Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 91 of 153
Found at i:28739050 original size:33 final size:32
Alignment explanation
Indices: 28738978--28739054 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
28738968 TAGATATATG
* **
28738978 TGTAAGACCATAACTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
* *
28739010 TGATAAGATCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
28739044 TGTAAGACCAT
1 TGTAAGACCAT
28739055 GGCAAGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:28739066 original size:105 final size:105
Alignment explanation
Indices: 28738873--28739066 Score: 273
Period size: 105 Copynumber: 1.8 Consensus size: 105
28738863 AATGTTTAAA
* ***
28738873 TGTAAGACCATAACTGGGCTATGACATTTTAATGAAAAGACCATAACTGGGTTATGGCACTTTGA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACTACAA
**
28738938 ACGTAAGACCATGGTTGGACCATGGCATTATAGATATATG
66 ACGTAAGACCATGGAAGGACCATGGCATTATAGATATATG
* * * *
28738978 TGTAAGACCATAACTGGGCTATGGCATTCTGATGATAAGATCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACTACAA
*
28739043 ATGTAAGACCATGGCAAGG-CCATG
66 ACGTAAGACCATGG-AAGGACCATG
28739067 ACAATGCATG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 75 0.97
106 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACTACAA
ACGTAAGACCATGGAAGGACCATGGCATTATAGATATATG
Found at i:28740261 original size:16 final size:17
Alignment explanation
Indices: 28740240--28740272 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28740230 AAAGGGTCAG
28740240 AAAAAGA-AAAATTACA
1 AAAAAGACAAAATTACA
*
28740256 AAAAAGACCAAATTACA
1 AAAAAGACAAAATTACA
28740273 TAATGTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.12, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAGACAAAATTACA
Found at i:28744054 original size:14 final size:14
Alignment explanation
Indices: 28744035--28744063 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28744025 AAATGAGAAA
28744035 AGCAACTTAGATAG
1 AGCAACTTAGATAG
28744049 AGCAACTTAGATAG
1 AGCAACTTAGATAG
28744063 A
1 A
28744064 ACTAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGCAACTTAGATAG
Found at i:28745958 original size:24 final size:23
Alignment explanation
Indices: 28745928--28745987 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
28745918 TTATATATAA
28745928 TAATTATTTTATAAAAAATAATT
1 TAATTATTTTATAAAAAATAATT
* *
28745951 TAATT-TATATATCAAAATATAATT
1 TAATTAT-TTTAT-AAAAAATAATT
*
28745975 TAATAATTTTATA
1 TAATTATTTTATA
28745988 TTTGAGTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 18 0.60
25 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTATTTTATAAAAAATAATT
Found at i:28751256 original size:13 final size:14
Alignment explanation
Indices: 28751236--28751275 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
28751226 TCCTTATTAT
28751236 TCGAATTATAAAGG
1 TCGAATTATAAAGG
*
28751250 T-GAATTAT-AATG
1 TCGAATTATAAAGG
28751262 TCGAATTATAAAGG
1 TCGAATTATAAAGG
28751276 CACTCCGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (14 bp):
TCGAATTATAAAGG
Found at i:28753471 original size:28 final size:28
Alignment explanation
Indices: 28753430--28753484 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
28753420 ATGACTGTAT
* *
28753430 AAAATTTTTTAATAAATAAAA-AATATAC
1 AAAATTATTAAAT-AATAAAATAATATAC
*
28753458 AAAATTATTAAATATTAAAATAATATA
1 AAAATTATTAAATAATAAAATAATATA
28753485 ATATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAATTATTAAATAATAAAATAATATAC
Found at i:28754632 original size:32 final size:30
Alignment explanation
Indices: 28754579--28754643 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
28754569 ATTTATTTTA
*
28754579 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
*
28754609 TTGTTAATTTATTATTATTATTTTAGAGGCAT
1 TTGTTAA-TT-TTATTATTATTTTAAAGGCAT
28754641 TTG
1 TTG
28754644 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 7 0.23
31 2 0.06
32 22 0.71
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:28755275 original size:34 final size:32
Alignment explanation
Indices: 28755231--28755344 Score: 108
Period size: 34 Copynumber: 3.5 Consensus size: 32
28755221 CAATATTTAA
*
28755231 AAAAAAACTAAATCCAATTTTAATTAATTTTCTT
1 AAAAACACTAAATCCAA-TTTAATTAATTTT-TT
*
28755265 AAAAACACTAAAACCAAATTTAATTAATTTATTT
1 AAAAACACTAAATCC-AATTTAATTAATTT-TTT
* * *
28755299 AAAATCCCTAAA-CCGTAATTTAATTAA--TTTA
1 AAAAACACTAAATCC--AATTTAATTAATTTTTT
28755330 AAAAACACTAAATCC
1 AAAAACACTAAATCC
28755345 TGATTTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
31 12 0.18
32 3 0.04
33 2 0.03
34 48 0.71
35 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (32 bp):
AAAAACACTAAATCCAATTTAATTAATTTTTT
Found at i:28755405 original size:21 final size:21
Alignment explanation
Indices: 28755376--28755446 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
28755366 TAAAACCTAG
* *
28755376 AACCTTAAATTATTTTAACAA
1 AACCCTAAATTATTCTAACAA
** * * **
28755397 AACCCTAAATCCTACAAACCT
1 AACCCTAAATTATTCTAACAA
28755418 AACCCTAAATTATTCTAACAA
1 AACCCTAAATTATTCTAACAA
28755439 AACCCTAA
1 AACCCTAA
28755447 CCCTAAAAAA
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
AACCCTAAATTATTCTAACAA
Found at i:28755458 original size:42 final size:43
Alignment explanation
Indices: 28755367--28755465 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
28755357 AAAAATTTCT
* * *
28755367 AAAACCTAGAACCTTAAATTATTTTAACAAAACCCTAAATCCTA
1 AAAACCTA-AACCCTAAATTATTCTAACAAAACCCTAAACCCTA
*
28755411 CAAACCT-AACCCTAAATTATTCTAACAAAACCCT-AACCCTAA
1 AAAACCTAAACCCTAAATTATTCTAACAAAACCCTAAACCCT-A
28755453 AAAACCCTAAACC
1 AAAA-CCTAAACC
28755466 AAAAAACCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
41 5 0.11
42 29 0.62
43 3 0.06
44 10 0.21
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.22
Consensus pattern (43 bp):
AAAACCTAAACCCTAAATTATTCTAACAAAACCCTAAACCCTA
Found at i:28755469 original size:15 final size:16
Alignment explanation
Indices: 28755432--28755476 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
28755422 CTAAATTATT
*
28755432 CTAACAAAACCCTAACC
1 CTAA-AAAACCCTAAAC
28755449 CTAAAAAACCCTAAAC
1 CTAAAAAACCCTAAAC
28755465 C-AAAAAACCCTA
1 CTAAAAAACCCTA
28755477 GGGACTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.41
16 12 0.44
17 4 0.15
ACGTcount: A:0.53, C:0.36, G:0.00, T:0.11
Consensus pattern (16 bp):
CTAAAAAACCCTAAAC
Found at i:28764170 original size:17 final size:16
Alignment explanation
Indices: 28764136--28764185 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
28764126 TTGTAAAATA
28764136 AAAACAAATAACAA-A-
1 AAAACAAATAA-AACAT
*
28764151 AAATCAAATAAAACAT
1 AAAACAAATAAAACAT
*
28764167 AAAACTAAATAAAATAT
1 AAAAC-AAATAAAACAT
28764184 AA
1 AA
28764186 GTAATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
16 4 0.14
17 12 0.41
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAACAAATAAAACAT
Found at i:28764448 original size:30 final size:30
Alignment explanation
Indices: 28764414--28764474 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
28764404 TCCATGTGCT
* *
28764414 AAGCCATGTGAGCCATATGGCAGTGTGGCC
1 AAGCCATGTGAGCCACATGACAGTGTGGCC
*
28764444 AAGCCATGTGAGCCACATGACCGTGTGGCC
1 AAGCCATGTGAGCCACATGACAGTGTGGCC
28764474 A
1 A
28764475 GACCGTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.18
Consensus pattern (30 bp):
AAGCCATGTGAGCCACATGACAGTGTGGCC
Found at i:28764790 original size:13 final size:13
Alignment explanation
Indices: 28764772--28764801 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28764762 GACACACCCA
28764772 TGTGTCCAAACCG
1 TGTGTCCAAACCG
*
28764785 TGTGTCCAAGCCG
1 TGTGTCCAAACCG
28764798 TGTG
1 TGTG
28764802 AATTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (13 bp):
TGTGTCCAAACCG
Found at i:28767300 original size:5 final size:6
Alignment explanation
Indices: 28767278--28767308 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
28767268 AATTGAAACA
28767278 AAAATAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT
28767309 GGCTAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:28767306 original size:25 final size:26
Alignment explanation
Indices: 28767250--28767306 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
28767240 AACAAAAAAC
* * *
28767250 AATAGAATATAAAAATTAAATTGAAA
1 AATAAAATATAAAAATAAAAATGAAA
*
28767276 CA-AAAATATAAAAATAAAAAT-AAA
1 AATAAAATATAAAAATAAAAATGAAA
28767300 AATAAAA
1 AATAAAA
28767307 ATGGCTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 4 0.16
25 20 0.80
26 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
AATAAAATATAAAAATAAAAATGAAA
Found at i:28768997 original size:18 final size:19
Alignment explanation
Indices: 28768976--28769012 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28768966 CACTGCTTGT
*
28768976 GTTAGAATTAC-TGAAAAG
1 GTTACAATTACATGAAAAG
28768994 GTTACAATTACATGAAAAG
1 GTTACAATTACATGAAAAG
28769013 ACACTCTTTA
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:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (19 bp):
GTTACAATTACATGAAAAG
Found at i:28771334 original size:22 final size:22
Alignment explanation
Indices: 28771309--28771353 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28771299 GCATTGAGAA
28771309 TGAGATTAAAATATGTTACTTT
1 TGAGATTAAAATATGTTACTTT
28771331 TGAGATTAAAATATGTTACTTT
1 TGAGATTAAAATATGTTACTTT
28771353 T
1 T
28771354 AGCACTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
TGAGATTAAAATATGTTACTTT
Found at i:28788218 original size:20 final size:20
Alignment explanation
Indices: 28788193--28788239 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
28788183 AATATCCAAA
28788193 CAATAATAATAAAATAGTAG
1 CAATAATAATAAAATAGTAG
* *
28788213 CAATAATAGTAAAATTGTAG
1 CAATAATAATAAAATAGTAG
28788233 CAA-AATA
1 CAATAATA
28788240 GTGAGAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (20 bp):
CAATAATAATAAAATAGTAG
Found at i:28794185 original size:20 final size:21
Alignment explanation
Indices: 28794160--28794198 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28794150 TAGCAGTTGT
28794160 GCTGCA-AATACTGTATAGCA
1 GCTGCATAATACTGTATAGCA
*
28794180 GCTGCATATTACTGTATAG
1 GCTGCATAATACTGTATAG
28794199 TGTCGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (21 bp):
GCTGCATAATACTGTATAGCA
Found at i:28794638 original size:24 final size:24
Alignment explanation
Indices: 28794611--28794659 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28794601 ATTTAAGCGC
28794611 TTAATTTTGATTTTGACTTTATGT
1 TTAATTTTGATTTTGACTTTATGT
28794635 TTAATTTTGATTTTGACTTTATGT
1 TTAATTTTGATTTTGACTTTATGT
28794659 T
1 T
28794660 GGGGGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (24 bp):
TTAATTTTGATTTTGACTTTATGT
Found at i:28805197 original size:49 final size:49
Alignment explanation
Indices: 28805140--28805234 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
28805130 ACAGAATCGT
*
28805140 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAATAGAGAAACTAACAAA
1 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAACAAA
28805189 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAAC
1 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAAC
28805235 GCCAGATTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.58, C:0.07, G:0.29, T:0.05
Consensus pattern (49 bp):
AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAACAAA
Found at i:28808909 original size:20 final size:19
Alignment explanation
Indices: 28808878--28808947 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 19
28808868 CTTGCGTTTC
28808878 TTCTTTCTTTCTTTTTTTT
1 TTCTTTCTTTCTTTTTTTT
28808897 TTCTTTCCTTTCTATTTCATTTTGT
1 TTCTTT-CTTTC--TTT--TTTT-T
*
28808922 TTCTTTCTTTCTCTTTTTAT
1 TTCTTTCTTTCT-TTTTTTT
28808942 TTCTTT
1 TTCTTT
28808948 TTCTTTTACT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
19 6 0.14
20 12 0.28
21 3 0.07
22 4 0.09
23 2 0.05
24 9 0.21
25 7 0.16
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (19 bp):
TTCTTTCTTTCTTTTTTTT
Found at i:28809015 original size:8 final size:8
Alignment explanation
Indices: 28809002--28809058 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
28808992 TTTTAAGTTT
28809002 TAATATTA
1 TAATATTA
28809010 TAATATTA
1 TAATATTA
28809018 TAATA-TA
1 TAATATTA
*
28809025 T-ATATTT
1 TAATATTA
28809032 TAACT-TTA
1 TAA-TATTA
28809040 -AATATTTA
1 TAATA-TTA
28809048 TAATATATA
1 TAATAT-TA
28809057 TA
1 TA
28809059 CACTTATGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
6 4 0.10
7 7 0.17
8 20 0.50
9 9 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (8 bp):
TAATATTA
Found at i:28809661 original size:21 final size:21
Alignment explanation
Indices: 28809637--28809687 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
28809627 GTGTCCCCTC
*
28809637 CACACGGGTATGTGTGGCCTT
1 CACACGGGCATGTGTGGCCTT
28809658 CACACGGGCATGTGTGGCCTT
1 CACACGGGCATGTGTGGCCTT
*
28809679 CACATGGGC
1 CACACGGGC
28809688 GTGTAGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (21 bp):
CACACGGGCATGTGTGGCCTT
Found at i:28813509 original size:21 final size:21
Alignment explanation
Indices: 28813484--28813525 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28813474 AAACTTACAA
28813484 AAACCCCATAAAACTCATTTC
1 AAACCCCATAAAACTCATTTC
28813505 AAACCCCATAAAACTCATTTC
1 AAACCCCATAAAACTCATTTC
28813526 TTAGGCAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCCCATAAAACTCATTTC
Found at i:28814609 original size:13 final size:13
Alignment explanation
Indices: 28814591--28814616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28814581 CAATAGTTAA
28814591 ATATATTAATAAT
1 ATATATTAATAAT
28814604 ATATATTAATAAT
1 ATATATTAATAAT
28814617 GGAACTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATTAATAAT
Found at i:28819223 original size:17 final size:16
Alignment explanation
Indices: 28819201--28819245 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28819191 TAGAATCAAG
*
28819201 TTGAGAAAATTATTTAA
1 TTGAG-AAATTAATTAA
28819218 TTGAGAAATTAATTAA
1 TTGAGAAATTAATTAA
28819234 TT-A-AAATTAATT
1 TTGAGAAATTAATT
28819246 TATGATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 12 0.44
17 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
TTGAGAAATTAATTAA
Found at i:28819255 original size:132 final size:131
Alignment explanation
Indices: 28819114--28819383 Score: 513
Period size: 132 Copynumber: 2.1 Consensus size: 131
28819104 TCATAGTGAA
* *
28819114 TATGTTGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGG
1 TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
28819179 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTAATTAAAATTAA
66 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATT-ATTAAAATTAA
28819244 TT
130 TT
28819246 TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
1 TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
28819311 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTATTAAAATTAAT
66 TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTATTAAAATTAAT
28819376 T
131 T
28819377 TATGATG
1 TATGATG
28819384 TTTATTTTGG
Statistics
Matches: 136, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 20 0.15
132 116 0.85
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.41
Consensus pattern (131 bp):
TATGATGAATGTAGAAATATTAAATGTATTTTCTCATAGGTTTTTTTACAGTAAAATTGTCACGA
TTTTAAGAGAATTAGAATCAAGTTGAGAAAATTATTTAATTGAGAAATTAATTATTAAAATTAAT
T
Found at i:28826713 original size:18 final size:19
Alignment explanation
Indices: 28826690--28826728 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28826680 CTTTTATGAT
28826690 TTAGTCCCTAAATCG-TAA
1 TTAGTCCCTAAATCGATAA
*
28826708 TTAGTCCCTAATTCGATAA
1 TTAGTCCCTAAATCGATAA
28826727 TT
1 TT
28826729 TTACCTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (19 bp):
TTAGTCCCTAAATCGATAA
Found at i:28827430 original size:13 final size:13
Alignment explanation
Indices: 28827412--28827438 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28827402 TCAAAGGATA
28827412 GATTTCTTTTATT
1 GATTTCTTTTATT
28827425 GATTTCTTTTATT
1 GATTTCTTTTATT
28827438 G
1 G
28827439 GTTTAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.11, T:0.67
Consensus pattern (13 bp):
GATTTCTTTTATT
Found at i:28828803 original size:31 final size:31
Alignment explanation
Indices: 28828768--28828828 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
28828758 TTAATAGCCT
* *
28828768 AATGACTTAAATAAAAACTTTTGAATAATTG
1 AATGACTTAAAGAAAAACTTTTAAATAATTG
* *
28828799 AATGACTTAAAGGAAAATTTTTAAATAATT
1 AATGACTTAAAGAAAAACTTTTAAATAATT
28828829 CAGTGACCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (31 bp):
AATGACTTAAAGAAAAACTTTTAAATAATTG
Found at i:28834240 original size:123 final size:123
Alignment explanation
Indices: 28834013--28834246 Score: 319
Period size: 123 Copynumber: 1.9 Consensus size: 123
28834003 ATTAATTATA
* *
28834013 CCCTGAATTGCACATACGTGCCTCTGTTTGTACTTCGGTACTCCTGAATTACACATACATGCCCC
1 CCCTAAATTGCACATACATGCCTCTGTTTGTACTTCGGTACTCCTGAATTACACATACATGCCCC
* ** *
28834078 TATTTGTACTTTGGTACCCCTGAATTGCACATACATGCCCTTATTTGTACTTTGGTAC
66 TATTTGTACTTCGGTACCCCTGAATAACACATACATGCCCCTATTTGTACTTTGGTAC
* * * *
28834136 CCCTAAATTGCACATACATGCC-CTTGTTTGTACTTTGGTAC-CATTGAATTGCACATAGATGCC
1 CCCTAAATTGCACATACATGCCTC-TGTTTGTACTTCGGTACTC-CTGAATTACACATACATGCC
* * *
28834199 CTTATTTGTACTTCGGTACCCTTGAATAACACATACGTGCCCCTATTT
64 CCTATTTGTACTTCGGTACCCCTGAATAACACATACATGCCCCTATTT
28834247 ACACTTCAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
122 2 0.02
123 94 0.98
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (123 bp):
CCCTAAATTGCACATACATGCCTCTGTTTGTACTTCGGTACTCCTGAATTACACATACATGCCCC
TATTTGTACTTCGGTACCCCTGAATAACACATACATGCCCCTATTTGTACTTTGGTAC
Found at i:28834253 original size:41 final size:41
Alignment explanation
Indices: 28834013--28834246 Score: 288
Period size: 41 Copynumber: 5.7 Consensus size: 41
28834003 ATTAATTATA
* * *
28834013 CCCTGAATTGCACATACGTGCCTCTGTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* * *
28834054 TCCTGAATTACACATACATGCCCCTATTTGTACTTTGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* *
28834095 CCCTGAATTGCACATACATGCCCTTATTTGTACTTTGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* * * *
28834136 CCCTAAATTGCACATACATGCCCTTGTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
** * *
28834177 CATTGAATTGCACATAGATGCCCTTATTTGTACTTCGGTAC
1 CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
* ** *
28834218 CCTTGAATAACACATACGTGCCCCTATTT
1 CCCTGAATTGCACATACATGCCCCTATTT
28834247 ACACTTCAAT
Statistics
Matches: 170, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 170 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (41 bp):
CCCTGAATTGCACATACATGCCCCTATTTGTACTTCGGTAC
Found at i:28843195 original size:30 final size:30
Alignment explanation
Indices: 28843161--28843223 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
28843151 ACTTAACAAG
28843161 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
28843191 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
28843221 CAA
1 CAA
28843224 TAAAATAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:28845131 original size:104 final size:104
Alignment explanation
Indices: 28844951--28845314 Score: 537
Period size: 104 Copynumber: 3.6 Consensus size: 104
28844941 TGTATATAAA
** * * *
28844951 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
28845015 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
28845055 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
28845120 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCCG
* *
28845160 AGGGGTTGCTAAGTGCCGA-T------TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
**
28845218 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
28845257 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
28845315 GATAACGGTT
Statistics
Matches: 237, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
97 24 0.10
98 69 0.29
104 119 0.50
105 25 0.11
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:28845234 original size:98 final size:97
Alignment explanation
Indices: 28844974--28845277 Score: 450
Period size: 98 Copynumber: 3.1 Consensus size: 97
28844964 TGCTGATTCC
* *
28844974 CCGATTT-ATGGGTGGTGCTATGTGCG-TGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGC
1 CCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTTGAAATGTGAAAGGGGGTTGC
28845037 TATGTGCTGATTCCCCCGAGGGGTTGCTAAGTG
65 TATGTGCTGATTCCCCCGAGGGGTTGCTAAGTG
*
28845070 CTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGG
1 CCGA-T------TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGG
28845135 GGTTGCTATGTGCTGATTCCCCCCGAGGGGTTGCTAAGTG
59 GGTTGCTATGTGCTGATT-CCCCCGAGGGGTTGCTAAGTG
* **
28845175 CCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAAGGGGGTTGCT
1 CCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCT
28845240 ATGTGCTGATTCCCCCGAGGGGTTGCTAAGTG
66 ATGTGCTGATTCCCCCGAGGGGTTGCTAAGTG
*
28845272 CTGATT
1 CCGATT
28845278 CCCCGATTCA
Statistics
Matches: 190, Mismatches: 8, Indels: 19
0.88 0.04 0.09
Matches are distributed among these distances:
96 3 0.02
97 27 0.14
98 68 0.36
103 2 0.01
104 65 0.34
105 25 0.13
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (97 bp):
CCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCT
ATGTGCTGATTCCCCCGAGGGGTTGCTAAGTG
Found at i:28847115 original size:31 final size:31
Alignment explanation
Indices: 28847058--28847571 Score: 277
Period size: 31 Copynumber: 16.8 Consensus size: 31
28847048 ATCCAATGCT
** * *
28847058 CAAATC-AATTCAACAATATATATTCATATA
1 CAAATCAAATTCGGCAATGTATAATCATATA
* **
28847088 CGAATCAAATTCGGCAACT-TATCTTCATATA
1 CAAATCAAATTCGGCAA-TGTATAATCATATA
* * **
28847119 CAAATCGATTTCGATAATGTATAATCATATA
1 CAAATCAAATTCGGCAATGTATAATCATATA
*
28847150 CAAAT-AAATTTCAGCAATGTATAATCATATA
1 CAAATCAAA-TTCGGCAATGTATAATCATATA
* **
28847181 CGAATC-AATTCGGCAACT-TATCTTCATATA
1 CAAATCAAATTCGGCAA-TGTATAATCATATA
* * ** *
28847211 TAAATCAATTTCGATAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAATCATATA
* *
28847242 CAAAT-AAATTTCAGCAATGTATAATTATATA
1 CAAATCAAA-TTCGGCAATGTATAATCATATA
* * **
28847273 CGAATC-AATTTGGCAACT-TATCTTCATATA
1 CAAATCAAATTCGGCAA-TGTATAATCATATA
* *** * *
28847303 CAAATCAATTTCTATAATATATAACCATATA
1 CAAATCAAATTCGGCAATGTATAATCATATA
*
28847334 CAAAT-AAATTTCAGCAATGTATAATCATATA
1 CAAATCAAA-TTCGGCAATGTATAATCATATA
* * * **
28847365 CGAATC-CATTCGACAACT-TATCTTCATATA
1 CAAATCAAATTCGGCAA-TGTATAATCATATA
* ** * *
28847395 CAAATCAATTTCGATAATATATAACCATATA
1 CAAATCAAATTCGGCAATGTATAATCATATA
* *
28847426 TAAAT-AAATTTCAGCAATGTATAATCATATA
1 CAAATCAAA-TTCGGCAATGTATAATCATATA
** **
28847457 TGAATC-AATTCGGCAACT-TATCTTCATATA
1 CAAATCAAATTCGGCAA-TGTATAATCATATA
* ** *
28847487 CAAATCAATTTCGATAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAATCATATA
*** **
28847518 CAAAT-AAATTTCAATAATGTATAATTGTATA
1 CAAATCAAA-TTCGGCAATGTATAATCATATA
* * *
28847549 CGAAT-TAATTTGGCAATGTATAA
1 CAAATCAAATTCGGCAATGTATAA
28847572 AACAATCAAA
Statistics
Matches: 361, Mismatches: 99, Indels: 48
0.71 0.19 0.09
Matches are distributed among these distances:
30 113 0.31
31 247 0.68
32 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATAATCATATA
Found at i:28847196 original size:92 final size:92
Alignment explanation
Indices: 28847058--28847564 Score: 800
Period size: 92 Copynumber: 5.5 Consensus size: 92
28847048 ATCCAATGCT
* * * *
28847058 CAAATCAA-TTCAACAATATATATTCATATACGAATCAAATTCGGCAACTTATCTTCATATACAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATC-AATTCGGCAACTTATCTTCATATACAA
* *
28847122 ATCGATTTCGATAATGTATAATCATATA
65 ATCAATTTCGATAATGTATAACCATATA
*
28847150 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATATAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
28847215 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* *
28847242 CAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
* *
28847307 TCAATTTCTATAATATATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* *
28847334 CAAATAAATTTCAGCAATGTATAATCATATACGAATCCATTCGACAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
*
28847399 TCAATTTCGATAATATATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
* *
28847426 TAAATAAATTTCAGCAATGTATAATCATATATGAATCAATTCGGCAACTTATCTTCATATACAAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
28847491 TCAATTTCGATAATGTATAACCATATA
66 TCAATTTCGATAATGTATAACCATATA
** ** * *
28847518 CAAATAAATTTCAATAATGTATAATTGTATACGAATTAATTTGGCAA
1 CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAA
28847565 TGTATAAAAC
Statistics
Matches: 384, Mismatches: 30, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
92 359 0.93
93 25 0.07
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (92 bp):
CAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAA
TCAATTTCGATAATGTATAACCATATA
Found at i:28849651 original size:73 final size:73
Alignment explanation
Indices: 28849574--28849736 Score: 177
Period size: 73 Copynumber: 2.2 Consensus size: 73
28849564 TGTATAACGT
* * * *
28849574 GAAGCT-CATAAGAGTCATAT-TTAGGAAACTCATGCGAGCCAATAACGGGTAGCTTCAAAGAGC
1 GAAGCTCCA-AAGAGCCATATATTAGGAAACTCAAGCGAGCC-ATAACGGGAAGCTCCAAAGAGC
28849637 CATTAATTAG
64 CATTAATTAG
* * ** * * *
28849647 GAAGCTCCAAATAGCCATATATTGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGAAGGGCCA
1 GAAGCTCCAAAGAGCCATATATTAGGAAACTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCA
28849712 TTAATTAG
66 TTAATTAG
*
28849720 GAAGCTTACAAAGAGCC
1 GAAGC-TCCAAAGAGCC
28849737 TTTAATCGGG
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
73 47 0.64
74 27 0.36
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (73 bp):
GAAGCTCCAAAGAGCCATATATTAGGAAACTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCA
TTAATTAG
Found at i:28849657 original size:25 final size:25
Alignment explanation
Indices: 28849624--28849752 Score: 95
Period size: 25 Copynumber: 5.2 Consensus size: 25
28849614 AATAACGGGT
* *
28849624 AGCTTCAAAGAGCCATTAATTAGGA
1 AGCTCCAAAGAGCCATTAATTGGGA
*
28849649 AGCTCCAAATAGCCA-TATATTGGGA
1 AGCTCCAAAGAGCCATTA-ATTGGGA
* * *
28849674 AG-TTCAAGCGAGCCA-T-ATCGGGA
1 AGCTCCAA-AGAGCCATTAATTGGGA
* * *
28849697 AGCTCCGAAGGGCCATTAATTAGGA
1 AGCTCCAAAGAGCCATTAATTGGGA
* * *
28849722 AGCTTACAAAGAGCCTTTAATCGGGA
1 AGC-TCCAAAGAGCCATTAATTGGGA
28849748 AGCTC
1 AGCTC
28849753 ATGAAGAGCC
Statistics
Matches: 78, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
23 13 0.17
24 10 0.13
25 36 0.46
26 19 0.24
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATTGGGA
Found at i:28853071 original size:18 final size:18
Alignment explanation
Indices: 28853050--28853095 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
28853040 TTTAAATCAA
* *
28853050 TAAAAATTTTAAAAATAT
1 TAAAAATATAAAAAATAT
28853068 TAAAAATATAAAAAATAT
1 TAAAAATATAAAAAATAT
*
28853086 TAAAATTATA
1 TAAAAATATA
28853096 GAAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATATAAAAAATAT
Found at i:28853104 original size:18 final size:17
Alignment explanation
Indices: 28853052--28853100 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
28853042 TAAATCAATA
*
28853052 AAAATTTTAAAAATATT
1 AAAATTATAAAAATATT
*
28853069 AAAAATATAAAAAATATT
1 AAAATTAT-AAAAATATT
*
28853087 AAAATTATAGAAAT
1 AAAATTATAAAAAT
28853101 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATATT
Found at i:28853321 original size:10 final size:9
Alignment explanation
Indices: 28853300--28853436 Score: 76
Period size: 9 Copynumber: 14.0 Consensus size: 9
28853290 ATAAAAGGTG
28853300 ATAAAAATT
1 ATAAAAATT
28853309 ATAAAAATAT
1 ATAAAAAT-T
*
28853319 ATAGGAAAAAT
1 ATA--AAAATT
* *
28853330 GTATAAATT
1 ATAAAAATT
**
28853339 ATTAAATTTTT
1 A-TAAA-AATT
28853350 ATACAAAATT
1 ATA-AAAATT
*
28853360 ATTTAAAATTTT
1 A--TAAAA-ATT
*
28853372 AGAAAAAATT
1 ATAA-AAATT
*
28853382 ATAAAAGTT
1 ATAAAAATT
*
28853391 ATAAAAAAT
1 ATAAAAATT
28853400 ATAATAAATT
1 ATAA-AAATT
* *
28853410 ATTAAAAGT
1 ATAAAAATT
28853419 ATAAAAATT
1 ATAAAAATT
28853428 ATAAAAATT
1 ATAAAAATT
28853437 TATGTCAAAG
Statistics
Matches: 95, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
9 47 0.49
10 26 0.27
11 13 0.14
12 9 0.09
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28853371 original size:22 final size:22
Alignment explanation
Indices: 28853334--28853383 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
28853324 AAAAATGTAT
* * *
28853334 AAATTA-TTAAATTTTTATACA
1 AAATTATTTAAAATTTTAGAAA
28853355 AAATTATTTAAAATTTTAGAAA
1 AAATTATTTAAAATTTTAGAAA
28853377 AAATTAT
1 AAATTAT
28853384 AAAAGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATTATTTAAAATTTTAGAAA
Found at i:28853398 original size:19 final size:19
Alignment explanation
Indices: 28853374--28853439 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
28853364 AAAATTTTAG
*
28853374 AAAAAATTATAAAAGTTAT
1 AAAAAATTATAAAAATTAT
28853393 AAAAAA-TATAATAAATTAT
1 AAAAAATTATAA-AAATTAT
* *
28853412 -TAAAAGTATAAAAATTAT
1 AAAAAATTATAAAAATTAT
*
28853430 AAAAATTTAT
1 AAAAAATTAT
28853440 GTCAAAGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAT
Found at i:28853439 original size:28 final size:28
Alignment explanation
Indices: 28853375--28853436 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
28853365 AAATTTTAGA
28853375 AAAAATTA-TAAAAGTTATAAAAAATAT
1 AAAAATTATTAAAAGTTATAAAAAATAT
*
28853402 AATAAATTATTAAAAG-TATAAAAATTAT
1 AA-AAATTATTAAAAGTTATAAAAAATAT
28853430 AAAAATT
1 AAAAATT
28853437 TATGTCAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.22
28 19 0.59
29 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATTATTAAAAGTTATAAAAAATAT
Found at i:28853690 original size:49 final size:47
Alignment explanation
Indices: 28853619--28853712 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 47
28853609 TATATAACAT
**
28853619 TTTTTTAACATTTTTCTAAATTTTTG-ATATTTTTATATTTTTCTGTA
1 TTTTTTAACATTTTTCTAAATTTAAGTAT-TTTTTATATTTTTCTGTA
* *
28853666 TTTTTTAACATTTTTTTATTAATTTAAGTATTTTTTATCTTTTTCTG
1 TTTTTTAACATTTTTCTA--AATTTAAGTATTTTTTATATTTTTCTG
28853713 CCACATGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 17 0.43
49 21 0.52
50 2 0.05
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (47 bp):
TTTTTTAACATTTTTCTAAATTTAAGTATTTTTTATATTTTTCTGTA
Found at i:28854437 original size:26 final size:26
Alignment explanation
Indices: 28854408--28854462 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
28854398 TGAAAAATAA
28854408 GTAAATTTTTGTGTAATTAGATATTT
1 GTAAATTTTTGTGTAATTAGATATTT
*
28854434 GTAAATTTTTGTGTATTTAGATATTT
1 GTAAATTTTTGTGTAATTAGATATTT
28854460 GTA
1 GTA
28854463 TGTCAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (26 bp):
GTAAATTTTTGTGTAATTAGATATTT
Found at i:28854643 original size:2 final size:2
Alignment explanation
Indices: 28854636--28854662 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28854626 CTTTAAGTGT
28854636 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 T
28854663 TACCAACTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28854983 original size:43 final size:43
Alignment explanation
Indices: 28854936--28855121 Score: 122
Period size: 43 Copynumber: 4.3 Consensus size: 43
28854926 CTTTTCCCTA
*
28854936 AAACGCCGCAAAAGACCCTGATCCATAACGGCGC-TTCGACCAC
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTC-ACCAC
* * * ** * *
28854979 AAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
* ** ** ** **
28855022 AAACGCCGCTAAAGACCATGATCTTTAGGGGCGCTTTTTCTGC
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
* * ** * * * *
28855065 AAACGCCGCGAAAGACCCTTATCTTTAGCGGTGCTTTTACCAA
1 AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
*
28855108 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
28855122 GCCAACACCT
Statistics
Matches: 114, Mismatches: 28, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
43 111 0.97
44 3 0.03
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCTGATCCATAACGGCGCTTTCACCAC
Found at i:28855055 original size:86 final size:85
Alignment explanation
Indices: 28854914--28855121 Score: 200
Period size: 86 Copynumber: 2.4 Consensus size: 85
28854904 AAGATTAGGG
* * * *
28854914 TCTTTAGTGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCATAACGGCGCTTCGACCAC
1 TCTTTAGCGGCGC-TTTCCCCAAAACGCCGCTAAAGACCATGATCCATAACGGCGCTTCGACCAC
*
28854979 AAACGCCACTAAAGAACCTAA
65 AAACGCCACGAAAGAACCTAA
** ** *** **
28855000 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGATCTTTAGGGGCGCTTTTTCTGC
1 TCTTTAGCGGCGCTTTCCCCA-AAACGCCGCTAAAGACCATGATCCATAACGGCGCTTCGACCAC
* * *
28855065 AAACGCCGCGAAAGACCCTTA
65 AAACGCCACGAAAGAACCTAA
* * * *
28855086 TCTTTAGCGGTGCTTTTACCAAAAACGCCACTAAAG
1 TCTTTAGCGGCGC-TTTCCCCAAAACGCCGCTAAAG
28855122 GCCAACACCT
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
85 7 0.07
86 86 0.87
87 6 0.06
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTCCCCAAAACGCCGCTAAAGACCATGATCCATAACGGCGCTTCGACCACA
AACGCCACGAAAGAACCTAA
Found at i:28855134 original size:86 final size:86
Alignment explanation
Indices: 28854978--28855146 Score: 203
Period size: 86 Copynumber: 2.0 Consensus size: 86
28854968 GCTTCGACCA
* * * * **
28854978 CAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGA
1 CAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCAACA
*
28855043 TCTTTAGGGGCGCTTTTTCTG
66 CCTTTAGGGGCGCTTTTTCTG
* * * * * *
28855064 CAAACGCCGCGAAAGACCCTTATCTTTAGCGGTGCTTTTACCAAAAACGCCACTAAAGGCCAACA
1 CAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCAACA
* *
28855129 CCTTTAGTGGCGTTTTTT
66 CCTTTAGGGGCGCTTTTT
28855147 TTTGAAAAAC
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (86 bp):
CAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCAACA
CCTTTAGGGGCGCTTTTTCTG
Found at i:28855134 original size:129 final size:129
Alignment explanation
Indices: 28854896--28855140 Score: 278
Period size: 129 Copynumber: 1.9 Consensus size: 129
28854886 TTAGTGGAAG
** * *
28854896 CGCCGCTAAAGATTAGGGTCTTTAGTGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCA
1 CGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCA
* * *
28854961 TAACGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCACAAA
66 TAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGCGGCGCTTTCCCCACAAA
* * * * * *
28855025 CGCCGCTAAAGACCATGATCTTTAGGGGCGCTTTT-TCTGCAAACGCCGCGAAAGACCCTTATCT
1 CGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCCT-AAAACGCCGCAAAAGACCCTGATCC
* * * ** * *
28855089 TTAGCGGTGCTTTTACCAAAAACGCCACTAAAG-GCCAACACCTTTAGTGGCG
65 ATAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCAA-ACCTTTAGCGGCG
28855141 TTTTTTTTTG
Statistics
Matches: 94, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
128 5 0.05
129 89 0.95
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.22
Consensus pattern (129 bp):
CGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCCA
TAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGCGGCGCTTTCCCCACAAA
Found at i:28857667 original size:22 final size:22
Alignment explanation
Indices: 28857626--28857679 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
28857616 TTATATTTTC
* *
28857626 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
28857649 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
28857670 -TAAAAGTTTT
1 ATTAAAGTTTT
28857680 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:28857694 original size:21 final size:21
Alignment explanation
Indices: 28857628--28857694 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
28857618 ATATTTTCAT
*
28857628 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
28857650 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
28857670 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
28857691 TAAA
1 TAAA
28857695 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:28857727 original size:21 final size:20
Alignment explanation
Indices: 28857701--28857744 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
28857691 TAAATTTTAG
28857701 TTTTTTATTTCCTTT-TTATAT
1 TTTTTTATTT--TTTCTTATAT
28857722 TTTTTTATTTTTTCTTATAT
1 TTTTTTATTTTTTCTTATAT
28857742 TTT
1 TTT
28857745 GGTCCTGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTATTTTTTCTTATAT
Found at i:28858544 original size:89 final size:88
Alignment explanation
Indices: 28858419--28858668 Score: 437
Period size: 89 Copynumber: 2.8 Consensus size: 88
28858409 CCAAACCCCT
*
28858419 ACCCCTAAACCCTAAACATTATCTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCT-AACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
*
28858484 CCCTAACTCGATCCCGAATCACTA
65 CCCTAACTCGACCCCGAATCACTA
28858508 ACCCCTAACCCTTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAACCC-TAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
* *
28858573 CCCTAAATTGACCCCGAATCACTA
65 CCCTAACTCGACCCCGAATCACTA
28858597 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAA-CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
28858662 CCCTAAC
65 CCCTAAC
28858669 CCCTAAACAT
Statistics
Matches: 154, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
88 5 0.03
89 146 0.95
90 3 0.02
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.27
Consensus pattern (88 bp):
ACCCCTAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAAC
CCTAACTCGACCCCGAATCACTA
Found at i:28858666 original size:63 final size:66
Alignment explanation
Indices: 28858589--28858735 Score: 201
Period size: 66 Copynumber: 2.3 Consensus size: 66
28858579 ATTGACCCCG
*
28858589 AATCACTAACCCCTAACCCCTAAACATTATTTAATA-TATA-AA-TTAAAAAACACTAATTAATC
1 AATC-CTAAACCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAAAACACTAATTAATC
28858651 TA
65 TA
* * * *
28858653 AATCCTAAACCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCT
1 AATCCTAAACCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAAAACACTAATTAATCT
28858718 A
66 A
* *
28858719 AACCCTAAACTCTAACC
1 AATCCTAAACCCTAACC
28858736 TAACACCGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
63 30 0.41
64 8 0.11
65 2 0.03
66 33 0.45
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.32
Consensus pattern (66 bp):
AATCCTAAACCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAAAACACTAATTAATCT
A
Found at i:28859294 original size:41 final size:41
Alignment explanation
Indices: 28859236--28859472 Score: 336
Period size: 41 Copynumber: 5.8 Consensus size: 41
28859226 AAATGTTTTT
* *
28859236 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGTA-C-GAGCATTA
1 GCGGCGCTTATTAAAAAACGCCGCTAAA-G-ACCTGAGCATTA
*
28859277 GCGGCGCTTATTAAAAAACGCCACTAAAGACCTGAGCATTA
1 GCGGCGCTTATTAAAAAACGCCGCTAAAGACCTGAGCATTA
* *
28859318 GCGGCGCTTATTAAAAAACGCCGCTAAAGACTTGAGAATTA
1 GCGGCGCTTATTAAAAAACGCCGCTAAAGACCTGAGCATTA
*
28859359 GCGGCGCTTATTAAAAAACGCCGCTAAAGACCTGAACATTA
1 GCGGCGCTTATTAAAAAACGCCGCTAAAGACCTGAGCATTA
* *
28859400 GTGGCGCTTATTTAAAAACGCCGCTAAAGACCTGAGCATTA
1 GCGGCGCTTATTAAAAAACGCCGCTAAAGACCTGAGCATTA
* *
28859441 GCGGCGCTT-TTCAGAAAATGCCGCTAAAGACC
1 GCGGCGCTTATT-AAAAAACGCCGCTAAAGACC
28859473 CCAAAAAACT
Statistics
Matches: 177, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 4 0.02
41 172 0.97
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTATTAAAAAACGCCGCTAAAGACCTGAGCATTA
Found at i:28859934 original size:14 final size:15
Alignment explanation
Indices: 28859915--28859945 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28859905 ATGTGAGTTT
28859915 TAAATATATTT-TTA
1 TAAATATATTTGTTA
28859929 TAAATATATTTGTTA
1 TAAATATATTTGTTA
28859944 TA
1 TA
28859946 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TAAATATATTTGTTA
Found at i:28860486 original size:27 final size:27
Alignment explanation
Indices: 28860437--28860503 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
28860427 GATGAAGCCA
*
28860437 AAATTTTTTTAG-GAAAGTTAAATTAT
1 AAATTTTATTAGAGAAAGTTAAATTAT
28860463 AAATTTTATTAGAGAAAGTTAAATTAT
1 AAATTTTATTAGAGAAAGTTAAATTAT
28860490 AAATTTTATTAGAG
1 AAATTTTATTAGAG
28860504 GTATAATGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 11 0.28
27 28 0.72
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (27 bp):
AAATTTTATTAGAGAAAGTTAAATTAT
Found at i:28866320 original size:416 final size:416
Alignment explanation
Indices: 28865549--28866380 Score: 1664
Period size: 416 Copynumber: 2.0 Consensus size: 416
28865539 ACTGAAACTA
28865549 AACGAACACTAAACGAAGGAAAATAAATAAATTAGGGAAAATCAAGAAGAAGAAAAGAAGAGAAA
1 AACGAACACTAAACGAAGGAAAATAAATAAATTAGGGAAAATCAAGAAGAAGAAAAGAAGAGAAA
28865614 GATGGAAAAACTCAGAGAATTTCGGCAAGAGGAGAGAGAGAAGAATAGACGGCTGAATTTTTTTT
66 GATGGAAAAACTCAGAGAATTTCGGCAAGAGGAGAGAGAGAAGAATAGACGGCTGAATTTTTTTT
28865679 TGGAAAAGAGAGTCAAAATTCGGTTATGGGAAAAAATAAAATAAAATCCCGATAACCCCCAAAAT
131 TGGAAAAGAGAGTCAAAATTCGGTTATGGGAAAAAATAAAATAAAATCCCGATAACCCCCAAAAT
28865744 CTCTTAATCTTCTCCCCTAATTCCCACTACACATCAACTACTTAGAATCCCCCAATTACACAACT
196 CTCTTAATCTTCTCCCCTAATTCCCACTACACATCAACTACTTAGAATCCCCCAATTACACAACT
28865809 CTATCCCGAAATCTGAGCAAAAAATAATACCCTTGCCTGCATAGGGATTTGAATGCAAGATCTTC
261 CTATCCCGAAATCTGAGCAAAAAATAATACCCTTGCCTGCATAGGGATTTGAATGCAAGATCTTC
28865874 ACCATAATAACACACCATTTAACCACCAAACCAACAGGCCCATTCTAATGTAATTTACCCAACAA
326 ACCATAATAACACACCATTTAACCACCAAACCAACAGGCCCATTCTAATGTAATTTACCCAACAA
28865939 TCAAATAAAAGCCTATTAAACAAGAG
391 TCAAATAAAAGCCTATTAAACAAGAG
28865965 AACGAACACTAAACGAAGGAAAATAAATAAATTAGGGAAAATCAAGAAGAAGAAAAGAAGAGAAA
1 AACGAACACTAAACGAAGGAAAATAAATAAATTAGGGAAAATCAAGAAGAAGAAAAGAAGAGAAA
28866030 GATGGAAAAACTCAGAGAATTTCGGCAAGAGGAGAGAGAGAAGAATAGACGGCTGAATTTTTTTT
66 GATGGAAAAACTCAGAGAATTTCGGCAAGAGGAGAGAGAGAAGAATAGACGGCTGAATTTTTTTT
28866095 TGGAAAAGAGAGTCAAAATTCGGTTATGGGAAAAAATAAAATAAAATCCCGATAACCCCCAAAAT
131 TGGAAAAGAGAGTCAAAATTCGGTTATGGGAAAAAATAAAATAAAATCCCGATAACCCCCAAAAT
28866160 CTCTTAATCTTCTCCCCTAATTCCCACTACACATCAACTACTTAGAATCCCCCAATTACACAACT
196 CTCTTAATCTTCTCCCCTAATTCCCACTACACATCAACTACTTAGAATCCCCCAATTACACAACT
28866225 CTATCCCGAAATCTGAGCAAAAAATAATACCCTTGCCTGCATAGGGATTTGAATGCAAGATCTTC
261 CTATCCCGAAATCTGAGCAAAAAATAATACCCTTGCCTGCATAGGGATTTGAATGCAAGATCTTC
28866290 ACCATAATAACACACCATTTAACCACCAAACCAACAGGCCCATTCTAATGTAATTTACCCAACAA
326 ACCATAATAACACACCATTTAACCACCAAACCAACAGGCCCATTCTAATGTAATTTACCCAACAA
28866355 TCAAATAAAAGCCTATTAAACAAGAG
391 TCAAATAAAAGCCTATTAAACAAGAG
28866381 TAAGACCTAA
Statistics
Matches: 416, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
416 416 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (416 bp):
AACGAACACTAAACGAAGGAAAATAAATAAATTAGGGAAAATCAAGAAGAAGAAAAGAAGAGAAA
GATGGAAAAACTCAGAGAATTTCGGCAAGAGGAGAGAGAGAAGAATAGACGGCTGAATTTTTTTT
TGGAAAAGAGAGTCAAAATTCGGTTATGGGAAAAAATAAAATAAAATCCCGATAACCCCCAAAAT
CTCTTAATCTTCTCCCCTAATTCCCACTACACATCAACTACTTAGAATCCCCCAATTACACAACT
CTATCCCGAAATCTGAGCAAAAAATAATACCCTTGCCTGCATAGGGATTTGAATGCAAGATCTTC
ACCATAATAACACACCATTTAACCACCAAACCAACAGGCCCATTCTAATGTAATTTACCCAACAA
TCAAATAAAAGCCTATTAAACAAGAG
Found at i:28866995 original size:26 final size:26
Alignment explanation
Indices: 28866966--28867015 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28866956 CAGTGGCTGG
28866966 TTTGACCAACTGATTCTATTAACTAA
1 TTTGACCAACTGATTCTATTAACTAA
*
28866992 TTTGACCAACTGATTTTATTAACT
1 TTTGACCAACTGATTCTATTAACT
28867016 GTTTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTGACCAACTGATTCTATTAACTAA
Found at i:28867113 original size:115 final size:115
Alignment explanation
Indices: 28866982--28867212 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
28866972 CAACTGATTC
*
28866982 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAATCTTAAT
1 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
28867047 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
66 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
28867097 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
1 TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
28867162 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
66 TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
28867212 T
1 T
28867213 TCTATTGTTA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (115 bp):
TATTAACTAATTTGACCAACTGATTTTATTAACTGTTTATTTAAAAGTGTTTGATAAAACTTAAT
TGATAGATAAAAGCTGATATGTGTAAAATGACAAATACGGGTATGCCACA
Found at i:28869214 original size:9 final size:9
Alignment explanation
Indices: 28869200--28869267 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
28869190 CTCTCTCACA
28869200 ATAAAAATT
1 ATAAAAATT
28869209 ATAAAAAATT
1 AT-AAAAATT
*
28869219 AAAATAAATT
1 ATAA-AAATT
28869229 -TAAAAAATT
1 AT-AAAAATT
28869238 CA-AAAAATT
1 -ATAAAAATT
*
28869247 ATAGAAATT
1 ATAAAAATT
* *
28869256 CTAAAATTT
1 ATAAAAATT
28869265 ATA
1 ATA
28869268 TTTTTAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
8 1 0.02
9 30 0.65
10 15 0.33
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28869217 original size:10 final size:10
Alignment explanation
Indices: 28869202--28869249 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
28869192 CTCTCACAAT
28869202 AAAAATTATA
1 AAAAATTATA
28869212 AAAAATTA-A
1 AAAAATTATA
28869221 AATAAATT-TA
1 AA-AAATTATA
*
28869231 AAAAATT-CA
1 AAAAATTATA
28869240 AAAAATTATA
1 AAAAATTATA
28869250 GAAATTCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:28869234 original size:19 final size:19
Alignment explanation
Indices: 28869202--28869249 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
28869192 CTCTCACAAT
28869202 AAAAATTATAAAAAATTAA
1 AAAAATTATAAAAAATTAA
*
28869221 AATAAATT-TAAAAAATTCA
1 AA-AAATTATAAAAAATTAA
28869240 AAAAATTATA
1 AAAAATTATA
28869250 GAAATTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAAAAATTAA
Found at i:28869254 original size:18 final size:19
Alignment explanation
Indices: 28869202--28869267 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 19
28869192 CTCTCACAAT
*
28869202 AAAAATTATAAAAAATTAA
1 AAAAATTATAAAAAATTCA
28869221 AATAAATT-TAAAAAATTCA
1 AA-AAATTATAAAAAATTCA
* *
28869240 AAAAATTAT-AGAAATTCT
1 AAAAATTATAAAAAATTCA
*
28869258 AAAATTTATA
1 AAAAATTATA
28869268 TTTTTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 20 0.50
19 15 0.38
20 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATTATAAAAAATTCA
Found at i:28876073 original size:11 final size:11
Alignment explanation
Indices: 28876057--28876082 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28876047 TTTTTTAATA
28876057 TTATTTAATTT
1 TTATTTAATTT
28876068 TTATTTAATTT
1 TTATTTAATTT
28876079 TTAT
1 TTAT
28876083 AATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:28876093 original size:29 final size:30
Alignment explanation
Indices: 28876041--28876111 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
28876031 ATAAGGGTTA
* *
28876041 ATTTCATTTTTTAATATTATTTAAT-TTTT
1 ATTTAATTTTTTAATATTAATTAATATTTT
28876070 ATTTAATTTTTATAAT-TTAATTAATATTTT
1 ATTTAATTTTT-TAATATTAATTAATATTTT
28876100 -TTATAATTTTTT
1 ATT-TAATTTTTT
28876112 TTTATAATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (30 bp):
ATTTAATTTTTTAATATTAATTAATATTTT
Found at i:28876192 original size:41 final size:41
Alignment explanation
Indices: 28876135--28876213 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
28876125 GTAGATCCAA
* *
28876135 TGTTACAATGTTTTATTCGTAATCTACCTGGTCCTCCAGAG
1 TGTTACAACGTTTTATTCATAATCTACCTGGTCCTCCAGAG
*
28876176 TGTTACAACGTTTTATTCATAATCTATCTGGTCCTCCA
1 TGTTACAACGTTTTATTCATAATCTACCTGGTCCTCCA
28876214 TCACTGTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (41 bp):
TGTTACAACGTTTTATTCATAATCTACCTGGTCCTCCAGAG
Found at i:28878245 original size:29 final size:29
Alignment explanation
Indices: 28878213--28878292 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
28878203 AAAACAAAAT
*
28878213 ACATCTTGTCAAAATAATTTTTTCAGAAC
1 ACATCTTGTCAAAATTATTTTTTCAGAAC
** *
28878242 ACATCACGTCAAATTTATTTTTTCAGAAC
1 ACATCTTGTCAAAATTATTTTTTCAGAAC
*
28878271 -CTATCTTGTTAAAATTATTTTT
1 AC-ATCTTGTCAAAATTATTTTT
28878293 CCCATAACAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (29 bp):
ACATCTTGTCAAAATTATTTTTTCAGAAC
Found at i:28887175 original size:13 final size:13
Alignment explanation
Indices: 28887157--28887181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28887147 CTAAATCGTA
28887157 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
28887170 ATTTTAGTAAAA
1 ATTTTAGTAAAA
28887182 CCTTTTTGGT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:28888264 original size:19 final size:19
Alignment explanation
Indices: 28888237--28888301 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
28888227 AATTTGATAC
*
28888237 TTAACTTAATAGTAATTTG
1 TTAATTTAATAGTAATTTG
**
28888256 TTAATTTAATA-TGAAAGTG
1 TTAATTTAATAGT-AATTTG
*
28888275 ATT-ATCTTAATAGTATTTTG
1 -TTAAT-TTAATAGTAATTTG
28888295 TTAATTT
1 TTAATTT
28888302 TTAAAAGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 1 0.03
19 20 0.57
20 13 0.37
21 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (19 bp):
TTAATTTAATAGTAATTTG
Found at i:28891361 original size:22 final size:23
Alignment explanation
Indices: 28891333--28891439 Score: 85
Period size: 25 Copynumber: 4.4 Consensus size: 23
28891323 CACTGATGAA
*
28891333 CAGAGAGCACAGATGTGC-TAAT
1 CAGAGAGCACAGACGTGCATAAT
*
28891355 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACAGACGTGC-A-TAAT
*
28891380 CAGAGAGCACCA-ACATGCTAATAAT
1 CAGAGAGCA-CAGACGTGC--ATAAT
*
28891405 CAGATAGCACCA-ACGTGCTAATAAT
1 CAGAGAGCA-CAGACGTGC--ATAAT
28891430 CAGAGAGCAC
1 CAGAGAGCAC
28891440 GCTAAAGTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.22
24 1 0.01
25 53 0.74
26 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (23 bp):
CAGAGAGCACAGACGTGCATAAT
Found at i:28891385 original size:25 final size:25
Alignment explanation
Indices: 28891351--28891439 Score: 133
Period size: 25 Copynumber: 3.6 Consensus size: 25
28891341 ACAGATGTGC
** *
28891351 TAATCAGAGAGCACTGACGTGCTAG
1 TAATCAGAGAGCACCAACGTGCTAA
*
28891376 TAATCAGAGAGCACCAACATGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
*
28891401 TAATCAGATAGCACCAACGTGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
28891426 TAATCAGAGAGCAC
1 TAATCAGAGAGCAC
28891440 GCTAAAGTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (25 bp):
TAATCAGAGAGCACCAACGTGCTAA
Found at i:28892412 original size:5 final size:5
Alignment explanation
Indices: 28892402--28892444 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
28892392 TTATTTCGTT
28892402 TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
28892445 TAACTTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:28899020 original size:6 final size:6
Alignment explanation
Indices: 28899009--28899039 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28898999 CAGGTAAGGC
28899009 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
28899040 GTTGTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:28899697 original size:17 final size:15
Alignment explanation
Indices: 28899658--28899689 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28899648 TTTAAACATA
*
28899658 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28899673 ATTATAATTAAATAT
1 ATTATAATTAAATAT
28899688 AT
1 AT
28899690 AATTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28899746 original size:54 final size:54
Alignment explanation
Indices: 28899688--28899866 Score: 137
Period size: 60 Copynumber: 3.1 Consensus size: 54
28899678 AATTAAATAT
28899688 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
* * * * * * *
28899742 ATAATATATGATACTATAAAATATAAATTAA-CATAATTATTATTAAAT-ATATTATATTTAAAA
1 ATAAT-T-T-A-A-TA-AAATTCTTAA-TAATC--AA-TATTCTTATATGA-ATT-TA-CTCAAA
*
28899805 TAT
53 T-C
*
28899808 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
28899862 ATAAT
1 ATAAT
28899867 ATATGATACT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 6 0.07
56 3 0.03
57 13 0.14
58 4 0.04
59 5 0.05
60 15 0.16
61 5 0.05
62 4 0.04
63 13 0.14
64 3 0.03
65 6 0.07
66 5 0.05
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
Found at i:28899838 original size:120 final size:120
Alignment explanation
Indices: 28899647--28900086 Score: 810
Period size: 120 Copynumber: 3.7 Consensus size: 120
28899637 ATTTAATCAT
28899647 ATTTAAACATAATTATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
28899711 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
28899767 AATTAACATAATTATTATTAAATATATTATATTTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
28899832 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
28899887 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
28899952 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
28900007 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
28900072 TTAATATTCTTATAT
66 TTAATATTCTTATAT
28900087 AAGCACCAAA
Statistics
Matches: 312, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
119 29 0.09
120 283 0.91
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:28899929 original size:18 final size:17
Alignment explanation
Indices: 28899908--28899942 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28899898 TTATTATTAA
*
28899908 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28899926 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28899943 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28900049 original size:18 final size:17
Alignment explanation
Indices: 28900028--28900062 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28900018 TTATTATTAA
*
28900028 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28900046 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28900063 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28905666 original size:48 final size:48
Alignment explanation
Indices: 28905611--28905705 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
28905601 TCATTATTTA
* *
28905611 CAGTGCATTATTTTCGAACATTTAGATAGGTTCAGTGTATTAGTTTTC
1 CAGTGCATTATTTTCGAACATTGAGATAGGTTCAGTGCATTAGTTTTC
* *
28905659 CAGTGCATTATTTTCGAACATTGAGATAGGTTTAGTGCATTATTTTT
1 CAGTGCATTATTTTCGAACATTGAGATAGGTTCAGTGCATTAGTTTT
28905706 AGTGCACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (48 bp):
CAGTGCATTATTTTCGAACATTGAGATAGGTTCAGTGCATTAGTTTTC
Found at i:28905773 original size:21 final size:21
Alignment explanation
Indices: 28905747--28905787 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28905737 TCCATACTCA
28905747 TATTTATTAATATTTTTAACC
1 TATTTATTAATATTTTTAACC
*
28905768 TATTTATTAATTTTTTTAAC
1 TATTTATTAATATTTTTAAC
28905788 TGGAATCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTATTAATATTTTTAACC
Found at i:28909825 original size:21 final size:21
Alignment explanation
Indices: 28909778--28909821 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
28909768 TGGCTGATTG
*
28909778 AGAA-AACAAAATATAGGAGA
1 AGAAGAACAAAAAATAGGAGA
*
28909798 AGAAGAACAAAAAATTGG-GA
1 AGAAGAACAAAAAATAGGAGA
28909818 AGAA
1 AGAA
28909822 AGAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.64, C:0.05, G:0.23, T:0.09
Consensus pattern (21 bp):
AGAAGAACAAAAAATAGGAGA
Found at i:28909832 original size:21 final size:22
Alignment explanation
Indices: 28909778--28909832 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 22
28909768 TGGCTGATTG
28909778 AGAAAACAAAATATAGGAGAAGA
1 AGAAAA-AAAATATAGGAGAAGA
28909801 AGAACAAAAAAT-T-GG-GAAGAA
1 AGAA-AAAAAATATAGGAGAAG-A
28909822 AGAAAAGAAAA
1 AGAAAA-AAAA
28909833 GGAAAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 1 0.03
23 9 0.31
24 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (22 bp):
AGAAAAAAAATATAGGAGAAGA
Found at i:28912252 original size:19 final size:19
Alignment explanation
Indices: 28912203--28912259 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
28912193 AAAATTATAA
* *
28912203 AAAAATTCAAAATAATTTTT
1 AAAAATTCTAAAT-ATTTAT
*
28912223 AAAAA-TATAAATATTTAT
1 AAAAATTCTAAATATTTAT
28912241 AAAAATTCTAAA-ATTTAT
1 AAAAATTCTAAATATTTAT
28912259 A
1 A
28912260 TTTTAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.53
19 10 0.31
20 5 0.16
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCTAAATATTTAT
Found at i:28917945 original size:24 final size:24
Alignment explanation
Indices: 28917918--28917969 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
28917908 TTTCTAGAAG
*
28917918 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGTATTTATGAGCATAATAT
*
28917942 ATTTAGTATTTATTAGCATAATAT
1 ATTTAGTATTTATGAGCATAATAT
28917966 ATTT
1 ATTT
28917970 CACTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATGAGCATAATAT
Found at i:28917980 original size:24 final size:24
Alignment explanation
Indices: 28917935--28917981 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28917925 ATTTATGAGT
* *
28917935 ATAATATATTTAGTATTTATTAGC
1 ATAATATATTTACTATTCATTAGC
28917959 ATAATATATTTCACT-TTCATTAG
1 ATAATATATTT-ACTATTCATTAG
28917982 AATTAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (24 bp):
ATAATATATTTACTATTCATTAGC
Found at i:28923278 original size:42 final size:43
Alignment explanation
Indices: 28923231--28923339 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 43
28923221 TCCAGTTTGT
28923231 TTCCACGTTGCTTTCTTTTTTGTCTAGATT-AGTTGTGATTGC
1 TTCCACGTTGCTTTCTTTTTTGTCTAGATTCAGTTGTGATTGC
* *
28923273 TTCCACGTTGCTTCCTTTTTTGTCTAGATTCAGTTGTGGTTGC
1 TTCCACGTTGCTTTCTTTTTTGTCTAGATTCAGTTGTGATTGC
*
28923316 TTCCACATTGC-TTCTTTTTTGTCT
1 TTCCACGTTGCTTTCTTTTTTGTCT
28923340 TTTTCTTGGT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 41 0.66
43 21 0.34
ACGTcount: A:0.10, C:0.20, G:0.17, T:0.52
Consensus pattern (43 bp):
TTCCACGTTGCTTTCTTTTTTGTCTAGATTCAGTTGTGATTGC
Found at i:28929437 original size:42 final size:41
Alignment explanation
Indices: 28929390--28929470 Score: 144
Period size: 42 Copynumber: 2.0 Consensus size: 41
28929380 ACTTTCTCTT
28929390 TCCCTAATGCCTCGATCATCTTCGCCCCCAAATCGTAAATG
1 TCCCTAATGCCTCGATCATCTTCGCCCCCAAATCGTAAATG
*
28929431 NTCCCTAATGCCTCGATCATCTTCGCCCCTAAATCGTAAA
1 -TCCCTAATGCCTCGATCATCTTCGCCCCCAAATCGTAAA
28929471 CGGTCTCCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.25, C:0.36, G:0.11, T:0.27
Consensus pattern (41 bp):
TCCCTAATGCCTCGATCATCTTCGCCCCCAAATCGTAAATG
Found at i:28930170 original size:96 final size:96
Alignment explanation
Indices: 28930037--28930232 Score: 311
Period size: 96 Copynumber: 2.0 Consensus size: 96
28930027 TTGAAATGGA
* * * *
28930037 AGAGAATGATGAAGTAAGCTATTGATAAAGCCTGTGTTCTGAACGCTTGTTTTCAGTTTTGGGTC
1 AGAGAATGATGAAGAAAGCTATTAATAAAACCTGTGTTCCGAACGCTTGTTTTCAGTTTTGGGTC
28930102 TAGGGTAAAGTTCTAATTTTTGAATTGTTTT
66 TAGGGTAAAGTTCTAATTTTTGAATTGTTTT
* * *
28930133 AGAGAGTGATGAAGAAAGCTTTTAATAAAACCTGTGTTCCGAAGGCTTGTTTTCAGTTTTGGGTC
1 AGAGAATGATGAAGAAAGCTATTAATAAAACCTGTGTTCCGAACGCTTGTTTTCAGTTTTGGGTC
* *
28930198 TAGGGTAAAGTTCTAATTTTTGGATTTTTTT
66 TAGGGTAAAGTTCTAATTTTTGAATTGTTTT
28930229 AGAG
1 AGAG
28930233 TTTGGGCCTT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (96 bp):
AGAGAATGATGAAGAAAGCTATTAATAAAACCTGTGTTCCGAACGCTTGTTTTCAGTTTTGGGTC
TAGGGTAAAGTTCTAATTTTTGAATTGTTTT
Found at i:28932512 original size:23 final size:24
Alignment explanation
Indices: 28932486--28932543 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
28932476 CTATTTTCAA
*
28932486 ATTTATTAATAT-T-TTTGAAAAAT
1 ATTTATTAATATGTATAT-AAAAAT
*
28932509 ATTTAAT-ATATGTATATAAAAAT
1 ATTTATTAATATGTATATAAAAAT
*
28932532 ATTTATAAATAT
1 ATTTATTAATAT
28932544 CTAACAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 4 0.14
23 18 0.64
24 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
ATTTATTAATATGTATATAAAAAT
Found at i:28938002 original size:14 final size:15
Alignment explanation
Indices: 28937977--28938005 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28937967 TTGCAAGCAC
28937977 TAATACTTTTTATTG
1 TAATACTTTTTATTG
28937992 TAATA-TTTTTATTG
1 TAATACTTTTTATTG
28938006 GGTAAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (15 bp):
TAATACTTTTTATTG
Found at i:28938240 original size:23 final size:23
Alignment explanation
Indices: 28938196--28938240 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28938186 TAATAATGAG
* *
28938196 TTATAATAAATTATATTTATATT
1 TTATAATAAATTAAATTGATATT
* *
28938219 TTATTATAATTTAAATTGATAT
1 TTATAATAAATTAAATTGATAT
28938241 ATTTCATATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATAATAAATTAAATTGATATT
Found at i:28945426 original size:138 final size:137
Alignment explanation
Indices: 28945086--28945467 Score: 594
Period size: 133 Copynumber: 2.8 Consensus size: 137
28945076 ATAATAAATT
*
28945086 AATAAATTAATATAACATATCAATTATATTAATAAACACAATTCCCTAAACATTAAATAAACTCA
1 AATAAATTAATATAACATATCAATTATATTAATAAACACAATTCCCAAAACATTAAATAAACTCA
* * *
28945151 AATAACCAATTATAAAAAATATGCTCATACCTTAAATACAAAAAATCGATATAACTTAAATACGA
66 AATAACCAATTATAAAAAATATGCTTATACCTTAAATACAAAAAATCAATATAACTTAAATACAA
28945216 AATAATA
131 AATAATA
* *
28945223 AAT--A--AATATAACATGTCAATTATATTAATAAATACAATTCCCAAAACATTAAATAAACTCA
1 AATAAATTAATATAACATATCAATTATATTAATAAACACAATTCCCAAAACATTAAATAAACTCA
* * *
28945284 AATAACCAATTATAAAAAAATATGCTTATATCTTAAAAACGAAAAATCAATATAACTTAAATACA
66 AATAACCAATTAT-AAAAAATATGCTTATACCTTAAATACAAAAAATCAATATAACTTAAATACA
28945349 AAATAATA
130 AAATAATA
* * *
28945357 AATAAATTAATATAACATATGAATTATATTAATAAACACAACTCCCCAAACATTAAATAAACTCA
1 AATAAATTAATATAACATATCAATTATATTAATAAACACAATTCCCAAAACATTAAATAAACTCA
*
28945422 AATAACCAATAATAAAAAATATG-TTCATACCTTAAATACAAAAAAT
66 AATAACCAATTATAAAAAATATGCTT-ATACCTTAAATACAAAAAAT
28945468 ATTGTGGAAT
Statistics
Matches: 221, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
133 67 0.30
134 56 0.25
135 1 0.00
136 3 0.01
137 30 0.14
138 64 0.29
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (137 bp):
AATAAATTAATATAACATATCAATTATATTAATAAACACAATTCCCAAAACATTAAATAAACTCA
AATAACCAATTATAAAAAATATGCTTATACCTTAAATACAAAAAATCAATATAACTTAAATACAA
AATAATA
Found at i:28945615 original size:115 final size:114
Alignment explanation
Indices: 28945489--28945745 Score: 293
Period size: 114 Copynumber: 2.2 Consensus size: 114
28945479 TAACATTCTT
* * * *
28945489 CAAAAACATTAATAAAAAAAATTAATCAAAC-CAAAATACTAACTTAAAGCTAATAAAACACAAC
1 CAAAAACATTAATAAAACAAATTAATCAAACTCAAAATACAAACCTAAAACTAA-AAAA-AC-AC
* * *
28945553 AACAAAAAAACAACATTTCAAGTAAATACG-AAAAACTAATATAAGATACCA
63 AACAAAAAAACAACATTCCAAGTAAATACGAAAAAAATAATATAAGATACAA
* ***
28945604 CAAAAACATTAATAAAACAAATTAATCATACTTTCAATACAAACCTAAAACTAAAAAAACACAAC
1 CAAAAACATTAATAAAACAAATTAATCAAACTCAAAATACAAACCTAAAACTAAAAAAACACAAC
* * * *** *
28945669 AAAAAAATATCCTTCCCCTTAAATACGAAAAAAATGATATAAGATACAA
66 AAAAAAACAACATTCCAAGTAAATACGAAAAAAATAATATAAGATACAA
* *
28945718 CAATAACATTAATAAAACAAACTAATCA
1 CAAAAACATTAATAAAACAAATTAATCA
28945746 TACATTTAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
113 25 0.21
114 46 0.38
115 33 0.28
116 16 0.13
ACGTcount: A:0.60, C:0.18, G:0.03, T:0.20
Consensus pattern (114 bp):
CAAAAACATTAATAAAACAAATTAATCAAACTCAAAATACAAACCTAAAACTAAAAAAACACAAC
AAAAAAACAACATTCCAAGTAAATACGAAAAAAATAATATAAGATACAA
Found at i:28945804 original size:34 final size:35
Alignment explanation
Indices: 28945761--28945826 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28945751 TTAATACAAA
28945761 TTTAAATATAATAAAAC-A-TATAAAAAATCATTCT
1 TTTAAATATAA-AAAACTATTATAAAAAATCATTCT
*
28945795 TTTAAATATAAAAAACTATTATAAAATATCAT
1 TTTAAATATAAAAAACTATTATAAAAAATCAT
28945827 ACAAACAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (35 bp):
TTTAAATATAAAAAACTATTATAAAAAATCATTCT
Found at i:28956835 original size:13 final size:13
Alignment explanation
Indices: 28956819--28956843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28956809 TTTGATACTT
28956819 GATTTTGATTTGA
1 GATTTTGATTTGA
28956832 GATTTTGATTTG
1 GATTTTGATTTG
28956844 TTTTTTTCTT
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:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (13 bp):
GATTTTGATTTGA
Found at i:28958584 original size:23 final size:23
Alignment explanation
Indices: 28958558--28958611 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
28958548 GTTAATTATT
28958558 CGTACCTCCACTCACTAATCCCC
1 CGTACCTCCACTCACTAATCCCC
28958581 CGTACCTCCACTCACTAATCCCC
1 CGTACCTCCACTCACTAATCCCC
*
28958604 CATACCTC
1 CGTACCTC
28958612 ATGGATCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.52, G:0.04, T:0.22
Consensus pattern (23 bp):
CGTACCTCCACTCACTAATCCCC
Found at i:28980160 original size:23 final size:23
Alignment explanation
Indices: 28980127--28980170 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28980117 CCGTTACACA
28980127 GCTCTTAGTGAGCTTCCCGATAG
1 GCTCTTAGTGAGCTTCCCGATAG
*
28980150 GCTCTTTGTGAGCTTCCCGAT
1 GCTCTTAGTGAGCTTCCCGAT
28980171 TAAATGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.14, C:0.27, G:0.25, T:0.34
Consensus pattern (23 bp):
GCTCTTAGTGAGCTTCCCGATAG
Found at i:28985456 original size:29 final size:28
Alignment explanation
Indices: 28985401--28985456 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
28985391 TCGATACTGG
**
28985401 ATCGATACTTAGTAAAATTTTTGAAAAA
1 ATCGATACTTAGTAAAAAATTTGAAAAA
28985429 ATCGATACTTAGTAAAAAAATTTGAAAA
1 ATCGATACTTAGT-AAAAAATTTGAAAA
28985457 CAGAATGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (28 bp):
ATCGATACTTAGTAAAAAATTTGAAAAA
Found at i:28986029 original size:23 final size:25
Alignment explanation
Indices: 28985983--28986041 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
28985973 CTAAAGTGGT
* *
28985983 AACAAAAAAAAACTTTAGGTACCTA
1 AACAAAAAAAAACATTAGGCACCTA
*
28986008 GACAAAAAAAAA-ATTA-GCACCTA
1 AACAAAAAAAAACATTAGGCACCTA
28986031 AACAAAAAAAA
1 AACAAAAAAAA
28986042 GTTGCATAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.53
24 3 0.10
25 11 0.37
ACGTcount: A:0.64, C:0.15, G:0.07, T:0.14
Consensus pattern (25 bp):
AACAAAAAAAAACATTAGGCACCTA
Found at i:28990110 original size:50 final size:50
Alignment explanation
Indices: 28989999--28990245 Score: 212
Period size: 50 Copynumber: 4.8 Consensus size: 50
28989989 ATTTGGGTAA
* *
28989999 AGAGATCCCATGTAAGACCATGTCTGGGACATGCCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
28990055 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
28990105 AGAGGTCTCC-CGTAAGACCATGTCTGGAACATAGCATGGGCACCGATATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
28990155 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * * *
28990204 AAACATCACATGTAAGACCATATCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28990246 TGTTATTATC
Statistics
Matches: 163, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 43 0.26
50 74 0.45
51 2 0.01
53 3 0.02
55 2 0.01
56 38 0.23
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28992623 original size:42 final size:43
Alignment explanation
Indices: 28992564--28992673 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 43
28992554 ATTTACGTGC
* * *
28992564 AAGACCATGTCTGGGACATTGGCGTCG-TATATAATTACATGT
1 AAGACCATGTCTGGGACAGTGGCATCGTTATATAATTACATAT
* * * *
28992606 AAGACCCTGTGTGGGACAGTGGCATCGTTATTTGATTACATAT
1 AAGACCATGTCTGGGACAGTGGCATCGTTATATAATTACATAT
*
28992649 AAGACCACGTCTGGGA-AGTTGGCAT
1 AAGACCATGTCTGGGACAG-TGGCAT
28992674 TGTACGAGCT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
42 25 0.45
43 31 0.55
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
AAGACCATGTCTGGGACAGTGGCATCGTTATATAATTACATAT
Found at i:28993202 original size:23 final size:23
Alignment explanation
Indices: 28993172--28993219 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
28993162 TGGTTTAATC
*
28993172 TTGGTTTTAATACTTATGTGTAT
1 TTGGTTTTAATACTTATGTATAT
28993195 TTGGTTTTAATACTTATGTATAT
1 TTGGTTTTAATACTTATGTATAT
28993218 TT
1 TT
28993220 CACGGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.58
Consensus pattern (23 bp):
TTGGTTTTAATACTTATGTATAT
Found at i:28999109 original size:11 final size:11
Alignment explanation
Indices: 28999092--28999130 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28999082 TTTTTGGAGT
28999092 TTACAATATAA
1 TTACAATATAA
* *
28999103 ATACAATACAA
1 TTACAATATAA
*
28999114 TTATAATATAA
1 TTACAATATAA
28999125 TTACAA
1 TTACAA
28999131 ATACATGCCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (11 bp):
TTACAATATAA
Found at i:29006277 original size:9 final size:9
Alignment explanation
Indices: 29006255--29006310 Score: 52
Period size: 8 Copynumber: 6.8 Consensus size: 9
29006245 TGTCACATCA
29006255 ATAAATAATT
1 ATAAA-AATT
29006265 -TAAAAATT
1 ATAAAAATT
29006273 ATAAAAA-T
1 ATAAAAATT
*
29006281 A-AAAAA-A
1 ATAAAAATT
29006288 AT-AAAATT
1 ATAAAAATT
29006296 AT-AAAATT
1 ATAAAAATT
29006304 ATAAAAA
1 ATAAAAA
29006311 AATAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 10 0.25
8 16 0.40
9 14 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:29006297 original size:23 final size:24
Alignment explanation
Indices: 29006267--29006317 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
29006257 AAATAATTTA
29006267 AAAATTATAAAAATA-AAAAAAAT
1 AAAATTATAAAAATATAAAAAAAT
*
29006290 AAAATTATAAAATTATAAAAAAAT
1 AAAATTATAAAAATATAAAAAAAT
29006314 AAAA
1 AAAA
29006318 AAAGAGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATTATAAAAATATAAAAAAAT
Found at i:29010315 original size:60 final size:61
Alignment explanation
Indices: 29010249--29010402 Score: 215
Period size: 61 Copynumber: 2.5 Consensus size: 61
29010239 TATATTAATT
* **
29010249 TAATATTTTAT-TATAAATTATATTAGAATATTTTATT-TCATATTTTTTGAAATTTGA-AAA
1 TAATATTTTATAT-TAAATTATATTAAAATATTTTATTATCATATTTCCTGAAATTT-ATAAA
* *
29010309 TAATATTTTATATTAAATTATATTAAAATGTTTTATTATTATATTTCCTGAAATTTATAAA
1 TAATATTTTATATTAAATTATATTAAAATATTTTATTATCATATTTCCTGAAATTTATAAA
*
29010370 TAATAATTTATATTAAATTATATTAAAATATTT
1 TAATATTTTATATTAAATTATATTAAAATATTT
29010403 AAAACATTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
60 34 0.40
61 50 0.60
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (61 bp):
TAATATTTTATATTAAATTATATTAAAATATTTTATTATCATATTTCCTGAAATTTATAAA
Found at i:29010735 original size:3 final size:3
Alignment explanation
Indices: 29010727--29010753 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29010717 ATTCATCCAA
29010727 CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC
29010754 ATCTTTAATG
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:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:29012874 original size:28 final size:28
Alignment explanation
Indices: 29012811--29012889 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
29012801 CATTCAGTAC
**
29012811 TTGCCACAAAGGCTT-TCCTATCCAGAGTT
1 TTGCCACAAAGG-TTGTCCT-TTTAGAGTT
29012840 TTGCCACAAAGGTTGTCCTTTTAGAGTT
1 TTGCCACAAAGGTTGTCCTTTTAGAGTT
* * *
29012868 TTTCCACGAAGGTTTTCCTTTT
1 TTGCCACAAAGGTTGTCCTTTT
29012890 CATCCAGTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 28 0.64
29 16 0.36
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (28 bp):
TTGCCACAAAGGTTGTCCTTTTAGAGTT
Found at i:29013086 original size:60 final size:60
Alignment explanation
Indices: 29012962--29013090 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
29012952 GGTTTATCAT
* * * * * * *
29012962 AAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCATTATTTACATCCAATACTCACTAG
1 AAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATCATTTACATCCAATACTCACCAC
* * * **
29013022 AAAGGCTTTCCTATCCAGAGTTGTGCCACAAATGCATCATTTACATCTAGTACTTGCCAC
1 AAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATCATTTACATCCAATACTCACCAC
29013082 AAAGGCTTT
1 AAAGGCTTT
29013091 TGCTTTCCCA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (60 bp):
AAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATCATTTACATCCAATACTCACCAC
Found at i:29013293 original size:53 final size:53
Alignment explanation
Indices: 29013211--29013313 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
29013201 TGAATTTTTC
* * * * *
29013211 TCATGTGATGCCATAATCCACCAATTACGATTTTACACGATATAGTCTTCTTT
1 TCATATGATACCATAACCCACCAACTACGATCTTACACGATATAGTCTTCTTT
* *
29013264 TCATATGATACCATAACCCACCAGCTACGATCTTACACGATATGGTCTTC
1 TCATATGATACCATAACCCACCAACTACGATCTTACACGATATAGTCTTC
29013314 AACGCTATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (53 bp):
TCATATGATACCATAACCCACCAACTACGATCTTACACGATATAGTCTTCTTT
Found at i:29019722 original size:18 final size:17
Alignment explanation
Indices: 29019696--29019757 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
29019686 AAAACAGTCT
29019696 AAAAATAATAGTAAATA
1 AAAAATAATAGTAAATA
* *
29019713 AAAAAGTAATA-TATATT
1 AAAAA-TAATAGTAAATA
29019730 AAAAATAATAGTAAATA
1 AAAAATAATAGTAAATA
*
29019747 ATAAAGTAATA
1 A-AAAATAATA
29019758 TATATATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.14
17 19 0.51
18 13 0.35
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAAATAATAGTAAATA
Found at i:29019733 original size:34 final size:35
Alignment explanation
Indices: 29019695--29019771 Score: 129
Period size: 34 Copynumber: 2.2 Consensus size: 35
29019685 AAAAACAGTC
29019695 TAAAAATAATAGTAAATAAAAAAGTAATATATAT-
1 TAAAAATAATAGTAAATAAAAAAGTAATATATATA
*
29019729 TAAAAATAATAGTAAATAATAAAGTAATATATATA
1 TAAAAATAATAGTAAATAAAAAAGTAATATATATA
*
29019764 TAGAAATA
1 TAAAAATA
29019772 TAATCAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 33 0.82
35 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (35 bp):
TAAAAATAATAGTAAATAAAAAAGTAATATATATA
Found at i:29019829 original size:25 final size:24
Alignment explanation
Indices: 29019777--29019842 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
29019767 AAATATAATC
* *
29019777 AAAT-ATAATAATAATAACAATAT
1 AAATAATAATAAAAATAACAATAG
* *
29019800 AAATAGTGATGAAAAATAACAATAG
1 AAATAATAAT-AAAAATAACAATAG
*
29019825 CAATAATAATAAAAATAA
1 AAATAATAATAAAAATAA
29019843 TTAAATGATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 4 0.12
24 11 0.32
25 19 0.56
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (24 bp):
AAATAATAATAAAAATAACAATAG
Done.