGCTTGACCTAT-TTTAGGAAAATAG-GTTCGACTTAAAAGTA-AAAAGACCTTGACTTTATTC
*
2262956 T
63 A
* * * * * * *
2262957 GGTGTTTGACCTATTTCTAGAAAAATATGTTCAACTTAAAAGGAAAAAAACCTTGACTTT
1 AG-GCTTGACCTATTT-TAGGAAAATAGGTTCGACTTAAAAGTAAAAAGACCTTGACTTT
2263017 GTTTTGAGGC
Statistics
Matches: 243, Mismatches: 56, Indels: 36
0.73 0.17 0.11
Matches are distributed among these distances:
63 53 0.22
64 56 0.23
65 126 0.52
66 8 0.03
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (63 bp):
AGGCTTGACCTATTTTAGGAAAATAGGTTCGACTTAAAAGTAAAAAGACCTTGACTTTATTCA
Found at i:2263111 original size:129 final size:128
Alignment explanation
Indices: 2262836--2263135 Score: 295
Period size: 129 Copynumber: 2.3 Consensus size: 128
2262826 TCAAGGTTGA
* * * * ** * *
2262836 ACCTATATT-TAGGAAAATAGGCTCGACTTAAAAGTAAAAGGAGCTTGACTTTGTTTTGAGGCTT
1 ACCTAT-TTCTAGAAAAATAGGTTCAACTTAAAAGGAAAAAAACCTTGACTTTGTTTTGAGGCTC
* * * * * *
2262900 AACCGATGTTTAGGAAAATGAGTTCAACTTAAAAAGAAAAGATCTCGACTTTATTTTGGTGTTTG
65 AACCGATGTTTAGGAAAAAGAGTTC-ACCTAAAAAGAAAAGATCTCAACTTCATTTTGGAGCTTG
*
2262965 ACCTATTTCTAGAAAAATATGTTCAACTTAAAAGGAAAAAAACCTTGACTTTGTTTTGAGGCTCA
1 ACCTATTTCTAGAAAAATAGGTTCAACTTAAAAGGAAAAAAACCTTGACTTTGTTTTGAGGCTCA
* * * *
2263030 ACCTATTTTTAGGAAACAAGA-TTGC-CCTAAAAGGAAAATGA-CATTAACTTCATTTTGGAGCT
66 ACCGATGTTTAGGAAA-AAGAGTT-CACCTAAAAAGAAAA-GATC-TCAACTTCATTTTGGAGCT
2263092 TG
127 TG
* * * *
2263094 ACCTATTTCTA-AGAAAATGGGTTCAATTTGATAGGAAAAAAA
1 ACCTATTTCTAGA-AAAATAGGTTCAACTTAAAAGGAAAAAAA
2263136 TTTTGGTAGT
Statistics
Matches: 141, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
128 15 0.11
129 122 0.87
130 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (128 bp):
ACCTATTTCTAGAAAAATAGGTTCAACTTAAAAGGAAAAAAACCTTGACTTTGTTTTGAGGCTCA
ACCGATGTTTAGGAAAAAGAGTTCACCTAAAAAGAAAAGATCTCAACTTCATTTTGGAGCTTG
Found at i:2265982 original size:19 final size:18
Alignment explanation
Indices: 2265958--2266020 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
2265948 ATCGATATAA
2265958 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2265977 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
2265990 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
2266009 TGTATCGATACA
1 TGTATCGATACA
2266021 ATGTATTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2265985 original size:32 final size:32
Alignment explanation
Indices: 2265944--2266026 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
2265934 TTTCACCGAT
*
2265944 TTGTATCGATATAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
2265976 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
2266008 TTGTATCGATACAATGTAT
1 TTGTATCGATACAATGTAT
2266027 TGCTATGAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:2266000 original size:13 final size:13
Alignment explanation
Indices: 2265945--2266001 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2265935 TTCACCGATT
*
2265945 TGTATCGATATAA
1 TGTATCGATACAA
2265958 TGTATCGATACATAA
1 TGTATCGATAC--AA
2265973 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2265990 TGTATCGATACA
1 TGTATCGATACA
2266002 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2266128 original size:52 final size:52
Alignment explanation
Indices: 2266085--2266209 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
2266075 CACTGATCTT
2266085 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
2266137 TGTATCGATACCTACAGGCAAATTTGCCCAGATGTCTCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
2266189 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
2266210 TTTTTCATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:2268924 original size:88 final size:88
Alignment explanation
Indices: 2268817--2268982 Score: 323
Period size: 88 Copynumber: 1.9 Consensus size: 88
2268807 AGATTGCAAT
2268817 AGTTACAAAACCCAAAAAATAAATACCAAGATCTGCACTAATACTAGAGATTGCATGAAAGGGTC
1 AGTTACAAAACCCAAAAAATAAATACCAAGATCTGCACTAATACTAGAGATTGCATGAAAGGGTC
2268882 TAAGAGTTAATTAGTATTTCAAG
66 TAAGAGTTAATTAGTATTTCAAG
*
2268905 AGTTACAAAACCCAAAAAATAAATACCAAGATCTGTACTAATACTAGAGATTGCATGAAAGGGTC
1 AGTTACAAAACCCAAAAAATAAATACCAAGATCTGCACTAATACTAGAGATTGCATGAAAGGGTC
2268970 TAAGAGTTAATTA
66 TAAGAGTTAATTA
2268983 CAATCATGAG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (88 bp):
AGTTACAAAACCCAAAAAATAAATACCAAGATCTGCACTAATACTAGAGATTGCATGAAAGGGTC
TAAGAGTTAATTAGTATTTCAAG
Found at i:2271487 original size:19 final size:18
Alignment explanation
Indices: 2271448--2271488 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2271438 TAAGATTTTA
*
2271448 TATTTTATATTTTTTATT
1 TATTTTATATTTTTTAAT
*
2271466 TATTTTTTATTTTTGTAAT
1 TATTTTATATTTTT-TAAT
2271485 TATT
1 TATT
2271489 AATTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
TATTTTATATTTTTTAAT
Found at i:2275822 original size:12 final size:12
Alignment explanation
Indices: 2275805--2275837 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2275795 TGTGATGATG
2275805 AAAGAAAAATGA
1 AAAGAAAAATGA
2275817 AAAG-AAAATGA
1 AAAGAAAAATGA
*
2275828 AAATAAAAAT
1 AAAGAAAAAT
2275838 TTATGCACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (12 bp):
AAAGAAAAATGA
Found at i:2276444 original size:13 final size:13
Alignment explanation
Indices: 2276426--2276450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2276416 ATATTGCTTA
2276426 GTATCGATACATT
1 GTATCGATACATT
2276439 GTATCGATACAT
1 GTATCGATACAT
2276451 GTTCTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2276467 original size:32 final size:33
Alignment explanation
Indices: 2276407--2276468 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2276397 CACCCAGATA
2276407 TATCGATACATATTGCTTAGTATCGATACATTG
1 TATCGATACATATTGCTTAGTATCGATACATTG
* *
2276440 TATCGATACATGTT-CTTTGTATCGATACA
1 TATCGATACATATTGCTTAGTATCGATACA
2276469 CCGTAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (33 bp):
TATCGATACATATTGCTTAGTATCGATACATTG
Found at i:2276585 original size:52 final size:52
Alignment explanation
Indices: 2276526--2276634 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
2276516 GTTCATAATT
*
2276526 GAATTGTATCGATACATGGTAAATTGTATCGATACATTGAGCCCAACAGCTA
1 GAATTGTATCGATACATGATAAATTGTATCGATACATTGAGCCCAACAGCTA
* * * * * *
2276578 TAATTGTATTGATATATTATGAATTGTATCGATACATTGAGCCCAACGGCTA
1 GAATTGTATCGATACATGATAAATTGTATCGATACATTGAGCCCAACAGCTA
2276630 GAATT
1 GAATT
2276635 TCAAATGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (52 bp):
GAATTGTATCGATACATGATAAATTGTATCGATACATTGAGCCCAACAGCTA
Found at i:2277096 original size:35 final size:34
Alignment explanation
Indices: 2277057--2277122 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
2277047 TAAGTGATTG
* * *
2277057 AGAGGTTTTATTTTAGCCTTTGTAAAAGATAGGAA
1 AGAGGTTCTATCTTAGCCTTCG-AAAAGATAGGAA
2277092 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
1 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
2277123 TGTTGTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTCGAAAAGATAGGAA
Found at i:2279280 original size:34 final size:34
Alignment explanation
Indices: 2279092--2279365 Score: 122
Period size: 34 Copynumber: 8.3 Consensus size: 34
2279082 CGGGTCTAAT
* * *
2279092 TCTTTTAAATCATTTAGTAAGATATGAGTTTGAC
1 TCTTTTAACTCATTTAATAGGATATGAGTTTGAC
* * **
2279126 TCGTTTAACTTATGCAGA-AGG--AT-A-TTTGAC
1 TCTTTTAACTCATTTA-ATAGGATATGAGTTTGAC
* * * *
2279156 T-TTTTGAC-CTATTTAGTAGGATATGGGCTTGA-
1 TCTTTTAACTC-ATTTAATAGGATATGAGTTTGAC
* * * * *
2279188 TTTTTTAACTCTTTTACTTGGATACGAGTTTGAC
1 TCTTTTAACTCATTTAATAGGATATGAGTTTGAC
** ** * * * *
2279222 GATTTTAACTTGTTCAAAAAGATATAAGTTTGAC
1 TCTTTTAACTCATTTAATAGGATATGAGTTTGAC
* *
2279256 TCTTTTAACTCGTTTAATAGGATATGATTTTGA-
1 TCTTTTAACTCATTTAATAGGATATGAGTTTGAC
* * *
2279289 -CTTTTAAC-CTATTTAGA-AGGCTATGGGCTTGAC
1 TCTTTTAACTC-ATTTA-ATAGGATATGAGTTTGAC
* * ** *
2279322 TCTTTTAACTCATTTAGTAAGATACAAGTTTGAA
1 TCTTTTAACTCATTTAATAGGATATGAGTTTGAC
2279356 TCTTTTAACT
1 TCTTTTAACT
2279366 TGCTCAAAAG
Statistics
Matches: 170, Mismatches: 54, Indels: 32
0.66 0.21 0.12
Matches are distributed among these distances:
29 11 0.06
30 7 0.04
31 4 0.02
32 26 0.15
33 27 0.16
34 94 0.55
35 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (34 bp):
TCTTTTAACTCATTTAATAGGATATGAGTTTGAC
Found at i:2279329 original size:66 final size:67
Alignment explanation
Indices: 2279150--2279354 Score: 189
Period size: 66 Copynumber: 3.1 Consensus size: 67
2279140 CAGAAGGATA
* * * * * * *
2279150 TTTGACTTTTTGACCTATTTAGTAGGATATGGGCTTGA-TTTTTTAACTCTTTTACTTGGATACG
1 TTTGACATTTTAACCTATTTAGAAGGATATGGGCTTGACTCTTTTAACTCATTTAATAGGATACG
2279214 AG
66 AG
* * * * * ** * * *
2279216 TTTGACGATTTTAACTTGTTCAAAAAGATATAAGTTTGACTCTTTTAACTCGTTTAATAGGATAT
1 TTTGAC-ATTTTAACCTATTTAGAAGGATATGGGCTTGACTCTTTTAACTCATTTAATAGGATAC
*
2279281 GAT
65 GAG
* * * *
2279284 TTTGAC-TTTTAACCTATTTAGAAGGCTATGGGCTTGACTCTTTTAACTCATTTAGTAAGATACA
1 TTTGACATTTTAACCTATTTAGAAGGATATGGGCTTGACTCTTTTAACTCATTTAATAGGATACG
2279348 AG
66 AG
2279350 TTTGA
1 TTTGA
2279355 ATCTTTTAAC
Statistics
Matches: 105, Mismatches: 32, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
66 56 0.53
67 21 0.20
68 28 0.27
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.43
Consensus pattern (67 bp):
TTTGACATTTTAACCTATTTAGAAGGATATGGGCTTGACTCTTTTAACTCATTTAATAGGATACG
AG
Found at i:2279708 original size:45 final size:44
Alignment explanation
Indices: 2279659--2279751 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
2279649 GTGGTGTAAT
* * *
2279659 TGCAACTGTCATCTAATGGTGTAGATGCACGTGAAATAATGCAAA
1 TGCAAATGTCATCTAAT-GTGTAGATGCACATGAAACAATGCAAA
* * * *
2279704 TGCAAATGTTATTTAATGTGTAGATGCACATGTAACAATGGAAA
1 TGCAAATGTCATCTAATGTGTAGATGCACATGAAACAATGCAAA
2279748 TGCA
1 TGCA
2279752 TGTATGAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 27 0.66
45 14 0.34
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (44 bp):
TGCAAATGTCATCTAATGTGTAGATGCACATGAAACAATGCAAA
Found at i:2281096 original size:20 final size:22
Alignment explanation
Indices: 2281061--2281100 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2281051 TGTTTCCTTA
2281061 TCTTTTCTTCCCTTTTAATTTT
1 TCTTTTCTTCCCTTTTAATTTT
2281083 TCTTTT-TT-CCTTTTAATT
1 TCTTTTCTTCCCTTTTAATT
2281101 GTAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (22 bp):
TCTTTTCTTCCCTTTTAATTTT
Found at i:2295643 original size:21 final size:21
Alignment explanation
Indices: 2295619--2295664 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2295609 TGATGTATAA
2295619 ATACCTCGACCTAATATATCG
1 ATACCTCGACCTAATATATCG
*
2295640 ATACCTCGACCTAATGTATCG
1 ATACCTCGACCTAATATATCG
2295661 ATAC
1 ATAC
2295665 ATTGTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (21 bp):
ATACCTCGACCTAATATATCG
Found at i:2298961 original size:18 final size:18
Alignment explanation
Indices: 2298921--2298962 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2298911 TTGATTTGAT
* * *
2298921 TAAAAATGAACCAATAAC
1 TAAAAATAAAACAATAAA
2298939 T-AAAATAAAACAATAAA
1 TAAAAATAAAACAATAAA
2298956 TAAAAAT
1 TAAAAAT
2298963 GTTTTAGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (18 bp):
TAAAAATAAAACAATAAA
Found at i:2299455 original size:34 final size:34
Alignment explanation
Indices: 2299393--2299460 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2299383 ATCCCATGAA
*
2299393 AAATATAACAATTGGTAGCGGTACTAGAAAGAAG
1 AAATATAACAATTGGTAGCGGTAATAGAAAGAAG
* *
2299427 AAATATAACAATTTGTA-CTGTTAATAGAAAGAAG
1 AAATATAACAATTGGTAGC-GGTAATAGAAAGAAG
2299461 TTCTTATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (34 bp):
AAATATAACAATTGGTAGCGGTAATAGAAAGAAG
Found at i:2299949 original size:25 final size:25
Alignment explanation
Indices: 2299912--2299967 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
2299902 AGATGTAACG
*
2299912 TAACACGTGATAGAAAAACGT-AGTA
1 TAACACGTAATAGAAAAACGTGA-TA
*
2299937 TAACACGTAATAGGAAAACGTGATA
1 TAACACGTAATAGAAAAACGTGATA
2299962 TAACAC
1 TAACAC
2299968 ATGACAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (25 bp):
TAACACGTAATAGAAAAACGTGATA
Found at i:2301657 original size:13 final size:13
Alignment explanation
Indices: 2301641--2301675 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2301631 TCAAAAACTT
2301641 TTTTAAAAAATAA
1 TTTTAAAAAATAA
*
2301654 TTTTAAAAAATTA
1 TTTTAAAAAATAA
2301667 TTCTTAAAA
1 TT-TTAAAA
2301676 TTTTTAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:2301717 original size:20 final size:20
Alignment explanation
Indices: 2301677--2301718 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
2301667 TTCTTAAAAT
2301677 TTTTAAAGATAAATTTTTATC
1 TTTTAAAGAT-AATTTTTATC
2301698 TTTTAAAGAT-ATTGTTTATC
1 TTTTAAAGATAATT-TTTATC
2301718 T
1 T
2301719 CTAATTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 7 0.35
21 10 0.50
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAAGATAATTTTTATC
Found at i:2303485 original size:15 final size:14
Alignment explanation
Indices: 2303461--2303502 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2303451 AACTAATGAA
2303461 ATTT-ATTAATTTT
1 ATTTAATTAATTTT
2303474 ATTATAATTAATTTTT
1 ATT-TAATTAA-TTTT
2303490 ATTTAATATAATT
1 ATTTAAT-TAATT
2303503 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 1 0.04
15 11 0.44
16 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTAATTAATTTT
Found at i:2303491 original size:16 final size:15
Alignment explanation
Indices: 2303461--2303502 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2303451 AACTAATGAA
2303461 ATTT-ATTAA-TTTT
1 ATTTAATTAATTTTT
2303474 ATTATAATTAATTTTT
1 ATT-TAATTAATTTTT
2303490 ATTTAATATAATT
1 ATTTAAT-TAATT
2303503 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 1 0.04
15 9 0.36
16 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTAATTAATTTTT
Found at i:2309463 original size:36 final size:36
Alignment explanation
Indices: 2309416--2309488 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
2309406 TTAAAGTGGA
2309416 CAAACTTGGGAGAATCATGGTAATAGTAGATAGGTT
1 CAAACTTGGGAGAATCATGGTAATAGTAGATAGGTT
* * * *
2309452 CAAACTTGGGAGAATCTTGGTACTCGTGGATAGGTT
1 CAAACTTGGGAGAATCATGGTAATAGTAGATAGGTT
2309488 C
1 C
2309489 CTAAGGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (36 bp):
CAAACTTGGGAGAATCATGGTAATAGTAGATAGGTT
Found at i:2320791 original size:20 final size:20
Alignment explanation
Indices: 2320722--2320801 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 20
2320712 AATTTCCAAA
2320722 ATGTATCGATACATGT-TTCT
1 ATGTATCGATACAT-TATTCT
* *
2320742 GTGTATCGATACATTTGGAAATTCA
1 ATGTATCGATACA-TT----ATTCT
2320767 ATGTATCGATACATTATTCT
1 ATGTATCGATACATTATTCT
*
2320787 TTGTATCGATACATT
1 ATGTATCGATACATT
2320802 GTATTGATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 31 0.63
21 1 0.02
24 2 0.04
25 15 0.31
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTATTCT
Found at i:2320805 original size:13 final size:13
Alignment explanation
Indices: 2320787--2320825 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2320777 ACATTATTCT
2320787 TTGTATCGATACA
1 TTGTATCGATACA
*
2320800 TTGTATTGATACA
1 TTGTATCGATACA
*
2320813 CTGTATCGATACA
1 TTGTATCGATACA
2320826 GGGGGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2323345 original size:13 final size:13
Alignment explanation
Indices: 2323327--2323352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2323317 TACACAGAGT
2323327 ATGTATCGATACA
1 ATGTATCGATACA
2323340 ATGTATCGATACA
1 ATGTATCGATACA
2323353 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2323369 original size:33 final size:32
Alignment explanation
Indices: 2323309--2323372 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
2323299 TAGCCAAACT
* **
2323309 TGTATCGATACACAGAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
2323341 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACA-CAAAAAATGTATCGATACA
2323373 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:2328831 original size:163 final size:162
Alignment explanation
Indices: 2328651--2329356 Score: 457
Period size: 162 Copynumber: 4.3 Consensus size: 162
2328641 TTTAAACATC
* * * * * * *
2328651 AAAATTCTTCAAATATTATCAATTAATCCCA-ATCAAATCAGTTTTGAAAAATTCTTTTATTTTT
1 AAAATTCATCAAATATTAT-AATTAATCCCATATCAAATCAGTTCTCAAAAATCCATTCATTTTC
*
2328715 ATGAATTTTTTATTTTTTCCTTGAAA-TT-TTTTTCCAAAATACGGAGTTTTCTACTCCATAAAT
65 ATAAATTTTTTA-TTTTTCCTTGAAATTTCTTTTTCCAAAATACGGAGTTTTCTACTCCAT-AA-
*
2328778 TTTTTTC-AGAGGTATTTTTCTT-AGTTTTTAATTTTT
127 TTTTTTCGAG-GGGATTTTTCTTGA-TTTTTAATTTTT
* * ** * * *
2328814 AAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTCTCAAAGATCCATTCATTTTCA
1 AAAATTCATCAAATATTATAATTAATCCCATATCAAATCAGTTCTCAAAAATCCATTCATTTTCA
* * * *
2328879 TAAATTTTTTATTTTTCCTTGAAATTCTTCTTTTTTCGAAATACGGAGTTTTTTACTTCATAATT
66 TAAATTTTTTATTTTTCCTTGAAA-T-TTCTTTTTCCAAAATACGGAGTTTTCTACTCCATAATT
2328944 TTTTCGAGGGGATTTTTCTTGATTTTTAATTTTT
129 TTTTCGAGGGGATTTTTCTTGATTTTTAATTTTT
* * * ** * * * * * * *
2328978 AAAAGTCATCAAATATTATTATTTATTTCAGATTAATTCA-TT-TCAAAAATTCATGCAGTTCCA
1 AAAATTCATCAAATATTATAATTAATCCCATATCAAATCAGTTCTCAAAAATCCATTCATTTTCA
* ** * * * * *
2329041 TGAATTTTGAATTTTTCCTTAAAATTTTCCTTTTTTCGAAATACGGAGTTTT-TACTTCGTAAAT
66 TAAATTTTTTATTTTTCCTTGAAA-TTT-CTTTTTCCAAAATACGGAGTTTTCTACTCCAT-AAT
* * *
2329105 TCTTTCGAAGTGATTTTTCTTG-TTTTCTAATTTTT
128 TTTTTCGAGGGGATTTTTCTTGATTTT-TAATTTTT
* * * *** * * * * * * *
2329140 AAAAGTCATCAAATATTATTATTTATTTAATATTAATTTAGTT-TAAAAAAATTCATGCATTTCC
1 AAAATTCATCAAATATTATAATTAATCCCATATCAAATCAGTTCT-CAAAAATCCATTCATTTTC
* ** * * * * * * *
2329204 ATAAGTTTTGAATTTTTTCCTTGAAATTCCCTATCTCCAAAAAACCGAGTTTTCTACGCTATAAA
65 ATAAATTTTTTA-TTTTTCCTTGAAATT-TCTTTTTCCAAAATACGGAGTTTTCTACTCCAT-AA
* * ** *
2329269 TTTTTTCG-GGAGAATTTTTCTCGATTTAAAAATTTT
127 TTTTTTCGAGG-GGATTTTTCTTGATTTTTAATTTTT
* * * * * *
2329305 AAAATTTATCTAATATTGTCATTGAACTCCCAT-T-AATTCAGTTTTCAAAAAT
1 AAAATTCATCAAATATTATAATT-AA-TCCCATATCAAATCAGTTCTCAAAAAT
2329357 TTAATTTATT
Statistics
Matches: 448, Mismatches: 75, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
161 13 0.03
162 148 0.33
163 58 0.13
164 113 0.25
165 80 0.18
166 33 0.07
167 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (162 bp):
AAAATTCATCAAATATTATAATTAATCCCATATCAAATCAGTTCTCAAAAATCCATTCATTTTCA
TAAATTTTTTATTTTTCCTTGAAATTTCTTTTTCCAAAATACGGAGTTTTCTACTCCATAATTTT
TTCGAGGGGATTTTTCTTGATTTTTAATTTTT
Found at i:2328981 original size:164 final size:164
Alignment explanation
Indices: 2328726--2329231 Score: 631
Period size: 162 Copynumber: 3.1 Consensus size: 164
2328716 TGAATTTTTT
* * * *
2328726 ATTTTTTCCTTGAAA--TT-TTTTTCCAAAATACGGAGTTTTCTACTCCATAAATTTTTTTC-AG
1 ATTTTTTCCTTGAAATTTTCTTTTTTCGAAATACGGAGTTTTTTACTTCATAAA-TTTTTTCGAG
* *
2328787 AGGTATTTTTCTT-AGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAA
65 -GGGATTTTTCTTGA-TTTTTAATTTTTAAAAGTCATCAAATATTATTATTTATTTCATATTAAA
* * * * **
2328851 TTAGTTCTCAAAGATCCATTCATTTTCATAAATTTTTT
128 TTAGTT-TCAAAAATTCATGCATTTCCATAAATTTTGA
2328889 A-TTTTTCCTTGAAATTCTTCTTTTTTCGAAATACGGAGTTTTTTACTTCAT-AATTTTTTCGAG
1 ATTTTTTCCTTGAAATT-TTCTTTTTTCGAAATACGGAGTTTTTTACTTCATAAATTTTTTCGAG
*
2328952 GGGATTTTTCTTGATTTTTAATTTTTAAAAGTCATCAAATATTATTATTTATTTCAGATT-AATT
65 GGGATTTTTCTTGATTTTTAATTTTTAAAAGTCATCAAATATTATTATTTATTTCATATTAAATT
* *
2329016 CA-TTTCAAAAATTCATGCAGTTCCATGAATTTTGA
130 -AGTTTCAAAAATTCATGCATTTCCATAAATTTTGA
* * * *
2329051 A-TTTTTCCTTAAAATTTTCCTTTTTTCGAAATACGGAG-TTTTTACTTCGTAAATTCTTTCGAA
1 ATTTTTTCCTTGAAATTTT-CTTTTTTCGAAATACGGAGTTTTTTACTTCATAAATTTTTTCGAG
* * *
2329114 GTGATTTTTCTTG-TTTTCTAATTTTTAAAAGTCATCAAATATTATTATTTATTTAATATTAATT
65 GGGATTTTTCTTGATTTT-TAATTTTTAAAAGTCATCAAATATTATTATTTATTTCATATTAAAT
* *
2329178 TAGTTTAAAAAAATTCATGCATTTCCATAAGTTTTGA
129 TAGTTT-CAAAAATTCATGCATTTCCATAAATTTTGA
2329215 ATTTTTTCCTTGAAATT
1 ATTTTTTCCTTGAAATT
2329232 CCCTATCTCC
Statistics
Matches: 301, Mismatches: 28, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
161 17 0.06
162 133 0.44
163 13 0.04
164 90 0.30
165 21 0.07
166 27 0.09
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (164 bp):
ATTTTTTCCTTGAAATTTTCTTTTTTCGAAATACGGAGTTTTTTACTTCATAAATTTTTTCGAGG
GGATTTTTCTTGATTTTTAATTTTTAAAAGTCATCAAATATTATTATTTATTTCATATTAAATTA
GTTTCAAAAATTCATGCATTTCCATAAATTTTGA
Found at i:2338832 original size:52 final size:52
Alignment explanation
Indices: 2338764--2338882 Score: 211
Period size: 52 Copynumber: 2.3 Consensus size: 52
2338754 GAAAATTTCA
* *
2338764 GCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCTT
1 GCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCT
*
2338816 GCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCT
1 GCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCT
2338868 GCATGTATCGATACA
1 GCATGTATCGATACA
2338883 AAGATCGGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
GCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCT
Found at i:2338895 original size:52 final size:52
Alignment explanation
Indices: 2338764--2338902 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 52
2338754 GAAAATTTCA
* *
2338764 GCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCTT
1 GCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCT
*** *
2338816 GCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCT
1 GCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCT
*
2338868 GCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 GCATGTATCGATACATAAGAT-AGTGTATCGATACA
2338903 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
GCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCT
Found at i:2338909 original size:13 final size:13
Alignment explanation
Indices: 2338891--2338915 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2338881 CAAAGATCGG
2338891 TGTATCGATACAA
1 TGTATCGATACAA
2338904 TGTATCGATACA
1 TGTATCGATACA
2338916 TTTCTTTGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2338976 original size:13 final size:13
Alignment explanation
Indices: 2338958--2338982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2338948 TAAAAAAATA
2338958 TGTATCGATACAT
1 TGTATCGATACAT
2338971 TGTATCGATACA
1 TGTATCGATACA
2338983 ATATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2349132 original size:86 final size:85
Alignment explanation
Indices: 2349040--2349235 Score: 212
Period size: 86 Copynumber: 2.2 Consensus size: 85
2349030 AACTTCATTG
* * * * *
2349040 ATCTTTTACATAATCGGATGGAGTGAACAATTGAATCCATCGATCTTTTGCCTAACTGAATAAAG
1 ATCTTTTAC-TAATCGGATGAAGTGAACAACTGAATCAATCGATCTTTTACCTAACCGAATAAAG
* *
2349105 TTAATGAAAGAAAACTTTATC
65 CTAATGAAAGAAAAATTTATC
* * * * *
2349126 ATCTTTTGTCTAATCGGATAAAGTGAACAACTGACTCAATTGGTCTTTTACCTAACCGAATAAAG
1 ATCTTTT-ACTAATCGGATGAAGTGAACAACTGAATCAATCGATCTTTTACCTAACCGAATAAAG
* *
2349191 CTGATGAAAGAAAAATTTATG
65 CTAATGAAAGAAAAATTTATC
*
2349212 ATTTTTTTTACCTAATCGGATGAA
1 A--TCTTTTA-CTAATCGGATGAA
2349236 CCAAACTTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
86 71 0.80
87 1 0.01
88 17 0.19
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (85 bp):
ATCTTTTACTAATCGGATGAAGTGAACAACTGAATCAATCGATCTTTTACCTAACCGAATAAAGC
TAATGAAAGAAAAATTTATC
Found at i:2353527 original size:146 final size:146
Alignment explanation
Indices: 2352944--2353525 Score: 1101
Period size: 146 Copynumber: 4.0 Consensus size: 146
2352934 TGTTTGAACT
* * *
2352944 CATTTAATCACGAATCCATACTTGAAAATTAACTTTACCCTAAGATTGTGATATTTACTTAGTAA
1 CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
2353009 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
66 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
2353074 GGAAAATCGATTTTAA
131 GGAAAATCGATTTTAA
2353090 CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
1 CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
2353155 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
66 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
2353220 GGAAAATCGATTTTAA
131 GGAAAATCGATTTTAA
*
2353236 CATTTAATCACGAATCCATACCTGAAAATTGACTTTACCCCAAGATTGTGATATTTACTTGGTAA
1 CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
2353301 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
66 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
* *
2353366 GGAAAATCAATTTTCA
131 GGAAAATCGATTTTAA
2353382 CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
1 CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
*
2353447 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGTAGGTTTTT
66 AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
2353512 GGAAAATCGATTTT
131 GGAAAATCGATTTT
2353526 CAAATGCAAA
Statistics
Matches: 427, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
146 427 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (146 bp):
CATTTAATCACGAATCCATACCTGAAAATTAACTTTACCCCAAGATTGTGATATTTACTTGGTAA
AAACTTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATGCTTAACTTGTGGGAGGTTTTT
GGAAAATCGATTTTAA
Found at i:2354052 original size:52 final size:52
Alignment explanation
Indices: 2353975--2354081 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
2353965 TGGGTAGAGA
2353975 TGGATTGGAGTTGTGTAGTGACCAAGGAGGAAGTGTTTGGAGGTGTTTTCTT
1 TGGATTGGAGTTGTGTAGTGACCAAGGAGGAAGTGTTTGGAGGTGTTTTCTT
2354027 TGGATTGGAGTTGTGTAGTGACCAAGGAGGAAGTGTTTGGAGGTGTTTTCTT
1 TGGATTGGAGTTGTGTAGTGACCAAGGAGGAAGTGTTTGGAGGTGTTTTCTT
2354079 TGG
1 TGG
2354082 GAGCTATAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.19, C:0.06, G:0.39, T:0.36
Consensus pattern (52 bp):
TGGATTGGAGTTGTGTAGTGACCAAGGAGGAAGTGTTTGGAGGTGTTTTCTT
Found at i:2354633 original size:20 final size:20
Alignment explanation
Indices: 2354608--2354645 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2354598 AAAAAAAGAT
2354608 AGAATGTATTGATACATTGA
1 AGAATGTATTGATACATTGA
2354628 AGAATGTATTGATACATT
1 AGAATGTATTGATACATT
2354646 CATATGGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (20 bp):
AGAATGTATTGATACATTGA
Found at i:2354680 original size:20 final size:20
Alignment explanation
Indices: 2354655--2354692 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2354645 TCATATGGGT
2354655 AAAAATGTATCGATACATTG
1 AAAAATGTATCGATACATTG
2354675 AAAAATGTATCGATACAT
1 AAAAATGTATCGATACAT
2354693 CTGGGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAAATGTATCGATACATTG
Found at i:2354682 original size:48 final size:44
Alignment explanation
Indices: 2354610--2354706 Score: 131
Period size: 48 Copynumber: 2.1 Consensus size: 44
2354600 AAAAAGATAG
* * *
2354610 AATGTATTGATACATTGAAGAATGTATTGATACATTCATATGGGTAAA
1 AATGTATCGATACATTGAAAAATGTATCGATACA-TC---TGGGTAAA
2354658 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAA
1 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAA
2354702 AATGT
1 AATGT
2354707 GACTTTTCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 13 0.28
47 2 0.04
48 31 0.67
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (44 bp):
AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAA
Found at i:2358366 original size:20 final size:21
Alignment explanation
Indices: 2358332--2358370 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2358322 GACACAAAGC
*
2358332 AAATTGTATCTATACATTTGG
1 AAATTGTATCGATACATTTGG
2358353 AAATT-TATCGATACATTT
1 AAATTGTATCGATACATTT
2358371 ACTTATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
AAATTGTATCGATACATTTGG
Found at i:2359223 original size:40 final size:41
Alignment explanation
Indices: 2359147--2359224 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
2359137 ACTTAAAGAT
*
2359147 GATGCCACCAACTGGTGTAAGCTTTTAAAAAGAAAAAAGAAG
1 GATGCCACCAACTGATGTAAGC-TTTAAAAAGAAAAAAGAAG
* *
2359189 GATGCCACCAACTTATGTAGGC-TTAAAAAGAAAAAA
1 GATGCCACCAACTGATGTAAGCTTTAAAAAGAAAAAA
2359225 AGGAAAGGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 14 0.42
42 19 0.58
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (41 bp):
GATGCCACCAACTGATGTAAGCTTTAAAAAGAAAAAAGAAG
Found at i:2359500 original size:68 final size:68
Alignment explanation
Indices: 2359373--2359532 Score: 239
Period size: 68 Copynumber: 2.3 Consensus size: 68
2359363 AAGGGATGCT
* * *
2359373 ACCAACTTGTGTGGGCTTAAACAAAGAAAAAAGGAAAGACGTCTTGCTCTTTGAGGACTAAAAGG
1 ACCAACTTGTGTGGGCTTAAA-AAAGAAAAAAGGAAAAACGCCTTGCTCTTTGAAGACTAAAAGG
*
2359438 TGCC
65 AGCC
* *
2359442 ACCAACTTATGTGGGCTTAAAAAAGGAAAAAGGAAAAACGCCTTGCTCTTTGAAGACTAAAAGGA
1 ACCAACTTGTGTGGGCTTAAAAAAGAAAAAAGGAAAAACGCCTTGCTCTTTGAAGACTAAAAGGA
2359507 GCC
66 GCC
* *
2359510 ACCAACTTGTGTGGACTTTAAAA
1 ACCAACTTGTGTGGGCTTAAAAA
2359533 GGGTTACCAC
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 62 0.76
69 20 0.24
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (68 bp):
ACCAACTTGTGTGGGCTTAAAAAAGAAAAAAGGAAAAACGCCTTGCTCTTTGAAGACTAAAAGGA
GCC
Found at i:2359518 original size:180 final size:175
Alignment explanation
Indices: 2359150--2359532 Score: 446
Period size: 179 Copynumber: 2.1 Consensus size: 175
2359140 TAAAGATGAT
* *
2359150 GCCACCAACTGGTGTAAGCTTTTAAAAAGAAAAAAGAAGGATGCCACCAACTTATGTAGGCTTAA
1 GCCACCAACTTGTGT-GGC-TTTAAAAAGAAAAAAGAAGGATGCCACCAACTTATGTAGGCTTAA
* * *
2359215 AAAGAAAAAAAGGAAAGGCGTCCTGCTCTTTGAGAACTAAAAGGTGCTACCAGCTTATATGGACT
64 AAAGAAAAAAAGGAAAGACGTCCTGCTCTTTGAGAACTAAAAGGTGCCACCAACTTATATGGACT
* *** * * *
2359280 TAAAAGGGAAAAAGGAAAGGTGTTCTACTCTTTGAGGACTAAAAAGT
129 TAAAAAGGAAAAAGGAAAAACGCTCTACTCTTTGAAGACTAAAAAGA
* * * * * *
2359327 GCCATCAACTTGTGTGTGCTTTAAAGAGGAAAAAGAAAGGGATGCTACCAACTTGTGTGGGCTTA
1 GCCACCAACTTGTGTG-GCTTTAAAAAGAAAAAAG-AA-GGATGCCACCAACTTATGTAGGCTTA
* * *
2359392 AACAA-AGAAAAAAGGAAAGACGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGG
63 AA-AAGA-AAAAAAGGAAAGACGTCCTGCTCTTTGAGAACTAAAAGGTGCCACCAACTTATATGG
* * *
2359456 GCTTAAAAAAGGAAAAAGGAAAAACGC-CTTGCTCTTTGAAGACTAAAAGGA
126 ACTT-AAAAAGGAAAAAGGAAAAACGCTC-TACTCTTTGAAGACTAAAAAGA
2359507 GCCACCAACTTGTGTGGACTTTAAAA
1 GCCACCAACTTGTGTGG-CTTTAAAA
2359533 GGGTTACCAC
Statistics
Matches: 172, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
176 14 0.08
177 17 0.10
178 26 0.15
179 58 0.34
180 57 0.33
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (175 bp):
GCCACCAACTTGTGTGGCTTTAAAAAGAAAAAAGAAGGATGCCACCAACTTATGTAGGCTTAAAA
AGAAAAAAAGGAAAGACGTCCTGCTCTTTGAGAACTAAAAGGTGCCACCAACTTATATGGACTTA
AAAAGGAAAAAGGAAAAACGCTCTACTCTTTGAAGACTAAAAAGA
Found at i:2359545 original size:31 final size:30
Alignment explanation
Indices: 2359508--2359595 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
2359498 CTAAAAGGAG
*
2359508 CCACCAACTTGTGTGGACTTTAAAAGGGTTA
1 CCACCAACTTATGTGG-CTTTAAAAGGGTTA
* * *
2359539 CCACCAACTTTTGTGGGCTTTAGAAGGGTTT
1 CCACCAACTTATGT-GGCTTTAAAAGGGTTA
*
2359570 CCATCAACTTATGTAGGCTTTAAAAG
1 CCACCAACTTATGT-GGCTTTAAAAG
2359596 AAAAAGATGC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
31 47 0.96
32 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (30 bp):
CCACCAACTTATGTGGCTTTAAAAGGGTTA
Found at i:2359657 original size:34 final size:33
Alignment explanation
Indices: 2359591--2359661 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
2359581 TGTAGGCTTT
* * *
2359591 AAAAGAAAAAGATGCCATGGAGTTGTGGACTTA
1 AAAAGAAAAAGAGGCCACGGAGTTGTGCACTTA
*
2359624 AAAAGAAAAAGGGGGCCACGGAGTTGTGCACTTA
1 AAAAGAAAAA-GAGGCCACGGAGTTGTGCACTTA
2359658 AAAA
1 AAAA
2359662 AGGGTGCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 10 0.30
34 23 0.70
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (33 bp):
AAAAGAAAAAGAGGCCACGGAGTTGTGCACTTA
Found at i:2359670 original size:29 final size:29
Alignment explanation
Indices: 2359603--2359718 Score: 126
Period size: 29 Copynumber: 3.9 Consensus size: 29
2359593 AAGAAAAAGA
2359603 TGCCATGGAGTTGTGGACTTAAAAAGAAAAAGGG
1 TGCCATGGAGTTGTGGACTT----A-AAAAAGGG
* * *
2359637 GGCCACGGAGTTGTGCACTTAAAAAAGGG
1 TGCCATGGAGTTGTGGACTTAAAAAAGGG
* *
2359666 TGCCATGGAGTTGTGGACTTTAAAAA-TG
1 TGCCATGGAGTTGTGGACTTAAAAAAGGG
*
2359694 TGCTATGGAGTTGTGGACTTAAAAA
1 TGCCATGGAGTTGTGGACTTAAAAA
2359719 GAAAAAGATT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 24 0.33
29 30 0.42
30 1 0.01
34 17 0.24
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (29 bp):
TGCCATGGAGTTGTGGACTTAAAAAAGGG
Found at i:2360901 original size:13 final size:13
Alignment explanation
Indices: 2360883--2360908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2360873 CAATTTTTTG
2360883 TGTATCGATACAT
1 TGTATCGATACAT
2360896 TGTATCGATACAT
1 TGTATCGATACAT
2360909 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2360973 original size:21 final size:21
Alignment explanation
Indices: 2360947--2361022 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2360937 CTGCCAAGAA
*
2360947 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2360968 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2360988 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2361009 ATGTATCGATACAT
1 ATGTATCGATACAT
2361023 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2360993 original size:20 final size:20
Alignment explanation
Indices: 2360968--2361040 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2360958 CATCTTTTTT
2360968 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2360988 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2361009 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2361029 ATGTATCGATAC
1 ATGTATCGATAC
2361041 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2361004 original size:41 final size:41
Alignment explanation
Indices: 2360947--2361040 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2360937 CTGCCAAGAA
*
2360947 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2360988 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2361029 ATGTATCGATAC
1 ATGTATCGATAC
2361041 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2363501 original size:13 final size:13
Alignment explanation
Indices: 2363483--2363521 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2363473 ATAATCACCC
*
2363483 TGTATCGATACAG
1 TGTATCGATACAA
2363496 TGTATCGATACAA
1 TGTATCGATACAA
2363509 TGTATCGATACAA
1 TGTATCGATACAA
2363522 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2363532 original size:20 final size:20
Alignment explanation
Indices: 2363507--2363585 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
2363497 GTATCGATAC
2363507 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2363527 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
2363552 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
2363572 CATGTATCGATACA
1 AATGTATCGATACA
2363586 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2365620 original size:15 final size:15
Alignment explanation
Indices: 2365600--2365630 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2365590 ATTTCGTTTG
*
2365600 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2365615 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2365630 G
1 G
2365631 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2369709 original size:13 final size:13
Alignment explanation
Indices: 2369691--2369716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2369681 CAATTTTTTG
2369691 TGTATCGATACAT
1 TGTATCGATACAT
2369704 TGTATCGATACAT
1 TGTATCGATACAT
2369717 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2369781 original size:21 final size:21
Alignment explanation
Indices: 2369755--2369830 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2369745 CTGCCAAGAA
*
2369755 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2369776 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2369796 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2369817 ATGTATCGATACAT
1 ATGTATCGATACAT
2369831 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2369801 original size:20 final size:20
Alignment explanation
Indices: 2369776--2369848 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2369766 CATCTTTTTT
2369776 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2369796 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2369817 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2369837 ATGTATCGATAC
1 ATGTATCGATAC
2369849 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2369812 original size:41 final size:41
Alignment explanation
Indices: 2369755--2369848 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2369745 CTGCCAAGAA
*
2369755 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2369796 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2369837 ATGTATCGATAC
1 ATGTATCGATAC
2369849 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2379436 original size:13 final size:13
Alignment explanation
Indices: 2379418--2379443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2379408 TACACCAAGT
2379418 ATGTATCGATACA
1 ATGTATCGATACA
2379431 ATGTATCGATACA
1 ATGTATCGATACA
2379444 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2379441 original size:32 final size:33
Alignment explanation
Indices: 2379400--2379463 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2379390 TAGCCAAACT
**
2379400 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
2379432 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
2379464 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:2381690 original size:21 final size:21
Alignment explanation
Indices: 2381657--2381701 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2381647 TTGCAAGTTG
*
2381657 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2381679 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2381699 AAA
1 AAA
2381702 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2383510 original size:15 final size:15
Alignment explanation
Indices: 2383490--2383520 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2383480 TAAAAATGTC
*
2383490 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2383505 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2383520 C
1 C
2383521 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2385789 original size:20 final size:20
Alignment explanation
Indices: 2385746--2385791 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2385736 AAATCTTTTG
2385746 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2385767 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2385787 CAAAA
1 CAAAA
2385792 CCAGTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2388176 original size:13 final size:13
Alignment explanation
Indices: 2388158--2388183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2388148 TACACCAAGT
2388158 ATGTATCGATACA
1 ATGTATCGATACA
2388171 ATGTATCGATACA
1 ATGTATCGATACA
2388184 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2388181 original size:32 final size:33
Alignment explanation
Indices: 2388140--2388203 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2388130 TAGCCAAACT
**
2388140 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
2388172 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
2388204 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:2389569 original size:52 final size:51
Alignment explanation
Indices: 2389494--2389628 Score: 175
Period size: 51 Copynumber: 2.6 Consensus size: 51
2389484 GCTTGCATGT
*
2389494 ATCGATA-AATTAAAGAATGTATCGATACATTT-GGTTCAAAAGCCCAGAATGC
1 ATCGATACAA-TAAAGAATGTATCGATACATTTAGG-TCAAAA-CCCAAAATGC
* * *
2389546 ATCGATACAATGAAGAATGTATCGATATATTTAGGTCAAAACCCAAAATGT
1 ATCGATACAATAAAGAATGTATCGATACATTTAGGTCAAAACCCAAAATGC
* *
2389597 ATCGATACAATAAAAAATGTATCAATACATTT
1 ATCGATACAATAAAGAATGTATCGATACATTT
2389629 TCATTCCAGA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
51 36 0.49
52 33 0.45
53 4 0.05
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (51 bp):
ATCGATACAATAAAGAATGTATCGATACATTTAGGTCAAAACCCAAAATGC
Found at i:2389720 original size:20 final size:20
Alignment explanation
Indices: 2389695--2389746 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2389685 CATTTGAAAC
*
2389695 ATGTATTGATAAATTCACTT
1 ATGTATCGATAAATTCACTT
* *
2389715 ATGTATCAATACATTCACTT
1 ATGTATCGATAAATTCACTT
2389735 ATTGTATCGATA
1 A-TGTATCGATA
2389747 CAAATTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (20 bp):
ATGTATCGATAAATTCACTT
Found at i:2389742 original size:21 final size:20
Alignment explanation
Indices: 2389707--2389748 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2389697 GTATTGATAA
2389707 ATTCACTTATGTATCAATAC
1 ATTCACTTATGTATCAATAC
*
2389727 ATTCACTTATTGTATCGATAC
1 ATTCACTTA-TGTATCAATAC
2389748 A
1 A
2389749 AATTATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (20 bp):
ATTCACTTATGTATCAATAC
Found at i:2395835 original size:38 final size:37
Alignment explanation
Indices: 2395792--2395889 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
2395782 CTAGTTTCAA
*
2395792 CCGTGCCACCAGTTAAGAATAGTGATTTTTGTTTTGAT
1 CCGTGCCACC-GGTAAGAATAGTGATTTTTGTTTTGAT
* *
2395830 CCGTGCCATCGGTAAGAATAGTGATTTTTGTTTTGAA
1 CCGTGCCACCGGTAAGAATAGTGATTTTTGTTTTGAT
* * *
2395867 CTGTACCACCGGATTAGAATAGT
1 CCGTGCCACCGG-TAAGAATAGT
2395890 CGTTTTGGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
37 34 0.65
38 18 0.35
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (37 bp):
CCGTGCCACCGGTAAGAATAGTGATTTTTGTTTTGAT
Found at i:2398313 original size:22 final size:20
Alignment explanation
Indices: 2398278--2398320 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2398268 GTAATAGCAT
2398278 TATTTTTTTTTCAAAAATCA
1 TATTTTTTTTTCAAAAATCA
*
2398298 TATTTATTGTTTTCAAAATTCA
1 TATTT-TT-TTTTCAAAAATCA
2398320 T
1 T
2398321 GCATCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTTTTTTTCAAAAATCA
Found at i:2401250 original size:1 final size:1
Alignment explanation
Indices: 2401244--2401271 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2401234 AAGGTCCATC
2401244 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2401272 CCTTTTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2405413 original size:28 final size:29
Alignment explanation
Indices: 2405355--2405427 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
2405345 TAAATAAATT
*
2405355 ATTCGTAAAATTAATTAAAATAGAGATAA
1 ATTCGTAAAATTAATTAAAATAGAGAAAA
2405384 ATTCGT-AAA-TATATTAAAATA-AGTAAAA
1 ATTCGTAAAATTA-ATTAAAATAGAG-AAAA
*
2405412 ATTCACTAAAATTAAT
1 ATTC-GTAAAATTAAT
2405428 AAACTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 4 0.11
28 19 0.51
29 7 0.19
30 5 0.14
31 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (29 bp):
ATTCGTAAAATTAATTAAAATAGAGAAAA
Found at i:2405435 original size:14 final size:14
Alignment explanation
Indices: 2405416--2405442 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2405406 GTAAAAATTC
2405416 ACTAAAATTAATAA
1 ACTAAAATTAATAA
2405430 ACTAAAATTAATA
1 ACTAAAATTAATA
2405443 TTATATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
ACTAAAATTAATAA
Found at i:2409114 original size:21 final size:21
Alignment explanation
Indices: 2409081--2409121 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2409071 CTAAGTAAAA
2409081 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2409102 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2409122 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2409186 original size:20 final size:19
Alignment explanation
Indices: 2409161--2409231 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
2409151 ACCTTGAAAA
2409161 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
2409181 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
2409200 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
2409221 GTATCGATACA
1 GTATCGATACA
2409232 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:2409284 original size:53 final size:53
Alignment explanation
Indices: 2409201--2409337 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
2409191 AAATTGCATA
2409201 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
2409255 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCATATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
2409308 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
2409338 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:2409417 original size:13 final size:13
Alignment explanation
Indices: 2409399--2409424 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2409389 ACATATTTGT
2409399 GTGTATCGATACA
1 GTGTATCGATACA
2409412 GTGTATCGATACA
1 GTGTATCGATACA
2409425 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:2412950 original size:55 final size:55
Alignment explanation
Indices: 2412877--2413665 Score: 1109
Period size: 55 Copynumber: 14.3 Consensus size: 55
2412867 TGGCATTTTC
2412877 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
2412932 CAGTCCCCAAAAAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCCTTC
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
2412987 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-TTTT
1 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
2413041 CCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 -CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
2413096 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCCTT
1 -CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
2413152 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
2413206 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCCTT
1 -CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
2413262 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
2413316 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCTCCTTT
1 -CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
2413372 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
2413426 CCAGTCCTCAAAGAGCAGGACACCTTTCATAGCCCACACAAGTTGGTGGCACCTTT
1 -CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * *
2413482 CAATCCCCAAAGAGCAGGACTCCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
2413536 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 -CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
2413592 CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
2413647 TACTCCTCAATGAGCAGGA
1 CAGTCCTCAAAGAGCAGGA
2413666 TACACTTTAT
Statistics
Matches: 665, Mismatches: 50, Indels: 38
0.88 0.07 0.05
Matches are distributed among these distances:
54 22 0.03
55 622 0.94
56 21 0.03
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:2413059 original size:110 final size:110
Alignment explanation
Indices: 2412866--2413665 Score: 1338
Period size: 110 Copynumber: 7.3 Consensus size: 110
2412856 TTCGACATAT
2412866 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
2412931 TCAGTCCCCAAAAAGCAGGACACCTCTT-AAAGCCCACACAAGTTG
66 TCAGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTG
*** *
2412976 GTGGCGCCTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
2413040 TCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
66 T-CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
*
2413086 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCCT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
*
2413151 TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
66 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
*
2413196 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCCT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
2413261 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
66 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
*
2413306 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCTCCTT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
2413371 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
66 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
*
2413416 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCATAGCCCACACAAGTTGGTGGCACCT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCT
* *
2413480 TTCAATCCCCAAAGAGCAGGACTCCTTTCAAAGCCCACCCAAGTTG
65 TTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
2413526 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
1 GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
2413591 TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTG
66 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
* * *
2413636 GTGGCACTTTT-TACTCCTCAATGAGCAGGA
1 GTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
2413666 TACACTTTAT
Statistics
Matches: 656, Mismatches: 28, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
109 7 0.01
110 641 0.98
111 8 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (110 bp):
GTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTG
Found at i:2414366 original size:21 final size:21
Alignment explanation
Indices: 2414342--2414418 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
2414332 AAAAATTTCA
2414342 AATGTATCGATACATTTATAG
1 AATGTATCGATACATTTATAG
* * *
2414363 AATGTATCGATGCATTTGTGG
1 AATGTATCGATACATTTATAG
* *
2414384 AATGTATCAATACATTCTACA-
1 AATGTATCGATACATT-TATAG
2414405 AATGTATCGATACA
1 AATGTATCGATACA
2414419 GGGTCCCAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
21 45 0.98
22 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTATAG
Found at i:2414478 original size:19 final size:19
Alignment explanation
Indices: 2414454--2414521 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2414444 AATTCAACAA
2414454 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2414473 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2414488 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
2414505 ATTGTTTCGATACATAA
1 TTTGTATCGATACATAA
2414522 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2414493 original size:13 final size:13
Alignment explanation
Indices: 2414475--2414499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2414465 ACATAAGTTT
2414475 TGTATCGATACAA
1 TGTATCGATACAA
2414488 TGTATCGATACA
1 TGTATCGATACA
2414500 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2414497 original size:32 final size:32
Alignment explanation
Indices: 2414456--2414518 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2414446 TTCAACAATT
*
2414456 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
2414488 TGTATCGATACATAAGTATTGTTTCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2414519 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2414579 original size:13 final size:13
Alignment explanation
Indices: 2414561--2414586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2414551 CATTTTTCTG
2414561 TGTATCGATACAT
1 TGTATCGATACAT
2414574 TGTATCGATACAT
1 TGTATCGATACAT
2414587 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2414582 original size:33 final size:33
Alignment explanation
Indices: 2414541--2414607 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2414531 GCCAAGGAAA
***
2414541 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2414574 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2414607 T
1 T
2414608 TGGAAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2416966 original size:51 final size:54
Alignment explanation
Indices: 2416891--2417022 Score: 153
Period size: 51 Copynumber: 2.5 Consensus size: 54
2416881 AGTTTCTCAA
* * * * * * * *
2416891 TTCTCCACTATCGGAGATATTCCAACTCCGATTTTATTTTCAAAACACTA-ATT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAATACAAT
*
2416944 TTC-T-ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAATACCAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAATA-CAAT
2416997 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
2417023 CCCGTTAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
51 37 0.57
53 8 0.12
54 1 0.02
55 19 0.29
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (54 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAATACAAT
Found at i:2417076 original size:28 final size:27
Alignment explanation
Indices: 2417009--2417081 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2416999 CTTCACAATC
*
2417009 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2417036 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
*
2417064 GGGGACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2417082 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:2417124 original size:79 final size:79
Alignment explanation
Indices: 2417035--2417239 Score: 236
Period size: 79 Copynumber: 2.6 Consensus size: 79
2417025 CGTTAATCAT
*
2417035 CGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGACACTCCAACCCCGGCTTTATTCCCAAA--A
1 CGGGGATACTCCAACCCCGTTATTTTC-GAGGGGACACTCCAACCCCGACTTTATTCCCAAATCA
* *
2417097 TACTGATTTCTCATAAT
65 T-C-GATTTCTCACAAC
* * * * * ** *
2417114 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAATCAT
2417179 CGATTTCTCACAAC
66 CGATTTCTCACAAC
* * *
2417193 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCG
2417240 TTATTATCTC
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
79 99 0.93
80 5 0.05
81 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAATCAT
CGATTTCTCACAAC
Found at i:2418854 original size:13 final size:13
Alignment explanation
Indices: 2418816--2418856 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
2418806 ACTATTCATG
*
2418816 TATCGATACAGTG
1 TATCGATACAGTA
*
2418829 TATCAATACAGTA
1 TATCGATACAGTA
2418842 TATCGATACAGTA
1 TATCGATACAGTA
2418855 TA
1 TA
2418857 AATAGTATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
TATCGATACAGTA
Found at i:2418937 original size:20 final size:20
Alignment explanation
Indices: 2418912--2418964 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2418902 TTCAAATGCA
2418912 TGTATTGATACATTATGAAT
1 TGTATTGATACATTATGAAT
2418932 TGTATTGATACATTATGAAT
1 TGTATTGATACATTATGAAT
*
2418952 TGTATCGATACAT
1 TGTATTGATACAT
2418965 AGGAGCGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATTGATACATTATGAAT
Found at i:2419383 original size:32 final size:32
Alignment explanation
Indices: 2419341--2419431 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 32
2419331 AAGTGATTAA
2419341 AAGGTTCTATCTTAGCCTTAAAAGATA-GTGT
1 AAGGTTCTATCTTAGCCTTAAAAGATAGGTGT
2419372 AGAGGTTCTATCTTAGCCTTTGTAAAAGATATGGGTGT
1 A-AGGTTCTATCTTAGCC--T-TAAAAGATA--GGTGT
* *
2419410 AAGGTTATACCTTAGCCTTAAA
1 AAGGTTCTATCTTAGCCTTAAA
2419432 GGTAAACAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
31 1 0.02
32 16 0.31
34 5 0.10
35 10 0.20
37 14 0.27
38 5 0.10
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (32 bp):
AAGGTTCTATCTTAGCCTTAAAAGATAGGTGT
Found at i:2421102 original size:84 final size:84
Alignment explanation
Indices: 2420929--2421089 Score: 193
Period size: 84 Copynumber: 1.9 Consensus size: 84
2420919 ACTCAAAGAA
* * ** *
2420929 GAAAATAAATCAATAAGTATAGAGAATGATATTCTTGAAAAGAACTTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTATAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
2420994 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
2421013 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTATAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
2421076 AA-AAGAAATGAGTT
64 AATAAGAAA-GAGTT
2421090 GCAAGTGGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 55 0.85
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTATAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:2424397 original size:13 final size:13
Alignment explanation
Indices: 2424359--2424399 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
2424349 ACTATTCATG
*
2424359 TATCGATACAGTG
1 TATCGATACAGTA
*
2424372 TATCAATACAGTA
1 TATCGATACAGTA
2424385 TATCGATACAGTA
1 TATCGATACAGTA
2424398 TA
1 TA
2424400 AATAGTATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
TATCGATACAGTA
Found at i:2424910 original size:32 final size:33
Alignment explanation
Indices: 2424869--2424956 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 33
2424859 TGATTAAAAA
2424869 GTTCTATCTTAGCCTTAAAAGAT-A-GTGTAGAG
1 GTTCTATCTTAGCCTTAAAAGATAAGGTGTA-AG
2424901 GTTCTATCTTAGCCTTTGTAAAAGATAAGGGTGTAAG
1 GTTCTATCTTAGCC--T-TAAAAGATAA-GGTGTAAG
* *
2424938 GTTATACCTTAGCCTTAAA
1 GTTCTATCTTAGCCTTAAA
2424957 GGTAAACAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
32 14 0.29
34 5 0.10
35 9 0.19
36 1 0.02
37 14 0.29
38 5 0.10
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (33 bp):
GTTCTATCTTAGCCTTAAAAGATAAGGTGTAAG
Found at i:2428658 original size:20 final size:21
Alignment explanation
Indices: 2428610--2428668 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
2428600 AAAAATCCAG
2428610 AATGTATCGATACAATTGTAAGT
1 AATGTATCGATAC-ATT-TAAGT
2428633 -ATGTATCGATACATTTAA-T
1 AATGTATCGATACATTTAAGT
2428652 AATGTATCGATACATTT
1 AATGTATCGATACATTT
2428669 TCTTGGCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 3 0.09
22 12 0.34
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTAAGT
Found at i:2430572 original size:20 final size:20
Alignment explanation
Indices: 2430527--2430583 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2430517 CAAAACCCAG
**
2430527 AATGTATTGATACA-AAGCA
1 AATGTATTGATACATTTGCA
*
2430546 AATTGTATTGATACATTTGGA
1 AA-TGTATTGATACATTTGCA
*
2430567 AATGTATCGATACATTT
1 AATGTATTGATACATTT
2430584 ACTTATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.06
20 26 0.81
21 4 0.12
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (20 bp):
AATGTATTGATACATTTGCA
Found at i:2430686 original size:21 final size:21
Alignment explanation
Indices: 2430662--2430736 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
2430652 ATTTGAGACA
2430662 TGTATCGATACATTCACTAAT
1 TGTATCGATACATTCACTAAT
*
2430683 TGTATTGATACATTCACTAAT
1 TGTATCGATACATTCACTAAT
*
2430704 TGTATCGATACATTTACTAAT
1 TGTATCGATACATTCACTAAT
2430725 TGTATCGATACA
1 TGTATCGATACA
2430737 AATTGTAGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCACTAAT
Found at i:2433658 original size:80 final size:81
Alignment explanation
Indices: 2433414--2433704 Score: 254
Period size: 80 Copynumber: 3.6 Consensus size: 81
2433404 ATTTTTAGTG
* * * * *
2433414 AAAACTGAGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCTAGAGAT-AAAGAAT
1 AAAAATGAGGTTGGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTATCCCCAGAGATGAAA-ATT
* * *
2433478 TCGGTATTGTAGAAGTA
65 TTGATATTTTAGAAGTA
* ** * * *
2433495 AAAGAATGGGGTTTAAGTATCCCCTTAGAGATGG--GGGTTGAAGTATCCCTC-GATATGAAAAT
1 AAA-AATGAGGTTGGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTATCCC-CAGAGATGAAAAT
** * * *
2433557 GCT-ACAATTTGGAAGTA
64 TTTGATATTTTAGAAGTA
* * *
2433574 AAAAATGGGGTTGGAGTATTCCCTCGGAGATGGTAGGGTTGGAGTATCCCCAGAGATGAAAATTT
1 AAAAATGAGGTTGGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTATCCCCAGAGATGAAAATTT
*
2433639 TGATGTTTTAGAAGTA
66 TGATATTTTAGAAGTA
* * * *
2433655 AAAACA--AGGTTGGAATATCCCCTCGGAGATGGCAAGGTTGGAGTATCCCC
1 AAAA-ATGAGGTTGGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTATCCCC
2433705 TTATAAATGG
Statistics
Matches: 168, Mismatches: 34, Indels: 17
0.77 0.16 0.08
Matches are distributed among these distances:
78 25 0.15
79 13 0.08
80 83 0.49
81 20 0.12
82 27 0.16
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (81 bp):
AAAAATGAGGTTGGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTATCCCCAGAGATGAAAATTT
TGATATTTTAGAAGTA
Found at i:2433714 original size:28 final size:28
Alignment explanation
Indices: 2433659--2433732 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
2433649 GAAGTAAAAA
* * *
2433659 CAAGGTTGGAATATCCCCTCGGAGATGG
1 CAAGGTTGGAGTATCCCCTCAGAAATGG
* *
2433687 CAAGGTTGGAGTATCCCCTTATAAATGG
1 CAAGGTTGGAGTATCCCCTCAGAAATGG
* * *
2433715 TAGGGTTAGAGTATCCCC
1 CAAGGTTGGAGTATCCCC
2433733 AAAGATGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (28 bp):
CAAGGTTGGAGTATCCCCTCAGAAATGG
Found at i:2433727 original size:108 final size:108
Alignment explanation
Indices: 2433603--2433811 Score: 303
Period size: 108 Copynumber: 1.9 Consensus size: 108
2433593 TCCCTCGGAG
* *
2433603 ATGGTAGGGTTGGAGTATCCCCAGAGATGA-AAATTTTGATGTTTTAGAAGTAAAAACAAGGTTG
1 ATGGTAGGGTTAGAGTATCCCCAAAGATGATAAA-TTTGATGTTTTAGAAGTAAAAACAAGGTTG
* *
2433667 GAATATCCCCTCGGAGATGGCAAGGTTGGAGTATCCCCTTATAA
65 GAATATCCCCTCAGAGATGGCAAGGTTGAAGTATCCCCTTATAA
* *
2433711 ATGGTAGGGTTAGAGTATCCCCAAAGATGATAAATTTGATGTTTTAGAAGTAAAAATAGGGTTGG
1 ATGGTAGGGTTAGAGTATCCCCAAAGATGATAAATTTGATGTTTTAGAAGTAAAAACAAGGTTGG
* * * **
2433776 AGTATTCTCTCAGAGATGGCGGGGTTGAAGTATCCC
66 AATATCCCCTCAGAGATGGCAAGGTTGAAGTATCCC
2433812 TAGAAATGAA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 86 0.97
109 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (108 bp):
ATGGTAGGGTTAGAGTATCCCCAAAGATGATAAATTTGATGTTTTAGAAGTAAAAACAAGGTTGG
AATATCCCCTCAGAGATGGCAAGGTTGAAGTATCCCCTTATAA
Found at i:2440382 original size:20 final size:20
Alignment explanation
Indices: 2440353--2440390 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2440343 ACAAGGTCTA
* *
2440353 GTATCGATACATTCACTTAT
1 GTATCAATACATTAACTTAT
2440373 GTATCAATACATTAACTT
1 GTATCAATACATTAACTT
2440391 GTTATATCGA
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:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
GTATCAATACATTAACTTAT
Found at i:2441132 original size:21 final size:21
Alignment explanation
Indices: 2441103--2441158 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2441093 GTTGGGACCT
*
2441103 TGTATCGATACATGGAAGGCA
1 TGTACCGATACATGGAAGGCA
2441124 TGTACCGATACATGGAAGGCA
1 TGTACCGATACATGGAAGGCA
2441145 TGTACCGATACATG
1 TGTACCGATACATG
2441159 TAAGCAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (21 bp):
TGTACCGATACATGGAAGGCA
Found at i:2443850 original size:53 final size:53
Alignment explanation
Indices: 2443730--2443903 Score: 129
Period size: 53 Copynumber: 3.3 Consensus size: 53
2443720 GTTGCTCATT
* * * * * * * *
2443730 TCAAGATTAAGCCTAATGATGCTAAT-AGGTTAGTTCTGGCTAATTGGCTAAT-
1 TCAAGATTAAGCCTAATAATGCTAGTAAGCTAATTTC-AGCTAATTGTCCAATA
* * **
2443782 TAAAGATTTAGGCCTAATAATGCTAGTTGGCTAATTTCAGCTAATTAGTCC-ATA
1 TCAAGA-TTAAGCCTAATAATGCTAGTAAGCTAATTTCAGCTAATT-GTCCAATA
* * * * ** *
2443836 TCAAGATTAAGCCTAGTGATGCTAGTAATCTAGTTTTGGCTAATTTTCCAATA
1 TCAAGATTAAGCCTAATAATGCTAGTAAGCTAATTTCAGCTAATTGTCCAATA
2443889 TCAAGATTAAGCCTA
1 TCAAGATTAAGCCTA
2443904 GTGAAGTTGA
Statistics
Matches: 95, Mismatches: 22, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
52 8 0.08
53 74 0.78
54 13 0.14
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (53 bp):
TCAAGATTAAGCCTAATAATGCTAGTAAGCTAATTTCAGCTAATTGTCCAATA
Done.