Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 54 of 138
Found at i:11208659 original size:12 final size:11
Alignment explanation
Indices: 11208637--11208698 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
11208627 AAAAAAATAA
11208637 AAAAATAAAAT
1 AAAAATAAAAT
*
11208648 AAAAATGGAAAT
1 AAAAAT-AAAAT
11208660 AAAAATAAAAAAT
1 AAAAAT--AAAAT
11208673 AAAAATAAAAT
1 AAAAATAAAAT
11208684 -AAAATAAAAT
1 AAAAATAAAAT
11208694 AAAAA
1 AAAAA
11208699 GTATTAAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
10 10 0.22
11 15 0.33
12 10 0.22
13 10 0.22
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:11209584 original size:4 final size:4
Alignment explanation
Indices: 11209577--11209748 Score: 70
Period size: 4 Copynumber: 42.8 Consensus size: 4
11209567 AAGGAAGGAA
* * * * *
11209577 AAAT AAAT AAAT AAAT AAAT AAAT AAAG ATAAT ATAT TAAT TAAT AGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* * * * * *
11209626 AAA- CAAT -AAT TAAC AGAT AAAT -AAT AACAT --AT AAAT AGAC AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
* * * *
11209670 AAAT ATAT AAAT ATAAT AACAT ATAAA AACAT ACAT TAAT AAAT AGTAAT
1 AAAT AAAT AAAT A-AAT AA-AT A-AAT AA-AT AAAT AAAT AAAT A--AAT
* *
11209720 -AAT AAAG AAAT AAAT -AAT AAAT ACAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
11209749 AGATAAAGGA
Statistics
Matches: 123, Mismatches: 30, Indels: 30
0.67 0.16 0.16
Matches are distributed among these distances:
2 2 0.02
3 14 0.11
4 87 0.71
5 16 0.13
6 4 0.03
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:11209637 original size:18 final size:18
Alignment explanation
Indices: 11209614--11209652 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11209604 GATAATATAT
*
11209614 TAATTAATAGATAAACAA
1 TAATTAACAGATAAACAA
*
11209632 TAATTAACAGATAAATAA
1 TAATTAACAGATAAACAA
11209650 TAA
1 TAA
11209653 CATATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (18 bp):
TAATTAACAGATAAACAA
Found at i:11209653 original size:14 final size:15
Alignment explanation
Indices: 11209630--11209662 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
11209620 ATAGATAAAC
11209630 AATAATTAACAGATA
1 AATAATTAACAGATA
*
11209645 AATAA-TAACATATA
1 AATAATTAACAGATA
11209659 AATA
1 AATA
11209663 GACAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (15 bp):
AATAATTAACAGATA
Found at i:11209737 original size:28 final size:27
Alignment explanation
Indices: 11209642--11209742 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 27
11209632 TAATTAACAG
* *
11209642 ATAAATAATAACATAT-A-AATAGACAA
1 ATAAATAATAA-ATATAATAATAAAAAA
11209668 ATAAATATATAAATATAATAACATATAAAAA
1 ATAAATA-ATAAATATAAT-A-ATA-AAAAA
* *
11209699 CATACATTAATAAATAGTAATAATAAAGAA
1 -ATA-AATAATAAATA-TAATAATAAAAAA
11209729 ATAAATAATAAATA
1 ATAAATAATAAATA
11209743 CATAAAAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
26 11 0.18
27 5 0.08
28 10 0.16
29 4 0.07
30 7 0.11
31 6 0.10
32 11 0.18
33 7 0.11
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (27 bp):
ATAAATAATAAATATAATAATAAAAAA
Found at i:11209821 original size:25 final size:25
Alignment explanation
Indices: 11209771--11209821 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11209761 AAAACAATAT
* ** *
11209771 ATATAAAATATAAAATAAGTATAAA
1 ATATAAAATACAAAATAAAAAAAAA
11209796 ATATAAAATACAAAATAAAAAAAAA
1 ATATAAAATACAAAATAAAAAAAAA
11209821 A
1 A
11209822 ACAAAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
ATATAAAATACAAAATAAAAAAAAA
Found at i:11212181 original size:19 final size:19
Alignment explanation
Indices: 11212157--11212227 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
11212147 AGGTTTAAAG
*
11212157 TTTAGGGTTTAGGTCAGGA
1 TTTAGGGTTTAGATCAGGA
*
11212176 TTTAGGGTTT-GATCTAGGG
1 TTTAGGGTTTAGATC-AGGA
* *
11212195 TTTGGGGTTT-GATTTTAGGA
1 TTTAGGGTTTAGA--TCAGGA
11212215 TTTAGGGTTTAGA
1 TTTAGGGTTTAGA
11212228 CAAAGGTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.07
19 24 0.57
20 12 0.29
21 3 0.07
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (19 bp):
TTTAGGGTTTAGATCAGGA
Found at i:11215877 original size:20 final size:20
Alignment explanation
Indices: 11215810--11215932 Score: 99
Period size: 20 Copynumber: 6.2 Consensus size: 20
11215800 ATGTGAAATT
11215810 TTTGTGAAATT-ATCG-T-AA
1 TTTGTGAAATTAAT-GTTGAA
* * *
11215828 TTTGTGAAACTATTGTAGAA
1 TTTGTGAAATTAATGTTGAA
*
11215848 TTTGTGAAATTAATGTTTAA
1 TTTGTGAAATTAATGTTGAA
**
11215868 TTTGTGAAATTGGTGTTGAA
1 TTTGTGAAATTAATGTTGAA
* * *
11215888 TTTATAAAGATTAATGTTAAA
1 TTTGTGAA-ATTAATGTTGAA
* * *
11215909 ATTATGAAATTGATGTTGAA
1 TTTGTGAAATTAATGTTGAA
11215929 TTTG
1 TTTG
11215933 ATAATTTCCA
Statistics
Matches: 80, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
18 11 0.14
19 1 0.01
20 53 0.66
21 15 0.19
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.45
Consensus pattern (20 bp):
TTTGTGAAATTAATGTTGAA
Found at i:11215889 original size:40 final size:40
Alignment explanation
Indices: 11215810--11215932 Score: 119
Period size: 41 Copynumber: 3.1 Consensus size: 40
11215800 ATGTGAAATT
* *
11215810 TTTGTGAAATT-ATCG--TAATTTGTGAAACT-ATTGTAGAA
1 TTTGTGAAATTAAT-GTTTAATTTGTGAAATTGA-TGTTGAA
*
11215848 TTTGTGAAATTAATGTTTAATTTGTGAAATTGGTGTTGAA
1 TTTGTGAAATTAATGTTTAATTTGTGAAATTGATGTTGAA
* * * * *
11215888 TTTATAAAGATTAATGTTAAAATTATGAAATTGATGTTGAA
1 TTTGTGAA-ATTAATGTTTAATTTGTGAAATTGATGTTGAA
11215929 TTTG
1 TTTG
11215933 ATAATTTCCA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
38 12 0.17
39 2 0.03
40 25 0.36
41 31 0.44
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.45
Consensus pattern (40 bp):
TTTGTGAAATTAATGTTTAATTTGTGAAATTGATGTTGAA
Found at i:11216200 original size:21 final size:21
Alignment explanation
Indices: 11216149--11216200 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
11216139 CCAAATCAAA
** *
11216149 GAAATAAAACAATCCCAAGAT
1 GAAATAAAGTAATCCCAAGAG
* *
11216170 GAAATGAAGTAATCCTAAGAG
1 GAAATAAAGTAATCCCAAGAG
11216191 GAAATAAAGT
1 GAAATAAAGT
11216201 CAATTTTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.17, T:0.17
Consensus pattern (21 bp):
GAAATAAAGTAATCCCAAGAG
Found at i:11216359 original size:20 final size:20
Alignment explanation
Indices: 11216331--11216368 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11216321 TTCTTTTGCA
*
11216331 TGGATGTTTATGGATATTGT
1 TGGAAGTTTATGGATATTGT
11216351 TGGAAGTTTATGGATATT
1 TGGAAGTTTATGGATATT
11216369 TAAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (20 bp):
TGGAAGTTTATGGATATTGT
Found at i:11216379 original size:20 final size:20
Alignment explanation
Indices: 11216334--11216401 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
11216324 TTTTGCATGG
**
11216334 ATGTTTATGGATATTGTTGGA
1 ATGTTTATGGATATT-TAAGA
*
11216355 A-GTTTATGGATATTTAAAA
1 ATGTTTATGGATATTTAAGA
* * *
11216374 ATGTTTATTGATAGTTATGA
1 ATGTTTATGGATATTTAAGA
11216394 ATGTTTAT
1 ATGTTTAT
11216402 ACATGGATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.08
20 35 0.90
21 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (20 bp):
ATGTTTATGGATATTTAAGA
Found at i:11219892 original size:15 final size:16
Alignment explanation
Indices: 11219875--11219931 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
11219865 AAATATTATT
11219875 AAATTATTTAAAATTA
1 AAATTATTTAAAATTA
* ** *
11219891 AAAATACAATAATATT-
1 AAATTA-TTTAAAATTA
*
11219907 AAATTATTTGAAATTA
1 AAATTATTTAAAATTA
11219923 AAATTATTT
1 AAATTATTT
11219932 TAACTAGTAA
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
AAATTATTTAAAATTA
Found at i:11220380 original size:72 final size:72
Alignment explanation
Indices: 11220176--11220554 Score: 254
Period size: 72 Copynumber: 5.3 Consensus size: 72
11220166 GTAGTGGATG
* * * * *
11220176 TTAAAATTTT--AATTTTAATAAAAACTGCATTTCTAAG-ATAAAAAATATAGTGAATGTTGAAA
1 TTAAAATTTTGAAATTTTAAGAAAAATTGTATTT-TGAGCATAAAAAATATAGTGGATGTTGAAA
11220238 CTTTATTT
65 CTTTATTT
* * * *** * * * * * *
11220246 TTAAAATTTTGAAATGTTAACAAATA-CCAAGTTTTGAGCTTAAGAAATGTAATAGATATTGAAA
1 TTAAAATTTTGAAATTTTAAGAAAAATTGTA-TTTTGAGCATAAAAAATATAGTGGATGTTGAAA
*
11220310 TTTTATTT
65 CTTTATTT
* * * *
11220318 TTGAAATTCTGAAATTTTAAGAAAGATTGTATTTTGAGCATAAAAAATGTAGTGGATGTTGAAAC
1 TTAAAATTTTGAAATTTTAAGAAAAATTGTATTTTGAGCATAAAAAATATAGTGGATGTTGAAAC
*
11220383 ATTATTT
66 TTTATTT
* ** * ** * * * *
11220390 TCAAAATCATG-GA--TTAA-AAAAATAATGTTTTGAGCAT-TAAAACATAGTGAATGTTTGAAA
1 TTAAAATTTTGAAATTTTAAGAAAAATTGTATTTTGAGCATAAAAAATATAGTGGATG-TTGAAA
*
11220450 CTTTCTTT
65 CTTTATTT
* * ** * * *
11220458 TCAAAATTTTAAAATTAAAAAAAAAAATTGTATTTTGAGCATAAAAAACATAATGGATGTTGAAA
1 TTAAAATTTTGAAATT-TTAAGAAAAATTGTATTTTGAGCATAAAAAATATAGTGGATGTTGAAA
*
11220523 TTTTATTT
65 CTTTATTT
* **
11220531 TTGAAATTTTTTAATTTTAAGAAA
1 TTAAAATTTTGAAATTTTAAGAAA
11220555 TACTATAATT
Statistics
Matches: 231, Mismatches: 66, Indels: 22
0.72 0.21 0.07
Matches are distributed among these distances:
67 12 0.05
68 36 0.16
69 5 0.02
70 10 0.04
71 5 0.02
72 108 0.47
73 42 0.18
74 13 0.06
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (72 bp):
TTAAAATTTTGAAATTTTAAGAAAAATTGTATTTTGAGCATAAAAAATATAGTGGATGTTGAAAC
TTTATTT
Found at i:11220521 original size:73 final size:71
Alignment explanation
Indices: 11220343--11220540 Score: 206
Period size: 68 Copynumber: 2.8 Consensus size: 71
11220333 TTTAAGAAAG
** * ** **
11220343 ATTGTATTTTGAGCATAAAAAATGTAGTGGATGTTGAAACATTATTTTCAAAATCATGGATTAAA
1 ATTGTATTTTGAGCATAAAAAACATAGTGGATGTTGAAACTTTATTTTCAAAATTTTAAATTAAA
*
11220408 AAAATA
66 AAAAAA
* * *
11220414 A-TG--TTTTGAGCAT-TAAAACATAGTGAATGTTTGAAACTTTCTTTTCAAAATTTTAAAATTA
1 ATTGTATTTTGAGCATAAAAAACATAGTGGATG-TTGAAACTTTATTTTCAAAATTTT-AAATT-
11220475 AAAAAAAAA
63 AAAAAAAAA
* * **
11220484 ATTGTATTTTGAGCATAAAAAACATAATGGATGTTGAAATTTTATTTTTGAAATTTT
1 ATTGTATTTTGAGCATAAAAAACATAGTGGATGTTGAAACTTTATTTTCAAAATTTT
11220541 TTAATTTTAA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
67 12 0.12
68 30 0.29
69 3 0.03
70 11 0.11
71 3 0.03
73 30 0.29
74 13 0.13
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (71 bp):
ATTGTATTTTGAGCATAAAAAACATAGTGGATGTTGAAACTTTATTTTCAAAATTTTAAATTAAA
AAAAAA
Found at i:11224058 original size:26 final size:27
Alignment explanation
Indices: 11224009--11224059 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
11223999 TCATTGGTTA
* *
11224009 AAACGACGTCGTTTTGGGTCTTTCTCT
1 AAACGACGTCATTTTGAGTCTTTCTCT
*
11224036 AAACGACG-CATTTTGAGTTTTTCT
1 AAACGACGTCATTTTGAGTCTTTCT
11224060 TTCCTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (27 bp):
AAACGACGTCATTTTGAGTCTTTCTCT
Found at i:11224854 original size:19 final size:18
Alignment explanation
Indices: 11224830--11224882 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
11224820 TGCTACTTTC
* *
11224830 TGTTTTTCTCTTTTTTTGT
1 TGTTTTTAT-TTTTTTTAT
11224849 TGTTTTTATTTTTTTTATT
1 TGTTTTTATTTTTTTTA-T
*
11224868 TTTTTTTATTTTTTT
1 TGTTTTTATTTTTTT
11224883 ATATAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.06, C:0.04, G:0.06, T:0.85
Consensus pattern (18 bp):
TGTTTTTATTTTTTTTAT
Found at i:11224863 original size:9 final size:9
Alignment explanation
Indices: 11224840--11224882 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
11224830 TGTTTTTCTC
*
11224840 TTTTTTTGT
1 TTTTTTTAT
*
11224849 TGTTTTTAT
1 TTTTTTTAT
11224858 TTTTTTTATT
1 TTTTTTTA-T
11224868 TTTTTTTAT
1 TTTTTTTAT
11224877 TTTTTT
1 TTTTTT
11224883 ATATAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.07, C:0.00, G:0.05, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:11224864 original size:10 final size:10
Alignment explanation
Indices: 11224851--11224882 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
11224841 TTTTTTGTTG
11224851 TTTTTA-TTT
1 TTTTTATTTT
11224860 TTTTTATTTT
1 TTTTTATTTT
11224870 TTTTTATTTT
1 TTTTTATTTT
11224880 TTT
1 TTT
11224883 ATATAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:11225333 original size:88 final size:87
Alignment explanation
Indices: 11225210--11225388 Score: 234
Period size: 88 Copynumber: 2.0 Consensus size: 87
11225200 GGTCTTACAG
* * *
11225210 AATCGACTGGGATAACATCACAAGTTAAAAAATAAAGAATCGATCATGATAAAACCGCGAATCGA
1 AATCGACTGGGATAACATCACAAGTCAAAAAATAAAGAATCGATCAGGATAAAACCACGAATCGA
11225275 AATTATGCCCGGAGATCTTATAA
66 AATTATGCCCGGAGATCTTA-AA
* * * * *
11225298 AATCGACTGGGATAAC-TCCATAAGTCAAAAGATAAAGAATCGATCGGGATAATACCATGAATCG
1 AATCGACTGGGATAACAT-CACAAGTCAAAAAATAAAGAATCGATCAGGATAAAACCACGAATCG
* * *
11225362 AATTTATGCCTGGAGGTCTTAAA
65 AAATTATGCCCGGAGATCTTAAA
11225385 AATC
1 AATC
11225389 ATGTTCGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 7 0.09
88 72 0.91
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (87 bp):
AATCGACTGGGATAACATCACAAGTCAAAAAATAAAGAATCGATCAGGATAAAACCACGAATCGA
AATTATGCCCGGAGATCTTAAA
Found at i:11225439 original size:110 final size:110
Alignment explanation
Indices: 11225274--11225631 Score: 446
Period size: 110 Copynumber: 3.3 Consensus size: 110
11225264 CCGCGAATCG
* * * * * * * * *
11225274 AAATTATGCCCGGAGATCTTATAAAATCGACTGGGATAACTCCATAAGTCAAAAGATAAAGAATC
1 AAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACAACAAGACAAAAGATAAAGAATC
** * *
11225339 GATCGGGATAATACCATGAATCGAATTTATGCCTGGAGGTCTTAA
66 GATCGGGATAATACCGCGAATCAAATTTATGCCCGGAGGTCTTAA
** * *
11225384 AAATCATGTTCGGAGGTCTTACAGAATCGATTGAGATAATACAACAAGACAAAAGATAAAGAATC
1 AAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACAACAAGACAAAAGATAAAGAATC
* *
11225449 GATCGGGATAATATCGCGAATCAAATTTATGCCCGAAGGTCTTAA
66 GATCGGGATAATACCGCGAATCAAATTTATGCCCGGAGGTCTTAA
* * * * *
11225494 AAATCATGCCCAGAGGTCTTACAGAATCTACTGAGATAACACCATAAGTCAAAAGATAAAGAATC
1 AAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACAACAAGACAAAAGATAAAGAATC
** * *
11225559 GATCAAGATAACACCGCGAATCAAATTTATGCCCGGAGGTCTTAG
66 GATCGGGATAATACCGCGAATCAAATTTATGCCCGGAGGTCTTAA
* *
11225604 AAATCATGCCCGGAAGTCTTATAGAATC
1 AAATCATGCCCGGAGGTCTTACAGAATC
11225632 ATGTTCGGAG
Statistics
Matches: 211, Mismatches: 37, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
110 211 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (110 bp):
AAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACAACAAGACAAAAGATAAAGAATC
GATCGGGATAATACCGCGAATCAAATTTATGCCCGGAGGTCTTAA
Found at i:11225640 original size:23 final size:23
Alignment explanation
Indices: 11225587--11225654 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
11225577 AATCAAATTT
*
11225587 ATGCCCGGAGGTCTTAGA-AATC
1 ATGCCCGGAGGTCTTACAGAATC
* *
11225609 ATGCCCGGAAGTCTTATAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
**
11225632 ATGTTCGGAGGTCTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
11225655 GATTGAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (23 bp):
ATGCCCGGAGGTCTTACAGAATC
Found at i:11225681 original size:132 final size:133
Alignment explanation
Indices: 11225506--11225761 Score: 415
Period size: 132 Copynumber: 1.9 Consensus size: 133
11225496 ATCATGCCCA
* *
11225506 GAGGTCTTACAGAATCTACTGAGATAACACCATAAGTCAAAAGATAAAGAATCGATCAAGATAAC
1 GAGGTCTTACAGAATCGACTGAGATAACACCACAAGTCAAAAGATAAAGAATCGATCAAGATAAC
*
11225571 ACCGCGAATCAAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGGAAGTCTTATAGAATCATGT
66 ACCGCGAATCAAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGGAAGTCTTACAGAATCATGT
11225636 TCG
131 TCG
* * *
11225639 GAGGTCTTACAGAATCGATTGA-ATAACACCACAAGTCAAAAGATAAAGAATCGATTAGGATAAC
1 GAGGTCTTACAGAATCGACTGAGATAACACCACAAGTCAAAAGATAAAGAATCGATCAAGATAAC
* * * *
11225703 ACCGCGAATCAAATTTATGCTCGGAGGTCTTATAAATCATGCTCGGAGGTCTTACAGAA
66 ACCGCGAATCAAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGGAAGTCTTACAGAA
11225762 GCAACTGAGA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
132 93 0.82
133 20 0.18
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (133 bp):
GAGGTCTTACAGAATCGACTGAGATAACACCACAAGTCAAAAGATAAAGAATCGATCAAGATAAC
ACCGCGAATCAAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGGAAGTCTTACAGAATCATGT
TCG
Found at i:11225690 original size:110 final size:109
Alignment explanation
Indices: 11225604--11225871 Score: 333
Period size: 110 Copynumber: 2.4 Consensus size: 109
11225594 GAGGTCTTAG
* * * *
11225604 AAATCATGCCCGGAAGTCTTATAGAATCATGTTCGGAGGTCTTACAGAATCGATTGA-ATAACAC
1 AAATCATGCCCGGAAGTCTTATA-AATCATGCTCGGAGGTCTTACAGAAGCAACTGAGATAACAC
*
11225668 CACAAGTCAAAAGATAAAGAATCGATTAGGATAACACCGCGAATCA
65 CACAAGTCAAAAGATAAAGAATCAATTA-GATAACACCGCGAATCA
* * * *
11225714 AATTTATGCTCGGAGGTCTTATAAATCATGCTCGGAGGTCTTACAGAAGCAACTGAGATAACACC
1 AAATCATGCCCGGAAGTCTTATAAATCATGCTCGGAGGTCTTACAGAAGCAACTGAGATAACACC
* * *
11225779 ACAAGTCAAAAGATAAAGAATCGATCAGTATAACACCGTGAATCA
66 ACAAGTCAAAAGATAAAGAATCAATTAG-ATAACACCGCGAATCA
* * * * *
11225824 AATTTATGCTC-GAAGGTCTTAGAAATCATGCTCGAAGGTCTTACAGAA
1 AAATCATGCCCGGAA-GTCTTATAAATCATGCTCGGAGGTCTTACAGAA
11225872 TCATGCCCGG
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
109 32 0.23
110 110 0.77
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (109 bp):
AAATCATGCCCGGAAGTCTTATAAATCATGCTCGGAGGTCTTACAGAAGCAACTGAGATAACACC
ACAAGTCAAAAGATAAAGAATCAATTAGATAACACCGCGAATCA
Found at i:11225877 original size:23 final size:22
Alignment explanation
Indices: 11225829--11225893 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 22
11225819 AATCAAATTT
*
11225829 ATGCTCGAAGGTCTTAGAAATC
1 ATGCTCGAAGGTCTTACAAATC
11225851 ATGCTCGAAGGTCTTACAGAATC
1 ATGCTCGAAGGTCTTACA-AATC
* *
11225874 ATGCCCGGAGGTCTTACAAA
1 ATGCTCGAAGGTCTTACAAA
11225894 ATTGATTGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (22 bp):
ATGCTCGAAGGTCTTACAAATC
Found at i:11226007 original size:23 final size:23
Alignment explanation
Indices: 11225980--11226029 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
11225970 AGATCTTAAA
* *
11225980 AATCATGTTCGGAGGTCTTATAG
1 AATCATGCTCGGAGCTCTTATAG
*
11226003 AATCATGCTCGGAGCTTTTATAG
1 AATCATGCTCGGAGCTCTTATAG
11226026 AATC
1 AATC
11226030 GATTGGGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (23 bp):
AATCATGCTCGGAGCTCTTATAG
Found at i:11226140 original size:23 final size:23
Alignment explanation
Indices: 11226104--11226161 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
11226094 ATGTCTGAAA
*
11226104 GTCTTAGA-AATCATGCAT-GGAG
1 GTCTTACAGAATCATG-ATCGGAG
* *
11226126 GTCTTATAGAATCATGTTCGGAG
1 GTCTTACAGAATCATGATCGGAG
11226149 GTCTTACAGAATC
1 GTCTTACAGAATC
11226162 GACTAGGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (23 bp):
GTCTTACAGAATCATGATCGGAG
Found at i:11226384 original size:22 final size:23
Alignment explanation
Indices: 11226358--11226426 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
11226348 CGAATCAAAT
*
11226358 TTATGCCCGAAGGTCTTAGA-AA
1 TTATGCCCGAAGGTCTTACAGAA
*
11226380 TTATGCCCGAAGATCTTACAGAA
1 TTATGCCCGAAGGTCTTACAGAA
* * * *
11226403 TCATGTCCGGAGGTCTTATAGAA
1 TTATGCCCGAAGGTCTTACAGAA
11226426 T
1 T
11226427 CGACTGAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 18 0.46
23 21 0.54
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (23 bp):
TTATGCCCGAAGGTCTTACAGAA
Found at i:11226517 original size:22 final size:22
Alignment explanation
Indices: 11226486--11226542 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
11226476 TATCACGAAT
*
11226486 CAAATTTATGCCTGGAGGTCTTA
1 CAAAATTATGCCT-GAGGTCTTA
* *
11226509 -GAAATTATGTTCTGAGGTCTTA
1 CAAAATTATG-CCTGAGGTCTTA
11226531 CAAAATTATGCC
1 CAAAATTATGCC
11226543 CAAAGGTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTATGCCTGAGGTCTTA
Found at i:11226666 original size:155 final size:155
Alignment explanation
Indices: 11226499--11226818 Score: 428
Period size: 155 Copynumber: 2.1 Consensus size: 155
11226489 ATTTATGCCT
* * * *
11226499 GGAGGTCTTAGAAATTATGTTCT-GAGGTCTTACAAAATTATGCCCAAAGGTCTTACAGAATCGA
1 GGAGGTCTTAGAAATCATGTT-TGGAGATCTTACAAAATCATGCACAAAGGTCTTACAGAATCGA
* * *
11226563 CTGTGATAACACCACAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTAT
65 CTGTGATAACACCACAAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGAATCAAATTTAT
* *
11226628 GCTCGGAAGTCTTAGAAATCATACT-C
130 GCCCAGAAGTCTTAGAAATCAT-CTCC
* ***
11226654 GGAGGTCTTAGAAATCATGTTTGGAGATCTTACAGAATCATGCATGGAGGTCTTACAGAATCGAC
1 GGAGGTCTTAGAAATCATGTTTGGAGATCTTACAAAATCATGCACAAAGGTCTTACAGAATCGAC
** * * *
11226719 TGTGATAACACCGTAAGTTAAAAAATAAAAAATCGATCGGGATAACATCGCGAATCAAATTTATG
66 TGTGATAACACCACAAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGAATCAAATTTATG
* *
11226784 CCCAGAGGTCTTAGAAATCATGTCC
131 CCCAGAAGTCTTAGAAATCATCTCC
11226809 GGAGGTCTTA
1 GGAGGTCTTA
11226819 CAGAATCGAC
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
154 2 0.01
155 141 0.99
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (155 bp):
GGAGGTCTTAGAAATCATGTTTGGAGATCTTACAAAATCATGCACAAAGGTCTTACAGAATCGAC
TGTGATAACACCACAAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGAATCAAATTTATG
CCCAGAAGTCTTAGAAATCATCTCC
Found at i:11226679 original size:22 final size:22
Alignment explanation
Indices: 11226626--11226708 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
11226616 AATCGAATTT
* *
11226626 ATGCTCGGAAGTCTTAGAAATC
1 ATGCTTGGAGGTCTTAGAAATC
* *
11226648 ATACTCGGAGGTCTTAGAAATC
1 ATGCTTGGAGGTCTTAGAAATC
* * *
11226670 ATGTTTGGAGATCTTACAGAATC
1 ATGCTTGGAGGTCTTAGA-AATC
*
11226693 ATGCATGGAGGTCTTA
1 ATGCTTGGAGGTCTTA
11226709 CAGAATCGAC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 33 0.66
23 17 0.34
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (22 bp):
ATGCTTGGAGGTCTTAGAAATC
Found at i:11226701 original size:23 final size:23
Alignment explanation
Indices: 11226666--11226715 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
11226656 AGGTCTTAGA
**
11226666 AATCATGTTTGGAGATCTTACAG
1 AATCATGCATGGAGATCTTACAG
*
11226689 AATCATGCATGGAGGTCTTACAG
1 AATCATGCATGGAGATCTTACAG
11226712 AATC
1 AATC
11226716 GACTGTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (23 bp):
AATCATGCATGGAGATCTTACAG
Found at i:11226805 original size:531 final size:526
Alignment explanation
Indices: 11225592--11227160 Score: 1522
Period size: 531 Copynumber: 3.0 Consensus size: 526
11225582 AATTTATGCC
** * * *
11225592 CGGAGGTCTTAGAAATCATGCCCGGA-AGTCTTATAGAATCATGTTCGGAGGTCTTACAGAATCG
1 CGGAGGTCTTAGAAATCATGTTCGGAGA-TCTTACAGAATCATGATAGGAGGTCTTACAGAATCG
* * *
11225656 AT-TGAATAACACCACAAGTCAAAAGATAAAGAATCGATTAGGATAACACCGCGAATCAAATTTA
65 ATGTG-ATAACACC-GAAGT-AAAAAATAAAGAATCGA-TAGGATAACATCGCGAATCAAATTTA
* * *
11225720 TGCTCGGAGGTCTTATAAATCATG-CTCGGAGGTCTTACAGAAGCAACTGAGATAACACCACAAG
126 TGCTCGGAGGTCTTACAAATCATGTCT-GGAGGTCTTACAGAATCGACTG-GATAACACCACAAG
* * ** *
11225784 TCAAAAGATAAAGAATCGA-TCAGTATAACACCGTGAATCAAATTTATGCTCGAAGGTCTTAGAA
189 TCAAAAGATAAAGAATTGATTC-GGATAACACCACGAATCAAATTTATGCCCGAAGGTCTTAGAA
* * * * * *
11225848 ATCATGCTCGAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATTGATTG-GAATAACACT
253 ATCATGCCCGAAGGTCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAG-ATAACAC-
* * * * * * *
11225912 ATAAGTCAAAAGATAAAGAATCGATCGGGATGACACCACAAATCGAATTTATGCCCAGAGATCTT
316 ACAAGTCAAAAGATAAAGAATCGATCGAGATAATA-CACGAATCGAATTTATGCCTAGAGGTCTT
* * * * * * * * * * *
11225977 AAAAATCATGTTCGGAGGTCTTATAGAATCATGCTCGGAGCTTTTATAGAATCGATTGGGATAAA
380 AGAAATCATGTTCAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAAC
* * * * * * *
11226042 ACCACAAGTCAAAAGATAAATAATCAATCAAG-TAACACTGCGAATGGAATTTATG-TCTGAAAG
445 ACCACAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGCTCTGAAAG
*
11226105 TCTTAGAAATCATGCAT
510 TCTTAGAAATCATACAT
* * *** * *
11226122 -GGAGGTCTTATAGAATCATGTTCGGAGGTCTTACAGAATC--GACTAGGATAACAT-CATAACT
1 CGGAGGTCTTAGA-AATCATGTTCGGAGATCTTACAGAATCATGA-TAGGAGGTCTTACAGAA-T
* * * * * * * * * *** * * * * ** *
11226183 CAAAAGATAAAGAATCAATCG-AG-ATAACATCACGAATCGATTTTAT-GCCTGGAGGCCTTAAA
63 C-GATG-T-GATAA-C-ACCGAAGTAAAAAATAAAGAATCGATAGGATAACATCG-CG-AATCAA
* * * * *
11226245 AATTAGGCTTGGAGGTCTTACAGAATCATGTCTGGAGGTCTTACAAAATCGATTAGGATAACACC
121 ATTTATGCTCGGAGGTCTTACA-AATCATGTCTGGAGGTCTTACAGAATCGACT-GGATAACACC
* * * *
11226310 ACAAGTCAAAAAATAAAAAATTAATTCGGATAACATCACGAATCAAATTTATGCCCGAAGGTCTT
184 ACAAGTCAAAAGATAAAGAATTGATTCGGATAACACCACGAATCAAATTTATGCCCGAAGGTCTT
* *
11226375 AGAAATTATGCCCGAAGATCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAGATAAC
249 AGAAATCATGCCCGAAGGTCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAGATAAC
* * *
11226440 ATCACAAGTCAAAAGATAAAGAATCGATTGAGATAATATCACGAATCAAATTTATGCCTGGAGGT
314 A-CACAAGTCAAAAGATAAAGAATCGATCGAGATAATA-CACGAATCGAATTTATGCCTAGAGGT
* * * ** *
11226505 CTTAGAAATTATGTTCTGAGGTCTTACAAAATTATGCCCAAAGGTCTTACAGAATCGACTGTGAT
377 CTTAGAAATCATGTTCAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCGACTGAGAT
*
11226570 AACACCACAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGCTC-GG
442 AACACCACAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGCTCTGA
11226634 AAGTCTTAGAAATCATAC-T
507 AAGTCTTAGAAATCATACAT
*
11226653 CGGAGGTCTTAGAAATCATGTTTGGAGATCTTACAGAATCATGCAT-GGAGGTCTTACAGAATCG
1 CGGAGGTCTTAGAAATCATGTTCGGAGATCTTACAGAATCATG-ATAGGAGGTCTTACAGAATCG
* *
11226717 ACTGTGATAACACCGTAAGTTAAAAAATAAAAAATCGATCGGGATAACATCGCGAATCAAATTTA
65 A-TGTGATAACACCG-AAG-TAAAAAATAAAGAATCGAT-AGGATAACATCGCGAATCAAATTTA
* * * * * *
11226782 TGCCCAGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAGAATCGACTGGGATTACACCATAAGT
126 TGCTCGGAGGTCTTACAAATCATGTCTGGAGGTCTTACAGAATCGACT-GGATAACACCACAAGT
* * * *
11226847 CGAAAGATAAAGAATTGATTGGGATAACACCACGAATCGAAA-TTATGTCCGAAAGTCTTAGAAA
190 CAAAAGATAAAGAATTGATTCGGATAACACCACGAATC-AAATTTATGCCCGAAGGTCTTAGAAA
** * ** *
11226911 TCATGCCCGGTGGTCTTATAGAATCATGTCCAAAGGTCTTATAGAATGGACTGAGATAACACCAC
254 TCATGCCCGAAGGTCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAGATAACA-CAC
** * *
11226976 AAGTTGAAAGATAAAGAATCAATCGAGATAATAC-CGTAAATCGAATTTATG-TTCAGAGGTCTT
318 AAGTCAAAAGATAAAGAATCGATCGAGATAATACACG--AATCGAATTTATGCCT-AGAGGTCTT
** * * *
11227039 AGAAATCATGCACAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCAACTGAAAAAAC
380 AGAAATCATGTTCAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAAC
* * * * *
11227104 TCCATAAGTCAAAAAATAAAGAATCGATCGAGATAATATCGTGAATCAAATTTATGC
445 ACCACAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGC
11227161 CCAGAGGTCT
Statistics
Matches: 830, Mismatches: 173, Indels: 71
0.77 0.16 0.07
Matches are distributed among these distances:
528 10 0.01
529 26 0.03
530 64 0.08
531 607 0.73
532 105 0.13
533 12 0.01
534 6 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (526 bp):
CGGAGGTCTTAGAAATCATGTTCGGAGATCTTACAGAATCATGATAGGAGGTCTTACAGAATCGA
TGTGATAACACCGAAGTAAAAAATAAAGAATCGATAGGATAACATCGCGAATCAAATTTATGCTC
GGAGGTCTTACAAATCATGTCTGGAGGTCTTACAGAATCGACTGGATAACACCACAAGTCAAAAG
ATAAAGAATTGATTCGGATAACACCACGAATCAAATTTATGCCCGAAGGTCTTAGAAATCATGCC
CGAAGGTCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAGATAACACACAAGTCAAA
AGATAAAGAATCGATCGAGATAATACACGAATCGAATTTATGCCTAGAGGTCTTAGAAATCATGT
TCAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAAGTCA
AAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGCTCTGAAAGTCTTAGAAATC
ATACAT
Found at i:11226883 original size:110 final size:110
Alignment explanation
Indices: 11226689--11226935 Score: 300
Period size: 110 Copynumber: 2.2 Consensus size: 110
11226679 GATCTTACAG
** * * *
11226689 AATCATGCATGGAGGTCTTACAGAATCGACTGTGATAACACCGTAAGTTAAAAAATAAAAAATCG
1 AATCATGCCCGGAGGTCTTACAGAATCGACTGGGATAACACCATAAGTCAAAAAATAAAAAATCG
* * *
11226754 ATCGGGATAACATCGCGAATC-AAATTTATGCCC-AGAGGTCTTAGA
66 ATCGGGATAACACCACGAATCGAAA-TTATGCCCGA-AAGTCTTAGA
* * * * * *
11226799 AATCATGTCCGGAGGTCTTACAGAATCGACTGGGATTACACCATAAGTCGAAAGATAAAGAATTG
1 AATCATGCCCGGAGGTCTTACAGAATCGACTGGGATAACACCATAAGTCAAAAAATAAAAAATCG
* *
11226864 ATTGGGATAACACCACGAATCGAAATTATGTCCGAAAGTCTTAGA
66 ATCGGGATAACACCACGAATCGAAATTATGCCCGAAAGTCTTAGA
* *
11226909 AATCATGCCCGGTGGTCTTATAGAATC
1 AATCATGCCCGGAGGTCTTACAGAATC
11226936 ATGTCCAAAG
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
110 112 0.97
111 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (110 bp):
AATCATGCCCGGAGGTCTTACAGAATCGACTGGGATAACACCATAAGTCAAAAAATAAAAAATCG
ATCGGGATAACACCACGAATCGAAATTATGCCCGAAAGTCTTAGA
Found at i:11227071 original size:23 final size:23
Alignment explanation
Indices: 11227029--11227092 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
11227019 AATTTATGTT
*
11227029 CAGAGGTCTTA-GAAATCATGCA
1 CAGAGGTCTTACAAAATCATGCA
*
11227051 CAGAGGTCTTACAAAATCATGCC
1 CAGAGGTCTTACAAAATCATGCA
* *
11227074 CGGAGGTCTTACAGAATCA
1 CAGAGGTCTTACAAAATCA
11227093 ACTGAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 11 0.30
23 26 0.70
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (23 bp):
CAGAGGTCTTACAAAATCATGCA
Found at i:11227140 original size:133 final size:130
Alignment explanation
Indices: 11225719--11227194 Score: 996
Period size: 133 Copynumber: 11.1 Consensus size: 130
11225709 AATCAAATTT
* * * *
11225719 ATGCTCGGAGGTCTTATA-AATCATGCTCGGAGGTCTTACAGAAGCAACTGAGATAACACCACAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
* *
11225783 GTCAAAAGATAAAGAATCGATC-AGTATAACACCGTGAATCAAATTTATGCTCGAAGGTCTTAGA
66 GTCAAAAGATAAAGAATCGATCGAG-ATAACACC--GAATCGAATTTATGC-CGGAGGTCTTAGA
11225847 AATC
127 AATC
* * * * * *
11225851 ATGCTCGAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATTGATTG-GAATAACACTATA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAG-ATAACACCACA
* * * * * *
11225915 AGTCAAAAGATAAAGAATCGATCGGGATGACACCACAAATCGAATTTATGCCCAGAGATCTTAAA
65 AGTCAAAAGATAAAGAATCGATCGAGATAACA-C-CGAATCGAATTTATG-CCGGAGGTCTTAGA
11225980 AATC
127 AATC
* * * * * * * * *
11225984 ATGTTCGGAGGTCTTATAGAATCATGCTCGGAGCTTTTATAGAATCGATTGGGATAAAACCACAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
* * * * * * *
11226049 GTCAAAAGATAAATAATCAATCAAG-TAACACTGCGAATGGAATTTATGTCTGAAAGTCTTAGAA
66 GTCAAAAGATAAAGAATCGATCGAGATAACAC--CGAATCGAATTTATG-CCGGAGGTCTTAGAA
11226113 ATC
128 ATC
* ** * *
11226116 ATGCAT-GGAGGTCTTATAGAATCATGTTCGGAGGTCTTACAGAATCGACT-AGGATAACATCAT
1 ATGC-TCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGA-GATAACACCAC
* * * * *
11226179 AACTCAAAAGATAAAGAATCAATCGAGATAACATCACGAATCGATTTTATGCCTGGAGGCCTTAA
64 AAGTCAAAAGATAAAGAATCGATCGAGATAACA-C-CGAATCGAATTTATGCC-GGAGGTCTTAG
*
11226244 AAATT
126 AAATC
* * * * * *
11226249 AGGCTTGGAGGTCTTACAGAATCATGTCTGGAGGTCTTACAAAATCGA-TTAGGATAACACCACA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGA-GATAACACCACA
* * ** * *
11226313 AGTCAAAAAATAAAAAATTAATTCG-GATAACATCACGAATCAAATTTATGCCCGAAGGTCTTAG
65 AGTCAAAAGATAAAGAATCGA-TCGAGATAACA-C-CGAATCGAATTTATG-CCGGAGGTCTTAG
*
11226377 AAATT
126 AAATC
* * * * * *
11226382 ATGCCCGAAGATCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAGATAACATCACAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
* * *
11226447 GTCAAAAGATAAAGAATCGATTGAGATAATATCACGAATCAAATTTATGCCTGGAGGTCTTAGAA
66 GTCAAAAGATAAAGAATCGATCGAGATAACA-C-CGAATCGAATTTATGCC-GGAGGTCTTAGAA
*
11226512 ATT
128 ATC
* * * * ** *
11226515 ATGTTCTGAGGTCTTACAAAATTATGCCCAAAGGTCTTACAGAATCGACTGTGATAACACCACAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
* *
11226580 GTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGCTCGGAAGTCTTAGAA
66 GTCAAAAGATAAAGAATCGATCGAGATAACACC--GAATCGAATTTATGC-CGGAGGTCTTAGAA
11226645 ATC
128 ATC
* * *** * * ***
11226648 ATACTCGGAGGTCTTAGA-AATCATGTTTGGAGATCTTACAGAATC-ATGCATGGAGGTCTTA-C
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGA--C-T-GAGATAACACC
* *** ** *** * * * * * **
11226710 AGAA-TCGACTGTGATAACACCGTAAGTTAAAAAATAAAAAATCG-ATCGGGATAACAT--CGCG
62 ACAAGTC-A-AAAGATAA-A--G-AA-TCGATCGAGATAACACCGAATC-GAAT-TTATGCCG-G
* * *
11226771 A-ATC--A-AATTT
117 AGGTCTTAGAAATC
* * * * * * *
11226781 ATGCCCAGAGGTCTTAGA-AATCATGTCCGGAGGTCTTACAGAATCGACTGGGATTACACCATAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
* * * * * * *
11226845 GTCGAAAGATAAAGAATTGATTGGGATAACACCACGAATCGAAATTATGTCCGAAAGTCTTAGAA
66 GTCAAAAGATAAAGAATCGATCGAGATAACA-C-CGAATCGAATTTATG-CCGGAGGTCTTAGAA
11226910 ATC
128 ATC
* * * * ** * *
11226913 ATGCCCGGTGGTCTTATAGAATCATGTCCAAAGGTCTTATAGAATGGACTGAGATAACACCACAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
** * * * *
11226978 GTTGAAAGATAAAGAATCAATCGAGATAATACCGTAAATCGAATTTATGTTCAGAGGTCTTAGAA
66 GTCAAAAGATAAAGAATCGATCGAGATAACACCG--AATCGAATTTATG-CCGGAGGTCTTAGAA
11227043 ATC
128 ATC
* * * * * * * *
11227046 ATGCACAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCAACTGAAAAAACTCCATAA
1 ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
* * * * *
11227111 GTCAAAAAATAAAGAATCGATCGAGATAATATCGTGAATCAAATTTATGCCCAGAGGTCTT-GAA
66 GTCAAAAGATAAAGAATCGATCGAGATAACA-C-CGAATCGAATTTATG-CCGGAGGTCTTAGAA
*
11227175 AGTT
128 A-TC
* *
11227179 ATGCTCGAAAGTCTTA
1 ATGCTCGGAGGTCTTA
11227195 AAGATTACGT
Statistics
Matches: 1051, Mismatches: 237, Indels: 111
0.75 0.17 0.08
Matches are distributed among these distances:
125 7 0.01
126 4 0.00
127 5 0.00
128 4 0.00
129 5 0.00
130 9 0.01
131 11 0.01
132 174 0.17
133 773 0.74
134 22 0.02
135 10 0.01
136 5 0.00
137 5 0.00
138 5 0.00
139 4 0.00
140 8 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (130 bp):
ATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGAGATAACACCACAA
GTCAAAAGATAAAGAATCGATCGAGATAACACCGAATCGAATTTATGCCGGAGGTCTTAGAAATC
Found at i:11227214 original size:398 final size:395
Alignment explanation
Indices: 11225719--11227222 Score: 1283
Period size: 398 Copynumber: 3.8 Consensus size: 395
11225709 AATCAAATTT
* ** * *
11225719 ATGCTCGGAGGTCTTATA-AATCATG-CTCGGAGGTCTTACAGAAGCAACTGAGATAACACCACA
1 ATGCACGGAGGTCTTATAGAATCATGTC-CAAAGGTCTTACAGAATCGACTGAGATAACACCACA
* * *
11225782 AGTCAAAAGATAAAGAATCGATC-AGTATAACACCGTGAATCAAATTTATGCTCGAAGGTCTTAG
65 AGTCAAAAGATAAAGAATCAATCGAG-ATAACACCGTGAATCGAATTTATGCTCGGAGGTCTTAG
* * * *
11225846 AAATCATGCTC-GAAGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATTGATTGGAATAACA
129 AAATCATGCACAG-AGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATCGACTGAAATAACA
* * * * * * * *
11225910 CTATAAGTCAAAAGATAAAGAATCGATCGGGATGACACCACAAATCGAATTTATGCCCAGAGATC
193 CCATAAGTCAAAAAATAAAAAATCGATCGGGATAACATCACGAATCAAATTTATGCCCAGAGGTC
* * * * * * * * * * *
11225975 TTAAAAATCATGTTCGGAGGTCTTATAGAATCATGCTCGGAGCTTTTATAGAATCGATTGGGATA
258 TT-GAAATTATGCTCGAAAGTCTTA-AGATTCGT-C-CGGAGGTCTTACAGAATCGACTGGGATA
* * * ** ** * * *
11226040 AAACCACAAGTCAAAAGATAAATAATCAATCAAG-TAACACTGCGAATGGAATTTATGTCTGAAA
319 ACACCACAAGTCAAAAGATAAAGAATCGATTGAGATAACACCACGAATCGAAATTATGTCCGAAA
11226104 GTCTTAGAAATC
384 GTCTTAGAAATC
* * ** * *
11226116 ATGCATGGAGGTCTTATAGAATCATGTTCGGAGGTCTTACAGAATCGACT-AGGATAACATCATA
1 ATGCACGGAGGTCTTATAGAATCATGTCCAAAGGTCTTACAGAATCGACTGA-GATAACACCACA
* * ** * * *
11226180 ACTCAAAAGATAAAGAATCAATCGAGATAACATCACGAATCGATTTTATGC-CTGGAGGCCTTAA
65 AGTCAAAAGATAAAGAATCAATCGAGATAACACCGTGAATCGAATTTATGCTC-GGAGGTCTTAG
* * *** * * * *
11226244 AAATTAGGCTTGGAGGTCTTACAGAATCATGTCTGGAGGTCTTACAAAATCGA-TTAGGATAACA
129 AAATCATGCACAGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATCGACTGA-AATAACA
* **
11226308 CCACAAGTCAAAAAATAAAAAATTAATTC-GGATAACATCACGAATCAAATTTATGCCC-GAAGG
193 CCATAAGTCAAAAAATAAAAAATCGA-TCGGGATAACATCACGAATCAAATTTATGCCCAG-AGG
* * * *
11226371 TCTTAGAAATTATGCCCG-AAGATCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGACTGAG
256 TCTT-GAAATTATGCTCGAAAG-TCTTA-AGATTC--GTCCGGAGGTCTTACAGAATCGACTGGG
* * *
11226435 ATAACATCACAAGTCAAAAGATAAAGAATCGATTGAGATAATATCACGAATC-AAATTTATG-CC
316 ATAACACCACAAGTCAAAAGATAAAGAATCGATTGAGATAACACCACGAATCGAAA-TTATGTCC
* * *
11226498 TGGAGGTCTTAGAAATT
380 -GAAAGTCTTAGAAATC
** * * * * * *
11226515 ATGTTCTGAGGTCTTACAAAATTATGCCCAAAGGTCTTACAGAATCGACTGTGATAACACCACAA
1 ATGCACGGAGGTCTTATAGAATCATGTCCAAAGGTCTTACAGAATCGACTGAGATAACACCACAA
* * *
11226580 GTCAAAAAATAAAGAATCGATCGAGATAACACCGTGAATCGAATTTATGCTCGGAAGTCTTAGAA
66 GTCAAAAGATAAAGAATCAATCGAGATAACACCGTGAATCGAATTTATGCTCGGAGGTCTTAGAA
* **
11226645 ATCATACTCGGAGGTCTTAGAAATCATGTTTGGAGATCTTACAGAATCATGCATGGAGGTCTTAC
131 ATC--A-T-----G-C------A-CA------GAGGTCTTACAGAATCATGCCCGGAGGTCTTAC
* ** * * *
11226710 AGAATCGACTGTGATAACACCGTAAGTTAAAAAATAAAAAATCGATCGGGATAACATCGCGAATC
174 AAAATCGACTGAAATAACACCATAAGTCAAAAAATAAAAAATCGATCGGGATAACATCACGAATC
11226775 AAATTTATGCCCAGAGGTC------TTA-----GAAA-TC-----A-T-GTCCGGAGGTCTTACA
239 AAATTTATGCCCAGAGGTCTTGAAATTATGCTCGAAAGTCTTAAGATTCGTCCGGAGGTCTTACA
* * * * *
11226821 GAATCGACTGGGATTACACCATAAGTCGAAAGATAAAGAATTGATTGGGATAACACCACGAATCG
304 GAATCGACTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATTGAGATAACACCACGAATCG
11226886 AAATTATGTCCGAAAGTCTTAGAAATC
369 AAATTATGTCCGAAAGTCTTAGAAATC
* * * *
11226913 ATGCCCGGTGGTCTTATAGAATCATGTCCAAAGGTCTTATAGAATGGACTGAGATAACACCACAA
1 ATGCACGGAGGTCTTATAGAATCATGTCCAAAGGTCTTACAGAATCGACTGAGATAACACCACAA
** * * * *
11226978 GTTGAAAGATAAAGAATCAATCGAGATAATACCGTAAATCGAATTTATGTTCAGAGGTCTTAGAA
66 GTCAAAAGATAAAGAATCAATCGAGATAACACCGTGAATCGAATTTATGCTCGGAGGTCTTAGAA
* * * * *
11227043 ATCATGCACAGAGGTCTTACAAAATCATGCCCGGAGGTCTTACAGAATCAACTGAAAAAACTCCA
131 ATCATGCACAGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATCGACTGAAATAACACCA
* * * **
11227108 TAAGTCAAAAAATAAAGAATCGATCGAGATAATATCGTGAATCAAATTTATGCCCAGAGGTCTTG
196 TAAGTCAAAAAATAAAAAATCGATCGGGATAACATCACGAATCAAATTTATGCCCAGAGGTCTTG
*
11227173 AAAGTTATGCTCGAAAGTCTTAAAGATTACGTCCAGAGGTCTTACA-AATC
261 AAA-TTATGCTCGAAAGTCTT-AAGATT-CGTCCGGAGGTCTTACAGAATC
11227223 TTAAAATCTT
Statistics
Matches: 886, Mismatches: 154, Indels: 134
0.75 0.13 0.11
Matches are distributed among these distances:
376 102 0.12
382 2 0.00
383 4 0.00
388 4 0.00
389 3 0.00
390 1 0.00
395 2 0.00
396 2 0.00
397 26 0.03
398 480 0.54
399 143 0.16
400 2 0.00
401 2 0.00
402 1 0.00
407 1 0.00
408 3 0.00
409 1 0.00
410 2 0.00
414 3 0.00
420 2 0.00
421 98 0.11
422 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (395 bp):
ATGCACGGAGGTCTTATAGAATCATGTCCAAAGGTCTTACAGAATCGACTGAGATAACACCACAA
GTCAAAAGATAAAGAATCAATCGAGATAACACCGTGAATCGAATTTATGCTCGGAGGTCTTAGAA
ATCATGCACAGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAAAATCGACTGAAATAACACCA
TAAGTCAAAAAATAAAAAATCGATCGGGATAACATCACGAATCAAATTTATGCCCAGAGGTCTTG
AAATTATGCTCGAAAGTCTTAAGATTCGTCCGGAGGTCTTACAGAATCGACTGGGATAACACCAC
AAGTCAAAAGATAAAGAATCGATTGAGATAACACCACGAATCGAAATTATGTCCGAAAGTCTTAG
AAATC
Found at i:11227437 original size:41 final size:41
Alignment explanation
Indices: 11227345--11227449 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 41
11227335 TTCTGAGAAA
*
11227345 GGTTCC-CTTTAAACAGAGGCTTTGAAATCTTGATTGAAATT
1 GGTTCCTC-TTAAACAGAGGCTTTGAAATCTTGATTGAAATC
*
11227386 GGTTCCTCTTAAGCAGAGGCTTTGAAATCTTGATTGAGAA-C
1 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTGA-AATC
** *
11227427 GGTTTTTCTTAAACAGAGACTTT
1 GGTTCCTCTTAAACAGAGGCTTT
11227450 AAAACTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 53 0.95
42 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (41 bp):
GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTGAAATC
Found at i:11229175 original size:17 final size:17
Alignment explanation
Indices: 11229149--11229201 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
11229139 AAAAATGTCC
*
11229149 CTTTTGTTTTTTTTTTT
1 CTTTTTTTTTTTTTTTT
11229166 CTTTTTTTTTTGTTTTTT
1 CTTTTTTTTTT-TTTTTT
* *
11229184 CATTTTTTTGTTTTTTT
1 CTTTTTTTTTTTTTTTT
11229201 C
1 C
11229202 ATGCCCCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.85
Consensus pattern (17 bp):
CTTTTTTTTTTTTTTTT
Found at i:11229788 original size:9 final size:9
Alignment explanation
Indices: 11229776--11229800 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11229766 CTTTTTCTAT
11229776 TTTTTTTAA
1 TTTTTTTAA
11229785 TTTTTTTAA
1 TTTTTTTAA
11229794 TTTTTTT
1 TTTTTTT
11229801 TTAAAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:11236152 original size:16 final size:15
Alignment explanation
Indices: 11236105--11236152 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
11236095 ATCATATAAG
11236105 AATAAATAAAACAAACT
1 AATAAATAAAA-AAA-T
11236122 AA-AAATAACAAAAAT
1 AATAAATAA-AAAAAT
11236137 AATAATATAAAAAAAT
1 AATAA-ATAAAAAAAT
11236153 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.11
16 17 0.61
17 8 0.29
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAATAAAAAAAT
Found at i:11237054 original size:28 final size:30
Alignment explanation
Indices: 11237021--11237093 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 30
11237011 AAGGGGTTCC
11237021 GAGAGCTTTTTCGAAAAATGA-GGTTTC-A
1 GAGAGCTTTTTCGAAAAATGAGGGTTTCGA
*
11237049 GAGAGC-TTTTC-AGAAATGAGGGTTTCGA
1 GAGAGCTTTTTCGAAAAATGAGGGTTTCGA
* *
11237077 TAGAGCTTTTTGGAAAA
1 GAGAGCTTTTTCGAAAA
11237094 GAGGGGTCCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 7 0.19
27 11 0.30
28 12 0.32
29 4 0.11
30 3 0.08
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (30 bp):
GAGAGCTTTTTCGAAAAATGAGGGTTTCGA
Found at i:11237097 original size:28 final size:27
Alignment explanation
Indices: 11237012--11237098 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
11237002 GGTTTTCTAA
* * *
11237012 AGGGGTTCCGAGAGCTTTTTCGAAAA-
1 AGGGTTTCAGAGAGCTTTTTAGAAAAG
* *
11237038 ATGAGGTTTCAGAGAGCTTTTCAGAAATG
1 A-G-GGTTTCAGAGAGCTTTTTAGAAAAG
* *
11237067 AGGGTTTCGATAGAGCTTTTTGGAAAAG
1 AGGGTTTC-AGAGAGCTTTTTAGAAAAG
11237095 AGGG
1 AGGG
11237099 GTCCGAGCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.02
27 7 0.15
28 39 0.81
29 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (27 bp):
AGGGTTTCAGAGAGCTTTTTAGAAAAG
Found at i:11237383 original size:9 final size:9
Alignment explanation
Indices: 11237344--11237393 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
11237334 TTTTTTAAAA
*
11237344 ATTATTATT
1 ATTATTAAT
*
11237353 ATTATTATT
1 ATTATTAAT
*
11237362 ATTATTATT
1 ATTATTAAT
*
11237371 ATTATTAAA
1 ATTATTAAT
11237380 ATTATTAAT
1 ATTATTAAT
*
11237389 GTTAT
1 ATTAT
11237394 ACTAAAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
ATTATTAAT
Found at i:11237386 original size:3 final size:3
Alignment explanation
Indices: 11237344--11237377 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11237334 TTTTTTAAAA
11237344 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11237378 AAATTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11237962 original size:17 final size:17
Alignment explanation
Indices: 11237942--11237974 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11237932 TTGAAAAATT
11237942 AAAAGAAAAA-CAAAAAC
1 AAAA-AAAAATCAAAAAC
11237959 AAAAAAAAATCAAAAA
1 AAAAAAAAATCAAAAA
11237975 ATTAGTAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAAAATCAAAAAC
Found at i:11241001 original size:53 final size:53
Alignment explanation
Indices: 11240860--11241003 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 53
11240850 TTGCTTTTAA
11240860 TTTTTTTTATT-AAGCTAGTGCTTTTCTTTGATTTGAAAACATTGTTTTCATT
1 TTTTTTTTATTAAAGCTAGTGCTTTTCTTTGATTTGAAAACATTGTTTTCATT
* * * * * * *
11240912 ATTATTTTA-TAAAACTGGTGTTTTTCTTTGATTTGAAAGC-TCTGTTTTTATT
1 TTTTTTTTATTAAAGCTAGTGCTTTTCTTTGATTTGAAAACAT-TGTTTTCATT
* *
11240964 TTTTTTTTATTAAAGCTTGTGCTTTGCTTTGATTTGAAAA
1 TTTTTTTTATTAAAGCTAGTGCTTTTCTTTGATTTGAAAA
11241004 TAGGGTAATG
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
51 2 0.03
52 48 0.64
53 25 0.33
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.56
Consensus pattern (53 bp):
TTTTTTTTATTAAAGCTAGTGCTTTTCTTTGATTTGAAAACATTGTTTTCATT
Found at i:11269277 original size:16 final size:16
Alignment explanation
Indices: 11269256--11269287 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11269246 TCGTTTACAG
11269256 CTCTATTTCAACCCGA
1 CTCTATTTCAACCCGA
*
11269272 CTCTATTTCAATCCGA
1 CTCTATTTCAACCCGA
11269288 TCCGGAGAGC
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:0.25, C:0.34, G:0.06, T:0.34
Consensus pattern (16 bp):
CTCTATTTCAACCCGA
Found at i:11269956 original size:18 final size:18
Alignment explanation
Indices: 11269930--11269966 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11269920 TCGTGAGCCA
11269930 TACCCATAGCTCTCTCAC
1 TACCCATAGCTCTCTCAC
* *
11269948 TACCGATAGTTCTCTCAC
1 TACCCATAGCTCTCTCAC
11269966 T
1 T
11269967 CCTTCTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.08, T:0.32
Consensus pattern (18 bp):
TACCCATAGCTCTCTCAC
Found at i:11288445 original size:25 final size:25
Alignment explanation
Indices: 11288415--11288495 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
11288405 TCGAACGTGA
*
11288415 GAAGAGTCAAATGTTCGAGATGTGG
1 GAAGAGTCAAATGTTCGAGATATGG
** *
11288440 GAAGAG-CTGATGGTTCGAGACATGG
1 GAAGAGTCAAAT-GTTCGAGATATGG
* *
11288465 GAAGAGTTGACA-GTTCGAGATATGG
1 GAAGAG-TCAAATGTTCGAGATATGG
11288490 GAAGAG
1 GAAGAG
11288496 CTTGGTTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
24 3 0.07
25 41 0.91
27 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.38, T:0.21
Consensus pattern (25 bp):
GAAGAGTCAAATGTTCGAGATATGG
Found at i:11288870 original size:52 final size:52
Alignment explanation
Indices: 11288784--11288887 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
11288774 GGACAAGAAT
11288784 ACTTGCAAAAGAAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTG
1 ACTTGCAAAAGAAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTG
* * * *
11288836 ACTTGCAAGAGAAGAATTCTAAGAG-GAGAGGGATTCTTAATGGGTAAGTTTG
1 ACTTGCAAAAGAAGAATTCCAAGAGAAAGA-GGATTCTTAATAGGTAAGTTTG
11288888 TATGGTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
51 3 0.06
52 44 0.94
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (52 bp):
ACTTGCAAAAGAAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTG
Found at i:11299847 original size:22 final size:22
Alignment explanation
Indices: 11299822--11299876 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
11299812 CGCGCTTGGC
11299822 CAGCGCATTCTTTCAAAGAGAA
1 CAGCGCATTCTTTCAAAGAGAA
11299844 CAGCGCATTCTTTCAAAGAGAA
1 CAGCGCATTCTTTCAAAGAGAA
11299866 CAGCGCATTCT
1 CAGCGCATTCT
11299877 AGCACTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (22 bp):
CAGCGCATTCTTTCAAAGAGAA
Found at i:11312551 original size:27 final size:29
Alignment explanation
Indices: 11312498--11312551 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
11312488 TAAAATAAAC
*
11312498 AAAAATTATCATGCAAATAATGTAATAAT
1 AAAAATTATCATGCAAATAATATAATAAT
11312527 AAAAA-TATCATGC-AATAATATAATA
1 AAAAATTATCATGCAAATAATATAATA
11312552 TATCATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTATCATGCAAATAATATAATAAT
Found at i:11312669 original size:18 final size:18
Alignment explanation
Indices: 11312642--11312678 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11312632 AGTCATACAA
* *
11312642 AATCATACAATCAAATAT
1 AATCACACAAACAAATAT
11312660 AATCACACAAACAAATAT
1 AATCACACAAACAAATAT
11312678 A
1 A
11312679 TTAATAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (18 bp):
AATCACACAAACAAATAT
Found at i:11312728 original size:20 final size:18
Alignment explanation
Indices: 11312691--11312729 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
11312681 AATAATCATG
*
11312691 TAATCAAATTAAATATAA
1 TAATCAAATGAAATATAA
11312709 TAATACAAATGAATATATAA
1 TAAT-CAAATGAA-ATATAA
11312729 T
1 T
11312730 CATATCATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
TAATCAAATGAAATATAA
Found at i:11312772 original size:24 final size:24
Alignment explanation
Indices: 11312721--11312773 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
11312711 ATACAAATGA
* * *
11312721 ATATATAATCATATCATGCAATAG
1 ATATACAATCACATCATGCAAAAG
*
11312745 ATATACAATCACATCATGCAAAAT
1 ATATACAATCACATCATGCAAAAG
11312769 ATATA
1 ATATA
11312774 TTATAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (24 bp):
ATATACAATCACATCATGCAAAAG
Found at i:11312865 original size:8 final size:8
Alignment explanation
Indices: 11312821--11312913 Score: 57
Period size: 8 Copynumber: 11.1 Consensus size: 8
11312811 AATTACAATT
11312821 AAAATAAA
1 AAAATAAA
11312829 AAATAGTAAA
1 AAA-A-TAAA
*
11312839 AAAATATA
1 AAAATAAA
**
11312847 ATTAT-AA
1 AAAATAAA
11312854 AAAATAAA
1 AAAATAAA
11312862 AAAATAAA
1 AAAATAAA
11312870 ACAAA-AAA
1 A-AAATAAA
11312878 TAGAAA-AAGA
1 -A-AAATAA-A
11312888 AAAATAAAA
1 AAAAT-AAA
*
11312897 AAAAGAAA
1 AAAATAAA
*
11312905 AAAAGAAA
1 AAAATAAA
11312913 A
1 A
11312914 GAAAAACCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
7 4 0.06
8 38 0.55
9 17 0.25
10 10 0.14
ACGTcount: A:0.81, C:0.01, G:0.05, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:11312868 original size:21 final size:21
Alignment explanation
Indices: 11312823--11312907 Score: 57
Period size: 23 Copynumber: 3.9 Consensus size: 21
11312813 TTACAATTAA
* *
11312823 AATAAAAAATAGTAAAAAAATAT
1 AATAAAAAA-AAT-AAAAAAGAT
*
11312846 AATTATAAAAAATAAAAAA-AT
1 AA-TAAAAAAAATAAAAAAGAT
*
11312867 AA-AACAAAAAATAGAAAAAGAAA
1 AATAA-AAAAAATA-AAAAAG-AT
*
11312890 AATAAAAAAAAGAAAAAA
1 AATAAAAAAAATAAAAAA
11312908 AGAAAAGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.02
20 8 0.16
21 9 0.18
22 11 0.22
23 14 0.27
24 8 0.16
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (21 bp):
AATAAAAAAAATAAAAAAGAT
Found at i:11312914 original size:13 final size:13
Alignment explanation
Indices: 11312854--11312919 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
11312844 ATAATTATAA
* *
11312854 AAAATAAAAAAAT
1 AAAAGAAAAAAAG
*
11312867 AAAACAAAAAATAG
1 AAAAGAAAAAA-AG
*
11312881 AAAAAGAAAAATAAAA
1 -AAAAG-AAAA-AAAG
11312897 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
11312910 AAAAGAAAAA
1 AAAAGAAAAA
11312920 CCTTCTGATC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 23 0.52
14 5 0.11
15 9 0.20
16 5 0.11
17 2 0.05
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.06
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:11312917 original size:34 final size:34
Alignment explanation
Indices: 11312853--11312919 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
11312843 TATAATTATA
*
11312853 AAAAATAAAAAAATAAAACAAAAAATAGAAAAAG
1 AAAAATAAAAAAATAAAACAAAAAAAAGAAAAAG
11312887 AAAAATAAAAAAA-AGAAA-AAAAGAAAAGAAAAA
1 AAAAATAAAAAAATA-AAACAAAA-AAAAGAAAAA
11312920 CCTTCTGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.85, C:0.01, G:0.07, T:0.06
Consensus pattern (34 bp):
AAAAATAAAAAAATAAAACAAAAAAAAGAAAAAG
Found at i:11312919 original size:14 final size:14
Alignment explanation
Indices: 11312859--11312919 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
11312849 TATAAAAAAT
* *
11312859 AAAAAAATAAAACA
1 AAAAAAAGAAAAGA
*
11312873 AAAAATAGAAAAAGA
1 AAAAAAAG-AAAAGA
*
11312888 AAAATAAAAAAAAG-
1 AAAA-AAAGAAAAGA
11312902 AAAAAAAGAAAAGA
1 AAAAAAAGAAAAGA
11312916 AAAA
1 AAAA
11312920 CCTTCTGATC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.21
14 14 0.37
15 14 0.37
16 2 0.05
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:11313884 original size:15 final size:14
Alignment explanation
Indices: 11313862--11313891 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
11313852 CATTAAAATC
11313862 AAAACTAAATTAAA
1 AAAACTAAATTAAA
11313876 AAAATCTAAATTAAA
1 AAAA-CTAAATTAAA
11313891 A
1 A
11313892 TCAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAACTAAATTAAA
Found at i:11318117 original size:21 final size:20
Alignment explanation
Indices: 11318083--11318126 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
11318073 TATTTTTTTC
11318083 TTTCCTTTTTTGTAATTTAA
1 TTTCCTTTTTTGTAATTTAA
*
11318103 TTTCTTTTTTGTGTAATTTAA
1 TTTCCTTTTT-TGTAATTTAA
11318124 TTT
1 TTT
11318127 TTGTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTCCTTTTTTGTAATTTAA
Found at i:11318267 original size:3 final size:3
Alignment explanation
Indices: 11318261--11318292 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11318251 AATAATAATA
11318261 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
11318293 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:11318938 original size:22 final size:22
Alignment explanation
Indices: 11318913--11319001 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 22
11318903 TTTTACTTGG
*
11318913 AGGTCTTAAGGATTGTGCCTGA
1 AGGTCTTAAGGATTATGCCTGA
** *
11318935 AGGT-TTTGGAGATTATG-CTTA
1 AGGTCTTAAG-GATTATGCCTGA
*
11318956 GAGGTCTTAAGGATTATGCATGGA
1 -AGGTCTTAAGGATTATGCCT-GA
*
11318980 A-GTCTTAAAGATTATGCCTGA
1 AGGTCTTAAGGATTATGCCTGA
11319001 A
1 A
11319002 AATTTTACAC
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
21 9 0.17
22 37 0.71
23 5 0.10
24 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (22 bp):
AGGTCTTAAGGATTATGCCTGA
Found at i:11318992 original size:44 final size:44
Alignment explanation
Indices: 11318912--11318996 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
11318902 ATTTTACTTG
* * * **
11318912 GAGGTCTTAAGGATTGTGCCTGAAGGTTTTGGAGATTATGCTTA
1 GAGGTCTTAAGGATTATGCATGAAGGTCTTAAAGATTATGCTTA
11318956 GAGGTCTTAAGGATTATGCATGGAA-GTCTTAAAGATTATGC
1 GAGGTCTTAAGGATTATGCAT-GAAGGTCTTAAAGATTATGC
11318997 CTGAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.91
45 3 0.09
ACGTcount: A:0.27, C:0.09, G:0.29, T:0.34
Consensus pattern (44 bp):
GAGGTCTTAAGGATTATGCATGAAGGTCTTAAAGATTATGCTTA
Found at i:11319202 original size:106 final size:104
Alignment explanation
Indices: 11319015--11319224 Score: 242
Period size: 106 Copynumber: 2.0 Consensus size: 104
11319005 TTTACACATC
* * *
11319015 TCAAAATCTTTGAATTCTCCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCT
1 TCAAAATCTTTGAATGCTCCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATATTTTACT
* *
11319080 CGAAGGTCTTAGAGATTATGCCCGAAGGTCATAGAGATT
66 AGAAGGTCTTAAAGATTATGCCCGAAGGTCATAGAGATT
* * * * *
11319119 TCAAAATTTTTGAATGCTCTTTATACATTAGAGGTATTGAAACTTTAAAATTTTAAAATATTTTA
1 TCAAAATCTTTGAATGCTCCTCATA-A-TAGAGGCATTGAAACTTTAAAAATTTAAAATATTTT-
* * * * **
11319184 ACTAG-AGTTTTTAAAGATTGTGTCCGAAGGTTTTAGAGATT
63 ACTAGAAGGTCTTAAAGATTATGCCCGAAGGTCATAGAGATT
11319225 ATGATCGAAG
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
104 21 0.24
105 1 0.01
106 62 0.71
107 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (104 bp):
TCAAAATCTTTGAATGCTCCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATATTTTACT
AGAAGGTCTTAAAGATTATGCCCGAAGGTCATAGAGATT
Found at i:11319223 original size:22 final size:22
Alignment explanation
Indices: 11319192--11319240 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
11319182 TAACTAGAGT
*
11319192 TTTTAAAGATTGTG-TCCGAAGG
1 TTTTAAAGATTATGAT-CGAAGG
*
11319214 TTTTAGAGATTATGATCGAAGG
1 TTTTAAAGATTATGATCGAAGG
11319236 TTTTA
1 TTTTA
11319241 TAAATCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (22 bp):
TTTTAAAGATTATGATCGAAGG
Found at i:11319346 original size:126 final size:128
Alignment explanation
Indices: 11319080--11319346 Score: 308
Period size: 126 Copynumber: 2.1 Consensus size: 128
11319070 ATGTTTTGCT
* * * * * *
11319080 CGAAGGTCTTAGAGATTATGCCCGAAGGTCATAGAGATTTCAAAATTTTTGAATGCTCTTTATAC
1 CGAAGGTCTTAGAGATTATGACCGAAGGTCATAGAAATCTCAAAATCTTTGAATGCTCCTCATAC
* * **
11319145 ATTAGAGGTATTGAAACTTTAAAATTTTAAAATATTTTAACTAGAGTTTTTAAAGATTGTGTC
66 ATTAGAGGTATTGAAACTTTAAAATTTTAAAATATTTTAACTAGAGGTCTTAAAGATTGTACC
* * ** *
11319208 CGAAGGTTTTAGAGATTATGATCGAAGGTTTTATAAATCTCAAAATCTTTGAATGCTCCTCATA-
1 CGAAGGTCTTAGAGATTATGACCGAAGGTCATAGAAATCTCAAAATCTTTGAATGCTCCTCATAC
* * * **
11319272 A-TAGAGGTATTGAAACTTTAAATTTTTAAAATATTTT-TCTTGGAGGTCTTAGGGATTGTACC
66 ATTAGAGGTATTGAAACTTTAAAATTTTAAAATATTTTAAC-TAGAGGTCTTAAAGATTGTACC
11319334 C-AGAGGTCTTAGA
1 CGA-AGGTCTTAGA
11319347 AATTTGTTTG
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
125 2 0.02
126 60 0.52
127 1 0.01
128 53 0.46
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (128 bp):
CGAAGGTCTTAGAGATTATGACCGAAGGTCATAGAAATCTCAAAATCTTTGAATGCTCCTCATAC
ATTAGAGGTATTGAAACTTTAAAATTTTAAAATATTTTAACTAGAGGTCTTAAAGATTGTACC
Found at i:11319618 original size:18 final size:18
Alignment explanation
Indices: 11319595--11319661 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
11319585 TCCATCAAAT
*
11319595 GATGTGAATGCAAATGTC
1 GATGTGAATGCAAATATC
*
11319613 GATGTGAATGCAAATATT
1 GATGTGAATGCAAATATC
* *
11319631 AATGTGAATGCAAATATT
1 GATGTGAATGCAAATATC
* *
11319649 AATGCGAATGCAA
1 GATGTGAATGCAA
11319662 GAATGTGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.28
Consensus pattern (18 bp):
GATGTGAATGCAAATATC
Found at i:11321050 original size:85 final size:85
Alignment explanation
Indices: 11320961--11321116 Score: 222
Period size: 85 Copynumber: 1.8 Consensus size: 85
11320951 TTTACTTAGG
* * * * * *
11320961 ATTCTAATTGAAACTTTATTCACTTTTTACCCTAAATTCTCATCTCTGAGGTACATATCTTTCTT
1 ATTCTAACTAAAACTTCATTCACTTTTTACCCTAAATTCTCATATCTAAAGTACATATCTTTCTT
11321026 TTCTTTGCTCCATTTTTTTT
66 TTCTTTGCTCCATTTTTTTT
* ** *
11321046 ATTCTAACTAAAACTTCATTCACTTTTTGCTTTAAATTCTCATATCTAAAGTACATGTCTTTCTT
1 ATTCTAACTAAAACTTCATTCACTTTTTACCCTAAATTCTCATATCTAAAGTACATATCTTTCTT
11321111 TTCTTT
66 TTCTTT
11321117 ACTCTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.51
Consensus pattern (85 bp):
ATTCTAACTAAAACTTCATTCACTTTTTACCCTAAATTCTCATATCTAAAGTACATATCTTTCTT
TTCTTTGCTCCATTTTTTTT
Found at i:11321129 original size:15 final size:14
Alignment explanation
Indices: 11321103--11321157 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 14
11321093 AAAGTACATG
*
11321103 TCTTTCTTTTCTTTAC
1 TCTTT-TTTTCTTT-T
11321119 TCTTTTTTTCTGTTT
1 TCTTTTTTTCT-TTT
*
11321134 TCTTTTTTTTTTTTT
1 TC-TTTTTTTCTTTT
11321149 TCTTTTTTT
1 TCTTTTTTT
11321158 TCCTTTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.20
15 13 0.37
16 15 0.43
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (14 bp):
TCTTTTTTTCTTTT
Found at i:11321135 original size:22 final size:22
Alignment explanation
Indices: 11321109--11321156 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
11321099 CATGTCTTTC
11321109 TTTTCTTTACTCTTTTTTTCTG
1 TTTTCTTTACTCTTTTTTTCTG
** * *
11321131 TTTTCTTTTTTTTTTTTTTCTT
1 TTTTCTTTACTCTTTTTTTCTG
11321153 TTTT
1 TTTT
11321157 TTCCTTTCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTCTTTACTCTTTTTTTCTG
Found at i:11321144 original size:10 final size:10
Alignment explanation
Indices: 11321105--11321163 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
11321095 AGTACATGTC
*
11321105 TTTCTTTTCT
1 TTTCTTTTTT
* *
11321115 TTACTCTTTT
1 TTTCTTTTTT
11321125 TTTCTGTTTTCT
1 TTTCT-TTTT-T
*
11321137 TTTTTTTTTT
1 TTTCTTTTTT
11321147 TTTCTTTTTT
1 TTTCTTTTTT
*
11321157 TTCCTTT
1 TTTCTTT
11321164 CACTTTTGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 27 0.69
11 7 0.18
12 5 0.13
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:11321158 original size:15 final size:15
Alignment explanation
Indices: 11321119--11321158 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
11321109 TTTTCTTTAC
*
11321119 TCTTTTTTTCTGTTT
1 TCTTTTTTTTTGTTT
*
11321134 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTGTTT
11321149 TCTTTTTTTT
1 TCTTTTTTTT
11321159 CCTTTCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (15 bp):
TCTTTTTTTTTGTTT
Found at i:11328683 original size:19 final size:19
Alignment explanation
Indices: 11328661--11328723 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
11328651 TTTTCTTTCC
11328661 TTTTTTTTTAATTTAATTT
1 TTTTTTTTTAATTTAATTT
* *
11328680 TTTTTGTATAATTTAATTT
1 TTTTTTTTTAATTTAATTT
*
11328699 TTTTAATTAATTAATTTAATTT
1 TTTT--TT-TTTAATTTAATTT
11328721 TTT
1 TTT
11328724 ATATTTTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 21 0.58
21 1 0.03
22 14 0.39
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTTTTAATTTAATTT
Found at i:11331904 original size:51 final size:51
Alignment explanation
Indices: 11331822--11331970 Score: 147
Period size: 51 Copynumber: 2.9 Consensus size: 51
11331812 TTGATTTATG
* ** * *
11331822 TTTTAATGAGAATTGATGCTGAAATCCAATCCCAAAAATCTCTC-CCTATCA
1 TTTTAATGAGAATTGATTCTGAAATTAAATCCTAAAAATCTCTCAAC-ATCA
* * * * * *
11331873 TTTTAATGTGAATTGATTATGGAATTAAATCCTGACAATCTTTCAACATCA
1 TTTTAATGAGAATTGATTCTGAAATTAAATCCTAAAAATCTCTCAACATCA
** *
11331924 TTTTCAATGCCAATTGATTCTAAAATTAAATCCTAAAAATCTCTCAA
1 TTTT-AATGAGAATTGATTCTGAAATTAAATCCTAAAAATCTCTCAA
11331971 TTGCCATTGA
Statistics
Matches: 77, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
51 42 0.55
52 35 0.45
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (51 bp):
TTTTAATGAGAATTGATTCTGAAATTAAATCCTAAAAATCTCTCAACATCA
Found at i:11331965 original size:52 final size:51
Alignment explanation
Indices: 11331849--11331970 Score: 129
Period size: 52 Copynumber: 2.4 Consensus size: 51
11331839 GCTGAAATCC
* * ** **
11331849 AATCCCAAAAATCTCTC-CCTATCATTTTAATGTGAATTGATTATGGAATTA
1 AATCCTAAAAATCTCTCAAC-ATCATTTTAATGCCAATTGATTATAAAATTA
* * * *
11331900 AATCCTGACAATCTTTCAACATCATTTTCAATGCCAATTGATTCTAAAATTA
1 AATCCTAAAAATCTCTCAACATCATTTT-AATGCCAATTGATTATAAAATTA
11331952 AATCCTAAAAATCTCTCAA
1 AATCCTAAAAATCTCTCAA
11331971 TTGCCATTGA
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
51 21 0.38
52 35 0.62
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (51 bp):
AATCCTAAAAATCTCTCAACATCATTTTAATGCCAATTGATTATAAAATTA
Found at i:11332598 original size:120 final size:119
Alignment explanation
Indices: 11332473--11332749 Score: 286
Period size: 119 Copynumber: 2.3 Consensus size: 119
11332463 TAGAACTGCT
* * * * * *
11332473 AGTCAGGAAATGATCTGGACTAAACTGAGATTGAATGATTGATATGAAACCACCAGTCGAAAAGA
1 AGTCAGGAAATGATCTGGCCTAAGCTGAGATCGAATGATCGAGACGAAACCACCAGTC-AAAAGA
** * * * * * *
11332538 TAAAGTGACCAGGATCGAGTTCAAA-TCAAAGATGATTGATCAGGACAAAATTGCG
65 TAAAGCAACCAAGACCAAG-TCAAAGTCAAAGATGACTAATCAGGACAAAATCGCG
* * ** * ** *
11332593 AGTCAGAAAATGATTTGGCCTAAGCCAAGATCGAATGATCGAGACGAAATCATGAGTCTAAAGAT
1 AGTCAGGAAATGATCTGGCCTAAGCTGAGATCGAATGATCGAGACGAAACCACCAGTCAAAAGAT
* * * *
11332658 AAGGCAACCAAGACCAAGTCAAAGTCGAAGATGACTAATCGGGACAAAATCGTG
66 AAAGCAACCAAGACCAAGTCAAAGTCAAAGATGACTAATCAGGACAAAATCGCG
*
11332712 AGTCAAGAAATGATCTGGCCTAAGCTGAGATCGAATGA
1 AGTCAGGAAATGATCTGGCCTAAGCTGAGATCGAATGA
11332750 CTGGGACAAA
Statistics
Matches: 125, Mismatches: 31, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
118 5 0.04
119 75 0.60
120 45 0.36
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (119 bp):
AGTCAGGAAATGATCTGGCCTAAGCTGAGATCGAATGATCGAGACGAAACCACCAGTCAAAAGAT
AAAGCAACCAAGACCAAGTCAAAGTCAAAGATGACTAATCAGGACAAAATCGCG
Found at i:11332840 original size:118 final size:118
Alignment explanation
Indices: 11332611--11333421 Score: 419
Period size: 118 Copynumber: 6.8 Consensus size: 118
11332601 AATGATTTGG
** * * * * * * *
11332611 CCTAAGCCAAGATCGAATGATCGAGACGAAATCATGAGTC-TAAAGATAAGGCAACCAAGACCAA
1 CCTAAGCTGAGATCGAATGATCGAGACAAAATC--GAGTCAAAAAGATAAAGTAACTAGGACCGA
* * * * * * * ** **
11332675 GTCAAAGTCGAAGATGACTAATCGGGACAAAATCGTGAGTCAAGAAATGATCTGG
64 GTCAAGGTCGAAAATGACTGATCGAGATAGAACCACGAGTCAAGAAATGATCTAA
* * * * *
11332730 CCTAAGCTGAGATCGAATGA-CTGGGACAAAATCGAGACAAAAAGATAAATTGACTAGGATCGAG
1 CCTAAGCTGAGATCGAATGATC-GAGACAAAATCGAGTCAAAAAGATAAAGTAACTAGGACCGAG
* * *
11332794 TTAAGGTCGAAGATGACTGATCGAGATAGAACCACGAGTCAAGAAATGATCTAG
65 TCAAGGTCGAAAATGACTGATCGAGATAGAACCACGAGTCAAGAAATGATCTAA
* * * * *
11332848 CCTAAG-TCAAGATCAAATGATCGAGATAAAA-CCATGGTCTAAAA-ATAAAGTAACTAGGACCG
1 CCTAAGCT-GAGATCGAATGATCGAGACAAAATCGA--GTCAAAAAGATAAAGTAACTAGGACCG
** * * * * * * * * *
11332910 AGTTGAGGTCGAAGATGACTGACCAAGAT-GAAATCATGAGTTAGGAAATAATATAA
63 AGTCAAGGTCGAAAATGACTGATCGAGATAG-AACCACGAGTCAAGAAATGATCTAA
* * * * * * * * ** *
11332966 CTTGAGCCGAGATCGAACGATTGGGATAAAATTGTGAGT-TTAAAGATAAAGCAACT-GGACCGA
1 CCTAAGCTGAGATCGAATGATCGAGACAAAA-T-CGAGTCAAAAAGATAAAGTAACTAGGACCGA
* *
11333029 GTCAAGGTCGAAAATGACTGATC-ACGATAGAACTACGAGTCAAAAAATGATCTAA
64 GTCAAGGTCGAAAATGACTGATCGA-GATAGAACCACGAGTCAAGAAATGATCTAA
* * * * * * * *
11333084 CCTGAGTTGATATCAAATGATCGAGACAAAATCATGAGTTAAAAAGATAAAGTGACCAGGACCAA
1 CCTAAGCTGAGATCGAATGATCGAGACAAAATC--GAGTCAAAAAGATAAAGTAACTAGGACCGA
* * * * *
11333149 GTCAAGGTC-AAAGATGACTGACCGAGAT-GAAATCACTAGTCAAAAAATGATCTGA
64 GTCAAGGTCGAAA-ATGACTGATCGAGATAG-AACCACGAGTCAAGAAATGATCTAA
* * * * ** ** * *
11333204 CTTGAA-CCGAGATCGAATGA-CCAGAACAAAACTATGAGTTGAAAAGATAAAACAAATAGGATC
1 CCT-AAGCTGAGATCGAATGATCGAG-ACAAAA-T-CGAGTCAAAAAGATAAAGTAACTAGGACC
* ** * * * ** * * **
11333267 GAGTCGAGGTAAAAAATGATTGATC-AGGGTGGAACCGTGACTTAAGAAATGATCTGG
62 GAGTCAAGGTCGAAAATGACTGATCGA-GATAGAACCACGAGTCAAGAAATGATCTAA
* * * * * * * *
11333324 CCTAAGCTAATATCGAATGATCGAGACAAAATTGCAAGTC-AAAAGATAAAATGACCAAGATCGA
1 CCTAAGCTGAGATCGAATGATCGAGACAAAA-T-CGAGTCAAAAAGATAAAGTAACTAGGACCGA
*
11333388 GTCAAGGTCGAAAATGACTGATCGGGATAGAACC
64 GTCAAGGTCGAAAATGACTGATCGAGATAGAACC
11333422 GCAAGTTAGA
Statistics
Matches: 521, Mismatches: 140, Indels: 62
0.72 0.19 0.09
Matches are distributed among these distances:
117 10 0.02
118 241 0.46
119 114 0.22
120 145 0.28
121 11 0.02
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (118 bp):
CCTAAGCTGAGATCGAATGATCGAGACAAAATCGAGTCAAAAAGATAAAGTAACTAGGACCGAGT
CAAGGTCGAAAATGACTGATCGAGATAGAACCACGAGTCAAGAAATGATCTAA
Found at i:11334621 original size:7 final size:8
Alignment explanation
Indices: 11334601--11334631 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
11334591 TTTTTTATGT
11334601 TTTTTTCTC
1 TTTTTTC-C
11334610 TTTTTTCC
1 TTTTTTCC
11334618 TTTTTTCC
1 TTTTTTCC
11334626 TTTTTT
1 TTTTTT
11334632 TTGGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCC
Found at i:11338483 original size:19 final size:19
Alignment explanation
Indices: 11338461--11338501 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
11338451 AAGAGTAAAT
11338461 AAAAATA-AA-CAAAATAAG
1 AAAAATAGAATCAAAAT-AG
11338479 AAAAATAGAATCAAAATAG
1 AAAAATAGAATCAAAATAG
11338498 AAAA
1 AAAA
11338502 TGGAGTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAATAGAATCAAAATAG
Found at i:11339063 original size:51 final size:52
Alignment explanation
Indices: 11338999--11339145 Score: 181
Period size: 51 Copynumber: 2.8 Consensus size: 52
11338989 TTGATTTCTG
* **
11338999 TTTTATTGAGAATTGATTTTGAAATCCAATCCCAAAAATCTCTCC-CTATCA-
1 TTTTAATGAGAATTGATTTTGAAATTAAATCCCAAAAATCTCTCCAC-ATCAT
* * * * *
11339050 TTTTAATGTGAATTGATTATGGAATTAAATCCTAACAATCTCTCCACATCAT
1 TTTTAATGAGAATTGATTTTGAAATTAAATCCCAAAAATCTCTCCACATCAT
**
11339102 TTTTAATGCCAATTGATTTTGAAATTAAATCCCAAAAATCTCTC
1 TTTTAATGAGAATTGATTTTGAAATTAAATCCCAAAAATCTCTC
11339146 AATTACGGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
51 41 0.51
52 39 0.49
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (52 bp):
TTTTAATGAGAATTGATTTTGAAATTAAATCCCAAAAATCTCTCCACATCAT
Found at i:11339128 original size:52 final size:51
Alignment explanation
Indices: 11339009--11339145 Score: 177
Period size: 52 Copynumber: 2.7 Consensus size: 51
11338999 TTTTATTGAG
** **
11339009 AATTGATTTTGAAATCCAATCCCAAAAATCTCTCCCTATCATTTTAATGTG
1 AATTGATTTTGAAATTAAATCCCAAAAATCTCTCCCTATCATTTTAATGCC
* * * *
11339060 AATTGATTATGGAATTAAATCCTAACAATCTCTCCAC-ATCATTTTTAATGCC
1 AATTGATTTTGAAATTAAATCCCAAAAATCTCTCC-CTATCA-TTTTAATGCC
11339112 AATTGATTTTGAAATTAAATCCCAAAAATCTCTC
1 AATTGATTTTGAAATTAAATCCCAAAAATCTCTC
11339146 AATTACGGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 33 0.46
52 39 0.54
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (51 bp):
AATTGATTTTGAAATTAAATCCCAAAAATCTCTCCCTATCATTTTAATGCC
Found at i:11339285 original size:49 final size:51
Alignment explanation
Indices: 11339217--11339321 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 51
11339207 AAAAAAATAA
* * *
11339217 AATAATTATCAAAAGGAATAACTATTGGAAGTGTTT-CTT-TAAAATATG-G
1 AATAATTATAAAAAAGAATAACTATTGGAA-TGTTTCCTTACAAAATATGAG
*
11339266 AATAATTATAAAAAAGAATAACTTTTGGAATGTTTCCTTACAAAATATGAG
1 AATAATTATAAAAAAGAATAACTATTGGAATGTTTCCTTACAAAATATGAG
11339317 AATAA
1 AATAA
11339322 GTGTGGGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
48 5 0.10
49 30 0.61
50 8 0.16
51 6 0.12
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (51 bp):
AATAATTATAAAAAAGAATAACTATTGGAATGTTTCCTTACAAAATATGAG
Found at i:11339482 original size:48 final size:48
Alignment explanation
Indices: 11339357--11339579 Score: 292
Period size: 48 Copynumber: 4.6 Consensus size: 48
11339347 ATAAGAATAG
* * *
11339357 TTAAAAGAAATAGGTAATGGGAGTGTTTTCC-TAAAAAATAAGAAAATTA
1 TTAAAAGGAATAGGTAAT-GGAGTG-TTTCCTTTAAAAATAGGAAAATTA
* *
11339406 TTAAAAAGAATAGGTGATTGGAGTGTTT-CTATTAAAAATAGGAAAATTA
1 TTAAAAGGAATAGGT-AATGGAGTGTTTCCT-TTAAAAATAGGAAAATTA
*
11339455 TTAAAAGGAATAGGTAAAT-GAGTGTTT-CTTGTAAAAATAGGGAAATTA
1 TTAAAAGGAATAGGT-AATGGAGTGTTTCCTT-TAAAAATAGGAAAATTA
*
11339503 TTAAAAGGAATAGGTAATGGAGTGTTTCCTTTAAAAATAGAAAAATTA
1 TTAAAAGGAATAGGTAATGGAGTGTTTCCTTTAAAAATAGGAAAATTA
*
11339551 TTAAAAGGAATAGGTAATGGAATGTTTCC
1 TTAAAAGGAATAGGTAATGGAGTGTTTCC
11339580 CTAAAAAAAT
Statistics
Matches: 156, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
47 5 0.03
48 95 0.61
49 54 0.35
50 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.31
Consensus pattern (48 bp):
TTAAAAGGAATAGGTAATGGAGTGTTTCCTTTAAAAATAGGAAAATTA
Found at i:11339587 original size:48 final size:48
Alignment explanation
Indices: 11339332--11339587 Score: 277
Period size: 48 Copynumber: 5.3 Consensus size: 48
11339322 GTGTGGGAAC
* * *
11339332 GTTTCCCTAAAAAATATAAGAA-TAGTTAAAAGAAATAGGTAATGGGAGT
1 GTTTCCCTAAAAAATAGAAAAATTA-TTAAAAGGAATAGGTAAT-GGAGT
* * *
11339381 GTTTTCCTAAAAAATA-AGAAAATTATTAAAAAGAATAGGTGATTGGAGT
1 GTTTCCCTAAAAAATAGA-AAAATTATTAAAAGGAATAGGT-AATGGAGT
** * *
11339430 GTTTCTATTAAAAATAGGAAAATTATTAAAAGGAATAGGTAAAT-GAGT
1 GTTTCCCTAAAAAATAGAAAAATTATTAAAAGGAATAGGT-AATGGAGT
* * **
11339478 GTTT-CTTGTAAAAATAGGGAAATTATTAAAAGGAATAGGTAATGGAGT
1 GTTTCCCT-AAAAAATAGAAAAATTATTAAAAGGAATAGGTAATGGAGT
* * *
11339526 GTTTCCTTTAAAAATAGAAAAATTATTAAAAGGAATAGGTAATGGAAT
1 GTTTCCCTAAAAAATAGAAAAATTATTAAAAGGAATAGGTAATGGAGT
11339574 GTTTCCCTAAAAAA
1 GTTTCCCTAAAAAA
11339588 ATATGATAAA
Statistics
Matches: 179, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
47 4 0.02
48 97 0.54
49 74 0.41
50 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (48 bp):
GTTTCCCTAAAAAATAGAAAAATTATTAAAAGGAATAGGTAATGGAGT
Found at i:11339604 original size:36 final size:36
Alignment explanation
Indices: 11339559--11339677 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 36
11339549 TATTAAAAGG
* *
11339559 AATAGGTAATGGAATGTTTCCC-TAAAAAAATATGATA
1 AATAAGTAATGG-ATGTTTCCCTTAAAAAAATAGGA-A
* *
11339596 AA-AAGTAATGGGTGTTTCCCTTAAGAAAATAGGAA
1 AATAAGTAATGGATGTTTCCCTTAAAAAAATAGGAA
* * * * * *
11339631 AATAAGTAATGAATATTTTTCTTTAAAAAAATAGTAG
1 AATAAGTAATGGAT-GTTTCCCTTAAAAAAATAGGAA
11339668 AATAAGTAAT
1 AATAAGTAAT
11339678 ACAAATATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
35 11 0.16
36 28 0.42
37 28 0.42
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (36 bp):
AATAAGTAATGGATGTTTCCCTTAAAAAAATAGGAA
Found at i:11339614 original size:35 final size:37
Alignment explanation
Indices: 11339559--11339677 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 37
11339549 TATTAAAAGG
* *
11339559 AATAGGTAATGGAATGTTTCCC-TAAAAAAATATGATA
1 AATAAGTAATGGAATGTTTCCCTTAAAAAAATAGGA-A
* *
11339596 AA-AAGTAATGG-GTGTTTCCCTTAAGAAAATAGGAA
1 AATAAGTAATGGAATGTTTCCCTTAAAAAAATAGGAA
* * * * *
11339631 AATAAGTAAT-GAATATTTTTCTTTAAAAAAATAGTAG
1 AATAAGTAATGGAAT-GTTTCCCTTAAAAAAATAGGAA
11339668 AATAAGTAAT
1 AATAAGTAAT
11339678 ACAAATATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
35 12 0.18
36 27 0.40
37 28 0.42
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (37 bp):
AATAAGTAATGGAATGTTTCCCTTAAAAAAATAGGAA
Found at i:11339698 original size:39 final size:37
Alignment explanation
Indices: 11339621--11339698 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
11339611 TTCCCTTAAG
* * **
11339621 AAAATAGGAAAATAAGTAATGAATATTTTTCTTTAAA
1 AAAATAGGAAAATAAGTAATAAATATTTTCCTAAAAA
* *
11339658 AAAATAGTAGAATAAGTAATACAAATATTTTCCTAAAAA
1 AAAATAGGAAAATAAGTAAT--AAATATTTTCCTAAAAA
11339697 AA
1 AA
11339699 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
37 18 0.55
39 15 0.45
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (37 bp):
AAAATAGGAAAATAAGTAATAAATATTTTCCTAAAAA
Found at i:11339709 original size:37 final size:37
Alignment explanation
Indices: 11339629--11339733 Score: 92
Period size: 37 Copynumber: 2.8 Consensus size: 37
11339619 AGAAAATAGG
* * **
11339629 AAAATAAGTAATGAATATTTTTCTTTAAAAAAATAGT
1 AAAATAAGTAATAAATATTTTTCTCTAAAAAAATAAA
*
11339666 AGAATAAGTAATACAA-ATATTTTC-CTAAAAAAATAAA
1 AAAATAAGTAATA-AATAT-TTTTCTCTAAAAAAATAAA
*
11339703 AAAATAAGTCATGAGAATATTTTT-T-TAAAAA
1 AAAATAAGTAAT-A-AATATTTTTCTCTAAAAA
11339734 GTAGGAGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
37 39 0.71
38 14 0.25
39 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (37 bp):
AAAATAAGTAATAAATATTTTTCTCTAAAAAAATAAA
Found at i:11342780 original size:26 final size:26
Alignment explanation
Indices: 11342751--11342800 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
11342741 AGGGTTCGAG
*
11342751 TTTCATTAACGG-TTTTGATTTTAGGA
1 TTTCATTAA-GGTTTTTAATTTTAGGA
*
11342777 TTTCATTTAGGTTTTTAATTTTAG
1 TTTCATTAAGGTTTTTAATTTTAG
11342801 AGTTTTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (26 bp):
TTTCATTAAGGTTTTTAATTTTAGGA
Found at i:11345146 original size:28 final size:27
Alignment explanation
Indices: 11345109--11345200 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 27
11345099 GGCCTAATTG
11345109 TATTATTATTTTTATATGTTTTATTTAT
1 TATTATTATTTTTATAT-TTTTATTTAT
* *
11345137 TATTATTATTTTTTTATTATTATATTTAC
1 TATTATTATTTTTATATT-TT-TATTTAT
11345166 TATTATATTATTTTTATA-TTTTATTTAT
1 TA-T-TATTATTTTTATATTTTTATTTAT
*
11345194 TTTTATT
1 TATTATT
11345201 TGGTTTTCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.07
27 2 0.04
28 25 0.45
29 10 0.18
30 2 0.04
31 12 0.22
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (27 bp):
TATTATTATTTTTATATTTTTATTTAT
Found at i:11345154 original size:17 final size:17
Alignment explanation
Indices: 11345127--11345197 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 17
11345117 TTTTTATATG
11345127 TTTTATTTATTATTATTA
1 TTTT-TTTATTATTATTA
11345145 TTTTTTTATTATTA-TA
1 TTTTTTTATTATTATTA
**
11345161 -TTTACTATTA-TATTA
1 TTTTTTTATTATTATTA
*
11345176 TTTTTATATT-TTATTTA
1 TTTTTTTATTATTA-TTA
11345193 TTTTT
1 TTTTT
11345198 ATTTGGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
14 2 0.04
15 10 0.22
16 11 0.24
17 18 0.40
18 4 0.09
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTATTATTATTA
Found at i:11345198 original size:17 final size:18
Alignment explanation
Indices: 11345114--11345199 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 18
11345104 AATTGTATTA
*
11345114 TTATTTTTATATGTTTTAT
1 TTATTTTTATA-CTTTTAT
*
11345133 TTATTATTATTA-TTTT-T
1 TTATTTTTA-TACTTTTAT
*
11345150 TTATTATTATATTTACTATTAT
1 TTATT-TT-TA--TACTTTTAT
11345172 ATTATTTTTATA-TTTTAT
1 -TTATTTTTATACTTTTAT
11345190 TTATTTTTAT
1 TTATTTTTAT
11345200 TTGGTTTTCG
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
17 16 0.29
18 10 0.18
19 12 0.21
20 5 0.09
21 5 0.09
22 3 0.05
23 5 0.09
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (18 bp):
TTATTTTTATACTTTTAT
Found at i:11345199 original size:23 final size:23
Alignment explanation
Indices: 11345127--11345201 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
11345117 TTTTTATATG
*
11345127 TTTTATTTATTAT-TATTA-TT-T
1 TTTTATTT-TTATATTTTATTTAT
*
11345148 TTTTATTATTATA-TTTACTATTA-
1 TTTTATTTTTATATTTTA-T-TTAT
*
11345171 TATTATTTTTATATTTTATTTAT
1 TTTTATTTTTATATTTTATTTAT
11345194 TTTTATTT
1 TTTTATTT
11345202 GGTTTTCGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 7 0.17
21 7 0.17
22 3 0.07
23 21 0.50
24 4 0.10
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTATATTTTATTTAT
Found at i:11345207 original size:28 final size:27
Alignment explanation
Indices: 11345109--11345201 Score: 98
Period size: 29 Copynumber: 3.3 Consensus size: 27
11345099 GGCCTAATTG
11345109 TATTA-TTATTTTTATATGTTTTATTTAT
1 TATTATTTATTTTTATA--TTTTATTTAT
* * *
11345137 TATTATTATTTTTTTATTATTATATTTAC
1 TATTATT-TATTTTTA-TATTTTATTTAT
11345166 TATTATATTATTTTTATATTTTATTTAT
1 TATTAT-TTATTTTTATATTTTATTTAT
*
11345194 TTTTATTT
1 TATTATTT
11345202 GGTTTTCGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.04
28 20 0.37
29 22 0.41
30 8 0.15
31 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (27 bp):
TATTATTTATTTTTATATTTTATTTAT
Found at i:11345522 original size:5 final size:5
Alignment explanation
Indices: 11345494--11345556 Score: 101
Period size: 5 Copynumber: 12.4 Consensus size: 5
11345484 CATTTTCTAA
11345494 TTATT TT-TGT TTATT TTATGT TTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTAT-T TTATT TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT
11345545 TTATT TTATT TT
1 TTATT TTATT TT
11345557 GTTCTTAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
4 1 0.02
5 48 0.87
6 6 0.11
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:11345671 original size:34 final size:34
Alignment explanation
Indices: 11345600--11345676 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
11345590 GAATAATCGG
11345600 GATTGAACCACAAACCGAAAATAAAGATGACTAA
1 GATTGAACCACAAACCGAAAATAAAGATGACTAA
* **
11345634 GATTAAACCACAATTCGTAAAATAAAAGATGA-T-A
1 GATTGAACCACAAACCG-AAAAT-AAAGATGACTAA
11345668 GATTGAACC
1 GATTGAACC
11345677 GCACATCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 23 0.62
35 6 0.16
36 8 0.22
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (34 bp):
GATTGAACCACAAACCGAAAATAAAGATGACTAA
Found at i:11345850 original size:35 final size:35
Alignment explanation
Indices: 11345811--11345877 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
11345801 AAGCAACTGG
*
11345811 GATTGAGCTGCAAGTTAAGAAATAAAAATGATTGA
1 GATTGAACTGCAAGTTAAGAAATAAAAATGATTGA
* * *
11345846 GATTGAATTGCAAGTTGAGAAATAAAGATGAT
1 GATTGAACTGCAAGTTAAGAAATAAAAATGAT
11345878 CGGGACTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (35 bp):
GATTGAACTGCAAGTTAAGAAATAAAAATGATTGA
Found at i:11347032 original size:15 final size:15
Alignment explanation
Indices: 11347013--11347063 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
11347003 ATCCTTTTCC
11347013 TTTTTCCTTTTTT-T
1 TTTTTCCTTTTTTAT
*
11347027 TATTTTTCTTGTTTTAT
1 T-TTTTCCTT-TTTTAT
*
11347044 TTTTTCATTTTTTCAT
1 TTTTTCCTTTTTT-AT
11347060 TTTT
1 TTTT
11347064 CATTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.37
16 16 0.53
17 2 0.07
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTCCTTTTTTAT
Found at i:11347064 original size:15 final size:15
Alignment explanation
Indices: 11347007--11347069 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
11346997 GTTTGTATCC
* *
11347007 TTTTCCTTTTTCCTTT
1 TTTTCATTTTT-CATT
*
11347023 TTTTTATTTTTC-TT
1 TTTTCATTTTTCATT
11347037 GTTTT-ATTTTTTCATT
1 -TTTTCA-TTTTTCATT
11347053 TTTTCATTTTTCATT
1 TTTTCATTTTTCATT
11347068 TT
1 TT
11347070 CTTTAGGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 3 0.07
15 26 0.63
16 12 0.29
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTCATTTTTCATT
Found at i:11353419 original size:10 final size:9
Alignment explanation
Indices: 11353404--11353463 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
11353394 ACTTTGCTTG
11353404 AAAAAAAGA
1 AAAAAAAGA
11353413 CAAAAAAA-A
1 -AAAAAAAGA
11353422 AAGAAAAA-A
1 AA-AAAAAGA
11353431 AAAAGAAAGA
1 AAAA-AAAGA
11353441 AAAACAAAGA
1 AAAA-AAAGA
* *
11353451 CAAAGAAGA
1 AAAAAAAGA
11353460 AAAA
1 AAAA
11353464 CAAAAAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.09
9 19 0.44
10 20 0.47
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:11353422 original size:13 final size:13
Alignment explanation
Indices: 11353404--11353470 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
11353394 ACTTTGCTTG
11353404 AAAAAAAGACAAA
1 AAAAAAAGACAAA
11353417 AAAAAAAG--AAA
1 AAAAAAAGACAAA
11353428 AAAAAAAGA-AAGA
1 AAAAAAAGACAA-A
11353441 AAAACAAAGACAAA
1 AAAA-AAAGACAAA
*
11353455 GAAGAAAA-ACAAA
1 -AAAAAAAGACAAA
11353468 AAA
1 AAA
11353471 TGAATAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
11 11 0.23
12 4 0.09
13 18 0.38
14 9 0.19
15 5 0.11
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAGACAAA
Found at i:11354484 original size:51 final size:51
Alignment explanation
Indices: 11354414--11354529 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
11354404 TCATATAGAT
* *
11354414 TTTTTTAAAAGTTTAAAGGCCTCT-TTTTAGAGTAAGCCATTTTCAAACAAGA
1 TTTTTT-AAAGTTTAAAGGCCTCTATTTAAG-GGAAGCCATTTTCAAACAAGA
* **
11354466 TTTTTTAAAGTTTCAAGGCCTCTATTTAAGGGGGGCCATTTTCAAACAAGA
1 TTTTTTAAAGTTTAAAGGCCTCTATTTAAGGGAAGCCATTTTCAAACAAGA
*
11354517 TCTTTTAAAGTTT
1 TTTTTTAAAGTTT
11354530 TAATACCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 46 0.81
52 11 0.19
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (51 bp):
TTTTTTAAAGTTTAAAGGCCTCTATTTAAGGGAAGCCATTTTCAAACAAGA
Found at i:11355637 original size:142 final size:142
Alignment explanation
Indices: 11355368--11355624 Score: 324
Period size: 142 Copynumber: 1.8 Consensus size: 142
11355358 CACACATTGG
**
11355368 GAGGTGTGAAATTAACAAAATGCCCTTTAGGGATATTTTTGTAATTTGACCTTCTCGAGGTTAAT
1 GAGGTGTGAAATTAACAAAATGCCCTTTAGGGATATTTTTGTAATTTGACCTTCTCGAGCATAAT
* * * * * *
11355433 TTTTTATGAAACTTTTTATATCATAATTTTACAATATTTGATTTTTTTTATACATTTGAAATCAC
66 TTTTTATGAAAATTTTTAGATCATAATTTTACAATATTTAATATTTTTGATACATTTAAAATCAC
11355498 AATAGTCCTCGA
131 AATAGTCCTCGA
* * * *
11355510 GAGGTGTGAAATT-ACTAAAATTCACC-TTAGGGGTATTTTTGTAATTTTACCTTCTTGAGCATA
1 GAGGTGTGAAATTAAC-AAAATGC-CCTTTAGGGATATTTTTGTAATTTGACCTTCTCGAGCATA
*
11355573 GA-TTTTTATGAAAATTTTTAGATC-TCAATTTTATAATATTTAATGATTTTTG
64 -ATTTTTTATGAAAATTTTTAGATCAT-AATTTTACAATATTTAAT-ATTTTTG
11355625 GTGTTTTAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
141 3 0.03
142 87 0.89
143 8 0.08
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (142 bp):
GAGGTGTGAAATTAACAAAATGCCCTTTAGGGATATTTTTGTAATTTGACCTTCTCGAGCATAAT
TTTTTATGAAAATTTTTAGATCATAATTTTACAATATTTAATATTTTTGATACATTTAAAATCAC
AATAGTCCTCGA
Found at i:11356565 original size:50 final size:52
Alignment explanation
Indices: 11356501--11356633 Score: 166
Period size: 50 Copynumber: 2.6 Consensus size: 52
11356491 GATTTAAAAG
*
11356501 ATGGTTTTCTTCCTTTCATGTTCAGTTTGCACCTG-T-TAGTAAAAAAGAAA
1 ATGGTTTTCTTCCTTTCATGTTCAGTTTGCACCTGCTAGAGTAAAAAAGAAA
* * * *
11356551 ATGGCTTTCTTCCTTTCA-GATCAGTTTGCACTTGCTAGAGTAAAAAAGAAT
1 ATGGTTTTCTTCCTTTCATGTTCAGTTTGCACCTGCTAGAGTAAAAAAGAAA
* * *
11356602 AT-GTTTTATTCCTTTTATGTTCGGTTTGCACC
1 ATGGTTTTCTTCCTTTCATGTTCAGTTTGCACC
11356634 AAGTAACGCA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 14 0.20
50 30 0.43
51 25 0.36
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (52 bp):
ATGGTTTTCTTCCTTTCATGTTCAGTTTGCACCTGCTAGAGTAAAAAAGAAA
Found at i:11356935 original size:53 final size:51
Alignment explanation
Indices: 11356861--11356992 Score: 140
Period size: 53 Copynumber: 2.5 Consensus size: 51
11356851 AAAGATGGTT
* * *
11356861 TTCTTCCTTTCATGTTTGGTTTACA-CTTGTTAGTGTAAAAAAAAAAAGGTCGC
1 TTCTTCCTTTCATGTTCGGTTTACACCTT-TTAGAGT--AAAAAAAAAGATCGC
* * * * *
11356914 TTCTTCCTTTCATGATCGGTTTGCACCTTTTTGAGTAAAAAAGAAGATGGC
1 TTCTTCCTTTCATGTTCGGTTTACACCTTTTAGAGTAAAAAAAAAGATCGC
*
11356965 TTACTTCCTTTCATGTTCGGTTTGCACC
1 TT-CTTCCTTTCATGTTCGGTTTACACC
11356993 CAGTAATGCC
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
51 14 0.21
52 24 0.35
53 27 0.40
54 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (51 bp):
TTCTTCCTTTCATGTTCGGTTTACACCTTTTAGAGTAAAAAAAAAGATCGC
Found at i:11357101 original size:52 final size:52
Alignment explanation
Indices: 11357038--11357182 Score: 143
Period size: 52 Copynumber: 2.8 Consensus size: 52
11357028 AAGATGGTTG
* * * *
11357038 TCTTTCTTTCATGTTCGATTTACACCTATTAGTGCCAAAAAGA-AAAT-GGTT
1 TCTTCCTTTCATGTTCGATTTGCACCTATTAATGCCAAAAA-ATAAATAGCTT
* * * **
11357089 TGCTTCCTTTCATGTTC-AGTTTGCACCTGTTACTGTCAAAAAATAGGTAGCTT
1 T-CTTCCTTTCATGTTCGA-TTTGCACCTATTAATGCCAAAAAATAAATAGCTT
* *
11357142 TCTTCCTTTCATGTTTGGTTTGCACCTATTAATGCCAAAAA
1 TCTTCCTTTCATGTTCGATTTGCACCTATTAATGCCAAAAA
11357183 TGGTTTCTGG
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
51 3 0.04
52 69 0.91
53 4 0.05
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (52 bp):
TCTTCCTTTCATGTTCGATTTGCACCTATTAATGCCAAAAAATAAATAGCTT
Found at i:11357164 original size:175 final size:174
Alignment explanation
Indices: 11356440--11357182 Score: 681
Period size: 176 Copynumber: 4.2 Consensus size: 174
11356430 TTTTGTTTTA
* * * * * ** *
11356440 TTCCTTTCTTGTTCGGGTTACATCTAGTAA--CACAAAAAAAAAAAGTTTCTAGATTTAAAAGAT
1 TTCCTTTCATGTTCGGTTTGCACCCAGTAATGCAC-AAAAAAAATGGTTTCTGGATTTAAAAGAT
* *
11356503 GGTTTTCTTCCTTTCATGTTC-AGTTTGCACCTGTTAGT-AAAAAAGAAAATGGCTTTCTTCCTT
65 GGTTTTCTTCCTTTCATGTTCGA-TTTACACCTGTTAGTGAAAAAAAAAAATGGCTTTCTTCCTT
* * * * *
11356566 TCA-GATCAGTTTGCACTTGCTAGAGTAAAAAAGAATAT-GTTTTA
129 TCATGATCAGTTTGCACCTGTTAGAGTAAAAAAGAAGATAGCTTTC
* * * * * *
11356610 TTCCTTTTATGTTCGGTTTGCACCAAGTAACGCAAAAAAAAAAAAAAAAATAGTTTTTGGATTTA
1 TTCCTTTCATGTTCGGTTTGCACCCAGTAATGC-------ACAAAAAAAATGGTTTCTGGATTTA
* * * * **
11356675 AAAGACGGTTTTCTTCCTTTCTTGTTCGGTTTGCACCCCTTAGTGTCAAAAAAAAAAAGGTGGCT
59 AAAGATGGTTTTCTTCCTTTCATGTTCGATTTACACCTGTTAGTG--AAAAAAAAAAA--TGGCT
* *
11356740 TTCTTTCTTTCATGATC-GATTTGCTCCTGTTAGAGTAAAAAAGAAGATCA-CTTTC
120 TTCTTCCTTTCATGATCAG-TTTGCACCTGTTAGAGTAAAAAAGAAGAT-AGCTTTC
* * *
11356795 TTCTTTTCATGTTCGGTTTACACCCAGTAACT-TA-AAAAAAAA-GGTTTCTGGATTTAAAAGAT
1 TTCCTTTCATGTTCGGTTTGCACCCAGTAA-TGCACAAAAAAAATGGTTTCTGGATTTAAAAGAT
* * * *
11356857 GGTTTTCTTCCTTTCATGTTTGGTTTACACTTGTTAGTGTAAAAAAAAAAA-GGTCGCTTCTTCC
65 GGTTTTCTTCCTTTCATGTTCGATTTACACCTGTTAGTG-AAAAAAAAAAATGG-C-TTTCTTCC
* * * * *
11356921 TTTCATGATCGGTTTGCACCTTTTTGAGTAAAAAAGAAGATGGCTTAC
127 TTTCATGATCAGTTTGCACCTGTTAGAGTAAAAAAGAAGATAGCTTTC
11356969 TTCCTTTCATGTTCGGTTTGCACCCAGTAATGC-CAAAAGAAAATGGTTTCTGGATTTAAAAGAT
1 TTCCTTTCATGTTCGGTTTGCACCCAGTAATGCACAAAA-AAAATGGTTTCTGGATTTAAAAGAT
* * * * *
11357033 GGTTGTCTTTCTTTCATGTTCGATTTACACCTATTAGTGCCAAAAAGAAAATGG-TTTGCTTCCT
65 GGTTTTCTTCCTTTCATGTTCGATTTACACCTGTTAGTG-AAAAAAAAAAATGGCTTT-CTTCCT
* ** * *
11357097 TTCATGTTCAGTTTGCACCTGTTACTGTCAAAAAA-TAGGTAGCTTTC
128 TTCATGATCAGTTTGCACCTGTTAGAGT-AAAAAAGAAGATAGCTTTC
* * *
11357144 TTCCTTTCATGTTTGGTTTGCACCTATTAATGC-CAAAAA
1 TTCCTTTCATGTTCGGTTTGCACCCAGTAATGCACAAAAA
11357183 TGGTTTCTGG
Statistics
Matches: 470, Mismatches: 72, Indels: 58
0.78 0.12 0.10
Matches are distributed among these distances:
170 24 0.05
172 3 0.01
173 2 0.00
174 81 0.17
175 87 0.19
176 118 0.25
177 10 0.02
178 59 0.13
179 1 0.00
181 10 0.02
183 17 0.04
184 29 0.06
185 29 0.06
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (174 bp):
TTCCTTTCATGTTCGGTTTGCACCCAGTAATGCACAAAAAAAATGGTTTCTGGATTTAAAAGATG
GTTTTCTTCCTTTCATGTTCGATTTACACCTGTTAGTGAAAAAAAAAAATGGCTTTCTTCCTTTC
ATGATCAGTTTGCACCTGTTAGAGTAAAAAAGAAGATAGCTTTC
Found at i:11361435 original size:59 final size:58
Alignment explanation
Indices: 11361328--11361439 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 58
11361318 TCAAAAAATG
* **
11361328 TTTTAAAGAAAAGTTGAAAGTATTAATTTTCTTTGAAGGTAAAATTTTTAAAAGATATT
1 TTTTAAAGAAAAGTTG-AAGTATTAATTTTCCTTGAAAATAAAATTTTTAAAAGATATT
* **
11361387 TTTTGAAGAAAAGTTG-AGTATATCAATTTTCCTTGAAAATAATTTTTTTAAAA
1 TTTTAAAGAAAAGTTGAAGTAT-T-AATTTTCCTTGAAAATAAAATTTTTAAAA
11361440 AAAATACATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 5 0.11
58 1 0.02
59 39 0.87
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (58 bp):
TTTTAAAGAAAAGTTGAAGTATTAATTTTCCTTGAAAATAAAATTTTTAAAAGATATT
Found at i:11361678 original size:59 final size:59
Alignment explanation
Indices: 11361447--11361679 Score: 233
Period size: 59 Copynumber: 3.9 Consensus size: 59
11361437 AAAAAAATAC
* *
11361447 ATTTCTTAAGAAACATTTTTTAATGAAAAGTTGAAAGTA-CTAATTTTCCTTAAAAATAAAA
1 ATTTCTTAA-AAACATTTTTTGATGAAAAGTTGAAAGTATC-AATTTTCCTTGAAAAT-AAA
** * * *
11361508 ATTTCAAAAAAACATTTTTTTGA-GAAAAAGTTGAAAGTATCCATTTTTCTT-AAAGGTAAA
1 ATTTCTTAAAAACA-TTTTTTGATG-AAAAGTTGAAAGTATCAATTTTCCTTGAAA-ATAAA
* * * * *
11361568 ATTT-TCAAAAGATATTTTTTGAAGAAAAGTTGAGAGTATCAATTTTTCTTGAAAATAAA
1 ATTTCTTAAAA-ACATTTTTTGATGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA
* *
11361627 ATTT-TTAAAAATATTTTTCTGATGAAAAGTTGAAAGTATTAATTTTCCTTGAA
1 ATTTCTTAAAAACATTTTT-TGATGAAAAGTTGAAAGTATCAATTTTCCTTGAA
11361680 TAAAAGCATT
Statistics
Matches: 147, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
58 8 0.05
59 79 0.54
60 22 0.15
61 37 0.25
62 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (59 bp):
ATTTCTTAAAAACATTTTTTGATGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA
Found at i:11368563 original size:15 final size:14
Alignment explanation
Indices: 11368545--11368610 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
11368535 ATAAAAAATT
11368545 GAAAAAAATTGAAAA
1 GAAAAAAA-TGAAAA
*
11368560 GAAAAAGAA-AAAAA
1 GAAAAA-AATGAAAA
**
11368574 GAAAAAGTTGTAAAA
1 GAAAAAAATG-AAAA
*
11368589 GAAAAGAAAAGAAAA
1 GAAAA-AAATGAAAA
11368604 GAAAAAA
1 GAAAAAA
11368611 CAAAGGCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
14 12 0.30
15 24 0.60
16 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.08
Consensus pattern (14 bp):
GAAAAAAATGAAAA
Found at i:11368563 original size:29 final size:28
Alignment explanation
Indices: 11368547--11368610 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
11368537 AAAAAATTGA
11368547 AAAAAATTG-AAAAGAAAAAGAAAAAAAG
1 AAAAAATTGTAAAAGAAAAA-AAAAAAAG
*
11368575 AAAAAGTTGTAAAAGAAAAGAAAAGAAAAG
1 AAAAAATTGTAAAAGAAAA-AAAA-AAAAG
11368605 AAAAAA
1 AAAAAA
11368611 CAAAGGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 8 0.26
29 12 0.39
30 11 0.35
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.08
Consensus pattern (28 bp):
AAAAAATTGTAAAAGAAAAAAAAAAAAG
Found at i:11368945 original size:38 final size:38
Alignment explanation
Indices: 11368894--11368968 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
11368884 ATATAATGAA
* *
11368894 GGCAAAACTCCCCCTCAATTTGTGCATCCTAATCCAAT
1 GGCAAAACTCCCCCTCAATTTATGCATCATAATCCAAT
*
11368932 GGCAAAACTCCCCCTCATTTTATGCATCATAATCCAA
1 GGCAAAACTCCCCCTCAATTTATGCATCATAATCCAA
11368969 CACAACTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.27
Consensus pattern (38 bp):
GGCAAAACTCCCCCTCAATTTATGCATCATAATCCAAT
Found at i:11369607 original size:16 final size:16
Alignment explanation
Indices: 11369573--11369607 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11369563 ATACAAGCTC
**
11369573 ATACCAATTGTTATGG
1 ATACCAATTGTTAAAG
11369589 ATACCAATTGTTAAAG
1 ATACCAATTGTTAAAG
11369605 ATA
1 ATA
11369608 TGTAATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (16 bp):
ATACCAATTGTTAAAG
Found at i:11380675 original size:3 final size:3
Alignment explanation
Indices: 11380669--11380705 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
11380659 TTTTTTTAAT
11380669 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11380706 ATAAAACCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11383431 original size:5 final size:5
Alignment explanation
Indices: 11383421--11383474 Score: 58
Period size: 5 Copynumber: 11.0 Consensus size: 5
11383411 GACTCTTATC
* * *
11383421 ATTTT ATTTT ATTCT ATTTT GTTTT ATTTT ATTTT -TTTT GATTTT -TTTG
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT
11383470 ATTTT
1 ATTTT
11383475 TTGAAAAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
4 7 0.17
5 29 0.73
6 4 0.10
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:11383473 original size:19 final size:19
Alignment explanation
Indices: 11383422--11383476 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
11383412 ACTCTTATCA
* *
11383422 TTTTATTTTATTCTATTTTG
1 TTTTATTTGATT-TTTTTTG
*
11383442 TTTTATTTTATTTTTTTTG
1 TTTTATTTGATTTTTTTTG
11383461 ATTTT-TTTGATTTTTT
1 -TTTTATTTGATTTTTT
11383477 GAAAAGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.13, C:0.02, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTATTTGATTTTTTTTG
Found at i:11383775 original size:34 final size:34
Alignment explanation
Indices: 11383737--11383865 Score: 132
Period size: 34 Copynumber: 3.8 Consensus size: 34
11383727 GACAAACCCA
* *
11383737 CAAGTCAAGAACATGGATGATCGGGATAAAACCG
1 CAAGTCAAGAACAAGGATGATTGGGATAAAACCG
* * * *
11383771 CAAGTCAAGAACAAAGATGTTTGAGATAAAATCG
1 CAAGTCAAGAACAAGGATGATTGGGATAAAACCG
* * * *
11383805 TAAGTCAAGAAAAAGGATGATTAGGATAAAACCA
1 CAAGTCAAGAACAAGGATGATTGGGATAAAACCG
* * * *
11383839 CAAGCCAAAAATAAAGATGATTGGGAT
1 CAAGTCAAGAACAAGGATGATTGGGAT
11383866 GAAGTTGCAA
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.18
Consensus pattern (34 bp):
CAAGTCAAGAACAAGGATGATTGGGATAAAACCG
Done.