Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 5 of 222
Found at i:1499470 original size:23 final size:23
Alignment explanation
Indices: 1499403--1499474 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
1499393 TATTATTAAA
* *
1499403 ATTTATATTTACATATAA-ATAT
1 ATTTATATATATATATAATATAT
* **
1499425 ATTTATATATGTA-ATTTTGATAT
1 ATTTATATATATATATAAT-ATAT
*
1499448 ATTTATATGTATATATAATATAT
1 ATTTATATATATATATAATATAT
1499471 ATTT
1 ATTT
1499475 TTTAAACTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 2 0.05
22 10 0.26
23 23 0.61
24 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTATATATATATATAATATAT
Found at i:1499560 original size:67 final size:71
Alignment explanation
Indices: 1499486--1499620 Score: 188
Period size: 67 Copynumber: 1.9 Consensus size: 71
1499476 TTAAACTAAT
* *
1499486 ATATAATTTATTAAGAAACTAAAAATTAG-GCT-ATA-A-ATATATATATATGAAAAATATTTAA
1 ATATAATTTATCAAGAAACTAAAAATTAGTGCTAATATATATATATATATAAGAAAAATATTTAA
1499547 ATGTAC
66 ATGTAC
* *
1499553 ATATAATTTATCAATAAACTAAAAATTAGATTGTTAATATATATATATATATAAGAAAAATATTT
1 ATATAATTTATCAAGAAACTAAAAATTAG--TGCTAATATATATATATATATAAGAAAAATATTT
1499618 AAA
64 AAA
1499621 AACAACGATA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 27 0.47
70 2 0.03
71 3 0.05
72 1 0.02
73 25 0.43
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (71 bp):
ATATAATTTATCAAGAAACTAAAAATTAGTGCTAATATATATATATATATAAGAAAAATATTTAA
ATGTAC
Found at i:1499815 original size:13 final size:14
Alignment explanation
Indices: 1499792--1499832 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1499782 AATTATTATT
*
1499792 TTAAGTATAAAATA
1 TTAATTATAAAATA
*
1499806 TT-TTTATAAAAT-
1 TTAATTATAAAATA
1499818 TTAATTATAAAATA
1 TTAATTATAAAATA
1499832 T
1 T
1499833 ATAAAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 2 0.09
13 17 0.77
14 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
TTAATTATAAAATA
Found at i:1500270 original size:20 final size:20
Alignment explanation
Indices: 1500228--1500271 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1500218 ACATTTTGGG
*
1500228 TTTTTTTTTTATTTTTGTAA
1 TTTTTTTTTTATTTTTCTAA
*
1500248 TTTTTTCTTTTCTTTTTCT-A
1 TTTTTT-TTTTATTTTTCTAA
1500268 TTTT
1 TTTT
1500272 ATAAATATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTTATTTTTCTAA
Found at i:1507515 original size:31 final size:31
Alignment explanation
Indices: 1507479--1507544 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
1507469 AGATATGATC
1507479 TTTTAAATACACGAAAATATTAGAACTCGAA
1 TTTTAAATACACGAAAATATTAGAACTCGAA
1507510 TTTTAAATACACGAAAATATTAGAACTCGAA
1 TTTTAAATACACGAAAATATTAGAACTCGAA
1507541 TTTT
1 TTTT
1507545 TTGTATTACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (31 bp):
TTTTAAATACACGAAAATATTAGAACTCGAA
Found at i:1512348 original size:3 final size:3
Alignment explanation
Indices: 1512340--1512366 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1512330 TAAAATAAGA
1512340 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1512367 TATGACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1527886 original size:17 final size:17
Alignment explanation
Indices: 1527864--1527897 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1527854 CATTTACGAG
1527864 CCAAATGTCGTTTTTAA
1 CCAAATGTCGTTTTTAA
*
1527881 CCAAATGTGGTTTTTAA
1 CCAAATGTCGTTTTTAA
1527898 AAGATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
CCAAATGTCGTTTTTAA
Found at i:1528839 original size:21 final size:21
Alignment explanation
Indices: 1528791--1528832 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1528781 TTTTCCTAGG
* *
1528791 ATGTGAATTAGATTGAATTGA
1 ATGTAAATTAGATTAAATTGA
*
1528812 ATGTAAATTATATTAAATTGA
1 ATGTAAATTAGATTAAATTGA
1528833 TGCTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGTAAATTAGATTAAATTGA
Found at i:1529422 original size:24 final size:24
Alignment explanation
Indices: 1529395--1529453 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1529385 GCTATCTGAT
1529395 GCTACCCGTTAATTGCTCTTCGAA
1 GCTACCCGTTAATTGCTCTTCGAA
* *
1529419 GCTACCCGTTGATTGCTCTTCGGA
1 GCTACCCGTTAATTGCTCTTCGAA
*
1529443 GCTACCTGTTA
1 GCTACCCGTTA
1529454 TAGGCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.34
Consensus pattern (24 bp):
GCTACCCGTTAATTGCTCTTCGAA
Found at i:1531684 original size:36 final size:36
Alignment explanation
Indices: 1531636--1531707 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1531626 GGTTGGTGTC
*
1531636 GGTGTTTGAGGGTCAAGCTAAATCTGAGCTTAGATT
1 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1531672 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1531708 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (36 bp):
GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
Found at i:1533865 original size:26 final size:26
Alignment explanation
Indices: 1533843--1533894 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1533833 ACAAAAATTT
1533843 TATTTTAAAAATAAAAAAGAAAAAAA
1 TATTTTAAAAATAAAAAAGAAAAAAA
* *
1533869 TATTTTAAAATTAAAAAA-ATAAAAA
1 TATTTTAAAAATAAAAAAGAAAAAAA
1533894 T
1 T
1533895 TATATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAAGAAAAAAA
Found at i:1534579 original size:21 final size:18
Alignment explanation
Indices: 1534536--1534585 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 18
1534526 TATGGAAAAA
1534536 TGAATTTTTAAAATTTTT
1 TGAATTTTTAAAATTTTT
1534554 T--ATTTTTAAATTATTTTTT
1 TGAATTTTTAAA--A-TTTTT
1534573 TGAATTTTTAAAA
1 TGAATTTTTAAAA
1534586 ATCAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
16 9 0.33
18 2 0.07
19 7 0.26
21 9 0.33
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TGAATTTTTAAAATTTTT
Found at i:1535972 original size:15 final size:15
Alignment explanation
Indices: 1535925--1535972 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1535915 AACTGATAAT
1535925 ATTTTCCGTAAAATG
1 ATTTTCCGTAAAATG
*
1535940 A-TTGCCAGTAAAAT-
1 ATTTTCC-GTAAAATG
1535954 ATTTTCCGTAAAATG
1 ATTTTCCGTAAAATG
1535969 ATTT
1 ATTT
1535973 CTGGAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (15 bp):
ATTTTCCGTAAAATG
Found at i:1535973 original size:14 final size:14
Alignment explanation
Indices: 1535927--1535973 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
1535917 CTGATAATAT
1535927 TTTCCGTAAAATGA
1 TTTCCGTAAAATGA
*
1535941 TTGCCAGTAAAAT-A
1 TTTCC-GTAAAATGA
1535955 TTTTCCGTAAAATGA
1 -TTTCCGTAAAATGA
1535970 TTTC
1 TTTC
1535974 TGGAAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (14 bp):
TTTCCGTAAAATGA
Found at i:1535995 original size:20 final size:20
Alignment explanation
Indices: 1535970--1536009 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1535960 CGTAAAATGA
*
1535970 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1535990 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1536010 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1535999 original size:34 final size:35
Alignment explanation
Indices: 1535955--1536021 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1535945 CAGTAAAATA
*
1535955 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
1535989 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1536022 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1536025 original size:14 final size:15
Alignment explanation
Indices: 1535949--1536025 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1535939 GATTGCCAGT
* *
1535949 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
1535963 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
1535977 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
1535997 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
1536012 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
1536026 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:1539099 original size:4 final size:4
Alignment explanation
Indices: 1539090--1539116 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1539080 GGTATGCATC
1539090 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1539117 CTTACTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:1540397 original size:45 final size:45
Alignment explanation
Indices: 1540313--1540399 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
1540303 CAATAGAAGT
* *
1540313 TCATTACAAATCTTAACCTTTCATATCCTCCTCCTATTGGAGCAG
1 TCATTACAAATCTCAACCTTTCATATCCTCCTCCAATTGGAGCAG
* * *
1540358 TCATTACAAATCTCAACCCTTT-ATCTCCTCTTTCAATTGGAG
1 TCATTACAAATCTCAA-CCTTTCATATCCTCCTCCAATTGGAG
1540400 ATCTCAACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.37
Consensus pattern (45 bp):
TCATTACAAATCTCAACCTTTCATATCCTCCTCCAATTGGAGCAG
Found at i:1543448 original size:63 final size:62
Alignment explanation
Indices: 1543337--1543526 Score: 263
Period size: 63 Copynumber: 3.0 Consensus size: 62
1543327 GATCTCAATC
* * * *
1543337 CTTCGTCTACTCCTTTTATTGGAGCTTCAATAGAAGGTCATTACAAATCTTAGCCCTTCATCT
1 CTTCATCT-CTCCTTCTATTGGAGCTCCAATAGAAGGTCATTACAAATCTCAGCCCTTCATCT
* * *
1543400 TTTCATCTTCTCCTTCTATTGGAGCTCCAATAGAAGGTCAATATAAATCTCAGCCCTTCATCT
1 CTTCATC-TCTCCTTCTATTGGAGCTCCAATAGAAGGTCATTACAAATCTCAGCCCTTCATCT
* * *
1543463 CTTCATCTCATCTTTCTATTTGAGCTCCAATAGAATGTCATTACAAATCTCAGCCCTTCATCT
1 CTTCATCTC-TCCTTCTATTGGAGCTCCAATAGAAGGTCATTACAAATCTCAGCCCTTCATCT
1543526 C
1 C
1543527 CTCCTTTCTC
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
62 2 0.02
63 109 0.97
64 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (62 bp):
CTTCATCTCTCCTTCTATTGGAGCTCCAATAGAAGGTCATTACAAATCTCAGCCCTTCATCT
Found at i:1544425 original size:16 final size:17
Alignment explanation
Indices: 1544395--1544427 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1544385 TCTTCTTTTT
1544395 TTTCCTCTCATTTTCCC
1 TTTCCTCTCATTTTCCC
1544412 TTTCCTCT-ATTTTCCC
1 TTTCCTCTCATTTTCCC
1544428 ACCCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTCCTCTCATTTTCCC
Found at i:1548596 original size:3 final size:3
Alignment explanation
Indices: 1548573--1548655 Score: 64
Period size: 3 Copynumber: 27.0 Consensus size: 3
1548563 CTTTTTACAC
* *
1548573 TTA TCTA TTCA TTA TTA -TA TTA TTA -TA TCA -TA TTA TTA TTT TTGAA
1 TTA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A
* *
1548619 TTA TTA GTA TTA TTA TTA TTAA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
1548656 GTTTTATTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
2 5 0.08
3 48 0.75
4 9 0.14
5 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1548603 original size:19 final size:20
Alignment explanation
Indices: 1548581--1548655 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
1548571 ACTTATCTAT
1548581 TCATTATTA-TATTATTATA
1 TCATTATTATTATTATTATA
*
1548600 TCA-TATTATTATTTTTGA-A
1 TCATTATTATTATTATT-ATA
* *
1548619 TTATTAGTATTATTATTAT-
1 TCATTATTATTATTATTATA
* *
1548638 TAATTATTATCATTATTA
1 TCATTATTATTATTATTA
1548656 GTTTTATTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 5 0.11
19 28 0.62
20 12 0.27
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (20 bp):
TCATTATTATTATTATTATA
Found at i:1549051 original size:4 final size:4
Alignment explanation
Indices: 1549042--1549079 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
1549032 ATACATATCT
1549042 TTTA TTTA TTT- TCTTCA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA T-TT-A TTTA TTTA TTTA TTTA TTTA T
1549080 ATGTCCGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 27 0.87
5 2 0.06
6 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1550269 original size:20 final size:20
Alignment explanation
Indices: 1550237--1550301 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
1550227 TTATATTTGG
1550237 TATTTTGTAATCTATACATA
1 TATTTTGTAATCTATACATA
*
1550257 TATTTATGT-ATCTTTACATA
1 TATTT-TGTAATCTATACATA
*
1550277 TATATATTTTAAT-TCATACATA
1 TAT-T-TTGTAATCT-ATACATA
1550299 TAT
1 TAT
1550302 ATACGCACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 18 0.49
21 7 0.19
22 12 0.32
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.52
Consensus pattern (20 bp):
TATTTTGTAATCTATACATA
Found at i:1550434 original size:20 final size:20
Alignment explanation
Indices: 1550395--1550434 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1550385 ATGCATATAT
* * *
1550395 TTTCTTAATATGTATTCATA
1 TTTCATAATATATATACATA
1550415 TTTCATAATATATATACATA
1 TTTCATAATATATATACATA
1550435 CATATATACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTCATAATATATATACATA
Found at i:1557678 original size:2 final size:2
Alignment explanation
Indices: 1557673--1557699 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1557663 ATATATACAT
1557673 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1557700 CCTGCAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1569027 original size:17 final size:17
Alignment explanation
Indices: 1569005--1569038 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1568995 CTTTGAAATT
1569005 TTTTTCAAATATATATG
1 TTTTTCAAATATATATG
* *
1569022 TTTTTCAGATTTATATG
1 TTTTTCAAATATATATG
1569039 CTCTAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTTCAAATATATATG
Found at i:1585423 original size:9 final size:9
Alignment explanation
Indices: 1585409--1585442 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1585399 ATCTCTTATA
1585409 AAACAAAAG
1 AAACAAAAG
*
1585418 AAACAATAAT
1 AAACAA-AAG
1585428 AAACAAAAG
1 AAACAAAAG
1585437 AAACAA
1 AAACAA
1585443 TAATAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (9 bp):
AAACAAAAG
Found at i:1585433 original size:19 final size:19
Alignment explanation
Indices: 1585409--1585448 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1585399 ATCTCTTATA
1585409 AAACAAAAGAAACAATAAT
1 AAACAAAAGAAACAATAAT
1585428 AAACAAAAGAAACAATAAT
1 AAACAAAAGAAACAATAAT
1585447 AA
1 AA
1585449 TACACTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (19 bp):
AAACAAAAGAAACAATAAT
Found at i:1592276 original size:129 final size:127
Alignment explanation
Indices: 1592034--1592305 Score: 316
Period size: 129 Copynumber: 2.1 Consensus size: 127
1592024 CGGTAAGAAC
* * * *
1592034 ACCCGACTCGGTAGGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATATGGGTTGTCC
1 ACCCGACCCGGTAAGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATACGGGTTATCC
*
1592099 ACTCGTCCCGAAACATAACTAGTGACCATATCACAATAAAGTCCGAGTCACATATGAGCTATCA
66 ACTCGTCCAGAAACATAACTAGTGACCATAT--CAATAAAGTCCGAGTCACATATGAGCTATCA
* * *
1592163 ACCCGACCCGGTAAGAAACTAGTGACGATGTTTATAACCGAGTCCGAATATCATACGGGTTATCC
1 ACCCGACCCGGTAAGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATACGGGTTATCC
* * ** * * * *
1592228 ACTTGATCCAGTAGGA-AACTAGTGAAACGATAGT-AGTAGAA-TCTGAGTCACATATGGGCTAT
66 ACTCG-TCCAGAAACATAACTAGTG--ACCATA-TCAATA-AAGTCCGAGTCACATATGAGCTAT
1592290 CA
126 CA
1592292 ACCCGACCCGGTAA
1 ACCCGACCCGGTAA
1592306 AATCCGAGTA
Statistics
Matches: 122, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
129 108 0.89
130 8 0.07
131 5 0.04
132 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (127 bp):
ACCCGACCCGGTAAGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATACGGGTTATCC
ACTCGTCCAGAAACATAACTAGTGACCATATCAATAAAGTCCGAGTCACATATGAGCTATCA
Found at i:1596491 original size:17 final size:17
Alignment explanation
Indices: 1596471--1596506 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1596461 TTTTTTTGAA
1596471 TTAGTGAATTTTGTGAT
1 TTAGTGAATTTTGTGAT
1596488 TTAGTGAATTTTGTGAT
1 TTAGTGAATTTTGTGAT
1596505 TT
1 TT
1596507 TAAAAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (17 bp):
TTAGTGAATTTTGTGAT
Found at i:1601684 original size:19 final size:20
Alignment explanation
Indices: 1601649--1601691 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1601639 CTTTTGTAAA
1601649 TTTTTATACTTTCATATATT
1 TTTTTATACTTTCATATATT
1601669 TTTTTATA-TTAT-ATATATT
1 TTTTTATACTT-TCATATATT
1601688 TTTT
1 TTTT
1601692 AAAATTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTATACTTTCATATATT
Found at i:1603687 original size:30 final size:30
Alignment explanation
Indices: 1603653--1603723 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
1603643 GTATTACAAA
* *
1603653 TATATTTTTACATAATTTATTTCATCCCAT
1 TATATTTTTACATAACTTATTTCAACCCAT
1603683 TATATTTTTACATAACTTATTTCAACCCAT
1 TATATTTTTACATAACTTATTTCAACCCAT
*
1603713 CATATTTTTAC
1 TATATTTTTAC
1603724 TTCTCCTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (30 bp):
TATATTTTTACATAACTTATTTCAACCCAT
Found at i:1609595 original size:18 final size:18
Alignment explanation
Indices: 1609574--1609608 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1609564 CTTGTTTTCG
1609574 ATACTCTTCTTCAATACT
1 ATACTCTTCTTCAATACT
1609592 ATACTCTTCTTCAATAC
1 ATACTCTTCTTCAATAC
1609609 GAAGATGATT
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:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
ATACTCTTCTTCAATACT
Found at i:1611621 original size:19 final size:20
Alignment explanation
Indices: 1611578--1611620 Score: 65
Period size: 17 Copynumber: 2.3 Consensus size: 20
1611568 TCTTTTGTAA
1611578 ATTTTTATACTTTCATATAT
1 ATTTTTATACTTTCATATAT
1611598 ATTTTTATA--TT-ATATAT
1 ATTTTTATACTTTCATATAT
1611615 ATTTTT
1 ATTTTT
1611621 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.52
18 2 0.09
20 9 0.39
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTATACTTTCATATAT
Found at i:1613629 original size:5 final size:5
Alignment explanation
Indices: 1613621--1613646 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1613611 ATGATATGAG
1613621 TGTCA TGTCA TGTCA TGTCA TGTCA T
1 TGTCA TGTCA TGTCA TGTCA TGTCA T
1613647 TACACATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TGTCA
Found at i:1616505 original size:27 final size:22
Alignment explanation
Indices: 1616442--1616503 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
1616432 ATTTATACTT
1616442 AATATAATATTTTATTTTTATTA
1 AATA-AATATTTTATTTTTATTA
1616465 AATAAATATTTTATTTTTATTA
1 AATAAATATTTTATTTTTATTA
1616487 AATAAATATTTTATTTT
1 AATAAATATTTTATTTT
1616504 ATACTTAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATAAATATTTTATTTTTATTA
Found at i:1619172 original size:6 final size:6
Alignment explanation
Indices: 1619161--1619195 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
1619151 TCCAAATATA
1619161 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
1619196 TCATTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:1621957 original size:28 final size:29
Alignment explanation
Indices: 1621926--1621980 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
1621916 AATCAAAGTA
1621926 AAAAAATCAAAATCAAAA-TAAAAAAAAT
1 AAAAAATCAAAATCAAAAGTAAAAAAAAT
*
1621954 AAAAAATCAAAGTCAAAAGTAAAAAAA
1 AAAAAATCAAAATCAAAAGTAAAAAAA
1621981 GAAATCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (29 bp):
AAAAAATCAAAATCAAAAGTAAAAAAAAT
Found at i:1621976 original size:29 final size:28
Alignment explanation
Indices: 1621920--1622005 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
1621910 AGAAAAAATC
*
1621920 AAAGTAAAAAAATCAAAATCAAAATAAAA
1 AAAG-AAAAAAATCAAAGTCAAAATAAAA
1621949 AAA-ATAAAAAATCAAAGTCAAAAGTAAAA
1 AAAGA-AAAAAATCAAAGTCAAAA-TAAAA
** *
1621978 AAAGAAATCAATCAAAGTTAAAATAAAA
1 AAAGAAAAAAATCAAAGTCAAAATAAAA
1622006 TATGAAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.02
28 22 0.44
29 26 0.52
30 1 0.02
ACGTcount: A:0.72, C:0.07, G:0.06, T:0.15
Consensus pattern (28 bp):
AAAGAAAAAAATCAAAGTCAAAATAAAA
Found at i:1622386 original size:7 final size:7
Alignment explanation
Indices: 1622374--1622406 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1622364 GGATTTCAAA
1622374 AAAAATG
1 AAAAATG
1622381 AAAAATG
1 AAAAATG
*
1622388 -AGAATG
1 AAAAATG
1622394 AAAAATG
1 AAAAATG
1622401 AAAAAT
1 AAAAAT
1622407 AGAGAGGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:1622395 original size:13 final size:13
Alignment explanation
Indices: 1622377--1622401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1622367 TTTCAAAAAA
1622377 AATGAAAAATGAG
1 AATGAAAAATGAG
1622390 AATGAAAAATGA
1 AATGAAAAATGA
1622402 AAAATAGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (13 bp):
AATGAAAAATGAG
Found at i:1623780 original size:87 final size:87
Alignment explanation
Indices: 1623629--1623803 Score: 269
Period size: 87 Copynumber: 2.0 Consensus size: 87
1623619 AGATCAGTGA
* * *
1623629 AGATGAAAAACAAAGCCTTGCCTTCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
1623694 CTTCCTGCGTTAATAGCAAAGC
66 CTTCCTACGTTAATAGCAAAGC
* * *
1623716 AGATCAAAAACGAAGCCTTGCCTCCATCGGTTGCAGTGGAGTTGGTTGAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
1623781 CTTCCTATGTTAATAGCGAAGC
66 CTTCCTACGTTAATAGCAAAGC
1623803 A
1 A
1623804 TCTTGCTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTACGTTAATAGCAAAGC
Found at i:1623884 original size:116 final size:116
Alignment explanation
Indices: 1623687--1623902 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 116
1623677 AAGATAGCAG
* * *
1623687 ATCTTGCCTTCCTGCGTTAATAGCAAAGCAGATCAAAAACGAAGCCTTGCCTCCATCGGTTGCAG
1 ATCTTGCCTTCCTGCGTCAACAGCAAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAG
* * * *
1623752 TGGAGTTGGTTGAAGATAGCAGATCTTGCCTTCCTATGTTAATAGCGAAGC
66 TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCTATGTTAATAGCGAAGC
* * * *
1623803 ATCTTGCTTTCCTGCGTCAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAG
1 ATCTTGCCTTCCTGCGTCAACAGCAAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAG
1623868 TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCT
66 TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCT
1623903 GCATCGACAG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (116 bp):
ATCTTGCCTTCCTGCGTCAACAGCAAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAG
TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCTATGTTAATAGCGAAGC
Found at i:1634878 original size:22 final size:22
Alignment explanation
Indices: 1634836--1634879 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1634826 AATTACAAAT
**
1634836 TATTTGAGAATTTATGGTTTTA
1 TATTTGAGAATTTATACTTTTA
1634858 TATTTGAGAATTTATACTTTTA
1 TATTTGAGAATTTATACTTTTA
1634880 GAGGAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (22 bp):
TATTTGAGAATTTATACTTTTA
Found at i:1642817 original size:8 final size:7
Alignment explanation
Indices: 1642729--1642815 Score: 50
Period size: 7 Copynumber: 11.9 Consensus size: 7
1642719 TATTTATACA
*
1642729 TTTAATT
1 TTTAAAT
1642736 TTTAATAT
1 TTTAA-AT
1642744 TTTAATAT
1 TTTAA-AT
**
1642752 TTTATCT
1 TTTAAAT
* *
1642759 TTCAGAT
1 TTTAAAT
1642766 TTTAAA-
1 TTTAAAT
* *
1642772 ATTCAAT
1 TTTAAAT
*
1642779 TTCAATATT
1 TTTAA-A-T
1642788 TTTGAAAT
1 TTT-AAAT
1642796 TTTAAAT
1 TTTAAAT
1642803 TTTAAAT
1 TTTAAAT
1642810 TTTAAA
1 TTTAAA
1642816 ATTAAAATAA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
6 4 0.07
7 33 0.54
8 18 0.30
9 4 0.07
10 2 0.03
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (7 bp):
TTTAAAT
Found at i:1655815 original size:15 final size:15
Alignment explanation
Indices: 1655777--1655814 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1655767 TTATAGTTTT
1655777 TATATTTTACAATTA
1 TATATTTTACAATTA
*
1655792 TATAATTTTATAA-TA
1 TAT-ATTTTACAATTA
1655807 TATATTTT
1 TATATTTT
1655815 TTTGATGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTTACAATTA
Found at i:1656084 original size:20 final size:20
Alignment explanation
Indices: 1656059--1656097 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1656049 ATGCATTGTT
1656059 TTATATT-TTTGTAATATATA
1 TTATATTATTT-TAATATATA
1656079 TTATATTATTTTAATATAT
1 TTATATTATTTTAATATAT
1656098 TATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTATATTATTTTAATATATA
Found at i:1661116 original size:44 final size:44
Alignment explanation
Indices: 1660999--1661173 Score: 148
Period size: 44 Copynumber: 4.1 Consensus size: 44
1660989 TAGGGGGACG
* *
1660999 AGATTTGTGGTTTTAGTCTGCTCCACTGCAA-TGTCAGGGAGATA
1 AGATCTGTGGTTTTAATCTGCTCCACTGCAACT-TCAGGGAGATA
* *** * *
1661043 AGA-C--TGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATA
1 AGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
*
1661084 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 AGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
* * * **
1661128 GGAT-TGT-TTTCTTATATCTGCTCCACTACTGCTT-AGGGAGATA
1 AGATCTGTGGTT-TTA-ATCTGCTCCACTGCAACTTCAGGGAGATA
1661171 AGA
1 AGA
1661174 CTTGATGCGA
Statistics
Matches: 103, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
41 31 0.30
42 4 0.04
43 17 0.17
44 51 0.50
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (44 bp):
AGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
Found at i:1661343 original size:131 final size:131
Alignment explanation
Indices: 1661192--1661921 Score: 1208
Period size: 131 Copynumber: 5.5 Consensus size: 131
1661182 GATCTGCTGT
* * * * * *
1661192 ACTACTACTTAGGGAGATAAGATCTATAATCTTTAACCTATTCCACTGCTGCTTAGGAAGATAGG
1 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
* **
1661257 ACTGGTGGCTTAAATCAGCTTCCTACTATCTTGGGAAGATAAGATTCATCGTCTTCGATCCGCTC
66 ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
1661322 C
131 C
*
1661323 ACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
1 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
1661388 ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
66 ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
1661453 C
131 C
1661454 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
1 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
1661519 ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
66 ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
1661584 C
131 C
1661585 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
1 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
* * *
1661650 ACTGGTGGCTTAAATCTGCTTCCTACTATCTCGGGAAGATAAGATTCGTCGTCTTTGATCCGCTC
66 ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
1661715 C
131 C
* * *
1661716 ACTTCTGCTTAGGGAGATAAGATCTACCATCTTCAACCTACTCCACTGCTGCTTAGGGAGATAGA
1 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGAT---
* *
1661781 ACTGGTAGCTGGTAGCTTAAATCTTCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGA
63 A--GG-A-CTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGA
*
1661846 TCTGCTCC
124 TCCGCTCC
* *
1661854 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTTCTCAGGGAGATAAG
1 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
1661919 ACT
66 ACT
1661922 TGTAGTTTCA
Statistics
Matches: 566, Mismatches: 26, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
131 442 0.78
132 1 0.00
133 1 0.00
134 1 0.00
135 1 0.00
136 2 0.00
137 1 0.00
138 117 0.21
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (131 bp):
ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGG
ACTGGTGGCTTAAATCTGCTTCCTACTATCTTGGGAAGATAAGATTCGCCGTCTTCGATCCGCTC
C
Found at i:1661887 original size:44 final size:44
Alignment explanation
Indices: 1661143--1661919 Score: 277
Period size: 44 Copynumber: 17.7 Consensus size: 44
1661133 GTTTTCTTAT
* * * *
1661143 ATCTGCTCCACTACTGCTTAGGGAGATAAGA-CT--TG-ATGCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
** * * * *
1661183 ATCTGCTGTACTACTACTTAGGGAGATAAGATCTATAATCTTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* ** * * * *** * *
1661227 ACCTATTCCACTGCTGCTTAGGAAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* *
1661270 ATCAGCTTCCTACTA-T-CTT-GGGAAGATAAGAT-T-CATCGTCTTCG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGATCTACA--GTCTTCA
* * *
1661314 ATCCGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * *** * *
1661358 ACCTACTCCACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * *
1661401 ATCTGCTTCCTACTA-T-CTT-GGGAAGATAAGAT-TCGCCGTCTTCG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGATCT-ACAGTCTTCA
* *
1661445 ATCCGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * *** * *
1661489 ACCTACTCCACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * *
1661532 ATCTGCTTCCTACTA-T-CTT-GGGAAGATAAGAT-TCGCCGTCTTCG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGATCT-ACAGTCTTCA
* *
1661576 ATCCGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * *** * *
1661620 ACCTACTCCACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* **
1661663 ATCTGCTTCCTACTA-T-C-TCGGGAAGATAAGATTCGT-C-GTCTTTG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGA-TC-TACAGTCTTCA
* *
1661707 ATCCGCTCCACTTCTGCTTAGGGAGATAAGATCTACCA-TCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA-CAGTCTTCA
* * * * * *
1661751 ACCTACTCCACTGCTGCTTAGGGAGAT-AGAACTGGTAGCTGGTAGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAG-A-T-CTA-C-AGT--CTTCA
* * * *
1661801 ATCTTCTTCCTACTA-T-CTT-GGGAAGATAAGAT-TCGCCGTCTTCG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGATCT-ACAGTCTTCA
*
1661845 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * *
1661889 ACCTACTCCACTGCTTCTCAGGGAGATAAGA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGA
1661920 CTTGTAGTTT
Statistics
Matches: 530, Mismatches: 146, Indels: 118
0.67 0.18 0.15
Matches are distributed among these distances:
40 28 0.05
41 2 0.00
42 31 0.06
43 101 0.19
44 295 0.56
45 34 0.06
46 7 0.01
47 2 0.00
48 1 0.00
49 4 0.01
50 16 0.03
51 6 0.01
52 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
Found at i:1662463 original size:45 final size:46
Alignment explanation
Indices: 1662410--1662497 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
1662400 AGCTCGAAAT
*
1662410 GAATAAATTAATCAAGATAGCAAATTTTGTC-AGAATACAAAATGA
1 GAATAAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAATGA
* **
1662455 GAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAAAA
1 GAATAAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAA
1662498 AATAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 28 0.74
46 10 0.26
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (46 bp):
GAATAAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAATGA
Found at i:1663310 original size:12 final size:12
Alignment explanation
Indices: 1663258--1663327 Score: 58
Period size: 12 Copynumber: 5.9 Consensus size: 12
1663248 CCGGTAGAGT
1663258 TTTTTTGTTTT-
1 TTTTTTGTTTTG
*
1663269 TTATTTTCTTGTT-
1 TT-TTTTGTT-TTG
*
1663282 TTTTTTGGGTTTG
1 TTTTTT-GTTTTG
1663295 --TTTTGTTTTG
1 TTTTTTGTTTTG
1663305 TTTTTTGTTTTG
1 TTTTTTGTTTTG
*
1663317 CTTTTTGTTTT
1 TTTTTTGTTTT
1663328 TGCTTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.10
11 6 0.12
12 32 0.67
13 5 0.10
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.80
Consensus pattern (12 bp):
TTTTTTGTTTTG
Found at i:1663328 original size:13 final size:12
Alignment explanation
Indices: 1663295--1663335 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
1663285 TTTGGGTTTG
*
1663295 TTTTGTTTTGTT
1 TTTTGTTTTGCT
1663307 TTTTGTTTTGCT
1 TTTTGTTTTGCT
1663319 TTTTGTTTTTGCT
1 TTTTG-TTTTGCT
1663332 TTTT
1 TTTT
1663336 TTTACCTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (12 bp):
TTTTGTTTTGCT
Found at i:1663334 original size:12 final size:11
Alignment explanation
Indices: 1663260--1663327 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 11
1663250 GGTAGAGTTT
1663260 TTTTGTTTTT-
1 TTTTGTTTTTG
* *
1663270 TATT-TTCTTG
1 TTTTGTTTTTG
*
1663280 TTTT-TTTTGG
1 TTTTGTTTTTG
*
1663290 GTTTG-TTTTG
1 TTTTGTTTTTG
1663300 TTTTGTTTTTTG
1 TTTTG-TTTTTG
1663312 TTTTGCTTTTTG
1 TTTTG-TTTTTG
1663324 TTTT
1 TTTT
1663328 TGCTTTTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
9 4 0.09
10 21 0.47
12 20 0.44
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.79
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:1670444 original size:54 final size:54
Alignment explanation
Indices: 1670385--1670542 Score: 280
Period size: 54 Copynumber: 2.9 Consensus size: 54
1670375 GGTTGAGTGA
*
1670385 ATTAGACTAGAGATGTTCATTTGTTGGGCCGAGGGCCAATTCCAAAAAAATTAT
1 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAATTAT
*
1670439 ATTAGACTAGAGATGTTCATTTGCTCGGCCGAGGGCCAATTCCAAAAAAATTAT
1 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAATTAT
* *
1670493 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGTCAGTTCCAAAAAAA
1 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAA
1670543 GTTCTAGGCC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (54 bp):
ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAATTAT
Found at i:1671022 original size:28 final size:27
Alignment explanation
Indices: 1670983--1671052 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
1670973 ATACATATCT
1670983 AATTATTT-ATATTTAGTTA-TATAATA
1 AATTATTTAATATTTA-TTATTATAATA
*
1671009 AATTATATTAATATTTTATTATTTTAATA
1 AATTAT-TTAATA-TTTATTATTATAATA
*
1671038 AATTATTTAGTATTT
1 AATTATTTAATATTT
1671053 CAATTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.16
27 5 0.13
28 11 0.29
29 16 0.42
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
AATTATTTAATATTTATTATTATAATA
Found at i:1671093 original size:15 final size:17
Alignment explanation
Indices: 1671064--1671100 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1671054 AATTTTATTT
1671064 TAATAATGAATTTTAAA
1 TAATAATGAATTTTAAA
1671081 -AATAATG-ATTTTAAA
1 TAATAATGAATTTTAAA
1671096 TAATA
1 TAATA
1671101 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATGAATTTTAAA
Found at i:1674609 original size:14 final size:14
Alignment explanation
Indices: 1674576--1674610 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1674566 TATAATATTC
*
1674576 AAATAATAACAACA
1 AAATAGTAACAACA
1674590 AAATAGTAACAACA
1 AAATAGTAACAACA
*
1674604 TAATAGT
1 AAATAGT
1674611 GATATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:1686560 original size:3 final size:3
Alignment explanation
Indices: 1686552--1686598 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1686542 TTTAGCAATT
*
1686552 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1686599 GTTTTTATGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1707054 original size:3 final size:3
Alignment explanation
Indices: 1707046--1707101 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1707036 TTTAGCAATT
*
1707046 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1707094 TTA TTA TT
1 TTA TTA TT
1707102 GTTTTTATGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1710943 original size:18 final size:19
Alignment explanation
Indices: 1710901--1710943 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
1710891 CTCCCCCCCC
1710901 TTTATTCACATAAAAAATA
1 TTTATTCACATAAAAAATA
*
1710920 TATATT-AC-TAAAAAATAA
1 TTTATTCACATAAAAAAT-A
1710938 TTTATT
1 TTTATT
1710944 TTTTAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTATTCACATAAAAAATA
Found at i:1714722 original size:48 final size:45
Alignment explanation
Indices: 1714670--1715155 Score: 225
Period size: 48 Copynumber: 10.6 Consensus size: 45
1714660 CTCCACCACC
* * * *
1714670 GCCTTATGTGTATAAATCTCCACCACCACCACCTAAACATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC--AACA-AAGGAGAA
* *
1714718 GCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * ******* *
1714763 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC--AAAGGAGA-A
* * * * * ***** * *
1714811 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * *
1714859 TCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1714907 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* *
1714949 GCCTTATGAATACAAGTCTCCACCACCACCACC--GAAA-GAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * * ***** * *
1714991 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * * *
1715039 TCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1715087 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
*
1715129 GCCTTATGAATACAAGTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACC
1715156 TCCATCTCCA
Statistics
Matches: 343, Mismatches: 78, Indels: 40
0.74 0.17 0.09
Matches are distributed among these distances:
42 108 0.31
43 5 0.01
45 40 0.12
46 4 0.01
47 6 0.02
48 172 0.50
49 4 0.01
50 4 0.01
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (45 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
Found at i:1714838 original size:27 final size:26
Alignment explanation
Indices: 1714800--1714888 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
1714790 ACCATCACCT
*
1714800 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
1714827 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
1714848 TCTCCACCACCTCCTTATGTGTATAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
1714875 TCTCCACCACCTCC
1 TCTCCACCACCTCC
1714889 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 2 0.04
25 2 0.04
26 1 0.02
27 27 0.56
ACGTcount: A:0.21, C:0.45, G:0.06, T:0.28
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:1714946 original size:42 final size:42
Alignment explanation
Indices: 1714900--1715155 Score: 269
Period size: 42 Copynumber: 5.8 Consensus size: 42
1714890 CCAAAGCATG
1714900 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1714942 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
* * **
1714984 AAGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCA---CCACCACC-GA
*** * ** ** * * *
1715030 TCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCA
1 AGGA-GA-AGCCTTATGAATACAAGTCTCCACCACCACCACC---G-A
1715078 TGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 --AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1715122 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1715156 TCCATCTCCA
Statistics
Matches: 173, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
42 107 0.62
44 1 0.01
45 14 0.08
46 1 0.01
47 1 0.01
48 47 0.27
49 1 0.01
50 1 0.01
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.18
Consensus pattern (42 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1715048 original size:180 final size:182
Alignment explanation
Indices: 1714622--1715263 Score: 772
Period size: 180 Copynumber: 3.5 Consensus size: 182
1714612 CACCCCCTCC
* * * * * * *
1714622 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
*
1714687 CTCCACCACCACCACCTAAA-CATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
66 CTCCACCACCTCCACC-AAAGCATGAGGAGAAGCCTTATGAATACAAGTCT---CCACCACCACC
* * * ***** *
1714751 ACCAAAGGAGAAGCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
127 ACCGAAGGAGAAGCCTTATGAATACAAGTCTCCA---CCACCACCACC-TCAAAGACACA
* *
1714811 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1714876 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
* *
1714941 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC-GAAAGAGA-A
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTCAAAGACACA
*
1714991 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
*
1715056 CTCCTCCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
* * * ** *
1715121 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCTCCATCACCACC
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTCAAAGA-CACA
* * * * * * * * ** *
1715174 TCCATACT-ACTATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACT-ACTACAA
1 GCCTTA-TGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA-TGTGTATAA
* *
1715237 GTCCCCACCACCACCACCAAAGCATGA
64 GTCTCCACCACCTCCACCAAAGCATGA
1715264 AGAACAACCA
Statistics
Matches: 400, Mismatches: 47, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
180 165 0.41
181 3 0.01
182 1 0.00
183 82 0.20
184 2 0.00
186 43 0.11
188 3 0.01
189 101 0.25
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (182 bp):
GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTCAAAGACACA
Found at i:1715210 original size:138 final size:137
Alignment explanation
Indices: 1714942--1715204 Score: 415
Period size: 138 Copynumber: 1.9 Consensus size: 137
1714932 CCACCACCGA
1714942 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
* * ** * *
1715007 TCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACC
66 TCTCCACCACCTCCATCACC-TATCCACCACCTCCATATGACTATAAATCTCCACCACCTCCACC
1715072 AAAGCATG
130 AAAGCATG
*
1715080 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
*
1715145 TCTCCACCACCTCCATCTCC-AT-CACCACCTCCATACT-ACTATAAATCTCCACCACCTCCA
66 TCTCCACCACCTCCATCACCTATCCACCACCTCCATA-TGACTATAAATCTCCACCACCTCCA
1715205 TCACCATCAC
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
135 31 0.27
136 2 0.02
138 83 0.72
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.20
Consensus pattern (137 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
TCTCCACCACCTCCATCACCTATCCACCACCTCCATATGACTATAAATCTCCACCACCTCCACCA
AAGCATG
Found at i:1715223 original size:48 final size:48
Alignment explanation
Indices: 1715139--1715738 Score: 501
Period size: 48 Copynumber: 12.4 Consensus size: 48
1715129 GCCTTATGAA
* *
1715139 TACAAGTCTCCACCACCTCCATCTCCAT---CACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * *
1715184 TATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * * ** * * *
1715232 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCACCATATTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * * *
1715283 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * *
1715331 TACAAGTCCCCACCACCTCCTTCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
** * * * *
1715379 TACAAGTCTCCACCACCACCAAAACACGT-A-GAGCAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATCAC-CATCACCA-CCACCTCCATACTAC
* * * * *
1715427 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * * *
1715475 TATAAATCTCCACCACCACCTTCACCATCTCCACCACCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * *
1715523 TACAAGTCCCCACCACCTCCATCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * * ** * *
1715571 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * *
1715622 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* ** * ** *
1715670 TACAAATCTCCACCACCACCCCCA-CATTACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCAC-CACCTCCATACTAC
*
1715718 TACAAATCTCCACCACCACCA
1 TACAAGTCTCCACCACCACCA
1715739 GTGAAGTCTC
Statistics
Matches: 439, Mismatches: 102, Indels: 25
0.78 0.18 0.04
Matches are distributed among these distances:
45 25 0.06
47 9 0.02
48 322 0.73
49 10 0.02
50 7 0.02
51 66 0.15
ACGTcount: A:0.30, C:0.47, G:0.03, T:0.19
Consensus pattern (48 bp):
TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
Found at i:1715245 original size:27 final size:26
Alignment explanation
Indices: 1715167--1715248 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 26
1715157 CCATCTCCAT
* *
1715167 CACCACCTCCATACTACTATAAATCTC
1 CACCACCTCCATACTACTA-CAATCAC
1715194 CACCACCTCCAT-C-AC--C-ATCAC
1 CACCACCTCCATACTACTACAATCAC
*
1715215 CACCACCTCCATACTACTACAAGTCCC
1 CACCACCTCCATACTACTACAA-TCAC
1715242 CACCACC
1 CACCACC
1715249 ACCACCAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 16 0.35
22 1 0.02
23 2 0.04
25 3 0.07
26 2 0.04
27 22 0.48
ACGTcount: A:0.30, C:0.50, G:0.01, T:0.18
Consensus pattern (26 bp):
CACCACCTCCATACTACTACAATCAC
Found at i:1715566 original size:144 final size:143
Alignment explanation
Indices: 1715139--1715734 Score: 518
Period size: 147 Copynumber: 4.1 Consensus size: 143
1715129 GCCTTATGAA
* * *
1715139 TACAAGTCTCCACCACCTCCATCTCCAT---CACCACCTCCATACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * *
1715201 TCCATCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCA--ACACCAT-AA-
* * * *
1715266 AACAACCACCATATTAC
127 AGCACCCCCCATACTAC
* * * * * * * *
1715283 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTACTACAAGTCCCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * * *
1715348 TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCTCCACCACCACCAAAACACGTAGAGC
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACAC-CATAAAGC
*
1715413 AACCCCCATACTAC
130 ACCCCCCATACTAC
* * * *
1715427 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * * * * *
1715492 ACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACCTCCATCTCCAT-CACCA
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACACCATAAAGCA
1715556 CCTCCTCCATACTAC
131 CC-CC-CCATACTAC
* * * * * ** * * *
1715571 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTACTACAAGTCTCCACC
1 TACAAGTCTCCACCACCTCCATC--ACCAT-CACCACCACCACCATACTACTACAAATCTCCACC
* * * * * * ** * *
1715636 ACCACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACCACCCCCA-CATTAC
63 ACCACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACACCATAAA
* *
1715700 GTCTCACCACCATACTAC
128 G-CAC-CCCCCATACTAC
*
1715718 TACAAATCTCCACCACC
1 TACAAGTCTCCACCACC
1715735 ACCAGTGAAG
Statistics
Matches: 376, Mismatches: 64, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
142 4 0.01
143 4 0.01
144 170 0.45
145 4 0.01
146 8 0.02
147 182 0.48
148 3 0.01
149 1 0.00
ACGTcount: A:0.30, C:0.47, G:0.03, T:0.19
Consensus pattern (143 bp):
TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACACCATAAAGCA
CCCCCCATACTAC
Found at i:1715680 original size:24 final size:23
Alignment explanation
Indices: 1715653--1715734 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
1715643 TCACCATCTC
1715653 CTCCACCACCTTACTACTACAAAT
1 CTCCACCACC-TACTACTACAAAT
** * *
1715677 CTCCACCACC-ACCCCCAC-ATT
1 CTCCACCACCTACTACTACAAAT
1715698 ACGTCTCACCACCATACTACTACAAAT
1 -C-TC-CACCACC-TACTACTACAAAT
1715725 CTCCACCACC
1 CTCCACCACC
1715735 ACCAGTGAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 2 0.05
24 24 0.55
25 2 0.05
26 6 0.14
27 2 0.05
ACGTcount: A:0.30, C:0.49, G:0.01, T:0.20
Consensus pattern (23 bp):
CTCCACCACCTACTACTACAAAT
Found at i:1715802 original size:6 final size:6
Alignment explanation
Indices: 1715791--1715830 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
1715781 ACTCCTTACT
*
1715791 ACCCCC ACCCCC ACCCTC ACCCCC ACCCCC ACCCCC ACCC
1 ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCC
1715831 ACATCCGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.80, G:0.00, T:0.03
Consensus pattern (6 bp):
ACCCCC
Found at i:1716932 original size:36 final size:36
Alignment explanation
Indices: 1716885--1716973 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 36
1716875 GTACTACTAT
* * * *
1716885 AAGTCTCCACCTCCTCCGGCTCCCACTTACGTTTAC
1 AAGTCACCACCTCCTCCAGCACCAACTTACGTTTAC
* * *
1716921 AAGTCACCACCTCCACCATCACCAACTTATGTTTAC
1 AAGTCACCACCTCCTCCAGCACCAACTTACGTTTAC
* *
1716957 AAGTCACCTCCACCTCC
1 AAGTCACCACCTCCTCC
1716974 TGTGTACTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.24, C:0.44, G:0.08, T:0.25
Consensus pattern (36 bp):
AAGTCACCACCTCCTCCAGCACCAACTTACGTTTAC
Found at i:1717071 original size:150 final size:150
Alignment explanation
Indices: 1716876--1717153 Score: 493
Period size: 150 Copynumber: 1.9 Consensus size: 150
1716866 GCCACCACCG
*
1716876 TACTACTATAAGTCTCCACCTCCTCCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
* * *
1716941 ACCAACTTATGTTTACAAGTCACCTCCACCTCCTGTGTACTACTACAAGTCTCCACCACCACCAA
66 ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACCAA
1717006 AGCATGTGGAACAACCTCCA
131 AGCATGTGGAACAACCTCCA
*
1717026 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
* *
1717091 GCCGACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACC
66 ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACC
1717154 CACTTATGTC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 121 1.00
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (150 bp):
TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACCAA
AGCATGTGGAACAACCTCCA
Found at i:1717082 original size:36 final size:36
Alignment explanation
Indices: 1717035--1717123 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
1717025 ATACTACTAT
* * *
1717035 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1717071 AAGTCACCACCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1717107 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
1717124 TGTGTACTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.24, C:0.43, G:0.10, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1717673 original size:21 final size:21
Alignment explanation
Indices: 1717649--1717733 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
1717639 CTACTACAAG
1717649 TCTCCCCCACCACCATCACCA
1 TCTCCCCCACCACCATCACCA
* * *
1717670 TCTCCTCCTCCACCATACTATTACAAA
1 TCT-C-CC-CCACC--ACCATCAC-CA
*
1717697 TCTCCTCCACCACCATCACCA
1 TCTCCCCCACCACCATCACCA
* *
1717718 TCTCCTCCTCCACCAT
1 TCTCCCCCACCACCAT
1717734 ACTACTACAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
21 19 0.38
22 7 0.14
23 2 0.04
24 10 0.20
25 1 0.02
26 7 0.14
27 4 0.08
ACGTcount: A:0.24, C:0.53, G:0.00, T:0.24
Consensus pattern (21 bp):
TCTCCCCCACCACCATCACCA
Found at i:1717682 original size:24 final size:24
Alignment explanation
Indices: 1717650--1717732 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
1717640 TACTACAAGT
*
1717650 CTCCCCCACCACCATCACCATCTC
1 CTCCTCCACCACCATCACCATCTC
* * **
1717674 CTCCTCCACCATACTATTA-CAAAT-
1 CTCCTCCACC--ACCATCACCATCTC
1717698 CTCCTCCACCACCATCACCATCTC
1 CTCCTCCACCACCATCACCATCTC
1717722 CTCCTCCACCA
1 CTCCTCCACCA
1717733 TACTACTACA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
24 30 0.65
25 3 0.07
26 5 0.11
ACGTcount: A:0.24, C:0.54, G:0.00, T:0.22
Consensus pattern (24 bp):
CTCCTCCACCACCATCACCATCTC
Found at i:1717712 original size:240 final size:238
Alignment explanation
Indices: 1717442--1718479 Score: 1374
Period size: 240 Copynumber: 4.3 Consensus size: 238
1717432 AGAGGAGCCC
*
1717442 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * * * * * *
1717507 CCCACCACCACCAAAACATGTGGAGCAACCTCCATAC-TACTACAAATCACCCCCACCACCATCG
66 CCCACCACCACCAAAACATGTAGAGGAGCCCCCATACAT-CTACAAATCTCCTCCACCACCATCA
* ** *
1717571 CCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAG-CATGTAGAGGAGCCCC
130 CCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACC--AGCCATGTACACCA-CCAC
*
1717635 CATACTACTACAAGTCTCCCCCACCACCATCACCATCTCCTCCTCCA
192 CATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
1717682 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
*
1717747 CCCACCACCACCGAAACATGTAGAGGAGCCCCCATACATCTACAAATCTCCTCCACCACCATCAC
66 CCCACCACCACCAAAACATGTAGAGGAGCCCCCATACATCTACAAATCTCCTCCACCACCATCAC
* * * ** *
1717812 CATCTCCTCCTCCACCATACTACTACAAGTCTCCACCACCCCCGAAG-CATGTAGAGGAGCCCCC
131 CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACC--AGCCATGTACACCA-CCACC
1717876 ATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
193 ATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
*
1717922 CCATACTATTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * *
1717987 CCCACCACCACCGAAACATGTAGAGGAGCCTCCATACATCTACAAATCTCCTCCACCACCATCGC
66 CCCACCACCACCAAAACATGTAGAGGAGCCCCCATACATCTACAAATCTCCTCCACCACCATCAC
* * *
1718052 CATCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGCCCAT-TCCCCACCACCACC
131 CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAG-CCATGT--ACACCACCACC
* * * *
1718116 ATACTACTACAAGTCTCCACCACCACCA--GTCCACTCCCCACCCCCA
193 ATACTACTACAAGTCTCCCCCACCACCATCG-CCA-TCTCCTCCTCCA
* * * * * * * *
1718162 CCATACTATTACAAGTCTCCACCACCACCTTCTCCTTCACCACCTCCACCATACTATTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* *
1718227 CCCACCACCACCAAAACACGTAGAGGAGCCCCCATACATTTACAAATCTCCTCCACCACCATCAC
66 CCCACCACCACCAAAACATGTAGAGGAGCCCCCATACATCTACAAATCTCCTCCACCACCATCAC
* * * *
1718292 CATCTCCTCCTCCACCATATTATTACAAGTCCCCACCACCACCAGTCCACTCTCCACCACCACCA
131 CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAG-CCA-TGTACACCACCACCA
* * *
1718357 TACTATTACAAATC-CCCTCCTCCACCATCGCCATCTCCTCCTCCA
194 TACTACTACAAGTCTCCC-CCACCACCATCGCCATCTCCTCCTCCA
* * * * * *
1718402 CCATACTACTACAAATCCCCACCACCACCAGT--CCACTCTCCACCCCCACCATACTACTACAAA
1 CCATACTATTACAAATCTCCTCCACCACCA-TCACCA-TCTCCTCCTCCACCATACTACTACAAG
1718465 TCCCCACCACCACCA
64 TCCCCACCACCACCA
1718480 TCTCCTTCAC
Statistics
Matches: 724, Mismatches: 60, Indels: 28
0.89 0.07 0.03
Matches are distributed among these distances:
238 3 0.00
239 8 0.01
240 703 0.97
241 8 0.01
242 2 0.00
ACGTcount: A:0.29, C:0.47, G:0.05, T:0.19
Consensus pattern (238 bp):
CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
CCCACCACCACCAAAACATGTAGAGGAGCCCCCATACATCTACAAATCTCCTCCACCACCATCAC
CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAGCCATGTACACCACCACCATA
CTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
Found at i:1717922 original size:24 final size:24
Alignment explanation
Indices: 1717890--1717972 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1717880 TACTACAAGT
*
1717890 CTCCCCCACCACCATCGCCATCTC
1 CTCCTCCACCACCATCGCCATCTC
* ** **
1717914 CTCCTCCACCATACTAT-TACAAAT-
1 CTCCTCCACC--ACCATCGCCATCTC
1717938 CTCCTCCACCACCATCGCCATCTC
1 CTCCTCCACCACCATCGCCATCTC
1717962 CTCCTCCACCA
1 CTCCTCCACCA
1717973 TACTACTACA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 30 0.68
25 3 0.07
26 4 0.09
ACGTcount: A:0.22, C:0.54, G:0.02, T:0.22
Consensus pattern (24 bp):
CTCCTCCACCACCATCGCCATCTC
Found at i:1718156 original size:21 final size:21
Alignment explanation
Indices: 1718081--1718164 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 21
1718071 CTATTACAAG
* *
1718081 TCCCCACCACCACCAGCCCAT
1 TCCCCACCACCACCAGTCCAC
1718102 TCCCCACCACCACCA-TACTACTAC
1 TCCCCACCACCACCAGT-C--C-AC
*
1718126 AAGTCTCCACCACCACCAGTCCAC
1 ---TCCCCACCACCACCAGTCCAC
*
1718150 TCCCCACCCCCACCA
1 TCCCCACCACCACCA
1718165 TACTATTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
21 29 0.58
23 1 0.02
24 3 0.06
25 1 0.02
27 15 0.30
28 1 0.02
ACGTcount: A:0.26, C:0.58, G:0.04, T:0.12
Consensus pattern (21 bp):
TCCCCACCACCACCAGTCCAC
Found at i:1718205 original size:96 final size:96
Alignment explanation
Indices: 1717206--1718701 Score: 724
Period size: 96 Copynumber: 15.6 Consensus size: 96
1717196 GCAGCCCCCG
* * * * * * * *
1717206 TACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCCC
* *
1717271 ACCACCACCAGTTCACTCTCCACCACCACCA
66 ACCACCACCAGTCCACTCTCCACCCCCACCA
* * *** **** ** * *
1717302 TACTACTACAAGT-CCCACCACCACCA-AAACATGTGGAGCAACCTCCATACTACTACAAATCTC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCA-CCTCCACCATACTACTACAAATCCC
* * * *
1717365 CTCCTCCACCA-TCGC-CATCTCCTCCACCACCA
65 CACCACCACCAGTC-CAC-TCTCCACCCCCACCA
* *** * ** *
1717397 TACTACTACAAATCCCCACCACCACCA-AAACATGTAGAGGAGC-CC-CCATACTACTACAAATC
1 TACTATTACAAATCCCCACCACCACCATCTCCA--T-CACCACCTCCACCATACTACTACAAATC
* * * *
1717459 TCCTCCACCACCA-T-CACCATCTCCTCCTCCACCA
63 CCCACCACCACCAGTCCA-C-TCTCCACCCCCACCA
* * *** **** ** *
1717493 TACTACTACAAGTCCCCACCACCACCA-AAACATGTGGAGCAACCTCCATACTACTACAAATCAC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCA-CCTCCACCATACTACTACAAATC-C
* *
1717557 CC-CCACCACCA-TCGC-CATCTCCTCCTCCACCA
64 CCACCACCACCAGTC-CAC-TCTCCACCCCCACCA
* * * ** * ** * *
1717589 TACTACTACAAGTCCCCACCACCACCGAAGCATGTA-GAGGAGC-CC-CCATACTACTACAAGTC
1 TACTATTACAAATCCCCACCACCACC--ATC-TCCATCACCACCTCCACCATACTACTACAAATC
* *
1717651 TCCC-CCACCACCA-T-CACCATCTCCTCCTCCACCA
63 -CCCACCACCACCAGTCCA-C-TCTCCACCCCCACCA
* * * * * *
1717685 TACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCCC
** * ** **
1717750 ACCACCACC-G-AAACATGTAGAGGAGCCC-CCA
66 ACCACCACCAGTCCAC-TCTCCA--CCCCCACCA
* * * * * * *
1717781 TAC-ATCTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCTC
1 TACTAT-TACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCC
* * ** **
1717845 CACCACCCCCGAAG--CA-TGTAGAGGAGCCC-CCA
65 CACCACCACC--AGTCCACTCTCCA--CCCCCACCA
* * * * * * *
1717877 TACTACTACAAGTCTCCC-CCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATCTC
1 TACTATTACAAATC-CCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCC
* * *
1717941 CTCCACCACCA-TCGC-CATCTCCTCCTCCACCA
65 CACCACCACCAGTC-CAC-TCTCCACCCCCACCA
* * * ** * **
1717973 TACTACTACAAGTCCCCACCACCACCGAAACATGTA-GAGGAGCCT---CCATAC-ATCTACAAA
1 TACTATTACAAATCCCCACCACCACC--ATC-TCCATCACCA-CCTCCACCATACTA-CTACAAA
* * * *
1718033 TCTCCTCCACCACCA-TCGC-CATCTCCTCCACCACCA
61 TCCCCACCACCACCAGTC-CAC-TCTCCACCCCCACCA
* * * * * *
1718069 TACTATTACAAGTCCCCACCACCACCAGC-CCATTCCCCACCACCACCATACTACTACAAGTCTC
1 TACTATTACAAATCCCCACCACCACCATCTCCA-TCACCACCTCCACCATACTACTACAAATCCC
*
1718133 CACCACCACCAGTCCACTCCCCACCCCCACCA
65 CACCACCACCAGTCCACTCTCCACCCCCACCA
* * * * * *
1718165 TACTATTACAAGTCTCCACCACCACCTTCTCCTTCACCACCTCCACCATACTATTACAAGTCCCC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCCC
*** * ** **
1718230 ACCACCACCAAAACAC-GTAGAGGAGCCC-CCA
66 ACCACCACCAGTCCACTCTCCA--CCCCCACCA
* * * * * * * *
1718261 TAC-ATTTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATATTATTACAAGTCCC
1 TACTA-TTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCC
*
1718325 CACCACCACCAGTCCACTCTCCACCACCACCA
65 CACCACCACCAGTCCACTCTCCACCCCCACCA
* * * * *
1718357 TACTATTACAAATCCCCTCCTCCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCCC
1718422 ACCACCACCAGTCCACTCTCCACCCCCACCA
66 ACCACCACCAGTCCACTCTCCACCCCCACCA
* *
1718453 TACTACTACAAATCCCCACCACCACCATCTCCTTCACCACCTCCACCATACTACTACAAATCACC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATC-CC
* ** ** * *
1718518 C-CCACCTCCAGTGAAGGCTCCAGCACCTACC-
65 CACCACCACCAGTCCACTCTCCA-CCCCCACCA
* * * * * * * *
1718549 TACCATTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCCCCATACTACTACAAATCTCC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATC-CC
* *
1718614 C-CCACCACCAGCCCACTCTCC-CTCACCACCA
65 CACCACCACCAGTCCACTCTCCAC-CCCCACCA
* * * * * *
1718645 TACTACTACAAATCTCCACCTCCTCCATCTCCCTCACCACCTCCTCCATACTACTAC
1 TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTAC
1718702 CACTCACCTC
Statistics
Matches: 1143, Mismatches: 191, Indels: 132
0.78 0.13 0.09
Matches are distributed among these distances:
92 1 0.00
93 7 0.01
94 17 0.01
95 93 0.08
96 971 0.85
97 34 0.03
98 6 0.01
99 13 0.01
100 1 0.00
ACGTcount: A:0.28, C:0.48, G:0.05, T:0.19
Consensus pattern (96 bp):
TACTATTACAAATCCCCACCACCACCATCTCCATCACCACCTCCACCATACTACTACAAATCCCC
ACCACCACCAGTCCACTCTCCACCCCCACCA
Found at i:1718471 original size:27 final size:27
Alignment explanation
Indices: 1718345--1718523 Score: 92
Period size: 27 Copynumber: 7.3 Consensus size: 27
1718335 AGTCCACTCT
*
1718345 CCACCACCACCATACTATTACAAATCC
1 CCACCACCACCATACTACTACAAATCC
* * * *
1718372 CCTCCTCCACCAT-C-GC--C--ATCT
1 CCACCACCACCATACTACTACAAATCC
* *
1718393 CCTCCTCCACCATACTACTACAAATCC
1 CCACCACCACCATACTACTACAAATCC
*
1718420 CCACCACCACCAGT-C--C-AC---TCT
1 CCACCACCACCA-TACTACTACAAATCC
*
1718441 CCACCCCCACCATACTACTACAAATCC
1 CCACCACCACCATACTACTACAAATCC
* *
1718468 CCACCACCACCAT-CT-C--C--TTCA
1 CCACCACCACCATACTACTACAAATCC
*
1718489 CCACCTCCACCATACTACTACAAATCAC
1 CCACCACCACCATACTACTACAAATC-C
1718517 CC-CCACC
1 CCACCACC
1718524 TCCAGTGAAG
Statistics
Matches: 112, Mismatches: 19, Indels: 42
0.65 0.11 0.24
Matches are distributed among these distances:
20 1 0.01
21 44 0.39
22 3 0.03
23 5 0.04
24 4 0.04
25 4 0.04
26 3 0.03
27 45 0.40
28 3 0.03
ACGTcount: A:0.28, C:0.53, G:0.01, T:0.18
Consensus pattern (27 bp):
CCACCACCACCATACTACTACAAATCC
Found at i:1722672 original size:2 final size:2
Alignment explanation
Indices: 1722660--1722689 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1722650 GATCCTTCCC
1722660 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1722690 AAAGGAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1725528 original size:15 final size:15
Alignment explanation
Indices: 1725508--1725537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1725498 TAAAATTTTG
1725508 GGGTCATTGCAAGTT
1 GGGTCATTGCAAGTT
*
1725523 GGGTCATTTCAAGTT
1 GGGTCATTGCAAGTT
1725538 CCGATTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (15 bp):
GGGTCATTGCAAGTT
Found at i:1728221 original size:5 final size:5
Alignment explanation
Indices: 1728213--1728238 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1728203 TATAATATGC
1728213 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
1728239 ATGCTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1730723 original size:28 final size:31
Alignment explanation
Indices: 1730668--1730725 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
1730658 TTTATATATG
1730668 TAATTATATTAAAATAAATAGAAGTAATTAC
1 TAATTATATTAAAATAAATAGAAGTAATTAC
* *
1730699 TAATT-TATTCAAA-AATTAGAA-TAATTA
1 TAATTATATTAAAATAAATAGAAGTAATTA
1730726 AATTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 7 0.28
30 7 0.28
31 5 0.20
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (31 bp):
TAATTATATTAAAATAAATAGAAGTAATTAC
Found at i:1738194 original size:33 final size:33
Alignment explanation
Indices: 1738139--1738214 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
1738129 CAGGCACAAT
**
1738139 CAAGTGCTAATATGTACAGCCAACC-GACACAGC
1 CAAGTGCTAATACATACAGCCAACCTG-CACAGC
* *
1738172 CAAGTGCTAATCCATACGGCCAACCTGCACAGC
1 CAAGTGCTAATACATACAGCCAACCTGCACAGC
**
1738205 CTGGTGCTAA
1 CAAGTGCTAA
1738215 CGCATATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (33 bp):
CAAGTGCTAATACATACAGCCAACCTGCACAGC
Found at i:1738912 original size:6 final size:6
Alignment explanation
Indices: 1738901--1738931 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1738891 AGTATGGGTA
*
1738901 GCATGG GCATGG GCATGG GCATGG GAATGG G
1 GCATGG GCATGG GCATGG GCATGG GCATGG G
1738932 TGGTGGACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.52, T:0.16
Consensus pattern (6 bp):
GCATGG
Found at i:1741132 original size:33 final size:32
Alignment explanation
Indices: 1741094--1741271 Score: 108
Period size: 33 Copynumber: 5.4 Consensus size: 32
1741084 TAATATGTAC
1741094 AGCCAACCGACACAGCCAAGTGCTAATCCATAT
1 AGCCAACCG-CACAGCCAAGTGCTAATCCATAT
* **
1741127 GGCCAACCTGCACAGCCTGGTGCTAA-CGCATAT
1 AGCCAACC-GCACAGCCAAGTGCTAATC-CATAT
* * * * * *
1741160 -GACCAACTTGGACAACCTAGTTCTAATGCATAT
1 AG-CCAAC-CGCACAGCCAAGTGCTAATCCATAT
* ** * * *
1741193 AGCCAATCTGTGCAGCCGAGTGTTAATCCTTAT
1 AGCCAA-CCGCACAGCCAAGTGCTAATCCATAT
* * *
1741226 AGCCAACCGCCACAGCCAGGTGCTAATCCCTAC
1 AGCCAACCG-CACAGCCAAGTGCTAATCCATAT
1741259 AGCCAACCTGCAC
1 AGCCAACC-GCAC
1741272 GGTTTAACTC
Statistics
Matches: 111, Mismatches: 25, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
32 4 0.04
33 103 0.93
34 4 0.04
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.20
Consensus pattern (32 bp):
AGCCAACCGCACAGCCAAGTGCTAATCCATAT
Found at i:1747960 original size:27 final size:27
Alignment explanation
Indices: 1747922--1747977 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1747912 TACTCTCTAA
1747922 CATCTTCAAGTTCTTCATCACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
*
1747949 CATCTTCAAGTTCTTCATGACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
1747976 CA
1 CA
1747978 GTGGAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (27 bp):
CATCTTCAAGTTCTTCATCACCATTTT
Found at i:1749383 original size:23 final size:24
Alignment explanation
Indices: 1749332--1749383 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1749322 TGGATTGGTG
*
1749332 ATTTAATATAAATATAATTATAATT
1 ATTTAATAT-AATATAATTATAATA
1749357 ATTTAATAT-ATATAATTA-ATATA
1 ATTTAATATAATATAATTATA-ATA
1749380 ATTT
1 ATTT
1749384 TTTTAGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
25 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAATATAATATAATTATAATA
Found at i:1749937 original size:8 final size:8
Alignment explanation
Indices: 1749924--1749952 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1749914 ATTTAAGTAA
1749924 ATATTATT
1 ATATTATT
1749932 ATATTATT
1 ATATTATT
1749940 ATATTATT
1 ATATTATT
1749948 ATATT
1 ATATT
1749953 GTATTGTTAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTATT
Found at i:1750047 original size:13 final size:12
Alignment explanation
Indices: 1750002--1750067 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
1749992 AAAAGAATAG
* *
1750002 AAAGAAAAGAAC
1 AAAGAGAAGAAA
1750014 AAAGTAGAACG-AA
1 AAAG-AGAA-GAAA
*
1750027 ATAGAGAAGAAA
1 AAAGAGAAGAAA
1750039 AAGAGAGAAAGAAA
1 AA-AGAG-AAGAAA
*
1750053 AATGAGAAGAAA
1 AAAGAGAAGAAA
1750065 AAA
1 AAA
1750068 TTAGGGTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 1 0.02
12 19 0.44
13 14 0.33
14 9 0.21
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (12 bp):
AAAGAGAAGAAA
Found at i:1753408 original size:12 final size:12
Alignment explanation
Indices: 1753391--1753418 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1753381 ACAACCACCC
1753391 ATCACAACATTT
1 ATCACAACATTT
1753403 ATCACAACATTT
1 ATCACAACATTT
1753415 ATCA
1 ATCA
1753419 TCATACTCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCACAACATTT
Found at i:1767806 original size:18 final size:18
Alignment explanation
Indices: 1767761--1767806 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1767751 TAGTTTTTTT
1767761 TTTTCAATTTAAGTTTAA
1 TTTTCAATTTAAGTTTAA
*
1767779 TTGTT-AATTTAATTTTAA
1 TT-TTCAATTTAAGTTTAA
*
1767797 TTTTCTATTT
1 TTTTCAATTT
1767807 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTCAATTTAAGTTTAA
Found at i:1769775 original size:21 final size:22
Alignment explanation
Indices: 1769749--1769790 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1769739 TGACCTTTCC
*
1769749 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
1769770 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
1769791 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:1769776 original size:11 final size:10
Alignment explanation
Indices: 1769749--1769790 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
1769739 TGACCTTTCC
1769749 AAGGTATGGG
1 AAGGTATGGG
*
1769759 TAGGTATGGG
1 AAGGTATGGG
1769769 AAAGGTATGGG
1 -AAGGTATGGG
1769780 CAAGGTATGGG
1 -AAGGTATGGG
1769791 GTATATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:1773861 original size:18 final size:18
Alignment explanation
Indices: 1773838--1773930 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
1773828 CCCAACTACT
*
1773838 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1773856 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
1773874 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
1773892 ATATACGTGAATAGTGCT
1 GTATACGTGAATAGTACC
*
1773910 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
1773928 GTA
1 GTA
1773931 AACGGTCGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1773890 original size:36 final size:36
Alignment explanation
Indices: 1773838--1773930 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
1773828 CCCAACTACT
* *
1773838 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACATGAATAGTACCGTATACGTGAATAGTGCC
* *
1773874 GTATACATGAATAGTACCATATACGTGAATAGTGCT
1 GTATACATGAATAGTACCGTATACGTGAATAGTGCC
1773910 GTATACATGAATAGTACCGTA
1 GTATACATGAATAGTACCGTA
1773931 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (36 bp):
GTATACATGAATAGTACCGTATACGTGAATAGTGCC
Found at i:1774490 original size:21 final size:22
Alignment explanation
Indices: 1774464--1774505 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1774454 TGACCTTTCC
*
1774464 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
1774485 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
1774506 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:1774491 original size:11 final size:10
Alignment explanation
Indices: 1774464--1774505 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
1774454 TGACCTTTCC
1774464 AAGGTATGGG
1 AAGGTATGGG
*
1774474 TAGGTATGGG
1 AAGGTATGGG
1774484 AAAGGTATGGG
1 -AAGGTATGGG
1774495 CAAGGTATGGG
1 -AAGGTATGGG
1774506 GTATATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:1780523 original size:20 final size:20
Alignment explanation
Indices: 1780485--1780521 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1780475 CAATGTCGCA
1780485 ACACCCACTTGATATTTTCG
1 ACACCCACTTGATATTTTCG
1780505 ACACCCACTTGA-ATTTT
1 ACACCCACTTGATATTTT
1780522 TCTTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (20 bp):
ACACCCACTTGATATTTTCG
Found at i:1785224 original size:12 final size:12
Alignment explanation
Indices: 1785207--1785232 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1785197 ATCACAGAAA
1785207 TCGCAAATGCAC
1 TCGCAAATGCAC
1785219 TCGCAAATGCAC
1 TCGCAAATGCAC
1785231 TC
1 TC
1785233 TCCATCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (12 bp):
TCGCAAATGCAC
Found at i:1785247 original size:6 final size:6
Alignment explanation
Indices: 1785236--1785280 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1785226 TGCACTCTCC
1785236 ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATC
1 ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATC
1785281 AGGTGGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (6 bp):
ATCTGA
Found at i:1789880 original size:19 final size:18
Alignment explanation
Indices: 1789858--1789897 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1789848 AATAAAACAC
*
1789858 TAAAAATTTATTTTAAAAA
1 TAAAAAGTT-TTTTAAAAA
1789877 TAAAAAAGTTTTTTAAAAA
1 T-AAAAAGTTTTTTAAAAA
1789896 TA
1 TA
1789898 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.05
19 11 0.58
20 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAAAGTTTTTTAAAAA
Found at i:1798418 original size:31 final size:32
Alignment explanation
Indices: 1798347--1798425 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
1798337 AAATTAATAA
* * *
1798347 TAATAAAATTATATTTTTATTTTTCTTAAAAT
1 TAATAAAATTATAATTTAATTTTTCTAAAAAT
*
1798379 TAATAAAATTTTAATTTAATTTTT-TAAAAAT
1 TAATAAAATTATAATTTAATTTTTCTAAAAAT
*
1798410 T-ATAAAAATAATAATT
1 TAAT-AAAATTATAATT
1798426 AAAAATTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.05
31 17 0.43
32 21 0.52
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TAATAAAATTATAATTTAATTTTTCTAAAAAT
Found at i:1798645 original size:19 final size:18
Alignment explanation
Indices: 1798609--1798652 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1798599 GTTACCAAAA
1798609 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
*
1798627 TATAAATATTTAG-GTTTT
1 TATAAAT-TTTAGAATTTT
*
1798645 TAAAAATT
1 TATAAATT
1798653 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:1813151 original size:727 final size:728
Alignment explanation
Indices: 1811734--1813200 Score: 1978
Period size: 727 Copynumber: 2.0 Consensus size: 728
1811724 CTTGTCTCAA
* *
1811734 AAACAAGGTGAATGGATGTTCATGATTTGTATTCTTAATAACTTGTAATGACGATTGTGATGCAC
1 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGACGATTGTGATGCAC
*
1811799 ATTCAATATGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCGTGGTACT
66 ATTCAATATGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCTCTTCGCCGTGGTACT
* * * *
1811864 TGGCATACCTTGCAAGAGAGTCGTTTGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
131 CGACATACCTTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
*
1811929 ACATGATTGAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAATCAGGAGA
196 ACATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAATCAGGAGA
* *
1811994 AAAGTGTGTACACATTGCTAATGGTTCCCAACATCCAAAGCACTTACTAACATCTTTGAGTTTTT
261 AAAGTGTGTACACATTGCTAATGGTTCCCAACACCCAAAGCACTTACT-ACATC--T-A---TTC
*
1812059 TATCACCATTTTCAGTGGAAATCAATGGATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTA
319 TATCA-CATGTTCA-T----ATC-A---ATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTA
* * * * * *
1812124 TTCTCAGCAATATTAAGTGTAAACAAAGCACATTTAATATGAAATTCCAATTCACAACTAGAGCA
374 TTCTCAGCAATATTAAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATCACAAC-AGAGCA
* ** * * *
1812189 GTGATAAACAGACTTGTCACCAAATTCATGGCAGAAACTGCAAAAGTACGCTCCAGATAAATGAG
438 GTGATAAACAAACTCATCACCAAATTCATCGCAAAAACTGCAAAAGTACGCTCCAGATAAATAAG
* * *
1812254 GTGACTTTTGCATAAGAAGAAGAGGATGGTTGAGATGAAAAGGGTGATTAAGCTCCAAAGGTGCC
503 GTGACTTTTGCAGAAGAAGAAGAGGATGGATGAGATGAAAAGGATGATTAAGCTCCAAAGGTGCC
* *
1812319 TCGGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGTAGCAGACAC
568 TCGGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACAC
*
1812384 CTTATCCCCACACCTGGAGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTGATTCA
633 CTTATCCCCACACCTGGAGCAATCAGTTACACCACTTTGATTGTCGATCAGCTGCTCTTGATTCA
1812449 ACATAAGAAACAGGGGATGTTGGTGCTCATT
698 ACATAAGAAACAGGGGATGTTGGTGCTCATT
**
1812480 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGGTGATTGTGATGCAC
1 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGACGATTGTGATGCAC
*
1812545 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCACTTTCCGTACTTCGC
66 ATTCAATATGAACAACAAACTTACAAGGAGAACAACCAT-AAAAAA---A---TCC-T-CTTCGC
* * *
1812610 CTTGTTACTCGACATATCTTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTT
122 CGTGGTACTCGACATACCTTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTT
1812675 GCGATGG-CACCCATGATTCAGTTTGAAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCC
187 GCGATGGTCA--CATGATTCAGTTTG-AAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCC
* * * *** *
1812739 ACAGTCAGGAGAAAAGTGTGTATA-ATTTGTTAATGGTTCCTGGCACCCAAAGCACTTA-T-TAT
249 ACAATCAGGAGAAAAGTGTGTACACA-TTGCTAATGGTTCCCAACACCCAAAGCACTTACTACAT
*
1812801 C-A-TCT-TCA-A-GTTC-T-TC-ATCTTGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCT
313 CTATTCTATCACATGTTCATATCAATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCT
**
1812858 CAGCAATATTAAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATGGC-A-AGAGCAGTGAT
378 CAGCAATATTAAATGTAAACAAAGCACATTAAATACGAAAGTCAAAATCACAACAGAGCAGTGAT
* *** * * * *
1812921 AAACAAACTCATTACCGCCTTTATCGCAAAAATTGCAAATGTAC-CGTCCAGATGAATAAGGTG-
443 AAACAAACTCATCACCAAATTCATCGCAAAAACTGCAAAAGTACGC-TCCAGATAAATAAGGTGA
1812984 CATTTTGCAGAAGAAGAAGAGGAT-GATGAGGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTC
507 C-TTTTGCAGAAGAAGAAGAGGATGGATGA-GATGAAAAGGATGATTAAGCTCCAAAGGTGCCTC
1813048 GGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACACCT
570 GGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACACCT
* * * * *
1813113 TCTCCCCACACCTGGAGCAATGAGTTACACCACTTTGATTGTGGATCAGCTGGTCTTGATTCAAG
635 TATCCCCACACCTGGAGCAATCAGTTACACCACTTTGATTGTCGATCAGCTGCTCTTGATTCAAC
*
1813178 ATAAGAAGCAGGGGATGTTGGTG
700 ATAAGAAACAGGGGATGTTGGTG
1813201 GCCATAATTG
Statistics
Matches: 646, Mismatches: 59, Indels: 51
0.85 0.08 0.07
Matches are distributed among these distances:
726 6 0.01
727 256 0.40
729 1 0.00
730 83 0.13
735 2 0.00
740 1 0.00
742 3 0.00
743 1 0.00
745 3 0.00
746 101 0.16
747 5 0.01
750 2 0.00
753 3 0.00
754 6 0.01
755 71 0.11
756 15 0.02
757 87 0.13
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (728 bp):
AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGACGATTGTGATGCAC
ATTCAATATGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCTCTTCGCCGTGGTACT
CGACATACCTTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
ACATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAATCAGGAGA
AAAGTGTGTACACATTGCTAATGGTTCCCAACACCCAAAGCACTTACTACATCTATTCTATCACA
TGTTCATATCAATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCTCAGCAATATTAAA
TGTAAACAAAGCACATTAAATACGAAAGTCAAAATCACAACAGAGCAGTGATAAACAAACTCATC
ACCAAATTCATCGCAAAAACTGCAAAAGTACGCTCCAGATAAATAAGGTGACTTTTGCAGAAGAA
GAAGAGGATGGATGAGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTCGGCACATACCTTGTGA
AGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACACCTTATCCCCACACCTGGA
GCAATCAGTTACACCACTTTGATTGTCGATCAGCTGCTCTTGATTCAACATAAGAAACAGGGGAT
GTTGGTGCTCATT
Found at i:1814155 original size:25 final size:24
Alignment explanation
Indices: 1814103--1814156 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1814093 TGGATTGGTG
*
1814103 ATTTAATATAAATATAATTATAATT
1 ATTTAATAT-AATATAATTATAAAT
1814128 ATTTAATAT-ATATAATTAATATAAT
1 ATTTAATATAATATAATT-ATA-AAT
1814153 ATTT
1 ATTT
1814157 TTTAGGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 8 0.31
24 3 0.12
25 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAATATAATATAATTATAAAT
Found at i:1836149 original size:3 final size:3
Alignment explanation
Indices: 1836143--1836169 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1836133 AAAAAACGAC
1836143 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1836170 CTAAATTTTG
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):
AAT
Found at i:1842026 original size:13 final size:13
Alignment explanation
Indices: 1842008--1842044 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1841998 AGAACGAAAT
1842008 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
1842021 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
1842035 -GAGAA-AAAAA
1 AGAGAAGAAAAA
1842045 TCTAAGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 2 0.09
13 7 0.30
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:1842031 original size:14 final size:14
Alignment explanation
Indices: 1842008--1842044 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1841998 AGAACGAAAT
1842008 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
1842021 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
1842035 -GAGAAA-AAAA
1 AGAGAAAGAAAA
1842045 TCTAAGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:1850243 original size:28 final size:27
Alignment explanation
Indices: 1850207--1850331 Score: 107
Period size: 28 Copynumber: 4.6 Consensus size: 27
1850197 ACTTCATAAA
1850207 ATTTTATAATTTTTTTATATTTCTATAT
1 ATTTTATAATTTTTTTATATTT-TATAT
** *
1850235 ATTTTATAATTTTTACGAT-TTTTATAAA
1 ATTTTATAATTTTT-TTATATTTTAT-AT
*
1850263 ATTTTATAATTTTTTTATATTTTTTAT
1 ATTTTATAATTTTTTTATATTTTATAT
*
1850290 GATTTT-TATATTTTTTTCTAACTTTTA-AT
1 -ATTTTATA-ATTTTTTTAT-A-TTTTATAT
1850319 A-TTTA-AATTTTTT
1 ATTTTATAATTTTTT
1850332 ATTAAAATTT
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
26 7 0.09
27 12 0.15
28 52 0.65
29 5 0.06
30 4 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
ATTTTATAATTTTTTTATATTTTATAT
Found at i:1850248 original size:9 final size:9
Alignment explanation
Indices: 1850208--1850304 Score: 72
Period size: 9 Copynumber: 10.4 Consensus size: 9
1850198 CTTCATAAAA
1850208 TTTTATAAT
1 TTTTATAAT
*
1850217 TTTTTTATAT
1 TTTTATA-AT
*
1850227 TTCTAT-AT
1 TTTTATAAT
1850235 ATTTTATAAT
1 -TTTTATAAT
**
1850245 TTTTACGAT
1 TTTTATAAT
*
1850254 TTTTATAAAA
1 TTTTAT-AAT
1850264 TTTTATAATTT
1 TTTTATAA--T
*
1850275 TTTTATATT
1 TTTTATAAT
*
1850284 TTTTATGAT
1 TTTTATAAT
1850293 TTTTAT-AT
1 TTTTATAAT
1850301 TTTT
1 TTTT
1850305 TTCTAACTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
8 8 0.12
9 39 0.57
10 15 0.22
11 7 0.10
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1850267 original size:20 final size:19
Alignment explanation
Indices: 1850242--1850299 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
1850232 TATATTTTAT
1850242 AATTTTTACGATTTTTATAA
1 AATTTTTA-GATTTTTATAA
* *
1850262 AATTTTATA-ATTTTTTTAT
1 AATTTT-TAGATTTTTATAA
*
1850281 ATTTTTTATGATTTTTATA
1 AATTTTTA-GATTTTTATA
1850300 TTTTTTTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 14 0.45
21 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
AATTTTTAGATTTTTATAA
Found at i:1850273 original size:56 final size:59
Alignment explanation
Indices: 1850161--1850284 Score: 175
Period size: 56 Copynumber: 2.2 Consensus size: 59
1850151 TTTTGCGAAA
*
1850161 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTCATAAAATTTTATAATTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTCATAAAATTTTATAATTTT
* * *
1850220 TTTATATTTCTATATA-TTT-TATAA-TTT-TTACGATTTTTATAAAATTTTATAATTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGA-CTTCATAAAATTTTATAATTTT
1850276 TTTATATTT
1 TTTATATTT
1850285 TTTATGATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
55 6 0.10
56 32 0.53
57 5 0.08
58 3 0.05
59 14 0.23
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.61
Consensus pattern (59 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTCATAAAATTTTATAATTTT
Found at i:1850305 original size:20 final size:20
Alignment explanation
Indices: 1850208--1850322 Score: 82
Period size: 19 Copynumber: 6.0 Consensus size: 20
1850198 CTTCATAAAA
*
1850208 TTTTATAATTTTTTTATA-T
1 TTTTATAATTTTTATATATT
*
1850227 TTCTAT-ATATTTTATA-A-T
1 TTTTATAAT-TTTTATATATT
** **
1850245 TTTTACGATTTTTATA-AAA
1 TTTTATAATTTTTATATATT
*
1850264 TTTTATAATTTTTTTATATT
1 TTTTATAATTTTTATATATT
*
1850284 TTTTATGATTTTTATAT-TT
1 TTTTATAATTTTTATATATT
* *
1850303 TTTTCTAACTTTTA-ATATT
1 TTTTATAATTTTTATATATT
1850322 T
1 T
1850323 AAATTTTTTA
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
18 18 0.24
19 42 0.55
20 16 0.21
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATAATTTTTATATATT
Found at i:1850386 original size:20 final size:20
Alignment explanation
Indices: 1850361--1850401 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1850351 TATGTAATTC
* *
1850361 ATTTATTCTATTTTTTTATA
1 ATTTATTCTAATTTTTAATA
1850381 ATTTATTCTAATTTTTAATA
1 ATTTATTCTAATTTTTAATA
1850401 A
1 A
1850402 AAAGAATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTATTCTAATTTTTAATA
Found at i:1850595 original size:91 final size:91
Alignment explanation
Indices: 1850400--1850608 Score: 246
Period size: 91 Copynumber: 2.3 Consensus size: 91
1850390 AATTTTTAAT
* * * *
1850400 AAAAAGAATGGGCTTAATTGC-TTTTTTGAAAAAGCTTGAGGGTCTTTTTGATGCATTTTGAAAG
1 AAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAACTTGAGGGTCTTTTTAATGCATTTTGAAAG
* *
1850464 TTCAAGTATCCAATTGAGTGCAAAAA
66 TTCAAATATCCAAATGAGTGCAAAAA
* * * * * *
1850490 AAAATGTAGAGGCTTAATTACTTTTTTTGAAAAAATTTGAGGG-CTTTTTTAATGTATTTTGAAA
1 AAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAACTTGAGGGTC-TTTTTAATGCATTTTGAAA
1850554 GTTCAAATA-CTCAAATGAGTG-AAAAA
65 GTTCAAATATC-CAAATGAGTGCAAAAA
*
1850580 AAAAGAGCAGGGGCTTAATTGTTTTTTTT
1 AAAA-AGCAGGGGCTTAATTGCTTTTTTT
1850609 TTTCATTTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
90 27 0.27
91 72 0.73
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (91 bp):
AAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAACTTGAGGGTCTTTTTAATGCATTTTGAAAG
TTCAAATATCCAAATGAGTGCAAAAA
Done.