Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 124 of 208
Found at i:40808552 original size:4 final size:4
Alignment explanation
Indices: 40808543--40808601 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
40808533 TTATTAAATC
40808543 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
40808591 TGTA TGTA TGT
1 TGTA TGTA TGT
40808602 CATTGTATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:40809675 original size:23 final size:21
Alignment explanation
Indices: 40809627--40809676 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
40809617 AGTGTGGTGT
40809627 TAATATGCATAATGAAAAAAA
1 TAATATGCATAATGAAAAAAA
*
40809648 GAATATG-ATAATGTGAACAAAAA
1 TAATATGCATAA--TGAA-AAAAA
40809671 TAATAT
1 TAATAT
40809677 AAGCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 6 0.25
22 4 0.17
23 10 0.42
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.26
Consensus pattern (21 bp):
TAATATGCATAATGAAAAAAA
Found at i:40810676 original size:6 final size:6
Alignment explanation
Indices: 40810667--40810728 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
40810657 AAAGAAAAGA
* * * *
40810667 AAAATC AAAATC AAAATC AAAGTC AAAATG AAAATG AAAA-- ACAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
40810713 AAAAATC AAAAT- AAAA
1 -AAAATC AAAATC AAAA
40810729 AAAATAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.06
5 4 0.08
6 36 0.75
7 5 0.10
ACGTcount: A:0.69, C:0.11, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:40811663 original size:7 final size:7
Alignment explanation
Indices: 40811651--40811688 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
40811641 TCTGAGTCAA
40811651 AAAAATG
1 AAAAATG
40811658 AAAAATG
1 AAAAATG
*
40811665 -AGAATG
1 AAAAATG
40811671 AAAAATG
1 AAAAATG
40811678 AAAAATG
1 AAAAATG
40811685 AAAA
1 AAAA
40811689 TGGAGAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:40811674 original size:20 final size:20
Alignment explanation
Indices: 40811651--40811690 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40811641 TCTGAGTCAA
*
40811651 AAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAATG
40811671 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
40811691 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:40811690 original size:13 final size:14
Alignment explanation
Indices: 40811651--40811688 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
40811641 TCTGAGTCAA
40811651 AAAAATGAAAAATG
1 AAAAATGAAAAATG
*
40811665 -AGAATGAAAAATG
1 AAAAATGAAAAATG
40811678 AAAAATGAAAA
1 AAAAATGAAAA
40811689 TGGAGAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:40811879 original size:9 final size:9
Alignment explanation
Indices: 40811865--40811895 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40811855 GTTAAACGAA
40811865 TCGAGTTAT
1 TCGAGTTAT
*
40811874 TCGAGTTAA
1 TCGAGTTAT
40811883 TCGAGTTAT
1 TCGAGTTAT
40811892 TCGA
1 TCGA
40811896 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40811966 original size:9 final size:9
Alignment explanation
Indices: 40811949--40811985 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40811939 TGAGTTTTCG
40811949 AATTCGAAT
1 AATTCGAAT
*
40811958 AACTCGAAT
1 AATTCGAAT
*
40811967 AATTTGAAT
1 AATTCGAAT
40811976 AATTCGAAT
1 AATTCGAAT
40811985 A
1 A
40811986 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40813017 original size:5 final size:5
Alignment explanation
Indices: 40813007--40813032 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40812997 CTCGAAAATT
40813007 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
40813033 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:40814430 original size:50 final size:49
Alignment explanation
Indices: 40814275--40814656 Score: 203
Period size: 50 Copynumber: 7.7 Consensus size: 49
40814265 TCAGTGGAGC
* * * * *
40814275 AGATTAAAGCCATAATGGTGAATCTTGCTTTCCCTGACATTGCGGTTAAAA
1 AGATTAAA-CCACAACGGTGAATCTTAC-CTCCCTGGCATTGCGGTTAAAA
* * ** * * ** * ** *
40814326 AGATTAAAGCTACATA-AGCAAATCTTACCTCTCAGGCGGTGCAGTGGAAT
1 AGATTAAA-CCACA-ACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
** *
40814376 AGATTAAACCAACAACGGTGAATCTTACCTTTCTGACATTGCGGTTAAAA
1 AGATTAAACC-ACAACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
* * * * * * * * *
40814426 AGATTAAAGCTACAGCAGCGAATCTTATCTCCCAGGTAGTGCAG-TAAAA
1 AGATTAAA-CCACAACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
* ** *
40814475 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAA
1 AGATTAAA-CCACAACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
* * * * * *** *
40814525 AGATTAAAGCTACAGCAGTGAATCTTATCTCCCAGGTGGTGCAG-TAAAA
1 AGATTAAA-CCACAACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
* * * *
40814574 AGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACATTGCGATTAAAA
1 AGATTAAA-CCACAACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
* * * *
40814624 AGATTAAAGCTACAGCAGCGAATCTTACCTCCC
1 AGATTAAA-CCACAACGGTGAATCTTACCTCCC
40814657 AAGCGATGCA
Statistics
Matches: 239, Mismatches: 86, Indels: 13
0.71 0.25 0.04
Matches are distributed among these distances:
49 74 0.31
50 143 0.60
51 21 0.09
52 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (49 bp):
AGATTAAACCACAACGGTGAATCTTACCTCCCTGGCATTGCGGTTAAAA
Found at i:40814483 original size:49 final size:50
Alignment explanation
Indices: 40814321--40814657 Score: 252
Period size: 50 Copynumber: 6.8 Consensus size: 50
40814311 ACATTGCGGT
** ** * *
40814321 TAAAAAGATTAAAGCTACATAAGCAAATCTTACCTCTCAGGCGGTGC-AG
1 TAAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCAGGCAGTGCGAG
* * * * * * ** * * *
40814370 TGGAATAGATTAAACCAACAACGGTGAATCTTACCTTTCTGACATTGCG-G
1 T-AAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCAGGCAGTGCGAG
* * *
40814420 TTAAAAAGATTAAAGCTACAGCAGCGAATCTTATCTCCCAGGTAGTGC-AG
1 -TAAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCAGGCAGTGCGAG
* * * * ** * * *
40814470 TAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGAT
1 TAAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCAGGCAGTGCGAG
* **
40814520 TAAAAAGATTAAAGCTACAGCAGTGAATCTTATCTCCCAGGTGGTGC-AG
1 TAAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCAGGCAGTGCGAG
* * * * * * *
40814569 TAAAAAGATTAAAGCCACAAC-GATGAATCTTGCCTCCCTGACATTGCGAT
1 TAAAAAGATTAAAGCTACAGCAG-TGAATCTTACCTCCCAGGCAGTGCGAG
*
40814619 TAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCA
1 TAAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCA
40814658 AGCGATGCAG
Statistics
Matches: 213, Mismatches: 67, Indels: 15
0.72 0.23 0.05
Matches are distributed among these distances:
48 1 0.00
49 74 0.35
50 136 0.64
51 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (50 bp):
TAAAAAGATTAAAGCTACAGCAGTGAATCTTACCTCCCAGGCAGTGCGAG
Found at i:40814526 original size:99 final size:100
Alignment explanation
Indices: 40814248--40814751 Score: 542
Period size: 99 Copynumber: 5.0 Consensus size: 100
40814238 AAAACAAAGC
* * * * ** * *
40814248 CTTACTTCCCAGATAGTTCAGTGGAGCAGATTAAAGCCATAATGGTGAATCTTG-CTTTCCCTGA
1 CTTACCTCCCAGGTAGTGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTT--CTGA
* ** *
40814312 CATTGCGGTTAAAAAGATTAAAGCTACATAAGCAAAT
64 CATTGCGATTAAAAAGATTAAAGCTACAGCAGCGAAT
* ** * * *
40814349 CTTACCTCTCAGGCGGTGCAGTGGAATAGATTAAA-CCAACAACGGTGAATCTTACCTTTCTGAC
1 CTTACCTCCCAGGTAGTGCAGTGAAAAAGATTAAAGCC-ACAACGGTGAATCTTGCCTTTCTGAC
*
40814413 ATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGAAT
65 ATTGCGATTAAAAAGATTAAAGCTACAGCAGCGAAT
* *
40814449 CTTATCTCCCAGGTAGTGCAGT-AAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCA
1 CTTACCTCCCAGGTAGTGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACA
*
40814513 TTGCGATTAAAAAGATTAAAGCTACAGCAGTGAAT
66 TTGCGATTAAAAAGATTAAAGCTACAGCAGCGAAT
* * * **
40814548 CTTATCTCCCAGGTGGTGCAGT-AAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACA
1 CTTACCTCCCAGGTAGTGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACA
40814612 TTGCGATTAAAAAGATTAAAGCTACAGCAGCGAAT
66 TTGCGATTAAAAAGATTAAAGCTACAGCAGCGAAT
* * *
40814647 CTTACCTCCCAAGCG-A-TGCAGTGGAACAGATTAAAGCCA-AATTGGTGAATCTTG--TTTCTC
1 CTTACCTCCC-AG-GTAGTGCAGTGAAAAAGATTAAAGCCACAA-CGGTGAATCTTGCCTTTCT-
* * ***
40814707 CGACATTGC-AGTTAAAAATATTAAAGCCACAATGGCGAAT
62 -GACATTGCGA-TTAAAAAGATTAAAGCTACAGCAGCGAAT
40814747 CTTAC
1 CTTAC
40814752 TTTCCAAAAG
Statistics
Matches: 350, Mismatches: 43, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
98 3 0.01
99 179 0.51
100 123 0.35
101 41 0.12
102 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (100 bp):
CTTACCTCCCAGGTAGTGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACA
TTGCGATTAAAAAGATTAAAGCTACAGCAGCGAAT
Found at i:40814678 original size:149 final size:150
Alignment explanation
Indices: 40814275--40814738 Score: 350
Period size: 149 Copynumber: 3.1 Consensus size: 150
40814265 TCAGTGGAGC
* * * * *
40814275 AGATTAAAGCCATAATGGTGAATCTTGCTTTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACA
1 AGATTAAAGCCACAACGATGAATCTTGC-CTCCCTGACATTGCGATTAAAAAGATTAAAGCTACA
* * * * *
40814340 TA-AGCAAATCTTACCTCTCAGGCGGTGCAGTGGAATAGATTAAACCAACAACGGTGAATCTTAC
65 -ACAGCGAATCTTACCTCTCAGGCGATGCAGTGGAAAAGATTAAAGCAACAACAGTGAATCTTAC
** * * *
40814404 CTTTCTGACATTGCGGTTAAAA
129 CTCCCAGACAGTGCAGTTAAAA
* * * ** * ** * * *
40814426 AGATTAAAGCTACAGC-AGCGAATCTTATCTCCCAGGTAGTGC-AGTAAAAAGATTAAAGCCACA
1 AGATTAAAGCCACAACGA-TGAATCTTGCCTCCCTGACATTGCGATTAAAAAGATTAAAGCTACA
* * * * * ** * *
40814489 ACGGTGAATCTTGCCTTTCTGGC-ATTGC-GATTAAAAAGATTAAAGCTACAGCAGTGAATCTTA
65 ACAGCGAATCTTACCTCTCAGGCGA-TGCAG-TGGAAAAGATTAAAGCAACAACAGTGAATCTTA
* ***
40814552 TCTCCCAGGTGGTGCAG-TAAAA
128 CCTCCCAGACAGTGCAGTTAAAA
*
40814574 AGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACATTGCGATTAAAAAGATTAAAGCTACAG
1 AGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACATTGCGATTAAAAAGATTAAAGCTACAA
* * * *** ***
40814639 CAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCAA-ATTGGTGAATCTTGTT
66 CAGCGAATCTTACCTCTCAGGCGATGCAGTGGAAAAGATTAAAG-CAACAACAGTGAATCTTACC
*
40814703 TCTCC-GACATTGCAGTTAAAA
130 TC-CCAGACAGTGCAGTTAAAA
*
40814724 ATATTAAAGCCACAA
1 AGATTAAAGCCACAA
40814739 TGGCGAATCT
Statistics
Matches: 230, Mismatches: 72, Indels: 23
0.71 0.22 0.07
Matches are distributed among these distances:
148 38 0.17
149 139 0.60
150 34 0.15
151 19 0.08
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (150 bp):
AGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACATTGCGATTAAAAAGATTAAAGCTACAA
CAGCGAATCTTACCTCTCAGGCGATGCAGTGGAAAAGATTAAAGCAACAACAGTGAATCTTACCT
CCCAGACAGTGCAGTTAAAA
Found at i:40815017 original size:44 final size:43
Alignment explanation
Indices: 40814771--40815246 Score: 179
Period size: 44 Copynumber: 10.9 Consensus size: 43
40814761 GTTACGAGTT
* * * ** *
40814771 ACAA-ATCCTATCTCCCTGATATTATAGTGGAGTGGATCGAAG
1 ACAAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * *
40814813 AACCAA-AGTCTTATCCCCCTGAAGA-TACAGTGGGGCAAATTGAAA
1 -A-CAAGA-TCTTATCTCCCTG-AGATTACAGTGGAGCAGATTGAAG
* * * * * * *
40814858 ATAAAGGATCTCATCTCTCTGA-AGTTACAGTAGAGCAGATCGCAT
1 A-CAA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAG
* * * **
40814903 AC-AG-TCTTATCTCCCTGAGGTTACAGTGGAGTAAACCGAAG
1 ACAAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
*
40814944 A-ATTTTAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG
1 ACA----AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* *
40814990 CCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
1 ACA-AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
** * * * * *
40815034 ACACTATCCTATCTCCCTGA-AGTTACAGTAGAGCGGATTAAAA
1 ACAAGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAG
* * * * ** * * *
40815077 AAAAGGATATTATCTCTCT-AAAGTTACAGCAGAGTAGATCGCA-
1 ACAA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAG
* * * * ***
40815120 TC-AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAAAG
1 ACAAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * *
40815162 A-ATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG
1 ACA----AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * *
40815208 ACACA-ATCCTATCTCCCTGA-AGTTACTGTGGAGCGGATT
1 ACA-AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT
40815247 AAAATAATAC
Statistics
Matches: 322, Mismatches: 84, Indels: 54
0.70 0.18 0.12
Matches are distributed among these distances:
41 54 0.17
42 4 0.01
43 63 0.20
44 76 0.24
45 51 0.16
46 72 0.22
47 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
ACAAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
Found at i:40815176 original size:174 final size:174
Alignment explanation
Indices: 40814994--40815337 Score: 503
Period size: 174 Copynumber: 2.0 Consensus size: 174
40814984 TTGAAGCCAG
* *
40814994 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTA
* * *
40815059 CAGTAGAGCGGATTAAAA-AAAAGGATATTATCTCTCTAAAGTTACAGCAGAGTAGATCGCAT-C
66 CAGTAGAGCGGATTAAAATAAAA-CATATTATCTCTCTAAAGTTACAGCAGAGCAGAGCGCATCC
* *
40815122 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAAAGAATTTC
130 A-GTCTTATCTCCCTGAAGTTACAGTGGAGCAGACCAAAGAATTTC
*
40815168 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTA
* * * * * * *
40815233 CTGTGGAGCGGATTAAAATAATACATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGCGCATCCA
66 CAGTAGAGCGGATTAAAATAAAACATATTATCTCTCTAAAGTTACAGCAGAGCAGAGCGCATCCA
* *
40815298 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAA
131 GTCTTATCTCCCTGAAGTTACAGTGGAGCAGACCAAAGAA
40815338 ACCTATCCTA
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
174 146 0.97
175 5 0.03
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (174 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTA
CAGTAGAGCGGATTAAAATAAAACATATTATCTCTCTAAAGTTACAGCAGAGCAGAGCGCATCCA
GTCTTATCTCCCTGAAGTTACAGTGGAGCAGACCAAAGAATTTC
Found at i:40815274 original size:218 final size:218
Alignment explanation
Indices: 40814855--40815285 Score: 591
Period size: 218 Copynumber: 2.0 Consensus size: 218
40814845 GGGCAAATTG
* * * *
40814855 AAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGCAGATCGCATACAGTCTTATCTCCCTG
1 AAAAAAAAGGATATCATCTCTCTAAAGTTACAGCAGAGCAGATCGCATACAGTCTTATCTCCCTG
* * *
40814920 AGGTTACAGTGGAGTAAACCGAAGAATTTTAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGAT
66 AGGTTACAGTGGAGTAAACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGAT
* * * * * *
40814985 TGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTATCCTATCTCC
131 CGAAGACACAGATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAACACTATCCTATCTCC
40815050 CTGAAGTTACAGTAGAGCGGATT
196 CTGAAGTTACAGTAGAGCGGATT
* *
40815073 AAAAAAAAGGATATTATCTCTCTAAAGTTACAGCAGAGTAGATCGCAT-CAGGTCTTATCTCCCT
1 AAAAAAAAGGATATCATCTCTCTAAAGTTACAGCAGAGCAGATCGCATACA-GTCTTATCTCCCT
*
40815137 GAGGTTACAGTGGAGTAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGA
65 GAGGTTACAGTGGAGTAAACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGA
* * * * *
40815202 TCGAAGACACA-ATCCTATCTCCCTGA-AGTTACTGTGGAGCGGATTAAAATAATAC-ATCTTAT
130 TCGAAGACACAGATCCTATCTCCCTGAGA-TTACAGCGGAGCAGATT-AAA-AACACTATCCTAT
* *
40815264 CTCTCTGAAGTTGCAGTAGAGC
192 CTCCCTGAAGTTACAGTAGAGC
40815286 AGAGCGCATC
Statistics
Matches: 186, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
216 1 0.01
217 30 0.16
218 152 0.82
219 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (218 bp):
AAAAAAAAGGATATCATCTCTCTAAAGTTACAGCAGAGCAGATCGCATACAGTCTTATCTCCCTG
AGGTTACAGTGGAGTAAACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGAT
CGAAGACACAGATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAACACTATCCTATCTCC
CTGAAGTTACAGTAGAGCGGATT
Found at i:40815324 original size:85 final size:84
Alignment explanation
Indices: 40814953--40815364 Score: 290
Period size: 87 Copynumber: 4.8 Consensus size: 84
40814943 GAATTTTAGA
* * *** * *
40814953 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGATTAC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATT-AAAAAATAGATCTTATCTCTCTGAAG-TTAC
* * * *
40815017 AGCGGAGCAGATTGAAGACACTA-
64 AGCAGAGCAGATCGCA-TC-C-AG
* * * * *
40815040 TCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAAAAAAGGATATTATCTCTCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAATA-GATCTTATCTCTCTGAAGTTACA
*
40815105 GCAGAGTAGATCGCAT-CAGG
65 GCAGAGCAGATCGCATCCA-G
* ** ** * * *
40815125 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA-AA-AT-AGATCTTATCTCTCTGAAGTTA
* * * *
40815190 CAGCGGAGCAGATCGAAGACACAA
63 CAGCAGAGCAGATCGCA-TC-CAG
* * * *
40815214 TCCTATCTCCCTGAAGTTACTGTGGAGCGGATTAAAATAATACATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA-AATAGATCTTATCTCTCTGAAGTTACA
* *
40815279 GTAGAGCAGAGCGCATCCAG
65 GCAGAGCAGATCGCATCCAG
* * ** *** *
40815299 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACCTATCCTATCTCTCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA-AAATAGATCTTATCTCTCTGAAGTTACA
40815364 G
65 G
40815365 TGGAGCGGAT
Statistics
Matches: 250, Mismatches: 63, Indels: 26
0.74 0.19 0.08
Matches are distributed among these distances:
83 1 0.00
84 1 0.00
85 84 0.34
86 8 0.03
87 119 0.48
88 5 0.02
89 30 0.12
90 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (84 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAATAGATCTTATCTCTCTGAAGTTACAG
CAGAGCAGATCGCATCCAG
Found at i:40815371 original size:129 final size:128
Alignment explanation
Indices: 40815170--40815547 Score: 474
Period size: 129 Copynumber: 2.9 Consensus size: 128
40815160 AGAATTTCAG
* * * *
40815170 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCG-AAGACACAATCCTATCTCCCTGAAGTTAC
1 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAAGAAACAATCCTATCTCTCTGAAGTTAC
* *
40815234 TGTGGAGCGGATTAAAATAATACATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGCGCATCCA
66 AGTGGAGCGGATTAAAAT-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGCGCATCCA
* * *
40815298 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGAAACCTATCCTATCTCTCTGAAGTTA
1 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAAGAAA-CAATCCTATCTCTCTGAAGTTA
* * *
40815362 CAGTGGAGCGGATTAAAACTACAGATCTTATCTCTCTGAAGTTGCAGTAAAGCAGATCGCATCCA
65 CAGTGGAGCGGATTAAAA-TATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGCGCATCCA
* * ** * *
40815427 ATCTTATTTCCCTGAAGTTGCAACGGAGCAGATTAAAAAAAATCAATCCTATCT-TCCTAAAGTT
1 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAAGAAA-CAATCCTATCTCT-CTGAAGTT
* * * * *
40815491 GCAGTGAAGTGGATTAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
64 ACAGTGGAGCGGATTAAAAT-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
40815548 TCGCGTCAGA
Statistics
Matches: 215, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
127 2 0.01
128 33 0.15
129 108 0.50
130 72 0.33
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (128 bp):
ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAAGAAACAATCCTATCTCTCTGAAGTTAC
AGTGGAGCGGATTAAAATATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGCGCATCCA
Found at i:40815394 original size:44 final size:43
Alignment explanation
Indices: 40814821--40815464 Score: 293
Period size: 44 Copynumber: 14.9 Consensus size: 43
40814811 AGAACCAAAG
* * * * *
40814821 TCTTATCCCCCTGAAGATACAGTGGGGCAAATTGAAAATAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATACA-GA
* * * ***
40814866 TCTCATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCATACAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGA
* * * ** **
40814907 TCTTATCTCCCTGAGGTTACAGTGGAGTAAACCGAAGAATTTTAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TACAGA
* *** *
40814953 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATACAGA
* * * *
40814997 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATT-GAAGACACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATACA-GA
* * * * *
40815040 TCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAAAAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACA-GA
* * * ** * *** *
40815084 TATTATCTCTCTAAAGTTACAGCAGAGTAGA-TCGCAT-CAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGA
* * ** *
40815125 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TACAGA
* * * * *
40815171 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACACA-A
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-TAAAATACAGA
* * * * *
40815214 TCCTATCTCCCTGAAGTTACTGTGGAGCGGATTAAAATAATACA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAT-ACAGA
* * * **** *
40815258 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-GCGCATCCAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGA
* ** * **
40815299 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACCTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATACAGA
* * *
40815343 TCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAACTACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA-TACAGA
* * ** *** *
40815387 TCTTATCTCTCTGAAGTTGCAGTAAAGCAGA-TCGCATCCA-A
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGA
* * **
40815428 TCTTATTTCCCTGAAGTTGCAACGGAGCAGATTAAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA
40815465 AAAATCAATC
Statistics
Matches: 438, Mismatches: 138, Indels: 49
0.70 0.22 0.08
Matches are distributed among these distances:
41 106 0.24
42 14 0.03
43 71 0.16
44 153 0.35
45 29 0.07
46 65 0.15
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGA
Found at i:40817759 original size:16 final size:16
Alignment explanation
Indices: 40817738--40817776 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40817728 AACGTATACA
40817738 TATATATACATACTTT
1 TATATATACATACTTT
*
40817754 TATATATACATGCTTT
1 TATATATACATACTTT
*
40817770 CATATAT
1 TATATAT
40817777 CTCCATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:40817776 original size:34 final size:34
Alignment explanation
Indices: 40817736--40817800 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
40817726 ATAACGTATA
*
40817736 CATATATATACATACTTTTATATATACATGCTTT
1 CATATATATACATAATTTTATATATACATGCTTT
* * * *
40817770 CATATATCTCCATAATTTTATGTATATATGC
1 CATATATATACATAATTTTATATATACATGC
40817801 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (34 bp):
CATATATATACATAATTTTATATATACATGCTTT
Found at i:40821583 original size:7 final size:8
Alignment explanation
Indices: 40821573--40821600 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40821563 GAAAAAAATC
40821573 AAAATAAA
1 AAAATAAA
40821581 AAAATAAA
1 AAAATAAA
40821589 AAAATAAA
1 AAAATAAA
40821597 AAAA
1 AAAA
40821601 AGAAGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:40821658 original size:55 final size:49
Alignment explanation
Indices: 40821563--40821670 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 49
40821553 AAATGAAAAT
*
40821563 GAAAAAAATCAAAATAAAAAAATAAAAAAATAAAAAAAAGAAGAAAGAA
1 GAAAAAAATCAAAATAAAAAAATAAAAAAAGAAAAAAAAGAAGAAAGAA
** *
40821612 GAAAAAAATCAAAATCAAGATCAAAATGAAAATGAGAAAAAGAAAGAAGAATGAA
1 GAAAAAAATCAAAAT-AA-A--AAAAT-AAAAAAAGAAAAA-AAAGAAGAAAGAA
40821667 -AAAA
1 GAAAA
40821671 GAGAAATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
49 15 0.31
50 2 0.04
51 1 0.02
53 5 0.10
54 14 0.29
55 12 0.24
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.09
Consensus pattern (49 bp):
GAAAAAAATCAAAATAAAAAAATAAAAAAAGAAAAAAAAGAAGAAAGAA
Found at i:40822595 original size:6 final size:7
Alignment explanation
Indices: 40822578--40822619 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
40822568 CTGAGTAAAA
40822578 AAAAATG
1 AAAAATG
40822585 AAAAATG
1 AAAAATG
40822592 AAAAATG
1 AAAAATG
40822599 -AAAATG
1 AAAAATG
40822605 AAAAATG
1 AAAAATG
40822612 -AAAATG
1 AAAAATG
40822618 AA
1 AA
40822620 GAGGCTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:40822602 original size:13 final size:13
Alignment explanation
Indices: 40822578--40822619 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
40822568 CTGAGTAAAA
40822578 AAAAATGAAAAATG
1 AAAAATG-AAAATG
40822592 AAAAATGAAAATG
1 AAAAATGAAAATG
40822605 AAAAATGAAAATG
1 AAAAATGAAAATG
40822618 AA
1 AA
40822620 GAGGCTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:40825366 original size:28 final size:28
Alignment explanation
Indices: 40825309--40825488 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
40825299 TAAATTGTGC
*
40825309 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
40825336 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
40825364 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
40825392 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
40825419 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
40825447 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
40825474 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40825489 GACTTAATAT
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
27 66 0.45
28 81 0.55
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:40825374 original size:55 final size:55
Alignment explanation
Indices: 40825309--40825488 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
40825299 TAAATTGTGC
*
40825309 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAG-TTGACTATGT
40825364 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
* * *
40825419 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
*
40825474 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40825489 GACTTAATAT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40825424 original size:83 final size:82
Alignment explanation
Indices: 40825309--40825488 Score: 306
Period size: 83 Copynumber: 2.2 Consensus size: 82
40825299 TAAATTGTGC
40825309 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
*
40825374 GTGCGAGTTTGACTATGT
66 GTGCGAG-TTGACTATAT
* *
40825392 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
*
40825457 GTGCGAGTTGATTATAT
66 GTGCGAGTTGACTATAT
*
40825474 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40825489 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 22 0.24
83 70 0.76
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
GTGCGAGTTGACTATAT
Found at i:40844961 original size:28 final size:28
Alignment explanation
Indices: 40844904--40845083 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
40844894 TAAATTGTGC
*
40844904 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
40844931 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
40844959 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
40844987 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
40845014 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
40845042 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
40845069 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40845084 GACTTAATAT
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
27 66 0.45
28 81 0.55
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:40844969 original size:55 final size:55
Alignment explanation
Indices: 40844904--40845083 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
40844894 TAAATTGTGC
*
40844904 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAG-TTGACTATGT
40844959 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
* * *
40845014 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
*
40845069 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40845084 GACTTAATAT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40845019 original size:83 final size:82
Alignment explanation
Indices: 40844904--40845083 Score: 306
Period size: 83 Copynumber: 2.2 Consensus size: 82
40844894 TAAATTGTGC
40844904 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
*
40844969 GTGCGAGTTTGACTATGT
66 GTGCGAG-TTGACTATAT
* *
40844987 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
*
40845052 GTGCGAGTTGATTATAT
66 GTGCGAGTTGACTATAT
*
40845069 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40845084 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 22 0.24
83 70 0.76
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
GTGCGAGTTGACTATAT
Found at i:40847456 original size:50 final size:49
Alignment explanation
Indices: 40847331--40847807 Score: 233
Period size: 50 Copynumber: 9.6 Consensus size: 49
40847321 GCAGTGAAGT
* * * * * *
40847331 AGATTAAAGCCATAACGGTGAATCTTACTTTCTCTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-CTCTCAGGCGTTGCAG-TAAAA
* * * ** * *
40847382 AGATTAAAGCTACATCAGCAAATCTTACCTCTCAGGCGGTTG-AGTGGAAT
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGC-GTTGCAGT-AAAA
* * * *
40847432 AGATTAAAGCCACAACGGTGAATCTTACCTCTCTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAG-TAAAA
* * * * * *
40847482 AGATTAAAGCTACAACAGCGAATCTTATCTCCCAAGCAG-TGCAGTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGC-GTTGCAGTAAAA
* * * * *
40847531 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGC-AGTAAAA
* *** * * * * **
40847581 AGATTAAAGCTACAGTAGCGAATCTTATCTCCCAGGTGGAGCAGTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGTAAAA
* * * * *
40847630 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGC-GATCAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAG-T-AAAA
* * * * * * * * * *
40847680 AGATTGAAGCTACAGCAGCGAATCTTACCTCCCAAGCGATGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGT-AAAA
* * *** * * * *
40847730 AGATTAAATCCA-AATTGGTGAATCTTGTTTCTCCGACATTACAGTTAAAA
1 AGATTAAAGCCACAA-CGGTGAATCTTACCTCTCAGGCGTTGCAG-TAAAA
* * *
40847780 ATATTAAAGCCACAATGGCGAATCTTAC
1 AGATTAAAGCCACAACGGTGAATCTTAC
40847808 TTTCCAAAAG
Statistics
Matches: 302, Mismatches: 111, Indels: 27
0.69 0.25 0.06
Matches are distributed among these distances:
48 1 0.00
49 77 0.25
50 194 0.64
51 30 0.10
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (49 bp):
AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGTAAAA
Found at i:40847583 original size:99 final size:101
Alignment explanation
Indices: 40847320--40847807 Score: 533
Period size: 99 Copynumber: 4.9 Consensus size: 101
40847310 TCCCAGGTAG
** * * * *
40847320 TGCAGTGAAGTAGATTAAAGCCATAACGGTGAATCTTACTTTCTCTGACATTGCGGTTAAAAAGA
1 TGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGC-CTCTCTGACATTGCGATTAAAAAGA
* * * * *
40847385 TTAAAGCTACATCAGCAAATCTTACCTCTCAGGCGGT
65 TTAAAGCTACAGCAGCGAATCTTACCTCCCAAGCGGA
* * * *
40847422 TG-AGTGGAATAGATTAAAGCCACAACGGTGAATCTTACCTCTCTGACATTGCGGTTAAAAAGAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACATTGCGATTAAAAAGAT
* * *
40847486 TAAAGCTACAACAGCGAATCTTATCTCCCAAGCAG-
66 TAAAGCTACAGCAGCGAATCTTACCTCCCAAGCGGA
* *
40847521 TGCAGT-AAAAAGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAAAGAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACATTGCGATTAAAAAGAT
* * * *
40847585 TAAAGCTACAGTAGCGAATCTTATCTCCCAGGTGGA
66 TAAAGCTACAGCAGCGAATCTTACCTCCCAAGCGGA
* *
40847621 -GCAGT-AAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCGATCAAAAAGAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACATTGCGATTAAAAAGAT
*
40847684 TGAAGCTACAGCAGCGAATCTTACCTCCCAAGC-GA
66 TAAAGCTACAGCAGCGAATCTTACCTCCCAAGCGGA
* * * * ** * * *
40847719 TGCAGTGGAACAGATTAAATCCA-AATTGGTGAATCTTGTTTCTCCGACATTAC-AGTTAAAAAT
1 TGCAGTGAAAAAGATTAAAGCCACAA-CGGTGAATCTTGCCTCTCTGACATTGCGA-TTAAAAAG
* ***
40847782 ATTAAAGCCACAATGGCGAATCTTAC
64 ATTAAAGCTACAGCAGCGAATCTTAC
40847808 TTTCCAAAAG
Statistics
Matches: 334, Mismatches: 46, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
98 2 0.01
99 179 0.54
100 118 0.35
101 33 0.10
102 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (101 bp):
TGCAGTGAAAAAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACATTGCGATTAAAAAGAT
TAAAGCTACAGCAGCGAATCTTACCTCCCAAGCGGA
Found at i:40848151 original size:129 final size:127
Alignment explanation
Indices: 40848008--40848382 Score: 448
Period size: 129 Copynumber: 2.9 Consensus size: 127
40847998 AGAATTTCAG
* * ** * * *
40848008 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGGTTAC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACA-ATCCTATCTCCCTGAAGTTAC
* *
40848073 AGTGGAGCGGATTAAAATAATAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAAAGCGCATCCA
65 AGTGAAGCGGATTAAAAT-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAAGCGCATCCA
* * * *
40848137 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGAAACCTATCCTATCTCTCTGAAGTTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AAGAAA-CAATCCTATCTCCCTGAAGTTA
* * *
40848201 CAGTGAAGCGGATTAAAACTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
64 CAGTGAAGCGGATTAAAA-TATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAAGCGCATCCA
* * * * * *
40848266 ATCTTATCTCCCTGAAGTTGCAATGGAGGAGATT-AAAAAATCAATCCTATCTTCCTAAAGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAA-CAATCCTATCTCCCTGAAGTTAC
* * *
40848330 AGTGAAGTGGATTAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
65 AGTGAAGCGGATTAAAAT-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
40848383 GATCGCGTCA
Statistics
Matches: 210, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
127 1 0.00
128 71 0.34
129 137 0.65
130 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (127 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTACA
GTGAAGCGGATTAAAATATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAAGCGCATCCA
Found at i:40848233 original size:44 final size:44
Alignment explanation
Indices: 40847877--40848303 Score: 214
Period size: 44 Copynumber: 9.8 Consensus size: 44
40847867 AGAACCAAAG
* * * * * *
40847877 TCTTATCCCCCTGAAGATGCAGTGGGGCAAATTGAAAA-TAAAAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAACT-ACAGA
* * * ***
40847922 TCTCATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCA-TACAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * ** * *
40847963 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AACTACAGA
* * * * *
40848009 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * *
40848053 TCTTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAA-TAATAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACT-ACAGA
* * ** *** *
40848097 TCTTATCTCTCTGAAGTTGCAGCAGAGCA-A--AGCGCATCCAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAC-TACAGA
* ** * **
40848138 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AACCTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ACTACAGA
* * * *
40848182 TCCTATCTCTCTGAAGTTACAGTGAAGCGGATTAAAACTACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * * *** *
40848226 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCA-TCCA-A
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * *
40848267 TCTTATCTCCCTGAAGTTGCAATGGAGGAGATTAAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA
40848304 AATCAATCCT
Statistics
Matches: 284, Mismatches: 83, Indels: 33
0.71 0.21 0.08
Matches are distributed among these distances:
41 81 0.29
42 11 0.04
43 8 0.03
44 126 0.44
45 28 0.10
46 30 0.11
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
Found at i:40848343 original size:43 final size:43
Alignment explanation
Indices: 40848264--40848346 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
40848254 AGATCGCATC
* * *
40848264 CAATCTTATCTCCCTGAAGTTGCAATGGAGGAGATTAAAAAAT
1 CAATCCTATCTCCCTAAAGTTGCAATGAAGGAGATTAAAAAAT
* *
40848307 CAATCCTATCTTCCTAAAGTTGCAGTGAAGTG-GATTAAAA
1 CAATCCTATCTCCCTAAAGTTGCAATGAAG-GAGATTAAAA
40848347 TGGTGGATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (43 bp):
CAATCCTATCTCCCTAAAGTTGCAATGAAGGAGATTAAAAAAT
Found at i:40850365 original size:13 final size:13
Alignment explanation
Indices: 40850347--40850372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40850337 TTTTTAAAAC
40850347 ATGTATTTTATAT
1 ATGTATTTTATAT
40850360 ATGTATTTTATAT
1 ATGTATTTTATAT
40850373 TTTATGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATGTATTTTATAT
Found at i:40850615 original size:16 final size:16
Alignment explanation
Indices: 40850594--40850632 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40850584 AACGTATACA
40850594 TATATATACATACTTT
1 TATATATACATACTTT
*
40850610 TATATATACATGCTTT
1 TATATATACATACTTT
*
40850626 CATATAT
1 TATATAT
40850633 CTCCATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:40850632 original size:34 final size:34
Alignment explanation
Indices: 40850592--40850656 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
40850582 ATAACGTATA
*
40850592 CATATATATACATACTTTTATATATACATGCTTT
1 CATATATATACATAATTTTATATATACATGCTTT
* * * *
40850626 CATATATCTCCATAATTTTATGTATATATGC
1 CATATATATACATAATTTTATATATACATGC
40850657 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (34 bp):
CATATATATACATAATTTTATATATACATGCTTT
Found at i:40853417 original size:39 final size:39
Alignment explanation
Indices: 40853295--40853504 Score: 316
Period size: 39 Copynumber: 5.3 Consensus size: 39
40853285 GCTCCTCGTT
* *
40853295 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40853335 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
40853375 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40853414 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40853453 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40853492 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40853505 ATCTTAGTCC
Statistics
Matches: 160, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 112 0.70
40 46 0.29
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:40853540 original size:78 final size:78
Alignment explanation
Indices: 40853295--40853556 Score: 293
Period size: 78 Copynumber: 3.3 Consensus size: 78
40853285 GCTCCTCGTT
* * *
40853295 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCC
* * **
40853358 GGATTTAGTAACTCGCA
62 GGAATTAGTATCTAACA
*
40853375 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
**
40853440 TTAGTATCTCGCA
66 TTAGTATCTAACA
* *
40853453 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
40853518 TATT-GTCA-CTTAACA
65 -ATTAGT-ATC-TAACA
40853533 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
40853557 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
78 84 0.51
79 57 0.35
80 23 0.14
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTAACA
Found at i:40861651 original size:39 final size:39
Alignment explanation
Indices: 40861506--40861714 Score: 307
Period size: 39 Copynumber: 5.3 Consensus size: 39
40861496 GCTCCTCGTT
* *
40861506 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40861546 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
40861586 CAAATGCCTTC-GGCTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40861624 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40861663 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40861702 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40861715 ATCTTAGTCC
Statistics
Matches: 158, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
38 32 0.20
39 81 0.51
40 43 0.27
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:40861750 original size:78 final size:78
Alignment explanation
Indices: 40861506--40861765 Score: 282
Period size: 78 Copynumber: 3.3 Consensus size: 78
40861496 GCTCCTCGTT
* * *
40861506 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCC
* * **
40861569 GGATTTAGTAACTCGCA
62 GGAATTAGTATCTAACA
*
40861586 CAAATGCCTTC-GGCTTAGCCCGGAATTAGTATCTCGTACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
**
40861650 TTAGTATCTCGCA
66 TTAGTATCTAACA
* *
40861663 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
40861728 TATT-GTCA-CTTAACA
65 -ATTAGT-ATC-TAACA
*
40861743 C-AA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGA
40861766 CATCATTCAA
Statistics
Matches: 161, Mismatches: 12, Indels: 16
0.85 0.06 0.08
Matches are distributed among these distances:
77 35 0.22
78 89 0.55
79 18 0.11
80 19 0.12
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTAACA
Found at i:40861750 original size:117 final size:117
Alignment explanation
Indices: 40861506--40861765 Score: 320
Period size: 117 Copynumber: 2.2 Consensus size: 117
40861496 GCTCCTCGTT
* *
40861506 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
40861570 GATTTAGTAACTCGCACAAATGCCTTCGGCTTAGCCCGGAATTAGTATCTCGTA
65 GAATTAGTAACTCGCACAAATGCCTTCGGCTTAGCCCGGAATTAGTATCTC-TA
*
40861624 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCG
* *
40861686 GAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CT-TAA
65 GAATTAGTAACTCGCACAAATGCCTTCGG--CTTAGCCCGGA-ATTAGT-ATCTCT-A
*
40861741 CACAA-GCCTTCGGACTTAGCCCGGA
1 CA-AATGCCTTCGGGCTTAGCCCGGA
40861766 CATCATTCAA
Statistics
Matches: 127, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
116 38 0.30
117 54 0.43
118 31 0.24
119 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (117 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCACAAATGCCTTCGGCTTAGCCCGGAATTAGTATCTCTA
Found at i:40869898 original size:146 final size:147
Alignment explanation
Indices: 40869590--40869900 Score: 349
Period size: 147 Copynumber: 2.1 Consensus size: 147
40869580 GTTTTACGCC
* *
40869590 CAGCGCTAGTCGGATAAATTGACAATAGGTGTGCCCAGCACTGGTCTGGTAAACCAACAATATTT
1 CAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTGGTCTGGTAAACCAACAATATTT
* * ** * *
40869655 TATGGCCAGTGCTAGTCGAATAAACTGACGATATTAAATCTGTGCCCAGCACTAATAGGATAAAC
66 TACGCCCAACGCAAGTCGAATAAACTGACGATATTAAATCTGTGCCCAACACTAATAGGATAAAC
* *
40869720 CAATATTGTTTTGCGTT
131 CAATATTGCTTTGCGCT
* * * * *
40869737 CAGCGCTAGTTGGATAAATCGACAATAGATGTTCCCAGCACTGGTC-GAGTAAATCGACAATGTT
1 CAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTGGTCTG-GTAAACCAACAATATT
* * * ** * * *
40869801 TTGCGCCCAACGCAAGTCGGAT-AATTGATTATATTAAATGTGTGCCCAACACTAGTCGGATAAA
65 TTACGCCCAACGCAAGTCGAATAAACTGACGATATTAAATCTGTGCCCAACACTAATAGGATAAA
**
40869865 CTGATATTGCTTTGCGC-
130 CCAATATTGCTTTGCGCT
*
40869882 CTAGTGCTAGTCGGATAAA
1 C-AGCGCTAGTCGGATAAA
40869901 CTGATGATAT
Statistics
Matches: 135, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
145 1 0.01
146 64 0.47
147 70 0.52
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (147 bp):
CAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTGGTCTGGTAAACCAACAATATTT
TACGCCCAACGCAAGTCGAATAAACTGACGATATTAAATCTGTGCCCAACACTAATAGGATAAAC
CAATATTGCTTTGCGCT
Found at i:40882558 original size:17 final size:17
Alignment explanation
Indices: 40882522--40882559 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40882512 CATCTTCCCA
*
40882522 TTAGTTTTAAATGTTAT
1 TTAGTTTTAAAGGTTAT
40882539 TTAGTATTTAAAGGTT-T
1 TTAGT-TTTAAAGGTTAT
40882556 TTAG
1 TTAG
40882560 CCATTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (17 bp):
TTAGTTTTAAAGGTTAT
Found at i:40889885 original size:95 final size:93
Alignment explanation
Indices: 40889712--40889888 Score: 239
Period size: 95 Copynumber: 1.9 Consensus size: 93
40889702 CATAATCGCT
* * **
40889712 CACTTGTTGTGAAATGTAATTGGTGTGTTCAAAAGATCATGAGGGTTCTGATGTCCAATTAAATA
1 CACTTGTTGTGAAATGTAATTGGTGAGTTCAAAAGATCATAAGGGTTCCAATGTCCAATTAAATA
40889777 TCCAAATAAAGAGAATACGATTGAGCTAC
66 TCCAAAT-AAGAGAATACGATTGAGCTAC
* * *
40889806 CACTTTTTGTGCAATGTTATTGGTGCAGTTCAAAAGATCATAAGGGTTTCCAATGTCCAATTAAA
1 CACTTGTTGTGAAATGTAATTGGTG-AGTTCAAAAGATCATAAGGG-TTCCAATGTCCAATTAAA
*
40889871 TTATCCAACT-AGAGAATA
64 -TATCCAAATAAGAGAATA
40889889 AAGTAACTAC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
94 22 0.31
95 26 0.36
96 16 0.22
97 8 0.11
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (93 bp):
CACTTGTTGTGAAATGTAATTGGTGAGTTCAAAAGATCATAAGGGTTCCAATGTCCAATTAAATA
TCCAAATAAGAGAATACGATTGAGCTAC
Found at i:40891784 original size:157 final size:157
Alignment explanation
Indices: 40891592--40891908 Score: 634
Period size: 157 Copynumber: 2.0 Consensus size: 157
40891582 GTTAAGTATT
40891592 TTAAGTTATTTAGGAGTTTTATGTCAACAAGAAAGTTTAGTTTAAAACTACTTATTGTTTAGGTT
1 TTAAGTTATTTAGGAGTTTTATGTCAACAAGAAAGTTTAGTTTAAAACTACTTATTGTTTAGGTT
40891657 AATTAAAGTTCTAGTATATTTAAAAGTTTTATTTAGATTTATTTAGCTAGACTATATAAAGGCAT
66 AATTAAAGTTCTAGTATATTTAAAAGTTTTATTTAGATTTATTTAGCTAGACTATATAAAGGCAT
40891722 TTGCATTGTACAACAATAAATTCGTTA
131 TTGCATTGTACAACAATAAATTCGTTA
40891749 TTAAGTTATTTAGGAGTTTTATGTCAACAAGAAAGTTTAGTTTAAAACTACTTATTGTTTAGGTT
1 TTAAGTTATTTAGGAGTTTTATGTCAACAAGAAAGTTTAGTTTAAAACTACTTATTGTTTAGGTT
40891814 AATTAAAGTTCTAGTATATTTAAAAGTTTTATTTAGATTTATTTAGCTAGACTATATAAAGGCAT
66 AATTAAAGTTCTAGTATATTTAAAAGTTTTATTTAGATTTATTTAGCTAGACTATATAAAGGCAT
40891879 TTGCATTGTACAACAATAAATTCGTTA
131 TTGCATTGTACAACAATAAATTCGTTA
40891906 TTA
1 TTA
40891909 TTCAACAACT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.43
Consensus pattern (157 bp):
TTAAGTTATTTAGGAGTTTTATGTCAACAAGAAAGTTTAGTTTAAAACTACTTATTGTTTAGGTT
AATTAAAGTTCTAGTATATTTAAAAGTTTTATTTAGATTTATTTAGCTAGACTATATAAAGGCAT
TTGCATTGTACAACAATAAATTCGTTA
Found at i:40891961 original size:28 final size:26
Alignment explanation
Indices: 40891930--40891984 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
40891920 TTCTTTTGAG
*
40891930 TTAATAAATTCTCTTTGAGTTTTTCTTT
1 TTAAGAAATTCTCTTT-AG-TTTTCTTT
* *
40891958 TTAAGAATTTTTCTTTAGTTTTCTTT
1 TTAAGAAATTCTCTTTAGTTTTCTTT
40891984 T
1 T
40891985 AGAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 13 0.54
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (26 bp):
TTAAGAAATTCTCTTTAGTTTTCTTT
Found at i:40891992 original size:26 final size:28
Alignment explanation
Indices: 40891941--40891995 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
40891931 TAATAAATTC
*
40891941 TCTTTGAGTTTTTCTTTTTAAGAATTTT
1 TCTTTGAGTTTTTCTTTTTAAAAATTTT
40891969 TCTTT-AG-TTTTC-TTTTAGAAAATTTT
1 TCTTTGAGTTTTTCTTTTTA-AAAATTTT
40891995 T
1 T
40891996 AACAATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 2 0.08
28 5 0.20
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (28 bp):
TCTTTGAGTTTTTCTTTTTAAAAATTTT
Found at i:40894419 original size:20 final size:20
Alignment explanation
Indices: 40894396--40894433 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40894386 AAAAGCATAC
*
40894396 AAAATTTTAAAATTATATTA
1 AAAATTATAAAATTATATTA
40894416 AAAATTATAAAATTATAT
1 AAAATTATAAAATTATAT
40894434 AGAATTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTATAAAATTATATTA
Found at i:40894445 original size:18 final size:20
Alignment explanation
Indices: 40894404--40894445 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
40894394 ACAAAATTTT
*
40894404 AAAATTATATTAAAAATTAT
1 AAAATTATATTAAAAATTAC
*
40894424 AAAATTATA-T-AGAATTAC
1 AAAATTATATTAAAAATTAC
40894442 AAAA
1 AAAA
40894446 ATCTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 1 0.05
20 9 0.45
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATTATATTAAAAATTAC
Found at i:40894864 original size:18 final size:18
Alignment explanation
Indices: 40894825--40894864 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40894815 GATTATTATG
*
40894825 TTATAATTTTTATATCTC
1 TTATAATTTTTATATCTA
40894843 TTATAATTTTTATGAT-TA
1 TTATAATTTTTAT-ATCTA
40894861 TTAT
1 TTAT
40894865 GTTTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATAATTTTTATATCTA
Found at i:40894945 original size:19 final size:19
Alignment explanation
Indices: 40894921--40895004 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
40894911 ATATTTCTAT
*
40894921 ATTTTTTAA-TTTTTATAA
1 ATTTTTAAATTTTTTATAA
40894939 CATTTTTAAATTTTTTATAA
1 -ATTTTTAAATTTTTTATAA
** * *
40894959 ATTTAAAATATTTTTTTCTAT
1 ATTTTTAA-A-TTTTTTATAA
* *
40894980 ATTTTTAGATTTTCTAATAA
1 ATTTTTAAATTTT-TTATAA
40895000 ATTTT
1 ATTTT
40895005 CTTTTATAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 18 0.36
20 19 0.38
21 13 0.26
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTTTAAATTTTTTATAA
Found at i:40895042 original size:18 final size:17
Alignment explanation
Indices: 40895007--40895055 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
40894997 TAAATTTTCT
40895007 TTTATAA-A-TTTTATA
1 TTTATAATATTTTTATA
40895022 TTTCAT-ATATTTTTATAA
1 TTT-ATAATATTTTTAT-A
*
40895040 TTTTTAATATTTTTAT
1 TTTATAATATTTTTAT
40895056 TGATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 3 0.11
17 7 0.25
18 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATAATATTTTTATA
Found at i:40896293 original size:19 final size:20
Alignment explanation
Indices: 40896263--40896327 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
40896253 AAAATATAAA
*
40896263 ATTTAGAATTTTTATAAA-T
1 ATTTTGAATTTTTATAAATT
* *
40896282 ATTTTG-AGTTTTAGAAATT
1 ATTTTGAATTTTTATAAATT
40896301 ATTTTGAATTTTTGA-AAATT
1 ATTTTGAATTTTT-ATAAATT
40896321 ATTTTGA
1 ATTTTGA
40896328 TTCTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 9 0.23
19 12 0.31
20 17 0.44
21 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:40896319 original size:20 final size:20
Alignment explanation
Indices: 40896263--40896327 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
40896253 AAAATATAAA
*
40896263 ATTTAGAATTTTT-ATAAA-T
1 ATTTTGAATTTTTGA-AAATT
* *
40896282 ATTTTGAGTTTTAG-AAATT
1 ATTTTGAATTTTTGAAAATT
40896301 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
40896321 ATTTTGA
1 ATTTTGA
40896328 TTCTTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.08
19 23 0.61
20 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:40897434 original size:11 final size:11
Alignment explanation
Indices: 40897412--40897462 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
40897402 AACTAATCCT
40897412 CTCTCAAATTTC
1 CTCTC-AATTTC
40897424 CTCTCAATTTC
1 CTCTCAATTTC
*
40897435 CTCTTAATTTC
1 CTCTCAATTTC
*
40897446 CTCTCAAGTTC
1 CTCTCAATTTC
40897457 CT-TCAA
1 CTCTCAA
40897463 AAATTCTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 4 0.11
11 27 0.75
12 5 0.14
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:40897485 original size:11 final size:11
Alignment explanation
Indices: 40897466--40897507 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
40897456 CCTTCAAAAA
40897466 TTCTCTTAAGT
1 TTCTCTTAAGT
*
40897477 TTTTCTTAAGT
1 TTCTCTTAAGT
*
40897488 TCCTCTTAAGT
1 TTCTCTTAAGT
40897499 TTCTCTTAA
1 TTCTCTTAA
40897508 CTCTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (11 bp):
TTCTCTTAAGT
Found at i:40897538 original size:24 final size:24
Alignment explanation
Indices: 40897511--40897556 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40897501 CTCTTAACTC
*
40897511 TATTTTTTTAAATAATTTTAAAAA
1 TATTTTTTAAAATAATTTTAAAAA
**
40897535 TATTTTTTAAAATTTTTTTAAA
1 TATTTTTTAAAATAATTTTAAA
40897557 CCGTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTTTAAAATAATTTTAAAAA
Found at i:40897552 original size:12 final size:12
Alignment explanation
Indices: 40897511--40897556 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
40897501 CTCTTAACTC
*
40897511 TATTTTTTTAAA
1 TATTTTTTAAAA
* *
40897523 TAATTTTAAAAA
1 TATTTTTTAAAA
40897535 TATTTTTTAAAA
1 TATTTTTTAAAA
40897547 T-TTTTTTAAA
1 TATTTTTTAAA
40897557 CCGTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTTTAAAA
Found at i:40898671 original size:7 final size:7
Alignment explanation
Indices: 40898659--40898683 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40898649 AGTCGATTGA
40898659 TATTTAG
1 TATTTAG
40898666 TATTTAG
1 TATTTAG
40898673 TATTTAG
1 TATTTAG
40898680 TATT
1 TATT
40898684 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:40899659 original size:21 final size:21
Alignment explanation
Indices: 40899635--40899680 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
40899625 CGAATCGAAA
40899635 GAACCAGAATCCCCAGCGGAG
1 GAACCAGAATCCCCAGCGGAG
*
40899656 GAACCAGAATCCCTAGCGGAG
1 GAACCAGAATCCCCAGCGGAG
40899677 GAAC
1 GAAC
40899681 AACAACCGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.30, G:0.28, T:0.07
Consensus pattern (21 bp):
GAACCAGAATCCCCAGCGGAG
Found at i:40899916 original size:23 final size:23
Alignment explanation
Indices: 40899864--40900322 Score: 192
Period size: 29 Copynumber: 18.3 Consensus size: 23
40899854 TTTGATGTAA
* *
40899864 TAAAAACCCTAACTTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
***
40899887 CCTAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40899910 TAAAAACCTTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
40899939 TAAAAACCCTAACATTAACCTAATTTAA-
1 TAAAAA-CC---C--TAACCTAATTTAAT
* **
40899967 TACAAAACCCTACCCTAATTGGAT
1 TA-AAAACCCTAACCTAATTTAAT
40899991 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
40900020 TAAAAACCCTAACCCTAACATAATTTAAT
1 TAAAAACCCTAA--C---C-TAATTTAAT
40900049 TAAAAACCCTAAACC----TTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
40900070 TAAAAACCCTAAACCTTAACTT-A-
1 TAAAAACCCT-AACC-TAATTTAAT
40900093 -AAAAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
*
40900114 TACAAAACCCTTACCTAATTTTAAT
1 TA-AAAACCCTAACCTAA-TTTAAT
40900139 TAAAAACCCTAACCCTACCTTAATTTAAT
1 TAAAAACCCT-A----ACC-TAATTTAAT
40900168 TAAAAACCTTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
40900197 TAAAAATCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
*
40900226 TAAAAACCCTAAACC---TTAAAT
1 TAAAAACCCT-AACCTAATTTAAT
* *
40900247 TAGAAACCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
*
40900269 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
***
40900292 CCTAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40900315 TAAAAACC
1 TAAAAACC
40900323 ATAAACAAAG
Statistics
Matches: 345, Mismatches: 33, Indels: 116
0.70 0.07 0.23
Matches are distributed among these distances:
20 12 0.03
21 45 0.13
22 20 0.06
23 82 0.24
24 20 0.06
25 9 0.03
26 3 0.01
27 10 0.03
28 6 0.02
29 120 0.35
30 8 0.02
31 3 0.01
34 1 0.00
35 6 0.02
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:40899993 original size:81 final size:81
Alignment explanation
Indices: 40899890--40900237 Score: 313
Period size: 81 Copynumber: 4.4 Consensus size: 81
40899880 ATTTAACCCT
* * *
40899890 AAACCCTAACCTAATTTAATTAAAAACCTTAACCCTAACCTAATTTAATTAAAAACCCTAACATT
1 AAACCCTAACCTAATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACT
*
40899955 AACCTAATTTAA-TACA
66 AACATAATTTAATTA-A
* * *
40899971 AAACCCTACCCTAATTGGATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
1 AAACCCTAACCTAATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACT
40900036 AACATAATTTAATTAA
66 AACATAATTTAATTAA
* *
40900052 AAACCCTAAACC---TT-AACTTAAAAACCCTAAACCT----TAACTT-A--AAAAACCCT-A-A
1 AAACCCT-AACCTAATTGAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACA
40900104 C---C-TAATTTAA-TACA
64 CTAACATAATTTAATTA-A
* * * *
40900118 AAACCCTTACCTAATTTTAATTAAAAACCCTAACCCT-ACCTTAATTTAATTAAAAACCTTAACC
1 AAACCCTAACCTAA-TTGAATTAAAAACCCTAACCCTAACC-TAATTTAATTAAAAACCCTAACA
*
40900182 CTAACCTAATTTAATTAAAA
64 CTAACATAATTTAATT--AA
*
40900202 ATCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
1 A----AACCCTAACCTAATTGAATTAAAAACCCTAA
40900238 ACCTTAAATT
Statistics
Matches: 220, Mismatches: 18, Indels: 52
0.76 0.06 0.18
Matches are distributed among these distances:
65 5 0.02
66 16 0.07
67 1 0.00
69 18 0.08
70 3 0.01
71 1 0.00
72 9 0.04
73 5 0.02
74 2 0.01
75 5 0.02
76 8 0.04
77 1 0.00
78 2 0.01
79 18 0.08
81 79 0.36
82 13 0.06
83 1 0.00
84 2 0.01
85 1 0.00
87 18 0.08
88 12 0.05
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (81 bp):
AAACCCTAACCTAATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACT
AACATAATTTAATTAA
Found at i:40900106 original size:21 final size:21
Alignment explanation
Indices: 40900044--40900103 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
40900034 CTAACATAAT
40900044 TTAA-TTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
40900064 TTAACTTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
40900085 TTAACTTAAAAAACCCTAA
1 TTAACTT-AAAAACCCTAA
40900104 CCTAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.11
21 23 0.61
22 11 0.29
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:40900184 original size:177 final size:176
Alignment explanation
Indices: 40899920--40900322 Score: 576
Period size: 177 Copynumber: 2.3 Consensus size: 176
40899910 TAAAAACCTT
* * ** * * **
40899920 AACCCTAACCTAATTTAATTA-AAAACCCTAACATTAACCTAATTTAATA-CAAAACCCTACCCT
1 AACCCTAACCTAATTTAA-CACAAAACCCTAAC-CTAATTTAATTAAAAACCCTAACCCTACCCT
*
40899983 AATTGGATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAA
64 AATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAA
*
40900048 TTAAAAACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTAAAA
129 TTAAAAACCCTAAACCTTAAATTAAAAACCCTAAACCTTAACTTAAAA
* * *
40900096 AACCCTAACCTAATTTAATACAAAACCCTTACCTAATTTTAATTAAAAACCCTAACCCTACCTTA
1 AACCCTAACCTAATTTAACACAAAACCCTAACCTAA-TTTAATTAAAAACCCTAACCCTACCCTA
* * * *
40900161 ATTTAATTAAAAACCTTAACCCTAACCTAATTTAATTAAAAATCCTAACCCTAACCTAATTTAAT
65 ATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAAT
* *
40900226 TAAAAACCCTAAACCTTAAATTAGAAACCCTAAACCTTAACTTTAAA
130 TAAAAACCCTAAACCTTAAATTAAAAACCCTAAACCTTAACTTAAAA
* *
40900273 AACCCTAACCTAATTTAACCCTAAACCCTAACCTAATTTAATTAAAAACC
1 AACCCTAACCTAATTTAACACAAAACCCTAACCTAATTTAATTAAAAACC
40900323 ATAAACAAAG
Statistics
Matches: 203, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
175 5 0.02
176 50 0.25
177 148 0.73
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (176 bp):
AACCCTAACCTAATTTAACACAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAA
TTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATT
AAAAACCCTAAACCTTAAATTAAAAACCCTAAACCTTAACTTAAAA
Found at i:40900236 original size:29 final size:29
Alignment explanation
Indices: 40899884--40900237 Score: 312
Period size: 29 Copynumber: 13.3 Consensus size: 29
40899874 AACTTAATTT
40899884 AACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
40899914 AACCTTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
**
40899943 AACCCTAACATTAACCTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
**
40899972 AACCCT-A--C---CCTAATTGGATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
40899995 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
40900024 AACCCTAACCCTAACATAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
40900053 AACCCT-A----AACC----TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* *
40900074 AACCCTAAACCT----TAACTT-A--AAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
40900096 AACCCTAA------CCTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
*
40900119 AACCCTTA-CCTAA--T--TTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
40900143 AACCCTAACCCT-ACCTTAATTTAATTAAA
1 AACCCTAACCCTAACC-TAATTTAATTAAA
*
40900172 AACCTTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
40900201 AATCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
40900230 AACCCTAA
1 AACCCTAA
40900238 ACCTTAAATT
Statistics
Matches: 270, Mismatches: 18, Indels: 73
0.75 0.05 0.20
Matches are distributed among these distances:
20 9 0.03
21 12 0.04
22 13 0.05
23 25 0.09
24 21 0.08
25 6 0.02
26 4 0.01
27 1 0.00
28 4 0.01
29 167 0.62
30 8 0.03
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:40900282 original size:21 final size:21
Alignment explanation
Indices: 40900221--40900290 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
40900211 CTAACCTAAT
40900221 TTAA-TTAAAAACCCTAAACC
1 TTAATTTAAAAACCCTAAACC
* *
40900241 TTAAATTAGAAACCCTAAACC
1 TTAATTTAAAAACCCTAAACC
40900262 TTAACTTTAAAAACCCT-AACC
1 TTAA-TTTAAAAACCCTAAACC
40900283 -TAATTTAA
1 TTAATTTAA
40900291 CCCTAAACCC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.11
20 7 0.16
21 23 0.51
22 10 0.22
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.29
Consensus pattern (21 bp):
TTAATTTAAAAACCCTAAACC
Found at i:40903714 original size:126 final size:126
Alignment explanation
Indices: 40903483--40903833 Score: 551
Period size: 126 Copynumber: 2.8 Consensus size: 126
40903473 CCCAAACATG
*
40903483 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* **
40903548 TAGAAGCGATTTTATACTATTTGCTCAGAAACGT-CAAAAAAATAATTATTTCTTTTGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATAATTATTTCTTCCG-GAC
* * * * *
40903609 TTACTGTAGCAAAAGCGCGTCCTCGATGGCGCGATTTCACAATTTCTTCTCACATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
40903674 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATAATTATTTCTTCCGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATAATTATTTCTTCCGGAC
* * *
40903735 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGTGATTTCACAAATTCTTCCCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
40903800 TAGAAGTGATTTTATACTATTTGATTAGAAACGT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGT
40903834 CAACTCGAAA
Statistics
Matches: 204, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
126 184 0.90
127 20 0.10
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATAATTATTTCTTCCGGAC
Found at i:40904876 original size:22 final size:21
Alignment explanation
Indices: 40904838--40904880 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
40904828 TTTTATAAGA
*
40904838 AATTTATCTTTTAAATAGAAAT
1 AATTTATCTATTAAATA-AAAT
40904860 AATTTATACTATT-AATAAAAT
1 AATTTAT-CTATTAAATAAAAT
40904881 CTTTAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTATCTATTAAATAAAAT
Found at i:40905496 original size:18 final size:18
Alignment explanation
Indices: 40905473--40905508 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40905463 AGCAAAACTT
*
40905473 TATTTTGATTTTCTTATG
1 TATTTTAATTTTCTTATG
*
40905491 TATTTTAATTTTTTTATG
1 TATTTTAATTTTCTTATG
40905509 CACACTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTCTTATG
Found at i:40906465 original size:3 final size:3
Alignment explanation
Indices: 40906459--40906485 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40906449 AAAACAACTT
40906459 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
40906486 GGTCTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40929893 original size:29 final size:29
Alignment explanation
Indices: 40929851--40930178 Score: 347
Period size: 29 Copynumber: 11.3 Consensus size: 29
40929841 TGTGCTAAAC
* * *
40929851 GATGGTCATAACCATCCCTTTTCATATTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
40929880 GATGGTTGTCACCATCCCTTTTCATA-TT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
** * *
40929908 CGATGGTCGGAACCATCCCTTTTCATTAATC
1 -GATGGTCGTCACCATCCCTTTTCA-TAGTT
*
40929939 GATAGTCGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *
40929968 GATGGTCATCACCATCCCTTTTCATAGTC
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *** *
40929997 GATAGTCAAAACTATCCCTTTTCATA-TT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* * * *
40930025 CAATTGTCGTCACTATCCATTTTCATAGTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
*
40930055 GATGGTTGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* ** * *
40930084 GATAGTCGAAACTATCCCTTTTCATATTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
40930113 GATGGTTGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
40930142 GATGGTCGTTC-CCATCCCTTTTCATAGTT
1 GATGGTCG-TCACCATCCCTTTTCATAGTT
*
40930171 GATAGTCG
1 GATGGTCG
40930179 AATTTATCCC
Statistics
Matches: 248, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
28 3 0.01
29 217 0.88
30 27 0.11
31 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATAGTT
Found at i:40930072 original size:87 final size:87
Alignment explanation
Indices: 40929861--40930202 Score: 470
Period size: 87 Copynumber: 3.9 Consensus size: 87
40929851 GATGGTCATA
* * * * * *
40929861 ACCATCCCTTTTCATATTTGATGGTTGTCACCATCCCTTTTCATATTCGATGGTCGGAACCATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
*
40929926 CTTTTCATTAATCGATAGTCGTC
66 CTTTTCA-TATTCGATAGTCGTC
* *
40929949 ACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTCGATAGTCAAAACTATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
* *
40930014 CTTTTCATATTCAATTGTCGTC
66 CTTTTCATATTCGATAGTCGTC
* * * *
40930036 ACTATCCATTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGTCGAAACTATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
* * *
40930101 CTTTTCATATTTGATGGTTGTC
66 CTTTTCATATTCGATAGTCGTC
* **
40930123 ACCATCCCTTTTCATAGTTGATGGTCGTTC-CCATCCCTTTTCATAGTTGATAGTCGAATTTATC
1 ACCATCCCTTTTCATAGTTGATGGTCG-TCACCATCCCTTTTCATAGTCGATAGTCGAAACTATC
40930187 CCTTTTCATATTCGAT
65 CCTTTTCATATTCGAT
40930203 GCTTATCAAT
Statistics
Matches: 226, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
87 160 0.71
88 66 0.29
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (87 bp):
ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
CTTTTCATATTCGATAGTCGTC
Found at i:40938270 original size:38 final size:39
Alignment explanation
Indices: 40938228--40938305 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
40938218 CTTATCACAT
*
40938228 ATTAAAGATGTTCAAATTATGACATAGTTAAA-ACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAATACTCAA
* *
40938266 ATTAATGATGTTCAAATTATGGCATAATTAAATACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAATACTCAA
40938305 A
1 A
40938306 CTTTCATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (39 bp):
ATTAAAGATGTTCAAATTATGACATAATTAAATACTCAA
Found at i:40950691 original size:18 final size:18
Alignment explanation
Indices: 40950670--40950709 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40950660 ATATTTAAAT
40950670 TTTTAATAATTTTTTAGA
1 TTTTAATAATTTTTTAGA
* *
40950688 TTTTCATGATTTTTTAGA
1 TTTTAATAATTTTTTAGA
40950706 TTTT
1 TTTT
40950710 TATACTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTAATAATTTTTTAGA
Found at i:40950749 original size:20 final size:21
Alignment explanation
Indices: 40950717--40950764 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
40950707 TTTTATACTT
40950717 TAAAAAGTCTATATA-TATTTAA
1 TAAAAA-T-TATATATTATTTAA
*
40950739 TAAAAATTATATATTTTTTAA
1 TAAAAATTATATATTATTTAA
40950760 TAAAA
1 TAAAA
40950765 TAAAGACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAAAATTATATATTATTTAA
Found at i:40953942 original size:27 final size:28
Alignment explanation
Indices: 40953910--40953965 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
40953900 AAGACCCATT
40953910 TTTAAC-ATTATTTATAGAAATGGGCCA
1 TTTAACAATTATTTATAGAAATGGGCCA
*
40953937 TTTAACAAATTATTTATCGAAATGGGCCA
1 TTTAAC-AATTATTTATAGAAATGGGCCA
40953966 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.23
29 20 0.77
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (28 bp):
TTTAACAATTATTTATAGAAATGGGCCA
Found at i:40962307 original size:17 final size:17
Alignment explanation
Indices: 40962256--40962300 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
40962246 GCAATAATTG
40962256 ACGTTTTGAAAATGAATA
1 ACGTTTTGAAAA-GAATA
*
40962274 ACGTTTTGCAAGAGAATA
1 ACGTTTTG-AAAAGAATA
40962292 AC-TTTTGAA
1 ACGTTTTGAA
40962301 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 5 0.20
18 15 0.60
19 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
ACGTTTTGAAAAGAATA
Found at i:40974904 original size:4 final size:4
Alignment explanation
Indices: 40974895--40974924 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
40974885 TACAGTTGAG
40974895 ATTT ATTT ATTT ATTT ATTT ATTT AGTTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT A
40974925 CTTAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:40979902 original size:37 final size:37
Alignment explanation
Indices: 40979852--40979930 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40979842 TTATTACGAA
* * *
40979852 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
40979889 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
40979926 GTCTT
1 GTCTT
40979931 TAGAGCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:40980219 original size:49 final size:47
Alignment explanation
Indices: 40980048--40980387 Score: 477
Period size: 47 Copynumber: 7.2 Consensus size: 47
40980038 CCCTTCGGGA
* * * * * *
40980048 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40980095 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** * *
40980141 C-TATCACGCATATACACTTTCACATTCATCACATTGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40980187 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40980236 CTTATCGCACATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40980283 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40980332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40980379 CTTATCACA
1 CTTATCACA
40980388 ATTTAGAATT
Statistics
Matches: 262, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
45 40 0.15
46 2 0.01
47 134 0.51
49 86 0.33
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40980270 original size:96 final size:96
Alignment explanation
Indices: 40980048--40980387 Score: 499
Period size: 96 Copynumber: 3.6 Consensus size: 96
40980038 CCCTTCGGGA
** * * * * ** * *
40980048 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATAC
*
40980111 ACTTTCACATTCATCACATCGGCCATTAAG-
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
40980141 C-TATCACGCATATACACTTTCACATTCATCACATTGGCCATTAAGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATAC
*
40980205 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
40980236 CTTATCGCACATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATAC
40980301 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
40980332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACA
40980388 ATTTAGAATT
Statistics
Matches: 224, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
92 43 0.19
93 1 0.00
94 36 0.16
95 1 0.00
96 143 0.64
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40981837 original size:13 final size:13
Alignment explanation
Indices: 40981819--40981843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40981809 TACTAAATTT
40981819 TCATGGATTCAAG
1 TCATGGATTCAAG
40981832 TCATGGATTCAA
1 TCATGGATTCAA
40981844 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:40988729 original size:11 final size:10
Alignment explanation
Indices: 40988713--40988742 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
40988703 CATCATTACC
40988713 TTTTTTCTTCT
1 TTTTTTCTT-T
40988724 TTTTTTCTTT
1 TTTTTTCTTT
40988734 TTTTTTCTT
1 TTTTTTCTT
40988743 ATCTCAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:40989480 original size:5 final size:5
Alignment explanation
Indices: 40989470--40989495 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40989460 TTACTTCGAC
40989470 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
40989496 TTAAGTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:40997966 original size:16 final size:15
Alignment explanation
Indices: 40997943--40997984 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
40997933 ATAAAATGAG
40997943 TGACTAAAATGAAAT
1 TGACTAAAATGAAAT
* *
40997958 CTTACTAAAGT-AAAT
1 -TGACTAAAATGAAAT
40997973 TGACTAAAATGA
1 TGACTAAAATGA
40997985 GTCTACAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 8 0.38
15 5 0.24
16 8 0.38
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (15 bp):
TGACTAAAATGAAAT
Found at i:41002069 original size:24 final size:24
Alignment explanation
Indices: 41002054--41002105 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41002044 AATCAAAGTC
41002054 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
41002078 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
41002102 AAAT
1 AAAT
41002106 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:41006427 original size:24 final size:24
Alignment explanation
Indices: 41006400--41006449 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
41006390 TCAAAGTCAC
* *
41006400 ATATATTATGCTAATAAATGCTAA
1 ATATATTATACTAATAAATACTAA
*
41006424 ATATATTATACTCATAAATACTAA
1 ATATATTATACTAATAAATACTAA
41006448 AT
1 AT
41006450 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATATTATACTAATAAATACTAA
Found at i:41009212 original size:45 final size:45
Alignment explanation
Indices: 41009163--41009395 Score: 403
Period size: 45 Copynumber: 5.2 Consensus size: 45
41009153 TCGGCCATGG
* * * *
41009163 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
41009208 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
41009253 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
41009298 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
41009343 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
41009388 TGCTTCCT
1 TGCTTCCT
41009396 TAATTTCATG
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 181 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:41014757 original size:21 final size:20
Alignment explanation
Indices: 41014733--41014781 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
41014723 AAACTTAAAA
41014733 TGAATTTCAATCACTTTTTTT
1 TGAATTTCAAT-ACTTTTTTT
* * **
41014754 TGAATTCCGATTTTTTTTTT
1 TGAATTTCAATACTTTTTTT
41014774 TGAATTTC
1 TGAATTTC
41014782 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.59
Consensus pattern (20 bp):
TGAATTTCAATACTTTTTTT
Found at i:41015626 original size:45 final size:45
Alignment explanation
Indices: 41015575--41015807 Score: 403
Period size: 45 Copynumber: 5.2 Consensus size: 45
41015565 TCGACCATGG
* * * *
41015575 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
41015620 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
41015665 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
41015710 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
41015755 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
41015800 TGCTTCCT
1 TGCTTCCT
41015808 TAATTTCATG
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 181 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:41018127 original size:196 final size:196
Alignment explanation
Indices: 41017793--41018188 Score: 765
Period size: 196 Copynumber: 2.0 Consensus size: 196
41017783 TAAAGGCTTG
41017793 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
1 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
*
41017858 GTTCACCCAATATGATTATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
66 GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
41017923 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
131 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
41017988 A
196 A
*
41017989 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTTAATCTCTTTGGGTTATATTT
1 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
41018054 GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
66 GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
*
41018119 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACTCGTAGTCATGTTACTTTTCC
131 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
41018184 A
196 A
41018185 TCTA
1 TCTA
41018189 TCATGTAATT
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 197 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (196 bp):
TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
A
Found at i:41019880 original size:43 final size:43
Alignment explanation
Indices: 41019811--41019946 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
41019801 TTTTAAAAAT
* * *
41019811 AAACGCTGCTAAA-AGTCATGATCTTTAACGGCGCTT-TTCTCAC
1 AAACGCCGCTAAAGA-TCATGACCTTTAACGGCGCTTCTAC-CAC
* * *
41019854 AAATGCCGCTAAAGATCATGACCTTTAGCGGTGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTACCAC
* * * *
41019897 AAACGCTGCTAAAGAACATGACCTTTAACGACGCTTATACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTACCAC
41019940 AAACGCC
1 AAACGCC
41019947 ACTATAAAGA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
43 74 0.96
44 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTACCAC
Found at i:41021264 original size:33 final size:33
Alignment explanation
Indices: 41021227--41021382 Score: 126
Period size: 33 Copynumber: 4.6 Consensus size: 33
41021217 AATATGAAGG
41021227 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * * *
41021260 GGTTGCTAAGTGCTGATTCGACTGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTC-CCCG-A-C--T-CAT-T---GGT
*
41021303 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
41021330 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
41021363 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
41021383 ACCGTATCTT
Statistics
Matches: 97, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
27 18 0.19
28 5 0.05
31 2 0.02
32 2 0.02
33 40 0.41
34 2 0.02
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
40 1 0.01
41 1 0.01
43 20 0.21
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:41021306 original size:76 final size:73
Alignment explanation
Indices: 41021217--41021497 Score: 212
Period size: 76 Copynumber: 3.8 Consensus size: 73
41021207 GAGTACATTG
*
41021217 AATATGAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCGAC
1 AATATAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTC-AC
*
41021282 TGTATCTTT
65 CGTATCTTT
* *
41021291 AAATATAAAGGGGGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-GGTTGCTAAGTGCTGATTCC
1 -AATATAAA-GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCA
41021350 CCG-A---TT
64 CCGTATCTTT
* * *
41021356 CAT-T---GGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGGTTGCTAAGT
1 AATATAAAGG-GGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CAT-T---GGTGGTTGCTAAGT
*
41021417 GCTGATTCCACCATATCTTT
55 GCTGATT-CACCGTATCTTT
* * *
41021437 GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGA
1 -AATAT-AAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGA
41021498 ATCCACCGAT
Statistics
Matches: 163, Mismatches: 14, Indels: 57
0.70 0.06 0.24
Matches are distributed among these distances:
59 2 0.01
60 18 0.11
61 1 0.01
62 2 0.01
63 1 0.01
64 2 0.01
65 2 0.01
66 1 0.01
68 1 0.01
69 2 0.01
70 20 0.12
71 2 0.01
72 2 0.01
73 1 0.01
75 12 0.07
76 56 0.34
77 3 0.02
78 1 0.01
79 1 0.01
80 1 0.01
81 3 0.02
82 2 0.01
83 1 0.01
84 1 0.01
85 3 0.02
86 20 0.12
87 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (73 bp):
AATATAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCACC
GTATCTTT
Found at i:41021405 original size:103 final size:103
Alignment explanation
Indices: 41021223--41021425 Score: 361
Period size: 103 Copynumber: 2.0 Consensus size: 103
41021213 ATTGAATATG
* *
41021223 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCGACTGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
41021288 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
41021326 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
41021391 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCC
41021426 ACCATATCTT
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:41021424 original size:43 final size:43
Alignment explanation
Indices: 41021363--41021468 Score: 185
Period size: 43 Copynumber: 2.5 Consensus size: 43
41021353 ATTCATTGGT
* *
41021363 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAAGG
*
41021406 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAAGG
41021449 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
41021469 CCGAATCACT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAAGG
Found at i:41025393 original size:22 final size:22
Alignment explanation
Indices: 41025337--41025402 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
41025327 GTATGTTTGT
* *
41025337 AAAGTTGGGGGTTTCAAGGGGGG
1 AAAGTTGGGGATTT-TAGGGGGG
* *
41025360 AAA-TTAGAGATTTTAGGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
*
41025381 AAAGTTGGGGA-TTTCGGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
41025402 A
1 A
41025403 GGGGATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 20 0.57
22 12 0.34
23 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.47, T:0.24
Consensus pattern (22 bp):
AAAGTTGGGGATTTTAGGGGGG
Found at i:41025592 original size:123 final size:124
Alignment explanation
Indices: 41025448--41025684 Score: 377
Period size: 123 Copynumber: 1.9 Consensus size: 124
41025438 TAAAATTATT
* * ** * *
41025448 TTTTGCGGCATTTTTCATAAAAATGTGACAAAAAATTATTTCATTTGGAATAAAACGATATTGTT
1 TTTTGCGGCATTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
* *
41025513 TTGCTATATAAAATGGCGCTA-TTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
66 TTGCTATATAAAATGACACTATTTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
*
41025571 TTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
1 TTTTGCGGCATTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
*
41025636 TTGCTATATAAAATGACACTATTTTTTTTAAAGTAAAATTATTTTTTGT
66 TTGCTATATAAAATGACACTATTTTTTTAAAAGTAAAATTATTTTTTGT
41025685 GGCGTTTTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
123 77 0.75
124 26 0.25
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (124 bp):
TTTTGCGGCATTTTCCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
TTGCTATATAAAATGACACTATTTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
Found at i:41026640 original size:7 final size:7
Alignment explanation
Indices: 41026630--41026668 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
41026620 CCCTAAATTA
*
41026630 CTAACTC
1 CTAACCC
41026637 CTAACCC
1 CTAACCC
*
41026644 CAAACCC
1 CTAACCC
*
41026651 TTAACCC
1 CTAACCC
41026658 CTAACCC
1 CTAACCC
41026665 CTAA
1 CTAA
41026669 ACCTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:41026655 original size:21 final size:22
Alignment explanation
Indices: 41026631--41026671 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41026621 CCTAAATTAC
*
41026631 TAACTCCTAACCCC-AAACCCT
1 TAACCCCTAACCCCTAAACCCT
41026652 TAACCCCTAACCCCTAAACC
1 TAACCCCTAACCCCTAAACC
41026672 TTATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (22 bp):
TAACCCCTAACCCCTAAACCCT
Found at i:41026816 original size:96 final size:96
Alignment explanation
Indices: 41026646--41026826 Score: 281
Period size: 96 Copynumber: 1.9 Consensus size: 96
41026636 CCTAACCCCA
* * *
41026646 AACCCTTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
1 AACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTAA
*
41026711 ACCCCAAACCCTAACCTGACCTCGAATCCCT
66 ACCCCAAACCCCAACCTGACCTCGAATCCCT
* *
41026742 AACCCCTAACCTCTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAACTAATCTAA
1 AACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTAA
** *
41026807 ACCTTAAACCCCAACTTGAC
66 ACCCCAAACCCCAACCTGAC
41026827 ACCAAATCCA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.42, C:0.30, G:0.02, T:0.26
Consensus pattern (96 bp):
AACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTAA
ACCCCAAACCCCAACCTGACCTCGAATCCCT
Found at i:41026835 original size:96 final size:96
Alignment explanation
Indices: 41026646--41026855 Score: 278
Period size: 96 Copynumber: 2.2 Consensus size: 96
41026636 CCTAACCCCA
* * *
41026646 AACCCTTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
1 AACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTAA
* * *
41026711 ACCCCAAACCCTAACCTGACCTCGAATCCCT
66 ACCCCAAACCCCAACCTGACCTCAAATCCAT
* *
41026742 AACCCCTAACCTCTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAACTAATCTAA
1 AACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTAA
** *
41026807 ACCTTAAACCCCAACTTGACAC-CAAATCCAT
66 ACCCCAAACCCCAACCTGAC-CTCAAATCCAT
* *
41026838 AAACCCTAAATCCCTAAC
1 AACCCCT-AACCCCTAAC
41026856 TCTTAACCTC
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 89 0.91
97 9 0.09
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.25
Consensus pattern (96 bp):
AACCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAACTAATCTAA
ACCCCAAACCCCAACCTGACCTCAAATCCAT
Found at i:41026933 original size:14 final size:15
Alignment explanation
Indices: 41026916--41026949 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41026906 CTTAAATCAG
41026916 AATCTCTAA-TCCAT
1 AATCTCTAATTCCAT
*
41026930 AATCCCTAATTCCAT
1 AATCTCTAATTCCAT
41026945 AATCT
1 AATCT
41026950 ATAAACCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:41035795 original size:41 final size:41
Alignment explanation
Indices: 41035735--41035933 Score: 193
Period size: 41 Copynumber: 4.9 Consensus size: 41
41035725 AAATGTTTTT
* *
41035735 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCTCGAACATTA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
41035776 GCGGCGCTTATTGATAAACGCCGTTAAAGCCCCTAGCATTA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
41035817 GAGGCGCTTCTTGAAAAATGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * * *** * *
41035858 GCTGTGCTT-TATCAAAAACGCCACTAAAAATCTGAGCACTA
1 GCGGCGCTTCT-TGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
41035899 GTGGCGCTTTTTTAAAAACACCGCTAAAGCCCCGA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGA
41035934 AAGGTAGAAA
Statistics
Matches: 123, Mismatches: 33, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
40 1 0.01
41 121 0.98
42 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:41036016 original size:41 final size:41
Alignment explanation
Indices: 41035970--41036078 Score: 94
Period size: 40 Copynumber: 2.7 Consensus size: 41
41035960 CAGGTTTTTT
41035970 GCGGCGTTTTTTGGAAAAACGCCGCTAATGCTCGATCTTTA
1 GCGGCGTTTTTTGGAAAAACGCCGCTAATGCTCGATCTTTA
* ** * ** * * *
41036011 GCGGCG-ATTTACGTAAGGCGCTGGTAATGCTCGATTTTTA
1 GCGGCGTTTTTTGGAAAAACGCCGCTAATGCTCGATCTTTA
* ***
41036051 GCCGCGTTTTTTGTCCAAACGCCGCTAA
1 GCGGCGTTTTTTGGAAAAACGCCGCTAA
41036079 AAATGCCGCT
Statistics
Matches: 47, Mismatches: 20, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
40 30 0.64
41 17 0.36
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (41 bp):
GCGGCGTTTTTTGGAAAAACGCCGCTAATGCTCGATCTTTA
Found at i:41045213 original size:804 final size:803
Alignment explanation
Indices: 41043659--41045270 Score: 2587
Period size: 804 Copynumber: 2.0 Consensus size: 803
41043649 AGCCAACCAG
* * *
41043659 TCCATAGTCCAAAAGATACATCAACAACCCCAAATAAGTAATAAATTTTAGGCATTAATGGAAAA
1 TCCATAGTCCAAAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAATGAAAAA
*
41043724 CAGTCTAAAATTTACGTGTGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
66 CAGTCTAAAATTTACGTATGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
* * *
41043789 TTACCTGTACAGATAAAACAGAGGAAGGGTGAGTTTTCGCAAACTCAGTGTGTAATCCTCACAGA
131 TTACCTGTACAGATAAAACAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
* * ** *
41043854 AAACATGCATACAGATAATCAACAGAATTCAGTTAAATACAGTCTGGGGCCCGTGGCCATCACAG
196 AAACATGCATACAGATAATCAAAAAAATTCAGTTAAATACAGTCTGGGGCCCAAGCCCATCACAG
* *
41043919 AATTGTTTGGGCCTTAGCCCATTCAGATAAAGTCTCATAAATACATTAGGGCCTTGGCCCATATC
261 AATTGTTTGGGACTTAGCCCATTCAGATAAAGTCTCAAAAATACATTAGGGCCTTGGCCCATATC
* **
41043984 AGATACAGAATGCAGATACAGTAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTTGGTC
326 AGATACAGAATGCAGATACAATAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCGTC
* *
41044049 CAACCCTACACACTATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGTTGTACCAAA
391 CAACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGCTGTACCAAA
* * * *
41044114 ATGTGGCACATAATTAGAAGGTTGCAGCTGGGCTGCCAGATAATAGGCTTAATAGCCTTTCAGGC
456 ATGTGGCACATAATCAGAAGGTTGCAGCTGAGCTGCCAGATAACAGGCTTAATAGCCTTTCAGAC
* *
41044179 ACTTCCTCTAAATATCATCAACCCACCCCGATGCAATGCAACATACAAAATATGTCATGCCATTA
521 ACTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCATTA
* *
41044244 TGAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCGGTATAGAAATCCGACAGACAG
586 TGAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCAGTATAGAAATCAGACAGACAG
* *
41044309 ATCAAACATATAGGAGTCTAAGTAAAACTTATCGGCCCTACAGTAGGTCCACAGTCGACTTGGGC
651 ATCAAACATATAGGAGTCTAAGTAAAACTTACCGACCCTACAGTAGGTCCACAGTCGACTTGGGC
* *
41044374 GACCTGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCTCACACGCCCATATTGCCCACTCGGC
716 GACCCGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCTCACACGCCCATATGGCCCACTCGGC
* *
41044439 CCAAATTGACCTTGGCCACGTGA
781 CCAAATTGACCGTGGCCACATGA
* *
41044462 TCCATAGTCTAGAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAATGAAAAA
1 TCCATAGTCCAAAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAATGAAAAA
* * * * * *
41044527 TAGTCTAAAATTTACGTATGGCCACCATCGAGTCCTTCACTGCATCGACCCGTCAAGTCTGGGGT
66 CAGTCTAAAATTTACGTATGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
* *
41044592 TTACCTGTACAGATTAAGCAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
131 TTACCTGTACAGATAAAACAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
* *
41044657 AAACATGCATACAGATAATCAAAAAAATTTAGTTAGATACAGTCTGGGGCCCAAGCCCATCACA-
196 AAACATGCATACAGATAATCAAAAAAATTCAGTTAAATACAGTCTGGGGCCCAAGCCCATCACAG
* * * *
41044721 AATTTAGTTTGGGATTTAGCCTATTCAGATACAGTCTTAAAAATACATTAGGGCCTTGGCCCATA
261 AA-TT-GTTTGGGACTTAGCCCATTCAGATAAAGTCTCAAAAATACATTAGGGCCTTGGCCCATA
* *
41044786 TTAGATACAGAATGCAGATACAATAAATCAGAATCCTACCTACCAGCCTCTACACACCATCTCCG
324 TCAGATACAGAATGCAGATACAATAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCG
* * * *
41044851 TCTAATCCTACACACCATGTGGGTATTAAATCAACTCACCCATCCCTACACACCATGCTGTACCA
389 TCCAACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGCTGTACCA
*
41044916 AAATGTGGCACATAATCAGAAGGTTGCAGTTGAGCTGCCAGATAACAGGCTTAATAGCCTTTCAG
454 AAATGTGGCACATAATCAGAAGGTTGCAGCTGAGCTGCCAGATAACAGGCTTAATAGCCTTTCAG
41044981 ACACTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCAT
519 ACACTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCAT
* * * *
41045046 TATGCAATTAATATTACATACATTCAGATATCATAAGTCATGCTTAGTATAGAAATCAGATAGAC
584 TATGAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCAGTATAGAAATCAGACAGAC
* * * *
41045111 AGATCACACATATAGGGGTCTAAGTAAAGCTTACCGACCCTACAGTAGGTTCACAGTCGACTTGG
649 AGATCAAACATATAGGAGTCTAAGTAAAACTTACCGACCCTACAGTAGGTCCACAGTCGACTTGG
* * *
41045176 GTGACCCGTGCAACCTTACAGAACTTTTCAGAAAAATGGGCTCACACGCCCATGTGGCCCACTCG
714 GCGACCCGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCTCACACGCCCATATGGCCCACTCG
*
41045241 GCCCAAATTGGCCGTGGCCACATGA
779 GCCCAAATTGACCGTGGCCACATGA
41045266 TCCAT
1 TCCAT
41045271 TTTTAATGTA
Statistics
Matches: 739, Mismatches: 68, Indels: 3
0.91 0.08 0.00
Matches are distributed among these distances:
802 2 0.00
803 237 0.32
804 500 0.68
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (803 bp):
TCCATAGTCCAAAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAATGAAAAA
CAGTCTAAAATTTACGTATGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
TTACCTGTACAGATAAAACAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
AAACATGCATACAGATAATCAAAAAAATTCAGTTAAATACAGTCTGGGGCCCAAGCCCATCACAG
AATTGTTTGGGACTTAGCCCATTCAGATAAAGTCTCAAAAATACATTAGGGCCTTGGCCCATATC
AGATACAGAATGCAGATACAATAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCGTC
CAACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGCTGTACCAAA
ATGTGGCACATAATCAGAAGGTTGCAGCTGAGCTGCCAGATAACAGGCTTAATAGCCTTTCAGAC
ACTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCATTA
TGAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCAGTATAGAAATCAGACAGACAG
ATCAAACATATAGGAGTCTAAGTAAAACTTACCGACCCTACAGTAGGTCCACAGTCGACTTGGGC
GACCCGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCTCACACGCCCATATGGCCCACTCGGC
CCAAATTGACCGTGGCCACATGA
Found at i:41049363 original size:27 final size:27
Alignment explanation
Indices: 41049325--41049379 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
41049315 ATTTGAAATG
41049325 TCAGTGTCACACGGGTAATACACTCAA
1 TCAGTGTCACACGGGTAATACACTCAA
41049352 TCAGTGTCACACGGGTAATACACTCAA
1 TCAGTGTCACACGGGTAATACACTCAA
41049379 T
1 T
41049380 GTGTACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (27 bp):
TCAGTGTCACACGGGTAATACACTCAA
Found at i:41049746 original size:26 final size:26
Alignment explanation
Indices: 41049711--41049767 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
41049701 TAAAAGCCAA
* * *
41049711 AATCAGGAAGTTCACAAAGAACTTTT
1 AATCAAGAAGCTCACAAAGAACCTTT
* *
41049737 AATCAAGAAGCTCACGAAGAGCCTTT
1 AATCAAGAAGCTCACAAAGAACCTTT
41049763 AATCA
1 AATCA
41049768 GGAGCTCCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (26 bp):
AATCAAGAAGCTCACAAAGAACCTTT
Found at i:41055960 original size:24 final size:25
Alignment explanation
Indices: 41055907--41055957 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
41055897 ATTGTAAATC
*
41055907 AATAAATATATGTACAAAAATTTAA
1 AATAAATATATATACAAAAATTTAA
41055932 AATAAATA-ATATACAAGAAATTTAA
1 AATAAATATATATACAA-AAATTTAA
41055957 A
1 A
41055958 TAAGCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
AATAAATATATATACAAAAATTTAA
Found at i:41060187 original size:10 final size:10
Alignment explanation
Indices: 41060174--41060331 Score: 64
Period size: 9 Copynumber: 15.9 Consensus size: 10
41060164 ATTTTTTTAA
*
41060174 ATTTTAAAAT
1 ATTTTTAAAT
*
41060184 ATTTTTACAT
1 ATTTTTAAAT
*
41060194 ACTTTTTTAAT
1 A-TTTTTAAAT
*
41060205 -TTTTTTAA-
1 ATTTTTAAAT
41060213 ATTTTTAAAT
1 ATTTTTAAAT
41060223 ATTTTTAAAAT
1 ATTTTT-AAAT
*
41060234 ACTTTTTTTAAT
1 A--TTTTTAAAT
*
41060246 -TTTTT-TA-
1 ATTTTTAAAT
*
41060253 ATTTTAAAAT
1 ATTTTTAAAT
*
41060263 AATTTTTTTAAT
1 -A-TTTTTAAAT
**
41060275 -TTTTTTTA-
1 ATTTTTAAAT
*
41060283 ATTTTAAAAT
1 ATTTTTAAAT
41060293 ATTTTTAAAAT
1 ATTTTT-AAAT
*
41060304 ACTTTTT-TA-
1 A-TTTTTAAAT
*
41060313 ATTTTTAAAA
1 ATTTTTAAAT
41060323 ATTTTTAAA
1 ATTTTTAAA
41060332 ATAAAAATGG
Statistics
Matches: 113, Mismatches: 18, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
8 10 0.09
9 35 0.31
10 30 0.27
11 18 0.16
12 15 0.13
13 5 0.04
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:41060220 original size:40 final size:40
Alignment explanation
Indices: 41060164--41060334 Score: 195
Period size: 39 Copynumber: 4.5 Consensus size: 40
41060154 AAATATATTT
*
41060164 ATTTTTTTAAATTTTAAAATATTTTT-ACATACTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
*
41060203 ATTTTTTTAAATTTTTAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTA
41060244 ATTTTTTT-AATTTT-AAA-A----T--AAT--TTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
*
41060273 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
**
41060313 ATTTTTAAAAATTTTTAAAATA
1 ATTTTTTTAAA-TTTTAAAATA
41060335 AAAATGGGCT
Statistics
Matches: 113, Mismatches: 5, Indels: 26
0.78 0.03 0.18
Matches are distributed among these distances:
29 15 0.13
30 6 0.05
31 3 0.03
32 4 0.04
34 1 0.01
36 1 0.01
38 4 0.04
39 28 0.25
40 26 0.23
41 25 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:41060257 original size:8 final size:9
Alignment explanation
Indices: 41060164--41060287 Score: 68
Period size: 9 Copynumber: 12.6 Consensus size: 9
41060154 AAATATATTT
41060164 ATTTTTTTA
1 ATTTTTTTA
* **
41060173 AATTTTAAA
1 ATTTTTTTA
*
41060182 ATATTTTTA
1 ATTTTTTTA
41060191 CATACTTTTTTA
1 -AT--TTTTTTA
41060203 ATTTTTTTA
1 ATTTTTTTA
* *
41060212 AATTTTTAA
1 ATTTTTTTA
41060221 ATATTTTTAAAATA
1 AT-TTTTT----TA
*
41060235 CTTTTTTTA
1 ATTTTTTTA
41060244 ATTTTTTTA
1 ATTTTTTTA
**
41060253 ATTTTAAAATA
1 ATTTT--TTTA
41060264 ATTTTTTTA
1 ATTTTTTTA
41060273 ATTTTTTTTA
1 A-TTTTTTTA
41060283 ATTTT
1 ATTTT
41060288 AAAATATTTT
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
9 48 0.56
10 16 0.19
11 9 0.10
12 6 0.07
13 5 0.06
14 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:41060258 original size:29 final size:28
Alignment explanation
Indices: 41060225--41060328 Score: 129
Period size: 30 Copynumber: 3.5 Consensus size: 28
41060215 TTTTAAATAT
41060225 TTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTAAAATA-TTTTTTTAATTTTTTTAA
41060254 TTTTAAAATAATTTTTTTAATTTTTTTTAA
1 TTTTAAAAT-ATTTTTTTAA-TTTTTTTAA
**
41060284 TTTTAAAATATTTTTAAAATACTTTTTTAA
1 TTTTAAAATATTTTTTTAAT--TTTTTTAA
41060314 TTTTTAAAA-ATTTTT
1 -TTTTAAAATATTTTT
41060329 AAAATAAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
28 1 0.01
29 26 0.38
30 33 0.49
31 8 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTAAAATATTTTTTTAATTTTTTTAA
Found at i:41060298 original size:11 final size:11
Alignment explanation
Indices: 41060284--41060334 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
41060274 TTTTTTTTAA
41060284 TTTTAAAATAT
1 TTTTAAAATAT
41060295 TTTTAAAATACT
1 TTTTAAAATA-T
*
41060307 TTTT--TA-AT
1 TTTTAAAATAT
41060315 TTTTAAAA-AT
1 TTTTAAAATAT
41060325 TTTTAAAATA
1 TTTTAAAATA
41060335 AAAATGGGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 5 0.15
9 1 0.03
10 12 0.35
11 11 0.32
12 5 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41060326 original size:70 final size:71
Alignment explanation
Indices: 41060165--41060335 Score: 231
Period size: 70 Copynumber: 2.4 Consensus size: 71
41060155 AATATATTTA
* * * *
41060165 TTTTTTTAAATTTTAAAATATTTTTACAT-ACTTTTTTAATTTTTTTAAATTTTTAAATATTTTT
1 TTTTTTTAATTTTTAAAA-ATTTTAAAATAACTTTTTTAATTTTTTTAAATTTTAAAATATTTTT
41060229 AAAATAC
65 AAAATAC
** * *
41060236 TTTTTTTAATTTTT-TTAATTTTAAAATAATTTTTTTAATTTTTTTTAATTTTAAAATATTTTTA
1 TTTTTTTAATTTTTAAAAATTTTAAAATAACTTTTTTAATTTTTTTAAATTTTAAAATATTTTTA
41060300 AAATAC
66 AAATAC
41060306 -TTTTTTAATTTTTAAAAATTTTTAAAATAA
1 TTTTTTTAATTTTTAAAAA-TTTTAAAATAA
41060336 AAATGGGCTG
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 21 0.24
70 42 0.48
71 24 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (71 bp):
TTTTTTTAATTTTTAAAAATTTTAAAATAACTTTTTTAATTTTTTTAAATTTTAAAATATTTTTA
AAATAC
Found at i:41060329 original size:41 final size:41
Alignment explanation
Indices: 41060254--41060334 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
41060244 ATTTTTTTAA
* ***
41060254 TTTTAAAATAATTTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATAACTTTTTTAATTTTTAAAAATTTTAAAATAT
41060295 TTTTAAAAT-ACTTTTTTAATTTTTAAAAATTTTTAAAATA
1 TTTTAAAATAACTTTTTTAATTTTTAAAAA-TTTTAAAATA
41060335 AAAATGGGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.46
41 19 0.54
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (41 bp):
TTTTAAAATAACTTTTTTAATTTTTAAAAATTTTAAAATAT
Found at i:41060606 original size:20 final size:19
Alignment explanation
Indices: 41060583--41060643 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
41060573 TTTCTAGAAG
41060583 TTTAACTATTTTTTTATAAT
1 TTTAACTA-TTTTTTATAAT
*
41060603 TTTAA--ATTTTTTAGAA-
1 TTTAACTATTTTTTATAAT
* *
41060619 TTTAACTAATCTTTTATATT
1 TTTAACT-ATTTTTTATAAT
41060639 TTTAA
1 TTTAA
41060644 TTTTTCTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.15
17 9 0.27
18 1 0.03
19 8 0.24
20 10 0.30
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAACTATTTTTTATAAT
Done.