Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 102 of 444
Found at i:25095416 original size:4 final size:4
Alignment explanation
Indices: 25095407--25095438 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
25095397 TTAGAAGGAG
25095407 ATTA ATTA ATTA ATTA ATTA ATTAA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATT-A ATTA ATT
25095439 TCAATGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:25099198 original size:12 final size:12
Alignment explanation
Indices: 25099181--25099205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25099171 AACACCATTA
25099181 AAGCAATTTTCC
1 AAGCAATTTTCC
25099193 AAGCAATTTTCC
1 AAGCAATTTTCC
25099205 A
1 A
25099206 CCAAGATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (12 bp):
AAGCAATTTTCC
Found at i:25102671 original size:21 final size:19
Alignment explanation
Indices: 25102623--25102671 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
25102613 TACAAATTGT
25102623 TAAA-TAAAACCAGAATTA
1 TAAATTAAAACCAGAATTA
* *
25102641 TAAATAAAAACCATAGATTA
1 TAAATTAAAACCAGA-ATTA
25102661 CTAAATTAAAA
1 -TAAATTAAAA
25102672 TAGTTCTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 4 0.16
21 9 0.36
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.24
Consensus pattern (19 bp):
TAAATTAAAACCAGAATTA
Found at i:25105487 original size:22 final size:22
Alignment explanation
Indices: 25105458--25105527 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
25105448 TATTGAAGCT
*
25105458 TATCATATCTCATATCAGAGCA
1 TATCATATTTCATATCAGAGCA
* ** * *
25105480 TATTATATTTCGCATCAGAACG
1 TATCATATTTCATATCAGAGCA
*
25105502 TATCATATTTCATATCATAGCA
1 TATCATATTTCATATCAGAGCA
25105524 TATC
1 TATC
25105528 TTACCCCTAT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (22 bp):
TATCATATTTCATATCAGAGCA
Found at i:25120893 original size:46 final size:46
Alignment explanation
Indices: 25120837--25121004 Score: 159
Period size: 46 Copynumber: 3.6 Consensus size: 46
25120827 TCTCGTAGCT
25120837 GATGCATGTCCTAGACATGTCTTACACTGACTTATGTCTCAAGGCC
1 GATGCATGTCCTAGACATGTCTTACACTGACTTATGTCTCAAGGCC
* * * *
25120883 GATGCATGTCCCAGACATGTCTTACACTAGCAC-T-CGTCTCAATGCT
1 GATGCATGTCCTAGACATGTCTTACACT-G-ACTTATGTCTCAAGGCC
* * *
25120929 GAAGCCATGTCAC-AGACATGGTCTTACACTGGCTCTCATGATGT---GGCC
1 GATG-CATGTC-CTAGACAT-GTCTTACACTGACT-T-ATG-TCTCAAGGCC
25120977 GATGCATGTCCTAGACATGTCTTACACT
1 GATGCATGTCCTAGACATGTCTTACACT
25121005 AGCTCACAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
46 51 0.51
47 27 0.27
48 19 0.19
50 1 0.01
51 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCTAGACATGTCTTACACTGACTTATGTCTCAAGGCC
Found at i:25127022 original size:22 final size:22
Alignment explanation
Indices: 25126997--25127069 Score: 96
Period size: 22 Copynumber: 3.3 Consensus size: 22
25126987 TATTGAACGT
*
25126997 TATCGTATCTCATATCA-AAGCA
1 TATCATATCTCATATCAGAA-CA
25127019 TATCATA-CTTCATATCAGAACA
1 TATCATATC-TCATATCAGAACA
*
25127041 TATCATATTTCATATCAGAACA
1 TATCATATCTCATATCAGAACA
25127063 TATCATA
1 TATCATA
25127070 GCATATCCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.02
22 43 0.93
23 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (22 bp):
TATCATATCTCATATCAGAACA
Found at i:25138528 original size:23 final size:22
Alignment explanation
Indices: 25138484--25138554 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
25138474 CGATTACACT
* * *
25138484 AAAACACAAAATGGCAGCAAAG
1 AAAAAACAAAATGGAAGAAAAG
*
25138506 CAAAAAGCAAAATGGAAGAAAAG
1 -AAAAAACAAAATGGAAGAAAAG
*
25138529 AATAAAACAACA-GGAAGAAAAG
1 AA-AAAACAAAATGGAAGAAAAG
25138551 AAAA
1 AAAA
25138555 GAAAAGAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.05
22 14 0.34
23 25 0.61
ACGTcount: A:0.66, C:0.11, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAAACAAAATGGAAGAAAAG
Found at i:25141000 original size:20 final size:20
Alignment explanation
Indices: 25140977--25141018 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25140967 ATAAATATTT
*
25140977 AAAATTAGGAACAATAAATA
1 AAAATTAGAAACAATAAATA
**
25140997 AAAATTTTAAACAATAAATA
1 AAAATTAGAAACAATAAATA
25141017 AA
1 AA
25141019 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAATTAGAAACAATAAATA
Found at i:25148084 original size:25 final size:25
Alignment explanation
Indices: 25148056--25148106 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
25148046 AAAAATAATG
25148056 ATTTGGTCACCTTTATTTTAAATTA
1 ATTTGGTCACCTTTATTTTAAATTA
25148081 ATTTGGTCACCTTTATTTTAAATTA
1 ATTTGGTCACCTTTATTTTAAATTA
25148106 A
1 A
25148107 CTTCATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (25 bp):
ATTTGGTCACCTTTATTTTAAATTA
Found at i:25150933 original size:28 final size:28
Alignment explanation
Indices: 25150872--25150970 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
25150862 TCACAAATTG
** * *
25150872 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
25150901 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* * *
25150929 GCACTAAGTGTGCGAGTTCGACTATTTAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
25150958 GCACTAAGTGTGC
1 GCACTAAGTGTGC
25150971 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
28 30 0.50
29 30 0.50
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:25150969 original size:29 final size:28
Alignment explanation
Indices: 25150872--25150971 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 28
25150862 TCACAAATTG
* *
25150872 GCACTAAGTGTGCGGGTTC-AAATTATACA
1 GCACTAAGTGTGCGAGTTCGATATT-TA-A
* * *
25150901 GCACTAAGTGTGCAAGTTTGAT-TATATA
1 GCACTAAGTGTGCGAGTTCGATATTTA-A
25150929 GCACTAAGTGTGCGAGTTCGACTATTTAA
1 GCACTAAGTGTGCGAGTTCGA-TATTTAA
25150958 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
25150972 GGCTTATTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
28 22 0.37
29 33 0.56
30 4 0.07
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTCGATATTTAA
Found at i:25156953 original size:48 final size:48
Alignment explanation
Indices: 25156882--25157223 Score: 540
Period size: 48 Copynumber: 7.0 Consensus size: 48
25156872 CAAGATAAAT
* * *
25156882 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGCATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
25156930 ATATGTGTATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
25156978 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
25157026 ATATATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ----ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
25157078 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
25157126 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
25157174 ATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
25157222 AT
1 AT
25157224 GTGTGTATAT
Statistics
Matches: 274, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
48 229 0.84
52 45 0.16
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:25157051 original size:148 final size:145
Alignment explanation
Indices: 25156880--25157231 Score: 580
Period size: 148 Copynumber: 2.4 Consensus size: 145
25156870 TACAAGATAA
* *
25156880 ATATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGCATGAGATATGTGTATGTGGT
1 ATATATATAT-TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTGTATGTGGT
25156945 AAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT
65 AAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT
25157010 ATGAAATATGTATGAG
130 ATGAAATATGTATGAG
* *
25157026 ATATATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTG
1 --ATATATATAT-TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTGTATGTG
25157091 GTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
63 GTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
25157156 GTGTGAAATATGTATGAG
128 ATATGAAATATGTATGAG
* * *
25157174 ATATGTATATT-TGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAGATGTGTGTAT
1 ATATATATATTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTGTAT
25157232 ATTGTGGCCG
Statistics
Matches: 192, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
144 43 0.22
145 1 0.01
146 9 0.05
148 139 0.72
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (145 bp):
ATATATATATTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTGTATGTGGTA
AAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATA
TGAAATATGTATGAG
Found at i:25157424 original size:37 final size:37
Alignment explanation
Indices: 25157364--25157465 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
25157354 GGAAATATAT
25157364 TCCGGGTAAGA-CCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
25157400 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
25157437 TCTGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
25157466 GGACTATTCG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
36 11 0.18
37 51 0.82
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:25158581 original size:66 final size:66
Alignment explanation
Indices: 25158475--25158605 Score: 262
Period size: 66 Copynumber: 2.0 Consensus size: 66
25158465 CTCTTGGTGC
25158475 AAACTATTGCAATTTTGTTTGAGTGTAGGGTATGTATGTTGTGTGATTTTAATGAGCAAAATGCA
1 AAACTATTGCAATTTTGTTTGAGTGTAGGGTATGTATGTTGTGTGATTTTAATGAGCAAAATGCA
25158540 A
66 A
25158541 AAACTATTGCAATTTTGTTTGAGTGTAGGGTATGTATGTTGTGTGATTTTAATGAGCAAAATGCA
1 AAACTATTGCAATTTTGTTTGAGTGTAGGGTATGTATGTTGTGTGATTTTAATGAGCAAAATGCA
25158606 TGAATTTAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (66 bp):
AAACTATTGCAATTTTGTTTGAGTGTAGGGTATGTATGTTGTGTGATTTTAATGAGCAAAATGCA
A
Found at i:25158830 original size:31 final size:32
Alignment explanation
Indices: 25158792--25158864 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
25158782 TAGGTTGTAT
25158792 TATATATAATACATATGTGTGGGTT-TTG-TTA
1 TATATATAATACATATGTGT-GGTTCTTGATTA
*
25158823 TATATATAATATATATGTGTGGTTCTTGATTA
1 TATATATAATACATATGTGTGGTTCTTGATTA
25158855 TATATATAAT
1 TATATATAAT
25158865 GTATATGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 4 0.10
31 22 0.56
32 13 0.33
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (32 bp):
TATATATAATACATATGTGTGGTTCTTGATTA
Found at i:25160364 original size:21 final size:21
Alignment explanation
Indices: 25160335--25160382 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
25160325 TATAGTTTAG
*
25160335 GGTTTAGGGTTTAAGGTATAT
1 GGTTAAGGGTTTAAGGTATAT
*
25160356 GGTTAAGGGTTTAAGGTTTAT
1 GGTTAAGGGTTTAAGGTATAT
25160377 GAGTTA
1 G-GTTA
25160383 TCATTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (21 bp):
GGTTAAGGGTTTAAGGTATAT
Found at i:25160413 original size:16 final size:16
Alignment explanation
Indices: 25160392--25160423 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25160382 ATCATTTTAA
*
25160392 GGTTTATGGATTATGG
1 GGTTTAGGGATTATGG
25160408 GGTTTAGGGATTATGG
1 GGTTTAGGGATTATGG
25160424 TTTAAGGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.41
Consensus pattern (16 bp):
GGTTTAGGGATTATGG
Found at i:25160833 original size:7 final size:7
Alignment explanation
Indices: 25160807--25160877 Score: 88
Period size: 7 Copynumber: 9.9 Consensus size: 7
25160797 TATATTTTAT
25160807 GATTCAGG
1 GATT-AGG
* *
25160815 GTTTATG
1 GATTAGG
25160822 GATTAGG
1 GATTAGG
25160829 GATTAGG
1 GATTAGG
25160836 GATTAGG
1 GATTAGG
25160843 GATTAGG
1 GATTAGG
25160850 GATTAGG
1 GATTAGG
25160857 GATTATGG
1 GATTA-GG
*
25160865 GTTTAGG
1 GATTAGG
*
25160872 GTTTAG
1 GATTAG
25160878 ATTATTTAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
7 48 0.84
8 9 0.16
ACGTcount: A:0.24, C:0.01, G:0.39, T:0.35
Consensus pattern (7 bp):
GATTAGG
Found at i:25161099 original size:36 final size:36
Alignment explanation
Indices: 25161059--25161130 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
25161049 TTATGAATTA
* *
25161059 TGGTTCAAGGGCT-GGGGTTTAAGGTTTAGGGGTTAT
1 TGGTT-AAGGGCTACGGGTTCAAGGTTTAGGGGTTAT
* * *
25161095 TGGTTACGGGTTACGGGTTCAAGGTTTAGGGTTTAT
1 TGGTTAAGGGCTACGGGTTCAAGGTTTAGGGGTTAT
25161131 GGGTAGGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.17, C:0.07, G:0.39, T:0.38
Consensus pattern (36 bp):
TGGTTAAGGGCTACGGGTTCAAGGTTTAGGGGTTAT
Found at i:25161139 original size:13 final size:13
Alignment explanation
Indices: 25161121--25161145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25161111 GTTCAAGGTT
25161121 TAGGGTTTATGGG
1 TAGGGTTTATGGG
25161134 TAGGGTTTATGG
1 TAGGGTTTATGG
25161146 TTTAAGGTTT
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:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TAGGGTTTATGGG
Found at i:25161331 original size:14 final size:14
Alignment explanation
Indices: 25161295--25161331 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
25161285 GAAAAGAATG
*
25161295 AAATTATTTTGATT
1 AAATTATTTAGATT
25161309 AAATT-TTTAGATT
1 AAATTATTTAGATT
25161322 AAATTATTTA
1 AAATTATTTA
25161332 AGAGATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AAATTATTTAGATT
Found at i:25161410 original size:19 final size:19
Alignment explanation
Indices: 25161388--25161427 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
25161378 AATTGATAAC
*
25161388 AAATAAAAATTAAATACAA
1 AAATAAAAATGAAATACAA
*
25161407 AAATAAAAATGAAATATAA
1 AAATAAAAATGAAATACAA
25161426 AA
1 AA
25161428 TGGAGATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (19 bp):
AAATAAAAATGAAATACAA
Found at i:25161831 original size:21 final size:20
Alignment explanation
Indices: 25161794--25161832 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
25161784 CATCGCCGTC
*
25161794 CGCCGTCCTCACTGCTGCGT
1 CGCCGTCCTCACCGCTGCGT
*
25161814 CGCCGTCGCTCTCCGCTGC
1 CGCCGTC-CTCACCGCTGC
25161833 CGCAACCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.03, C:0.49, G:0.26, T:0.23
Consensus pattern (20 bp):
CGCCGTCCTCACCGCTGCGT
Found at i:25161883 original size:20 final size:20
Alignment explanation
Indices: 25161858--25161896 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25161848 ATGAAGGTTC
*
25161858 AGTTTTCTTGTTATGTCATT
1 AGTTTTCTTGTTATATCATT
25161878 AGTTTTCTTGTTATATCAT
1 AGTTTTCTTGTTATATCAT
25161897 CCAACCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.59
Consensus pattern (20 bp):
AGTTTTCTTGTTATATCATT
Found at i:25164749 original size:5 final size:5
Alignment explanation
Indices: 25164741--25164779 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
25164731 TTATTTAAAG
**
25164741 TTTTA TTTTA AAT-A TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
25164780 ATCACGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 2 0.07
5 27 0.93
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:25164868 original size:14 final size:13
Alignment explanation
Indices: 25164843--25164884 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 13
25164833 TTAAATTGTA
25164843 TTTAAAATTTTAT
1 TTTAAAATTTTAT
25164856 TTTAAATATTTTAT
1 TTTAAA-ATTTTAT
25164870 TTT---ATTTTAT
1 TTTAAAATTTTAT
25164880 TTTAA
1 TTTAA
25164885 TCATGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.38
13 6 0.23
14 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTAAAATTTTAT
Found at i:25164881 original size:104 final size:105
Alignment explanation
Indices: 25164461--25165257 Score: 1273
Period size: 105 Copynumber: 7.8 Consensus size: 105
25164451 TTATTTTAAA
25164461 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
25164526 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
66 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
*
25164566 TATTTTATTTTAATCATGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
25164631 ATTAAATTGTATTTAAAGTTTTATTTT-AA-A---TATTT
66 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
* *
25164666 TATTTTATTTTAATCACGAAAAATATTTT-TATACTTTTA-TTTATTTTTAAATTA--T--CT-A
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
25164724 ATTAAATT-TATTTAAAGTTTTATTTTAAATATTTTATTTTATTT
66 ATTAAATTGTATTTAAAGTTTTATTTT-AA-A---TATTTTATTT
*
25164768 TATTTTATTTTAATCACGAAAAATATTTTGTATACTTTTATTTTA-TTTTAAATTACCTAATTAA
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
*
25164832 ATTAAATTGTATTTAAAATTTTATTTTAAATATTTTATTT
66 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
*
25164872 TATTTTATTTTAATCATGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
* *
25164937 ATTAAATTGTATTTAAATTTTTATTTTAAATGTTTTATTT
66 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
25164977 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTA-TTTTAAATTACCTAATTAA
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
25165041 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
66 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
*
25165081 TATTTTATTTTAATCATGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
*
25165146 ATTAAATTGTATTT-AA----T-GTTT---TATTTTATTT
66 ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
25165177 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATATT
1 TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCT-A-ATT
25165242 AAATTAAATTGTATTT
64 AAATTAAATTGTATTT
25165258 TTAAATATTG
Statistics
Matches: 654, Mismatches: 16, Indels: 51
0.91 0.02 0.07
Matches are distributed among these distances:
92 18 0.03
93 9 0.01
94 2 0.00
95 1 0.00
96 69 0.11
97 1 0.00
98 34 0.05
99 13 0.02
100 34 0.05
102 34 0.05
103 21 0.03
104 162 0.25
105 226 0.35
107 2 0.00
108 11 0.02
109 17 0.03
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (105 bp):
TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTAATTAA
ATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTT
Found at i:25164974 original size:14 final size:13
Alignment explanation
Indices: 25164948--25164989 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 13
25164938 TTAAATTGTA
25164948 TTTAAATTTTTAT
1 TTTAAATTTTTAT
25164961 TTTAAATGTTTTAT
1 TTTAAAT-TTTTAT
25164975 TTT--A-TTTTAT
1 TTTAAATTTTTAT
25164985 TTTAA
1 TTTAA
25164990 TCACGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.35
12 1 0.04
13 7 0.27
14 9 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTAAATTTTTAT
Found at i:25165041 original size:209 final size:205
Alignment explanation
Indices: 25164306--25165257 Score: 1414
Period size: 209 Copynumber: 4.7 Consensus size: 205
25164296 ATTTTAAATA
*
25164306 TTTTATTTTATTTTTAAATTACTTAATTAAATTAAATTGTATTTAAAGTTTTATTTT--A-A---
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
25164365 -A---TATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
66 TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
25164426 ATTAAATTAAATTGTATTTAAAGTTTTATTTT-AA-A---TATTTTATTTTAATCACGAAAAATA
131 ATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTATTTTAATCACGAAAAATA
25164486 TTTTGTCTAC
196 TTTTGTCTAC
25164496 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
*
25164561 TATTTTATTTTATTTTAATCATGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
66 TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
25164626 ATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTATTTTAATCACGAAAAATA
131 ATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTATTTTAATCACGAAAAATA
*
25164691 TTTT-TATAC
196 TTTTGTCTAC
*
25164700 TTTTA-TTTATTTTTAAATTA--T--CT-AATTAAATT-TATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTT-AA-A---
*
25164758 TATTTTATTTTATTTTATTTTAATCACGAAAAATATTTTGTATACTTTTATTTTA-TTTTAAATT
61 TATTTTATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
*
25164822 ACCTAATTAAATTAAATTGTATTTAAAATTTTATTTTAAATATTTTATTTTATTTTATTTTAATC
126 ACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTT-AA-A---TATTTTATTTTATTTTAATC
*
25164887 ATGAAAAATATTTTGTCTAC
186 ACGAAAAATATTTTGTCTAC
* *
25164907 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAATTTTTATTTTAAATGTTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
25164972 TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTA-TTTTAAATTACCTA
66 TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
*
25165036 ATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTATTTTATTTTAATCATGAA
131 ATTAAATTAAATTGTATTTAAAGTTTTATTTT-AA-A---TATTTTATTTTATTTTAATCACGAA
25165101 AAATATTTTGTCTAC
191 AAATATTTTGTCTAC
*
25165116 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTT-AA----T-GTTT---TATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
25165172 TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
66 TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCT-
25165237 ATATTAAATTAAATTGTATTT
130 A-ATTAAATTAAATTGTATTT
25165258 TTAAATATTG
Statistics
Matches: 710, Mismatches: 16, Indels: 59
0.90 0.02 0.08
Matches are distributed among these distances:
190 56 0.08
192 1 0.00
193 1 0.00
197 19 0.03
198 11 0.02
199 2 0.00
200 145 0.20
201 61 0.09
202 57 0.08
203 38 0.05
204 10 0.01
205 29 0.04
206 33 0.05
207 9 0.01
208 17 0.02
209 190 0.27
210 1 0.00
212 2 0.00
213 11 0.02
214 17 0.02
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.57
Consensus pattern (205 bp):
TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
TATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCTA
ATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTATTTTAATCACGAAAAATA
TTTTGTCTAC
Found at i:25165172 original size:5 final size:5
Alignment explanation
Indices: 25165164--25165188 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25165154 GTATTTAATG
25165164 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
25165189 ATCACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:25165496 original size:9 final size:9
Alignment explanation
Indices: 25165480--25165533 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
25165470 ATATCATATC
25165480 TTACATAAT
1 TTACATAAT
*
25165489 TTACATAAG
1 TTACATAAT
* * * *
25165498 ATAAACAAC
1 TTACATAAT
25165507 TTACATAAT
1 TTACATAAT
*
25165516 TTACATAAC
1 TTACATAAT
25165525 TTACATAAT
1 TTACATAAT
25165534 ACATAAATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAT
Found at i:25165525 original size:18 final size:18
Alignment explanation
Indices: 25165480--25165566 Score: 65
Period size: 18 Copynumber: 4.9 Consensus size: 18
25165470 ATATCATATC
* *
25165480 TTACATAATTTACATAAG
1 TTACATAACTTACATAAT
* * *
25165498 ATAAACAACTTACATAAT
1 TTACATAACTTACATAAT
25165516 TTACATAACTTACATAA-
1 TTACATAACTTACATAAT
* *
25165533 -TACATAA-ATATAT-AT
1 TTACATAACTTACATAAT
25165548 TATATCATAACTTACATAA
1 T-TA-CATAACTTACATAA
25165567 CTTAATTATA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
14 1 0.02
15 4 0.08
16 7 0.14
17 2 0.04
18 32 0.63
19 4 0.08
20 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (18 bp):
TTACATAACTTACATAAT
Found at i:25170630 original size:13 final size:14
Alignment explanation
Indices: 25170614--25170642 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25170604 TTATAAATAT
25170614 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
25170627 TTATAATGGTTTAA
1 TTATAATGGTTTAA
25170641 TT
1 TT
25170643 CGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:25171388 original size:31 final size:32
Alignment explanation
Indices: 25171334--25171408 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
25171324 TTAGAATTAA
*
25171334 TGTTTTTGGTTGTATTTTTTATGCGAAATTTGC
1 TGTTTTTGGTTGCA-TTTTTATGCGAAATTTGC
* *
25171367 TGTTTTTGGTTGCA-TTTTATGCTATATTTGC
1 TGTTTTTGGTTGCATTTTTATGCGAAATTTGC
*
25171398 TATTTTTGGTT
1 TGTTTTTGGTT
25171409 AGATTTAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 25 0.66
33 13 0.34
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (32 bp):
TGTTTTTGGTTGCATTTTTATGCGAAATTTGC
Found at i:25178146 original size:18 final size:20
Alignment explanation
Indices: 25178102--25178146 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
25178092 AGCAATAAGC
25178102 TATTAATT-TAATATAAATG
1 TATTAATTATAATATAAATG
*
25178121 TGTT-ATTATAA-ATAAAT-
1 TATTAATTATAATATAAATG
25178138 TATTAATTA
1 TATTAATTA
25178147 ATTTTAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TATTAATTATAATATAAATG
Found at i:25179836 original size:42 final size:42
Alignment explanation
Indices: 25179784--25179967 Score: 172
Period size: 42 Copynumber: 4.4 Consensus size: 42
25179774 TTTTTTAGAA
* ** * *
25179784 AAAAACGCCGCTAAAGACCACGATCTTTCTCGGTGTTTTTAT
1 AAAAGCGCCGCTAAAGACCACGATCTTTAGCGGCGTCTTTAT
25179826 AAAAGCGCCGCTAAAGACCACGATCTTTAGCGGCGTCTTTAT
1 AAAAGCGCCGCTAAAGACCACGATCTTTAGCGGCGTCTTTAT
* * * * *
25179868 AAAAGCGTCGCTGAAGACCAAGACCTTTAGCGGCG-CTCTTAA
1 AAAAGCGCCGCTAAAGACCACGATCTTTAGCGGCGTCT-TTAT
** * * * * * *
25179910 AAAAATGCCGCCAAAGACCAGGACCTATAGCGGCGTTTTTTAA
1 AAAAGCGCCGCTAAAGACCACGATCTTTAGCGGCG-TCTTTAT
*
25179953 AAAAGTGCCGCTAAA
1 AAAAGCGCCGCTAAA
25179968 AGTACAGGTC
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 2 0.02
42 99 0.83
43 17 0.14
44 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGACCACGATCTTTAGCGGCGTCTTTAT
Found at i:25180094 original size:72 final size:72
Alignment explanation
Indices: 25180005--25180139 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
25179995 AAAAAACGTC
* *
25180005 GCTATAGGCCAAGAACTTTAGCGGCGCCTT-TTTAAAAAACGCCGCTATAGACCTGTACTTTTAC
1 GCTATAGACCAAGAACTTTAGCGGCG-CTTCTGTAAAAAACGCCGCTATAGACCTGTACTTTTAC
25180069 AAAAGCCT
65 AAAAGCCT
*
25180077 GCTATAGACGAAGAACTTTAGCGGCGCTTCTGTAAAAAACGCCGCTATAGACCTGTACTTTTA
1 GCTATAGACCAAGAACTTTAGCGGCGCTTCTGTAAAAAACGCCGCTATAGACCTGTACTTTTA
25180140 GCGGCGCTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 3 0.05
72 56 0.95
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (72 bp):
GCTATAGACCAAGAACTTTAGCGGCGCTTCTGTAAAAAACGCCGCTATAGACCTGTACTTTTACA
AAAGCCT
Found at i:25180171 original size:44 final size:43
Alignment explanation
Indices: 25180093--25180254 Score: 236
Period size: 43 Copynumber: 3.7 Consensus size: 43
25180083 GACGAAGAAC
* *
25180093 TTTAGCGGCGCTTCTGTAAAAAACGCCGCTATAGACCTGTACT
1 TTTAGCGGCGCTTTTGCAAAAAACGCCGCTATAGACCTGTACT
* * *
25180136 TTTAGCGGCGCTTTTGTAGAAAAATGCCGCTATAGACCTATACT
1 TTTAGCGGCGCTTTTGCA-AAAAACGCCGCTATAGACCTGTACT
*
25180180 TTTAGCGGCGCTTTTGCAAAAAAAGCCGCTATA-ATCCTGTACT
1 TTTAGCGGCGCTTTTGCAAAAAACGCCGCTATAGA-CCTGTACT
25180223 TTTAGCGGCGCTTTTGCAAAAAAACGCCGCTA
1 TTTAGCGGCGCTTTTGC-AAAAAACGCCGCTA
25180255 ATTTGCCCAG
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.01
43 55 0.50
44 53 0.49
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTGCAAAAAACGCCGCTATAGACCTGTACT
Found at i:25180223 original size:87 final size:87
Alignment explanation
Indices: 25180093--25180254 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
25180083 GACGAAGAAC
* * * *
25180093 TTTAGCGGCGCTTCTGTAAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTGTAGAAA
1 TTTAGCGGCGCTTCTGCAAAAAAAGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTGCAAAAA
*
25180158 AATGCCGCTATAGACCTATACT
66 AACGCCGCTATAGACCTATACT
*
25180180 TTTAGCGGCGCTTTTGCAAAAAAAGCCGCTATA-ATCCTGTACTTTTAGCGGCGCTTTTGCAAAA
1 TTTAGCGGCGCTTCTGCAAAAAAAGCCGCTATAGA-CCTGTACTTTTAGCGGCGCTTTTGCAAAA
25180244 AAACGCCGCTA
65 AAACGCCGCTA
25180255 ATTTGCCCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 67 0.99
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (87 bp):
TTTAGCGGCGCTTCTGCAAAAAAAGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTGCAAAAA
AACGCCGCTATAGACCTATACT
Found at i:25186216 original size:21 final size:21
Alignment explanation
Indices: 25186192--25186231 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25186182 AAATTAATTC
*
25186192 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
25186213 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
25186232 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:25190178 original size:10 final size:11
Alignment explanation
Indices: 25190157--25190190 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
25190147 AGTCAGTAAA
25190157 CAAAACCATTT
1 CAAAACCATTT
25190168 CAAAA-CATTT
1 CAAAACCATTT
*
25190178 CAAACCCATTT
1 CAAAACCATTT
25190189 CA
1 CA
25190191 GTAAACAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (11 bp):
CAAAACCATTT
Found at i:25191353 original size:15 final size:15
Alignment explanation
Indices: 25191333--25191363 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25191323 CAAATAATAA
*
25191333 TATATATATTTATCT
1 TATATACATTTATCT
25191348 TATATACATTTATCT
1 TATATACATTTATCT
25191363 T
1 T
25191364 CTAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATACATTTATCT
Found at i:25191426 original size:22 final size:22
Alignment explanation
Indices: 25191396--25191437 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25191386 ACTCTAAATT
25191396 TAAAACCCTAAACCTGAGACTC
1 TAAAACCCTAAACCTGAGACTC
* *
25191418 TAAACCCCTAAACCTTAGAC
1 TAAAACCCTAAACCTGAGAC
25191438 CACAAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.19
Consensus pattern (22 bp):
TAAAACCCTAAACCTGAGACTC
Found at i:25191785 original size:25 final size:25
Alignment explanation
Indices: 25191750--25191801 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
25191740 TTTCTAGCTA
25191750 ATAGTTAAACAAATGCTAATTCCAC
1 ATAGTTAAACAAATGCTAATTCCAC
*
25191775 ATAGTTCAACAAATGCTAATTCCAC
1 ATAGTTAAACAAATGCTAATTCCAC
25191800 AT
1 AT
25191802 TCAAAATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (25 bp):
ATAGTTAAACAAATGCTAATTCCAC
Found at i:25192256 original size:41 final size:41
Alignment explanation
Indices: 25192199--25192296 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
25192189 GGTTTATGAC
*
25192199 TTTTAGCGACGTTTTACCCAAAGCGCCGCTAATGATCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGATCTGGT
25192240 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGATCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGATCTGGT
*
25192281 TTTTAGCGGCGCTTTA
1 TTTTAGCGGCGTTTTA
25192297 GGTGATCTGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGATCTGGT
Found at i:25192303 original size:68 final size:68
Alignment explanation
Indices: 25192231--25192364 Score: 223
Period size: 68 Copynumber: 2.0 Consensus size: 68
25192221 GCGCCGCTAA
** *
25192231 TGATCTGGTTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGATCTGGTTTTTAGCGGCGCTTT
1 TGATCTGGTTTTTAGCGGAATTTTACCCAAAGCACCGCTAATGATCTGGTTTTTAGCGGCGCTTT
25192296 AGG
66 AGG
* *
25192299 TGATCTGGTTTTTAGCGGAATTTTACCTAAAGCACCGCTAATGATCTGGTTTTTAGCGGCGTTTT
1 TGATCTGGTTTTTAGCGGAATTTTACCCAAAGCACCGCTAATGATCTGGTTTTTAGCGGCGCTTT
25192364 A
66 A
25192365 CCTAAAGCGC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (68 bp):
TGATCTGGTTTTTAGCGGAATTTTACCCAAAGCACCGCTAATGATCTGGTTTTTAGCGGCGCTTT
AGG
Found at i:25192323 original size:27 final size:27
Alignment explanation
Indices: 25192272--25192323 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
25192262 GCGCCGCTAA
**
25192272 TGATCTGGTTTTTAGCGGCGCTTTAGG
1 TGATCTGGTTTTTAGCGGAACTTTAGG
*
25192299 TGATCTGGTTTTTAGCGGAATTTTA
1 TGATCTGGTTTTTAGCGGAACTTTA
25192324 CCTAAAGCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (27 bp):
TGATCTGGTTTTTAGCGGAACTTTAGG
Found at i:25192344 original size:41 final size:41
Alignment explanation
Indices: 25192299--25192381 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
25192289 GCGCTTTAGG
*
25192299 TGATCTGGTTTTTAGCGGAATTTTACCTAAAGCACCGCTAA
1 TGATCTGGTTTTTAGCGGAATTTTACCTAAAGCACAGCTAA
** *
25192340 TGATCTGGTTTTTAGCGGCGTTTTACCTAAAGCGCAGCTAA
1 TGATCTGGTTTTTAGCGGAATTTTACCTAAAGCACAGCTAA
25192381 T
1 T
25192382 TCTCTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (41 bp):
TGATCTGGTTTTTAGCGGAATTTTACCTAAAGCACAGCTAA
Found at i:25192403 original size:40 final size:41
Alignment explanation
Indices: 25192319--25192403 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
25192309 TTTAGCGGAA
* * * *
25192319 TTTTACCTAAAGCACCGCTAATGATCTGGTTTTTAGCGGCG
1 TTTTACCTAAAGCACAGCTAATGATCTGATTTTTACCAGCG
* **
25192360 TTTTACCTAAAGCGCAGCTAATTCTCT-ATTTTTACCAGCG
1 TTTTACCTAAAGCACAGCTAATGATCTGATTTTTACCAGCG
25192400 TTTT
1 TTTT
25192404 TTACTAAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 14 0.38
41 23 0.62
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (41 bp):
TTTTACCTAAAGCACAGCTAATGATCTGATTTTTACCAGCG
Found at i:25200156 original size:19 final size:19
Alignment explanation
Indices: 25200134--25200175 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
25200124 TTCCATTCAT
25200134 TTTCTTTCCTTCC-CTTTCC
1 TTTCTTTCCTTCCTCTTT-C
*
25200153 TTTCTTTCTTTCCTCTTTC
1 TTTCTTTCCTTCCTCTTTC
25200172 TTTC
1 TTTC
25200176 CCTTTCTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTCTTTCCTTCCTCTTTC
Found at i:25200436 original size:28 final size:28
Alignment explanation
Indices: 25200404--25200495 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 28
25200394 CTTTTACCCT
* * *
25200404 TTATTTTTATTTATTTATTTATTTTTAA
1 TTATTATTATTCATTTATTTATTATTAA
*
25200432 TTATTATTCTTCA-TTA-TTATTATT-A
1 TTATTATTATTCATTTATTTATTATTAA
* *
25200457 CTGTTATTATTCATTATATTTATTATTAA
1 TTATTATTATTCATT-TATTTATTATTAA
25200486 TTATT-TTATT
1 TTATTATTATT
25200496 ATTATAATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
25 11 0.22
26 8 0.16
27 5 0.10
28 23 0.45
29 4 0.08
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (28 bp):
TTATTATTATTCATTTATTTATTATTAA
Found at i:25200439 original size:3 final size:3
Alignment explanation
Indices: 25200431--25200516 Score: 68
Period size: 3 Copynumber: 28.0 Consensus size: 3
25200421 TTTATTTTTA
* * *
25200431 ATT ATT ATT CTT CATT ATT ATT ATT ACT GTT ATT ATT CATT A-T ATTT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT A-TT
* * *
25200478 ATT ATT AATT ATT -TT ATT ATT ATA ATT ATG AAT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25200517 CCTTTATTAC
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
2 4 0.06
3 51 0.78
4 10 0.15
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:25200514 original size:49 final size:49
Alignment explanation
Indices: 25200414--25200524 Score: 122
Period size: 49 Copynumber: 2.3 Consensus size: 49
25200404 TTATTTTTAT
* * *
25200414 TTATTTATTTATTTTTAATTATTATTCTTCATTATTATTATTACTGTTA
1 TTATTCATTTATTTTTAATTATTATTCTTCATTATTATAATTACTGATA
25200463 TTATTCATTATATTTATT-ATTAATTATT-TT-ATTATTATAATTA-TGAATA
1 TTATTCATT-TATTT-TTAATT-ATTATTCTTCATTATTATAATTACTG-ATA
*
25200512 TTATTCCTTTATT
1 TTATTCATTTATT
25200525 ACTATTTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
48 6 0.11
49 30 0.56
50 10 0.19
51 8 0.15
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (49 bp):
TTATTCATTTATTTTTAATTATTATTCTTCATTATTATAATTACTGATA
Found at i:25208686 original size:24 final size:24
Alignment explanation
Indices: 25208633--25208686 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
25208623 GTAAAATTCA
* * *
25208633 ATTTGATTCGAACTCGAATTACTT
1 ATTTGAGTCGAACTCGAATAACTG
*
25208657 ACTTGAGTCG-ACTCGAATAACTCG
1 ATTTGAGTCGAACTCGAATAACT-G
25208681 ATTTGA
1 ATTTGA
25208687 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (24 bp):
ATTTGAGTCGAACTCGAATAACTG
Found at i:25213874 original size:22 final size:22
Alignment explanation
Indices: 25213849--25213899 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
25213839 TTTACGGATC
25213849 ATAAACATAACACATAATTTTT
1 ATAAACATAACACATAATTTTT
25213871 ATAAACATAACACATAATTTTT
1 ATAAACATAACACATAATTTTT
*
25213893 ACAAACA
1 ATAAACA
25213900 AAACTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAACATAACACATAATTTTT
Found at i:25221371 original size:92 final size:94
Alignment explanation
Indices: 25221252--25221430 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 94
25221242 AGCATATCTG
*
25221252 TGCCGATGCCATGTCCCAGACATGGTCTTACACT-GAC-GCATCTC-GTAGCCGATGCATGTCCC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGACAGC-TCTCAGTAGCCGATGCATGTCCC
25221314 AGACATGTCTTACACTAGTACTCATTTCAA
65 AGACATGTCTTACACTAGTACTCATTTCAA
* *
25221344 TGCCAATGCCATGTCCTAGACATGGTCTTACACTGGACTAGCTCTCATGATGTGGCCGATGCATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGAC-AGCTCTC---A-GTAGCCGATGCATG
*
25221409 TCCCAGACTTGTCTTACACTAG
61 TCCCAGACATGTCTTACACTAG
25221431 CTCACAATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
92 32 0.43
93 3 0.04
94 4 0.05
95 2 0.03
99 34 0.45
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (94 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGACAGCTCTCAGTAGCCGATGCATGTCCCA
GACATGTCTTACACTAGTACTCATTTCAA
Found at i:25221937 original size:20 final size:20
Alignment explanation
Indices: 25221909--25221951 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
25221899 CTCTAAATTC
25221909 CAACAATTTCACATACTTA-A
1 CAACAATTTCACA-ACTTATA
* *
25221929 CAACTATTTTACAACTTATA
1 CAACAATTTCACAACTTATA
25221949 CAA
1 CAA
25221952 TATAGTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
CAACAATTTCACAACTTATA
Found at i:25224656 original size:43 final size:42
Alignment explanation
Indices: 25224600--25224793 Score: 246
Period size: 43 Copynumber: 4.5 Consensus size: 42
25224590 ATTTTTTAGA
*
25224600 AAAAAACACCGCTAAAGACCAGGACATTTAGCGGCGCTTTTAT
1 AAAAAACGCCGCTAAAGACCAGGAC-TTTAGCGGCGCTTTTAT
25224643 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTAT
1 AAAAAACGCCGCTAAAGACCAGGA-CTTTAGCGGCGCTTTTAT
* * *
25224686 AAAAAACACCGCTAAAGACCAGGATCTTTAGTGGCGCTCTTAT
1 AAAAAACGCCGCTAAAGACCAGGA-CTTTAGCGGCGCTTTTAT
* * *
25224729 AAAAAACGCCGCTAAATACCTA-TACTTTTAGCGGCGCTTTTTT
1 AAAAAACGCCGCTAAAGACC-AGGAC-TTTAGCGGCGCTTTTAT
* * *
25224772 AAAAAATGCTGCTAGAGACCAG
1 AAAAAACGCCGCTAAAGACCAG
25224794 CAATATATAT
Statistics
Matches: 132, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.02
43 128 0.97
44 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGACCAGGACTTTAGCGGCGCTTTTAT
Found at i:25225688 original size:18 final size:18
Alignment explanation
Indices: 25225656--25225693 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
25225646 TACAATATAG
25225656 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
25225675 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
25225692 TA
1 TA
25225694 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:25228726 original size:31 final size:31
Alignment explanation
Indices: 25228688--25228751 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
25228678 CCTTTTCATA
25228688 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
25228719 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
25228750 TT
1 TT
25228752 ATTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:25229022 original size:23 final size:24
Alignment explanation
Indices: 25228943--25229061 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
25228933 GCTTTATCAT
*
25228943 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
25228968 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
*
25228992 ATAACTGGGGTATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
25229015 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
25229039 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25229062 TCACTTTCTC
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 22 0.26
24 51 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:25229022 original size:47 final size:48
Alignment explanation
Indices: 25228943--25229061 Score: 161
Period size: 47 Copynumber: 2.5 Consensus size: 48
25228933 GCTTTATCAT
*
25228943 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* * **
25228992 ATAACTGGGGTATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
25229039 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25229062 TCACTTTCTC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
47 43 0.68
48 8 0.13
49 12 0.19
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:25229137 original size:20 final size:20
Alignment explanation
Indices: 25229112--25229171 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
25229102 TATGATTACC
25229112 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
25229132 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
25229152 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
25229172 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:25229142 original size:11 final size:11
Alignment explanation
Indices: 25229112--25229166 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
25229102 TATGATTACC
25229112 TCATGTGCATA
1 TCATGTGCATA
*
25229123 TCA--TACATA
1 TCATGTGCATA
25229132 TCATGTGCATA
1 TCATGTGCATA
* *
25229143 TCA--TACATT
1 TCATGTGCATA
25229152 TCATGTGCATA
1 TCATGTGCATA
25229163 TCAT
1 TCAT
25229167 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:25229246 original size:25 final size:25
Alignment explanation
Indices: 25229214--25229261 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25229204 ATACATAAAC
* * *
25229214 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
25229239 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
25229262 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:25233749 original size:53 final size:49
Alignment explanation
Indices: 25233679--25233777 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 49
25233669 TTATGTAATT
**
25233679 TATTTAAGTAATGATCAATATTAATACTATTTTGATAAAAATTAGTTATATTA
1 TATTTAAACAATGATCAATATT-AT--TATTTTGAT-AAAATTAGTTATATTA
* *
25233732 TATTTAAACAATGATCAATATTGTTATTTTGATAAAATTATTTATA
1 TATTTAAACAATGATCAATATTATTATTTTGATAAAATTAGTTATA
25233778 ATTGGCCCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 12 0.29
50 9 0.21
52 1 0.02
53 20 0.48
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (49 bp):
TATTTAAACAATGATCAATATTATTATTTTGATAAAATTAGTTATATTA
Found at i:25234503 original size:23 final size:24
Alignment explanation
Indices: 25234477--25234531 Score: 58
Period size: 28 Copynumber: 2.2 Consensus size: 24
25234467 AAGCAAGCTA
25234477 CATA-TATGGTAATAAAATTAATTC
1 CATATTATGGTAATAAAATTAA-TC
*
25234501 ATACTTATTATGGTAATAAAATTAATC
1 ---CATATTATGGTAATAAAATTAATC
25234528 CATA
1 CATA
25234532 CTGTAACACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 3 0.12
27 5 0.20
28 17 0.68
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.38
Consensus pattern (24 bp):
CATATTATGGTAATAAAATTAATC
Found at i:25235560 original size:27 final size:28
Alignment explanation
Indices: 25235530--25235629 Score: 116
Period size: 27 Copynumber: 3.7 Consensus size: 28
25235520 TTTAGTTTAC
25235530 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
25235557 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
25235584 TAAAATTACTGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
*
25235611 TAAAATTACCGAAGTACCC
1 TAAAATTACCGAAATACCC
25235630 CCGATTTACA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 4 0.06
27 57 0.90
28 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:25235598 original size:54 final size:54
Alignment explanation
Indices: 25235530--25235636 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
25235520 TTTAGTTTAC
* * *
25235530 TAAAATTACCGAAATACCCTTAG-TTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATA-CCTTAGACTTGTAAAAATACCGAAATACCCCCGATTTG
* * * *
25235584 TAAAATTACTGAAATACCTTCGACTTGTAAAATTACCGAAGTACCCCCGATTT
1 TAAAATTACCGAAATACCTTAGACTTGTAAAAATACCGAAATACCCCCGATTT
25235637 ACAGAATTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (54 bp):
TAAAATTACCGAAATACCTTAGACTTGTAAAAATACCGAAATACCCCCGATTTG
Found at i:25235835 original size:27 final size:27
Alignment explanation
Indices: 25235625--25235834 Score: 271
Period size: 27 Copynumber: 7.8 Consensus size: 27
25235615 ATTACCGAAG
*
25235625 TACCCCCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25235652 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25235679 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
25235706 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25235733 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
25235760 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25235787 TACCCT-TATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
25235813 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
25235835 TAAAATACCC
Statistics
Matches: 162, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 24 0.15
27 137 0.85
28 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:25235843 original size:27 final size:27
Alignment explanation
Indices: 25235733--25236009 Score: 98
Period size: 27 Copynumber: 10.2 Consensus size: 27
25235723 ATTACCGTTT
* *****
25235733 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ***
25235760 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ****
25235787 TACCCT-TATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
25235813 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
25235840 TACCCT-TAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAA
* * *** **
25235867 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
25235894 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
*
25235921 TACCC-CTGATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
*
25235948 TACCCTTGACTTTTTA-AAAATTA-TAGAAA
1 TACCCTCGA---TTTACAAAATTACTA-AAA
* * * * *
25235977 TACCATTGGTTTACAAAATTAGTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
25236004 TACCCT
1 TACCCT
25236010 TAGTTGTAGA
Statistics
Matches: 201, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
26 30 0.15
27 148 0.74
28 1 0.00
29 18 0.09
30 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:25235871 original size:80 final size:80
Alignment explanation
Indices: 25235571--25235954 Score: 193
Period size: 81 Copynumber: 4.8 Consensus size: 80
25235561 AATACTGAAA
** ** * * * * * * **
25235571 TACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTGTAAAATTACCGAAGTACCCCCGATT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTAGATTTATAAAATTACCAAAATA-CCCTTATT
25235636 TACAGAATTACCGTTT
65 TACAGAATTACCGTTT
* * **** * * * **** * *
25235652 TACCCCCGATTTACATAATTACCGTTTTACCCCT-GATTTACATAATTATCGTTTTACCCTCGAC
1 TACCCTCGATTTACAAAATTACCAAAATA-CCCTAGATTTATAAAATTACCAAAATACCCT-TAT
25235716 TTACAGAATTACCGTTT
64 TTACAGAATTACCGTTT
* **** * * * ***
25235733 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTATTT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTAGATTTATAAAATTACCAAAATACCCTTATTT
*
25235798 ACAGAATTACTGTTT
66 ACAGAATTACCGTTT
* * *
25235813 TACCCTCGATTTACAAAATTACTAAAATACCCTTAG-TTTGTAAAATTACCAAAATACCCTTGGT
1 TACCCTCGATTTACAAAATTACCAAAATACCC-TAGATTTATAAAATTACCAAAATACCCTT-AT
** ***
25235877 TT-GTGAAATTACCGAAA
64 TTACAG-AATTACCGTTT
* ** * *
25235894 TACCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAGTTA-CAGAAATACCCTT
1 TACCCTCGATTTACAAAATTACCAAAATA-CCCTAGATTTATAAAATTACCA-AAATACCCTT
25235955 GACTTTTTAA
Statistics
Matches: 237, Mismatches: 57, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
80 73 0.31
81 158 0.67
82 6 0.03
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (80 bp):
TACCCTCGATTTACAAAATTACCAAAATACCCTAGATTTATAAAATTACCAAAATACCCTTATTT
ACAGAATTACCGTTT
Found at i:25235886 original size:54 final size:54
Alignment explanation
Indices: 25235828--25236060 Score: 170
Period size: 54 Copynumber: 4.3 Consensus size: 54
25235818 TCGATTTACA
25235828 AAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTG
1 AAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTG
** * * * * **
25235882 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTT-AC
1 AAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTG
* * * * ***
25235935 AAAGTTAC-AGAAATACCCTTGACTTTTTAAAAATTA-TAGAAATACCATTGGTTTACA
1 AAA-TTACTA-AAATACCCTT-AGTTTGT-AAAATTACCA-AAATACCCTTGGTTTGTG
* * * * * **
25235992 AAATTAGTGAAATACCCTTAG-TTGTAGATTTACCAAAACACCCTT-GTAGGATG
1 AAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGGTTTG-TG
*
25236045 AAATGACTAAAATACC
1 AAATTACTAAAATACC
25236061 TTTATTAGGT
Statistics
Matches: 135, Mismatches: 35, Indels: 19
0.71 0.19 0.10
Matches are distributed among these distances:
52 2 0.01
53 29 0.21
54 62 0.46
55 7 0.05
56 32 0.24
57 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (54 bp):
AAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTG
Found at i:25236098 original size:27 final size:27
Alignment explanation
Indices: 25236068--25236131 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
25236058 ACCTTTATTA
25236068 GGTAAAATGATCGTAA-AGCCCCTGTAG
1 GGTAAAATGATCGTAATA-CCCCTGTAG
* *
25236095 GGTAAAGTGATCGTAATACCCCTGTAT
1 GGTAAAATGATCGTAATACCCCTGTAG
25236122 GGTAAAATGA
1 GGTAAAATGA
25236132 CGAATATGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
GGTAAAATGATCGTAATACCCCTGTAG
Found at i:25237389 original size:9 final size:9
Alignment explanation
Indices: 25237377--25237433 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
25237367 TTTGATAAAC
25237377 ATGATATGT
1 ATGATATGT
*
25237386 ATGATATGCAC
1 ATGATATG--T
25237397 ATGATATGT
1 ATGATATGT
*
25237406 ATGATATGCAC
1 ATGATATG--T
*
25237417 ATGACATGT
1 ATGATATGT
25237426 ATGATATG
1 ATGATATG
25237434 CACATGATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:25237400 original size:20 final size:20
Alignment explanation
Indices: 25237375--25237445 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
25237365 ATTTTGATAA
25237375 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
25237395 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
25237415 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
25237435 ACATGATATGT
1 ACATGATATGT
25237446 GACAGCCTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:25237402 original size:11 final size:11
Alignment explanation
Indices: 25237386--25237444 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 11
25237376 CATGATATGT
25237386 ATGATATGCAC
1 ATGATATGCAC
*
25237397 ATGATATG--T
1 ATGATATGCAC
25237406 ATGATATGCAC
1 ATGATATGCAC
* *
25237417 ATGACATG--T
1 ATGATATGCAC
25237426 ATGATATGCAC
1 ATGATATGCAC
25237437 ATGATATG
1 ATGATATG
25237445 TGACAGCCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 15 0.39
11 23 0.61
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:25239203 original size:40 final size:40
Alignment explanation
Indices: 25239124--25239281 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
25239114 TTCGAATGAT
* * * *
25239124 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
25239164 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
25239204 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
25239244 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
25239282 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:25239302 original size:80 final size:80
Alignment explanation
Indices: 25239124--25239311 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
25239114 TTCGAATGAT
* *
25239124 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
25239189 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
25239204 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
25239265 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
25239285 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
25239312 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:25241360 original size:23 final size:23
Alignment explanation
Indices: 25241330--25241377 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25241320 AGCAAGTAAC
25241330 TTGGGAGTTTTTCCAAACTGAGT
1 TTGGGAGTTTTTCCAAACTGAGT
25241353 TTGGGAGTTTTTCCAAACTGAGT
1 TTGGGAGTTTTTCCAAACTGAGT
25241376 TT
1 TT
25241378 CGGAAGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (23 bp):
TTGGGAGTTTTTCCAAACTGAGT
Found at i:25247299 original size:40 final size:40
Alignment explanation
Indices: 25247220--25247377 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
25247210 TTCGAATGAT
* * * *
25247220 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
25247260 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
25247300 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
25247340 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
25247378 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:25247398 original size:80 final size:80
Alignment explanation
Indices: 25247220--25247407 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
25247210 TTCGAATGAT
* *
25247220 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
25247285 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
25247300 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
25247361 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
25247381 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
25247408 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:25248905 original size:23 final size:24
Alignment explanation
Indices: 25248874--25248976 Score: 149
Period size: 23 Copynumber: 4.4 Consensus size: 24
25248864 AGGAAGTGCA
25248874 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
25248898 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
25248921 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
25248944 AAAAGGGCTT-TTCCCTAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
25248967 AAAAGAGGCT
1 AAAAG-GGCT
25248977 AGGCCTCCAG
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 61 0.82
24 13 0.18
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:25249219 original size:31 final size:31
Alignment explanation
Indices: 25249184--25249247 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
25249174 CGTTTATAGT
*
25249184 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
25249215 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
25249246 AA
1 AA
25249248 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:25250837 original size:467 final size:470
Alignment explanation
Indices: 25249957--25250860 Score: 1643
Period size: 467 Copynumber: 1.9 Consensus size: 470
25249947 GGGTGTTACA
*
25249957 CATACTTATTCATACTTAAGTTGAATCAAATAATAATTAAGTTGAACTAAAATATAAAAACTTAT
1 CATACTTATTCATACTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAACTTAT
25250022 TCATACTTATTCATACTTCAAATAATAATTAATACTATTTTGATAAAAATTAGTTATAACTTTTA
66 TCATACTTATTCATACTTCAAATAATAATTAATACTA--TT-AT----ATTAGTTATAACTTTTA
25250087 AAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAA
124 AAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAA
25250152 TATAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTT
189 TATAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTT
* *
25250217 ATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCATCATA
254 ATATAAATATTCAATAGCGATAGAACTTTTTTCAATCCTTCTTGAATTTTTTAAGATTCATCATA
* *
25250282 CGTGGCGTTGTTACACCTAGAGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAGCCCGTCA
319 CGTGGCGTTGTTACACCTACAGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCA
25250347 GGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAAGCTAC
384 GGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAAGCTAC
25250412 ATATATGGTAATAAAATTAATT
449 ATATATGGTAATAAAATTAATT
25250434 CATACTTATTCATACTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAACTTAT
1 CATACTTATTCATACTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAACTTAT
25250499 TCATACTTATTCATACTTCAAATAATAATTAATACTA-T-T-TTAGTTATAACTTTTAAAGACAT
66 TCATACTTATTCATACTTCAAATAATAATTAATACTATTATATTAGTTATAACTTTTAAAGACAT
*
25250561 TTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAATTTGAATATAATA
131 TTAAAAATATTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATA
*
25250626 ATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATATAAA
196 ATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATATAAA
25250691 TATTCAATAGCGATAGAACTTTTTTCAATCCTTCTTGAATTTTTTAAGATTCATCATACGTGGCG
261 TATTCAATAGCGATAGAACTTTTTTCAATCCTTCTTGAATTTTTTAAGATTCATCATACGTGGCG
* *
25250756 TTGTTACATCTACAGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACCTGTCAGGTTTCC
326 TTGTTACACCTACAGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCC
25250821 AGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGG
391 AGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGG
25250861 CTGGAGAGAA
Statistics
Matches: 418, Mismatches: 9, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
467 315 0.75
472 1 0.00
474 1 0.00
477 101 0.24
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (470 bp):
CATACTTATTCATACTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAACTTAT
TCATACTTATTCATACTTCAAATAATAATTAATACTATTATATTAGTTATAACTTTTAAAGACAT
TTAAAAATATTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATA
ATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATATAAA
TATTCAATAGCGATAGAACTTTTTTCAATCCTTCTTGAATTTTTTAAGATTCATCATACGTGGCG
TTGTTACACCTACAGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCC
AGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAAGCTACATATATG
GTAATAAAATTAATT
Found at i:25265539 original size:15 final size:15
Alignment explanation
Indices: 25265519--25265550 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25265509 AAATAATAAT
*
25265519 TTATATATATTTATC
1 TTATATACATTTATC
25265534 TTATATACATTTATC
1 TTATATACATTTATC
25265549 TT
1 TT
25265551 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:25266170 original size:25 final size:25
Alignment explanation
Indices: 25266142--25266195 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
25266132 TGGAAATTAT
25266142 ACATAGTTCAACAAATGCTAATTCC
1 ACATAGTTCAACAAATGCTAATTCC
25266167 ACATAGTTCAACAAATGCTAATTCC
1 ACATAGTTCAACAAATGCTAATTCC
25266192 ACAT
1 ACAT
25266196 TCAAAATCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (25 bp):
ACATAGTTCAACAAATGCTAATTCC
Found at i:25266402 original size:18 final size:18
Alignment explanation
Indices: 25266354--25266402 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 18
25266344 TTTCAAATAC
*
25266354 TAGTTAACTCCTAAACCA
1 TAGTTAACTCATAAACCA
*
25266372 TA--T-A-TCTTAAACCA
1 TAGTTAACTCATAAACCA
25266386 TAGTTAACTCATAAACC
1 TAGTTAACTCATAAACC
25266403 TGCTTAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 2 0.08
17 1 0.04
18 10 0.40
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (18 bp):
TAGTTAACTCATAAACCA
Found at i:25266682 original size:37 final size:38
Alignment explanation
Indices: 25266607--25266897 Score: 180
Period size: 41 Copynumber: 7.1 Consensus size: 38
25266597 TTTAGTGGCG
25266607 TTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTTAGCGCGT
1 TTTTACCAAAAGCGCCGCT-ATG--CTGG-TTTTTAGCGCGT
*
25266649 TTTTACCAAAAGCG-CTCTATGCTGGTTTTTAGCGGCG-
1 TTTTACCAAAAGCGCCGCTATGCTGGTTTTTAGC-GCGT
* * *
25266686 TTTTACCAAAAGCG-CTCTATGCTCTGTTTTTAGCGGGT
1 TTTTACCAAAAGCGCCGCTATGCT-GGTTTTTAGCGCGT
25266724 TTTTACCAAAAGCGCCGCTATGCTCTGG-TTTTAGCGGCGT
1 TTTTACCAAAAGCGCCGCTATG--CTGGTTTTTAGC-GCGT
* *
25266764 AGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGGTTTTTAGTGGCG-
1 -------TTTTACCAAAAGCGCCGCT-ATG--CTGGTTTTTAG-CGCGT
** * *
25266812 TTTTACTGAAAGCGCCACTAATGCTCTGTTTTTAGCGGCGTT
1 TTTTACCAAAAGCGCCGCT-ATGCT-GGTTTTTAGC-GCG-T
* * *
25266854 TTTTACTAAAA-CGCCGCTGTTGCTCTGTTTTTAGCGGCGT
1 TTTTACCAAAAGCGCCGCT-ATGCT-GGTTTTTAGC-GCGT
25266894 TTTT
1 TTTT
25266898 TCTTAAAACA
Statistics
Matches: 210, Mismatches: 18, Indels: 44
0.77 0.07 0.16
Matches are distributed among these distances:
37 33 0.16
38 30 0.14
39 15 0.07
40 23 0.11
41 49 0.23
42 24 0.11
47 18 0.09
48 9 0.04
49 9 0.04
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (38 bp):
TTTTACCAAAAGCGCCGCTATGCTGGTTTTTAGCGCGT
Found at i:25266775 original size:47 final size:49
Alignment explanation
Indices: 25266716--25266812 Score: 146
Period size: 47 Copynumber: 2.0 Consensus size: 49
25266706 GCTCTGTTTT
25266716 TAGCGGGTTTTTACCAAAAGCGCCGCT-ATGCTCTGG-TTTTAGCGGCG
1 TAGCGGGTTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCG
* *
25266763 TAGCGGCG-TTTTACCAAAAGCGTCGCTAATGCTCTGGTTTTTAGTGGCG
1 TAGCGG-GTTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCG
25266812 T
1 T
25266813 TTTACTGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 24 0.53
48 10 0.22
49 11 0.24
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.32
Consensus pattern (49 bp):
TAGCGGGTTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCG
Found at i:25266827 original size:88 final size:86
Alignment explanation
Indices: 25266678--25266852 Score: 246
Period size: 88 Copynumber: 2.0 Consensus size: 86
25266668 TGCTGGTTTT
* *
25266678 TAGCGGCGTTTTACCAAAAGCGCTCTATGCTCTGTTTTTAGCGGGTTTTTACCAAAAGCGCCGCT
1 TAGCGGCGTTTTACCAAAAGCGCGCTATGCTCTGTTTTTAGCGGGTTTTTACCAAAAGCGCCACT
25266743 -ATGCTCTGGTTTTAGCGGCG
66 AATGCTCTGGTTTTAGCGGCG
* **
25266763 TAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGGTTTTTAGTGGCG-TTTTACTGAAAGCGC
1 TAGCGGCGTTTTACCAAAAGCG-CGCT-ATGCTCT-GTTTTTAGCGG-GTTTTTACCAAAAGCGC
*
25266827 CACTAATGCTCTGTTTTTAGCGGCG
62 CACTAATGCTCTGGTTTTAGCGGCG
25266852 T
1 T
25266853 TTTTTACTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
85 22 0.28
86 3 0.04
87 7 0.09
88 26 0.33
89 21 0.27
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (86 bp):
TAGCGGCGTTTTACCAAAAGCGCGCTATGCTCTGTTTTTAGCGGGTTTTTACCAAAAGCGCCACT
AATGCTCTGGTTTTAGCGGCG
Found at i:25266897 original size:41 final size:41
Alignment explanation
Indices: 25266763--25266928 Score: 162
Period size: 41 Copynumber: 4.0 Consensus size: 41
25266753 TTTAGCGGCG
* * *
25266763 TAGCGGCG--TTTTACCAAAAGCGTCGCTAATGCTCTGGTTTT
1 TAGCGGCGTTTTTTACTAAAA-CGCCGCTATTGCTCT-GTTTT
* * * *
25266804 TAGTGGCG--TTTTACTGAAAGCGCCACTAATGCTCTGTTTT
1 TAGCGGCGTTTTTTACT-AAAACGCCGCTATTGCTCTGTTTT
*
25266844 TAGCGGCGTTTTTTACTAAAACGCCGCTGTTGCTCTGTTTT
1 TAGCGGCGTTTTTTACTAAAACGCCGCTATTGCTCTGTTTT
* *
25266885 TAGCGGCGTTTTTT-CTTAAAACACCGTTATTGCTCTGTATTT
1 TAGCGGCGTTTTTTAC-TAAAACGCCGCTATTGCTCTGT-TTT
25266927 TA
1 TA
25266929 AAAATTTTGG
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
40 13 0.12
41 79 0.74
42 15 0.14
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (41 bp):
TAGCGGCGTTTTTTACTAAAACGCCGCTATTGCTCTGTTTT
Found at i:25269903 original size:74 final size:74
Alignment explanation
Indices: 25269782--25269932 Score: 259
Period size: 74 Copynumber: 2.0 Consensus size: 74
25269772 CATTTACTAT
* * *
25269782 ATAAAAATAAAATTTATAAACGGTAGAAGTTGTCACACTATCAATATATAGTTATGGCATGTATA
1 ATAAAAATAAAAGTTATAAACGGTAGAAGTTGTCACACTATCAATATACAATTATGGCATGTATA
25269847 GCTAGACCC
66 GCTAGACCC
25269856 ATAAAAATAAAAGTTATAAAC-GTCAGAAGTTGTCACACTATCAATATACAATTATGGCATGTAT
1 ATAAAAATAAAAGTTATAAACGGT-AGAAGTTGTCACACTATCAATATACAATTATGGCATGTAT
25269920 AGCTAGACCC
65 AGCTAGACCC
25269930 ATA
1 ATA
25269933 CTTTCGCTAG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
73 2 0.03
74 71 0.97
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (74 bp):
ATAAAAATAAAAGTTATAAACGGTAGAAGTTGTCACACTATCAATATACAATTATGGCATGTATA
GCTAGACCC
Found at i:25270246 original size:21 final size:20
Alignment explanation
Indices: 25270218--25270257 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
25270208 ACTTTGAAAC
25270218 AAGGAACACG-CTCGTGTGGA
1 AAGGAACACGTC-CGTGTGGA
25270238 AAGGTAACACGTCCGTGTGG
1 AAGG-AACACGTCCGTGTGG
25270258 CCATTTCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 13 0.72
22 1 0.06
ACGTcount: A:0.28, C:0.20, G:0.35, T:0.17
Consensus pattern (20 bp):
AAGGAACACGTCCGTGTGGA
Found at i:25271463 original size:46 final size:45
Alignment explanation
Indices: 25271362--25271578 Score: 190
Period size: 46 Copynumber: 4.7 Consensus size: 45
25271352 GCATATCTGT
* *
25271362 GCCGATGCCATGTTCCAGACATGGTCTTACACTGGC-TCATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACTTCATCTCG-AG
* * *
25271408 GCTGATGCATGTCCTAGACATGTCTTACACTGACTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGACTT-CATCTCGAG
* * *
25271454 GCCGATGCATGTCCCAGACATGTCTTACACT-AGCATTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGA-C-TTCATCTCGAG
* * * * * *
25271500 ACCGAAGCCATGTCCCAGATATGGTCTTACACTGGCTCTCATGAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACT-TCAT-CTCGAG
25271548 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
25271579 AGCTCATAAT
Statistics
Matches: 140, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
44 12 0.09
45 15 0.11
46 64 0.46
47 29 0.21
48 19 0.14
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACTTCATCTCGAG
Found at i:25277795 original size:31 final size:32
Alignment explanation
Indices: 25277757--25277831 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
25277747 CATTAAATCT
*
25277757 AACCAAAAACAACAAATATAGCAT-AAAATGC
1 AACCAAAAACAACAAATATAGCATAAAAATAC
* * *
25277788 AACCAAAAACAGCAAATTTCGCATAAAAAATAC
1 AACCAAAAACAACAAATATAGCAT-AAAAATAC
25277821 AACCAAAAACA
1 AACCAAAAACA
25277832 TTAATTCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 21 0.55
33 17 0.45
ACGTcount: A:0.61, C:0.21, G:0.05, T:0.12
Consensus pattern (32 bp):
AACCAAAAACAACAAATATAGCATAAAAATAC
Found at i:25278549 original size:13 final size:14
Alignment explanation
Indices: 25278523--25278551 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25278513 ACTAATGACG
25278523 AATTAAACCATTAT
1 AATTAAACCATTAT
25278537 AATTAAA-CATTAT
1 AATTAAACCATTAT
25278550 AA
1 AA
25278552 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:25283570 original size:9 final size:9
Alignment explanation
Indices: 25283556--25283622 Score: 59
Period size: 9 Copynumber: 7.7 Consensus size: 9
25283546 TAAGTATAAT
25283556 TAAGTTATG
1 TAAGTTATG
25283565 TAAGTTATG
1 TAAGTTATG
* * *
25283574 ATATGATATA
1 -TAAGTTATG
*
25283584 T-ATTTATG
1 TAAGTTATG
25283592 T-A-TTATG
1 TAAGTTATG
25283599 TAAGTTATG
1 TAAGTTATG
*
25283608 TAAATTATG
1 TAAGTTATG
25283617 TAAGTT
1 TAAGTT
25283623 GTTTATCTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 28 0.61
10 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:25283948 original size:5 final size:5
Alignment explanation
Indices: 25283938--25283962 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25283928 TTTTCGTGAT
25283938 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
25283963 CATTAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:25284172 original size:14 final size:13
Alignment explanation
Indices: 25284142--25284182 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
25284132 TTTTTCGTGA
25284142 TTAAAAT-AAAA-
1 TTAAAATAAAAAT
25284153 -TAAAATAAAACAT
1 TTAAAATAAAA-AT
25284166 TTAAAATAAAAAT
1 TTAAAATAAAAAT
25284179 TTAA
1 TTAA
25284183 TACAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.23
11 3 0.12
12 1 0.04
13 6 0.23
14 10 0.38
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAAAATAAAAAT
Found at i:25284353 original size:103 final size:105
Alignment explanation
Indices: 25283938--25284629 Score: 1048
Period size: 103 Copynumber: 6.7 Consensus size: 105
25283928 TTTTCGTGAT
** *
25283938 TAAAATAAAATAAAATAAAATAAAACATTAAATACAATTTAATTTAATTAGGTAATTTAAAAATA
1 TAAAATAAAAT-ATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATA
*
25284003 AAATAAAAGTAGACAAAATATTTTTCATGATTAAAATAAAA
65 AAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
25284044 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTTAATTAGGTAATTT-AA
1 TAAAATAAAATATTTAAAATAAAACTTTAAATAC-----AATTTAATTTAATTAGGTAATTTAAA
25284108 AATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
61 AATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
* *
25284153 TAAAATAAAACATTTAAAATAAAAATTT-AATACAATTTAATTTAATTAGGTAATTTAAAAATAA
1 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
*
25284217 AATAAAAGTAGACAAAATATTTTTCATGATTAAAATAAAA
66 AATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
25284257 TAAAATAAAATATTTAAAATAAAA-TTTAAATACAATTTAATTTAATTAGGTAATTT-AAAATAA
1 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
*
25284320 AATAAAAGTATACAAAATATTTTTCGTGATTAAAATAAAA
66 AATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
*
25284360 TAAAATAAAATATTTAAAATAAAACTTTAAATAC-----AATTTAATTAGATAATTTAAAAAT-A
1 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
25284419 AATAAAAGTAGA-AAAATATTTTTCGTGATTAAAATAAAATAAAA
66 AATAAAAGTAGACAAAATATTTTTCGTGA-T----TAAAATAAAA
25284463 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
1 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
25284528 AATAAAAGTAGACAAAATATTTTTCGTG------AT----
66 AATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
*
25284558 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTGAATTTAATTAGGTAATTTAAAAATAA
1 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
25284623 AATAAAA
66 AATAAAA
25284630 TATTTAAAAT
Statistics
Matches: 551, Mismatches: 14, Indels: 53
0.89 0.02 0.09
Matches are distributed among these distances:
95 71 0.13
98 16 0.03
99 32 0.06
100 5 0.01
103 139 0.25
104 106 0.19
105 20 0.04
106 11 0.02
108 28 0.05
109 85 0.15
110 38 0.07
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (105 bp):
TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
AATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAA
Found at i:25284486 original size:5 final size:5
Alignment explanation
Indices: 25284448--25284474 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
25284438 TTTTCGTGAT
25284448 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
25284475 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:25284493 original size:13 final size:14
Alignment explanation
Indices: 25284447--25284486 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
25284437 TTTTTCGTGA
*
25284447 TTAAAATAAAATAAA
1 TTAAAATAAAAT-AT
*
25284462 ATAAAATAAAATAT
1 TTAAAATAAAATAT
25284476 TTAAAATAAAA
1 TTAAAATAAAA
25284487 CTTTAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TTAAAATAAAATAT
Found at i:25287064 original size:20 final size:20
Alignment explanation
Indices: 25287036--25287074 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25287026 ATGGGGTTGG
*
25287036 ATGATATAACAAGAAAACTA
1 ATGACATAACAAGAAAACTA
25287056 ATGACATAACAAGAAAACT
1 ATGACATAACAAGAAAACT
25287075 GAACCTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.13, G:0.10, T:0.18
Consensus pattern (20 bp):
ATGACATAACAAGAAAACTA
Found at i:25287516 original size:19 final size:19
Alignment explanation
Indices: 25287494--25287538 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
25287484 GTAATCTCCA
25287494 TTTTATATTTTAA-TTTTAT
1 TTTTATA-TTTAATTTTTAT
*
25287513 TTTTGTATTTAATTTTTAT
1 TTTTATATTTAATTTTTAT
25287532 TTGTTAT
1 TT-TTAT
25287539 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 14 0.64
20 3 0.14
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTATATTTAATTTTTAT
Found at i:25287613 original size:13 final size:14
Alignment explanation
Indices: 25287590--25287626 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
25287580 TATTATCTCT
25287590 TAAATAATTTAATC
1 TAAATAATTTAATC
25287604 TAAA-AATTTAATC
1 TAAATAATTTAATC
*
25287617 AAAATAATTT
1 TAAATAATTT
25287627 CATTCTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATAATTTAATC
Found at i:25287768 original size:7 final size:7
Alignment explanation
Indices: 25287758--25287961 Score: 64
Period size: 7 Copynumber: 28.7 Consensus size: 7
25287748 TCTAATCTTG
25287758 TAAACCC
1 TAAACCC
25287765 TAAACCC
1 TAAACCC
25287772 TAAACCC
1 TAAACCC
25287779 TAAACCC
1 TAAACCC
*
25287786 T--ACTCA
1 TAAAC-CC
25287792 TAAACCC
1 TAAACCC
*
25287799 TAAACCT
1 TAAACCC
*
25287806 TGAACCCC
1 T-AAACCC
25287814 T-AACCC
1 TAAACCC
25287820 GT-AACCC
1 -TAAACCC
*
25287827 GT-AACCAA
1 -TAAACC-C
*
25287835 TAACCCC
1 TAAACCC
*
25287842 TAAACCT
1 TAAACCC
25287849 TAAACCC
1 TAAACCC
* *
25287856 -CAGCCC
1 TAAACCC
*
25287862 TTAAACCA
1 -TAAACCC
** *
25287870 TAATTCA
1 TAAACCC
25287877 TAAACCC
1 TAAACCC
*
25287884 TTAAA--G
1 -TAAACCC
*
25287890 TAGTAACTCA
1 TA--AAC-CC
25287900 TAAACCC
1 TAAACCC
25287907 TAAAACCC
1 T-AAACCC
* *
25287915 TTAACCA
1 TAAACCC
*
25287922 TATACCC
1 TAAACCC
* **
25287929 TAATCTG
1 TAAACCC
*
25287936 TAAACCA
1 TAAACCC
25287943 TAAACCC
1 TAAACCC
25287950 TAAACCC
1 TAAACCC
25287957 TAAAC
1 TAAAC
25287962 TATAAAGATA
Statistics
Matches: 143, Mismatches: 38, Indels: 32
0.67 0.18 0.15
Matches are distributed among these distances:
5 4 0.03
6 10 0.07
7 100 0.70
8 27 0.19
10 2 0.01
ACGTcount: A:0.41, C:0.36, G:0.03, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:25287784 original size:21 final size:21
Alignment explanation
Indices: 25287758--25287967 Score: 94
Period size: 21 Copynumber: 9.9 Consensus size: 21
25287748 TCTAATCTTG
*
25287758 TAAACCCTAAACCCTAAACCC
1 TAAACCCTAAACCATAAACCC
25287779 TAAACCCT--ACTCATAAACCC
1 TAAACCCTAAAC-CATAAACCC
* * *
25287799 TAAACCTTGAACCCCT-AACCC
1 TAAACCCT-AAACCATAAACCC
*
25287820 GT-AACCCGT-AACCAATAACCCC
1 -TAAACCC-TAAACC-ATAAACCC
* ** *
25287842 TAAACCTTAAACC-CCAGCCC
1 TAAACCCTAAACCATAAACCC
* **
25287862 TTAAACCATAATTCATAAACCC
1 -TAAACCCTAAACCATAAACCC
*
25287884 TTAAA--GTAGTAACTCATAAACCC
1 -TAAACCCTA--AAC-CATAAACCC
* *
25287907 TAAAACCCTTAACCATATACCC
1 T-AAACCCTAAACCATAAACCC
* **
25287929 TAATCTGTAAACCATAAACCC
1 TAAACCCTAAACCATAAACCC
*
25287950 TAAACCCTAAACTATAAA
1 TAAACCCTAAACCATAAA
25287968 GATAATTAAT
Statistics
Matches: 138, Mismatches: 33, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
19 2 0.01
20 24 0.17
21 59 0.43
22 36 0.26
23 16 0.12
25 1 0.01
ACGTcount: A:0.41, C:0.35, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACCC
Found at i:25287883 original size:43 final size:43
Alignment explanation
Indices: 25287758--25287888 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 43
25287748 TCTAATCTTG
* * *
25287758 TAAACCCTAAA-CCCTAAACCC-TAAACCCTACTCATAAA-CCC
1 TAAACCTTAAACCCCT-AACCCGTAAACCATAATCATAAACCCC
* * * *
25287799 TAAACCTTGAACCCCTAACCCGTAACCCGTAACCA-ATAACCCC
1 TAAACCTTAAACCCCTAACCCGTAAACCATAATCATA-AACCCC
* * *
25287842 TAAACCTTAAACCCC-AGCCCTTAAACCATAATTCATAAACCCT
1 TAAACCTTAAACCCCTAACCCGTAAACCATAA-TCATAAACCCC
25287885 TAAA
1 TAAA
25287889 GTAGTAACTC
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
41 15 0.21
42 27 0.38
43 28 0.39
44 1 0.01
ACGTcount: A:0.40, C:0.38, G:0.03, T:0.19
Consensus pattern (43 bp):
TAAACCTTAAACCCCTAACCCGTAAACCATAATCATAAACCCC
Found at i:25287886 original size:22 final size:23
Alignment explanation
Indices: 25287859--25287913 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
25287849 TAAACCCCAG
*
25287859 CCCTTAAACCA-TAATTCATAAA
1 CCCTTAAACCAGTAACTCATAAA
**
25287881 CCCTTAAAGTAGTAACTCATAAA
1 CCCTTAAACCAGTAACTCATAAA
*
25287904 CCCTAAAACC
1 CCCTTAAACC
25287914 CTTAACCATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.24
Consensus pattern (23 bp):
CCCTTAAACCAGTAACTCATAAA
Found at i:25288069 original size:7 final size:7
Alignment explanation
Indices: 25288059--25288144 Score: 66
Period size: 7 Copynumber: 12.3 Consensus size: 7
25288049 ACTAAATAAT
25288059 CTAAACC
1 CTAAACC
25288066 CTAAACC
1 CTAAACC
* *
25288073 ATAATCC
1 CTAAACC
*
25288080 CTAATCC
1 CTAAACC
25288087 CTAAACC
1 CTAAACC
*
25288094 CTAATCC
1 CTAAACC
*
25288101 ATAAACC
1 CTAAACC
* *
25288108 CTGAATC
1 CTAAACC
* *
25288115 ATAAAAC
1 CTAAACC
*
25288122 ATAAACC
1 CTAAACC
25288129 CTAAACC
1 CTAAACC
25288136 ACT-AACC
1 -CTAAACC
25288143 CT
1 CT
25288145 TGACCTTGAC
Statistics
Matches: 63, Mismatches: 15, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
6 2 0.03
7 59 0.94
8 2 0.03
ACGTcount: A:0.43, C:0.36, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:25288088 original size:21 final size:21
Alignment explanation
Indices: 25288059--25288144 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
25288049 ACTAAATAAT
25288059 CTAAACCCTAAACCATAATCC
1 CTAAACCCTAAACCATAATCC
* *
25288080 CTAATCCCTAAACCCTAATCC
1 CTAAACCCTAAACCATAATCC
* * * **
25288101 ATAAACCCTGAATCATAAAAC
1 CTAAACCCTAAACCATAATCC
*
25288122 ATAAACCCTAAACCACTAA-CC
1 CTAAACCCTAAACCA-TAATCC
25288143 CT
1 CT
25288145 TGACCTTGAC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
21 48 0.94
22 3 0.06
ACGTcount: A:0.43, C:0.36, G:0.01, T:0.20
Consensus pattern (21 bp):
CTAAACCCTAAACCATAATCC
Found at i:25288121 original size:15 final size:14
Alignment explanation
Indices: 25288060--25288119 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
25288050 CTAAATAATC
*
25288060 TAAACCCTAAACCA
1 TAAACCCTAATCCA
* *
25288074 TAATCCCTAATCCC
1 TAAACCCTAATCCA
25288088 TAAACCCTAATCCA
1 TAAACCCTAATCCA
25288102 TAAACCCTGAAT-CA
1 TAAACCCT-AATCCA
25288116 TAAA
1 TAAA
25288120 ACATAAACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 37 0.93
15 3 0.08
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACCCTAATCCA
Found at i:25289247 original size:31 final size:31
Alignment explanation
Indices: 25289206--25289269 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
25289196 CCTTTTCATA
*
25289206 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
25289237 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
25289268 TT
1 TT
25289270 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:25289514 original size:24 final size:24
Alignment explanation
Indices: 25289462--25289627 Score: 230
Period size: 24 Copynumber: 7.0 Consensus size: 24
25289452 GCTTTATCAT
*
25289462 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
25289487 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
25289511 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
25289534 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
25289558 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
25289582 ATAATTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
25289605 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25289628 TCACTTCCTC
Statistics
Matches: 127, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
23 42 0.33
24 73 0.57
25 12 0.09
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:25289538 original size:47 final size:48
Alignment explanation
Indices: 25289461--25289627 Score: 232
Period size: 47 Copynumber: 3.5 Consensus size: 48
25289451 TGCTTTATCA
* *
25289461 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
25289510 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* * *
25289557 GATAACTGGGGCATAAGCCCTTTTGATAATTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
25289604 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
25289628 TCACTTCCTC
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
47 70 0.65
48 25 0.23
49 13 0.12
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:25289562 original size:71 final size:71
Alignment explanation
Indices: 25289462--25289627 Score: 253
Period size: 71 Copynumber: 2.3 Consensus size: 71
25289452 GCTTTATCAT
* *
25289462 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
25289526 GCCCTTTA
64 GCCCTTTA
* * * *
25289534 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAATTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
25289599 CCTTTA
66 CCTTTA
25289605 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25289628 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 75 0.86
72 12 0.14
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:25289700 original size:9 final size:9
Alignment explanation
Indices: 25289686--25289742 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
25289676 ATCTCGTGTG
25289686 CATATCATA
1 CATATCATA
*
25289695 CATATCATGTG
1 CATATCA--TA
25289706 CATATCATA
1 CATATCATA
* *
25289715 CATGTCATGTG
1 CATATCA--TA
25289726 CATATCATA
1 CATATCATA
25289735 CATATCAT
1 CATATCAT
25289743 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:25289705 original size:20 final size:20
Alignment explanation
Indices: 25289682--25289744 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
25289672 GAACATCTCG
25289682 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
25289702 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
25289722 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
25289742 TGT
1 TGT
25289745 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Done.