Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 86 of 136
Found at i:28443849 original size:11 final size:11
Alignment explanation
Indices: 28443835--28443869 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28443825 TTTTGCTGCC
*
28443835 ATATCGTTATT
1 ATATTGTTATT
28443846 ATATTGTTATT
1 ATATTGTTATT
*
28443857 ATTTTGTTATT
1 ATATTGTTATT
28443868 AT
1 AT
28443870 TGTTTGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.63
Consensus pattern (11 bp):
ATATTGTTATT
Found at i:28443870 original size:11 final size:11
Alignment explanation
Indices: 28443840--28443870 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28443830 CTGCCATATC
*
28443840 GTTATTATATT
1 GTTATTATTTT
28443851 GTTATTATTTT
1 GTTATTATTTT
28443862 GTTATTATT
1 GTTATTATT
28443871 GTTTGGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (11 bp):
GTTATTATTTT
Found at i:28445054 original size:37 final size:37
Alignment explanation
Indices: 28445007--28445137 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 37
28444997 GATTAAATAA
28445007 AAATTATTAAAATATTATAAAAATTATTAAAAATTGT
1 AAATTATTAAAATATTATAAAAATTATTAAAAATTGT
* * * * **
28445044 AAATTGTTAAAAACATTAAAATTTGTAAAAAATA-TAGAAAAATAA
1 AAATTATT--AAA-A-T---A-TTATAAAAATTATTA-AAAATTGT
28445089 AAATTATTAAAATATTATAAAAATTATTAAAAATTGT
1 AAATTATTAAAATATTATAAAAATTATTAAAAATTGT
*
28445126 AAATTGTTAAAA
1 AAATTATTAAAA
28445138 ACATTAAAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 20
0.68 0.12 0.19
Matches are distributed among these distances:
37 33 0.46
38 3 0.04
39 3 0.04
40 1 0.01
41 2 0.03
42 1 0.01
43 3 0.04
44 3 0.04
45 22 0.31
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (37 bp):
AAATTATTAAAATATTATAAAAATTATTAAAAATTGT
Found at i:28445075 original size:36 final size:36
Alignment explanation
Indices: 28445035--28445159 Score: 92
Period size: 37 Copynumber: 3.2 Consensus size: 36
28445025 AAAAATTATT
28445035 AAAAATTGTAAATTGTTAAAAACATTAAAATTTGTA
1 AAAAATTGTAAATTGTTAAAAACATTAAAATTTGTA
* * *
28445071 AAAAATATAGAAAAATAAAAATTATTAAAATATTATAAAAATTAT-T-
1 AAAAAT-T-G-----T--AAATTGTTAAAA-A-CATTAAAATT-TGTA
28445117 AAAAATTGTAAATTGTTAAAAACATTAAAAATTTGTA
1 AAAAATTGTAAATTGTTAAAAACATT-AAAATTTGTA
28445154 AAAAAT
1 AAAAAT
28445160 ATAGAAAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 29
0.66 0.06 0.28
Matches are distributed among these distances:
35 3 0.04
36 14 0.21
37 18 0.26
38 1 0.01
39 1 0.01
43 1 0.01
44 1 0.01
45 12 0.18
46 7 0.10
47 9 0.13
48 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (36 bp):
AAAAATTGTAAATTGTTAAAAACATTAAAATTTGTA
Found at i:28445101 original size:82 final size:83
Alignment explanation
Indices: 28445001--28445169 Score: 331
Period size: 82 Copynumber: 2.0 Consensus size: 83
28444991 TACATTGATT
28445001 AAATAAAAATTATTAAAATATTATAAAAATTATTAAAAATTGTAAATTGTTAAAAACATT-AAAA
1 AAATAAAAATTATTAAAATATTATAAAAATTATTAAAAATTGTAAATTGTTAAAAACATTAAAAA
28445065 TTTGTAAAAAATATAGAA
66 TTTGTAAAAAATATAGAA
28445083 AAATAAAAATTATTAAAATATTATAAAAATTATTAAAAATTGTAAATTGTTAAAAACATTAAAAA
1 AAATAAAAATTATTAAAATATTATAAAAATTATTAAAAATTGTAAATTGTTAAAAACATTAAAAA
28445148 TTTGTAAAAAATATAGAA
66 TTTGTAAAAAATATAGAA
28445166 AAAT
1 AAAT
28445170 TGCAAAATTT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 60 0.70
83 26 0.30
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (83 bp):
AAATAAAAATTATTAAAATATTATAAAAATTATTAAAAATTGTAAATTGTTAAAAACATTAAAAA
TTTGTAAAAAATATAGAA
Found at i:28445121 original size:10 final size:10
Alignment explanation
Indices: 28445004--28445123 Score: 84
Period size: 10 Copynumber: 12.8 Consensus size: 10
28444994 ATTGATTAAA
28445004 TAAAAATTAT
1 TAAAAATTAT
28445014 TAAAATATTA-
1 TAAAA-ATTAT
28445024 TAAAAATTAT
1 TAAAAATTAT
*
28445034 TAAAAATT-G
1 TAAAAATTAT
*
28445043 T--AAATTGT
1 TAAAAATTAT
*
28445051 TAAAAA-CAT
1 TAAAAATTAT
28445060 T-AAAATT-T
1 TAAAAATTAT
*
28445068 GTAAAAAATA-
1 -TAAAAATTAT
28445078 TAGAAAA--A-
1 TA-AAAATTAT
28445086 TAAAAATTAT
1 TAAAAATTAT
28445096 TAAAATATTA-
1 TAAAA-ATTAT
28445106 TAAAAATTAT
1 TAAAAATTAT
28445116 TAAAAATT
1 TAAAAATT
28445124 GTAAATTGTT
Statistics
Matches: 89, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
7 9 0.10
8 9 0.10
9 15 0.17
10 48 0.54
11 8 0.09
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:28445136 original size:27 final size:27
Alignment explanation
Indices: 28445022--28445155 Score: 107
Period size: 26 Copynumber: 4.9 Consensus size: 27
28445012 ATTAAAATAT
*
28445022 TATAAAAATTATTAAAAATTGTAAATTG
1 TATAAAAA-CATTAAAAATTGTAAATTG
* ***
28445050 T-TAAAAACATTAAAATTTGTAAAAAA
1 TATAAAAACATTAAAAATTGTAAATTG
*
28445076 TATAGAAAA-A-TAAAAATTATTAAAATAT-
1 TATA-AAAACATTAAAAATT-GT-AAAT-TG
*
28445104 TATAAAAATTATTAAAAATTGTAAATTG
1 TATAAAAA-CATTAAAAATTGTAAATTG
28445132 T-TAAAAACATTAAAAATTTGTAAA
1 TATAAAAACATTAAAAA-TTGTAAA
28445156 AAATATAGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
26 30 0.35
27 28 0.33
28 17 0.20
29 2 0.02
30 8 0.09
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.35
Consensus pattern (27 bp):
TATAAAAACATTAAAAATTGTAAATTG
Found at i:28447533 original size:16 final size:15
Alignment explanation
Indices: 28447510--28447539 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28447500 ATATATTTAC
28447510 AAAAAAATGATGTTA
1 AAAAAAATGATGTTA
28447525 AAAATAAATGATGTT
1 AAAA-AAATGATGTT
28447540 TTGGTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
AAAAAAATGATGTTA
Found at i:28459972 original size:124 final size:125
Alignment explanation
Indices: 28459752--28460001 Score: 493
Period size: 124 Copynumber: 2.0 Consensus size: 125
28459742 TGGGGAGGGT
28459752 AAAACAGAAACGATTAGCTAATCCTTACTTTTGAAACGGAATGACTAATCGTTGTTGAAGCAGAG
1 AAAACAGAAACGATTAGCTAATCCTTACTTTTGAAACGGAATGACTAATCGTTGTTGAAGCAGAG
28459817 AAAATGAGGAATACATCCGTCTTGTAATAGGCCTGTAATAGGCAATACAT-AAACCAAAC
66 AAAATGAGGAATACATCCGTCTTGTAATAGGCCTGTAATAGGCAATACATCAAACCAAAC
28459876 AAAACAGAAACGATTAGCTAATCCTTACTTTTGAAACGGAATGACTAATCGTTGTTGAAGCAGAG
1 AAAACAGAAACGATTAGCTAATCCTTACTTTTGAAACGGAATGACTAATCGTTGTTGAAGCAGAG
28459941 AAAATGAGGAATACATCCGTCTTGTAATAGGCCTGTAATAGGCAATACATCAAACCAAAC
66 AAAATGAGGAATACATCCGTCTTGTAATAGGCCTGTAATAGGCAATACATCAAACCAAAC
28460001 A
1 A
28460002 CGGGATTAAG
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
124 115 0.92
125 10 0.08
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Consensus pattern (125 bp):
AAAACAGAAACGATTAGCTAATCCTTACTTTTGAAACGGAATGACTAATCGTTGTTGAAGCAGAG
AAAATGAGGAATACATCCGTCTTGTAATAGGCCTGTAATAGGCAATACATCAAACCAAAC
Found at i:28460488 original size:68 final size:68
Alignment explanation
Indices: 28460374--28460507 Score: 259
Period size: 68 Copynumber: 2.0 Consensus size: 68
28460364 TTGCAGCATG
*
28460374 AAGGTTTGAAGTTCTTCAAACCTTTCTTGGTAGTCCTCAATTGTTCCCTTCTGTGCTTCTTTATT
1 AAGGCTTGAAGTTCTTCAAACCTTTCTTGGTAGTCCTCAATTGTTCCCTTCTGTGCTTCTTTATT
28460439 GCA
66 GCA
28460442 AAGGCTTGAAGTTCTTCAAACCTTTCTTGGTAGTCCTCAATTGTTCCCTTCTGTGCTTCTTTATT
1 AAGGCTTGAAGTTCTTCAAACCTTTCTTGGTAGTCCTCAATTGTTCCCTTCTGTGCTTCTTTATT
28460507 G
66 G
28460508 AATTCTTCCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (68 bp):
AAGGCTTGAAGTTCTTCAAACCTTTCTTGGTAGTCCTCAATTGTTCCCTTCTGTGCTTCTTTATT
GCA
Found at i:28461593 original size:12 final size:12
Alignment explanation
Indices: 28461576--28461610 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
28461566 AGTTGTGTTT
*
28461576 GGCCCAACATCA
1 GGCCCATCATCA
28461588 GGCCCATCATCA
1 GGCCCATCATCA
28461600 GGCCCATCATC
1 GGCCCATCATC
28461611 CTTTAGTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.14
Consensus pattern (12 bp):
GGCCCATCATCA
Found at i:28468943 original size:21 final size:21
Alignment explanation
Indices: 28468917--28468964 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
28468907 ATATGTGAAG
28468917 TTTCTAGACCAGAAGTCCAAA
1 TTTCTAGACCAGAAGTCCAAA
** *
28468938 TTTCTAGATTAGAAGTCCGAA
1 TTTCTAGACCAGAAGTCCAAA
28468959 TTTCTA
1 TTTCTA
28468965 AATGTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (21 bp):
TTTCTAGACCAGAAGTCCAAA
Found at i:28477794 original size:2 final size:2
Alignment explanation
Indices: 28477789--28477821 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28477779 GAGAACTTCC
28477789 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
28477822 GCGTGGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:28479355 original size:50 final size:50
Alignment explanation
Indices: 28479291--28479388 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
28479281 TAGTAGATTA
28479291 GTTGAATATATATTCTACTTTATTTTTTTAGTAGATTAGTTGGATCTTCT
1 GTTGAATATATATTCTACTTTATTTTTTTAGTAGATTAGTTGGATCTTCT
*
28479341 GTTGCATATATATTCTACTTTATTTTTTTAGTAGATTAGTTGGATCTT
1 GTTGAATATATATTCTACTTTATTTTTTTAGTAGATTAGTTGGATCTT
28479389 TCATATTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.54
Consensus pattern (50 bp):
GTTGAATATATATTCTACTTTATTTTTTTAGTAGATTAGTTGGATCTTCT
Found at i:28482507 original size:26 final size:25
Alignment explanation
Indices: 28482470--28482531 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 25
28482460 TATAAGGACT
*
28482470 TATGAAATATTTTAACTTAGTATAAAA
1 TATGAAATATTTGAA-TTA-TATAAAA
28482497 TATG-AATATTTGAATTATAT-AAA
1 TATGAAATATTTGAATTATATAAAA
*
28482520 TAT-ACATATTTG
1 TATGAAATATTTG
28482532 TTTAAGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 13 0.41
24 3 0.09
25 3 0.09
26 9 0.28
27 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (25 bp):
TATGAAATATTTGAATTATATAAAA
Found at i:28483723 original size:27 final size:27
Alignment explanation
Indices: 28483693--28483746 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
28483683 GTGTTTCTAC
28483693 TGATTTAGGTTAGGCATTTTTTTTTTT
1 TGATTTAGGTTAGGCATTTTTTTTTTT
28483720 TGATTTAGGTTAGGCATTTTTTTTTTT
1 TGATTTAGGTTAGGCATTTTTTTTTTT
28483747 ACGGGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.19, T:0.63
Consensus pattern (27 bp):
TGATTTAGGTTAGGCATTTTTTTTTTT
Found at i:28505769 original size:22 final size:23
Alignment explanation
Indices: 28505726--28505776 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
28505716 AAATCCATAG
*
28505726 AATTAAAAAATAAAAAACGAATC
1 AATTCAAAAATAAAAAACGAATC
*
28505749 AATTCAAAAATAATAAA-GAATC
1 AATTCAAAAATAAAAAACGAATC
28505771 AATTCA
1 AATTCA
28505777 TTCTCAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.22
Consensus pattern (23 bp):
AATTCAAAAATAAAAAACGAATC
Found at i:28510257 original size:30 final size:29
Alignment explanation
Indices: 28510208--28510273 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
28510198 ACAGTTGGAT
* *
28510208 CTAAATTTTGAAATCTGAAAAGTA-AAGGGA
1 CTAAATTTTGAAATATG-AAACTACAA-GGA
28510238 CTAAATTTCTGAAA-ATGAAACTACAAGGA
1 CTAAATTT-TGAAATATGAAACTACAAGGA
28510267 CTAAATT
1 CTAAATT
28510274 CCAAATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 15 0.47
30 12 0.38
31 5 0.16
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (29 bp):
CTAAATTTTGAAATATGAAACTACAAGGA
Found at i:28513771 original size:46 final size:46
Alignment explanation
Indices: 28513719--28513995 Score: 509
Period size: 46 Copynumber: 6.0 Consensus size: 46
28513709 ACATTGCTAT
* *
28513719 AACTCAGTATGGTTTTCTTCCTTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
*
28513765 AACTCAGTATGGTTTTCTTCCTTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
28513811 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
28513857 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
28513903 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
**
28513949 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
28513995 A
1 A
28513996 CTTTGCCATG
Statistics
Matches: 227, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 227 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:28521613 original size:15 final size:16
Alignment explanation
Indices: 28521593--28521653 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
28521583 GGCAGCTTTG
28521593 GGTTTGG-TTTTTTTA
1 GGTTTGGATTTTTTTA
*
28521608 GGTTTGGAATTTTTTA
1 GGTTTGGATTTTTTTA
* *
28521624 AGTTTAGG-TCTTTTT-
1 GGTTT-GGATTTTTTTA
28521639 GAGTTTGGATTTTTT
1 G-GTTTGGATTTTTT
28521654 GAAATTTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
15 9 0.25
16 25 0.69
17 2 0.06
ACGTcount: A:0.13, C:0.02, G:0.25, T:0.61
Consensus pattern (16 bp):
GGTTTGGATTTTTTTA
Found at i:28521654 original size:15 final size:14
Alignment explanation
Indices: 28521589--28521655 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
28521579 TCGAGGCAGC
*
28521589 TTTGGGTTTGGTTT
1 TTTGAGTTTGGTTT
*
28521603 TTTTAGGTTTGGAATTT
1 TTTGA-GTTTGG--TTT
*
28521620 TTTAAGTTTAGGTCTT
1 TTTGAGTTT-GGT-TT
28521636 TTTGAGTTTGGATTT
1 TTTGAGTTTGG-TTT
28521651 TTTGA
1 TTTGA
28521656 AATTTGAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
14 3 0.07
15 16 0.37
16 15 0.35
17 9 0.21
ACGTcount: A:0.13, C:0.01, G:0.25, T:0.60
Consensus pattern (14 bp):
TTTGAGTTTGGTTT
Found at i:28522390 original size:25 final size:25
Alignment explanation
Indices: 28522338--28522391 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
28522328 AAATATTTTC
** *
28522338 TAAAATTAAATATTTTAATTAATGA
1 TAAAATTAAATATAATAATTAATAA
*
28522363 TAAAATTAAATATAATAATTACTAA
1 TAAAATTAAATATAATAATTAATAA
28522388 TAAA
1 TAAA
28522392 TGTAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
TAAAATTAAATATAATAATTAATAA
Found at i:28525289 original size:20 final size:20
Alignment explanation
Indices: 28525264--28525304 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28525254 ACTTGTCTCT
28525264 TTGTCTTAATATATATGTAA
1 TTGTCTTAATATATATGTAA
28525284 TTGTCTTAATATATATGTAA
1 TTGTCTTAATATATATGTAA
28525304 T
1 T
28525305 AGAAAGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
TTGTCTTAATATATATGTAA
Found at i:28535292 original size:83 final size:82
Alignment explanation
Indices: 28535153--28535328 Score: 239
Period size: 83 Copynumber: 2.1 Consensus size: 82
28535143 CCTTGGCCCT
* * *
28535153 AAAAATGAAAAATTGCTATTTCAATCCCCTAATCAATAATAAAATTATAAATTAATATATGGTGA
1 AAAAATAAAAAATTACTATTTCAATCCCCTAATAAATAATAAAATTATAAATTAATATATGGTGA
*
28535218 AATTTCACTTTGACCACC
66 AATTGCACTTTGACC-CC
* * * *
28535236 AAAAATAAAAAATTACTATTTTAGA-CCCCTCATAAATAATGAAATTGTAAATTAATATATGGTG
1 AAAAATAAAAAATTACTATTTCA-ATCCCCTAATAAATAATAAAATTATAAATTAATATATGGTG
*
28535300 AAATTGCACTTTGACCTC
65 AAATTGCACTTTGACCCC
28535318 -AAAATAAAAAA
1 AAAAATAAAAAA
28535329 AATATTTTTA
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
81 11 0.13
82 1 0.01
83 70 0.84
84 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (82 bp):
AAAAATAAAAAATTACTATTTCAATCCCCTAATAAATAATAAAATTATAAATTAATATATGGTGA
AATTGCACTTTGACCCC
Found at i:28539019 original size:31 final size:29
Alignment explanation
Indices: 28538977--28539042 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
28538967 TACACTACTA
28538977 GTCACCCAATTATCAGTAAATT-TCTTTTTTG
1 GTCACCCAATTAT---TAAATTGTCTTTTTTG
* *
28539008 GTCACCTAATTATTCAATTGTCTTTTTTG
1 GTCACCCAATTATTAAATTGTCTTTTTTG
28539037 GTCACC
1 GTCACC
28539043 AGAGGGCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 15 0.47
31 12 0.38
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (29 bp):
GTCACCCAATTATTAAATTGTCTTTTTTG
Found at i:28539197 original size:14 final size:14
Alignment explanation
Indices: 28539174--28539211 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28539164 GTAATTTGGT
28539174 CTCTCTCTCTCCCC
1 CTCTCTCTCTCCCC
* *
28539188 CTCTCCCTCTCCCT
1 CTCTCTCTCTCCCC
28539202 CTCTCTCTCT
1 CTCTCTCTCT
28539212 GTTTGGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCTCTCTCTCCCC
Found at i:28539201 original size:12 final size:12
Alignment explanation
Indices: 28539176--28539210 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28539166 AATTTGGTCT
*
28539176 CTCTCTCTCCCC
1 CTCTCTCTCTCC
*
28539188 CTCTCCCTCTCC
1 CTCTCTCTCTCC
28539200 CTCTCTCTCTC
1 CTCTCTCTCTC
28539211 TGTTTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:28552363 original size:202 final size:202
Alignment explanation
Indices: 28552017--28552409 Score: 642
Period size: 202 Copynumber: 1.9 Consensus size: 202
28552007 TAAACAAAGA
* *
28552017 ACAAAATTCTGTAACATCCCAAATCTAGCCTAGACGTCATAGCCAGATGCTGAAGGTTACATTGG
1 ACAAAATTCTGTAACACCCCAAACCTAGCCTAGACGTCATAGCCAGATGCTGAAGGTTACATTGG
* * * *
28552082 TTACCGAAATGGCAAAGTGAAATATTCAGATTCTTTTAAAACTCCTATTCTAAATAATATTAGAA
66 TCACCGAAATGGCAAAGTGAAACATCCAAATTCTTTTAAAACTCCTATTCTAAATAATATTAGAA
*
28552147 AAACTTGTGCATTTTACTTAGTTTAAATAAAACATCTTATCAAGCCGGCCAAGGATTATTAGACG
131 AAACTTGTGCATTTTACTTAGTTTAAATAAAACATCTTATCAAGCCGGCCAAGAATTATTAGACG
28552212 ACAAAAT
196 ACAAAAT
* * *
28552219 ACAAAATTCTTTAACACCCCAAACCTGGCCTAGACGTTATAGCCAGATGCTGAAGGTTACATTGG
1 ACAAAATTCTGTAACACCCCAAACCTAGCCTAGACGTCATAGCCAGATGCTGAAGGTTACATTGG
* * * *
28552284 TCACTGAAATGGCAAAGTGAAACGTCCAAATTCTTTTAAAACTCCTATTCTAACTAATTTTAGAA
66 TCACCGAAATGGCAAAGTGAAACATCCAAATTCTTTTAAAACTCCTATTCTAAATAATATTAGAA
* *
28552349 AAACTTGTGCATTTTCCTTAGTTTAAATAAAACATCTTATCAAGTCGGCCAAGAATTATTA
131 AAACTTGTGCATTTTACTTAGTTTAAATAAAACATCTTATCAAGCCGGCCAAGAATTATTA
28552410 CGCAACGTGA
Statistics
Matches: 175, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
202 175 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (202 bp):
ACAAAATTCTGTAACACCCCAAACCTAGCCTAGACGTCATAGCCAGATGCTGAAGGTTACATTGG
TCACCGAAATGGCAAAGTGAAACATCCAAATTCTTTTAAAACTCCTATTCTAAATAATATTAGAA
AAACTTGTGCATTTTACTTAGTTTAAATAAAACATCTTATCAAGCCGGCCAAGAATTATTAGACG
ACAAAAT
Found at i:28559399 original size:13 final size:14
Alignment explanation
Indices: 28559368--28559400 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28559358 AGACTTAAAG
*
28559368 GAAAAAGTTGCGAT
1 GAAAAAGTTACGAT
28559382 GAAAAAGTTACGAT
1 GAAAAAGTTACGAT
28559396 -AAAAA
1 GAAAAA
28559401 CAGTGAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (14 bp):
GAAAAAGTTACGAT
Found at i:28581261 original size:11 final size:11
Alignment explanation
Indices: 28581245--28581274 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28581235 TGTAGCCCAT
28581245 TTTTTGTTTTA
1 TTTTTGTTTTA
28581256 TTTTTGTTTTA
1 TTTTTGTTTTA
*
28581267 TGTTTGTT
1 TTTTTGTT
28581275 GACAGTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.13, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:28583644 original size:31 final size:31
Alignment explanation
Indices: 28583609--28583667 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28583599 ATTAAAATTA
* * *
28583609 AGAAAAATTGTTAATTTTTAGGATTAATATG
1 AGAAAAATTGTTAAGTTTAAAGATTAATATG
*
28583640 AGAAAAGTTGTTAAGTTTAAAGATTAAT
1 AGAAAAATTGTTAAGTTTAAAGATTAAT
28583668 GTAGATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (31 bp):
AGAAAAATTGTTAAGTTTAAAGATTAATATG
Found at i:28606042 original size:20 final size:20
Alignment explanation
Indices: 28606017--28606057 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28606007 TTTCCGTTTA
*
28606017 CTCCATCTAATGTTTAACCT
1 CTCCATCTAATATTTAACCT
28606037 CTCCATCTAATATTTAACCT
1 CTCCATCTAATATTTAACCT
28606057 C
1 C
28606058 AATGAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (20 bp):
CTCCATCTAATATTTAACCT
Found at i:28608875 original size:71 final size:72
Alignment explanation
Indices: 28608796--28608940 Score: 283
Period size: 71 Copynumber: 2.0 Consensus size: 72
28608786 ATTACTTTTA
28608796 AAAATATAATTTTAAATGCCACAGAAATAAATATAATATCAATTATTTAATAAATATATGT-AAC
1 AAAATATAATTTTAAATGCCACAGAAATAAATATAATATCAATTATTTAATAAATATATGTAAAC
28608860 CAATAAT
66 CAATAAT
28608867 AAAATATAATTTTAAATGCCACAGAAATAAATATAATATCAATTATTTAATAAATATATGTAAAC
1 AAAATATAATTTTAAATGCCACAGAAATAAATATAATATCAATTATTTAATAAATATATGTAAAC
28608932 CAATAAT
66 CAATAAT
28608939 AA
1 AA
28608941 CCCCCATTTA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 61 0.84
72 12 0.16
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (72 bp):
AAAATATAATTTTAAATGCCACAGAAATAAATATAATATCAATTATTTAATAAATATATGTAAAC
CAATAAT
Found at i:28610379 original size:24 final size:23
Alignment explanation
Indices: 28610351--28610405 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
28610341 TGATTTATAA
*
28610351 ATTTATTTCAACCTCATATATATTT
1 ATTTATTTCAACATCATA-AT-TTT
*
28610376 -TTTATCATCAACATCATAATTTT
1 ATTTAT-TTCAACATCATAATTTT
28610399 ATTTATT
1 ATTTATT
28610406 AATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
23 3 0.12
24 12 0.48
25 10 0.40
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATTTCAACATCATAATTTT
Found at i:28610460 original size:76 final size:77
Alignment explanation
Indices: 28610374--28610527 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 77
28610364 TCATATATAT
28610374 TTTTTATCATCAACATCATAATTTTATTTATTAATATATAAATTGTAATGAAAATAAAAAAAATT
1 TTTTTATCATCAACATCATAATTTTATTTATTAATATATAAATTGTAATGAAAATAAAAAAAATT
28610439 AT-ATCATTTTA
66 ATCATCATTTTA
28610450 TTTTTATCATCAACATCATAATTTTATTTATTAATATATAAATTGTAATGAAAATAAAAAAAATT
1 TTTTTATCATCAACATCATAATTTTATTTATTAATATATAAATTGTAATGAAAATAAAAAAAATT
28610515 ATCATCATTTTA
66 ATCATCATTTTA
28610527 T
1 T
28610528 GAAAATTAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 67 0.87
77 10 0.13
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (77 bp):
TTTTTATCATCAACATCATAATTTTATTTATTAATATATAAATTGTAATGAAAATAAAAAAAATT
ATCATCATTTTA
Found at i:28614511 original size:87 final size:89
Alignment explanation
Indices: 28614420--28614622 Score: 268
Period size: 87 Copynumber: 2.3 Consensus size: 89
28614410 AATTTTTTTT
* * * *
28614420 AAAAAGTAATTAAGCCCATGCTTTTTTTTTTGCACTCATTTGAGCACTTGAACTTTTAAAATTCA
1 AAAAAGCAATTAAGCCCATGCTTTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
*
28614485 TCAAAAAGT-CCCTCAAACTTAAAA
66 TCAAAAA-TACCCTCAAACTTTAAA
* * * *
28614509 AAAAAGCAATTAAGCCCCTAC--TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCA
1 AAAAAGCAATTAAGCCCATGCTTTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
*
28614572 TCAAAAATACCCTCAAACTTTTTCAA
66 TCAAAAATACCCTCAAAC--TTTAAA
28614598 AAAAAGCAATTAAGCCCATGCTTTT
1 AAAAAGCAATTAAGCCCATGCTTTT
28614623 ATTAAAAATT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
86 1 0.01
87 53 0.55
89 41 0.42
91 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (89 bp):
AAAAAGCAATTAAGCCCATGCTTTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
TCAAAAATACCCTCAAACTTTAAA
Found at i:28615046 original size:26 final size:26
Alignment explanation
Indices: 28615008--28615067 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
28614998 TTTTTATAAA
*
28615008 AAAATTGTAATTTTTAA-TAAATTTT
1 AAAATTTTAATTTTTAATTAAATTTT
28615033 AAAATTTTATATTTTTAATTAAATTTT
1 AAAATTTTA-ATTTTTAATTAAATTTT
*
28615060 AATATTTT
1 AAAATTTT
28615068 TTCTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 8 0.26
26 8 0.26
27 15 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
AAAATTTTAATTTTTAATTAAATTTT
Found at i:28615058 original size:38 final size:37
Alignment explanation
Indices: 28615015--28615102 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 37
28615005 AAAAAAATTG
*
28615015 TAATTTTTAATAAATTT-TAAAATTTTATATTTTTAA
1 TAATTTTTAATAAATTTCTAAAATTTAATATTTTTAA
* ** *
28615051 TTAAATTTTAATATTTTTTCTAAAATTTAATATTTTTTA
1 -TAATTTTTAATA-AATTTCTAAAATTTAATATTTTTAA
28615090 TAATTTTTAATAA
1 TAATTTTTAATAA
28615103 GAGCAGGGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
37 11 0.26
38 14 0.33
39 17 0.40
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (37 bp):
TAATTTTTAATAAATTTCTAAAATTTAATATTTTTAA
Found at i:28615098 original size:19 final size:19
Alignment explanation
Indices: 28615019--28615101 Score: 89
Period size: 19 Copynumber: 4.4 Consensus size: 19
28615009 AAATTGTAAT
**
28615019 TTTTAATAAATTTTA-AAA
1 TTTTAATATTTTTTATAAA
*
28615037 TTTT-ATATTTTTAATTAAA
1 TTTTAATATTTTTTA-TAAA
*
28615056 TTTTAATATTTTTTCTAAA
1 TTTTAATATTTTTTATAAA
* *
28615075 ATTTAATATTTTTTATAAT
1 TTTTAATATTTTTTATAAA
28615094 TTTTAATA
1 TTTTAATA
28615102 AGAGCAGGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
17 7 0.13
18 4 0.08
19 34 0.64
20 8 0.15
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATATTTTTTATAAA
Found at i:28616512 original size:21 final size:21
Alignment explanation
Indices: 28616487--28616526 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28616477 TCCTTCCATC
28616487 GTTCTTGCTAGTTTCTCCCTT
1 GTTCTTGCTAGTTTCTCCCTT
*
28616508 GTTCTTGCTGGTTTCTCCC
1 GTTCTTGCTAGTTTCTCCC
28616527 CTCATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.30, G:0.17, T:0.50
Consensus pattern (21 bp):
GTTCTTGCTAGTTTCTCCCTT
Found at i:28618629 original size:31 final size:31
Alignment explanation
Indices: 28618577--28618658 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
28618567 GGTGGAAGAA
28618577 ATTTTAAAAATAAAAAA-ATATAGGTAGTGT
1 ATTTTAAAAATAAAAAATATATAGGTAGTGT
*
28618607 ATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATAGGTAGTGT
28618638 ATTTTAAAAATAAAAAATATA
1 ATTTTAAAAATAAAAAATATA
28618659 GTTTATATTC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 17 0.34
31 33 0.66
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (31 bp):
ATTTTAAAAATAAAAAATATATAGGTAGTGT
Found at i:28619024 original size:39 final size:39
Alignment explanation
Indices: 28618981--28619061 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
28618971 ACTAAAGTGA
28618981 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
1 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
*
28619020 AAAGAAAACAATAGTTTAAGTAAAGCTTTAAAGATGAAC
1 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
28619059 AAA
1 AAA
28619062 TCGATTGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.21
Consensus pattern (39 bp):
AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
Found at i:28620242 original size:3 final size:3
Alignment explanation
Indices: 28620236--28620367 Score: 210
Period size: 3 Copynumber: 44.0 Consensus size: 3
28620226 TAATTACTTA
28620236 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28620284 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
28620332 ATT ATT AAT GTT ACT ATA ACT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28620368 TATATTAGTT
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28625422 original size:13 final size:14
Alignment explanation
Indices: 28625406--28625434 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28625396 CCAATTTTTT
28625406 TTAT-TTTTTAATA
1 TTATGTTTTTAATA
28625419 TTATGTTTTTAATA
1 TTATGTTTTTAATA
28625433 TT
1 TT
28625435 GAGAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTATGTTTTTAATA
Found at i:28635702 original size:3 final size:3
Alignment explanation
Indices: 28635694--28635725 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28635684 CCAGGTAGAT
28635694 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
28635726 TACTTTCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:28635958 original size:17 final size:16
Alignment explanation
Indices: 28635936--28635967 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28635926 GCTTCAACTG
28635936 TTTCTTTTTCTTTTTTT
1 TTTCTTTTT-TTTTTTT
28635953 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
28635968 GTGGAATCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:28635967 original size:12 final size:11
Alignment explanation
Indices: 28635940--28635966 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28635930 CAACTGTTTC
28635940 TTTTTCTTTTT
1 TTTTTCTTTTT
28635951 TTTTTCTTTTT
1 TTTTTCTTTTT
28635962 TTTTT
1 TTTTT
28635967 TGTGGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:28637343 original size:6 final size:6
Alignment explanation
Indices: 28637332--28637358 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28637322 TTTTAGGTGC
28637332 TTGGGG TTGGGG TTGGGG TTGGGG TTG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTG
28637359 TTAATAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.63, T:0.37
Consensus pattern (6 bp):
TTGGGG
Found at i:28640337 original size:16 final size:15
Alignment explanation
Indices: 28640311--28640340 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28640301 TACGTATGTG
28640311 TATATGTATATAAAT
1 TATATGTATATAAAT
28640326 TATATAGTATATAAA
1 TATAT-GTATATAAA
28640341 AATGTAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TATATGTATATAAAT
Found at i:28640427 original size:19 final size:19
Alignment explanation
Indices: 28640403--28640439 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28640393 TAAATGAACA
28640403 AATAATAACAATAATAATT
1 AATAATAACAATAATAATT
*
28640422 AATAATAACAGTAATAAT
1 AATAATAACAATAATAAT
28640440 ATCAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAATAACAATAATAATT
Found at i:28644919 original size:51 final size:51
Alignment explanation
Indices: 28644864--28645031 Score: 164
Period size: 51 Copynumber: 3.3 Consensus size: 51
28644854 AATTTTTAAT
*
28644864 TTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATA
1 TTTTAAATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATA
** * * * * * * * *
28644915 TTTTAAAATTTTTTATATTTTAAACAAAATAAACAAATATT-A-TT-TTTAAT-
1 TTTT-AAATTTTTT-TA-TCAAAATAGAACAAATAACTTTTAAGTTATGTCATA
*
28644965 TTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATA
1 TTTTAAATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATA
*
28645016 TTTTAAAATTTTTTAT
1 TTTTAAATTTTTTTAT
28645032 ATTTTAAACA
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
47 15 0.17
48 3 0.03
49 10 0.12
50 8 0.09
51 22 0.26
52 10 0.12
53 3 0.03
54 15 0.17
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (51 bp):
TTTTAAATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATA
Found at i:28644996 original size:101 final size:102
Alignment explanation
Indices: 28644855--28645079 Score: 409
Period size: 101 Copynumber: 2.2 Consensus size: 102
28644845 ATATGTCATA
28644855 ATTTTTAATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTA
1 ATTTTTAATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTA
28644920 AAATTTTTTATATTTTAAACAAAATA-AACAAATATT
66 AAATTTTTTATATTTTAAACAAAATACAACAAATATT
28644956 ATTTTTAATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTA
1 ATTTTTAATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTA
28645021 AAATTTTTTATATTTTAAACAAAATACAACAAATATT
66 AAATTTTTTATATTTTAAACAAAATACAACAAATATT
*
28645058 -TTTTAAATTTTATTATATTTTT
1 ATTTTTAA-TTT-TTATATTTTT
28645080 AATGATATCA
Statistics
Matches: 120, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
101 97 0.81
102 13 0.11
103 10 0.08
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (102 bp):
ATTTTTAATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTA
AAATTTTTTATATTTTAAACAAAATACAACAAATATT
Found at i:28645076 original size:59 final size:60
Alignment explanation
Indices: 28644962--28645078 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 60
28644952 TATTATTTTT
* * * * * *
28644962 AATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTAA
1 AATTTTTATATATTTTAAACAAAATACAACAAATAACTTTTAAATTATATCATATTTTAA
** * *
28645022 AATTTTT-TATATTTTAAACAAAATACAACAAATATTTTTTAAATTTTATTATATTTT
1 AATTTTTATATATTTTAAACAAAATACAACAAATAACTTTTAAATTATATCATATTTT
28645079 TAATGATATC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 40 0.85
60 7 0.15
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (60 bp):
AATTTTTATATATTTTAAACAAAATACAACAAATAACTTTTAAATTATATCATATTTTAA
Found at i:28647099 original size:59 final size:60
Alignment explanation
Indices: 28646985--28647101 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 60
28646975 CATAATTTTT
* * * * * *
28646985 AATTTTTATATTTTTTTATCAAAATAGAACAAATAACTTTTAAGTTATGTCATATTTTAA
1 AATTTTTATATATTTTAAACAAAATACAACAAATAACTTTTAAATTATATCATATTTTAA
** * *
28647045 AATTTTT-TATATTTTAAACAAAATACAACAAATATTTTTTAAATTTTATTATATTTT
1 AATTTTTATATATTTTAAACAAAATACAACAAATAACTTTTAAATTATATCATATTTT
28647102 TAATGATATC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 40 0.85
60 7 0.15
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (60 bp):
AATTTTTATATATTTTAAACAAAATACAACAAATAACTTTTAAATTATATCATATTTTAA
Found at i:28649420 original size:29 final size:28
Alignment explanation
Indices: 28649371--28649443 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 28
28649361 TATTAAAATT
*
28649371 ATACAT-AAATTTAA--TGTGCAATGTA
1 ATACATGAAATTTAATTTATGCAATGTA
* * * *
28649396 ATTCATGAATTTTAACTTTATGCAATTTT
1 ATACATGAAATTTAA-TTTATGCAATGTA
28649425 ATACATGAAATTTAATTTA
1 ATACATGAAATTTAATTTA
28649444 ATTTAATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 5 0.14
26 7 0.19
28 4 0.11
29 21 0.57
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (28 bp):
ATACATGAAATTTAATTTATGCAATGTA
Found at i:28655529 original size:22 final size:20
Alignment explanation
Indices: 28655501--28655540 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28655491 TTTACTCATT
28655501 ATTTATTTATATATATATTTAA
1 ATTTA-TTAT-TATATATTTAA
28655523 ATTTATTATTATATATTT
1 ATTTATTATTATATATTT
28655541 TGGAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATTATTATATATTTAA
Found at i:28655553 original size:22 final size:20
Alignment explanation
Indices: 28655504--28655563 Score: 50
Period size: 23 Copynumber: 2.8 Consensus size: 20
28655494 ACTCATTATT
28655504 TATTTA-TATATATATTTAAA
1 TATTTATTATATAT-TTTAAA
*
28655524 TTTATTATTATATATTTTGGAAA
1 TAT-TTATTATATATTTT--AAA
*
28655547 TATTTATGTATTTATTT
1 TATTTAT-TATATATTT
28655564 AATTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.06
21 6 0.19
22 11 0.34
23 13 0.41
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TATTTATTATATATTTTAAA
Found at i:28659949 original size:37 final size:39
Alignment explanation
Indices: 28659875--28659958 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 39
28659865 TTACATCCTT
*
28659875 TTGTTGAAACCTTAGTCTAAGAAAACTTATCAACCTTCA
1 TTGTTGAAACCTTAGTCTAAGAAAACCTATCAACCTTCA
* **
28659914 TTGTTGAAACCTTAG-CTCA-AAAACCTATCTTCCTTCA
1 TTGTTGAAACCTTAGTCTAAGAAAACCTATCAACCTTCA
*
28659951 TTGCTGAA
1 TTGTTGAA
28659959 TATCACCTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 22 0.55
38 3 0.08
39 15 0.38
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (39 bp):
TTGTTGAAACCTTAGTCTAAGAAAACCTATCAACCTTCA
Found at i:28660428 original size:18 final size:18
Alignment explanation
Indices: 28660401--28660451 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
28660391 AATTGTTCCA
*
28660401 GATTTGTAGGGATAGACT
1 GATTTCTAGGGATAGACT
*
28660419 GATTTCTAGGGATAAACT
1 GATTTCTAGGGATAGACT
* *
28660437 GATTTTTTGGGATAG
1 GATTTCTAGGGATAG
28660452 GATCCTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.37
Consensus pattern (18 bp):
GATTTCTAGGGATAGACT
Found at i:28665334 original size:16 final size:16
Alignment explanation
Indices: 28665283--28665334 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28665273 TGTGTATTAA
*
28665283 TAATGTATAAACTAAT
1 TAATTTATAAACTAAT
* *
28665299 TACTTCTATCAAA-GAAT
1 TAATT-TAT-AAACTAAT
28665316 TAATTTATAAACTAAT
1 TAATTTATAAACTAAT
28665332 TAA
1 TAA
28665335 GTCTACTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 3 0.11
16 12 0.43
17 10 0.36
18 3 0.11
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (16 bp):
TAATTTATAAACTAAT
Found at i:28667714 original size:181 final size:181
Alignment explanation
Indices: 28667410--28667946 Score: 966
Period size: 181 Copynumber: 3.0 Consensus size: 181
28667400 GACTCACCTA
*
28667410 ATTCTTATCCACTGCAGTTTTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
1 ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
*
28667475 CTCAATTGCTGACAATCTTATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
66 CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
*
28667540 TAGATTTACTCATTCAAAACTTAACATGCAAAGCTGGAACACTTATTACTC
131 TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
* *
28667591 ATTCTTATCCACTACAATTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
1 ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
*
28667656 CTCAATTGCTGACAATCTCATGCAAAAACTTTATACTCGTAGTCTTACTGTTCAGATACCATACA
66 CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
*
28667721 TAGATTTGCTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
131 TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
*
28667772 ATTCTTATCCACTGCAGTTCTAGGCTCCATTATTATTACTCTTGTACATACAAATTACTTATCAT
1 ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
* * *
28667837 CTTAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTATTGTTCAAATACCATACA
66 CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
*
28667902 TAGATTTACTCATTCAAAACTTAACATGCAGAGTTGGAACACTTA
131 TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTA
28667947 CCCTGATATG
Statistics
Matches: 340, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 340 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.35
Consensus pattern (181 bp):
ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
Found at i:28669141 original size:15 final size:15
Alignment explanation
Indices: 28669121--28669150 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28669111 AGTCTTTCTT
28669121 TCTAATAGTTTAGAA
1 TCTAATAGTTTAGAA
28669136 TCTAATAGTTTAGAA
1 TCTAATAGTTTAGAA
28669151 GGAGCATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TCTAATAGTTTAGAA
Found at i:28678299 original size:19 final size:19
Alignment explanation
Indices: 28678275--28678314 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28678265 CCTAGGGTCA
28678275 TCAAGCCTAAGGTTTAGGT
1 TCAAGCCTAAGGTTTAGGT
28678294 TCAAGCCTAAGGTTTAGGT
1 TCAAGCCTAAGGTTTAGGT
28678313 TC
1 TC
28678315 TTCCATTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (19 bp):
TCAAGCCTAAGGTTTAGGT
Found at i:28684624 original size:32 final size:31
Alignment explanation
Indices: 28684586--28684664 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
28684576 TTATTTTTAT
**
28684586 TTAAATTTGATTTTTAATTTTTTTAAAAAGAG
1 TTAAATTTGATTTTTAA-TACTTTAAAAAGAG
* *
28684618 TTAAATTTGACTATTAATACTTTAAAAAGAG
1 TTAAATTTGATTTTTAATACTTTAAAAAGAG
* *
28684649 TCAAATTGTTATTTTT
1 TTAAATT-TGATTTTT
28684665 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 18 0.47
32 20 0.53
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (31 bp):
TTAAATTTGATTTTTAATACTTTAAAAAGAG
Found at i:28684768 original size:16 final size:16
Alignment explanation
Indices: 28684749--28684779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28684739 CTAATTTTTT
*
28684749 ATTTTTATTTTTTTGC
1 ATTTTTATGTTTTTGC
28684765 ATTTTTATGTTTTTG
1 ATTTTTATGTTTTTG
28684780 AATAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.10, T:0.74
Consensus pattern (16 bp):
ATTTTTATGTTTTTGC
Found at i:28685007 original size:23 final size:25
Alignment explanation
Indices: 28684961--28685007 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
28684951 AATGTTAATA
*
28684961 ACTAAATTTAACTAAAAAATTATAG
1 ACTAAATTTAACTAAAAAAGTATAG
28684986 ACTAAA-TTAA-TAAAAAAGTATA
1 ACTAAATTTAACTAAAAAAGTATA
28685008 AACAAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 4 0.19
25 6 0.29
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (25 bp):
ACTAAATTTAACTAAAAAAGTATAG
Found at i:28685658 original size:28 final size:27
Alignment explanation
Indices: 28685595--28685660 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
28685585 TCATCATGAA
28685595 AAAGTAAAAGGAATCCTTTTTTTATAG
1 AAAGTAAAAGGAATCCTTTTTTTATAG
*
28685622 AAAGTAAAAGGAATCTTTTTTTTATAG
1 AAAGTAAAAGGAATCCTTTTTTTATAG
28685649 AAAGTGAAAAGG
1 AAAGT-AAAAGG
28685661 TTAGTCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (27 bp):
AAAGTAAAAGGAATCCTTTTTTTATAG
Found at i:28688032 original size:23 final size:24
Alignment explanation
Indices: 28688000--28688050 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
28687990 ATTCTATTTA
28688000 ATTTTTTTAT-ACA-ACTAGTTCT
1 ATTTTTTTATAACAGACTAGTTCT
*
28688022 ATTTTTATTATAATAGACTAGTTCT
1 ATTTTT-TTATAACAGACTAGTTCT
28688047 ATTT
1 ATTT
28688051 AATTAATCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 4 0.16
24 2 0.08
25 13 0.52
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (24 bp):
ATTTTTTTATAACAGACTAGTTCT
Found at i:28694945 original size:48 final size:48
Alignment explanation
Indices: 28694874--28694965 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
28694864 NNNNNNNNNN
28694874 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAATATTT
1 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAATATTT
*
28694922 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCCGAAAT
1 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAAT
28694966 TATGTATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (48 bp):
CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAATATTT
Found at i:28706284 original size:21 final size:22
Alignment explanation
Indices: 28706255--28706295 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28706245 ATTACATATT
*
28706255 TTTAGTTTT-AATTTTTCAAAA
1 TTTAGTTTTAAAATTTTCAAAA
*
28706276 TTTATTTTTAAAATTTTCAA
1 TTTAGTTTTAAAATTTTCAA
28706296 CCAATCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTAGTTTTAAAATTTTCAAAA
Found at i:28726818 original size:69 final size:69
Alignment explanation
Indices: 28726721--28726876 Score: 215
Period size: 69 Copynumber: 2.3 Consensus size: 69
28726711 ATTCACAAAT
* * * * *
28726721 ATTTGGACAGTAGTAAAAACATTTGGACAGCAGT-GACTTGTACCAAAAATAGACAGCATTTAAG
1 ATTTGGACAGCATTAATAACATTCGGACAGCA-TAGACTTGTACAAAAAATAGACAGCATTTAAG
*
28726785 TACTA
65 TACCA
* * *
28726790 ATTTGGACAGCATTAATAACATTCGGACAGCATAGATTTGTACAAAAAATGGACTGCATTTAAGT
1 ATTTGGACAGCATTAATAACATTCGGACAGCATAGACTTGTACAAAAAATAGACAGCATTTAAGT
28726855 ACCA
66 ACCA
28726859 ATTTGGACAGCATTAATA
1 ATTTGGACAGCATTAATA
28726877 TGCTAAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
68 1 0.01
69 76 0.99
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (69 bp):
ATTTGGACAGCATTAATAACATTCGGACAGCATAGACTTGTACAAAAAATAGACAGCATTTAAGT
ACCA
Found at i:28726871 original size:23 final size:23
Alignment explanation
Indices: 28726772--28726872 Score: 66
Period size: 23 Copynumber: 4.4 Consensus size: 23
28726762 ACCAAAAATA
*
28726772 GACAGCATTTAAGTACTAATTTG
1 GACAGCATTTAAGTACCAATTTG
* *
28726795 GACAGCA-TTAA-TAAC-ATTCG
1 GACAGCATTTAAGTACCAATTTG
* * **
28726815 GACAGCATAGATT-TGTACAAAAAATG
1 GACAGCAT---TTAAGTAC-CAATTTG
*
28726841 GACTGCATTTAAGTACCAATTTG
1 GACAGCATTTAAGTACCAATTTG
28726864 GACAGCATT
1 GACAGCATT
28726873 AATATGCTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
20 11 0.20
21 2 0.04
22 4 0.07
23 21 0.38
24 8 0.15
26 9 0.16
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
GACAGCATTTAAGTACCAATTTG
Found at i:28726939 original size:34 final size:33
Alignment explanation
Indices: 28726887--28726990 Score: 91
Period size: 38 Copynumber: 2.9 Consensus size: 33
28726877 TGCTAAAAAA
*
28726887 TGGACAGCATTTATACATGTAAAACAACCACATT
1 TGGACAACATTTA-ACATGTAAAACAACCACATT
*
28726921 TGGACAACATTATAACATGTAAAAAAAACAGCCACATT
1 TGGACAACATT-TAACATGT----AAAACAACCACATT
* * * *
28726959 TGGATATCATTGTAATATGCAAAACAACCACA
1 TGGACAACATT-TAACATGTAAAACAACCACA
28726991 CTTTAATACA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
34 27 0.47
35 2 0.04
38 28 0.49
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (33 bp):
TGGACAACATTTAACATGTAAAACAACCACATT
Found at i:28727815 original size:43 final size:41
Alignment explanation
Indices: 28727738--28727862 Score: 124
Period size: 43 Copynumber: 3.0 Consensus size: 41
28727728 AAAACACATA
* * * * *
28727738 TATCACATTCAATGCCATATCCCAGATATTGTCTTACATGT
1 TATCACATTCGATGCCATGTCCCAGACATGGTCTTACACGT
*
28727779 TATCACATCTCGATGCCACTGTCCCAGACAGGGTCTTACACGT
1 TATCACAT-TCGATGCCA-TGTCCCAGACATGGTCTTACACGT
* * * *
28727822 AATCTCATATTGATGTCAATGTCCCAGACATGGTCTTACAC
1 TATCACAT-TCGATG-CCATGTCCCAGACATGGTCTTACAC
28727863 AAAATTAAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 8 0.12
42 8 0.12
43 51 0.74
44 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (41 bp):
TATCACATTCGATGCCATGTCCCAGACATGGTCTTACACGT
Found at i:28731571 original size:13 final size:13
Alignment explanation
Indices: 28731553--28731579 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28731543 TACTTGGGAA
28731553 ATAAAAAAAAGTT
1 ATAAAAAAAAGTT
28731566 ATAAAAAAAAGTT
1 ATAAAAAAAAGTT
28731579 A
1 A
28731580 CATTGTCAAT
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:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAAAAAAAGTT
Found at i:28735332 original size:20 final size:20
Alignment explanation
Indices: 28735307--28735347 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28735297 TTTTTCATCA
28735307 TGAGGCAGGGAATAAAAACT
1 TGAGGCAGGGAATAAAAACT
28735327 TGAGGCAGGGAATAAAAACT
1 TGAGGCAGGGAATAAAAACT
28735347 T
1 T
28735348 TAAAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (20 bp):
TGAGGCAGGGAATAAAAACT
Found at i:28739236 original size:18 final size:18
Alignment explanation
Indices: 28739213--28739255 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28739203 ACCCAATCCA
*
28739213 AACCCAAGTATTC-AACCC
1 AACCCAAGTA-CCAAACCC
*
28739231 AACCCAATTACCAAACCC
1 AACCCAAGTACCAAACCC
28739249 AACCCAA
1 AACCCAA
28739256 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.44, C:0.42, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCAAACCC
Found at i:28739388 original size:9 final size:9
Alignment explanation
Indices: 28739359--28739416 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
28739349 GTAGTGATTC
28739359 AATTCGGTT
1 AATTCGGTT
* *
28739368 AATTTGGGT
1 AATTCGGTT
28739377 AATTCGGTT
1 AATTCGGTT
* *
28739386 AATACAGTT
1 AATTCGGTT
*
28739395 AATTCGGGT
1 AATTCGGTT
*
28739404 AATTCAGTT
1 AATTCGGTT
28739413 AATT
1 AATT
28739417 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28743207 original size:163 final size:163
Alignment explanation
Indices: 28742937--28743264 Score: 629
Period size: 163 Copynumber: 2.0 Consensus size: 163
28742927 TGTTTCATAG
* *
28742937 CTAGGTATTCATAGATGATTTTTTTGGTGATGCGAATTACTGTACAATAAGGAAAACAAAGGCTT
1 CTAGGTAGTCATAGATGATTTTTTTGGTGATGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
28743002 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
66 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
28743067 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
131 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
*
28743100 CTAGGTAGTCATAGATGATTTTTTTGGTGGTGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
1 CTAGGTAGTCATAGATGATTTTTTTGGTGATGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
28743165 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
66 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
28743230 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
131 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
28743263 CT
1 CT
28743265 TGTCAATGGC
Statistics
Matches: 162, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (163 bp):
CTAGGTAGTCATAGATGATTTTTTTGGTGATGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
Found at i:28749070 original size:6 final size:6
Alignment explanation
Indices: 28749059--28749091 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
28749049 TCTACGGTCT
28749059 GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GGT
1 GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GGT
28749092 GAATGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTTGA
Found at i:28749176 original size:36 final size:37
Alignment explanation
Indices: 28749126--28749197 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
28749116 ATAAAGTTTC
*
28749126 GGATAACTGAGTATTGAACTTATTAT-TTCTTAGGAT
1 GGATAACTGAGTATTGAACTTAGTATATTCTTAGGAT
* *
28749162 GGATAACTGGGTATTGTACTTAGTATATTCTTAGGA
1 GGATAACTGAGTATTGAACTTAGTATATTCTTAGGA
28749198 GGGCCTGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 23 0.72
37 9 0.28
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (37 bp):
GGATAACTGAGTATTGAACTTAGTATATTCTTAGGAT
Found at i:28768536 original size:23 final size:23
Alignment explanation
Indices: 28768506--28768574 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
28768496 TATGAGAGAA
*
28768506 TACCAAAAAAAAACATAAGGAAG
1 TACCAAAAAAAAATATAAGGAAG
* *
28768529 TACC--AAAAAATTATAAGGAAA
1 TACCAAAAAAAAATATAAGGAAG
* *
28768550 TACTAAAAAAAAATATGAGGAAG
1 TACCAAAAAAAAATATAAGGAAG
28768573 TA
1 TA
28768575 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.46
23 20 0.54
ACGTcount: A:0.62, C:0.09, G:0.13, T:0.16
Consensus pattern (23 bp):
TACCAAAAAAAAATATAAGGAAG
Found at i:28768542 original size:44 final size:42
Alignment explanation
Indices: 28768480--28768638 Score: 153
Period size: 44 Copynumber: 3.7 Consensus size: 42
28768470 ACATTGAGGG
* * *
28768480 AGGAAGTACTAACAATTATGAGAGAATACCAAAAAAAAACAT
1 AGGAAGTACAAAAAATTATAAGAGAATACCAAAAAAAAACAT
* *
28768522 AAGGAAGTACCAAAAAATTATAAG-GAAATACTAAAAAAAAATAT
1 -AGGAAGTA-CAAAAAATTATAAGAG-AATACCAAAAAAAAACAT
* * *
28768566 GAGGAAGTATAAAAAATTATGAGAGAACA-C-AAAAAAAACACT
1 -AGGAAGTACAAAAAATTATAAGAGAATACCAAAAAAAAACA-T
* *
28768608 AGAAATTACAAAAAAGTTATAAGAGAATACC
1 AGGAAGTACAAAAAA-TTATAAGAGAATACC
28768639 GAATAATATG
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 21 0.22
42 12 0.13
43 25 0.27
44 36 0.38
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (42 bp):
AGGAAGTACAAAAAATTATAAGAGAATACCAAAAAAAAACAT
Found at i:28768579 original size:21 final size:21
Alignment explanation
Indices: 28768511--28768581 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
28768501 GAGAATACCA
* *
28768511 AAAAAAAACATAAGGAAGTAC
1 AAAAAAAATATAAGGAAGTAT
* * *
28768532 CAAAAAATTATAAGGAAATACT
1 AAAAAAAATATAAGGAAGTA-T
*
28768554 AAAAAAAAATATGAGGAAGTAT
1 -AAAAAAAATATAAGGAAGTAT
28768576 AAAAAA
1 AAAAAA
28768582 TTATGAGAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 22 0.56
22 1 0.03
23 16 0.41
ACGTcount: A:0.66, C:0.06, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAAAAATATAAGGAAGTAT
Found at i:28769413 original size:19 final size:20
Alignment explanation
Indices: 28769370--28769418 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28769360 ATACACAAAA
* * *
28769370 AATAACAAAAATTATGAGCG
1 AATACCAAAAATTACGAGAG
28769390 AATACCAAAAATTACGAGAG
1 AATACCAAAAATTACGAGAG
28769410 -ATACCAAAA
1 AATACCAAAA
28769419 GAAATGAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (20 bp):
AATACCAAAAATTACGAGAG
Found at i:28769480 original size:20 final size:20
Alignment explanation
Indices: 28769457--28769661 Score: 91
Period size: 20 Copynumber: 10.3 Consensus size: 20
28769447 AAAAAGAGAG
28769457 GATGTACCAAAAATTATGAA
1 GATGTACCAAAAATTATGAA
** * *
28769477 GATGTATAAAAAAGTTACGAGG
1 GATGTACCAAAAA-TTATGA-A
*
28769499 GA-ATACCAAAAA-TATGAA
1 GATGTACCAAAAATTATGAA
*
28769517 G--GATACCAAAAATACATG--
1 GATG-TACCAAAAAT-TATGAA
* * * * *
28769535 GATGCACGAAAAAATACGAG
1 GATGTACCAAAAATTATGAA
* *
28769555 GATGCACCAAAAATTATAAA
1 GATGTACCAAAAATTATGAA
*
28769575 GATGTACAAAAAATTATGAGA
1 GATGTACCAAAAATTATGA-A
* * * *
28769596 GA-ATACTAAAAAATATGAG
1 GATGTACCAAAAATTATGAA
* ** **
28769615 GAAGTATAAAAAAAAAATGAA
1 GATGTA-CCAAAAATTATGAA
*
28769636 GATGTACCAAAAATTATAAA
1 GATGTACCAAAAATTATGAA
28769656 GATGTA
1 GATGTA
28769662 TAAATACCAA
Statistics
Matches: 134, Mismatches: 39, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
18 13 0.10
19 13 0.10
20 76 0.57
21 30 0.22
22 2 0.01
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
GATGTACCAAAAATTATGAA
Found at i:28769624 original size:19 final size:21
Alignment explanation
Indices: 28769582--28769627 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
28769572 AAAGATGTAC
28769582 AAAAAATTATGAGAGAATACT
1 AAAAAATTATGAGAGAATACT
28769603 AAAAAA-TATGAG-GAAGTA-T
1 AAAAAATTATGAGAGAA-TACT
28769622 AAAAAA
1 AAAAAA
28769628 AAAATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAAATTATGAGAGAATACT
Found at i:28769663 original size:41 final size:42
Alignment explanation
Indices: 28769555--28769665 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 42
28769545 AAAATACGAG
* * **
28769555 GATGCACCAAAAATTATAAAGATGTA-CAAAAAATTATGAGA
1 GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
* * * * * *
28769596 GA-ATACTAAAAAATATGAGGAAGTATAAAAAAAAAATGA-A
1 GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
28769636 GATGTACCAAAAATTATAAAGATGTATAAA
1 GATGTACCAAAAATTATAAAGATGTATAAA
28769666 TACCAAAAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
40 19 0.37
41 33 0.63
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (42 bp):
GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
Found at i:28771282 original size:20 final size:20
Alignment explanation
Indices: 28771259--28771463 Score: 91
Period size: 20 Copynumber: 10.3 Consensus size: 20
28771249 AAAAAGAGAG
28771259 GATGTACCAAAAATTATGAA
1 GATGTACCAAAAATTATGAA
** * *
28771279 GATGTATAAAAAAGTTACGAGG
1 GATGTACCAAAAA-TTATGA-A
*
28771301 GA-ATACCAAAAA-TATGAA
1 GATGTACCAAAAATTATGAA
*
28771319 G--GATACCAAAAATACATG--
1 GATG-TACCAAAAAT-TATGAA
* * * * *
28771337 GATGCACGAAAAAATACGAG
1 GATGTACCAAAAATTATGAA
* *
28771357 GATGCACCAAAAATTATAAA
1 GATGTACCAAAAATTATGAA
*
28771377 GATGTACAAAAAATTATGAGA
1 GATGTACCAAAAATTATGA-A
* * * *
28771398 GA-ATACTAAAAAATATGAG
1 GATGTACCAAAAATTATGAA
* ** **
28771417 GAAGTATAAAAAAAAAATGAA
1 GATGTA-CCAAAAATTATGAA
*
28771438 GATGTACCAAAAATTATAAA
1 GATGTACCAAAAATTATGAA
28771458 GATGTA
1 GATGTA
28771464 TAAATACCAA
Statistics
Matches: 134, Mismatches: 39, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
18 13 0.10
19 13 0.10
20 76 0.57
21 30 0.22
22 2 0.01
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
GATGTACCAAAAATTATGAA
Found at i:28771426 original size:19 final size:21
Alignment explanation
Indices: 28771384--28771429 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
28771374 AAAGATGTAC
28771384 AAAAAATTATGAGAGAATACT
1 AAAAAATTATGAGAGAATACT
28771405 AAAAAA-TATGAG-GAAGTA-T
1 AAAAAATTATGAGAGAA-TACT
28771424 AAAAAA
1 AAAAAA
28771430 AAAATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAAATTATGAGAGAATACT
Found at i:28771465 original size:41 final size:42
Alignment explanation
Indices: 28771357--28771467 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 42
28771347 AAAATACGAG
* * **
28771357 GATGCACCAAAAATTATAAAGATGTA-CAAAAAATTATGAGA
1 GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
* * * * * *
28771398 GA-ATACTAAAAAATATGAGGAAGTATAAAAAAAAAATGA-A
1 GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
28771438 GATGTACCAAAAATTATAAAGATGTATAAA
1 GATGTACCAAAAATTATAAAGATGTATAAA
28771468 TACCAAAAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
40 19 0.37
41 33 0.63
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (42 bp):
GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
Found at i:28772898 original size:3 final size:3
Alignment explanation
Indices: 28772890--28772927 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
28772880 TAGTCCATTC
*
28772890 TTA TTA TTA TT- TTA TTA TTA TCA TTA TT- TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28772928 ACTGTTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28772915 original size:17 final size:17
Alignment explanation
Indices: 28772890--28772927 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28772880 TAGTCCATTC
*
28772890 TTATTATTATTTTATTA
1 TTATCATTATTTTATTA
28772907 TTATCATTATTTTATTA
1 TTATCATTATTTTATTA
28772924 TTAT
1 TTAT
28772928 ACTGTTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATCATTATTTTATTA
Found at i:28795500 original size:21 final size:23
Alignment explanation
Indices: 28795458--28795500 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
28795448 GATCGAGACC
*
28795458 AACTATAGTGGTATCGCGATACT
1 AACTATAGTGGTATCGCAATACT
*
28795481 AACTAT-G-GGTATTGCAATAC
1 AACTATAGTGGTATCGCAATAC
28795501 CCAACTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (23 bp):
AACTATAGTGGTATCGCAATACT
Found at i:28796928 original size:20 final size:22
Alignment explanation
Indices: 28796903--28796944 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28796893 ACCTTAACTC
28796903 ATATTACA-AA-CCCAAACCCA
1 ATATTACACAAGCCCAAACCCA
*
28796923 ATATTACACAAGCCCAAGCCCA
1 ATATTACACAAGCCCAAACCCA
28796945 CAACCTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (22 bp):
ATATTACACAAGCCCAAACCCA
Found at i:28797139 original size:6 final size:6
Alignment explanation
Indices: 28797123--28797188 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
28797113 AGAAGAAAGA
* * * * *
28797123 AAAACAC AAAAAC AAAAAT AGAAAT AGAAGC AGAAAAAC AAAAAC AAAAAC
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAAAC A-AAA-AC AAAAAC AAAAAC
28797174 AAAAAC AAAAAC AAA
1 AAAAAC AAAAAC AAA
28797189 TATTTGTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
6 40 0.78
7 9 0.18
8 2 0.04
ACGTcount: A:0.77, C:0.14, G:0.06, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:28805371 original size:24 final size:24
Alignment explanation
Indices: 28805315--28805393 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
28805305 GTCCTCATCT
* *
28805315 TCTTCATCTTCACCTCGACCCTCG
1 TCTTCATCTTCATCTCGACCCTCA
28805339 TAC-TCATCTTCATCTCGACCCTCA
1 T-CTTCATCTTCATCTCGACCCTCA
* * *
28805363 TCTTTATCTTTATCTCCACCC-CTA
1 TCTTCATCTTCATCTCGACCCTC-A
28805387 TCTTCAT
1 TCTTCAT
28805394 TTTTGTCTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
23 2 0.04
24 43 0.93
25 1 0.02
ACGTcount: A:0.16, C:0.41, G:0.04, T:0.39
Consensus pattern (24 bp):
TCTTCATCTTCATCTCGACCCTCA
Found at i:28805402 original size:24 final size:25
Alignment explanation
Indices: 28805342--28805404 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
28805332 ACCCTCGTAC
* *
28805342 TCATCTTCATCTCGA-CCCTCATCT
1 TCATCTTTATCTCCACCCCTCATCT
*
28805366 TTATCTTTATCTCCACCCCT-ATCT
1 TCATCTTTATCTCCACCCCTCATCT
* *
28805390 TCATTTTTGTCTCCA
1 TCATCTTTATCTCCA
28805405 TCGTCTTCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.16, C:0.37, G:0.03, T:0.44
Consensus pattern (25 bp):
TCATCTTTATCTCCACCCCTCATCT
Found at i:28807450 original size:9 final size:9
Alignment explanation
Indices: 28807436--28807474 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
28807426 TTTCGAAGAA
28807436 AATTGAGAG
1 AATTGAGAG
28807445 AATTGAGAG
1 AATTGAGAG
*
28807454 AGTTTAGAGAG
1 A-ATT-GAGAG
28807465 AATTGAGAG
1 AATTGAGAG
28807474 A
1 A
28807475 GTTAGATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 16 0.62
10 4 0.15
11 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (9 bp):
AATTGAGAG
Found at i:28807465 original size:20 final size:20
Alignment explanation
Indices: 28807440--28807477 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28807430 GAAGAAAATT
28807440 GAGAGAATTGAGAGAGTTTA
1 GAGAGAATTGAGAGAGTTTA
28807460 GAGAGAATTGAGAGAGTT
1 GAGAGAATTGAGAGAGTT
28807478 AGATTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (20 bp):
GAGAGAATTGAGAGAGTTTA
Found at i:28809643 original size:108 final size:108
Alignment explanation
Indices: 28809421--28809716 Score: 364
Period size: 108 Copynumber: 2.8 Consensus size: 108
28809411 TAAATAGTTA
* * * * * * *
28809421 TATTCATTTAATATTATTAGTCTT-ATGTTTTTATGTGTCTAAATTTTATTTTGCTCACAATTTA
1 TATTCATTTAGTATTCTTAAT-TTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTA
* ** * *
28809485 ATC--TCTTTTTTCATTTTAATATTGTACATATTTCACGTGTTT
65 ATCTATTTTTTTTCATTTTAATATCATACAAATTTCACGTGTTG
* *
28809527 TATTCATTTAGTATTCTTAATTTGATGTATTTGTGTGTTTAAATTTCATTTTATTCACAATTTAA
1 TATTCATTTAGTATTCTTAATTTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTAA
*
28809592 TCTATTTTTTTTCATTTTAATATCATACAAATTTCATGTGTTG
66 TCTATTTTTTTTCATTTTAATATCATACAAATTTCACGTGTTG
* * * * *
28809635 TATTCATTTAGTATACTTAATCTGATGCATTTATGTGTTTAAATTTCGTTTTACTCACAAGTTAA
1 TATTCATTTAGTATTCTTAATTTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTAA
*
28809700 TCTAATTTTTTTGCATT
66 TCT-ATTTTTTTTCATT
28809717 CTAAGATTGA
Statistics
Matches: 163, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
105 2 0.01
106 55 0.34
108 94 0.58
109 12 0.07
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (108 bp):
TATTCATTTAGTATTCTTAATTTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTAA
TCTATTTTTTTTCATTTTAATATCATACAAATTTCACGTGTTG
Found at i:28810723 original size:26 final size:25
Alignment explanation
Indices: 28810692--28810742 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
28810682 TATTATTTTT
28810692 AATTTAGTAT-TTAACAATTTTATATA
1 AATTTA-TATATTAA-AATTTTATATA
*
28810718 AATTTATTTATTAAAATTTTATATA
1 AATTTATATATTAAAATTTTATATA
28810743 TAGTCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTTATATATTAAAATTTTATATA
Found at i:28815245 original size:8 final size:8
Alignment explanation
Indices: 28815234--28815267 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
28815224 GCCCTTCTGG
28815234 TTTTCTTT
1 TTTTCTTT
28815242 TTTTCTTT
1 TTTTCTTT
28815250 CATTTTCTTT
1 --TTTTCTTT
28815260 TTTTCTTT
1 TTTTCTTT
28815268 GCTTTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:28831598 original size:26 final size:26
Alignment explanation
Indices: 28831569--28831625 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
28831559 GGGTCTATTA
28831569 AGTTTAAGTGGGTCT-AAGGACCCTTG
1 AGTTTAAGTGGGT-TGAAGGACCCTTG
* * *
28831595 AGTTTGAGTTGGTTGAAGGACCTTTG
1 AGTTTAAGTGGGTTGAAGGACCCTTG
28831621 AGTTT
1 AGTTT
28831626 GAGTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (26 bp):
AGTTTAAGTGGGTTGAAGGACCCTTG
Found at i:28832006 original size:36 final size:36
Alignment explanation
Indices: 28831959--28832031 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
28831949 GGCCAAGATG
28831959 GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
1 GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
*
28831995 GCCATACCCAATGGGGTGACCATTGAGGGGTCGAGA
1 GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
28832031 G
1 G
28832032 GGACTAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.37, T:0.15
Consensus pattern (36 bp):
GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
Found at i:28837727 original size:82 final size:82
Alignment explanation
Indices: 28837590--28837744 Score: 310
Period size: 82 Copynumber: 1.9 Consensus size: 82
28837580 TATTTAACTC
28837590 ATAATTATTAATTAAATATATTTATGGACTCTTTTGTCGGAATTGTTGTAATACACCTAAAATTA
1 ATAATTATTAATTAAATATATTTATGGACTCTTTTGTCGGAATTGTTGTAATACACCTAAAATTA
28837655 CTATAGTATATCCCTGA
66 CTATAGTATATCCCTGA
28837672 ATAATTATTAATTAAATATATTTATGGACTCTTTTGTCGGAATTGTTGTAATACACCTAAAATTA
1 ATAATTATTAATTAAATATATTTATGGACTCTTTTGTCGGAATTGTTGTAATACACCTAAAATTA
28837737 CTATAGTA
66 CTATAGTA
28837745 AGATAATATC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (82 bp):
ATAATTATTAATTAAATATATTTATGGACTCTTTTGTCGGAATTGTTGTAATACACCTAAAATTA
CTATAGTATATCCCTGA
Found at i:28839396 original size:2 final size:2
Alignment explanation
Indices: 28839389--28839414 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28839379 AGGAGGAGGA
28839389 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
28839415 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28839419 original size:2 final size:2
Alignment explanation
Indices: 28839414--28839483 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
28839404 TATATATATA
28839414 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
28839456 TG TG TG TG TG TG TG TA TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28839484 AATATTCACC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28840266 original size:62 final size:57
Alignment explanation
Indices: 28840195--28840341 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 57
28840185 ATTGACGGTA
* *
28840195 AAAAAGATCTAGCCCAGACGGGTGATCCTATCCTGATATAGCCCTCCTAAAGAATATGTGTG
1 AAAAAGATCTAGCCCAGACGGGTGATCC--T--TGATATAGCCCTCCCAAAGAATATATG-G
* * *
28840257 AAAAAGATCTAGCCCGGACAGGTGAT-CTTGATATAGCCCTCCCGAAGAATATATGG
1 AAAAAGATCTAGCCCAGACGGGTGATCCTTGATATAGCCCTCCCAAAGAATATATGG
* * *
28840313 AAAATGGATTTAGCCCAGACGGGTAATCC
1 AAAA-AGATCTAGCCCAGACGGGTGATCC
28840342 AAATTAAGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.07
57 41 0.56
58 1 0.01
59 1 0.01
61 1 0.01
62 24 0.33
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCAGACGGGTGATCCTTGATATAGCCCTCCCAAAGAATATATGG
Found at i:28840483 original size:54 final size:54
Alignment explanation
Indices: 28840425--28840545 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
28840415 ATCTAGCATA
****
28840425 GACTGGTAATCCCGACAATACTCTAT-AAGTTTATATTACAAGGGATTTAGCCTG
1 GACTGGTAATCCCG-CAATAAGAAATGAAGTTTATATTACAAGGGATTTAGCCTG
*** * *
28840479 GACTGGTAATCCCGTTGTAAGAAATGAGGTTTATATTACAGGGGATTTAGCCTG
1 GACTGGTAATCCCGCAATAAGAAATGAAGTTTATATTACAAGGGATTTAGCCTG
28840533 GACTGGTAATCCC
1 GACTGGTAATCCC
28840546 ACTGTAAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 4 0.07
54 53 0.93
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (54 bp):
GACTGGTAATCCCGCAATAAGAAATGAAGTTTATATTACAAGGGATTTAGCCTG
Found at i:28840552 original size:54 final size:54
Alignment explanation
Indices: 28840449--28840563 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
28840439 ACAATACTCT
**
28840449 ATAA-GTTTATATTACAAGGGATTTAGCCTGGACTGGTAATCCCGTTGTAAGAA
1 ATAAGGTTTATATTACAAGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAA
* *
28840502 ATGAGGTTTATATTACAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAA
1 ATAAGGTTTATATTACAAGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAA
28840556 ATAAGGTT
1 ATAAGGTT
28840564 CGCGGAAGCG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 3 0.05
54 53 0.95
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (54 bp):
ATAAGGTTTATATTACAAGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAA
Found at i:28850560 original size:3 final size:3
Alignment explanation
Indices: 28850552--28850580 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28850542 CAAACAGACA
28850552 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
28850581 AACGAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:28851826 original size:28 final size:28
Alignment explanation
Indices: 28851774--28851827 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
28851764 TATAAGATAC
*
28851774 AGACAAAAAAATGAAAAACCCAAACCCA
1 AGACAAAAAAATGAAAAACCAAAACCCA
28851802 AGACAAAGTAAAATG-AAAA-CAAAACC
1 AGACAAA--AAAATGAAAAACCAAAACC
28851828 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 13 0.57
29 4 0.17
30 6 0.26
ACGTcount: A:0.65, C:0.20, G:0.09, T:0.06
Consensus pattern (28 bp):
AGACAAAAAAATGAAAAACCAAAACCCA
Found at i:28859460 original size:121 final size:121
Alignment explanation
Indices: 28859145--28859500 Score: 493
Period size: 121 Copynumber: 2.9 Consensus size: 121
28859135 TACCTAATTG
* *
28859145 AATTTTAATACGACACTATAATAACTTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
1 AATTTTAATACGACACTCTAATAACGTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
* *
28859210 TCAGAATTGTGGTCCCAAAACTACTGTTTCTGACACCACTGAAAATGAGTTATTACA
66 TCA-AATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGAGTTATTACA
* *
28859267 AATTTTAATACGACACTCTAATAACGTTGCAAATATTAAATAAATAATATTTACTAACTCATTGG
1 AATTTTAATACGACACTCTAATAACGTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
* * * * *
28859332 TCTAAATTGTGGTCTCAAAATTACGGTTTCCGACTCTACTG-AAATG-GTTTGTTACA
66 TC-AAATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGAG-TTATTACA
*
28859388 AATTTTTATACGACACTCTAATAATC-TTGTAAATATTAAATAAATAATATTTACTAACTCACTG
1 AATTTTAATACGACACTCTAATAA-CGTTGTAAATATTAAATAAATAATATTTACTAACTCACTG
* * * * *
28859452 ATCGAAATTGTAGTCCCAAAATAACTGTTTCTGACACCATTGAAAATGA
65 GTC-AAATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGA
28859501 CCTGTTACAA
Statistics
Matches: 205, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
120 1 0.00
121 103 0.50
122 100 0.49
123 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (121 bp):
AATTTTAATACGACACTCTAATAACGTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
TCAAATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGAGTTATTACA
Found at i:28859950 original size:40 final size:42
Alignment explanation
Indices: 28859905--28859986 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 42
28859895 GATAAAGCAG
28859905 GAAAACG-ATTCCTTGAGGAAGCG-ATT-TGTCCACGTGGACA
1 GAAAACGCA-TCCTTGAGGAAGCGCATTGTGTCCACGTGGACA
* *
28859945 GAAAACGCATCCTTGAGGGAGCGCTTTGTGTCCACGTGGACA
1 GAAAACGCATCCTTGAGGAAGCGCATTGTGTCCACGTGGACA
28859987 AAGTGCTCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 20 0.54
41 3 0.08
42 14 0.38
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (42 bp):
GAAAACGCATCCTTGAGGAAGCGCATTGTGTCCACGTGGACA
Found at i:28860663 original size:84 final size:83
Alignment explanation
Indices: 28860566--28860811 Score: 278
Period size: 96 Copynumber: 2.8 Consensus size: 83
28860556 AACAACTAGT
* * * *
28860566 TTTATTTTATTTTTCCTTAAAAACTCTAAATATTAAACCCCAATCTAATTTTTTTAAAATTTATA
1 TTTATTTAATTTTTCCTTAAAAAC-CTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATA
28860631 AAGTAACCCTAAACCCTAA
65 AAGTAACCCTAAACCCTAA
*
28860650 TTTATTTAATTTTTCCCTTAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAATTTTATA
1 TTTATTTAATTTTT-CCTTAAAAACCTAAACACTAAACCCTAATCTAATTTTTTTAAA----AT-
28860715 ATTAATTTACTCAAGTAACCCTAAACCCTAA
60 -TT-A--TA---AAGTAACCCTAAACCCTAA
* *
28860746 TTTATTTAATTTTTTCCTTAAAAAGCATAAACACTAAACTCTAATCTAA-TTTTTTAAAATTTAT
1 TTTATTTAA-TTTTTCCTTAAAAA-CCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTAT
28860810 AA
64 AA
28860812 TTAAGTTAAT
Statistics
Matches: 139, Mismatches: 8, Indels: 30
0.79 0.05 0.17
Matches are distributed among these distances:
84 44 0.32
85 9 0.06
87 2 0.01
88 2 0.01
89 1 0.01
90 4 0.03
91 1 0.01
92 2 0.01
93 2 0.01
96 45 0.32
97 27 0.19
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.42
Consensus pattern (83 bp):
TTTATTTAATTTTTCCTTAAAAACCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAA
AGTAACCCTAAACCCTAA
Found at i:28860671 original size:48 final size:47
Alignment explanation
Indices: 28860611--28860768 Score: 123
Period size: 48 Copynumber: 3.3 Consensus size: 47
28860601 AACCCCAATC
28860611 TAATTTTT--TTAAAATTTATAAAGTAACCCTAAACCCTAATTTATT
1 TAATTTTTCCTTAAAATTTATAAAGTAACCCTAAACCCTAATTTATT
** * * *
28860656 TAATTTTTCCCTTAAAACCCTA-AACACTAAACCCT-AA-TCTAATTTTTT
1 TAATTTTT-CCTTAAAA-TTTATAA-AGT-AACCCTAAACCCTAATTTATT
* * *
28860704 TAAATTTT--ATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATT
1 TAATTTTTCCTTAA--AATTTA-TAAAGTAACCCTAAACCCTAATTTATT
28860752 TAATTTTTTCCTTAAAA
1 TAA-TTTTTCCTTAAAA
28860769 AGCATAAACA
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
45 11 0.13
46 8 0.10
47 6 0.07
48 37 0.45
49 12 0.14
50 6 0.07
51 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (47 bp):
TAATTTTTCCTTAAAATTTATAAAGTAACCCTAAACCCTAATTTATT
Found at i:28860739 original size:96 final size:93
Alignment explanation
Indices: 28860623--28860870 Score: 352
Period size: 96 Copynumber: 2.6 Consensus size: 93
28860613 ATTTTTTTAA
28860623 AATTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCCTTAAAACCCTAAACACTAAAC
1 AATTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTT-CCTTAAAACCCTAAACACTAAAC
*
28860688 CCTAATCTAATTTTTTTAAATTTTATAATT
65 CCTAATCTAA-TTTTTTAAAATTTATAATT
* * *
28860718 AATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAAGCATAAACACTAA
1 AATTTA-TAAAGTAACCCTAAACCCTAATTTATTTAA-TTTTTCCTT-AAAACCCTAAACACTAA
*
28860783 ACTCTAATCTAATTTTTTAAAATTTATAATT
63 ACCCTAATCTAATTTTTTAAAATTTATAATT
* * * * *
28860814 AAGTTAATTAAGAAACCCTAAACCCTTATTTATTTAATTTTTCCTTAGAACCCTAAA
1 AA-TTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAACCCTAAA
28860871 ATCTAAAAAC
Statistics
Matches: 137, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
94 8 0.06
95 15 0.11
96 80 0.58
97 34 0.25
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (93 bp):
AATTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAACCCTAAACACTAAACC
CTAATCTAATTTTTTAAAATTTATAATT
Found at i:28864759 original size:3 final size:3
Alignment explanation
Indices: 28864741--28864786 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
28864731 GCCTTTTTTT
* *
28864741 TTA TT- TTA GTTA -TA TTA TTA TTA TTA TTA TTG CTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28864785 TT
1 TT
28864787 TACTCATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28865332 original size:107 final size:107
Alignment explanation
Indices: 28865133--28865345 Score: 295
Period size: 107 Copynumber: 2.0 Consensus size: 107
28865123 AAGGAAAATT
* * *
28865133 TTTCTAAATAAGGCAATATTTTACGTTTAGAAAATCGAGAAAATGTGCCCTAATGTGCTGGGTTT
1 TTTCTAAATAAGGCAATATTTTACATTTAGAAAATCGAGAAAACGTGCCCTAATGTGCTAGGTTT
* *
28865198 CGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAAA
66 CGATTTTCTCGTTCAACCAAATAGCCAAATATCCTCTTAAAA
* * * *
28865240 TTTC-AAAGTAAGGCAATGTTTTGCATTTGGAAAATTCGAGAAAACGTGCCCTAATGTGTTAGGT
1 TTTCTAAA-TAAGGCAATATTTTACATTTAGAAAA-TCGAGAAAACGTGCCCTAATGTGCTAGGT
**
28865304 TTCGA-TTTCTCGTTTGACCAAATAGCCAAATATCCTCTTAAA
64 TTCGATTTTCTCGTTCAACCAAATAGCCAAATATCCTCTTAAA
28865346 TCTCAAACCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
106 3 0.03
107 59 0.63
108 31 0.33
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (107 bp):
TTTCTAAATAAGGCAATATTTTACATTTAGAAAATCGAGAAAACGTGCCCTAATGTGCTAGGTTT
CGATTTTCTCGTTCAACCAAATAGCCAAATATCCTCTTAAAA
Done.