Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 133 of 144
Found at i:33434926 original size:16 final size:16
Alignment explanation
Indices: 33434896--33434925 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33434886 ATCACTTTAA
33434896 AAATTTTCGATTTTTC
1 AAATTTTCGATTTTTC
33434912 AAATTTT-GATTTTT
1 AAATTTTCGATTTTT
33434926 TGGTCACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
AAATTTTCGATTTTTC
Found at i:33435849 original size:40 final size:41
Alignment explanation
Indices: 33435805--33435884 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
33435795 TTTAATGATT
* * * *
33435805 ATCTTTTTTAATA-ATATCATCTGAATAAATTATTTTATGG
1 ATCTTTTTCAACACATACCATCTGAAGAAATTATTTTATGG
*
33435845 ATCTTTTTCACCACATACCATCTGAAGAAATTATTTTATG
1 ATCTTTTTCAACACATACCATCTGAAGAAATTATTTTATG
33435885 AATATTTCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 10 0.29
41 24 0.71
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (41 bp):
ATCTTTTTCAACACATACCATCTGAAGAAATTATTTTATGG
Found at i:33435876 original size:41 final size:41
Alignment explanation
Indices: 33435822--33435904 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
33435812 TTAATAATAT
* * * **
33435822 CATCTGAATAAATTATTTTATGGATCTTTTTCACCACATAC
1 CATCTGAAGAAATTATTTTATGAATATTTCCCACCACATAC
33435863 CATCTGAAGAAATTATTTTATGAATATTTCCCACCACATAC
1 CATCTGAAGAAATTATTTTATGAATATTTCCCACCACATAC
33435904 C
1 C
33435905 CTTTCTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (41 bp):
CATCTGAAGAAATTATTTTATGAATATTTCCCACCACATAC
Found at i:33436113 original size:21 final size:21
Alignment explanation
Indices: 33436065--33436113 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
33436055 TTTTGGGTTC
33436065 GAAGTTTTAAGTTCAATATTT
1 GAAGTTTTAAGTTCAATATTT
* **
33436086 -AAGGTTTTAGGTTTGATATTT
1 GAA-GTTTTAAGTTCAATATTT
33436107 GAAGTTT
1 GAAGTTT
33436114 GGGATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (21 bp):
GAAGTTTTAAGTTCAATATTT
Found at i:33442537 original size:3 final size:3
Alignment explanation
Indices: 33442529--33442555 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33442519 TTCACTCTCC
33442529 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
33442556 ATCATCATCC
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:33443242 original size:9 final size:9
Alignment explanation
Indices: 33443228--33443266 Score: 78
Period size: 9 Copynumber: 4.3 Consensus size: 9
33443218 AGACTATTAC
33443228 TAATTCAGT
1 TAATTCAGT
33443237 TAATTCAGT
1 TAATTCAGT
33443246 TAATTCAGT
1 TAATTCAGT
33443255 TAATTCAGT
1 TAATTCAGT
33443264 TAA
1 TAA
33443267 ATGAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (9 bp):
TAATTCAGT
Found at i:33443280 original size:3 final size:3
Alignment explanation
Indices: 33443272--33443322 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
33443262 GTTAAATGAA
33443272 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33443320 TAT
1 TAT
33443323 AAGTTCTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:33470221 original size:17 final size:17
Alignment explanation
Indices: 33470188--33470222 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33470178 TTTTTTACGT
*
33470188 TGTTTAATTTTCCTTTC
1 TGTTTAATTTGCCTTTC
*
33470205 TGTTTAATTTGCTTTTC
1 TGTTTAATTTGCCTTTC
33470222 T
1 T
33470223 AAATTTGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (17 bp):
TGTTTAATTTGCCTTTC
Found at i:33480325 original size:17 final size:18
Alignment explanation
Indices: 33480305--33480350 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
33480295 TTATTGAAAT
33480305 AATAAATTTTTATT-TTA
1 AATAAATTTTTATTATTA
*
33480322 AAT-AATTTATATTATTA
1 AATAAATTTTTATTATTA
**
33480339 TTTAAATTTTTA
1 AATAAATTTTTA
33480351 ATTAGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 9 0.39
17 7 0.30
18 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATAAATTTTTATTATTA
Found at i:33480453 original size:20 final size:22
Alignment explanation
Indices: 33480418--33480459 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
33480408 TTTAATATTA
*
33480418 TTTTAAAATTTTATAT-TAATT
1 TTTTAAAATTTAATATGTAATT
33480439 TTTTAAAA-TTAATATGTAATT
1 TTTTAAAATTTAATATGTAATT
33480460 AGATTTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTAAAATTTAATATGTAATT
Found at i:33480458 original size:21 final size:21
Alignment explanation
Indices: 33480407--33480459 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
33480397 AAATTATATT
33480407 ATTTAATATT-A--TTTTAAA
1 ATTTAATATTAATTTTTTAAA
*
33480425 ATTTTATATTAATTTTTTAAA
1 ATTTAATATTAATTTTTTAAA
33480446 A-TTAATATGTAATT
1 ATTTAATAT-TAATT
33480460 AGATTTGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 9 0.31
19 1 0.03
20 6 0.21
21 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTAATATTAATTTTTTAAA
Found at i:33483142 original size:71 final size:72
Alignment explanation
Indices: 33483045--33483187 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
33483035 TAAATGATGA
33483045 CACAAAATTAGTTTTTAAAAATAAGTAATATTGATTATTAATTTATAATAATAGATAACATATGA
1 CACAAAATTAGTTTTTAAAAATAAGTAATATTGATTATTAATTTATAATAATAGATAACATATGA
33483110 AAGAGGG
66 AAGAGGG
33483117 CACAAAATTAG-TTTTAAAAATAAGTAATATTGATTATTAATTTATAATAATAGATAACATATGA
1 CACAAAATTAGTTTTTAAAAATAAGTAATATTGATTATTAATTTATAATAATAGATAACATATGA
33483181 AAGAGGG
66 AAGAGGG
33483188 TAAAAGTATT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 60 0.85
72 11 0.15
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (72 bp):
CACAAAATTAGTTTTTAAAAATAAGTAATATTGATTATTAATTTATAATAATAGATAACATATGA
AAGAGGG
Found at i:33489715 original size:19 final size:19
Alignment explanation
Indices: 33489691--33489728 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
33489681 GAAAGTTAAT
33489691 AACAAATTTGATTACAGTG
1 AACAAATTTGATTACAGTG
33489710 AACAAATTTGATTACAGTG
1 AACAAATTTGATTACAGTG
33489729 GGTGACAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
AACAAATTTGATTACAGTG
Found at i:33490253 original size:16 final size:16
Alignment explanation
Indices: 33490208--33490257 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
33490198 TAAACCTAAT
*
33490208 TAATTAATTACTAAAA
1 TAATTAATTACAAAAA
33490224 T-A-TAATATA-AAAAA
1 TAATTAAT-TACAAAAA
*
33490238 TAATTAATTACCAAAA
1 TAATTAATTACAAAAA
33490254 TAAT
1 TAAT
33490258 ATTCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTACAAAAA
Found at i:33493283 original size:17 final size:16
Alignment explanation
Indices: 33493252--33493290 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
33493242 AACGCATTAC
*
33493252 CTTTCTCTTCTTCTTT
1 CTTTCTCTCCTTCTTT
33493268 CTTTCGTCTCCTTCTTT
1 CTTTC-TCTCCTTCTTT
33493285 CTTTCT
1 CTTTCT
33493291 TTCTTTCCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (16 bp):
CTTTCTCTCCTTCTTT
Found at i:33493502 original size:27 final size:27
Alignment explanation
Indices: 33493448--33493502 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
33493438 ACACCCTTTC
* *
33493448 GTGTCGTCACTTGAAGTTCCTCCTTTA
1 GTGTCGTCACTTGAAGTCCCTCCATTA
*
33493475 GTGTCGTCACTTTG-TGTCCCTCCATTA
1 GTGTCGTCAC-TTGAAGTCCCTCCATTA
33493502 G
1 G
33493503 GGTGTCAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (27 bp):
GTGTCGTCACTTGAAGTCCCTCCATTA
Found at i:33494305 original size:31 final size:30
Alignment explanation
Indices: 33494270--33494344 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
33494260 ATATATCATT
33494270 ATATTAAATTATTTAAATATCATTTATTATG
1 ATATTAAATT-TTTAAATATCATTTATTATG
* * * *
33494301 ATATTACAAATTTTAAATCTTATTTATTATT
1 ATATTA-AATTTTTAAATATCATTTATTATG
*
33494332 ATATTTAATTTTT
1 ATATTAAATTTTT
33494345 TAAAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 6 0.16
31 28 0.76
32 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
ATATTAAATTTTTAAATATCATTTATTATG
Found at i:33494346 original size:31 final size:30
Alignment explanation
Indices: 33494250--33494348 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
33494240 ATTAAATTAA
* * * *
33494250 TTTATAATTTATATATCATTATATTAAATTA
1 TTTA-AATTTATTTATTATTATATTTAATTT
* * **
33494281 TTTAAATATCATTTATTATGATA-TTACAAAT
1 TTTAAAT-TTATTTATTATTATATTTA-ATTT
33494312 TTTAAATCTTATTTATTATTATATTTAATTT
1 TTTAAAT-TTATTTATTATTATATTTAATTT
33494343 TTTAAA
1 TTTAAA
33494349 AATATTTTAT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
30 5 0.10
31 44 0.85
32 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
TTTAAATTTATTTATTATTATATTTAATTT
Found at i:33496880 original size:18 final size:17
Alignment explanation
Indices: 33496832--33496884 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
33496822 TAATGCTAAT
*
33496832 TTTTTAATTTTAATGAATA
1 TTTTTAATTTT--TAAATA
*
33496851 TTTTTTATTTTTAAATA
1 TTTTTAATTTTTAAATA
33496868 TTTTATAATTTTTAAAT
1 TTTT-TAATTTTTAAAT
33496885 TATATTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.30
18 11 0.37
19 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTAATTTTTAAATA
Found at i:33497008 original size:21 final size:20
Alignment explanation
Indices: 33496975--33497023 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
33496965 ACATCTTAAA
*
33496975 AAAATAGTGTTTTAATATGTT
1 AAAA-AGTGTTTTAATATCTT
* *
33496996 AAAAAGTGATTTTACTCTCTT
1 AAAAAGTG-TTTTAATATCTT
33497017 AAAAAGT
1 AAAAAGT
33497024 TGACAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (20 bp):
AAAAAGTGTTTTAATATCTT
Found at i:33497530 original size:29 final size:30
Alignment explanation
Indices: 33497472--33497560 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 30
33497462 ATATCAAAAT
* *
33497472 TATATATGAACTATGATTTAATGTGCAATTG
1 TATATATGAATTTTGATTTAATGT-CAATTG
* *
33497503 TATATATGAATTTTGATTTTATGT-AATTT
1 TATATATGAATTTTGATTTAATGTCAATTG
* * *
33497532 TACACATGAAATTTTGATTTGAT-TCAATT
1 TATATATG-AATTTTGATTTAATGTCAATT
33497561 TTTGTAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 11 0.22
30 17 0.35
31 21 0.43
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (30 bp):
TATATATGAATTTTGATTTAATGTCAATTG
Found at i:33497766 original size:30 final size:30
Alignment explanation
Indices: 33497694--33497778 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
33497684 GATTAAATCA
* * *
33497694 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCATGTATATAATTCAACC
* * * *
33497724 ACAATTAGAGTTTCATGTGTATAATTCCACT
1 A-AATTAAAGTTTCATGTATATAATTCAACC
*
33497755 AAATTAAAGTTT-ATGTATACAATT
1 AAATTAAAGTTTCATGTATATAATT
33497779 GCACACTAGA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 10 0.23
30 11 0.25
31 23 0.52
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATATAATTCAACC
Found at i:33498262 original size:33 final size:33
Alignment explanation
Indices: 33498184--33498267 Score: 77
Period size: 33 Copynumber: 2.5 Consensus size: 33
33498174 ATATCCAAAC
*
33498184 AATAACAACAAAATAGTAGCAACATAATAGTAA
1 AATAACAACAAAATAGTAGAAACATAATAGTAA
*
33498217 AATGAA-AGCAAAATAGTGAGAAAACA-ACA-AG-AA
1 AAT-AACAACAAAATAGT-AG-AAACATA-ATAGTAA
*
33498250 AATAACAACAAAACAGTA
1 AATAACAACAAAATAGTA
33498268 AAAAAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
32 3 0.07
33 27 0.64
34 7 0.17
35 5 0.12
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.13
Consensus pattern (33 bp):
AATAACAACAAAATAGTAGAAACATAATAGTAA
Found at i:33499123 original size:15 final size:15
Alignment explanation
Indices: 33499103--33499158 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
33499093 AGAGATTAGG
33499103 TTTTAATTTTAATTT
1 TTTTAATTTTAATTT
33499118 TTTTAATTTTAATGATT
1 TTTTAATTTTAAT--TT
*
33499135 TAATTTAAATTTAATTT
1 T--TTTAATTTTAATTT
*
33499152 TATTAAT
1 TTTTAAT
33499159 ATTATCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 17 0.50
17 6 0.18
19 11 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTAATTTTAATTT
Found at i:33499971 original size:19 final size:19
Alignment explanation
Indices: 33499949--33500010 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
33499939 ATTTTTTTTT
*
33499949 AAAATTTCAAATATTTATA
1 AAAATTTAAAATATTTATA
33499968 AAAATTTTAAAA-ATTTATA
1 AAAA-TTTAAAATATTTATA
* * *
33499987 TATATTTAAAAATATATATA
1 AAAATTT-AAAATATTTATA
33500007 AAAA
1 AAAA
33500011 ATTCCAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 3 0.09
19 17 0.50
20 14 0.41
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTAAAATATTTATA
Found at i:33499989 original size:27 final size:28
Alignment explanation
Indices: 33499944--33499999 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
33499934 AATCAATTTT
*
33499944 TTTTTAAAATTTCAAATAT-TTATAAAAA
1 TTTTAAAAATTTCAAATATATT-TAAAAA
*
33499972 TTTTAAAAATTT-ATATATATTTAAAAA
1 TTTTAAAAATTTCAAATATATTTAAAAA
33499999 T
1 T
33500000 ATATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTAAAAATTTCAAATATATTTAAAAA
Found at i:33500004 original size:16 final size:17
Alignment explanation
Indices: 33499973--33500006 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
33499963 TTATAAAAAT
33499973 TTTAAAAATTTATATATA
1 TTTAAAAA-TTATATATA
33499991 TTTAAAAA-TATATATA
1 TTTAAAAATTATATATA
33500007 AAAAATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAAAATTATATATA
Found at i:33505488 original size:26 final size:26
Alignment explanation
Indices: 33505457--33505509 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
33505447 TTTTATCTAT
33505457 TCTTGTAGTACGCTTTTTAGTCTTAC
1 TCTTGTAGTACGCTTTTTAGTCTTAC
*
33505483 TCTTGTAGTATGCTTTTTAGTCTTAC
1 TCTTGTAGTACGCTTTTTAGTCTTAC
33505509 T
1 T
33505510 TTTGCGAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (26 bp):
TCTTGTAGTACGCTTTTTAGTCTTAC
Found at i:33507553 original size:30 final size:30
Alignment explanation
Indices: 33507485--33507553 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
33507475 AATTTAATCA
*
33507485 AAATTAAAGTTTCATGTATACATTAGAACC
1 AAATCAAAGTTTCATGTATACATTAGAACC
*
33507515 ACAATCAAAGTTTTCTATGTATA-ATT-GCACC
1 A-AATCAAAG-TTTC-ATGTATACATTAGAACC
33507546 AAATCAAA
1 AAATCAAA
33507554 ATTCATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 8 0.24
31 12 0.35
32 7 0.21
33 7 0.21
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTTCATGTATACATTAGAACC
Found at i:33507963 original size:24 final size:21
Alignment explanation
Indices: 33507926--33507971 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
33507916 TTCATGCTAA
33507926 TTTTAAAATTTTTATGAATATTT
1 TTTTAAAATTTTTAT-AAT-TTT
*
33507949 TTTTTAAATATTTTATAATTTT
1 TTTTAAAAT-TTTTATAATTTT
33507971 T
1 T
33507972 AAATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 11 0.52
24 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTAAAATTTTTATAATTTT
Found at i:33508622 original size:31 final size:29
Alignment explanation
Indices: 33508581--33508660 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 29
33508571 ATGTTAAAAT
* *
33508581 TATATGTGAATTATGATTTAATGTGTAATTA
1 TATATATGAATTTTGATTT--TGTGTAATTA
*
33508612 TATATATGAATTTTGATTTTGTGTAATTT
1 TATATATGAATTTTGATTTTGTGTAATTA
*
33508641 TATACATGAAATTTTGATTT
1 TATATATG-AATTTTGATTT
33508661 GATCTAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.36
30 11 0.25
31 17 0.39
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.53
Consensus pattern (29 bp):
TATATATGAATTTTGATTTTGTGTAATTA
Found at i:33508649 original size:29 final size:30
Alignment explanation
Indices: 33508587--33508660 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 30
33508577 AAATTATATG
* *
33508587 TGAATTATGATTTAATGTGTAATTATATATA
1 TGAATTTTGATTT-ATGTGTAATTATATACA
*
33508618 TGAATTTTGATTT-TGTGTAATTTTATACA
1 TGAATTTTGATTTATGTGTAATTATATACA
33508647 TGAAATTTTGATTT
1 TG-AATTTTGATTT
33508661 GATCTAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 16 0.41
30 11 0.28
31 12 0.31
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (30 bp):
TGAATTTTGATTTATGTGTAATTATATACA
Found at i:33508669 original size:30 final size:29
Alignment explanation
Indices: 33508587--33508669 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
33508577 AAATTATATG
* * *
33508587 TGAATTATGATTTAATGTGTAATTATATATA
1 TGAATTTTGATTT--TGTCTAATTATATACA
* *
33508618 TGAATTTTGATTTTGTGTAATTTTATACA
1 TGAATTTTGATTTTGTCTAATTATATACA
33508647 TGAAATTTTGA-TTTGATCTAATT
1 TG-AATTTTGATTTTG-TCTAATT
33508670 CTTGTAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 20 0.43
30 14 0.30
31 12 0.26
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (29 bp):
TGAATTTTGATTTTGTCTAATTATATACA
Found at i:33511613 original size:24 final size:24
Alignment explanation
Indices: 33511566--33511614 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
33511556 TTTAACCCTA
* *
33511566 AATATTAATATAATTATTTTATTT
1 AATATTAATATAATAATTTAATTT
33511590 AATATTAATATAA-AATTTAAATTT
1 AATATTAATATAATAATTT-AATTT
33511614 A
1 A
33511615 TTCTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATTAATATAATAATTTAATTT
Found at i:33514322 original size:12 final size:12
Alignment explanation
Indices: 33514305--33514331 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33514295 ATCTTAAAAA
33514305 AGACTAAGAACC
1 AGACTAAGAACC
33514317 AGACTAAGAACC
1 AGACTAAGAACC
33514329 AGA
1 AGA
33514332 AGGCAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.22, G:0.19, T:0.07
Consensus pattern (12 bp):
AGACTAAGAACC
Found at i:33522578 original size:6 final size:7
Alignment explanation
Indices: 33522560--33522586 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
33522550 TCAATTCTCC
33522560 CAAAAAA
1 CAAAAAA
33522567 CAAAAAA
1 CAAAAAA
33522574 CAAAAAA
1 CAAAAAA
33522581 CAAAAA
1 CAAAAA
33522587 TGTAAACTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:33530657 original size:28 final size:28
Alignment explanation
Indices: 33530625--33530680 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
33530615 AATAACTAAG
33530625 GTAAGAGATGATTCAATTTTCATGGCAT
1 GTAAGAGATGATTCAATTTTCATGGCAT
33530653 GTAAGAGATGATTCAATTTTCATGGCAT
1 GTAAGAGATGATTCAATTTTCATGGCAT
33530681 ACATGTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (28 bp):
GTAAGAGATGATTCAATTTTCATGGCAT
Found at i:33534735 original size:23 final size:23
Alignment explanation
Indices: 33534709--33534829 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
33534699 ACACTAGCGC
33534709 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
33534732 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
33534755 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
33534780 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
33534803 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
33534826 GCTC
1 GCTC
33534830 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:33534778 original size:48 final size:46
Alignment explanation
Indices: 33534709--33534829 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
33534699 ACACTAGCGC
* *
33534709 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
33534755 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
33534803 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
33534830 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:33534858 original size:39 final size:39
Alignment explanation
Indices: 33534794--33534868 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
33534784 TCCGATTAGC
*
33534794 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
33534833 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
33534869 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:33534863 original size:23 final size:23
Alignment explanation
Indices: 33534828--33534921 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
33534818 CTTTGTGTGC
*
33534828 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
33534851 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
33534874 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
33534899 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
33534921 T
1 T
33534922 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:33539554 original size:17 final size:17
Alignment explanation
Indices: 33539534--33539567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33539524 TTAATCTTTC
*
33539534 AAATTATTAAAAAAATA
1 AAATTATGAAAAAAATA
*
33539551 AAATTATGAACAAAATA
1 AAATTATGAAAAAAATA
33539568 TTTGTCTTTT
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:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATTATGAAAAAAATA
Found at i:33551197 original size:419 final size:418
Alignment explanation
Indices: 33549908--33551906 Score: 1836
Period size: 442 Copynumber: 4.7 Consensus size: 418
33549898 AAATAAAGAG
* *
33549908 GTGTTGAGAGATGTAGTGTCCAGATGTAGCTCAA-ATAA-C-AACTTTAGACT-GCTACTGGGCA
1 GTGTTGAGAGATGTAGAGTCCAGATGTAGCTCAAGATAACCAAAC---A-AATAG-TACTGGGCA
* ** * * * *
33549969 ACGATGGATTCCATCAAGGGATGGCTAATAGATAGATTGGAAACCCAAACTACCTACCCCTTCCC
61 ACGATGGACTCTTTCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACTCCTTCCC
* * * *
33550034 TATCTTTTATTTTCCAGACATGTAACAGTCACTACCATCA-AATCTAAGGTAGACACCTGACTAC
126 TATCTTTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTGACTAC
* * * * * *
33550098 GTCTGGTTAGACTCATGGGA--CAAACAACTAACTATT-CATAGT--TTC-CAGAAAAACACC-A
191 GTCTGGTTAGACTCATGGAACTCAAACAACTAAATATTAAATAATAGTTCATAGACAAACACCTA
* *** * *
33550156 AAAATGCATCTATATTCAAAAGATACAAAAGTACAG-AAAGTATTTCCAAATGCA-TATGTTTAA
256 AAAATGCATC-A-A-T----AG-TA-AAAA-TA-AGTTAA-TA-TAAGAAGTG-AGCA--TTTAA
* * ** * * * * *
33550219 GTGTTATTATCATTTGCTTCACTGCCCCTTTAGAAAACAAACAGATTCACAAGACGTGATCCACT
305 GTGTTACTATCATTTG-TTTACTATCTC-TT----AACAAACAGATTCATAGGA-GTGGTCAAC-
* * ** * * * * *
33550284 ATATCCAAAATAAGGATGGCCTTCATGCTTGGATGTAT-AGATTGAATACTGATAGAAAGAT
362 ATATCCAAAATAAGAAT-GCC-TCATACAAGAATGCATAAG-TTGACTACTG-GAG-TAGAT
* * * ** * *
33550345 GT-TTCGAGAGATATAGTGTCCAGAAGTAGCTTGAG-TAACTAAACACATAGTACTGGGCAACGA
1 GTGTT-GAGAGATGTAGAGTCCAGATGTAGCTCAAGATAACCAAACAAATAGTACTGGGCAACGA
* ** *
33550408 TGGA--C-ATCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACAACTTTCCTATC
65 TGGACTCTTTCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACTCCTTCCCTATC
* *
33550470 TTTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAACGTAGACACCTGACTACATCT
130 TTTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTGACTACGTCT
* *
33550535 GGTTAGACTCGTGGAACAT-AAACAACTAAATATTAAATAATAGTTCATAAACAAACACCTAAAA
195 GGTTAGACTCATGGAAC-TCAAACAACTAAATATTAAATAATAGTTCATAGACAAACACCTAAAA
* *
33550599 ATGCATCAATAGTAAAAATAAGTTAATATAAGAATTGAGAGCATTTAAGTGCTACTATCATTTGC
259 ATGCATCAATAGTAAAAATAAGTTAATATAAGAA--GTGAGCATTTAAGTGTTACTATCATTTG-
* * *
33550664 TTTACTATCTCTTAACAAACAGATTCATAGGGGCGGCCAACATATCCAAAATAAGAATGGCCTCA
321 TTTACTATCTCTTAACAAACAGATTCATAGGAGTGGTCAACATATCCAAAATAAGAAT-GCCTCA
*
33550729 TACAAGAATGCATAAGTTGACTACTGGAGAAGAT
385 TACAAGAATGCATAAGTTGACTACTGGAGTAGAT
33550763 GTGTTGAGAGATGTAGAGTCCAGATGTAGCTCAAG-T-ACCAAACAAATAGTACTGGGCAACGAT
1 GTGTTGAGAGATGTAGAGTCCAGATGTAGCTCAAGATAACCAAACAAATAGTACTGGGCAACGAT
* * *
33550826 GGACTCTTTCAAGGGATGGCTAATAGACAGATTGGAAACCCAAACTATCAACTCCTTCCTTATCT
66 GGACTCTTTCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACTCCTTCCCTATCT
*
33550891 TTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTAACTACGTCTG
131 TTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTGACTACGTCTG
* *
33550956 ATTAGACTCATGGAACATAAAACAACTAAATATTAAATAATAGTTCATAGACAAACACCTAAAAA
196 GTTAGACTCATGGAAC-TCAAACAACTAAATATTAAATAATAGTTCATAGACAAACACCTAAAAA
* *
33551021 TGCATCACTAGTAAAAATAAGTTAATATAAGAAGTGAGCATTTAAATGTTACTATCATTTGATTT
260 TGCATCAATAGTAAAAATAAGTTAATATAAGAAGTGAGCATTTAAGTGTTACTATCATTTG-TTT
*
33551086 ACTATCTCTTAACAAACAGATCCATAGGAGTGGTCAACATATCCAAAATAAGAATCGCCTCATAC
324 ACTATCTCTTAACAAACAGATTCATAGGAGTGGTCAACATATCCAAAATAAGAAT-GCCTCATAC
*
33551151 AAAAATGCATAAGTTGACTACTGGAGTAGAT
388 AAGAATGCATAAGTTGACTACTGGAGTAGAT
* * * *
33551182 TTGTTGAGAGATGTAGTGTCCAGATGTAGCTCAAGTAATAACTAAATAAATAGTACTGGGCAACG
1 GTGTTGAGAGATGTAGAGTCCAGATGTAGCTCAAG--ATAACCAAACAAATAGTACTGGGCAACG
* *
33551247 ATGGACTCTTTCAATGGATGGCTAATAGATAGATTGGAAACCCAAACTATCAACTCCTTCCCTAT
64 ATGGACTCTTTCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACTCCTTCCCTAT
* * * * *
33551312 CCTTCATTTTCCAGACATGTAACAGTCCCTACCATCA-AATCTAAGGTAGACACCTGACTACGTC
129 CTTTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTGACTACGTC
* * * * * * * *
33551376 TGGTTGGACTCATGGGACCCAAACAAC-AATATATTAAATAATAGTTTACAGATATACAAC--AA
194 TGGTTAGACTCATGGAACTCAAACAACTAA-ATATTAAATAATAGTTCATAGACAAACACCTAAA
** * * * *
33551438 AATGCATCTGTATTCAAAAGATAAAG--AAGTACAGGAAGTATTTCCAAACGCATATATTAAGTG
258 AATGCATCAATAGT-AAAA-AT-AAGTTAA-TATAAGAAG----T---GA-GC--AT-TTAAGTG
* * * * * * ** * *
33551501 TTATTATAATTTGTTTCAGTATCCCGTTAAAAAACAAACTGATTCACAACA-TGCAATCCACTAT
308 TTACTATCATTTGTTT-ACTATCTC-TT----AACAAACAGATTCATAGGAGTG--GTCAAC-AT
* ** * * * **
33551565 ATCCAAAATAAGGATGACCTTCATACTTGAAGGCAT-AGATTGGCTGCATATA-TAAAGAT
364 ATCCAAAATAAGAATG-CC-TCATACAAGAATGCATAAG-TTGACTAC-TGGAGT--AGAT
33551624 GTGTTGAGAGATGTA-ATGTCCAGATGTAGCTCAAGTAATAA-CAGAACAAATAGTACTGGGCAA
1 GTGTTGAGAGATGTAGA-GTCCAGATGTAGCTCAAG--ATAACCA-AACAAATAGTACTGGGCAA
* * * * *
33551687 GGATGGACTCTTTCAAGGGATGTCTAACAGATAGAATGGAAACCCAAACCATCAACTACTTCCCT
62 CGATGGACTCTTTCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACTCCTTCCCT
* * *
33551752 ATCTTTTATTTTCCAGACATGTAACAGTCCCTACAACCATA-TCAAAGGTAGACACCTGACTATG
127 ATCTTTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTGACTACG
* * * * * *
33551816 TCTGGTTAGAATCATGGAACGCAAATAACTAAATATTAAATAACAGCTCATAGACAAACATCTAA
192 TCTGGTTAGACTCATGGAACTCAAACAACTAAATATTAAATAATAGTTCATAGACAAACACCTAA
* *
33551881 AAATGCATCAATATTCAAAATAAGTT
257 AAATGCATCAATAGTAAAAATAAGTT
33551907 GCTTTAAGAA
Statistics
Matches: 1326, Mismatches: 169, Indels: 128
0.82 0.10 0.08
Matches are distributed among these distances:
417 28 0.02
418 33 0.02
419 168 0.13
420 157 0.12
421 140 0.11
422 48 0.04
423 135 0.10
425 1 0.00
427 2 0.00
428 31 0.02
429 7 0.01
430 6 0.00
431 9 0.01
432 110 0.08
433 43 0.03
435 32 0.02
436 10 0.01
437 45 0.03
438 9 0.01
439 33 0.02
440 30 0.02
441 6 0.00
442 223 0.17
443 6 0.00
444 14 0.01
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (418 bp):
GTGTTGAGAGATGTAGAGTCCAGATGTAGCTCAAGATAACCAAACAAATAGTACTGGGCAACGAT
GGACTCTTTCAAGGGATGGCTAACAGATAGATTGGAAACCCAAACTATCAACTCCTTCCCTATCT
TTTATTTTCCAGACATGTAACAGTCCCTACAATCATATTCCAAGGTAGACACCTGACTACGTCTG
GTTAGACTCATGGAACTCAAACAACTAAATATTAAATAATAGTTCATAGACAAACACCTAAAAAT
GCATCAATAGTAAAAATAAGTTAATATAAGAAGTGAGCATTTAAGTGTTACTATCATTTGTTTAC
TATCTCTTAACAAACAGATTCATAGGAGTGGTCAACATATCCAAAATAAGAATGCCTCATACAAG
AATGCATAAGTTGACTACTGGAGTAGAT
Found at i:33553546 original size:21 final size:22
Alignment explanation
Indices: 33553522--33553568 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
33553512 TTTTATGTAT
*
33553522 TATTATA-TT-AAATTATTTAAA
1 TATTATATTTAAAATT-TTAAAA
*
33553543 TATTTTATTTAAAATTTTAAAA
1 TATTATATTTAAAATTTTAAAA
33553565 TATT
1 TATT
33553569 TCATGTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATATTTAAAATTTTAAAA
Found at i:33554640 original size:17 final size:18
Alignment explanation
Indices: 33554615--33554648 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33554605 GAATTTTAAA
33554615 ATTTGTCATTG-TATTTT
1 ATTTGTCATTGATATTTT
*
33554632 ATTTTTCATTGATATTT
1 ATTTGTCATTGATATTT
33554649 GTTTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (18 bp):
ATTTGTCATTGATATTTT
Found at i:33555598 original size:17 final size:17
Alignment explanation
Indices: 33555576--33555618 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
33555566 CAAATCATGT
33555576 AAAAAATATTAAAAAGG
1 AAAAAATATTAAAAAGG
33555593 AAAAAATATTAAAAAGG
1 AAAAAATATTAAAAAGG
33555610 AAAAAATAT
1 AAAAAATAT
33555619 GATTAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (17 bp):
AAAAAATATTAAAAAGG
Found at i:33560279 original size:29 final size:29
Alignment explanation
Indices: 33560237--33560294 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
33560227 TTTTTCTCTT
*
33560237 TTATCATCCAGAGCTGAGAGCTCGAAAAA
1 TTATCATACAGAGCTGAGAGCTCGAAAAA
*
33560266 TTATCATACAGAGCTGAGAGCTGGAAAAA
1 TTATCATACAGAGCTGAGAGCTCGAAAAA
33560295 ACTTACTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (29 bp):
TTATCATACAGAGCTGAGAGCTCGAAAAA
Found at i:33570947 original size:31 final size:29
Alignment explanation
Indices: 33570909--33570978 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
33570899 ATCTCAAAAC
*
33570909 TATACATGAACTATAGTTTAATGTGCAATTG
1 TATACATGAACTATAATTT--TGTGCAATTG
* * *
33570940 TATACATGAATTTTAATTTTGTGCAATTT
1 TATACATGAACTATAATTTTGTGCAATTG
33570969 TATACATGAA
1 TATACATGAA
33570979 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (29 bp):
TATACATGAACTATAATTTTGTGCAATTG
Found at i:33570972 original size:29 final size:30
Alignment explanation
Indices: 33570930--33570988 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
33570920 TATAGTTTAA
33570930 TGTGCAATTGTATACATG-AATTTTAATTT
1 TGTGCAATTGTATACATGAAATTTTAATTT
* *
33570959 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTAATTT
33570989 GGTCAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTAATTT
Found at i:33570995 original size:29 final size:29
Alignment explanation
Indices: 33570931--33570995 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
33570921 ATAGTTTAAT
*
33570931 GTGCAATTGTATACATGAATTTTAATTTT
1 GTGCAATTGTATACATGAATTTTAATTTG
* *
33570960 GTGCAATTTTATACATGAAATTTTGATTTG
1 GTGCAATTGTATACATG-AATTTTAATTTG
33570990 GT-CAAT
1 GTGCAAT
33570996 CTTTTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (29 bp):
GTGCAATTGTATACATGAATTTTAATTTG
Found at i:33571245 original size:29 final size:27
Alignment explanation
Indices: 33571179--33571245 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
33571169 AAGTTTTACG
* *
33571179 TGTATAATTGCATCAAATTAAAGTTCG
1 TGTATAATTGCATCAAATCAAAGTTCA
*
33571206 TGTATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTG--CATCAAATCAAAGTTCA
33571237 TGTATAATT
1 TGTATAATT
33571246 TTGAAATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 9 0.27
31 19 0.58
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCATCAAATCAAAGTTCA
Found at i:33571451 original size:20 final size:20
Alignment explanation
Indices: 33571426--33571463 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33571416 TATTTCCTAA
33571426 ATAATTAAACAAAATTATAC
1 ATAATTAAACAAAATTATAC
*
33571446 ATAATTAAAGAAAATTAT
1 ATAATTAAACAAAATTAT
33571464 TTAACATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
ATAATTAAACAAAATTATAC
Found at i:33576568 original size:7 final size:7
Alignment explanation
Indices: 33576558--33576602 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
33576548 ATAATTGATG
33576558 ATTGAAA
1 ATTGAAA
*
33576565 ATTGGAA
1 ATTGAAA
33576572 ATTGAAA
1 ATTGAAA
33576579 ATTGAAA
1 ATTGAAA
* **
33576586 ATCGAGG
1 ATTGAAA
33576593 ATTGAAA
1 ATTGAAA
33576600 ATT
1 ATT
33576603 TAGGATAGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (7 bp):
ATTGAAA
Found at i:33579933 original size:12 final size:12
Alignment explanation
Indices: 33579902--33579933 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
33579892 AATAAATTAT
33579902 TAAAATAT-ATG
1 TAAAATATAATG
33579913 TAAAA-ATAATG
1 TAAAATATAATG
33579924 TAAAATATAA
1 TAAAATATAA
33579934 ATTTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 13 0.68
12 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
TAAAATATAATG
Found at i:33581536 original size:30 final size:30
Alignment explanation
Indices: 33581500--33581561 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
33581490 TCGGGTTATA
*
33581500 GTGATTGGTGATGATGGACTTGTTGTTGAT
1 GTGATTGGTGATGATGGACTTCTTGTTGAT
33581530 GTGATTGGTGATGATGGACTTCTTGTTGAT
1 GTGATTGGTGATGATGGACTTCTTGTTGAT
33581560 GT
1 GT
33581562 TAACTTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.05, G:0.35, T:0.44
Consensus pattern (30 bp):
GTGATTGGTGATGATGGACTTCTTGTTGAT
Found at i:33581544 original size:15 final size:15
Alignment explanation
Indices: 33581500--33581545 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
33581490 TCGGGTTATA
33581500 GTGATTGGTGATGAT
1 GTGATTGGTGATGAT
* *
33581515 G-GACTTGTTGTTGAT
1 GTGA-TTGGTGATGAT
33581530 GTGATTGGTGATGAT
1 GTGATTGGTGATGAT
33581545 G
1 G
33581546 GACTTCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.41
Consensus pattern (15 bp):
GTGATTGGTGATGAT
Found at i:33581559 original size:15 final size:15
Alignment explanation
Indices: 33581511--33581560 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
33581501 TGATTGGTGA
33581511 TGATGGACTTGTTGT
1 TGATGGACTTGTTGT
* *
33581526 TGATGTGA-TTGGTGA
1 TGATG-GACTTGTTGT
*
33581541 TGATGGACTTCTTGT
1 TGATGGACTTGTTGT
33581556 TGATG
1 TGATG
33581561 TTAACTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.16, C:0.06, G:0.34, T:0.44
Consensus pattern (15 bp):
TGATGGACTTGTTGT
Found at i:33587801 original size:24 final size:23
Alignment explanation
Indices: 33587723--33587810 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
33587713 TTAATATTCA
*
33587723 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
* * *
33587746 CGAACATATTCATGAATATTAAA
1 CGAACATGTTCATGAACATTAAT
*
33587769 GGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
* *
33587793 TGAACATGTTCACGAACA
1 CGAACATGTTCATGAACA
33587811 ATGTTAATGA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.58
24 19 0.36
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:33607542 original size:45 final size:47
Alignment explanation
Indices: 33607477--33607571 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 47
33607467 AAATCTTGAG
*
33607477 ATACTAAATATTTAACTAAATTATGTAGTATTTATTATAAAATATTT
1 ATACTAAATATTTAACTAAATTATATAGTATTTATTATAAAATATTT
* * *
33607524 ATACT-AAT-TTTAATTAAATTATATAGTATTTATTATTAATTATTT
1 ATACTAAATATTTAACTAAATTATATAGTATTTATTATAAAATATTT
33607569 ATA
1 ATA
33607572 TTTAGTCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 36 0.82
46 3 0.07
47 5 0.11
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (47 bp):
ATACTAAATATTTAACTAAATTATATAGTATTTATTATAAAATATTT
Found at i:33607555 original size:20 final size:20
Alignment explanation
Indices: 33607485--33607555 Score: 52
Period size: 22 Copynumber: 3.3 Consensus size: 20
33607475 AGATACTAAA
* *
33607485 TATTTAACTAAATTATGTAG
1 TATTTAATTAAATTATATAG
* * *
33607505 TATTTATTATAAAATATTTATAC
1 TATTTA--ATTAAAT-TATATAG
33607528 TAATTTTAATTAAATTATATAG
1 T-A-TTTAATTAAATTATATAG
33607550 TATTTA
1 TATTTA
33607556 TTATTAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 10 0.26
21 1 0.03
22 11 0.29
23 11 0.29
24 1 0.03
25 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (20 bp):
TATTTAATTAAATTATATAG
Found at i:33608604 original size:2 final size:2
Alignment explanation
Indices: 33608597--33608625 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33608587 ATAAATTCAT
33608597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33608626 TATGATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33611245 original size:22 final size:21
Alignment explanation
Indices: 33611217--33611258 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33611207 ACTTTAGTCC
*
33611217 ATTAATTTTTTAAAAATTTTAA
1 ATTAA-TTATTAAAAATTTTAA
*
33611239 ATTAATTATTAAAATTTTTA
1 ATTAATTATTAAAAATTTTA
33611259 CCCAATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAATTATTAAAAATTTTAA
Found at i:33617665 original size:14 final size:14
Alignment explanation
Indices: 33617646--33617678 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33617636 TTCTTTCCAC
33617646 AAAGAAGCTTTGGA
1 AAAGAAGCTTTGGA
33617660 AAAGAAGCTTTGGA
1 AAAGAAGCTTTGGA
33617674 AAAGA
1 AAAGA
33617679 CTAACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.27, T:0.18
Consensus pattern (14 bp):
AAAGAAGCTTTGGA
Found at i:33632981 original size:17 final size:17
Alignment explanation
Indices: 33632959--33632997 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
33632949 AGGTGAAGAA
* * *
33632959 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
33632976 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
33632993 CTTGT
1 CTTGT
33632998 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:33633083 original size:23 final size:22
Alignment explanation
Indices: 33633039--33633087 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
33633029 AAATTCTTGT
* *
33633039 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGCT-AAA
33633062 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGCTAAA
33633084 TAAA
1 TAAA
33633088 CTAGACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.22
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCTAAA
Found at i:33637191 original size:51 final size:51
Alignment explanation
Indices: 33637115--33637214 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
33637105 ATCTGAAAAG
*
33637115 CTCCGATAAGAACTAGGAGAGAGAGACTGGAAAAGTAAGAGATAAGGCAAT
1 CTCCGATAACAACTAGGAGAGAGAGACTGGAAAAGTAAGAGATAAGGCAAT
* *
33637166 CTCCGATAACAACTAAGG-GAGAGAGATTGGAGAAGTAAGAGATAAGGCA
1 CTCCGATAACAACT-AGGAGAGAGAGACTGGAAAAGTAAGAGATAAGGCA
33637215 GTGGCTAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.93
52 3 0.07
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (51 bp):
CTCCGATAACAACTAGGAGAGAGAGACTGGAAAAGTAAGAGATAAGGCAAT
Found at i:33639497 original size:24 final size:20
Alignment explanation
Indices: 33639434--33639504 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 20
33639424 TATTAATCCT
33639434 TAATCAAGTATAAATAATTAA
1 TAAT-AAGTATAAATAATTAA
*
33639455 TAATAAGTACTATATAATTCAA
1 TAATAAGTA-TAAATAATT-AA
* *
33639477 TTAAATTTAGTATAAATAATTTA
1 -T-AA-TAAGTATAAATAATTAA
33639500 TAATA
1 TAATA
33639505 TATACTATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 6 0.15
21 14 0.35
22 3 0.08
23 2 0.05
24 10 0.25
25 5 0.12
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
TAATAAGTATAAATAATTAA
Found at i:33641423 original size:18 final size:19
Alignment explanation
Indices: 33641400--33641436 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
33641390 GCATCATATT
33641400 GGGTTGGACAA-GATAAAA
1 GGGTTGGACAATGATAAAA
*
33641418 GGGTTGGATAATGATAAAA
1 GGGTTGGACAATGATAAAA
33641437 ATTTCTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.03, G:0.32, T:0.22
Consensus pattern (19 bp):
GGGTTGGACAATGATAAAA
Found at i:33650663 original size:30 final size:32
Alignment explanation
Indices: 33650601--33650665 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
33650591 TAAAGTTATA
*
33650601 TTTTGTTTAGTATTTATTATTTTAAGTTATTTG
1 TTTTGTTTAG-ATTTAATATTTTAAGTTATTTG
33650634 TTTTGTTTA-ATTTAAT-TTTTAA-TTGATTTG
1 TTTTGTTTAGATTTAATATTTTAAGTT-ATTTG
33650664 TT
1 TT
33650666 ATTTAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (32 bp):
TTTTGTTTAGATTTAATATTTTAAGTTATTTG
Found at i:33650743 original size:5 final size:5
Alignment explanation
Indices: 33650728--33650757 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
33650718 GTTTGATTAT
33650728 TTTTAA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT
33650758 GTTAGTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:33650790 original size:20 final size:21
Alignment explanation
Indices: 33650749--33650790 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
33650739 TTTTATTTTA
*
33650749 TTTTATTTTGTTAGTAAGTAG
1 TTTTATTCTGTTAGTAAGTAG
33650770 TTTTATTCTGTTAGT-AGTAG
1 TTTTATTCTGTTAGTAAGTAG
33650790 T
1 T
33650791 AATTAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.57
Consensus pattern (21 bp):
TTTTATTCTGTTAGTAAGTAG
Found at i:33651156 original size:30 final size:32
Alignment explanation
Indices: 33651120--33651184 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
33651110 AACATTAGAT
*
33651120 AACAAATCAA-TTAAAA-ATTAAAT-TAAACAA
1 AACAAAT-AACTTAAAACAATAAATATAAACAA
33651150 AACAAATAACTTAAAACAATAAATACTAAACAA
1 AACAAATAACTTAAAACAATAAATA-TAAACAA
33651183 AA
1 AA
33651185 TATAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (32 bp):
AACAAATAACTTAAAACAATAAATATAAACAA
Found at i:33651438 original size:13 final size:12
Alignment explanation
Indices: 33651420--33651453 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
33651410 TCATTCTTCC
33651420 TTCTTTCTTTTCT
1 TTCTTTCTTTT-T
33651433 TTCTTTCTTTTT
1 TTCTTTCTTTTT
*
33651445 TTATTTCTT
1 TTCTTTCTT
33651454 CTCTGGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:33652643 original size:6 final size:6
Alignment explanation
Indices: 33652632--33652666 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
33652622 ACCTCTCTTT
33652632 TTCATC TTCATC TTCATC TTCATC TTCATC TTCAT
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCAT
33652667 TTTCTTCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
TTCATC
Found at i:33652939 original size:18 final size:16
Alignment explanation
Indices: 33652908--33652951 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
33652898 AGGTTTAGGT
*
33652908 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
33652925 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
33652939 TTAAAAATTTATT
1 TTAAAAATTTATT
33652952 CTCATCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:33653203 original size:12 final size:13
Alignment explanation
Indices: 33653186--33653215 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33653176 ATAAAAACCC
33653186 AAAAAT-TATAAA
1 AAAAATCTATAAA
33653198 AAAAATCTATAAA
1 AAAAATCTATAAA
33653211 AAAAA
1 AAAAA
33653216 AAAAGAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATCTATAAA
Found at i:33666977 original size:17 final size:18
Alignment explanation
Indices: 33666955--33666988 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33666945 ATAAAATTTT
33666955 ATAAAAATCAT-AAAAAA
1 ATAAAAATCATCAAAAAA
*
33666972 ATAAAATTCATCAAAAA
1 ATAAAAATCATCAAAAA
33666989 GGCCTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAAAATCATCAAAAAA
Found at i:33666987 original size:27 final size:28
Alignment explanation
Indices: 33666930--33666988 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
33666920 AAAAAAATAT
*
33666930 AAATCATAAAAAATTATAAAATTTTATAA
1 AAATCATAAAAAA-TATAAAATTTCATAA
33666959 AAATCATAAAAAA-ATAAAA-TTCATCAA
1 AAATCATAAAAAATATAAAATTTCAT-AA
33666986 AAA
1 AAA
33666989 GGCCTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 4 0.14
27 11 0.39
29 13 0.46
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (28 bp):
AAATCATAAAAAATATAAAATTTCATAA
Found at i:33671822 original size:12 final size:12
Alignment explanation
Indices: 33671805--33671831 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33671795 CTCTATGGCT
33671805 GATTTCACAACA
1 GATTTCACAACA
33671817 GATTTCACAACA
1 GATTTCACAACA
33671829 GAT
1 GAT
33671832 ATGCAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (12 bp):
GATTTCACAACA
Found at i:33677673 original size:31 final size:28
Alignment explanation
Indices: 33677594--33677673 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 28
33677584 TTTAGAAATT
*
33677594 TAATTAAAGAAA-ATTATATTAAAAATATA
1 TAATTAAA-AAATA-TATAATAAAAATATA
* *
33677623 TAATTAATAAATATTTAATAAAAATAATTA
1 TAATTAAAAAATATATAATAAAAAT-A-TA
*
33677653 TATTTTAAAAAATATATAATA
1 TA-ATTAAAAAATATATAATA
33677674 TGAATGAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
28 13 0.32
29 9 0.22
30 4 0.10
31 15 0.37
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
TAATTAAAAAATATATAATAAAAATATA
Found at i:33677674 original size:19 final size:19
Alignment explanation
Indices: 33677627--33677674 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
33677617 AATATATAAT
33677627 TAATAAATATTTAATAAAAA
1 TAAT-AATATTTAATAAAAA
* *
33677647 TAATTATATTTTA-AAAAA
1 TAATAATATTTAATAAAAA
33677665 TATATAATAT
1 TA-ATAATAT
33677675 GAATGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAATATTTAATAAAAA
Found at i:33679373 original size:18 final size:19
Alignment explanation
Indices: 33679350--33679385 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
33679340 TTTCAATGTA
*
33679350 TATTTTTAGAT-TTTTTAT
1 TATTTTTAAATATTTTTAT
33679368 TATTTTTAAATATTTTTA
1 TATTTTTAAATATTTTTA
33679386 ATATATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TATTTTTAAATATTTTTAT
Found at i:33680629 original size:3 final size:3
Alignment explanation
Indices: 33680621--33680652 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33680611 GTTCTCTGAG
33680621 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
33680653 TTGTGTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33685042 original size:22 final size:22
Alignment explanation
Indices: 33685001--33685042 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33684991 AACTATTAAA
* **
33685001 ATAATTAAATTACATTTTTATT
1 ATAATAAAATTACAAGTTTATT
33685023 ATAATAAAATTACAAGTTTA
1 ATAATAAAATTACAAGTTTA
33685043 ATTTCCACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAATAAAATTACAAGTTTATT
Found at i:33685392 original size:20 final size:20
Alignment explanation
Indices: 33685355--33685392 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33685345 TGTACTTTAA
*
33685355 ATTTCAAATTTTATATATTT
1 ATTTCAAATTTTACATATTT
33685375 ATTTC-AATTTTAACATAT
1 ATTTCAAATTTT-ACATAT
33685393 GTGAATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTCAAATTTTACATATTT
Found at i:33690143 original size:2 final size:2
Alignment explanation
Indices: 33690136--33690163 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33690126 CCCAGATTTG
33690136 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33690164 CAATCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33692865 original size:17 final size:17
Alignment explanation
Indices: 33692833--33692868 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33692823 TAAATTTGAC
**
33692833 TTATTATTATTTAAATT
1 TTATTATTATACAAATT
33692850 TTATTATTATACAAATT
1 TTATTATTATACAAATT
33692867 TT
1 TT
33692869 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTATTATACAAATT
Found at i:33696838 original size:24 final size:24
Alignment explanation
Indices: 33696811--33696856 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
33696801 GTGATAAAGA
33696811 TAAATTAGTTTTT-CTAGTAAAAAT
1 TAAATTAGTTTTTCCTA-TAAAAAT
*
33696835 TAAATTATTTTTTCCTATAAAA
1 TAAATTAGTTTTTCCTATAAAA
33696857 GCCCAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
TAAATTAGTTTTTCCTATAAAAAT
Found at i:33697173 original size:32 final size:32
Alignment explanation
Indices: 33697111--33697173 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
33697101 AACGTCGAGC
* **
33697111 AACTAAAATGATAAAAAAATATAATTACAATG
1 AACTAAAATAATAAAAAAATATAACAACAATG
**
33697143 AACTAAAATAATAAAAGTATATAACAACAAT
1 AACTAAAATAATAAAAAAATATAACAACAAT
33697174 ACTTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (32 bp):
AACTAAAATAATAAAAAAATATAACAACAATG
Found at i:33697495 original size:17 final size:17
Alignment explanation
Indices: 33697473--33697528 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
33697463 CTCTTGATTT
33697473 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
* **
33697490 TTAACCTTTCAT-GACC
1 TTAACCTTCCATCTTCC
*
33697506 TTTAACCTTCTATCTTCC
1 -TTAACCTTCCATCTTCC
33697524 TTAAC
1 TTAAC
33697529 TTTTCATATT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.21, C:0.34, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:33702631 original size:39 final size:40
Alignment explanation
Indices: 33702572--33702649 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
33702562 GATTCGATCC
33702572 AGTGAGAGTATGCTACTTGTAAAAGGTATGAAATATATAT
1 AGTGAGAGTATGCTACTTGTAAAAGGTATGAAATATATAT
*
33702612 AGTG-GAGTATGCTACTTGTAAAATGTATGAAATATATA
1 AGTGAGAGTATGCTACTTGTAAAAGGTATGAAATATATA
33702650 GAATACAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 33 0.89
40 4 0.11
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (40 bp):
AGTGAGAGTATGCTACTTGTAAAAGGTATGAAATATATAT
Found at i:33703446 original size:19 final size:20
Alignment explanation
Indices: 33703424--33703475 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
33703414 AATTTAACTT
33703424 TTAATATTTA-TATATTTAA
1 TTAATATTTATTATATTTAA
* *
33703443 TTAAT-TTGATTATTTTTAA
1 TTAATATTTATTATATTTAA
33703462 TTAA-ATTTAATTAT
1 TTAATATTT-ATTAT
33703476 TCACTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.11
19 19 0.70
20 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATATTTATTATATTTAA
Found at i:33703474 original size:20 final size:19
Alignment explanation
Indices: 33703438--33703476 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
33703428 TATTTATATA
*
33703438 TTTAATTAATTTGATTATT
1 TTTAATTAATTTAATTATT
33703457 TTTAATTAAATTTAATTATT
1 TTTAATT-AATTTAATTATT
33703477 CACTTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAATTAATTTAATTATT
Found at i:33703900 original size:6 final size:6
Alignment explanation
Indices: 33703889--33703917 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
33703879 TTACGTATAG
33703889 CTATGC CTATGC CTATGC CTATGC CTATG
1 CTATGC CTATGC CTATGC CTATGC CTATG
33703918 GCCCCCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (6 bp):
CTATGC
Found at i:33706268 original size:17 final size:16
Alignment explanation
Indices: 33706227--33706269 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
33706217 ATTATAATTC
*
33706227 CATTAATTTTTTAAAT
1 CATTAATTTTCTAAAT
*
33706243 CATACAATTTTCTACAAT
1 CAT-TAATTTTCTA-AAT
33706261 CATTAATTT
1 CATTAATTT
33706270 AAAATACCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (16 bp):
CATTAATTTTCTAAAT
Found at i:33711521 original size:25 final size:26
Alignment explanation
Indices: 33711472--33711521 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
33711462 GATTGAATTT
*
33711472 AAATAATAATGTAAATATTACAAAAC
1 AAATAATAATGTAAATATTAAAAAAC
* *
33711498 AAATACTAAT-TAAATTTTAAAAAA
1 AAATAATAATGTAAATATTAAAAAA
33711522 ACTAAACTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (26 bp):
AAATAATAATGTAAATATTAAAAAAC
Found at i:33712390 original size:2 final size:2
Alignment explanation
Indices: 33712383--33712436 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
33712373 GAACATGTTC
33712383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33712425 AT AT AT AT AT AT
1 AT AT AT AT AT AT
33712437 TCGTGGAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33713299 original size:27 final size:28
Alignment explanation
Indices: 33713242--33713299 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
33713232 GATATTTTAA
*
33713242 AATAAAAACACTTACTAAGTATCCATGT
1 AATAAAAACACTTACTAAGTATCAATGT
*
33713270 AATAAGAAACACTTA-TAA-TATCAATTT
1 AATAA-AAACACTTACTAAGTATCAATGT
33713297 AAT
1 AAT
33713300 GAATAGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 8 0.30
29 9 0.33
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (28 bp):
AATAAAAACACTTACTAAGTATCAATGT
Found at i:33725975 original size:13 final size:14
Alignment explanation
Indices: 33725959--33725991 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
33725949 ATAAAATAAC
33725959 AAAATAGGAA-ATA
1 AAAATAGGAATATA
*
33725972 AAAATATGAATATA
1 AAAATAGGAATATA
33725986 AAAATA
1 AAAATA
33725992 CATAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (14 bp):
AAAATAGGAATATA
Found at i:33731183 original size:24 final size:25
Alignment explanation
Indices: 33731137--33731183 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
33731127 TGTTTCATTA
*
33731137 AATAATTACATTAAAATGAAAATGT
1 AATAATTACATTAAAAAGAAAATGT
* *
33731162 AATATTTA-ATTAAAAAGCAAAT
1 AATAATTACATTAAAAAGAAAAT
33731184 TTTATTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (25 bp):
AATAATTACATTAAAAAGAAAATGT
Found at i:33731672 original size:30 final size:30
Alignment explanation
Indices: 33731615--33731674 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
33731605 AAATTAAACT
* *
33731615 TAAAAAAATTAAAAATATGTTTCTAAAAAA
1 TAAAAAAAATAAAAACATGTTTCTAAAAAA
*
33731645 TAAAAAAAATAAAAACACT-TTTTTAAAAAA
1 TAAAAAAAATAAAAACA-TGTTTCTAAAAAA
33731675 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (30 bp):
TAAAAAAAATAAAAACATGTTTCTAAAAAA
Found at i:33737162 original size:16 final size:16
Alignment explanation
Indices: 33737141--33737183 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
33737131 AATTTCAGTA
33737141 ATTATTGTTATTT-TTC
1 ATTATT-TTATTTCTTC
33737157 ATTATTTTATTTCTTC
1 ATTATTTTATTTCTTC
33737173 ATTTATTTTAT
1 A-TTATTTTAT
33737184 GTGAATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTATTTTATTTCTTC
Found at i:33755883 original size:6 final size:6
Alignment explanation
Indices: 33755872--33755975 Score: 72
Period size: 6 Copynumber: 18.0 Consensus size: 6
33755862 TTGAATTTAT
** * * *
33755872 TTTAAA TTTAAA TTTATT TTTAAA TTTGAA TTT--G TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * * **
33755918 TTTATT TTTAAA TTTGAA TTT--G TTAAAA TTTAAA TTTAAA TTTATG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33755964 TTTAAA TTTAAA
1 TTTAAA TTTAAA
33755976 ATTATTCTAA
Statistics
Matches: 72, Mismatches: 22, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
4 4 0.06
6 68 0.94
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:33755914 original size:16 final size:16
Alignment explanation
Indices: 33755893--33755954 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
33755883 ATTTATTTTT
*
33755893 AAATTTGAATTTGTTA
1 AAATTTAAATTTGTTA
* *
33755909 AAATTTAAATTTATTTTT
1 AAATTTAAA-TT-TGTTA
*
33755927 AAATTTGAATTTGTTA
1 AAATTTAAATTTGTTA
33755943 AAATTTAAATTT
1 AAATTTAAATTT
33755955 AAATTTATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 22 0.59
17 4 0.11
18 11 0.30
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTTGTTA
Found at i:33755916 original size:40 final size:37
Alignment explanation
Indices: 33755872--33755972 Score: 145
Period size: 34 Copynumber: 2.7 Consensus size: 37
33755862 TTGAATTTAT
33755872 TTTAAATTTAAATTTATTTTTAAATTTGAATTTGTTA
1 TTTAAATTTAAATTTATTTTTAAATTTGAATTTGTTA
33755909 ---AAATTTAAATTTATTTTTAAATTTGAATTTGTTAAAA
1 TTTAAATTTAAATTTATTTTTAAATTTGAATTTGTT---A
*
33755946 TTTAAATTTAAATTTATGTTTAAATTT
1 TTTAAATTTAAATTTATTTTTAAATTT
33755973 AAAATTATTC
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
34 33 0.58
37 1 0.02
40 23 0.40
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (37 bp):
TTTAAATTTAAATTTATTTTTAAATTTGAATTTGTTA
Found at i:33755972 original size:34 final size:34
Alignment explanation
Indices: 33755861--33755955 Score: 163
Period size: 34 Copynumber: 2.8 Consensus size: 34
33755851 CTAAACCCAT
* *
33755861 TTTGAATTTATTTTAAATTTAAATTTATTTTTAAA
1 TTTGAATTT-GTTAAAATTTAAATTTATTTTTAAA
33755896 TTTGAATTTGTTAAAATTTAAATTTATTTTTAAA
1 TTTGAATTTGTTAAAATTTAAATTTATTTTTAAA
33755930 TTTGAATTTGTTAAAATTTAAATTTA
1 TTTGAATTTGTTAAAATTTAAATTTA
33755956 AATTTATGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
34 49 0.84
35 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTGAATTTGTTAAAATTTAAATTTATTTTTAAA
Found at i:33759406 original size:18 final size:17
Alignment explanation
Indices: 33759383--33759416 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
33759373 GAAATGGAGT
33759383 AAACAAAAAAACAAAACA
1 AAACAAAAAAA-AAAACA
33759401 AAACAAAAAAAAAAAC
1 AAACAAAAAAAAAAAC
33759417 CTCTATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAACAAAAAAAAAAACA
Found at i:33770141 original size:2 final size:2
Alignment explanation
Indices: 33770129--33770172 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
33770119 ATGAGGCAAC
*
33770129 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
33770171 CT
1 CT
33770173 TGTTTTTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:33777104 original size:29 final size:28
Alignment explanation
Indices: 33777024--33777105 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 28
33777014 TTAAGTGTTT
*
33777024 CAATTTTTTTTTAACTTTT-AAG-GACC
1 CAATTTTTTTTTAACTTTTAAAGAAACC
*
33777050 CAATTTTTTTTT-ACTAATTTATAAGAAATC
1 CAATTTTTTTTTAACT--TTTA-AAGAAACC
*
33777080 TAATTTTTTTTTTAACTTTTAAAGAA
1 CAA-TTTTTTTTTAACTTTTAAAGAA
33777106 CCTAAAATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
25 3 0.07
26 12 0.26
27 3 0.07
29 8 0.17
30 8 0.17
31 9 0.20
32 3 0.07
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (28 bp):
CAATTTTTTTTTAACTTTTAAAGAAACC
Found at i:33787997 original size:16 final size:17
Alignment explanation
Indices: 33787976--33788009 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33787966 GTATGGGACA
*
33787976 AATATACA-AACATATC
1 AATATACATAACAAATC
33787992 AATATACATAACAAATC
1 AATATACATAACAAATC
33788009 A
1 A
33788010 TTATTAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
AATATACATAACAAATC
Found at i:33796163 original size:15 final size:15
Alignment explanation
Indices: 33796143--33796173 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33796133 TATTTATTTT
*
33796143 ATTTTATTTTTTATA
1 ATTTTATTATTTATA
33796158 ATTTTATTATTTATA
1 ATTTTATTATTTATA
33796173 A
1 A
33796174 ATAATAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTATTATTTATA
Found at i:33807555 original size:17 final size:17
Alignment explanation
Indices: 33807533--33807571 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
33807523 AGGTGTAGAA
* *
33807533 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
33807550 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
33807567 CTTGT
1 CTTGT
33807572 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:33814355 original size:29 final size:29
Alignment explanation
Indices: 33814303--33814359 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
33814293 GGGGTACAAA
33814303 TTTTTTTTTAGCTTTTAAGGGGCCCAAATT
1 TTTTTTTTTAGCTTTTAA-GGGCCCAAATT
33814333 TTTTTTTTTCAGCTTTTAA-GGCCCAAA
1 TTTTTTTTT-AGCTTTTAAGGGCCCAAA
33814360 AAATTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.31
30 9 0.35
31 9 0.35
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTTTTTTTAGCTTTTAAGGGCCCAAATT
Found at i:33816181 original size:59 final size:57
Alignment explanation
Indices: 33816113--33816540 Score: 401
Period size: 59 Copynumber: 7.2 Consensus size: 57
33816103 TTGATCATTG
*
33816113 CATGGCCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTGGGTGTTGGCCATGC
1 CATGGCCGACACCCCTTTTTATCTG-ATAAAAAATTAAATTTTT-GGTGTTGGCCATGC
* * * * *
33816172 CATGACCGACACCCCCTTTTTGTCAGATAAAAAATTTGAATTTTTTGTGTTGGCCATGC
1 CATGGCCGACA-CCCCTTTTTATCTGATAAAAAA-TTAAATTTTTGGTGTTGGCCATGC
* * * ** *
33816231 AATGGCCGACACTCCTTTTTTGTCAAATAAAAAATTCGAATTTTTGGTGTTGGCCATTG-
1 CATGGCCGACAC-CCCTTTTTATCTGATAAAAAATT-AAATTTTTGGTGTTGGCCA-TGC
* * *
33816290 CATGGCCGACACCTCTTTTTTATTTGGTAAAAAATTTCAAAATATTTTGGTGTTGGCCATTG-
1 CATGGCCGACACC-CCTTTTTATCTGATAAAAAA-TT--AAAT-TTTTGGTGTTGGCCA-TGC
* ** * * *
33816352 AATGGCCGATTCCCTTTTTTATCTGAAAAAAAATTAAATTTTTGGGTGTTGGCCATGT
1 CATGGCCGACACCCCTTTTTATCTGATAAAAAATTAAATTTTT-GGTGTTGGCCATGC
* * * * *
33816410 CATGGTCGACACTCCCTTTTTGTCAGATAAAAAATTAACTTTTTTGGTGTTGGCCATAC
1 CATGGCCGACAC-CCCTTTTTATCTGATAAAAAATTAA-ATTTTTGGTGTTGGCCATGC
* * * *
33816469 TATGGCCGACACCCCTATTTATCTGATAAAAAAATTAAATTTTTTGGTGCTAGCCATGC
1 CATGGCCGACACCCCTTTTTATCTGAT-AAAAAATTAAA-TTTTTGGTGTTGGCCATGC
*
33816528 AATGGCCGACACC
1 CATGGCCGACACC
33816541 AACTTTTCCT
Statistics
Matches: 308, Mismatches: 46, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
57 6 0.02
58 39 0.13
59 184 0.60
60 31 0.10
61 20 0.06
62 28 0.09
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (57 bp):
CATGGCCGACACCCCTTTTTATCTGATAAAAAATTAAATTTTTGGTGTTGGCCATGC
Found at i:33816503 original size:238 final size:240
Alignment explanation
Indices: 33816077--33816540 Score: 618
Period size: 238 Copynumber: 1.9 Consensus size: 240
33816067 TTTTTTCAGA
* * * *
33816077 TAAAAAATTTTCAAATTTTTTTGATGTTGATCATTGCATGGCCGACACCCCTTTTTATCTGAATA
1 TAAAAAATTTTCAAAATATTTTGATGTTGACCATTGAATGGCCGACACCCCTTTTTATCTGAATA
33816142 AAAAATCAAATTTTTGGGTGTTGGCCATGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAAT
66 AAAAATCAAATTTTTGGGTGTTGGCCATGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAAT
* * * * *
33816207 TTGAATTTTTTGTGTTGGCCATGCAATGGCCGACACTCCTTTTTTGTCAAATAAAAAATTCGAA-
131 TTGAATTTTTTGTGTTGGCCATACAATGGCCGACACCCCTTTTATCTCAAATAAAAAATT-AAAT
* *
33816271 TTTTTGGTGTTGGCCATTGC-ATGGCCGACACCTCTTTTTTATTTGG
195 TTTTTGGTGCTAGCCA-TGCAATGGCCGACACCTCTTTTTTATTTGG
* * ** *
33816317 TAAAAAA-TTTCAAAATATTTTGGTGTTGGCCATTGAATGGCCGATTCCCTTTTTTATCTGAA-A
1 TAAAAAATTTTCAAAATATTTTGATGTTGACCATTGAATGGCCGACACCCCTTTTTATCTGAATA
* * ** *
33816380 AAAAATTAAATTTTTGGGTGTTGGCCATGTCATGGTCGACACTCCCTTTTTGTCAGATAAAAAA-
66 AAAAATCAAATTTTTGGGTGTTGGCCATGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAAT
* * *
33816444 TT-AACTTTTTTGGTGTTGGCCATACTATGGCCGACACCCCTATTTATCTGATA-AAAAAATTAA
131 TTGAA-TTTTTT-GTGTTGGCCATACAATGGCCGACACCCCT-TTTATCTCAAATAAAAAATTAA
33816507 ATTTTTTGGTGCTAGCCATGCAATGGCCGACACC
193 ATTTTTTGGTGCTAGCCATGCAATGGCCGACACC
33816541 AACTTTTCCT
Statistics
Matches: 195, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
236 2 0.01
237 13 0.07
238 120 0.62
239 53 0.27
240 7 0.04
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (240 bp):
TAAAAAATTTTCAAAATATTTTGATGTTGACCATTGAATGGCCGACACCCCTTTTTATCTGAATA
AAAAATCAAATTTTTGGGTGTTGGCCATGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAAT
TTGAATTTTTTGTGTTGGCCATACAATGGCCGACACCCCTTTTATCTCAAATAAAAAATTAAATT
TTTTGGTGCTAGCCATGCAATGGCCGACACCTCTTTTTTATTTGG
Found at i:33817360 original size:24 final size:24
Alignment explanation
Indices: 33817333--33817387 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
33817323 AAAAAATAAT
*
33817333 AATTAGAATATACAGGAAATTAGA
1 AATTAAAATATACAGGAAATTAGA
33817357 AATTAAAATATACAGGAAATTAGA
1 AATTAAAATATACAGGAAATTAGA
33817381 AATTAAA
1 AATTAAA
33817388 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (24 bp):
AATTAAAATATACAGGAAATTAGA
Found at i:33817395 original size:30 final size:30
Alignment explanation
Indices: 33817348--33817424 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
33817338 GAATATACAG
* * * *
33817348 GAAATTAGAAATTAAAATATACAGGAAATTA
1 GAAATTA-AATTTAAAATAAAAACGAAATTA
33817379 GAAATTAAATTTAAAATAAAAACGAAATTA
1 GAAATTAAATTTAAAATAAAAACGAAATTA
*
33817409 CAAATTAAATTTAAAA
1 GAAATTAAATTTAAAA
33817425 AGTAAACGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 34 0.83
31 7 0.17
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (30 bp):
GAAATTAAATTTAAAATAAAAACGAAATTA
Found at i:33818224 original size:168 final size:165
Alignment explanation
Indices: 33817939--33818260 Score: 486
Period size: 168 Copynumber: 1.9 Consensus size: 165
33817929 TGTACTCGAA
33817939 AAATAATGTATTGTAAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATTTTAATT
1 AAATAATGTATTGTAAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATTTTAATT
* ** * *
33818004 TAAATATTCAAATTTGGTAAATAATATATTGTCAAATCAACTTATTATTTGATAAAAATTGTAAT
66 TAAATATTAAAATTTAATAAATAATATATTGTCAAATCAACTCATTATTTGATAAAAATT-AAAT
33818069 ATAATAAT-CTTTTTATTTAAATATTACAATTTAAT
130 ATAATAATACTTTTTATTTAAATATTACAATTTAAT
* *
33818104 AAATAATGTATTGTCAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATAATTTTT
1 AAATAATGTATTGTAAAATCAACTCATTATTTGATAAAAATTAT-A-AT-ATAATAATAATTTTA
* *
33818169 ATTTAAATATTAAAATTTAATAAATAATGTATTGTCAAATCAA-TACATTATTTGATATAAATTA
63 ATTTAAATATTAAAATTTAATAAATAATATATTGTCAAATCAACT-CATTATTTGATAAAAATTA
*
33818233 AATATAATAATAATTTTTTATTTAAATA
127 AATATAATAAT-ACTTTTTATTTAAATA
33818261 ATGTTAAATT
Statistics
Matches: 141, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
165 43 0.30
166 1 0.01
167 14 0.10
168 69 0.49
169 14 0.10
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (165 bp):
AAATAATGTATTGTAAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATTTTAATT
TAAATATTAAAATTTAATAAATAATATATTGTCAAATCAACTCATTATTTGATAAAAATTAAATA
TAATAATACTTTTTATTTAAATATTACAATTTAAT
Found at i:33818268 original size:86 final size:84
Alignment explanation
Indices: 33817939--33818260 Score: 483
Period size: 82 Copynumber: 3.9 Consensus size: 84
33817929 TGTACTCGAA
* *
33817939 AAATAATGTATTGTAAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAA-TTTTAAT
1 AAATAATGTATTGTCAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATTTTTTAT
* **
33818003 TTAAATATTCAAATTTGGT
66 TTAAATATTAAAATTTAAT
* * * *
33818022 AAATAATATATTGTCAAATCAACTTATTATTTGATAAAAATTGTAATATAATAAT--CTTTTTAT
1 AAATAATGTATTGTCAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATTTTTTAT
*
33818085 TTAAATATTACAATTTAAT
66 TTAAATATTAAAATTTAAT
33818104 AAATAATGTATTGTCAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATAATTTTT
1 AAATAATGTATTGTCAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAAT--TTTTT
33818169 ATTTAAATATTAAAATTTAAT
64 ATTTAAATATTAAAATTTAAT
*
33818190 AAATAATGTATTGTCAAATCAA-TACATTATTTGATATAAATTA-AATATAATAATAATTTTTTA
1 AAATAATGTATTGTCAAATCAACT-CATTATTTGATAAAAATTATAATATAATAATAATTTTTTA
33818253 TTTAAATA
65 TTTAAATA
33818261 ATGTTAAATT
Statistics
Matches: 218, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
82 73 0.33
83 65 0.30
85 15 0.07
86 65 0.30
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (84 bp):
AAATAATGTATTGTCAAATCAACTCATTATTTGATAAAAATTATAATATAATAATAATTTTTTAT
TTAAATATTAAAATTTAAT
Found at i:33823570 original size:119 final size:119
Alignment explanation
Indices: 33823378--33823593 Score: 271
Period size: 119 Copynumber: 1.8 Consensus size: 119
33823368 TTACCAGATA
**
33823378 AAAAAGAAGGTGTCGATTATGCAATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAAT
1 AAAAAGAAGGTGTCGACCATGCAATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAAT
* *
33823443 AGGAGTGTCGGCTATGGT-ATGACCAACACCAAAAAATTGAATTTTTTATCTGAC
66 AGGAGTGTCGACCAT-GTAATGACCAACACCAAAAAATTGAATTTTTTATCTGAC
* * *
33823497 AAAAAGAAGGTGTCGACCATTGC-ATGATCAACATC-TAAAAATTTGA-TTTTTTTATCTGATTA
1 AAAAAGAAGGTGTCGACCA-TGCAATGACCAACA-CAAAAAAATTTGATTTTTTTTATCAGA-TA
* *
33823559 AA-AGAGGGTGTCGACCATGTAATGGCCAACACCAA
63 AATAG-GAGTGTCGACCATGTAATGACCAACACCAA
33823594 TTTTTTTTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
118 16 0.19
119 63 0.76
120 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (119 bp):
AAAAAGAAGGTGTCGACCATGCAATGACCAACACAAAAAAATTTGATTTTTTTTATCAGATAAAT
AGGAGTGTCGACCATGTAATGACCAACACCAAAAAATTGAATTTTTTATCTGAC
Done.