Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 57 of 186
Found at i:17725760 original size:23 final size:23
Alignment explanation
Indices: 17725711--17725761 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
17725701 ATAAATAGTA
*
17725711 ATAGTGTTAGAAATATACTATAT
1 ATAGTGTTAGAAATATACTATAG
* *
17725734 ATAGTGTTTGAAGTATAC-ATAAG
1 ATAGTGTTAGAAATATACTAT-AG
17725757 ATAGT
1 ATAGT
17725762 AAAAATATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (23 bp):
ATAGTGTTAGAAATATACTATAG
Found at i:17726164 original size:9 final size:9
Alignment explanation
Indices: 17726135--17726174 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
17726125 AAATATAATA
*
17726135 AATAATAAT
1 AATAACAAT
*
17726144 AATAATAAT
1 AATAACAAT
17726153 AATAACAAT
1 AATAACAAT
*
17726162 AATAGCAAT
1 AATAACAAT
17726171 AATA
1 AATA
17726175 GTAAAAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (9 bp):
AATAACAAT
Found at i:17726174 original size:3 final size:3
Alignment explanation
Indices: 17726111--17726165 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
17726101 AAGTACCTAT
*
17726111 TAA TAA TAT TATA TAA -ATA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
17726158 CAA TAA TA
1 TAA TAA TA
17726166 GCAATAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 1 0.02
3 37 0.84
4 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17726359 original size:17 final size:17
Alignment explanation
Indices: 17726348--17726385 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
17726338 ATAATAGTAG
17726348 TAATGTAATAATAACGA
1 TAATGTAATAATAACGA
*
17726365 TAATGTAATAATAATGA
1 TAATGTAATAATAACGA
17726382 TAAT
1 TAAT
17726386 AATATTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (17 bp):
TAATGTAATAATAACGA
Found at i:17726376 original size:3 final size:3
Alignment explanation
Indices: 17726370--17726455 Score: 50
Period size: 3 Copynumber: 27.7 Consensus size: 3
17726360 AACGATAATG
* * * *
17726370 TAA TAA TAA TGA TAA TAA TAT TAA GT-A TAG T-A TAAA TAA TATG TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TA-A TA-A
* * *
17726417 TAA CAG TAA TAA TAA TAA GTAA CAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA
17726456 TAGAAATTCA
Statistics
Matches: 62, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
2 2 0.03
3 50 0.81
4 10 0.16
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17726445 original size:19 final size:19
Alignment explanation
Indices: 17726417--17726453 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17726407 AATATGTACA
*
17726417 TAACAGTAATAATAATAAG
1 TAACAATAATAATAATAAG
17726436 TAACAATAATAATAATAA
1 TAACAATAATAATAATAA
17726454 TATAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
TAACAATAATAATAATAAG
Found at i:17726513 original size:16 final size:16
Alignment explanation
Indices: 17726480--17726512 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17726470 AACTAAACAT
*
17726480 AATATAATAATATTAA
1 AATAAAATAATATTAA
17726496 AATAAAATAAT-TTAA
1 AATAAAATAATATTAA
17726511 AA
1 AA
17726513 AATACTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATAATATTAA
Found at i:17735585 original size:52 final size:52
Alignment explanation
Indices: 17735507--17735610 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
17735497 TAATGCTTAA
17735507 GATATATTAATTTCGGGTAAGTTGTGTTAAATTCCGTACGAACTTACTAAGC
1 GATATATTAATTTCGGGTAAGTTGTGTTAAATTCCGTACGAACTTACTAAGC
17735559 GATATATTAATTTCGGGTAAGTTGTGTTAAATTCCGTACGAACTTACTAAGC
1 GATATATTAATTTCGGGTAAGTTGTGTTAAATTCCGTACGAACTTACTAAGC
17735611 ATTGTGTTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (52 bp):
GATATATTAATTTCGGGTAAGTTGTGTTAAATTCCGTACGAACTTACTAAGC
Found at i:17736813 original size:38 final size:38
Alignment explanation
Indices: 17736762--17737055 Score: 201
Period size: 38 Copynumber: 7.0 Consensus size: 38
17736752 TCAGAATGAA
*
17736762 AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
*
17736800 AACGTGGTGCTAAGTGGATATACCACGATTACACAAATTGATACATGT
1 AACGTGGTGCTAAGTGGATATACCACG---------GTT-ATACATGT
* *
17736848 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG------T
* * *
17736895 AACGTGGTGTTCAGTGGATATACCACGGTTAAACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
* * * *
17736933 AACGTGGGGCTGAGTGGATATGCCACGGTTACATATATTGATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG--T
*
17736976 CATTAGCGTGGTGCTAAGTGGATATACCACGGTTAAACATGT
1 -A--A-CGTGGTGCTAAGTGGATATACCACGGTTATACATGT
* * *
17737018 AACGTGGTGCTAAGTGAATATGCCATGGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
17737056 TACTTTGAAA
Statistics
Matches: 203, Mismatches: 26, Indels: 54
0.72 0.09 0.19
Matches are distributed among these distances:
38 86 0.42
39 3 0.01
40 7 0.03
41 5 0.02
42 1 0.00
43 1 0.00
44 5 0.02
45 6 0.03
46 1 0.00
47 55 0.27
48 33 0.16
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (38 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
Found at i:17736921 original size:47 final size:47
Alignment explanation
Indices: 17736799--17737010 Score: 244
Period size: 47 Copynumber: 4.7 Consensus size: 47
17736789 GTTATACGTG
* * * *
17736799 TAACGTGGTGCTAAGTGGATATACCACGATTACACAAATTGATACAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
17736846 GTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT
1 -TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* * *
17736894 TAACGTGGTGTTCAGTGGATATACCACGGTTA-A-ACA-TG------
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* * *
17736932 TAACGTGGGGCTGAGTGGATATGCCACGGTTACATATATTGATTCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
17736979 TAGCGTGGTGCTAAGTGGATATACCACGGTTA
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA
17737011 AACATGTAAC
Statistics
Matches: 137, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
38 28 0.20
39 1 0.01
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 57 0.42
48 42 0.31
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (47 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
Found at i:17736954 original size:85 final size:85
Alignment explanation
Indices: 17736842--17737048 Score: 351
Period size: 85 Copynumber: 2.4 Consensus size: 85
17736832 ACAAATTGAT
* *
17736842 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGTTC
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
17736907 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
* * *
17736927 ACATGTAACGTGGGGCTGAGTGGATATGCCACGGTTACATATATTGATTCATTAGCGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
17736992 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
* *
17737012 ACATGTAACGTGGTGCTAAGTGAATATGCCATGGTTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
17737049 TACATGTTAC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 113 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
AGTGGATATACCACGGTTAA
Found at i:17742437 original size:38 final size:38
Alignment explanation
Indices: 17742386--17742679 Score: 219
Period size: 38 Copynumber: 7.0 Consensus size: 38
17742376 GGAATGAAAA
*
17742386 AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
*
17742424 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGGATATACCACG---------GTT-ATACATGT
* *
17742472 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG------T
* *
17742519 AACGTGGTGCTCAGTGGATATACCACGGTTAAACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
* *
17742557 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG--T
*
17742600 CATTAGCGTGGTGCTAAGTGGATATACCACGGTTAAACATGT
1 -A--A-CGTGGTGCTAAGTGGATATACCACGGTTATACATGT
* * * *
17742642 AACATGGTGCTAAGTGAATATGCCATGGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
17742680 TACTTTGAAA
Statistics
Matches: 207, Mismatches: 22, Indels: 54
0.73 0.08 0.19
Matches are distributed among these distances:
38 87 0.42
39 3 0.01
40 7 0.03
41 5 0.02
42 1 0.00
43 1 0.00
44 5 0.02
45 6 0.03
46 1 0.00
47 58 0.28
48 33 0.16
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (38 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
Found at i:17742545 original size:47 final size:47
Alignment explanation
Indices: 17742423--17742634 Score: 280
Period size: 47 Copynumber: 4.7 Consensus size: 47
17742413 GTTATACGTG
* * *
17742423 TAACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
17742470 GTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT
1 -TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* *
17742518 TAACGTGGTGCTCAGTGGATATACCACGGTTA-A-ACA-TG------
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
17742556 TAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
17742603 TAGCGTGGTGCTAAGTGGATATACCACGGTTA
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA
17742635 AACATGTAAC
Statistics
Matches: 143, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
38 30 0.21
39 1 0.01
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 60 0.42
48 43 0.30
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (47 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
Found at i:17742578 original size:85 final size:85
Alignment explanation
Indices: 17742466--17742672 Score: 369
Period size: 85 Copynumber: 2.4 Consensus size: 85
17742456 ACATATTGAT
*
17742466 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTC
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
17742531 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
*
17742551 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAGCGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
17742616 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
* * *
17742636 ACATGTAACATGGTGCTAAGTGAATATGCCATGGTTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
17742673 TACATGTTAC
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 117 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
AGTGGATATACCACGGTTAA
Found at i:17744916 original size:43 final size:42
Alignment explanation
Indices: 17744821--17744967 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 42
17744811 ATCAAGATAT
* * *
17744821 GATTACATGTAAGACCATGTCTGGGACATTGACATTGTATTAA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCG-ATTAA
17744864 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TTAA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATTAA
* * * * * *
17744905 TCGATTTCGTGTAAGACCCTGTCTGGGGCAGTGGCAACGATATAT
1 --GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGAT-TAA
* *
17744950 GATTACATGTAAAACCAT
1 GATTACGTGTAAGACCAT
17744968 ATTTGGGATA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.05
43 80 0.92
44 1 0.01
45 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATTAA
Found at i:17746357 original size:34 final size:34
Alignment explanation
Indices: 17746314--17746379 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
17746304 AATAAGATGT
17746314 CTTGAGATAATAGGGTTCATGCCACACGACCTAA
1 CTTGAGATAATAGGGTTCATGCCACACGACCTAA
*
17746348 CTTGAGATAATGGGGTTCATGCCACACGACCT
1 CTTGAGATAATAGGGTTCATGCCACACGACCT
17746380 GACTCCTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (34 bp):
CTTGAGATAATAGGGTTCATGCCACACGACCTAA
Found at i:17748255 original size:43 final size:42
Alignment explanation
Indices: 17748160--17748306 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 42
17748150 ATCAAGATAT
* * *
17748160 GATTACATGTAAGACCATGTCTGGGACATTGACATTGTATTAA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCG-ATTAA
17748203 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TTAA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATTAA
* * * * * *
17748244 TCGATTTCGTGTAAGACCCTGTCTGGGGCAGTGGCAACGATATAT
1 --GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGAT-TAA
* *
17748289 GATTACATGTAAAACCAT
1 GATTACGTGTAAGACCAT
17748307 ATTTGGGATA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.05
43 80 0.92
44 1 0.01
45 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATTAA
Found at i:17750575 original size:17 final size:17
Alignment explanation
Indices: 17750553--17750591 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
17750543 TTGTTCAATT
17750553 AAATTATCCGTTTGTCA
1 AAATTATCCGTTTGTCA
17750570 AAATTATCCGTTTGTCA
1 AAATTATCCGTTTGTCA
17750587 AAATT
1 AAATT
17750592 GGTTTTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (17 bp):
AAATTATCCGTTTGTCA
Found at i:17753449 original size:16 final size:16
Alignment explanation
Indices: 17753428--17753460 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17753418 TGTTTTCTCG
17753428 ACTTGAGTGGTTTTAT
1 ACTTGAGTGGTTTTAT
17753444 ACTTGAGTGGTTTTAT
1 ACTTGAGTGGTTTTAT
17753460 A
1 A
17753461 GTTTCACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.48
Consensus pattern (16 bp):
ACTTGAGTGGTTTTAT
Found at i:17757991 original size:16 final size:16
Alignment explanation
Indices: 17757966--17758016 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17757956 TTAATCATTA
*
17757966 ATTAATATAAAAATAT
1 ATTAAAATAAAAATAT
17757982 ATTAAAAT-AAAATAAT
1 ATTAAAATAAAAAT-AT
*
17757998 AGTAAAATAATAAAT-T
1 ATTAAAATAA-AAATAT
17758014 ATT
1 ATT
17758017 TTAACCAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.17
16 19 0.66
17 1 0.03
18 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTAAAATAAAAATAT
Found at i:17758512 original size:15 final size:15
Alignment explanation
Indices: 17758492--17758599 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
17758482 TTTATGGAAA
17758492 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
17758507 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
17758521 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
17758537 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
17758551 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
17758567 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
17758581 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
17758597 ATC
1 ATC
17758600 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:17758529 original size:30 final size:30
Alignment explanation
Indices: 17758486--17758609 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
17758476 TCCATATTTA
* *
17758486 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
17758516 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
17758546 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
17758576 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
17758607 TGG
1 TGG
17758610 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:17764465 original size:15 final size:16
Alignment explanation
Indices: 17764445--17764474 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17764435 TAAATTTATT
17764445 AAATTT-TATTTTTTA
1 AAATTTATATTTTTTA
17764460 AAATTTATATTTTTT
1 AAATTTATATTTTTT
17764475 GATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AAATTTATATTTTTTA
Found at i:17771777 original size:6 final size:6
Alignment explanation
Indices: 17771759--17771797 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
17771749 AAAGTCTAAG
* *
17771759 AAAATA ACAATA AACATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
17771798 TAGAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:17779055 original size:34 final size:34
Alignment explanation
Indices: 17778997--17779066 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
17778987 TTTAAATGGC
* * *
17778997 ATAAAATAGAATTAAAATATAATCATACG-AGAA
1 ATAAAATAAAATAAAAATAAAATCATACGAAGAA
*
17779030 ATAAAATAAAAATAAAAATAAAATCATATGAAGAA
1 ATAAAAT-AAAATAAAAATAAAATCATACGAAGAA
17779065 AT
1 AT
17779067 TGCTTCGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 7 0.23
34 18 0.58
35 6 0.19
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (34 bp):
ATAAAATAAAATAAAAATAAAATCATACGAAGAA
Found at i:17782022 original size:15 final size:15
Alignment explanation
Indices: 17781987--17782038 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17781977 TTAAGAATTT
*
17781987 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17782001 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17782015 TATTTAATAATAAT-
1 TATTTAATTATAATA
17782029 TATGTTAATT
1 TAT-TTAATT
17782039 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17782137 original size:16 final size:16
Alignment explanation
Indices: 17782116--17782157 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17782106 TTATTAAATT
*
17782116 ATATATTTTAATTATA
1 ATATATTTTAATAATA
17782132 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
17782147 AT-TATGTTTAA
1 ATATAT-TTTAA
17782158 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:17782142 original size:15 final size:15
Alignment explanation
Indices: 17782107--17782148 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17782097 TTAAGAATTT
*
17782107 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17782121 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17782135 TATTTAATAATAAT
1 TATTTAATTATAAT
17782149 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17782383 original size:45 final size:43
Alignment explanation
Indices: 17782283--17782392 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
17782273 TTTTCCATTA
17782283 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
17782322 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
17782367 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
17782393 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:17782394 original size:16 final size:16
Alignment explanation
Indices: 17782373--17782440 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
17782363 GATTTGCTAT
*
17782373 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
17782389 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
17782405 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17782421 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17782437 TACA
1 TACA
17782441 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17783188 original size:14 final size:15
Alignment explanation
Indices: 17783169--17783224 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
17783159 AATCTTCAAT
17783169 GATATG-CAATCTTA
1 GATATGACAATCTTA
17783183 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
17783200 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
17783218 GATATGA
1 GATATGA
17783225 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:17783195 original size:17 final size:17
Alignment explanation
Indices: 17783175--17783238 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 17
17783165 CAATGATATG
17783175 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
17783192 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
17783210 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
17783229 CAATCTTAGA
1 CAATCTTAGA
17783239 AGATATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.36
18 15 0.36
19 11 0.26
20 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:17783213 original size:35 final size:37
Alignment explanation
Indices: 17783167--17783245 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
17783157 ATAATCTTCA
17783167 ATGATATGCAATCTTAGATATG-ATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAATACAATCTTAGAT
17783203 ATGAT-TGCAATCTTAGATATGATATACAATCTTAGA-
1 ATGATATGCAATCTTAGATATGA-ATACAATCTTAGAT
17783239 A-GATATG
1 ATGATATG
17783246 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 19 0.47
36 8 0.20
37 13 0.32
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGAATACAATCTTAGAT
Found at i:17787867 original size:14 final size:15
Alignment explanation
Indices: 17787848--17787903 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
17787838 NNNNNNNNAT
17787848 GATATG-CAATCTTA
1 GATATGACAATCTTA
17787862 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
17787879 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
17787897 GATATGA
1 GATATGA
17787904 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:17787876 original size:17 final size:17
Alignment explanation
Indices: 17787854--17787917 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 17
17787844 NNATGATATG
17787854 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
17787871 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
17787889 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
17787906 TGCAATCTTAGA
1 --CAATCTTAGA
17787918 AGATATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.38
18 16 0.38
19 10 0.24
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:17787892 original size:35 final size:37
Alignment explanation
Indices: 17787846--17787924 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
17787836 NNNNNNNNNN
17787846 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
17787882 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
17787918 A-GATATG
1 ATGATATG
17787925 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:17787924 original size:17 final size:19
Alignment explanation
Indices: 17787846--17787917 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
17787836 NNNNNNNNNN
17787846 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
17787865 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
17787882 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
17787900 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
17787918 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:17787943 original size:22 final size:22
Alignment explanation
Indices: 17787846--17787940 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
17787836 NNNNNNNNNN
17787846 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
17787865 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
17787882 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
17787900 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
17787922 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
17787941 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:17795461 original size:30 final size:25
Alignment explanation
Indices: 17795403--17795455 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
17795393 TGAAGGAAAC
17795403 AAAAACCTAATATAATAGATAAAAT
1 AAAAACCTAATATAATAGATAAAAT
*
17795428 AAAAACCTAATATAATATATAAAA-
1 AAAAACCTAATATAATAGATAAAAT
17795452 AAAA
1 AAAA
17795456 GTAAAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.23
Consensus pattern (25 bp):
AAAAACCTAATATAATAGATAAAAT
Found at i:17798955 original size:16 final size:18
Alignment explanation
Indices: 17798916--17798957 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
17798906 TAAGTTTATA
17798916 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
17798933 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
17798950 A-ATTTATA
1 ATATTTATA
17798958 ACACATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:17799940 original size:16 final size:16
Alignment explanation
Indices: 17799919--17799949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17799909 TTTAAAAAAT
17799919 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
17799935 TTTCAAATTTATATG
1 TTTCAAATATATATG
17799950 CTATAACACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:17800510 original size:18 final size:18
Alignment explanation
Indices: 17800487--17800521 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17800477 TCTGAGTTAG
17800487 AAAGAAAATTTATTTTAT
1 AAAGAAAATTTATTTTAT
17800505 AAAGAAAATTTATTTTA
1 AAAGAAAATTTATTTTA
17800522 AAATTATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAAGAAAATTTATTTTAT
Found at i:17801797 original size:25 final size:25
Alignment explanation
Indices: 17801736--17801813 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
17801726 CACAAACGCA
*
17801736 GCTCTTTATGAGCATCTTGATATAG
1 GCTCTTTATGAGCATCCTGATATAG
** *
17801761 AATTTTTATGAGCATCCTGATATAG
1 GCTCTTTATGAGCATCCTGATATAG
* *
17801786 GCTCTTTGTGAGCTTCCTGATAT-G
1 GCTCTTTATGAGCATCCTGATATAG
17801810 GCTC
1 GCTC
17801814 GCTTGAACAT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 5 0.11
25 39 0.89
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTTATGAGCATCCTGATATAG
Found at i:17811805 original size:7 final size:7
Alignment explanation
Indices: 17811793--17811837 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
17811783 TGATGACTAA
17811793 TGCAACT
1 TGCAACT
17811800 TGCAACT
1 TGCAACT
17811807 TGCAACT
1 TGCAACT
17811814 TGCAACT
1 TGCAACT
17811821 TGCAACT
1 TGCAACT
17811828 TGCAACT
1 TGCAACT
17811835 TGC
1 TGC
17811838 TTTTTTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (7 bp):
TGCAACT
Found at i:17812905 original size:43 final size:43
Alignment explanation
Indices: 17812857--17812945 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
17812847 AGTGACACCC
17812857 CACTTAGTTAAAATCTTTATATACAACACTAGAAATTCTATCA
1 CACTTAGTTAAAATCTTTATATACAACACTAGAAATTCTATCA
17812900 CACTTAGTTAAAATCTTTATATACAACACTAGAAATTCTATCA
1 CACTTAGTTAAAATCTTTATATACAACACTAGAAATTCTATCA
17812943 CAC
1 CAC
17812946 GTATATACGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (43 bp):
CACTTAGTTAAAATCTTTATATACAACACTAGAAATTCTATCA
Found at i:17813615 original size:23 final size:23
Alignment explanation
Indices: 17813589--17813632 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17813579 TCAAATTATC
* *
17813589 ATTTTCTTAACCAACATTAAAAA
1 ATTTTATTAACCAAAATTAAAAA
17813612 ATTTTATTAACCAAAATTAAA
1 ATTTTATTAACCAAAATTAAA
17813633 CTTTAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTTTATTAACCAAAATTAAAAA
Found at i:17824671 original size:22 final size:22
Alignment explanation
Indices: 17824645--17824695 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
17824635 GGAGGCAATG
*
17824645 CACACGCCCGTGTACTTTGAAA
1 CACACCCCCGTGTACTTTGAAA
*
17824667 CACACCCCCGTGTGCTTTGAAA
1 CACACCCCCGTGTACTTTGAAA
17824689 CACACCC
1 CACACCC
17824696 TTGTTGTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (22 bp):
CACACCCCCGTGTACTTTGAAA
Found at i:17831754 original size:31 final size:31
Alignment explanation
Indices: 17831719--17831777 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
17831709 ACACGAGAAC
* *
17831719 GTGGGCCCACACGGGTAGTCCATACGGGCGT
1 GTGGGCCCACACAGGTAGTCCACACGGGCGT
*
17831750 GTGGGCCCACATAGGTAGTCCACACGGG
1 GTGGGCCCACACAGGTAGTCCACACGGG
17831778 TATGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.19, C:0.29, G:0.37, T:0.15
Consensus pattern (31 bp):
GTGGGCCCACACAGGTAGTCCACACGGGCGT
Found at i:17832100 original size:27 final size:25
Alignment explanation
Indices: 17832070--17832121 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
17832060 ACTGAATATA
17832070 AGCATGTATTAATGTACATCTGCATTG
1 AGCATGT-TTAAT-TACATCTGCATTG
* *
17832097 AGCATGTTTAGTTGCATCTGCATTG
1 AGCATGTTTAATTACATCTGCATTG
17832122 GGGTGGGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 4 0.17
27 7 0.30
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
AGCATGTTTAATTACATCTGCATTG
Found at i:17833681 original size:5 final size:5
Alignment explanation
Indices: 17833671--17833734 Score: 56
Period size: 5 Copynumber: 12.8 Consensus size: 5
17833661 ATACATTTCT
** * * * * *
17833671 TGTTC TGTTC TACTC TGTTC TGTTT TGTTC TGCTC TGTTC TATTT TGTTT
1 TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC
*
17833721 TGTTC TGTGC TGTT
1 TGTTC TGTTC TGTT
17833735 GTGCTATCAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.03, C:0.17, G:0.19, T:0.61
Consensus pattern (5 bp):
TGTTC
Found at i:17833699 original size:20 final size:20
Alignment explanation
Indices: 17833671--17833719 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
17833661 ATACATTTCT
*
17833671 TGTTCTGTTCTACTCTGTTC
1 TGTTTTGTTCTACTCTGTTC
*
17833691 TGTTTTGTTCTGCTCTGTTC
1 TGTTTTGTTCTACTCTGTTC
*
17833711 TATTTTGTT
1 TGTTTTGTT
17833720 TTGTTCTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.04, C:0.18, G:0.16, T:0.61
Consensus pattern (20 bp):
TGTTTTGTTCTACTCTGTTC
Found at i:17835511 original size:30 final size:30
Alignment explanation
Indices: 17835465--17835524 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
17835455 GCTATGTCAC
* * *
17835465 GACACCGAAGGTAGTCTTGCTTTTTTGGTT
1 GACACCAAAGGCAGTCTTGCTCTTTTGGTT
17835495 GACACCAAAGGCAGTCTTGCTCTTTTGGTT
1 GACACCAAAGGCAGTCTTGCTCTTTTGGTT
17835525 ATCCTGCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (30 bp):
GACACCAAAGGCAGTCTTGCTCTTTTGGTT
Found at i:17842777 original size:32 final size:32
Alignment explanation
Indices: 17842731--17842794 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
17842721 TTCTTTCTAA
17842731 ACTCAGTTTGAAAGAATTCCAACGTTACTCTT
1 ACTCAGTTTGAAAGAATTCCAACGTTACTCTT
* *
17842763 ACTCGGTTTGAAAGAATTCTAACGTTACTCTT
1 ACTCAGTTTGAAAGAATTCCAACGTTACTCTT
17842795 TCTCTCGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (32 bp):
ACTCAGTTTGAAAGAATTCCAACGTTACTCTT
Found at i:17844536 original size:38 final size:38
Alignment explanation
Indices: 17844494--17844570 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
17844484 TAATTTTTAC
*
17844494 AAAATCACCATGATGTATCTACCTATCCCTCAATACAT
1 AAAATCACCATGATCTATCTACCTATCCCTCAATACAT
17844532 AAAATCACCATGATCTATCTACCTATCCCTCAATACAT
1 AAAATCACCATGATCTATCTACCTATCCCTCAATACAT
17844570 A
1 A
17844571 TGGCCAGACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.29
Consensus pattern (38 bp):
AAAATCACCATGATCTATCTACCTATCCCTCAATACAT
Found at i:17850200 original size:12 final size:12
Alignment explanation
Indices: 17850183--17850209 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17850173 GGTATTCTCC
17850183 TACTACAAGTCA
1 TACTACAAGTCA
17850195 TACTACAAGTCA
1 TACTACAAGTCA
17850207 TAC
1 TAC
17850210 ACTGAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (12 bp):
TACTACAAGTCA
Found at i:17851993 original size:26 final size:26
Alignment explanation
Indices: 17851924--17851994 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
17851914 CGCAACAAGA
* **
17851924 CTGGCGAACCCTAGTTCATAACTTAC
1 CTGGTGAACCCTAGTTCGCAACTTAC
*
17851950 CTGGTGAACCCTTA-TTCGCAACTTAT
1 CTGGTGAACCC-TAGTTCGCAACTTAC
*
17851976 CTTGTGAACCCTAGTTCGC
1 CTGGTGAACCCTAGTTCGC
17851995 TAAGTAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 2 0.05
26 34 0.89
27 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.31
Consensus pattern (26 bp):
CTGGTGAACCCTAGTTCGCAACTTAC
Found at i:17853981 original size:23 final size:22
Alignment explanation
Indices: 17853943--17854003 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
17853933 GACACATAAA
*
17853943 GTGCCT-AAAACGACACACGAG
1 GTGCCTGAATACGACACACGAG
*
17853964 GTGCTTG-ATACGACACACGAG
1 GTGCCTGAATACGACACACGAG
17853985 GTGCCTGAAATACGACACA
1 GTGCCTG-AATACGACACA
17854004 TAAAGTGCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 24 0.71
23 10 0.29
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (22 bp):
GTGCCTGAATACGACACACGAG
Found at i:17854011 original size:23 final size:22
Alignment explanation
Indices: 17853932--17854017 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 22
17853922 GATCAGTATC
*
17853932 CGACACATAAAGTGCCTAAA-A
1 CGACACACAAAGTGCCTAAATA
* * **
17853953 CGACACACGAGGTG-CTTGATA
1 CGACACACAAAGTGCCTAAATA
* *
17853974 CGACACACGAGGTGCCTGAAATA
1 CGACACACAAAGTGCCT-AAATA
*
17853997 CGACACATAAAGTGCCTAAAT
1 CGACACACAAAGTGCCTAAAT
17854018 GGTAAAGCCG
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.06
21 26 0.50
22 6 0.12
23 17 0.33
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (22 bp):
CGACACACAAAGTGCCTAAATA
Found at i:17854411 original size:15 final size:15
Alignment explanation
Indices: 17854386--17854443 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
17854376 TCATATATAT
17854386 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
17854402 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
17854417 AATAATTTCAATCAA
1 TATAAATTCAATCAA
17854432 TATAAATTCAAT
1 TATAAATTCAAT
17854444 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:17855722 original size:5 final size:5
Alignment explanation
Indices: 17855714--17855775 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
17855704 TCTTTAGTTT
17855714 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
17855764 ATATA ATATA AT
1 ATATA ATATA AT
17855776 TAAAACATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:17855811 original size:8 final size:8
Alignment explanation
Indices: 17855798--17855826 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
17855788 TATCTTTATT
17855798 ATATAATA
1 ATATAATA
17855806 ATATAATA
1 ATATAATA
17855814 ATATAATA
1 ATATAATA
17855822 ATATA
1 ATATA
17855827 TTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:17857549 original size:46 final size:46
Alignment explanation
Indices: 17857392--17857665 Score: 352
Period size: 46 Copynumber: 6.0 Consensus size: 46
17857382 TTCGACATGA
* * * * * * *
17857392 TGCCATAGTATCTTTCAACTATGGTTTTACCCGTTT-TTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
** ** *
17857437 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCAGGT
** *
17857484 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
17857530 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
17857576 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
* * *
17857622 TGCCATGGTATCTTTCAACTATGGTCTTATACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAG
17857666 AGAGCACACT
Statistics
Matches: 209, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
45 27 0.13
46 142 0.68
47 40 0.19
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
Found at i:17858379 original size:3 final size:3
Alignment explanation
Indices: 17858371--17858405 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17858361 ATATATATAT
*
17858371 TCC TCC TCC TCC TCC TCC TCC TCT TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
17858406 TCCATTCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:17859699 original size:22 final size:22
Alignment explanation
Indices: 17859674--17859720 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
17859664 GTTTGCTTTG
17859674 TTTCTTCCTTTCTATT-CTTTTT
1 TTTCTTCCTTT-TATTCCTTTTT
*
17859696 TTTCTTTCTTTTATTCCTTTTT
1 TTTCTTCCTTTTATTCCTTTTT
17859718 TTT
1 TTT
17859721 ATATATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCTTCCTTTTATTCCTTTTT
Found at i:17864185 original size:37 final size:37
Alignment explanation
Indices: 17864143--17864337 Score: 255
Period size: 37 Copynumber: 5.0 Consensus size: 37
17864133 GGTAGTTTTA
17864143 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
**
17864180 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* *
17864217 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
17864254 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAA---GT-G
*
17864295 CTTTAGCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTG
1 -----GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
17864337 G
1 G
17864338 TAGCCTAGCT
Statistics
Matches: 140, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
37 102 0.73
40 2 0.01
41 1 0.01
42 1 0.01
43 2 0.01
46 32 0.23
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:17864234 original size:74 final size:78
Alignment explanation
Indices: 17864107--17864337 Score: 281
Period size: 74 Copynumber: 2.9 Consensus size: 78
17864097 TTTGAGTACT
**
17864107 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAAACAAAGTGATAAGTGG-AG--TTA--TACACTTATCTGATCAAGTGACAAAGT
17864172 GATAAGTGGCTACACTTA
61 GATAAGTGGCTACACTTA
*
17864190 TCTGATCAAGAAACAAAGTGATAAGT-G-G-T-TACACTTATCTGATCAAGAGACAAAGTGATAA
1 TCTGATCAAGAAACAAAGTGATAAGTGGAGTTATACACTTATCTGATCAAGTGACAAAGTGATAA
17864251 GTGGCTACACTTA
66 GTGGCTACACTTA
** * *
17864264 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGGCAAAGT
1 TCTGATCAAGAAACAAAGTGATAAGTGG-AG--TTA--TACACTTATCTGATCAAGTGACAAAGT
17864329 GATAAGTGG
61 GATAAGTGG
17864338 TAGCCTAGCT
Statistics
Matches: 131, Mismatches: 8, Indels: 18
0.83 0.05 0.11
Matches are distributed among these distances:
74 67 0.51
75 1 0.01
77 2 0.02
80 2 0.02
82 1 0.01
83 58 0.44
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (78 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGAGTTATACACTTATCTGATCAAGTGACAAAGTGATAA
GTGGCTACACTTA
Found at i:17864362 original size:45 final size:46
Alignment explanation
Indices: 17864254--17864377 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
17864244 GTGATAAGTG
* *
17864254 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
*
17864300 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGC-CTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
17864345 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
17864378 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 22 0.30
46 40 0.54
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
Found at i:17867589 original size:23 final size:23
Alignment explanation
Indices: 17867557--17867618 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
17867547 CATCAAAGTG
*
17867557 CCAGATTGAATTGCACTGTAGCA
1 CCAGAATGAATTGCACTGTAGCA
* *
17867580 CCAGAATGAATTGCATTGTAGCG
1 CCAGAATGAATTGCACTGTAGCA
17867603 CCAGAATGAATTGCAC
1 CCAGAATGAATTGCAC
17867619 CATAGAGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (23 bp):
CCAGAATGAATTGCACTGTAGCA
Found at i:17867631 original size:23 final size:23
Alignment explanation
Indices: 17867582--17867656 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
17867572 CTGTAGCACC
*** * *
17867582 AGAATGAATTGCATTGTAGCGCC
1 AGAATGAATTGCACCATAGAGCT
17867605 AGAATGAATTGCACCATAGAGCT
1 AGAATGAATTGCACCATAGAGCT
* * * * *
17867628 AGAACGAGTTGCCCCTTAGTGCT
1 AGAATGAATTGCACCATAGAGCT
17867651 AGAATG
1 AGAATG
17867657 CACCCACCAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (23 bp):
AGAATGAATTGCACCATAGAGCT
Found at i:17869983 original size:40 final size:39
Alignment explanation
Indices: 17869952--17870161 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
17869942 GGACTAAGAT
* *
17869952 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
17869992 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
17870032 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
17870072 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
17870112 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
17870151 CCGAAGGCATT
1 CCGAAGGCATT
17870162 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:17870115 original size:120 final size:120
Alignment explanation
Indices: 17869899--17870161 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
17869889 TTGAATGCTG
* *
17869899 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
17869963 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
17870019 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
17870082 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
17870138 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
17870162 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:17870181 original size:79 final size:80
Alignment explanation
Indices: 17869900--17870196 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
17869890 TGAATGCTGT
* ** * * * **
17869900 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
17869963 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
17869980 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
17870044 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
17870060 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
17870124 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
17870139 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
17870197 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:17873098 original size:241 final size:241
Alignment explanation
Indices: 17872660--17873141 Score: 847
Period size: 241 Copynumber: 2.0 Consensus size: 241
17872650 TGAACGTCGA
*
17872660 GACAGGACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
1 GACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
* * *
17872725 CTGTTACAAGTGCGGATCAGTTGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGGACAGAATG
66 CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAATG
* *
17872790 CAAATCAGAGTGGGAGACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
131 AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
17872855 GCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCG
196 GCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCG
* * *
17872901 GACAGAACGGAATGTCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTTCCTGACCGCTC
1 GACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
**
17872966 CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTTTGAACAGAATG
66 CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAATG
*
17873031 AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATATGGGCAAT
131 AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
*
17873096 GCTGGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCG
196 GCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCG
17873142 AAGCCCGTGC
Statistics
Matches: 228, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
241 228 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (241 bp):
GACAGAACGAAATGCCGATATTGCGGTAAATGGCATTCGGGGAGTTGTAGATTCCCTGACCGCTC
CTGTTACAAATGCGGATCAGTGGACCACTTCATTAAAGATTGCCCGAGGTTGTCGGAACAGAATG
AAAATCAGAGTGGGAAACCGGGTGCTACCACTGCTCGAGGTAGACCATCTGGAAATACGGGCAAT
GCTAGTGGTGGTCAGAGAGGATCTAGAGATGATATAACCAGATCCG
Found at i:17878169 original size:40 final size:40
Alignment explanation
Indices: 17878086--17878388 Score: 405
Period size: 40 Copynumber: 7.6 Consensus size: 40
17878076 TTGAATGCTG
* * * * * *
17878086 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
17878126 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
17878166 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17878206 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17878246 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
17878286 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17878326 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17878365 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
17878389 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:17880397 original size:13 final size:13
Alignment explanation
Indices: 17880375--17880408 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17880365 GGGTCACACA
* *
17880375 CCCATATGTGTTG
1 CCCATGTGTGTTC
17880388 CCCATGTGTGTTC
1 CCCATGTGTGTTC
17880401 CCCATGTG
1 CCCATGTG
17880409 CGACACATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.29, G:0.24, T:0.35
Consensus pattern (13 bp):
CCCATGTGTGTTC
Found at i:17880780 original size:22 final size:24
Alignment explanation
Indices: 17880752--17880800 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
17880742 TATGCTAAGC
* *
17880752 TACCAAACTTTAAACTA-TC-ACA
1 TACCAAAATATAAACTAGTCAACA
17880774 TACCAAAATATAAACTAGTCAACA
1 TACCAAAATATAAACTAGTCAACA
17880798 TAC
1 TAC
17880801 AACATAGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 2 0.09
24 6 0.26
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (24 bp):
TACCAAAATATAAACTAGTCAACA
Found at i:17882646 original size:7 final size:7
Alignment explanation
Indices: 17882636--17882660 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17882626 TCAATTTATC
17882636 ATTTCAT
1 ATTTCAT
17882643 ATTTCAT
1 ATTTCAT
17882650 ATTTCAT
1 ATTTCAT
17882657 ATTT
1 ATTT
17882661 GTCATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTCAT
Found at i:17882646 original size:14 final size:14
Alignment explanation
Indices: 17882629--17882689 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
17882619 TCACATATCA
17882629 ATTTATCATTTCAT
1 ATTTATCATTTCAT
17882643 ATTTCAT-ATTTCAT
1 ATTT-ATCATTTCAT
*
17882657 ATTTGTCATTTCAAT
1 ATTTATCATTTC-AT
* *
17882672 ATTTTCTCATCTCAT
1 A-TTTATCATTTCAT
17882687 ATT
1 ATT
17882690 CATTTCTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.03
14 22 0.55
15 8 0.20
16 9 0.22
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATCATTTCAT
Found at i:17883136 original size:16 final size:16
Alignment explanation
Indices: 17883094--17883139 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
17883084 TAATAATCAC
*
17883094 ATATTTCTTAATACAT
1 ATATTTCATAATACAT
17883110 ATATATTCATAAT-CAAT
1 ATAT-TTCATAATAC-AT
17883127 ATATTTCATAATA
1 ATATTTCATAATA
17883140 TACAAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTCATAATACAT
Found at i:17883140 original size:25 final size:26
Alignment explanation
Indices: 17883107--17883160 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
17883097 TTTCTTAATA
* * *
17883107 CATATATATTCATAATCAATATATTT
1 CATATATATACAAAATCAATACATTT
*
17883133 CATA-ATATACAAAATCAATCCATTT
1 CATATATATACAAAATCAATACATTT
17883158 CAT
1 CAT
17883161 TTCAATTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (26 bp):
CATATATATACAAAATCAATACATTT
Found at i:17884020 original size:18 final size:18
Alignment explanation
Indices: 17883997--17884035 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
17883987 AATATATATA
*
17883997 CATGCATTTACATTTAAC
1 CATGCATTTACACTTAAC
17884015 CATGCATTTACACTTAAC
1 CATGCATTTACACTTAAC
17884033 CAT
1 CAT
17884036 ATTTGACCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (18 bp):
CATGCATTTACACTTAAC
Found at i:17884850 original size:20 final size:20
Alignment explanation
Indices: 17884827--17884869 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
17884817 TGGCCCCTGT
*
17884827 ATTG-TTTATTTTATAATCTA
1 ATTGATTTAATTTATAAT-TA
*
17884847 ATTGATTTAATTTCTAATTA
1 ATTGATTTAATTTATAATTA
17884867 ATT
1 ATT
17884870 CCATGTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTGATTTAATTTATAATTA
Found at i:17886664 original size:3 final size:3
Alignment explanation
Indices: 17886656--17886681 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17886646 ATTCATATCC
17886656 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
17886682 ATTGTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:17887476 original size:15 final size:15
Alignment explanation
Indices: 17887456--17887484 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17887446 ATAGGTGAGG
17887456 GCACTTAGAATTTGT
1 GCACTTAGAATTTGT
17887471 GCACTTAGAATTTG
1 GCACTTAGAATTTG
17887485 AAGTATGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (15 bp):
GCACTTAGAATTTGT
Found at i:17892630 original size:15 final size:15
Alignment explanation
Indices: 17892610--17892646 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
17892600 GATTTCTTAT
17892610 GATCTTTTAGCTTTG
1 GATCTTTTAGCTTTG
17892625 GATCTTTTAGCTTTG
1 GATCTTTTAGCTTTG
17892640 GAT-TTTT
1 GATCTTTT
17892647 CTTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.14, C:0.11, G:0.19, T:0.57
Consensus pattern (15 bp):
GATCTTTTAGCTTTG
Found at i:17893270 original size:48 final size:48
Alignment explanation
Indices: 17893199--17893295 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
17893189 GGGTACTGGG
17893199 TAGGTGCTAGATGATGTATGAGTTGATTAATTTGTTCATTAAGGGCAT
1 TAGGTGCTAGATGATGTATGAGTTGATTAATTTGTTCATTAAGGGCAT
*
17893247 TAGGTGCTAGATGATGTATGAGTTGATTAATTTGTTCATTAATGGCAT
1 TAGGTGCTAGATGATGTATGAGTTGATTAATTTGTTCATTAAGGGCAT
17893295 T
1 T
17893296 CTTTATGGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.06, G:0.26, T:0.41
Consensus pattern (48 bp):
TAGGTGCTAGATGATGTATGAGTTGATTAATTTGTTCATTAAGGGCAT
Found at i:17896638 original size:156 final size:156
Alignment explanation
Indices: 17896354--17896666 Score: 493
Period size: 156 Copynumber: 2.0 Consensus size: 156
17896344 TGATATTGTA
* * ***
17896354 AATATTCATCATAATTTGGCCTCTTGAGCAATTGTAAGTGGAAGAAGTCCATCTCCTTAAACCTA
1 AATATTCATCATAATTTGGCCCCTTGAGCAATTCTAAGCAAAAGAAGTCCATCTCCTTAAACCTA
* *
17896419 GGCTAAATGAACAATGGGCTGAATATTATGAGAAGGTTGGCCATGTAGAGCCCAACATGTATCAT
66 GGCTAAATGAACAATGGGCTGAATATTATGAGAAGGTCGGCCATGTAGAGCCCAACATGTATCAC
17896484 GTATGTGGCCACATTTTTT-ACAATAC
131 GTATGTGGCCAC-TTTTTTCACAATAC
* * *
17896510 AATATTCATCATAATTTGGCCCCTTGAGCAATTCTAAGCAAAAGAAGTCCATCTCGTTGAACGTA
1 AATATTCATCATAATTTGGCCCCTTGAGCAATTCTAAGCAAAAGAAGTCCATCTCCTTAAACCTA
* * *
17896575 GGCTAAATGAACAATGGGCTGAATATTATGAGAAGGTCGGCTATGTAGAGCTCAATATGTATCAC
66 GGCTAAATGAACAATGGGCTGAATATTATGAGAAGGTCGGCCATGTAGAGCCCAACATGTATCAC
17896640 GTATGTGGCCACTTTTTTCACAATAC
131 GTATGTGGCCACTTTTTTCACAATAC
17896666 A
1 A
17896667 TACAATTAGG
Statistics
Matches: 143, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
155 6 0.04
156 137 0.96
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (156 bp):
AATATTCATCATAATTTGGCCCCTTGAGCAATTCTAAGCAAAAGAAGTCCATCTCCTTAAACCTA
GGCTAAATGAACAATGGGCTGAATATTATGAGAAGGTCGGCCATGTAGAGCCCAACATGTATCAC
GTATGTGGCCACTTTTTTCACAATAC
Found at i:17902401 original size:16 final size:16
Alignment explanation
Indices: 17902380--17902411 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17902370 GCAGGCTAGA
17902380 CAACCTATGCCTTTGT
1 CAACCTATGCCTTTGT
17902396 CAACCTATGCCTTTGT
1 CAACCTATGCCTTTGT
17902412 AACATGGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (16 bp):
CAACCTATGCCTTTGT
Found at i:17913477 original size:95 final size:95
Alignment explanation
Indices: 17913365--17913551 Score: 320
Period size: 95 Copynumber: 2.0 Consensus size: 95
17913355 TTAGTTCATG
* * *
17913365 TCATAGAAAGATTTTAACGAATCTTTTCTCACTTCACTTTGGTTAAATTCACGTAATACTTTTTA
1 TCATAGAAAGATTTTAACAAATCTTTTCTCACTTCACTTGGGTTAAATTCACGTAATACTCTTTA
17913430 TTCTTTAAATTTTCATGAACTCAGGATATT
66 TTCTTTAAATTTTCATGAACTCAGGATATT
* *
17913460 TCATAGAAAGATTTTAACAAATCTTTTCTCACTTCACTTGGGTTAAATTCTCGTAGTACTCTTTA
1 TCATAGAAAGATTTTAACAAATCTTTTCTCACTTCACTTGGGTTAAATTCACGTAATACTCTTTA
*
17913525 TTCTTTAAATTTTCATGAACTTAGGAT
66 TTCTTTAAATTTTCATGAACTCAGGAT
17913552 TAATATCAAC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (95 bp):
TCATAGAAAGATTTTAACAAATCTTTTCTCACTTCACTTGGGTTAAATTCACGTAATACTCTTTA
TTCTTTAAATTTTCATGAACTCAGGATATT
Found at i:17913823 original size:21 final size:21
Alignment explanation
Indices: 17913799--17913855 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
17913789 TAGGTTTTTT
17913799 AACAATTG-GGTGACATGGCCC
1 AACAA-TGAGGTGACATGGCCC
17913820 AAC-ATGAAGGTGACATGGCCC
1 AACAATG-AGGTGACATGGCCC
17913841 AAC-ATGAAGGTGACA
1 AACAATG-AGGTGACA
17913856 CGTAGACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 31 0.91
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.16
Consensus pattern (21 bp):
AACAATGAGGTGACATGGCCC
Found at i:17914034 original size:6 final size:6
Alignment explanation
Indices: 17914023--17914053 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17914013 AAAATTTTAG
17914023 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
17914054 TTCAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:17918687 original size:27 final size:27
Alignment explanation
Indices: 17918656--17918728 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 27
17918646 TAAGATATTC
17918656 ATAATAATATTAAATTT-TTTTATTTTT
1 ATAATAATATT-AATTTCTTTTATTTTT
17918683 ATAAT-ATA-T-ATTTCTTTTATTTTT
1 ATAATAATATTAATTTCTTTTATTTTT
* * *
17918707 CTAAAAATATTTAATTACTTTT
1 ATAATAATA-TTAATTTCTTTT
17918729 TAAAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.11
24 13 0.34
25 4 0.11
26 3 0.08
27 6 0.16
28 8 0.21
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
ATAATAATATTAATTTCTTTTATTTTT
Found at i:17922151 original size:50 final size:50
Alignment explanation
Indices: 17922076--17922236 Score: 286
Period size: 50 Copynumber: 3.2 Consensus size: 50
17922066 CCATGGCAAC
*
17922076 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
17922126 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
17922176 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
17922226 AAGTGATAAGT
1 AAGTGATAAGT
17922237 GATATACTCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 107 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:17924828 original size:27 final size:27
Alignment explanation
Indices: 17924793--17924848 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
17924783 CCCTTCAATT
17924793 TTGCCAATTATAACTCAAAATTTCAAA
1 TTGCCAATTATAACTCAAAATTTCAAA
17924820 TTGCCAATTATAACTCAAAATTTCAAA
1 TTGCCAATTATAACTCAAAATTTCAAA
17924847 TT
1 TT
17924849 AGGGTTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.36
Consensus pattern (27 bp):
TTGCCAATTATAACTCAAAATTTCAAA
Found at i:17935202 original size:40 final size:40
Alignment explanation
Indices: 17935129--17935207 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
17935119 ACACACTATG
* * * *
17935129 TGGGGATAAAATCGACCCACCCAGCCTTGCACACCAAGTA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
* *
17935169 TGGGGATAAAATCAACCCATCCAACCCTACACACTAAGT
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGT
17935208 GGTACCGTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:17942695 original size:21 final size:21
Alignment explanation
Indices: 17942669--17942729 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
17942659 CAACTCATAG
17942669 GAGTTTCAGTTTAACCCTTCT
1 GAGTTTCAGTTTAACCCTTCT
* * * * * *
17942690 GGGTTTCAATTCAGCTCTTTT
1 GAGTTTCAGTTTAACCCTTCT
*
17942711 GAGCTTCAGTTTAACCCTT
1 GAGTTTCAGTTTAACCCTT
17942730 ATAGGTCTCC
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (21 bp):
GAGTTTCAGTTTAACCCTTCT
Found at i:17946056 original size:18 final size:18
Alignment explanation
Indices: 17946017--17946056 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17946007 TGCAATAATT
*
17946017 CTAAAAATTTTTATGCAC
1 CTAAAAATTTTTATGCAA
*
17946035 CTAAAAATTTTTATGTAA
1 CTAAAAATTTTTATGCAA
17946053 CTAA
1 CTAA
17946057 TAACTAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (18 bp):
CTAAAAATTTTTATGCAA
Found at i:17956297 original size:21 final size:21
Alignment explanation
Indices: 17956268--17956308 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17956258 AGATTGATTC
17956268 TTGCAGTTCAAGTTTGGTTAT
1 TTGCAGTTCAAGTTTGGTTAT
*
17956289 TTGCGGTTCAAGTTTGGTTA
1 TTGCAGTTCAAGTTTGGTTA
17956309 CTTGTGGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.27, T:0.46
Consensus pattern (21 bp):
TTGCAGTTCAAGTTTGGTTAT
Found at i:17956321 original size:21 final size:21
Alignment explanation
Indices: 17956276--17956322 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17956266 TCTTGCAGTT
* **
17956276 CAAGTTTGGTTATTTGCGGTT
1 CAAGTTTGGTTACTTGCGGAA
*
17956297 CAAGTTTGGTTACTTGTGGAA
1 CAAGTTTGGTTACTTGCGGAA
17956318 CAAGT
1 CAAGT
17956323 AAAATCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (21 bp):
CAAGTTTGGTTACTTGCGGAA
Found at i:17957486 original size:46 final size:46
Alignment explanation
Indices: 17957419--17957510 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
17957409 AATCTGTATC
17957419 TAGTTTTAAACTTGAGTGGACAATGTCAGTTATGGCGACGGAGACG
1 TAGTTTTAAACTTGAGTGGACAATGTCAGTTATGGCGACGGAGACG
17957465 TAGTTTTAAACTTGAGTGGACAATGTCAGTTATGGCGACGGAGACG
1 TAGTTTTAAACTTGAGTGGACAATGTCAGTTATGGCGACGGAGACG
17957511 AATAAAATCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (46 bp):
TAGTTTTAAACTTGAGTGGACAATGTCAGTTATGGCGACGGAGACG
Found at i:17958478 original size:143 final size:143
Alignment explanation
Indices: 17958220--17958503 Score: 541
Period size: 143 Copynumber: 2.0 Consensus size: 143
17958210 ACAAGTTTTT
*
17958220 ATCTCCTTTTAATAAGGTTTTATTGATTCGGAATATAAAAGTGTGAACAAAACTCGATTCAATTC
1 ATCTCCTTTTAATAAGGTTTTATTGATTCGGAATACAAAAGTGTGAACAAAACTCGATTCAATTC
17958285 AAAAATTTCGATAAAAATTTTAAATTTTAAATTAAATAGATCAAGTTAATTAAATTATTCGAATC
66 AAAAATTTCGATAAAAATTTTAAATTTTAAATTAAATAGATCAAGTTAATTAAATTATTCGAATC
17958350 AATTCGAAGAATC
131 AATTCGAAGAATC
17958363 ATCTCCTTTTAATAAGGTTTTATTGATTCGGAATACAAAAGTGTGAACAAAACTCGATTCAATTC
1 ATCTCCTTTTAATAAGGTTTTATTGATTCGGAATACAAAAGTGTGAACAAAACTCGATTCAATTC
* *
17958428 AAAAATTTTGATAAAAATTTTAAATTTTGAATTAAATAGATCAAGTTAATTAAATTATTCGAATC
66 AAAAATTTCGATAAAAATTTTAAATTTTAAATTAAATAGATCAAGTTAATTAAATTATTCGAATC
17958493 AATTCGAAGAA
131 AATTCGAAGAA
17958504 AAAAATTAAA
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (143 bp):
ATCTCCTTTTAATAAGGTTTTATTGATTCGGAATACAAAAGTGTGAACAAAACTCGATTCAATTC
AAAAATTTCGATAAAAATTTTAAATTTTAAATTAAATAGATCAAGTTAATTAAATTATTCGAATC
AATTCGAAGAATC
Found at i:17960444 original size:32 final size:32
Alignment explanation
Indices: 17960403--17960465 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
17960393 AGTAAGTATG
17960403 ATATGAACTGCTTATACATTTATATTTGACTA
1 ATATGAACTGCTTATACATTTATATTTGACTA
17960435 ATATGAACTGCTTATACATTTATATTTGACT
1 ATATGAACTGCTTATACATTTATATTTGACT
17960466 TTGTGATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (32 bp):
ATATGAACTGCTTATACATTTATATTTGACTA
Found at i:17960635 original size:50 final size:50
Alignment explanation
Indices: 17960560--17960660 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
17960550 GAGGCCCTAA
*
17960560 GGATATATAGGGTGTGAATGGAGAGTGTTTAGCTTTATACTACACTTATG
1 GGATATATAGGGTGTGAATGGAGAGTGTTTAACTTTATACTACACTTATG
* * ** * *
17960610 GGATATGTGGGGTGTGTTTGGAGAGTGTTTAATTTTATGCTACACTTATG
1 GGATATATAGGGTGTGAATGGAGAGTGTTTAACTTTATACTACACTTATG
17960660 G
1 G
17960661 AGAAATAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.39
Consensus pattern (50 bp):
GGATATATAGGGTGTGAATGGAGAGTGTTTAACTTTATACTACACTTATG
Found at i:17962229 original size:42 final size:43
Alignment explanation
Indices: 17962158--17962259 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 43
17962148 TCCCGGACAT
* * *
17962158 GGTCTTACATGTAATTCAG-TATTGATGCCTTTGTTCCAAACAG
1 GGTCTTACACGTAAATCAGAT-TTGATGCCTATGTTCCAAACAG
* *
17962201 GGTCTTACACG-AAATCAGATTTGATGCCTATGTTCCAGACAT
1 GGTCTTACACGTAAATCAGATTTGATGCCTATGTTCCAAACAG
17962243 GGTCTTACACGTAAATC
1 GGTCTTACACGTAAATC
17962260 TTAAATCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 36 0.69
43 16 0.31
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAGATTTGATGCCTATGTTCCAAACAG
Found at i:17966527 original size:35 final size:35
Alignment explanation
Indices: 17966488--17966722 Score: 139
Period size: 35 Copynumber: 6.5 Consensus size: 35
17966478 TGATTCATTT
* *
17966488 AACTAGCGCTGGGTGCAAATATCGTTGGTTTATCC
1 AACTAGCGCTGGGCGCAAATATCGTCGGTTTATCC
** * * * *
17966523 AACTAAAGCTAGGTTCACTAATTATTCGTCGGTTTATCT
1 AACTAGCGCT-GG-GCGC-AAATA-TCGTCGGTTTATCC
* * * * * * *
17966562 GACTAGCGCTTGGCACAACTTTCGTCAGTTTATCT
1 AACTAGCGCTGGGCGCAAATATCGTCGGTTTATCC
* * * * * * * *
17966597 GACTAGTGCTGGGCACACAT-TTGTAGGTTCATCT
1 AACTAGCGCTGGGCGCAAATATCGTCGGTTTATCC
* *
17966631 GACTAGCGCTGGGCGCAAATATCGTTGGTTTATCC
1 AACTAGCGCTGGGCGCAAATATCGTCGGTTTATCC
* *
17966666 AACTAGAGCTGGGCTCACTAATTATTCGTCGGTTTATCC
1 AACTAGCGCTGGGCGCA--AA-TA-TCGTCGGTTTATCC
*
17966705 AACTAGCACTGGGCGCAA
1 AACTAGCGCTGGGCGCAA
17966723 CCTCTATCAA
Statistics
Matches: 153, Mismatches: 38, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
34 27 0.18
35 61 0.40
36 5 0.03
37 7 0.05
38 7 0.05
39 46 0.30
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (35 bp):
AACTAGCGCTGGGCGCAAATATCGTCGGTTTATCC
Found at i:17966662 original size:69 final size:72
Alignment explanation
Indices: 17966489--17966722 Score: 224
Period size: 74 Copynumber: 3.2 Consensus size: 72
17966479 GATTCATTTA
* * * *
17966489 ACTAGCGCTGGGTGCAAATATCGTTGGTTTATCCAACTAAAGCTAGGTTCACTAATTATTCGTCG
1 ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCT-GG-GCACTAATTATTCGTAG
*
17966554 GTTTATCTG
64 GTTCATCTG
* * * * ** ** *
17966563 ACTAGCGCTTGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGGGCAC-ACA-T-TT-GTAGG
1 ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCACTA-ATTATTCGTAGG
17966624 TTCATCTG
65 TTCATCTG
*
17966632 ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAATTATTCGTCG
1 ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG--CACTAATTATTCGTAG
* **
17966697 GTTTATCCA
64 GTTCATCTG
*
17966706 ACTAGCACTGGGCGCAA
1 ACTAGCGCTGGGCGCAA
17966723 CCTCTATCAA
Statistics
Matches: 125, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
69 49 0.39
70 2 0.02
71 6 0.05
72 6 0.05
73 4 0.03
74 58 0.46
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (72 bp):
ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCACTAATTATTCGTAGGT
TCATCTG
Found at i:17966809 original size:143 final size:143
Alignment explanation
Indices: 17966481--17966791 Score: 419
Period size: 143 Copynumber: 2.2 Consensus size: 143
17966471 ACATCGTTGA
* * * *
17966481 TTCATTTAACTAGCGCTGGGTGCAAATATCGTTGGTTTATCCAACTAAAGCTAGGTTCACTAATT
1 TTCATCTAACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCTCACTAATT
** * * * * * * *
17966546 ATTCGTCGGTTTATCTGACTAGCGCTTGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGGGC
66 ATTCGTCGGTTTATCCAACTAGCACTGGGCACAACTCTCATCAATTTATCTAACTAGTGCTGGGA
17966611 ACACATTTGTAGG
131 ACACATTTGTAGG
* *
17966624 TTCATCTGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAATT
1 TTCATCTAACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCTCACTAATT
* *
17966689 ATTCGTCGGTTTATCCAACTAGCACTGGGCGCAAC-CTCTATCAATTTATCTAATTAGTGCTGGG
66 ATTCGTCGGTTTATCCAACTAGCACTGGGCACAACTCTC-ATCAATTTATCTAACTAGTGCTGGG
* *
17966753 AACACATTTTTCGG
130 AACACATTTGTAGG
*
17966767 TTTATCTAACTAGCGCTGGG-GCAAA
1 TTCATCTAACTAGCGCTGGGCGCAAA
17966792 CTCTTTTGCG
Statistics
Matches: 146, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
142 7 0.05
143 139 0.95
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (143 bp):
TTCATCTAACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCTCACTAATT
ATTCGTCGGTTTATCCAACTAGCACTGGGCACAACTCTCATCAATTTATCTAACTAGTGCTGGGA
ACACATTTGTAGG
Found at i:17973761 original size:36 final size:36
Alignment explanation
Indices: 17973714--17973787 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
17973704 GATTTATTCG
17973714 ACCTTTTCATGGACATAAGCACATTACCAATTGAGA
1 ACCTTTTCATGGACATAAGCACATTACCAATTGAGA
17973750 ACCTTTTCATGGACATAAGCACATTACCAATTGAGA
1 ACCTTTTCATGGACATAAGCACATTACCAATTGAGA
17973786 AC
1 AC
17973788 TTATTGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (36 bp):
ACCTTTTCATGGACATAAGCACATTACCAATTGAGA
Found at i:17974484 original size:102 final size:101
Alignment explanation
Indices: 17974370--17974584 Score: 315
Period size: 102 Copynumber: 2.1 Consensus size: 101
17974360 CATGGCCCTG
* * *
17974370 CCATGGTCTTACATTCATAGTGC-CATAACCCAGTTATGGTCTTATTATCAGAATTCCATAACCC
1 CCATGGTCTTACATCCATAGT-CACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCC
*
17974434 AACCTATGATATTACATATGAACACTATCATGGTCCAA
65 -ACCTATGATATTACATATAAACACTATCATGGTCCAA
*
17974472 CCATGGTATTACATCCATAGTCACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCA
1 CCATGGTCTTACATCCATAGTCACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCA
* * * * *
17974537 GCTATGGTCTTACATATAAACACTGTCATGGTTCAA
66 CCTATGATATTACATATAAACACTATCATGGTCCAA
17974573 CCATGGTCTTAC
1 CCATGGTCTTAC
17974585 GTTTGAATAA
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
101 43 0.43
102 58 0.57
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (101 bp):
CCATGGTCTTACATCCATAGTCACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCA
CCTATGATATTACATATAAACACTATCATGGTCCAA
Found at i:17978832 original size:8 final size:9
Alignment explanation
Indices: 17978806--17978831 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
17978796 CATTTAATTT
17978806 TTAAAAAAA
1 TTAAAAAAA
17978815 TTAAAAAAA
1 TTAAAAAAA
17978824 TTAAAAAA
1 TTAAAAAA
17978832 TATTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:17985519 original size:11 final size:12
Alignment explanation
Indices: 17985493--17985523 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17985483 GAAAAGATGT
17985493 AAAATTCATGGA
1 AAAATTCATGGA
17985505 AAAATTCATGGA
1 AAAATTCATGGA
17985517 AAAATTC
1 AAAATTC
17985524 TAATTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (12 bp):
AAAATTCATGGA
Found at i:17985731 original size:20 final size:21
Alignment explanation
Indices: 17985677--17985731 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
17985667 TTTTCCTAAG
* * *
17985677 ATGTGAATTGGATTGAATTGA
1 ATGTAAATTGTATTAAATTGA
17985698 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGTATTAAATTGA
17985718 ATGTTAAATT-TATT
1 ATG-TAAATTGTATT
17985732 CGTATAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (21 bp):
ATGTAAATTGTATTAAATTGA
Found at i:17986227 original size:24 final size:25
Alignment explanation
Indices: 17986200--17986259 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
17986190 AGCTTCCAGT
* *
17986200 TAATGGCTCTC-TGAAGCTTATCGA
1 TAATGGCTCGCTTGAACCTTATCGA
*
17986224 TAATGGCTCGCTTGAACCTTCTCGA
1 TAATGGCTCGCTTGAACCTTATCGA
* *
17986249 TACTAGCTCGC
1 TAATGGCTCGC
17986260 ATGAGCTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (25 bp):
TAATGGCTCGCTTGAACCTTATCGA
Found at i:17986304 original size:24 final size:23
Alignment explanation
Indices: 17986272--17986323 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
17986262 GAGCTTTCCG
* *
17986272 ATTACGGCTTTTATTAGCCTCCC
1 ATTACGGCTCTTATGAGCCTCCC
*
17986295 AATTACGGCTCTTATGAGCTTCCC
1 -ATTACGGCTCTTATGAGCCTCCC
17986319 ATTAC
1 ATTAC
17986324 ATGGCTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (23 bp):
ATTACGGCTCTTATGAGCCTCCC
Found at i:17989449 original size:104 final size:104
Alignment explanation
Indices: 17989327--17989550 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
17989317 AATGGATATC
17989327 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
17989392 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
17989431 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
17989496 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
17989535 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
17989551 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:17989912 original size:29 final size:29
Alignment explanation
Indices: 17989879--17989942 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
17989869 TAATCCACCA
17989879 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
17989908 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
17989938 CCCAA
1 CCCAA
17989943 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:17989916 original size:30 final size:30
Alignment explanation
Indices: 17989886--17989942 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17989876 CCACCCAACT
17989886 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
17989915 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
17989943 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:17996954 original size:104 final size:103
Alignment explanation
Indices: 17996774--17997001 Score: 366
Period size: 104 Copynumber: 2.2 Consensus size: 103
17996764 TAACCGTTAT
* * * *
17996774 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCATCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
17996839 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATA
17996878 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
* *
17996943 AATCAGCACATAGCAACCCCCTTTTCATTTCAAATATA
66 AATCAGCACATAGCAACCCCCTTTACATTTCAAAGATA
***
17996981 CAATGGATATCGCACTTAGCA
1 TGGTGGATATCGCACTTAGCA
17997002 ACCCCTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 30 0.26
104 85 0.74
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTACATTTCAAAGATA
Found at i:18022709 original size:14 final size:14
Alignment explanation
Indices: 18022690--18022721 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
18022680 TCGACATTCC
18022690 GGTGAGTAATCAAT
1 GGTGAGTAATCAAT
18022704 GGTGAGTAATCAAT
1 GGTGAGTAATCAAT
18022718 GGTG
1 GGTG
18022722 TAATTCGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.28
Consensus pattern (14 bp):
GGTGAGTAATCAAT
Found at i:18023949 original size:3 final size:3
Alignment explanation
Indices: 18023941--18023967 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18023931 AAACTATATT
18023941 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
18023968 CCTATTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.