Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 97 of 196
Found at i:28676656 original size:32 final size:33
Alignment explanation
Indices: 28676587--28676656 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 33
28676577 ATACTGTAAT
* * ** *
28676587 GGGCTAAGGCCCACACTACACTTTTACTGTTTT
1 GGGCTAAAGCCCACACTACACTGTTACTGGATA
*
28676620 GGGCTAAAG-CCACACTATACTGTTACTGGATA
1 GGGCTAAAGCCCACACTACACTGTTACTGGATA
28676652 GGGCT
1 GGGCT
28676657 CAGGCCCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (33 bp):
GGGCTAAAGCCCACACTACACTGTTACTGGATA
Found at i:28697738 original size:20 final size:20
Alignment explanation
Indices: 28697686--28697738 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
28697676 ACATTTGTGC
*
28697686 CTCTATTTGCACTTTGGTGT
1 CTCTATTTGCACTTTGATGT
* * *
28697706 GTCTACTTACACTTTGATGT
1 CTCTATTTGCACTTTGATGT
*
28697726 CTCTGTTTGCACT
1 CTCTATTTGCACT
28697739 ACAGTGCCTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (20 bp):
CTCTATTTGCACTTTGATGT
Found at i:28704850 original size:43 final size:43
Alignment explanation
Indices: 28704778--28704928 Score: 112
Period size: 43 Copynumber: 3.6 Consensus size: 43
28704768 TTCGAGGTGT
* * * * * *
28704778 GATTTCGTGCAAGACCATTTCAGGAACATTGGCATCGGTATGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
* **
28704821 GATTACGTGTAAGACCATGTCTGGGACATTAGCA-CCTTAT-A
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
* ** *
28704862 TGATCTA--TGTAGGACCATGTCTGGGACAGAGGCATCGATATGT
1 -GAT-TACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
* * *
28704905 GATAACATGTAAGACCATATCTGG
1 GATTACGTGTAAGACCATGTCTGG
28704929 TATATGGCAT
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
41 25 0.30
42 14 0.17
43 45 0.54
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
Found at i:28714731 original size:5 final size:5
Alignment explanation
Indices: 28714717--28714762 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
28714707 TAAATATACA
*
28714717 ATAT- ATATG ATATG ATATG ATATG ATATG ATATG -TA-C ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATAT
28714763 ATGTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:28716888 original size:18 final size:18
Alignment explanation
Indices: 28716853--28716890 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28716843 GAAATATTTA
*
28716853 TTTTGATATTTTTAATAT
1 TTTTGATATTTATAATAT
28716871 TTTTGATATATTAT-ATAT
1 TTTTGATAT-TTATAATAT
28716889 TT
1 TT
28716891 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTGATATTTATAATAT
Found at i:28719917 original size:2 final size:2
Alignment explanation
Indices: 28719910--28719936 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28719900 TACTTGACTT
28719910 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28719937 GCTTTATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28732385 original size:27 final size:26
Alignment explanation
Indices: 28732329--28732401 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 26
28732319 AAAAGGGTAC
* *
28732329 AAAATATATACATGTACATATATAAA
1 AAAATATATACATATACATAGATAAA
*
28732355 AAAATTATATACATATATATAGATTATAA
1 AAAA-TATATACATATACATAGA-TA-AA
*
28732384 AAAAGATAATTACATATA
1 AAAATAT-A-TACATATA
28732402 TATAAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 4 0.11
27 15 0.39
28 4 0.11
29 7 0.18
30 8 0.21
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAATATATACATATACATAGATAAA
Found at i:28732385 original size:30 final size:30
Alignment explanation
Indices: 28732349--28732405 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28732339 CATGTACATA
*
28732349 TATAAAAAA-ATTATATACATATATATAGAT
1 TATAAAAAAGATAAT-TACATATATATAGAT
28732379 TATAAAAAAGATAATTACATATATATA
1 TATAAAAAAGATAATTACATATATATA
28732406 AACAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (30 bp):
TATAAAAAAGATAATTACATATATATAGAT
Found at i:28732578 original size:17 final size:17
Alignment explanation
Indices: 28732558--28732601 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
28732548 AGGAAATAAA
28732558 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
28732575 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
28732592 -ATATGTATAT
1 AAAATGTATAT
28732602 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:28732584 original size:27 final size:27
Alignment explanation
Indices: 28732554--28732605 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
28732544 AGTTAGGAAA
*
28732554 TAAAAAAATGTATATGTATATAAAATG
1 TAAAAAAATATATATGTATATAAAATG
***
28732581 TAAATGTATATATATGTATATAAAA
1 TAAAAAAATATATATGTATATAAAA
28732606 GTTATGCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (27 bp):
TAAAAAAATATATATGTATATAAAATG
Found at i:28732635 original size:61 final size:61
Alignment explanation
Indices: 28732514--28732642 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 61
28732504 TTTATCAAAA
* * * *
28732514 AAAATATAAAAGTATATATATGCATATAAAAGTTAGGAAATAAAAAAATGTATATGTATAT
1 AAAATGTAAAAGTATATATATGCATATAAAAGTTAGCAAATAAAAAAATGAATATATATAT
* * * *
28732575 AAAATGTAAATGTATATATATGTATATAAAAGTTATGCAAATAGAACAAT-AATATATATAT
1 AAAATGTAAAAGTATATATATGCATATAAAAGTTA-GCAAATAAAAAAATGAATATATATAT
*
28732636 AATATGT
1 AAAATGT
28732643 GCATGTGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 47 0.81
62 11 0.19
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.33
Consensus pattern (61 bp):
AAAATGTAAAAGTATATATATGCATATAAAAGTTAGCAAATAAAAAAATGAATATATATAT
Found at i:28732738 original size:12 final size:12
Alignment explanation
Indices: 28732721--28732754 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28732711 GTATATATAG
**
28732721 TAATAATAATGA
1 TAATAATAACAA
28732733 TAATAATAACAA
1 TAATAATAACAA
28732745 TAATAATAAC
1 TAATAATAAC
28732755 TTAATAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (12 bp):
TAATAATAACAA
Found at i:28732797 original size:11 final size:11
Alignment explanation
Indices: 28732783--28732807 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28732773 AATTTAATAA
28732783 AAATAATAAAT
1 AAATAATAAAT
28732794 AAATAATAAAT
1 AAATAATAAAT
28732805 AAA
1 AAA
28732808 AAAAGACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:28733107 original size:23 final size:22
Alignment explanation
Indices: 28733064--28733121 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
28733054 AAAGGGTATC
* *
28733064 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28733085 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
28733108 TTCATATCATATCT
1 TACAAATCATATCT
28733122 AAGATTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28733124 original size:19 final size:20
Alignment explanation
Indices: 28733091--28733147 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
28733081 AGATTACAAA
28733091 ATCATATC-T-TCTAAGATT
1 ATCATATCATATCTAAGATT
28733109 -TCATATCATATCTAAGATT
1 ATCATATCATATCTAAGATT
28733128 GAAT-ATATCATATCTAAGAT
1 --ATCATATCATATCTAAGAT
28733148 CATATCTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 9 0.26
21 16 0.47
22 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATCATATCATATCTAAGATT
Found at i:28733167 original size:14 final size:12
Alignment explanation
Indices: 28733134--28733159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28733124 GATTGAATAT
28733134 ATCATATCTAAG
1 ATCATATCTAAG
28733146 ATCATATCTAAG
1 ATCATATCTAAG
28733158 AT
1 AT
28733160 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:28735910 original size:33 final size:32
Alignment explanation
Indices: 28735863--28735972 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
28735853 TACGCGGTTC
* * *
28735863 TGTGAAATGGTAACAAATATCAGCTTTTCATTT
1 TGTGAAATGATAACAAATATCAAC-TTTAATTT
*
28735896 TGTGAAATGATAACAAAT-TAAAACTTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
* *
28735928 TGTAAAATGATAACAAATATCAACTTCAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* *
28735960 TTTTAAATGATAA
1 TGTGAAATGATAA
28735973 TAATATTCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
32 46 0.70
33 20 0.30
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:28737761 original size:22 final size:22
Alignment explanation
Indices: 28737707--28737772 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
28737697 GGTATTTGGG
* *
28737707 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
28737728 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* * *
28737750 ATTTGGTGCGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
28737773 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 19 0.50
22 14 0.37
23 5 0.13
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:28739892 original size:50 final size:50
Alignment explanation
Indices: 28739833--28739931 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
28739823 ATGTGAGTTC
* *
28739833 TCATATCGGTGCCCATGCCATGT-CTAAGACATGGTCTTATGGGGGACCTT
1 TCATATCGGTGCCAATGCCATGTCCT-AGACACGGTCTTATGGGGGACCTT
* *
28739883 TCATCTCGGTGCCAATGCCATGTCCTAGACACGGTCTTATGTGGGACCT
1 TCATATCGGTGCCAATGCCATGTCCTAGACACGGTCTTATGGGGGACCT
28739932 CTTATAACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 42 0.95
51 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (50 bp):
TCATATCGGTGCCAATGCCATGTCCTAGACACGGTCTTATGGGGGACCTT
Found at i:28742703 original size:11 final size:13
Alignment explanation
Indices: 28742657--28742707 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
28742647 GAATTAATTT
28742657 TTAATAAAAAATA
1 TTAATAAAAAATA
** *
28742670 TTTTTAGAAAATA
1 TTAATAAAAAATA
28742683 TTAATAAAAAATA
1 TTAATAAAAAATA
28742696 -TAATAAAAAATA
1 TTAATAAAAAATA
28742708 GATTTAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TTAATAAAAAATA
Found at i:28743240 original size:13 final size:13
Alignment explanation
Indices: 28743222--28743246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28743212 AAATATTAAT
28743222 AATTAATTTTGAA
1 AATTAATTTTGAA
28743235 AATTAATTTTGA
1 AATTAATTTTGA
28743247 GAACAATTGC
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTAATTTTGAA
Found at i:28751918 original size:16 final size:16
Alignment explanation
Indices: 28751893--28751926 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28751883 AAGAAAATCA
28751893 TAAACAGAGGATTGAT
1 TAAACAGAGGATTGAT
*
28751909 TAAACGGAGGATTGAT
1 TAAACAGAGGATTGAT
28751925 TA
1 TA
28751927 TACTTACGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
TAAACAGAGGATTGAT
Found at i:28752041 original size:6 final size:7
Alignment explanation
Indices: 28752032--28752078 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
28752022 AAAATAAAAA
28752032 AATTA-G
1 AATTAGG
28752038 AATTAGG
1 AATTAGG
*
28752045 ATTTAGG
1 AATTAGG
28752052 AATTAGG
1 AATTAGG
*
28752059 ACTTAGG
1 AATTAGG
*
28752066 ACTTAGG
1 AATTAGG
*
28752073 ACTTAG
1 AATTAG
28752079 TATTTAGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (7 bp):
AATTAGG
Found at i:28752050 original size:7 final size:7
Alignment explanation
Indices: 28752040--28752078 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
28752030 AAAATTAGAA
*
28752040 TTAGGAT
1 TTAGGAC
*
28752047 TTAGGAA
1 TTAGGAC
28752054 TTAGGAC
1 TTAGGAC
28752061 TTAGGAC
1 TTAGGAC
28752068 TTAGGAC
1 TTAGGAC
28752075 TTAG
1 TTAG
28752079 TATTTAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (7 bp):
TTAGGAC
Found at i:28752085 original size:21 final size:21
Alignment explanation
Indices: 28752032--28752078 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28752022 AAAATAAAAA
* *
28752032 AATTA-GAATTAGGATTTAGG
1 AATTAGGACTTAGGACTTAGG
28752052 AATTAGGACTTAGGACTTAGG
1 AATTAGGACTTAGGACTTAGG
*
28752073 ACTTAG
1 AATTAG
28752079 TATTTAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (21 bp):
AATTAGGACTTAGGACTTAGG
Found at i:28758782 original size:50 final size:50
Alignment explanation
Indices: 28758672--28758787 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
28758662 TTATAAGAGG
* * * * *
28758672 TCCCACATAAGACCGTGTCTAGGACATGGCGTTGGCACCGAGATGAAAGG
1 TCCCACGTAAGACCATGTCTAGGACATGGCATAGGCACCGAGATGAAAGC
* * *
28758722 TCCCCCGTAAGACCATGTTTAGGACATGGCATAGGCACCGATATGAGAA-C
1 TCCCACGTAAGACCATGTCTAGGACATGGCATAGGCACCGAGATGA-AAGC
*
28758772 TCCCATGTAAGACCAT
1 TCCCACGTAAGACCAT
28758788 ATCTGGGATA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 53 0.96
51 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTAGGACATGGCATAGGCACCGAGATGAAAGC
Found at i:28760467 original size:472 final size:472
Alignment explanation
Indices: 28759148--28761446 Score: 3617
Period size: 472 Copynumber: 4.9 Consensus size: 472
28759138 CATTGTACGA
* * * * * *
28759148 GAGAATTTAACGAATTAACTGTACTATTT-CGCTAACCTAGAAATTTTAGAAATTTTATGATAAG
1 GAGACTTTAACAAATTAACTGTACTATTTGC-CTAACCCAAAAATTCTGGAAATTTTATGATAAG
*** * * *
28759212 AAGATATATGAGTCTAGTTTTAGGAAAAATTTACATATCTAAATTTAGAGTTTCGT-AACTCAAG
65 AAGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTT-TTAAACTCGAG
*
28759276 TTATAATTAAATTAGTTACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
129 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* * *
28759341 TTTGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCTGGTTTGGACCTGAACCATTTTTGTT
194 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTAAACCATTTTTGTT
*
28759406 GCATGTTTTAGGGTCTCGAGGTCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
259 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
* *
28759471 TAAAAGCAAATTTTTATGCTCTGAACTAGTAAGTTAAGTCAGGTAACGCATCATGTTCGACTCC-
324 TAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCG
* *
28759535 AGCAACAGTCTCGGGTAAGGGGTGTTATTTATGATAGTTGATTTCTAGTGAATAGAGGTCAGAAC
389 A-CAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
* * *
28759600 AGTCGGACAGTGAAATAGGG
453 CGTCAGACAGTGAAACAGGG
* * *
28759620 GAGAGTTTAACAAATTAAATTTACTATTTTG-CTAACCCAAAAATTCTGGAAATTTTATGATAAG
1 GAGACTTTAACAAATTAACTGTACTA-TTTGCCTAACCCAAAAATTCTGGAAATTTTATGATAAG
* *
28759684 AAGATATGTGAGTCTAGTTTTAGGAAAAATTTACT-GATCTAAATTTTGAGTTTTTAAACTCGAG
65 AAGATATATGAGTCTAGTTTTAGGAAAAATTTA-TGGATCTAAATTTCGAGTTTTTAAACTCGAG
28759748 TTATAATTAAATTAGTGACTGTCACG-AAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
129 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* * *
28759812 TTTGATTTATTTAAGTATTTAGAAAAGTTTTAATGTTCCAC-GTTTGGACCTAAACTATTTTTGT
194 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCC-CGGTTTGGACCTAAACCATTTTTGT
* *
28759876 TGTATGTTTTAGGGTCTCGAGGGCCCTTTTTAGAGACATATTGATTGAACGTGAGCGAATTAATT
258 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* *
28759941 TTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAACGCATCATGCTCGACTCC
323 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
*
28760006 GACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
388 GACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
*
28760071 CGTCAGACAGTGAAACAAGG
453 CGTCAGACAGTGAAACAGGG
* * * * *
28760091 GAGACTTTAACGAATTAACTGAAGTATTTGCCGAACCCAAAAATTCTGGAAATTTTATGATAATA
1 GAGACTTTAACAAATTAACTGTACTATTTGCCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
28760156 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
66 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
*
28760221 ATAATTAAATTAGTAACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
131 ATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
** * * * *
28760286 TGATTTATTTACCTAATCAGAAAATTTTTAATGTTCCTGGTTTGGACTTTAACCATTTTTGTTGC
196 TGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTAAACCATTTTTGTTGC
28760351 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
261 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
* *
28760416 AAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAACGCATCATGCTCGACTCCGAC
326 AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
* *
28760481 AATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACCAT
391 AACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACCGT
* *
28760546 CAGACAGTGAAACATGA
456 CAGACAGTGAAACAGGG
*
28760563 GAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
1 GAGACTTTAACAAATTAACTGTACTATTTGCCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
* *
28760628 AAATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
66 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
* * *
28760693 ATAATTAAATTAGTGACTGTAACACAAGTGGATAGTTTTATTATGAATTGTGAAATAAATTATTT
131 ATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
*
28760758 TGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTTGC
196 TGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTAAACCATTTTTGTTGC
* * * *
28760823 ATGTTTTAGGGTCTTGAGGGTCCTTTTTAGGGACATATTGATTGAACATGAGAGAATTAATTTTA
261 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
*
28760888 AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCACGCTCGACTCCGAC
326 AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
* * *
28760953 AACGGTCTCGAGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGCTTAGAACCGT
391 AACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACCGT
*
28761018 CGGACAGTGAAACAGGG
456 CAGACAGTGAAACAGGG
*
28761035 GAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
1 GAGACTTTAACAAATTAACTGTACTATTTGCCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
* * *
28761100 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATTTAAATTTCAAATTTTTAAACTCGAGTT
66 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
* * * *
28761165 ATAATTAAATTAGTGACTGTCATGCAAGTGGATTGTTTTATTGTGAATAGTAAAATAAATTATTT
131 ATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
* * * * **
28761230 TGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCCGATTTAGACCTAAACTATTTCCGTTGC
196 TGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTAAACCATTTTTGTTGC
* * *
28761295 ATGTTTTAGTGTCTCGAGGGCCCTTTTTAAGGAC--ATTGATTGAACATGAGCGAATTAATTTTA
261 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
* * * * ** *
28761358 AAAGCAAATTTTTATGATTCGAACTAGTAAGTTAAGTCAGGTAACTCCTTGTGCTCGACTCCGGC
326 AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
28761423 AACGGTCTCGGGTAAGGGGTGTTA
391 AACGGTCTCGGGTAAGGGGTGTTA
28761447 CATCCCAGAA
Statistics
Matches: 1691, Mismatches: 126, Indels: 22
0.92 0.07 0.01
Matches are distributed among these distances:
470 113 0.07
471 431 0.25
472 1144 0.68
473 3 0.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (472 bp):
GAGACTTTAACAAATTAACTGTACTATTTGCCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
ATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
TGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTAAACCATTTTTGTTGC
ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
AACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACCGT
CAGACAGTGAAACAGGG
Found at i:28761205 original size:944 final size:943
Alignment explanation
Indices: 28759148--28761446 Score: 3678
Period size: 943 Copynumber: 2.4 Consensus size: 943
28759138 CATTGTACGA
* * * * * *
28759148 GAGAATTTAACGAATTAACTGTACTATTTCGCTAACCTAGAAATTTTAGAAATTTTATGATAAGA
1 GAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
*** * *
28759213 AGATATATGAGTCTAGTTTTAGGAAAAATTTACATATCTAAATTT-AGAGTTTCGT-AACTCAAG
66 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCA-AGTTT-TTAAACTCGAG
*
28759276 TTATAATTAAATTAGTTACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
129 TTATAATTAAATTAGTAACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
*
28759341 TTTGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCTGGTTTGGACCTGAACCATTTTTGTT
194 TTTGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGTT
*
28759406 GCATGTTTTAGGGTCTCGAGGTCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
259 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
* *
28759471 TAAAAGCAAATTTTTATGCTCTGAACTAGTAAGTTAAGTCAGGTAACGCATCATGTTCGACTCC-
324 TAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCG
* *
28759535 AGCAACAGTCTCGGGTAAGGGGTGTTATTTATGATAGTTGATTTCTAGTGAATAGAGGTCAGAAC
389 A-CAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
* * * * * *
28759600 AGTCGGACAGTGAAATAGGGGAGAGTTTAACAAATTAAATTTACTATTTTGCTAACCCAAAAATT
453 AGTCAGACAGTGAAACAGGAGAGACTTTAACAAATTAAATGTACTATTTGGCTAACCCAAAAATT
* * *
28759665 CTGGAAATTTTATGATAAGAAGATATGTGAGTCTAGTTTTAGGAAAAATTTACTGATCTAAATTT
518 CTGGAAATTTTATGATAAGAAAATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTT
*
28759730 TGAGTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGTCACGAAGTGGATAGTTTTATTATGA
583 CGAGTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGTCACGAAGTGGATAGTTTTATTATGA
*
28759795 ATAGTGAAATAAATTATTTTGATTTATTTAAGTATTTAGAAAAGTTTTAATGTTCCACGTTTGGA
648 ATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAAGTTTTAATGTTCCACGTTTGGA
* *
28759860 CCTAAACTATTTTTGTTGTATGTTTTAGGGTCTCGAGGGCCCTTTTTAGAGACATATTGATTGAA
713 CCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGAGACATATTGATTGAA
* *
28759925 CGTGAGCGAATTAATTTTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAACG
778 CATGAGAGAATTAATTTTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAACG
* * *
28759990 CATCATGCTCGACTCCGACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGT
843 CATCACGCTCGACTCCGACAACGGTCTCGAGTAAGGGGTGTTATTTATGATAATTGATTTCTAGT
*
28760055 GAATAGAGGTCAGAACCGTCAGACAGTGAAACAAGG
908 GAATAGAGCTCAGAACCGTCAGACAGTGAAACAAGG
* * * * *
28760091 GAGACTTTAACGAATTAACTGAAGTATTTGCCGAACCCAAAAATTCTGGAAATTTTATGATAATA
1 GAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
*
28760156 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCGAGTTTTTAAACTCGAGTT
66 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCAAGTTTTTAAACTCGAGTT
28760221 ATAATTAAATTAGTAACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
131 ATAATTAAATTAGTAACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
** * * * *
28760286 TGATTTATTTACCTAATCAGAAAATTTTTAATGTTCCTGGTTTGGACTTTAACCATTTTTGTTGC
196 TGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGTTGC
28760351 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
261 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
* *
28760416 AAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAACGCATCATGCTCGACTCCGAC
326 AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
*
28760481 AATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACCA-
391 AACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAA-CAG
* *
28760545 TCAGACAGTGAAACATGAGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCT
455 TCAGACAGTGAAACAGGAGAGACTTTAACAAATTAAATGTACTATTTGGCTAACCCAAAAATTCT
28760610 GGAAATTTTATGATAAGAAAATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCG
520 GGAAATTTTATGATAAGAAAATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCG
28760675 AGTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGTAACAC-AAGTGGATAGTTTTATTATGA
585 AGTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGT--CACGAAGTGGATAGTTTTATTATGA
* *
28760739 ATTGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCC-CGGTTTGG
648 ATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAAGTTTTAATGTTCCAC-GTTTGG
* * * *
28760803 ACCTGAACCATTTTTGTTGCATGTTTTAGGGTCTTGAGGGTCCTTTTTAGGGACATATTGATTGA
712 ACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGAGACATATTGATTGA
* *
28760868 ACATGAGAGAATTAATTTTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAAC
777 ACATGAGAGAATTAATTTTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAAC
28760933 GCATCACGCTCGACTCCGACAACGGTCTCGAGTAAGGGGTGTTATTTATGATAATTGATTTCTAG
842 GCATCACGCTCGACTCCGACAACGGTCTCGAGTAAGGGGTGTTATTTATGATAATTGATTTCTAG
* * *
28760998 TGAATAGAGCTTAGAACCGTCGGACAGTGAAACAGGG
907 TGAATAGAGCTCAGAACCGTCAGACAGTGAAACAAGG
*
28761035 GAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
1 GAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
* *
28761100 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATTTAAATTTCAAATTTTTAAACTCGAGTT
66 AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCAAGTTTTTAAACTCGAGTT
* * * * *
28761165 ATAATTAAATTAGTGACTGTCATGCAAGTGGATTGTTTTATTGTGAATAGTAAAATAAATTATTT
131 ATAATTAAATTAGTAACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
* * * * **
28761230 TGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCCGATTTAGACCTAAACTATTTCCGTTGC
196 TGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGTTGC
* * *
28761295 ATGTTTTAGTGTCTCGAGGGCCCTTTTTAAGGAC--ATTGATTGAACATGAGCGAATTAATTTTA
261 ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
* * * * ** *
28761358 AAAGCAAATTTTTATGATTCGAACTAGTAAGTTAAGTCAGGTAACTCCTTGTGCTCGACTCCGGC
326 AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
28761423 AACGGTCTCGGGTAAGGGGTGTTA
391 AACGGTCTCGGGTAAGGGGTGTTA
28761447 CATCCCAGAA
Statistics
Matches: 1246, Mismatches: 103, Indels: 15
0.91 0.08 0.01
Matches are distributed among these distances:
942 108 0.09
943 571 0.46
944 564 0.45
945 3 0.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (943 bp):
GAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAAGA
AGATATATGAGTCTAGTTTTAGGAAAAATTTATGGATCTAAATTTCAAGTTTTTAAACTCGAGTT
ATAATTAAATTAGTAACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTATTT
TGATTTATTTAAGTATTCAAAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGTTGC
ATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTTTA
AAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCGAC
AACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACAGT
CAGACAGTGAAACAGGAGAGACTTTAACAAATTAAATGTACTATTTGGCTAACCCAAAAATTCTG
GAAATTTTATGATAAGAAAATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGA
GTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGTCACGAAGTGGATAGTTTTATTATGAATA
GTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAAGTTTTAATGTTCCACGTTTGGACCT
AAACCATTTTTGTTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGAGACATATTGATTGAACAT
GAGAGAATTAATTTTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGCTAACGCAT
CACGCTCGACTCCGACAACGGTCTCGAGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAA
TAGAGCTCAGAACCGTCAGACAGTGAAACAAGG
Found at i:28765686 original size:13 final size:13
Alignment explanation
Indices: 28765631--28765687 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
28765621 TAATACTCTA
*
28765631 TTTTCAAGATATG
1 TTTTAAAGATATG
* *
28765644 TTTCT-AGGTTATG
1 TTT-TAAAGATATG
* *
28765657 TTTTTAAGTTATG
1 TTTTAAAGATATG
28765670 TTTTAAAGATATG
1 TTTTAAAGATATG
28765683 TTTTA
1 TTTTA
28765688 CGCATGCTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.03
13 35 0.95
14 1 0.03
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (13 bp):
TTTTAAAGATATG
Found at i:28766988 original size:25 final size:23
Alignment explanation
Indices: 28766926--28766989 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 23
28766916 CGAACCCATG
*
28766926 TTTTTATGCGAACTCATATTTTA
1 TTTTTATGCGAACTCATATTGTA
* * *
28766949 TGTTGTAGTGTGAACTCATGTTGTA
1 T-TTTTA-TGCGAACTCATATTGTA
28766974 CTTTTCTATGCGAACT
1 -TTTT-TATGCGAACT
28766990 ATAATAATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
23 1 0.03
24 4 0.13
25 23 0.74
26 3 0.10
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (23 bp):
TTTTTATGCGAACTCATATTGTA
Found at i:28772613 original size:22 final size:22
Alignment explanation
Indices: 28772585--28772628 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28772575 CAACTTATGT
28772585 AAGAATCATAACATGTTGGATG
1 AAGAATCATAACATGTTGGATG
28772607 AAGAATCATAACATGTTGGATG
1 AAGAATCATAACATGTTGGATG
28772629 TAACACCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (22 bp):
AAGAATCATAACATGTTGGATG
Found at i:28773397 original size:43 final size:43
Alignment explanation
Indices: 28773350--28773446 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
28773340 TATCCCAGAT
*
28773350 ATGGTATTATATGTTAACGCA-TATCGATGCCAATGTCCCAAAC
1 ATGGTATTACATGTTAACGCACT-TCGATGCCAATGTCCCAAAC
* ** * *
28773393 ATGGTCTTACATGTTTTCTCACTTCGATGCCAATGTCCCAGAC
1 ATGGTATTACATGTTAACGCACTTCGATGCCAATGTCCCAAAC
*
28773436 ATGGTCTTACA
1 ATGGTATTACA
28773447 CGAAATCACA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (43 bp):
ATGGTATTACATGTTAACGCACTTCGATGCCAATGTCCCAAAC
Found at i:28773612 original size:31 final size:31
Alignment explanation
Indices: 28773571--28773961 Score: 477
Period size: 31 Copynumber: 12.7 Consensus size: 31
28773561 ATCCAATGCT
* * *
28773571 CAAATC-AATTCGACAGTATATATCCATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773601 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773632 CAAATC-AATTC-AGCAATGAATATCCATATA
1 CAAATCAAATTCGA-CAATGTATATCTATATA
* * * *
28773662 CAATTCAAATTTGACAATGTATAACCATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773693 CAAATCAAATTCGACAATATATATCTATAAA
1 CAAATCAAATTCGACAATGTATATCTATATA
*
28773724 CAAATCAAATTCGACAATGTATATTTATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773755 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
* * *
28773785 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
*
28773816 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773847 CAAATC-AATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773877 CAATTCAAATTCGACAATGTATATCTATAAA
1 CAAATCAAATTCGACAATGTATATCTATATA
* * *
28773908 CAAATCAATTTCGTCAATGTATATCTATAAA
1 CAAATCAAATTCGACAATGTATATCTATATA
* *
28773939 GAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCGACAATGTATA
28773962 AAACATATAC
Statistics
Matches: 318, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
30 85 0.27
31 232 0.73
32 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGACAATGTATATCTATATA
Found at i:28773699 original size:92 final size:92
Alignment explanation
Indices: 28773571--28773961 Score: 507
Period size: 92 Copynumber: 4.2 Consensus size: 92
28773561 ATCCAATGCT
* * * * * *
28773571 CAAATCAATTCGACAGTATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATACAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGACAATGTATATCTATAAACAAA
* *
28773636 TC-AATTC-AGCAATGAATATCCATATA
66 TCAAATTCGA-CAATGTATATCTATATA
* * * * *
28773662 CAATTCAAATTTGACAATGTATAACCATATACAAATCAAATTCGACAATATATATCTATAAACAA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGACAATGTATATCTATAAACAA
*
28773727 ATCAAATTCGACAATGTATATTTATATA
65 ATCAAATTCGACAATGTATATCTATATA
* * * *
28773755 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGACAATGTATATCTATAAACAAA
*
28773820 TCAAATTCGGCAATGTATATCTATATA
66 TCAAATTCGACAATGTATATCTATATA
* * *
28773847 CAAATCAATTCGGCAATGTATATCTATAAACAATTCAAATTCGACAATGTATATCTATAAACAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGACAATGTATATCTATAAACAAA
* * *
28773912 TCAATTTCGTCAATGTATATCTATAAA
66 TCAAATTCGACAATGTATATCTATATA
*
28773939 GAAATCAAATTCGGCAATGTATA
1 CAAATC-AATTCGGCAATGTATA
28773962 AAACATATAC
Statistics
Matches: 262, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
91 5 0.02
92 216 0.82
93 40 0.15
94 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (92 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGACAATGTATATCTATAAACAAA
TCAAATTCGACAATGTATATCTATATA
Found at i:28773714 original size:123 final size:122
Alignment explanation
Indices: 28773571--28773961 Score: 509
Period size: 123 Copynumber: 3.2 Consensus size: 122
28773561 ATCCAATGCT
* * *
28773571 CAAATC-AATTCGACAGTATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATCAAATTCGACAATATATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* *
28773635 ATCAATTCAGCAATGAATATCCATATACAATTCAAATTTGACAATGTATAACCATATA
66 ATCAATTC-GCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
* * *
28773693 CAAATCAAATTCGACAATATATATCTATAAACAAATCAAATTCGACAATGTATATTTATATACAA
1 CAAATCAAATTCGACAATATATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* *
28773758 ATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
66 ATCAATTC-GCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
* * *
28773816 CAAATCAAATTCGGCAATGTATATCTATATACAAATC-AATTCGGCAATGTATATCTATAAACAA
1 CAAATCAAATTCGACAATATATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* * * * * * *
28773880 TTCAAATTCGACAATGTATATCTATAAACAAATC-AATTTCGTCAATGTATATCTATAAA
66 ATC-AATTCG-CAATGTATATCCATATACAAATCAAATTT-GACAATGTATAACCATATA
* * *
28773939 GAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCGACAATATATA
28773962 AAACATATAC
Statistics
Matches: 239, Mismatches: 26, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
122 37 0.15
123 202 0.85
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (122 bp):
CAAATCAAATTCGACAATATATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
ATCAATTCGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
Found at i:28780700 original size:26 final size:26
Alignment explanation
Indices: 28780664--28780732 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
28780654 CCCGTTATAT
*
28780664 GGCTCTTTGTGAGCTTCTTGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
28780690 GGCTCTTTGTGAGCTTCTCGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
28780716 GGCTCTTTGTGAGCTTC
1 GGCTCTTTGTGAGCTTC
28780733 CCAATATTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.41
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCTCGATTAAA
Found at i:28783183 original size:11 final size:11
Alignment explanation
Indices: 28783167--28783193 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28783157 CAAAAATTTA
28783167 ATCTTTGTAGG
1 ATCTTTGTAGG
28783178 ATCTTTGTAGG
1 ATCTTTGTAGG
28783189 ATCTT
1 ATCTT
28783194 AGCCTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (11 bp):
ATCTTTGTAGG
Found at i:28783257 original size:17 final size:17
Alignment explanation
Indices: 28783235--28783268 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28783225 AAAGACTTAA
28783235 TTAGTTTCTTCTTTCCC
1 TTAGTTTCTTCTTTCCC
* *
28783252 TTAGTTTTTTGTTTCCC
1 TTAGTTTCTTCTTTCCC
28783269 CTGAGGGGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.24, G:0.09, T:0.62
Consensus pattern (17 bp):
TTAGTTTCTTCTTTCCC
Found at i:28784952 original size:10 final size:10
Alignment explanation
Indices: 28784937--28784964 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28784927 TAATATAAAT
28784937 ATTATAAACA
1 ATTATAAACA
28784947 ATTATAAACA
1 ATTATAAACA
28784957 ATTATAAA
1 ATTATAAA
28784965 TTAGATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (10 bp):
ATTATAAACA
Found at i:28793597 original size:24 final size:23
Alignment explanation
Indices: 28793570--28793619 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
28793560 TATTTAATAT
*
28793570 TATTAGAATAAGGATTTTCAACCC
1 TATTAGAATAAGG-TTTACAACCC
*
28793594 TATTAGAATAAGGTTTACAAGCC
1 TATTAGAATAAGGTTTACAACCC
28793617 TAT
1 TAT
28793620 AAATAGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (23 bp):
TATTAGAATAAGGTTTACAACCC
Found at i:28798732 original size:40 final size:41
Alignment explanation
Indices: 28798662--28798745 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 41
28798652 AATTATGGAA
* * * *
28798662 TACTGAATATTGTTTTTGAGTATTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAT
* *
28798703 TACTGAATATT-TTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAT
28798743 TAC
1 TAC
28798746 GGAAGTAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 26 0.70
41 11 0.30
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAT
Found at i:28799022 original size:45 final size:45
Alignment explanation
Indices: 28798952--28799049 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
28798942 TGCCGACTAT
* *
28798952 TGTTACTGTTACCGATTCAATACTTTGTGTGTCGAATACTGTTAGC
1 TGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTA-C
* *
28798998 -GTTACTGTTACATATTCAACACTTTGTGTGTTGAATACTGTTAC
1 TGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTAC
28799042 TGTTACTG
1 TGTTACTG
28799050 CTACCGTTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (45 bp):
TGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTAC
Found at i:28801816 original size:22 final size:22
Alignment explanation
Indices: 28801790--28801866 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
28801780 CTAAATTAAG
28801790 AATAAAGAATATAATGTATATT
1 AATAAAGAATATAATGTATATT
* * *
28801812 AATAATGTCATATAAAGTTAATAACAATT
1 AATAAAG-AATATAATG-T-AT----ATT
28801841 AATAAAGAATATAATGTATATT
1 AATAAAGAATATAATGTATATT
28801863 AATA
1 AATA
28801867 TATTAATTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
22 13 0.31
23 7 0.17
24 1 0.02
25 2 0.05
26 2 0.05
27 1 0.02
28 7 0.17
29 9 0.21
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.35
Consensus pattern (22 bp):
AATAAAGAATATAATGTATATT
Found at i:28805185 original size:50 final size:50
Alignment explanation
Indices: 28805059--28805300 Score: 193
Period size: 50 Copynumber: 4.7 Consensus size: 50
28805049 GATAATAACA
* * ** * * *
28805059 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGTATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * **
28805108 TGCCAATGCCATATCACAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
28805158 TGCCCATGCCATGTCCCAAACATGGTCTTAC-GGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGG
* * * **
28805208 TGCCAACGCCATGTCCCAGACATGATCTTACATGAGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
28805264 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28805301 TTTCATTCCC
Statistics
Matches: 152, Mismatches: 31, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 77 0.51
51 1 0.01
53 2 0.01
56 34 0.22
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28817410 original size:25 final size:25
Alignment explanation
Indices: 28817375--28817433 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
28817365 AGCTATAAAC
* *
28817375 AGTAAGCTCATACGAGTTGAATATT
1 AGTAAGCTCATACGAGCTAAATATT
* *
28817400 AGTAAGGTCATGCGAGCTAAATATT
1 AGTAAGCTCATACGAGCTAAATATT
* *
28817425 GGCAAGCTC
1 AGTAAGCTC
28817434 TCTTGAGTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (25 bp):
AGTAAGCTCATACGAGCTAAATATT
Found at i:28824917 original size:26 final size:26
Alignment explanation
Indices: 28824880--28824935 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
28824870 TTCTTATTAG
*
28824880 ACTA-AGGGCGTGGTTAGCTTCATCT
1 ACTACAGGACGTGGTTAGCTTCATCT
28824905 ACTACAGGACGTGGTTAGCTTCATCT
1 ACTACAGGACGTGGTTAGCTTCATCT
28824931 ACTAC
1 ACTAC
28824936 TACAAGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (26 bp):
ACTACAGGACGTGGTTAGCTTCATCT
Found at i:28825333 original size:27 final size:27
Alignment explanation
Indices: 28825300--28825530 Score: 265
Period size: 27 Copynumber: 8.6 Consensus size: 27
28825290 ATAACAGTCA
28825300 GTATTTCGATAATTTTACCCATCGAGG
1 GTATTTCGATAATTTTACCCATCGAGG
*
28825327 GTCTTTCGATAATTTTACCCATCGAGG
1 GTATTTCGATAATTTTACCCATCGAGG
*
28825354 GTATTTCGATAATTTTACCCTTCG-GG
1 GTATTTCGATAATTTTACCCATCGAGG
* * *
28825380 GATATTTTGGTAATTTTACCTATC-AGGG
1 G-TATTTCGATAATTTTACCCATCGA-GG
* *
28825408 GTATTTCGATAATTTTACCCTTCGGGG
1 GTATTTCGATAATTTTACCCATCGAGG
*
28825435 GTATTT-TAGTAATTTTACCCATCGAGG
1 GTATTTCGA-TAATTTTACCCATCGAGG
*
28825462 GTATTTC-ATTAATTTTACACATCGAGG
1 GTATTTCGA-TAATTTTACCCATCGAGG
* * *
28825489 ATATTTC-AGTAGTTTGACCCATCGAGG
1 GTATTTCGA-TAATTTTACCCATCGAGG
*
28825516 GTATTTTGATAATTT
1 GTATTTCGATAATTT
28825531 AGGCCTATTA
Statistics
Matches: 172, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
26 4 0.02
27 164 0.95
28 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (27 bp):
GTATTTCGATAATTTTACCCATCGAGG
Found at i:28826315 original size:24 final size:23
Alignment explanation
Indices: 28826287--28826331 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
28826277 AAAAGAAAAA
28826287 GAAAA-TAGAGCAGAAAACGTACTC
1 GAAAACTAG-GCA-AAAACGTACTC
*
28826311 GAAAACTTGGCAAAAACGTAC
1 GAAAACTAGGCAAAAACGTAC
28826332 CAAACACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 8 0.42
25 2 0.11
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (23 bp):
GAAAACTAGGCAAAAACGTACTC
Found at i:28826748 original size:25 final size:25
Alignment explanation
Indices: 28826698--28826751 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
28826688 TGAACCTCTA
*
28826698 ACCTCCTTACCACACCTGTGATGCC
1 ACCTCCTTACCACACCTATGATGCC
*
28826723 ACCTCCTTGCCACACCTATG-TCGCC
1 ACCTCCTTACCACACCTATGAT-GCC
28826748 ACCT
1 ACCT
28826752 TGGCACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.19, C:0.46, G:0.11, T:0.24
Consensus pattern (25 bp):
ACCTCCTTACCACACCTATGATGCC
Found at i:28830049 original size:34 final size:35
Alignment explanation
Indices: 28830004--28830071 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
28829994 CCAGTAAAAT
*
28830004 ATTTTCCGTAAAATGATTT-CAGGAAAATGTTTTA
1 ATTTTCCGTAAAATGATTTACAGGAAAATATTTTA
* *
28830038 ATTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 ATTTTCCGTAAAATGATTTACAGGAAAATATTTT
28830072 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (35 bp):
ATTTTCCGTAAAATGATTTACAGGAAAATATTTTA
Found at i:28830075 original size:14 final size:15
Alignment explanation
Indices: 28830038--28830075 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28830028 AAATGTTTTA
*
28830038 ATTTTCTGTAAAATG
1 ATTTTCTGGAAAATG
*
28830053 ATTTACTGGAAAAT-
1 ATTTTCTGGAAAATG
28830067 ATTTTCTGG
1 ATTTTCTGG
28830076 TGTTTGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (15 bp):
ATTTTCTGGAAAATG
Found at i:28830478 original size:21 final size:21
Alignment explanation
Indices: 28830449--28830490 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28830439 ACGGAAATTG
28830449 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAAGACATTTTCCCT
* **
28830470 AAAATGTAATCCATTTTCCCT
1 AAAAGGTAAGACATTTTCCCT
28830491 TGTTTTGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAGGTAAGACATTTTCCCT
Found at i:28832349 original size:26 final size:26
Alignment explanation
Indices: 28832320--28832374 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
28832310 AACACACTAA
28832320 TATCGCAACAAAGCTACCAGTAACAG
1 TATCGCAACAAAGCTACCAGTAACAG
* *
28832346 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAACAAAGCTACCAGTAACAG
28832372 TAT
1 TAT
28832375 ACTTCCTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (26 bp):
TATCGCAACAAAGCTACCAGTAACAG
Found at i:28832556 original size:27 final size:27
Alignment explanation
Indices: 28832536--28832810 Score: 329
Period size: 27 Copynumber: 10.3 Consensus size: 27
28832526 GGGTATAAAA
* *
28832536 GTCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
28832563 ATCATTTTACCCTATAGGGGTATTTT-
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
28832589 GTCATTTTACCTTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
28832616 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
28832643 ATCATTTTACCCTATGGGGGTATTCTG
1 GTCATTTTACCCTATGGGGGTATTTTG
28832670 GTCATTTTACCCTAT-GGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* **
28832696 GTCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
28832723 ATCATTTTACCCTGTGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * * *
28832750 GTTATTTTACCTTGTGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
28832777 GTCATTTTATCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
28832804 GTCATTT
1 GTCATTT
28832811 ATTGACCTTT
Statistics
Matches: 214, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
26 49 0.23
27 165 0.77
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:28832642 original size:80 final size:79
Alignment explanation
Indices: 28832536--28832810 Score: 388
Period size: 80 Copynumber: 3.4 Consensus size: 79
28832526 GGGTATAAAA
* *
28832536 GTCATTTTACCCTGTGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTGTCATTTTACCT
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGTCATTTTACCT
28832601 TATAGGGGTATTTTG
66 TAT-GGGGTATTTTG
*
28832616 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTCTGGTCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATT-TTGTCATTTTACC
*
28832681 CTATGGGGTATTTTG
65 TTATGGGGTATTTTG
* * * *
28832696 GTCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTGTGGGGGTATTTTGGTTATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTT-GTCATTTTACC
* *
28832761 TTGTGGAGGTATTTCG
65 TTATGG-GGTATTTTG
* * * *
28832777 GTCATTTTATCCTGTGGGGGTAATTCGGTCATTT
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTT
28832811 ATTGACCTTT
Statistics
Matches: 174, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.01
80 122 0.70
81 51 0.29
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.44
Consensus pattern (79 bp):
GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGTCATTTTACCT
TATGGGGTATTTTG
Found at i:28832700 original size:107 final size:108
Alignment explanation
Indices: 28832537--28832810 Score: 349
Period size: 107 Copynumber: 2.6 Consensus size: 108
28832527 GGTATAAAAG
* *
28832537 TCATTTTACCCTGTGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTT-GTCATTTTACCT
1 TCATTTTACCCTGTGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCC
***
28832601 TAT-AGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGA
66 TATGA-GGGTATTTCAATCATTTTACCCTATGGGGGTATTTCGA
*
28832644 TCATTTTACCCTATGGGGGTA-TTCTGGTCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTGTGGGGGTATTTC-GGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACC
* * *
28832707 CTATGAGGGTATTTCAATCATTTTACCCTGTGGGGGTATTTTGG
65 CTATGAGGGTATTTCAATCATTTTACCCTATGGGGGTATTTCGA
* * * * * * * *
28832751 TTATTTTACCTTGTGGAGGTATTTCGGTCATTTTATCCTGTGGGGGTAATTCGGTCATTT
1 TCATTTTACCCTGTGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTTGGTCATTT
28832811 ATTGACCTTT
Statistics
Matches: 145, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
106 13 0.09
107 112 0.77
108 20 0.14
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (108 bp):
TCATTTTACCCTGTGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCC
TATGAGGGTATTTCAATCATTTTACCCTATGGGGGTATTTCGA
Found at i:28840614 original size:40 final size:40
Alignment explanation
Indices: 28840566--28840831 Score: 441
Period size: 40 Copynumber: 6.7 Consensus size: 40
28840556 GCAAACACCT
* * * *
28840566 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28840606 TTGCCTTCGGGTCTTAGCCCGGATATCA-T--CTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATAT-ATTAACTCGCATAA
* *
28840644 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28840684 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28840724 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28840764 TTGCCTTCGGGTCTTAGCCCGGATATA-TAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28840803 TTGCCTTCGGGTCTTAGCCCGGATATATT
1 TTGCCTTCGGGTCTTAGCCCGGATATATT
28840832 CCAATGCTCA
Statistics
Matches: 213, Mismatches: 8, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
37 1 0.00
38 33 0.15
39 39 0.18
40 139 0.65
41 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
Found at i:28847985 original size:14 final size:14
Alignment explanation
Indices: 28847966--28847992 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28847956 TGGATTTTTT
28847966 TAGAATTTTTGGTC
1 TAGAATTTTTGGTC
28847980 TAGAATTTTTGGT
1 TAGAATTTTTGGT
28847993 TGGGCCAACT
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:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (14 bp):
TAGAATTTTTGGTC
Found at i:28849208 original size:40 final size:40
Alignment explanation
Indices: 28849160--28849426 Score: 450
Period size: 40 Copynumber: 6.7 Consensus size: 40
28849150 GCAAACACCT
* * * *
28849160 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28849200 TTGCCTTCGGGTCTTAGCCCGGATATCA-T--CTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATAT-ATTAACTCGCATAA
* *
28849238 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28849278 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28849318 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28849358 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
28849398 TTGCCTTCGGGTCTTAGCCCGGATATATT
1 TTGCCTTCGGGTCTTAGCCCGGATATATT
28849427 CCAATGCTCA
Statistics
Matches: 215, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
37 1 0.00
38 33 0.15
40 180 0.84
41 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
Found at i:28853308 original size:16 final size:15
Alignment explanation
Indices: 28853282--28853315 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
28853272 ATAACTAGTA
*
28853282 TATAAATATATTTAT
1 TATAAATATATTAAT
28853297 TATAATATATATTAAT
1 TATAA-ATATATTAAT
28853313 TAT
1 TAT
28853316 TATCAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAAATATATTAAT
Found at i:28854885 original size:3 final size:3
Alignment explanation
Indices: 28854877--28854911 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28854867 CGAGGATCTC
28854877 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
28854912 TCCCACAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28856755 original size:43 final size:42
Alignment explanation
Indices: 28856578--28856756 Score: 160
Period size: 43 Copynumber: 4.2 Consensus size: 42
28856568 AAAAAATGCA
* * * ** * *
28856578 GCTATAGAACGTGACCTTTAGCGGCGCTTCTCATAAAAATGCC
1 GCTAAAGAACATGACCTTTAGC-GCGCTTTTCCCACAAACGCC
* * * *
28856621 GCTATAGAACATGGCCTTTAGCAGCGGTTTTCTCACAAACGCC
1 GCTAAAGAACATGACCTTTAGC-GCGCTTTTCCCACAAACGCC
* * * *
28856664 GTTAAAGAACATGACCTTTAGCGACGCTTTTACTACAAACGCA
1 GCTAAAGAACATGACCTTTAGCG-CGCTTTTCCCACAAACGCC
* * *
28856707 ACTAAAGAACATGACCTTTAGCTGCGCTTTTCCCACAACCTCC
1 GCTAAAGAACATGACCTTTAGC-GCGCTTTTCCCACAAACGCC
28856750 GCTAAAG
1 GCTAAAG
28856757 GTCATGTTCT
Statistics
Matches: 109, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 1 0.01
43 107 0.98
44 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
GCTAAAGAACATGACCTTTAGCGCGCTTTTCCCACAAACGCC
Found at i:28856769 original size:43 final size:43
Alignment explanation
Indices: 28856722--28856813 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
28856712 AGAACATGAC
* * * *
28856722 CTTTAGCTGCGCTTTTCCCACAA-CCTCCGCTAAAGGTCATGTT
1 CTTTAGCGGCACTTTTACCAAAAGCC-CCGCTAAAGGTCATGTT
* **
28856765 CTTTAGCGGCATTTTTAGTAAAAGCCCCGCTAAAGGTCATGTT
1 CTTTAGCGGCACTTTTACCAAAAGCCCCGCTAAAGGTCATGTT
28856808 CTTTAG
1 CTTTAG
28856814 TGGTGTTTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 39 0.95
44 2 0.05
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (43 bp):
CTTTAGCGGCACTTTTACCAAAAGCCCCGCTAAAGGTCATGTT
Found at i:28862481 original size:15 final size:15
Alignment explanation
Indices: 28862469--28862497 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28862459 TTTTGAAATG
28862469 CAAAATTTAGAAAAA
1 CAAAATTTAGAAAAA
28862484 CAAAATTTAGAAAA
1 CAAAATTTAGAAAA
28862498 GTTTGTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
CAAAATTTAGAAAAA
Found at i:28866479 original size:48 final size:48
Alignment explanation
Indices: 28866427--28866554 Score: 141
Period size: 48 Copynumber: 2.7 Consensus size: 48
28866417 GTATATTTTT
* * **
28866427 TTTCAAGCAACGAAAAGACTGAGAAAGAAAATGGACGGGAGTTTGGGA
1 TTTCAAGCAAAGAAAAGTCTGAGAAAGAAAATGGACAAGAGTTTGGGA
* * * * * *
28866475 TTTCAAGTAAAGAGAAGTCT-AGGAAAAAAAAGGGACAAGATTTTGGGG
1 TTTCAAGCAAAGAAAAGTCTGA-GAAAGAAAATGGACAAGAGTTTGGGA
*
28866523 TTTCAGGCAAAGAAAAGTCTGAGAAAGAAAAT
1 TTTCAAGCAAAGAAAAGTCTGAGAAAGAAAAT
28866555 AATTTGTGCG
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
47 1 0.02
48 61 0.97
49 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.28, T:0.19
Consensus pattern (48 bp):
TTTCAAGCAAAGAAAAGTCTGAGAAAGAAAATGGACAAGAGTTTGGGA
Found at i:28877263 original size:20 final size:20
Alignment explanation
Indices: 28877238--28877288 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
28877228 TACTGCTGAG
28877238 CAGAGGCACC-GTGGTGCAAA
1 CAGAGGCACCAGT-GTGCAAA
28877258 CAGAGGCACCAGTGTGCAAA
1 CAGAGGCACCAGTGTGCAAA
* *
28877278 AAGGGGCACCA
1 CAGAGGCACCA
28877289 AAGTGCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.33, C:0.25, G:0.33, T:0.08
Consensus pattern (20 bp):
CAGAGGCACCAGTGTGCAAA
Found at i:28877294 original size:20 final size:20
Alignment explanation
Indices: 28877251--28877336 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
28877241 AGGCACCGTG
* **
28877251 GTGCAAACAGAGGCACCAGT
1 GTGCAAAAAGAGGCACCAAA
*
28877271 GTGCAAAAAGGGGCACCAAA
1 GTGCAAAAAGAGGCACCAAA
** **
28877291 GTGCAATGAG-GGACACTGAA
1 GTGCAAAAAGAGG-CACCAAA
*
28877311 GTGCAAATAGAGGCACCAAA
1 GTGCAAAAAGAGGCACCAAA
28877331 GTGCAA
1 GTGCAA
28877337 TCTCGTACAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.04
20 48 0.92
21 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.30, T:0.10
Consensus pattern (20 bp):
GTGCAAAAAGAGGCACCAAA
Found at i:28888871 original size:19 final size:19
Alignment explanation
Indices: 28888847--28888938 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
28888837 AATCATATCT
28888847 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
28888866 TCTAAGATTACATATGATA
1 TCTAAGATTGCATATCATA
28888885 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
28888904 TCTAAGAGTACATATCATA
1 TCTAAGATTGCATATCATA
28888923 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28888939 CTTGAAGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28888890 original size:38 final size:38
Alignment explanation
Indices: 28888840--28888938 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
28888830 ATTTCAAAAT
*
28888840 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
*
28888876 CATATGATATCTAAGATTGCATATCATATCTAAGAGTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
28888914 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTGCATATC
28888939 CTTGAAGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 5 0.09
37 1 0.02
38 52 0.90
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
Found at i:28890343 original size:16 final size:16
Alignment explanation
Indices: 28890324--28890377 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
28890314 TTTGGTTCGT
*
28890324 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGC
*
28890340 TGTAATTGAATAGAGC
1 TGTAATGGAATAGAGC
* *
28890356 TGTAATGAAATAAAGC
1 TGTAATGGAATAGAGC
28890372 TGTAAT
1 TGTAAT
28890378 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:28892345 original size:15 final size:15
Alignment explanation
Indices: 28892325--28892356 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28892315 ATTGCACAAC
28892325 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
28892340 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
28892355 TT
1 TT
28892357 TCCTCCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTAATAGTAAAGCAT
Found at i:28904664 original size:15 final size:15
Alignment explanation
Indices: 28904644--28904674 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28904634 TATTGAGGAG
28904644 CCAATTAATAATTAA
1 CCAATTAATAATTAA
28904659 CCAATTAATAATTAA
1 CCAATTAATAATTAA
28904674 C
1 C
28904675 AAATGGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (15 bp):
CCAATTAATAATTAA
Found at i:28905222 original size:59 final size:59
Alignment explanation
Indices: 28905156--28905325 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
28905146 TCAAGTTTGT
*
28905156 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
28905215 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* *
28905274 TTTACTAATCAAATGGTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
28905326 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:28905357 original size:16 final size:16
Alignment explanation
Indices: 28905336--28905377 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
28905326 AATAATTTGA
*
28905336 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
28905352 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
28905368 TAGTTTTAAT
1 TAATTTTAAT
28905378 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:28908383 original size:19 final size:19
Alignment explanation
Indices: 28908351--28908392 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28908341 AAAGCAACAT
* *
28908351 AACATTAGTTCAAGTAAAC
1 AACATGAGTCCAAGTAAAC
*
28908370 AACATGAGTCCAAGTGAAC
1 AACATGAGTCCAAGTAAAC
28908389 AACA
1 AACA
28908393 ACACAATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (19 bp):
AACATGAGTCCAAGTAAAC
Found at i:28916697 original size:16 final size:16
Alignment explanation
Indices: 28916676--28916709 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28916666 TTGAGGAGTG
28916676 TTGAGAATCTTTGATA
1 TTGAGAATCTTTGATA
28916692 TTGAGAATCTTTGATA
1 TTGAGAATCTTTGATA
28916708 TT
1 TT
28916710 ATTAAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (16 bp):
TTGAGAATCTTTGATA
Found at i:28920016 original size:531 final size:531
Alignment explanation
Indices: 28919007--28921135 Score: 4015
Period size: 531 Copynumber: 4.0 Consensus size: 531
28918997 ACGAATATTC
* *
28919007 GAAAACAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGTAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
* *
28919072 GTGAAGTTTTTCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGATAGCCT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
28919137 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
*
28919202 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAGAGTGGAAAGGAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
28919267 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
28919332 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
326 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
28919397 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
391 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
28919462 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
*
28919527 CATGCAGATTT
521 CGTGCAGATTT
*
28919538 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCAATGCAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
28919603 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
28919668 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
28919733 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
* *
28919798 ATAAAATTGAAAAAAAAATTGAAGAAATAAATGAAAAATACGAGGAAAGGGTAGTGAGGAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
* *
28919863 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCTCAAAATATCGAAAGA
326 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
28919928 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
391 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
*
28919993 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGAAAATTTTAGCCACTGAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
28920058 CGTGCAGATTT
521 CGTGCAGATTT
28920069 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
*
28920134 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGATAGCCT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
28920199 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
28920264 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
* * *
28920329 ATAAAATTGAAAAAGAATTTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGAAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
28920394 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
326 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
28920459 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
391 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
28920524 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
28920589 CGTGCAGATTT
521 CGTGCAGATTT
*
28920600 GAAAAGAGATTCATATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
* *
28920665 GTGAAGTTTTCCAAGGGGATCATTGTTCATATACAAGTCATTCCGTACATACCCAATGAGAGCCT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
* * *
28920730 TTCCGTTCTAATTCATTTATAACATCTCTATCTTGTAATGAAAAGAAGACATAAAAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
* *
28920795 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAGAGTGGAAAGAAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
28920860 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
* *
28920925 TCCACTAACCAAGATAGGAACTTTTCTTCTGTTTCTACTTTTCAGGTTCCCAAAATACCGAAAGA
326 TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
*
28920990 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGTAAGGTTG
391 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
28921055 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
28921120 CGTGCAGATTT
521 CGTGCAGATTT
28921131 GAAAA
1 GAAAA
28921136 TTATTGATAA
Statistics
Matches: 1561, Mismatches: 37, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
531 1561 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (531 bp):
GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
TCCACTAACCAAGATAGGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
CGTGCAGATTT
Found at i:28924546 original size:82 final size:82
Alignment explanation
Indices: 28924404--28924559 Score: 267
Period size: 82 Copynumber: 1.9 Consensus size: 82
28924394 CTCCGCCAAT
* *
28924404 GATCACGAAGCAACTCAATTGTCTATTTATTACACCATTGGACATATTATTACCGAAAAATACAC
1 GATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATTATTACCGAAAAATACAC
28924469 AAAAAGAAACCACTAGC
66 AAAAAGAAACCACTAGC
* * *
28924486 GATCACGAAGCAACTCAACTGTCTATTTATTCCACCATTGGAAATATTATTACCGGAAAATGCAC
1 GATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATTATTACCGAAAAATACAC
28924551 AAAAAGAAA
66 AAAAAGAAA
28924560 ACATTCAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (82 bp):
GATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATTATTACCGAAAAATACAC
AAAAAGAAACCACTAGC
Found at i:28933172 original size:26 final size:28
Alignment explanation
Indices: 28933138--28933193 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
28933128 GGTTTGCGAG
*
28933138 AAGTAAAAAT-TTTGGAG-GTAAAGTAA
1 AAGTAAAAATGTTTGGAGAGAAAAGTAA
*
28933164 AAGTAAAAATGTTTTGAGAGAAAAGTAA
1 AAGTAAAAATGTTTGGAGAGAAAAGTAA
28933192 AA
1 AA
28933194 AGGTCGGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 6 0.23
28 10 0.38
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (28 bp):
AAGTAAAAATGTTTGGAGAGAAAAGTAA
Found at i:28935164 original size:42 final size:42
Alignment explanation
Indices: 28935113--28935200 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
28935103 TTTTCATATT
*
28935113 TTTTTACTTCAAGTAAGTTCATTTCTTGTCATTTTCTTGAAA
1 TTTTTACTTCAAGTAAGTTCAGTTCTTGTCATTTTCTTGAAA
* *
28935155 TTTTTACTTCAAGTGAGTTTAGTTCTTGTCATTTTCTTGAAA
1 TTTTTACTTCAAGTAAGTTCAGTTCTTGTCATTTTCTTGAAA
28935197 TTTT
1 TTTT
28935201 ATGTTTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.55
Consensus pattern (42 bp):
TTTTTACTTCAAGTAAGTTCAGTTCTTGTCATTTTCTTGAAA
Found at i:28935920 original size:23 final size:24
Alignment explanation
Indices: 28935890--28935997 Score: 150
Period size: 24 Copynumber: 4.6 Consensus size: 24
28935880 CATTATTGGG
*
28935890 AAAGGATGAATTGACGG-AAATGT
1 AAAGGATGAATTGAAGGAAAATGT
28935913 AAAGGATGAATTGAAGGAAAATGT
1 AAAGGATGAATTGAAGGAAAATGT
* *
28935937 AAAGGA-GAAACTGACGGAAAATGT
1 AAAGGATG-AATTGAAGGAAAATGT
*
28935961 AAAGGATGAATTGAAGG-TAATGT
1 AAAGGATGAATTGAAGGAAAATGT
28935984 AAAGGATGAATTGA
1 AAAGGATGAATTGA
28935998 TGACAAATTG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
23 36 0.47
24 39 0.51
25 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.20
Consensus pattern (24 bp):
AAAGGATGAATTGAAGGAAAATGT
Found at i:28941305 original size:13 final size:14
Alignment explanation
Indices: 28941289--28941318 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28941279 ATAATGAAGT
28941289 AATAAAT-AATAAA
1 AATAAATAAATAAA
28941302 AATAAATAAATAAA
1 AATAAATAAATAAA
28941316 AAT
1 AAT
28941319 TAGATTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:28944951 original size:21 final size:21
Alignment explanation
Indices: 28944909--28944951 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28944899 TCATTTTTAG
* **
28944909 CAACTTCCTCTTCTTCGGCAA
1 CAACTTCCTCTTCTACAACAA
*
28944930 CAACTTTCTCTTCTACAACAA
1 CAACTTCCTCTTCTACAACAA
28944951 C
1 C
28944952 TTCTGCTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.33
Consensus pattern (21 bp):
CAACTTCCTCTTCTACAACAA
Found at i:28957901 original size:40 final size:39
Alignment explanation
Indices: 28957829--28957934 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
28957819 CTTAGATAAA
* * * *
28957829 AAACGCTGCTAAAAATCAAGCATTACCTGCGCTTTTA-AG
1 AAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAGAG
* * *
28957868 AAAATGCCGCTAAAGATCGAGTATTAGCGGCGCTTTTAGAG
1 -AAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAGAG
28957909 AAACGCCGCTAAAAATGAGCATTAGC
1 AAACGCCGCTAAAAATGAGCATTAGC
28957935 AGTGTTTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 9 0.16
40 44 0.80
41 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (39 bp):
AAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTAGAG
Found at i:28958056 original size:41 final size:41
Alignment explanation
Indices: 28957993--28958343 Score: 441
Period size: 41 Copynumber: 8.6 Consensus size: 41
28957983 TATTTGAGTT
* * *
28957993 CTCGGGTCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATT
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
28958034 CTCGGGTCTTTAGCGACTTTTTTGAAGAAGAGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
*
28958075 CTTGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
28958116 CTCGGGTCTTTAGCGGCATTTTTGGAGAAGCGCCACTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* *
28958157 CTCGGGTCTTTAGAGGCATTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* ** * ****
28958198 TTCGGGTCTTTAGCGGTATTTTTGAAGACGCAATACTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * * *
28958239 CTCAGGTCTTTAGAGGCATTTTTGAAGAAGCGCTGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * * * *
28958280 CTCAGGTCTTTAGCGACGTTTTTGAAGAAGCACCACTAATT
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
28958321 CTCGGGTCTTTAGCGGCGTTTTT
1 CTCGGGTCTTTAGCGGCGTTTTT
28958344 AAAAAATCGC
Statistics
Matches: 268, Mismatches: 42, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 268 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (41 bp):
CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
Found at i:28963841 original size:5 final size:5
Alignment explanation
Indices: 28963831--28963861 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
28963821 TTAAATTTCA
28963831 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
28963862 TTTATTATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:28964127 original size:42 final size:43
Alignment explanation
Indices: 28963978--28964180 Score: 210
Period size: 43 Copynumber: 4.7 Consensus size: 43
28963968 TAATGGAAGT
* * ** * *
28963978 GCCGCTAAAGCTCATGACCTTTAGCGACGTTTGGGGGAAAAGC
1 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
** * * * *
28964021 ATCGCTGAAGGTCTTGTTCTTTAGCAGCGTTTTTGGGAAAAGC
1 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
* * * *
28964064 GCCACTAAAAGTCTTGGTCTTTAGTGGCGTTTGTGGGAGAA-C
1 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
* * *
28964106 GCCGCTAAAGGTCTTAGTCTTTAGCGACGTTTGTGGGAAAAGT
1 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
* *
28964149 GCCGCTAAAGGTCCTGGTCTTTAACGGCGTTT
1 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
28964181 TTTCTGGCGC
Statistics
Matches: 127, Mismatches: 32, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
42 36 0.28
43 91 0.72
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (43 bp):
GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
Found at i:28964143 original size:85 final size:85
Alignment explanation
Indices: 28964023--28964180 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 85
28964013 GGAAAAGCAT
* * * *
28964023 CGCTGAAGGTCTTGTTCTTTAGCAGCGTTTTTGGGAAAAGCGCCACTAAAAGTCTTGGTCTTTAG
1 CGCTAAAGGTCTTGTTCTTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAAGTCCTGGTCTTTAA
*
28964088 TGGCGTTTGTGGGAGAACGC
66 CGGCGTTTGTGGGAGAACGC
* * *
28964108 CGCTAAAGGTCTTAG-TCTTTAGC-GACGTTTGTGGGAAAAGTGCCGCTAAAGGTCCTGGTCTTT
1 CGCTAAAGGTCTT-GTTCTTTAGCAG-CGTTTGTGGGAAAAGCGCCACTAAAAGTCCTGGTCTTT
28964171 AACGGCGTTT
64 AACGGCGTTT
28964181 TTTCTGGCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.02
85 61 0.97
86 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (85 bp):
CGCTAAAGGTCTTGTTCTTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAAGTCCTGGTCTTTAA
CGGCGTTTGTGGGAGAACGC
Found at i:28965790 original size:9 final size:9
Alignment explanation
Indices: 28965706--28965829 Score: 65
Period size: 9 Copynumber: 13.3 Consensus size: 9
28965696 TTTCTATATA
28965706 TTTATAATT
1 TTTATAATT
28965715 TTT-TACGATT
1 TTTATA--ATT
28965725 TTTAT-ATT
1 TTTATAATT
**
28965733 TTTCCAATT
1 TTTATAATT
* *
28965742 CTTAAGTATTT
1 -TTTA-TAATT
*
28965753 TTTATATTT
1 TTTATAATT
*
28965762 TTTATTAAAAT
1 TTTA-T-AATT
*
28965773 TTAATAATT
1 TTTATAATT
28965782 TTTATAATT
1 TTTATAATT
*
28965791 TTTATAACT
1 TTTATAATT
*
28965800 TTTATTGATT
1 TTTA-TAATT
*
28965810 TTTAT-CTT
1 TTTATAATT
*
28965818 TTTATCATT
1 TTTATAATT
28965827 TTT
1 TTT
28965830 TGCCACATGT
Statistics
Matches: 88, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
8 15 0.17
9 44 0.50
10 20 0.23
11 9 0.10
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:28968572 original size:138 final size:138
Alignment explanation
Indices: 28968227--28968923 Score: 1006
Period size: 138 Copynumber: 5.0 Consensus size: 138
28968217 TAGAAAAATA
* * *
28968227 AATTATATTCTTTCCAAAA-ACTATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
* **
28968291 TATAATTGTTTATATTAATAAATTTGGCAAAATATATACAATTAATATTTTAAATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
*
28968356 TATATATATT
130 T-CATATATT
* * * *
28968366 AATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
* * *
28968431 TATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
28968496 CATATATT
131 CATATATT
* * *
28968504 AATTATATTCTTTCCAAAAGAACATTAATTTCCTTGTCTTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
* * * *
28968569 TATAACTATTTATATTAATAAATTCGGTAAAATGTATATACATTTAATATTTTGTATGAATCAAA
66 TATAATTGTTTATATTAATAAATTTGGTAAAA--TATATACAATTAATATTTTGTATGAATCAAA
28968634 TTCATATATT
129 TTCATATATT
* *
28968644 AATTATATTCTTTCCAAAAAAAATATTAGTTTCCATGTCTTTTATATTTTG-ACTGAAATTAATT
1 AATTATATTCTTTCC-AAAAGAATATTAATTTCCATGTCTTTTATATTTTGAAC-GAAATTAATT
*
28968708 AATATAATT-TTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTATGAATCAAA
64 AATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAA
28968772 TTCATATATT
129 TTCATATATT
* * * **
28968782 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGATTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
* * * *
28968847 TAT-ATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTAGTATGAACCACAT
66 TATAAT-TGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28968911 TCATATATT
130 TCATATATT
28968920 AATT
1 AATT
28968924 TTATCTATGT
Statistics
Matches: 505, Mismatches: 45, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
136 2 0.00
137 48 0.10
138 209 0.41
139 20 0.04
140 178 0.35
141 48 0.10
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:28968727 original size:278 final size:276
Alignment explanation
Indices: 28968227--28968923 Score: 1008
Period size: 278 Copynumber: 2.5 Consensus size: 276
28968217 TAGAAAAATA
* *
28968227 AATTATATTCTTTCC-AAA-AACTATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAAC-ATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTA
* * **
28968290 ATATAATTGTTTATATTAATAAATTTGGCAAAA-TATATACAATTAATATTTTAAATGAATCAAA
65 ATATAACTGTTTATATTAATAAATTTGGTAAAATTATATAC-ATTAATATTTTGTATGAATCAAA
* ** *
28968354 TTTATATATATTAATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACC
129 -TT-CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACC
*
28968419 GAAATTAATTAATATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAATATTTTGT
192 GAAATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGT
28968484 ATGAATCAAATTCATATATT
257 ATGAATCAAATTCATATATT
* *
28968504 AATTATATTCTTTCCAAAAGAACATTAATTTCCTTGTCTTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
* *
28968569 TATAACTATTTATATTAATAAATTCGGTAAAATGTATATACATTTAATATTTTGTATGAATCAAA
66 TATAACTGTTTATATTAATAAATTTGGTAAAAT-TATATACA-TTAATATTTTGTATGAATCAAA
* * *
28968634 TTCATATATTAATTATATTCTTTCCAAAAAAAATATTAGTTTCCATGTCTTTTATATTTTGACTG
129 TTCATATATTAATTATATTCTTTCC-AAAAAAATATTAATTTCCATATCTTTTATATTTTGACCG
* * *
28968699 AAATTAATTAATATAATT-TTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTA
193 AAATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTA
28968763 TGAATCAAATTCATATATT
258 TGAATCAAATTCATATATT
* * * * **
28968782 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGATTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
* * * *
28968847 TATATCTGTTTATATTAATAAATTTGGTAAAATATATATA-ATTAATATTTAGTATGAACCACAT
66 TATAACTGTTTATATTAATAAATTTGGTAAAAT-TATATACATTAATATTTTGTATGAATCAAAT
28968911 TCATATATTAATT
130 TCATATATTAATT
28968924 TTATCTATGT
Statistics
Matches: 378, Mismatches: 36, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
276 33 0.09
277 16 0.04
278 245 0.65
279 57 0.15
280 27 0.07
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (276 bp):
AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTGAACGAAATTAATTAA
TATAACTGTTTATATTAATAAATTTGGTAAAATTATATACATTAATATTTTGTATGAATCAAATT
CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCGAAA
TTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGA
ATCAAATTCATATATT
Found at i:28969009 original size:17 final size:17
Alignment explanation
Indices: 28968989--28969021 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28968979 TTTAACTATC
28968989 AAATTAAAT-TAATTCAA
1 AAATT-AATCTAATTCAA
28969006 AAATTAATCTAATTCA
1 AAATTAATCTAATTCA
28969022 TGTGACAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAATCTAATTCAA
Found at i:28976354 original size:27 final size:27
Alignment explanation
Indices: 28976300--28976363 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
28976290 TTTTATCCCA
*
28976300 GTAAAATTTT-GACCATTTTACCAGTG
1 GTAAAATTTTGGACCATTTTACCACTG
** *
28976326 GTAAAATTTTGGATGATTTTACCTCTG
1 GTAAAATTTTGGACCATTTTACCACTG
28976353 GTAAAATTTTG
1 GTAAAATTTTG
28976364 AGAGAACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (27 bp):
GTAAAATTTTGGACCATTTTACCACTG
Found at i:28980378 original size:23 final size:23
Alignment explanation
Indices: 28980348--28980396 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
28980338 TACGGAAGGA
*
28980348 AAACTTGTATTAGTAAATAAATT
1 AAACTTGTATTAGTAAATAAACT
*
28980371 AAACTTGTATTAGTAGATAAACT
1 AAACTTGTATTAGTAAATAAACT
28980394 AAA
1 AAA
28980397 TAAGATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (23 bp):
AAACTTGTATTAGTAAATAAACT
Found at i:28982335 original size:24 final size:24
Alignment explanation
Indices: 28982300--28982347 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28982290 AATTGATGTG
*
28982300 CAAATCAATGAGTTAAAGGGAGCT
1 CAAATCAATGAGTTAAAAGGAGCT
*
28982324 CAAATCAGTGAGTTAAAAGGAGCT
1 CAAATCAATGAGTTAAAAGGAGCT
28982348 GAGGTGGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (24 bp):
CAAATCAATGAGTTAAAAGGAGCT
Found at i:28983430 original size:33 final size:33
Alignment explanation
Indices: 28983393--28983482 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
28983383 ACGTTCATAG
* * *
28983393 TGCCATAACTCGGTTATGGTCTTATCATCAGAA
1 TGCCATAACCCAGCTATGGTCTTATCATCAGAA
* *
28983426 TGCCATAGCCCAGCTATGGTCTTATCATCAGTA
1 TGCCATAACCCAGCTATGGTCTTATCATCAGAA
* *
28983459 TGCCATAGCCCAACTATGGTCTTA
1 TGCCATAACCCAGCTATGGTCTTA
28983483 CATATATACA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (33 bp):
TGCCATAACCCAGCTATGGTCTTATCATCAGAA
Found at i:28987025 original size:42 final size:43
Alignment explanation
Indices: 28986915--28987026 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 43
28986905 CTCATACAAT
* * ** * *
28986915 GCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAATGAT
1 GCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACGAC
* * * * *
28986958 GCCATTGTCCCAGATAGGGTTTTACACATAATCATAT-ACGAC
1 GCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACGAC
28987000 GCCAATGTCCCAGACATGGTCTTACAC
1 GCCAATGTCCCAGACATGGTCTTACAC
28987027 GTAAATTTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
42 26 0.48
43 28 0.52
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACGAC
Found at i:28994925 original size:41 final size:41
Alignment explanation
Indices: 28994784--28994925 Score: 178
Period size: 41 Copynumber: 3.5 Consensus size: 41
28994774 TTTAAAATGA
* * *
28994784 TTCACTGGCATTAAGCCT-ACTAGACGTAAAGTCTAAAATAT
1 TTCACTAGCATTAAGCCTGA-TAGACGTAAAGTCTGAATTAT
* * *
28994825 TACACCAGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
* * **
28994866 TTCATTGGCATTAAGCCTGATAGGTGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
28994907 TTCACTAGCATTAAGCCTG
1 TTCACTAGCATTAAGCCTG
28994926 CTAAGTACAG
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (41 bp):
TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
Found at i:28994943 original size:82 final size:82
Alignment explanation
Indices: 28994784--28994944 Score: 202
Period size: 82 Copynumber: 2.0 Consensus size: 82
28994774 TTTAAAATGA
28994784 TTCACTGGCATTAAGCCTACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAGA
1 TTCACTGGCATTAAGCCTACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAGA
*
28994849 CGTAAAGTCTGAATTAT
66 CGTAAAGCCTGAATTAT
* ** * * * *
28994866 TTCATTGGCATTAAGCCTGA-TAGGTGTAAAGTCTGAATTATTTCACTAGCATTAAGCCTGCTA-
1 TTCACTGGCATTAAGCCT-ACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAG
28994929 A-GTACAGAGCCTGAAT
65 ACGTA-A-AGCCTGAAT
28994945 AACTCAGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 3 0.04
81 2 0.03
82 62 0.91
83 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (82 bp):
TTCACTGGCATTAAGCCTACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAGA
CGTAAAGCCTGAATTAT
Found at i:28997110 original size:29 final size:29
Alignment explanation
Indices: 28997068--28997136 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
28997058 CACAAATAAA
28997068 TTGTACA-AGTAGACCGAATTCTACTAATC
1 TTGTACACA-TAGACCGAATTCTACTAATC
28997097 TTGTACACATAGACCGAATTCTACTAATC
1 TTGTACACATAGACCGAATTCTACTAATC
28997126 TTGTACACATA
1 TTGTACACATA
28997137 CATATATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (29 bp):
TTGTACACATAGACCGAATTCTACTAATC
Found at i:28997638 original size:31 final size:31
Alignment explanation
Indices: 28997597--28997675 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
28997587 TTCGGCATTG
*
28997597 TATAACCATACACGAATCAAGATCGCCAATA
1 TATAATCATACACGAATCAAGATCGCCAATA
28997628 TATAATCATACACGAATCAAGATCGCCAATA
1 TATAATCATACACGAATCAAGATCGCCAATA
28997659 TATAATCATACACGAAT
1 TATAATCATACACGAAT
28997676 TAAATTCGGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (31 bp):
TATAATCATACACGAATCAAGATCGCCAATA
Found at i:29000662 original size:24 final size:24
Alignment explanation
Indices: 29000615--29000663 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29000605 GCCGCTATAG
*
29000615 AACATGACCTTTAGCGGCGCTTTT
1 AACATGACCTTTAGCGGCACTTTT
* *
29000639 AACATGACCTTTAGTGGCATTTTT
1 AACATGACCTTTAGCGGCACTTTT
29000663 A
1 A
29000664 TCGCAAACGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (24 bp):
AACATGACCTTTAGCGGCACTTTT
Found at i:29000706 original size:43 final size:43
Alignment explanation
Indices: 29000639--29000818 Score: 227
Period size: 43 Copynumber: 4.2 Consensus size: 43
29000629 CGGCGCTTTT
* ** * * *
29000639 AACATGACCTTTAGTGGCATTTTTATCGCAAACGCCGTTAAAA
1 AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
** *
29000682 AACATGATATTTAGCGGCGCTTTTATCACAAACGCCGCTAAAT
1 AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
* * *
29000725 AACATGCCCTTTAGCGGCACTTTTATCACAAATGCCGCTAAAG
1 AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
*
29000768 AACATGACCTTTAGCGGCGCTTCTT-TCACAAATGCCGCTAAAG
1 AACATGACCTTTAGCGGCGCTT-TTATCACAAACGCCGCTAAAG
29000811 AACATGAC
1 AACATGAC
29000819 TTGACTCTCC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 118 0.98
44 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
Found at i:29005292 original size:21 final size:21
Alignment explanation
Indices: 29005268--29005315 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
29005258 AATTGAAGTA
*
29005268 ACAAATGATGTAGAGGCAGAG
1 ACAAATGATGCAGAGGCAGAG
*
29005289 ACAAATGATGCAGAGGTAGAG
1 ACAAATGATGCAGAGGCAGAG
29005310 ACAAAT
1 ACAAAT
29005316 TTGATGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.29, T:0.15
Consensus pattern (21 bp):
ACAAATGATGCAGAGGCAGAG
Found at i:29005426 original size:19 final size:19
Alignment explanation
Indices: 29005398--29005435 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29005388 CCGAAAACTA
29005398 GAAGGCAGGAGACAACTTG
1 GAAGGCAGGAGACAACTTG
*
29005417 GAAGGTAGGAGACAACTTG
1 GAAGGCAGGAGACAACTTG
29005436 CAACAGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.37, T:0.13
Consensus pattern (19 bp):
GAAGGCAGGAGACAACTTG
Found at i:29007106 original size:7 final size:7
Alignment explanation
Indices: 29007096--29007208 Score: 52
Period size: 7 Copynumber: 15.7 Consensus size: 7
29007086 TAATAAAACA
29007096 TAAACCC
1 TAAACCC
29007103 TAAACCTC
1 TAAACC-C
29007111 T-AACCC
1 TAAACCC
*
29007117 TTAACCC
1 TAAACCC
*
29007124 ATAAACCA
1 -TAAACCC
*
29007132 TAATCCC
1 TAAACCC
29007139 TAAACCC
1 TAAACCC
* *
29007146 ATAATCCA
1 -TAAACCC
*
29007154 TAAACCT
1 TAAACCC
*
29007161 TAAA--A
1 TAAACCC
*
29007166 TAGGAACTCT
1 TA--AAC-CC
*
29007176 TAAACCT
1 TAAACCC
29007183 TAAACCC
1 TAAACCC
*
29007190 TAAACCA
1 TAAACCC
*
29007197 TAAACCT
1 TAAACCC
29007204 TAAAC
1 TAAAC
29007209 TATATGGATA
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
5 2 0.02
6 2 0.02
7 62 0.75
8 15 0.18
10 2 0.02
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:29007144 original size:29 final size:29
Alignment explanation
Indices: 29007094--29007164 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
29007084 AATAATAAAA
* *
29007094 CATAAACCCTAAACCTCTAACCCTTAACC
1 CATAAACCATAAACCTCTAACCCATAACC
* *
29007123 CATAAACCATAATCC-CTAAACCCATAATC
1 CATAAACCATAAACCTCT-AACCCATAACC
*
29007152 CATAAACCTTAAA
1 CATAAACCATAAA
29007165 ATAGGAACTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.06
29 33 0.94
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (29 bp):
CATAAACCATAAACCTCTAACCCATAACC
Found at i:29007147 original size:15 final size:15
Alignment explanation
Indices: 29007112--29007159 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
29007102 CTAAACCTCT
*
29007112 AACCCTTAA-CCCATA
1 AACCCATAATCCC-TA
29007127 AA-CCATAATCCCTA
1 AACCCATAATCCCTA
*
29007141 AACCCATAATCCATA
1 AACCCATAATCCCTA
29007156 AACC
1 AACC
29007160 TTAAAATAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCCTA
Found at i:29007164 original size:22 final size:22
Alignment explanation
Indices: 29007096--29007208 Score: 94
Period size: 22 Copynumber: 5.2 Consensus size: 22
29007086 TAATAAAACA
* *
29007096 TAAACCC-TAAACCTCTAACCCT
1 TAAACCCATAAACC-ATAAACCT
* *
29007118 T-AACCCATAAACCATAATCCC
1 TAAACCCATAAACCATAAACCT
*
29007139 TAAACCCATAATCCATAAACCT
1 TAAACCCATAAACCATAAACCT
*
29007161 TAAA---ATAGGAACTCTTAAACCT
1 TAAACCCATA--AAC-CATAAACCT
29007183 TAAACCC-TAAACCATAAACCT
1 TAAACCCATAAACCATAAACCT
29007204 TAAAC
1 TAAAC
29007209 TATATGGATA
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.04
21 26 0.35
22 43 0.58
24 2 0.03
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAACCCATAAACCATAAACCT
Found at i:29007195 original size:14 final size:14
Alignment explanation
Indices: 29007089--29007208 Score: 66
Period size: 14 Copynumber: 8.4 Consensus size: 14
29007079 CCTTGAATAA
*
29007089 TAAAACATAAACCC
1 TAAACCATAAACCC
*
29007103 TAAACC-TCTAACCC
1 TAAACCAT-AAACCC
* *
29007117 TTAACCCATAAACCA
1 -TAAACCATAAACCC
* *
29007132 TAATCCCTAAACCC
1 TAAACCATAAACCC
* *
29007146 ATAATCCATAAACCT
1 -TAAACCATAAACCC
*
29007161 TAAA--ATAGGAACTCT
1 TAAACCATA--AAC-CC
*
29007176 TAAACCTTAAACCC
1 TAAACCATAAACCC
*
29007190 TAAACCATAAACCT
1 TAAACCATAAACCC
29007204 TAAAC
1 TAAAC
29007209 TATATGGATA
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
12 3 0.04
13 1 0.01
14 45 0.55
15 30 0.37
16 1 0.01
17 2 0.02
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:29007346 original size:14 final size:14
Alignment explanation
Indices: 29007308--29007404 Score: 81
Period size: 14 Copynumber: 6.9 Consensus size: 14
29007298 ACTAGTTAAT
*
29007308 CTAAACCTTAAACCC
1 CTAAACCATAAA-CC
**
29007323 CTATCCCATAAACC
1 CTAAACCATAAACC
* *
29007337 CTAAATCATAAAAC
1 CTAAACCATAAACC
*
29007351 ATAAATCC-TAAACC
1 CTAAA-CCATAAACC
*
29007365 CTAAACC-TCAACC
1 CTAAACCATAAACC
29007378 CTTAAACCATAAACC
1 C-TAAACCATAAACC
*
29007393 ATAAACCATAAA
1 CTAAACCATAAA
29007405 GCTCGATCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
13 8 0.12
14 42 0.65
15 15 0.23
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:29007355 original size:21 final size:21
Alignment explanation
Indices: 29007329--29007404 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
29007319 ACCCCTATCC
*
29007329 CATAAACCCTAAATCATAAAA
1 CATAAACCCTAAACCATAAAA
* *
29007350 CATAAATCCTAAACCCT-AAA
1 CATAAACCCTAAACCATAAAA
* * *
29007370 CCTCAACCCTTAAACCATAAAC
1 CATAAACCC-TAAACCATAAAA
*
29007392 CATAAACCATAAA
1 CATAAACCCTAAA
29007405 GCTCGATCTA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 9 0.21
21 25 0.60
22 8 0.19
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.18
Consensus pattern (21 bp):
CATAAACCCTAAACCATAAAA
Found at i:29007367 original size:7 final size:7
Alignment explanation
Indices: 29007308--29007404 Score: 54
Period size: 7 Copynumber: 13.7 Consensus size: 7
29007298 ACTAGTTAAT
29007308 CTAAACC
1 CTAAACC
*
29007315 TTAAACCC
1 CTAAA-CC
*
29007323 CT-ATCC
1 CTAAACC
29007329 CATAAACC
1 C-TAAACC
*
29007337 CTAAATC
1 CTAAACC
* *
29007344 ATAAAAC
1 CTAAACC
* *
29007351 ATAAATC
1 CTAAACC
29007358 CTAAACC
1 CTAAACC
29007365 CTAAA-C
1 CTAAACC
*
29007371 CTCAACC
1 CTAAACC
29007378 CTTAAACC
1 C-TAAACC
*
29007386 ATAAACC
1 CTAAACC
*
29007393 ATAAACC
1 CTAAACC
*
29007400 ATAAA
1 CTAAA
29007405 GCTCGATCTA
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
6 8 0.11
7 52 0.72
8 12 0.17
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:29007442 original size:17 final size:17
Alignment explanation
Indices: 29007420--29007453 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29007410 ATCTATAGCA
29007420 GCATTTTTCGAAAAGCG
1 GCATTTTTCGAAAAGCG
29007437 GCATTTTTCGAAAAGCG
1 GCATTTTTCGAAAAGCG
29007454 ACGCTAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
GCATTTTTCGAAAAGCG
Found at i:29007655 original size:40 final size:40
Alignment explanation
Indices: 29007515--29008055 Score: 155
Period size: 40 Copynumber: 13.8 Consensus size: 40
29007505 TTTTGCGACG
* * * * ** *
29007515 TTTTTCAAAAAGCGCCACTAATGGTTGACCTATAGTGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
* * * **
29007555 TTTTGCAAAACGCACCAG-TAATGCTCGATCTATAGTGGCA
1 TTTTTCAAAAAGCGCC-GCTAATGCTCGATCTATAGCAGCA
*
29007595 TTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAGCAGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
* * * *
29007635 TTTTTCAAAAAGTGCTGCTAATGC-C-A-CTAAAGC-TCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
*** * ** ** ** * * * *
29007671 -ACAT-AAAATGACGGTG-TTGTGCTTAATTTTTTGCGGCA
1 TTTTTCAAAAAG-CGCCGCTAATGCTCGATCTATAGCAGCA
** * * * * * *
29007709 TTTTTTGAAAAGTGCTGCTAATGGTCAACCTATAGCGGC-
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
* * * * *
29007748 GTTTTCAAGAAGCGCCGCTAGTGCTCTATCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
** * * * *
29007788 TTTTTCATGAAGCGCCGCTAATTCTCGATCTATAACGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
* * *
29007828 TTTTCCAAAAA-CGCCGCTAATGC-C-A-CTAAAGC-TCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
*** * * ** ** * * * * **
29007863 -ACAT-AAAATAGGGGCG-TTGTGCTTAATTTTTTTGCGGTG
1 TTTTTCAAAA-AGCGCCGCTAATGCTCGA-TCTATAGCAGCA
* * * * *
29007902 TTTTTCAAAAAGAGCCGTTAATGGTCGACCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
* * **
29007942 TTTTTCAAGAAGCGCCGCGAATGCTCGATCTATAG-AGGTG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCA-GCA
* * * *
29007982 TTTTTCAAAAGGCGCCACTAATGCTCGATCTATAGCGGTA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
* * *
29008022 TTTTTTAAAAAGCGTCGCTAATGCTTGATCTATA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
29008056 ACGGTGTTTT
Statistics
Matches: 354, Mismatches: 124, Indels: 46
0.68 0.24 0.09
Matches are distributed among these distances:
33 4 0.01
34 14 0.04
35 8 0.02
36 9 0.03
37 10 0.03
38 7 0.02
39 46 0.13
40 247 0.70
41 9 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCA
Found at i:29008035 original size:80 final size:80
Alignment explanation
Indices: 29007897--29008066 Score: 216
Period size: 80 Copynumber: 2.1 Consensus size: 80
29007887 AATTTTTTTG
** * *
29007897 CGGTGTTTTTCAAAAAGAGCCGTTAATGGTCGACCTATAGCGGCATTTTTCAAGAAGCGCCGCGA
1 CGGTGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCGA
29007962 ATGCTCGATCTATAGA
66 ATGCTCGATCTATA-A
* * * * * * *
29007978 -GGTGTTTTTCAAAAGGCGCCACTAATGCTCGATCTATAGCGGTATTTTTTAAAAAGCGTCGCTA
1 CGGTGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCGA
*
29008042 ATGCTTGATCTATAA
66 ATGCTCGATCTATAA
29008057 CGGTGTTTTT
1 CGGTGTTTTT
29008067 TATCCAAACA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.01
80 75 0.99
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (80 bp):
CGGTGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCGA
ATGCTCGATCTATAA
Found at i:29008068 original size:40 final size:40
Alignment explanation
Indices: 29007897--29008066 Score: 180
Period size: 40 Copynumber: 4.2 Consensus size: 40
29007887 AATTTTTTTG
* * * * *
29007897 CGGTGTTTTTCAAAAAGAGCCGTTAATGGTCGACCTATAG
1 CGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAA
** * *
29007937 CGGCATTTTTCAAGAAGCGCCGCGAATGCTCGATCTATAGA
1 CGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA-A
* * *
29007978 -GGTGTTTTTCAAAAGGCGCCACTAATGCTCGATCTATAG
1 CGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAA
* * * *
29008017 CGGTATTTTTTAAAAAGCGTCGCTAATGCTTGATCTATAA
1 CGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAA
29008057 CGGTGTTTTT
1 CGGTGTTTTT
29008067 TATCCAAACA
Statistics
Matches: 104, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (40 bp):
CGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAA
Found at i:29010665 original size:11 final size:11
Alignment explanation
Indices: 29010651--29010689 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29010641 CCACCCTATC
29010651 ACCACCATACA
1 ACCACCATACA
* *
29010662 ACCACCACACC
1 ACCACCATACA
*
29010673 ACCACCATTCA
1 ACCACCATACA
29010684 ACCACC
1 ACCACC
29010690 GTAGCACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.54, G:0.00, T:0.08
Consensus pattern (11 bp):
ACCACCATACA
Found at i:29010701 original size:22 final size:22
Alignment explanation
Indices: 29010640--29010689 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
29010630 AACCCAAATC
* *
29010640 ACCACCCTATCACCACCATACA
1 ACCACCATACCACCACCATACA
* *
29010662 ACCACCACACCACCACCATTCA
1 ACCACCATACCACCACCATACA
29010684 ACCACC
1 ACCACC
29010690 GTAGCACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.54, G:0.00, T:0.10
Consensus pattern (22 bp):
ACCACCATACCACCACCATACA
Found at i:29014093 original size:11 final size:11
Alignment explanation
Indices: 29014079--29014112 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
29014069 GGTAAATTCA
29014079 TAAAAAATACT
1 TAAAAAATACT
29014090 TAAAAAATACT
1 TAAAAAATACT
29014101 TAAAAAATACT
1 TAAAAAATACT
29014112 T
1 T
29014113 TTAATTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAAATACT
Done.