Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 74 of 295
Found at i:21337419 original size:20 final size:20
Alignment explanation
Indices: 21337394--21337434 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
21337384 TGAGAACCAT
21337394 GAAAGCAGGAGCTTTATATG
1 GAAAGCAGGAGCTTTATATG
*
21337414 GAAAGCTGGAGCTTTATATG
1 GAAAGCAGGAGCTTTATATG
21337434 G
1 G
21337435 TTATCTTTTC
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:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (20 bp):
GAAAGCAGGAGCTTTATATG
Found at i:21341849 original size:42 final size:42
Alignment explanation
Indices: 21341797--21341897 Score: 193
Period size: 42 Copynumber: 2.4 Consensus size: 42
21341787 TCATAAATAC
*
21341797 TTGAATATAATTTCATTAAATTCCAGTTTCGTAAGCATAAGT
1 TTGAATATAATTTCATTAAATTCCAGTTTCATAAGCATAAGT
21341839 TTGAATATAATTTCATTAAATTCCAGTTTCATAAGCATAAGT
1 TTGAATATAATTTCATTAAATTCCAGTTTCATAAGCATAAGT
21341881 TTGAATATAATTTCATT
1 TTGAATATAATTTCATT
21341898 CTTCAAAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (42 bp):
TTGAATATAATTTCATTAAATTCCAGTTTCATAAGCATAAGT
Found at i:21342711 original size:5 final size:5
Alignment explanation
Indices: 21342701--21342736 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
21342691 TTATGTTTTA
21342701 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
21342737 AAACGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:21344026 original size:15 final size:15
Alignment explanation
Indices: 21344006--21344062 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
21343996 CGATGAATTT
*
21344006 ATTGAATTTATATTG
1 ATTGAAATTATATTG
21344021 ATTGAAATTA-ATTTG
1 ATTGAAATTATA-TTG
21344036 ATTGAAATTATATTG
1 ATTGAAATTATATTG
21344051 ATTG-AATTATAT
1 ATTGAAATTATAT
21344063 AATATATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
14 9 0.23
15 29 0.74
16 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:21344460 original size:21 final size:21
Alignment explanation
Indices: 21344434--21344498 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
21344424 GACTTTATCG
21344434 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* **
21344455 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
21344476 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
21344497 AT
1 AT
21344499 ACTGATCAGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:21349422 original size:20 final size:20
Alignment explanation
Indices: 21349379--21349441 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
21349369 ATTTTTCAAT
*
21349379 ATTTAA-ATATTTAATATTATA
1 ATTTAATATTTTTAAT-TTA-A
**
21349400 ATTTTCTATTTTTAATTTAA
1 ATTTAATATTTTTAATTTAA
*
21349420 ATTTAATATTTTTATTTTAA
1 ATTTAATATTTTTAATTTAA
21349440 AT
1 AT
21349442 AAACTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 20 0.57
21 7 0.20
22 8 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAATATTTTTAATTTAA
Found at i:21350324 original size:10 final size:10
Alignment explanation
Indices: 21350309--21350359 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
21350299 AAAAGAAGAG
21350309 AATTATTTAA
1 AATTATTTAA
*
21350319 AATTATTTAG
1 AATTATTTAA
*
21350329 AATCA--TAA
1 AATTATTTAA
*
21350337 AAATATTTAA
1 AATTATTTAA
*
21350347 AATTATTAAA
1 AATTATTTAA
21350357 AAT
1 AAT
21350360 AACATCCAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
8 5 0.16
10 27 0.84
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (10 bp):
AATTATTTAA
Found at i:21350357 original size:18 final size:19
Alignment explanation
Indices: 21350309--21350357 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
21350299 AAAAGAAGAG
*
21350309 AATTATTTAAAATTATTTAG
1 AATTA-TTAAAATTATTTAA
* *
21350329 AATCA-TAAAAATATTTAA
1 AATTATTAAAATTATTTAA
21350347 AATTATTAAAA
1 AATTATTAAAA
21350358 ATAACATCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 15 0.62
19 5 0.21
20 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTATTAAAATTATTTAA
Found at i:21350468 original size:10 final size:10
Alignment explanation
Indices: 21350455--21350543 Score: 63
Period size: 10 Copynumber: 8.9 Consensus size: 10
21350445 TCTTAAATAG
21350455 TTATAAAAAA
1 TTATAAAAAA
21350465 TTATAAAAAA
1 TTATAAAAAA
* *
21350475 TTGTTTAAAAA
1 TT-ATAAAAAA
* *
21350486 TTATTAAGAA
1 TTATAAAAAA
*
21350496 TTATAAGAAA
1 TTATAAAAAA
*
21350506 TTATAAATAA
1 TTATAAAAAA
* **
21350516 TAATTGAAAA
1 TTATAAAAAA
* *
21350526 TT-TTAAAAG
1 TTATAAAAAA
21350535 TTATAAAAA
1 TTATAAAAA
21350544 CTATATGTAT
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
9 7 0.12
10 45 0.75
11 8 0.13
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:21350910 original size:50 final size:52
Alignment explanation
Indices: 21350845--21350945 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 52
21350835 AAAAAAAAAA
*
21350845 ATTTCTTATAAATTTT-A-ATTTTTAAATAATTTTCTATAATA-TTTTTAATC
1 ATTTCTTATAAATTTTAATATTTTTAAACAATTTTCTATAA-AGTTTTTAATC
*
21350895 ATTTCTTATAGATTTTAATTATTTTTAAACAATTTTCTATAAAGTTTTTAA
1 ATTTCTTATAAATTTTAA-TATTTTTAAACAATTTTCTATAAAGTTTTTAA
21350946 GAACTATGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
50 15 0.33
51 1 0.02
52 1 0.02
53 28 0.62
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (52 bp):
ATTTCTTATAAATTTTAATATTTTTAAACAATTTTCTATAAAGTTTTTAATC
Found at i:21353412 original size:15 final size:15
Alignment explanation
Indices: 21353392--21353428 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
21353382 CTCTCGAACT
21353392 AATGCTTATCAGTAA
1 AATGCTTATCAGTAA
21353407 AATGCTTATCAGTAA
1 AATGCTTATCAGTAA
21353422 AATGCTT
1 AATGCTT
21353429 CATACGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (15 bp):
AATGCTTATCAGTAA
Found at i:21356377 original size:23 final size:22
Alignment explanation
Indices: 21356310--21356416 Score: 121
Period size: 23 Copynumber: 4.9 Consensus size: 22
21356300 CTTGATCATT
21356310 ATACGACACAT-AAGTGCCTGA
1 ATACGACACATGAAGTGCCTGA
*
21356331 A-ACGACACATGAGGTGCCTG-
1 ATACGACACATGAAGTGCCTGA
* *
21356351 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATGAAGTGCCTG-A
*
21356374 ATACGACACATAAAGTGCCTGA
1 ATACGACACATGAAGTGCCTGA
* *
21356396 TATACAACACATAAAGTGCCT
1 -ATACGACACATGAAGTGCCT
21356417 AATCAGAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
20 10 0.13
21 27 0.36
22 1 0.01
23 37 0.49
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (22 bp):
ATACGACACATGAAGTGCCTGA
Found at i:21356392 original size:44 final size:41
Alignment explanation
Indices: 21356310--21356397 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 41
21356300 CTTGATCATT
* * *
21356310 ATACGACACATAAGTGCCTGAAACGACACATGAGGTGCCTG
1 ATACGACACAGAAGTGCCTGAAACGACACATAAAGTGCCTG
*
21356351 ATACGACACACGAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 ATACGACACA-GAAGTGCCTG-AA-ACGACACATAAAGTGCCTG
21356395 ATA
1 ATA
21356398 TACAACACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 10 0.25
42 8 0.20
43 2 0.05
44 20 0.50
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (41 bp):
ATACGACACAGAAGTGCCTGAAACGACACATAAAGTGCCTG
Found at i:21357723 original size:15 final size:16
Alignment explanation
Indices: 21357691--21357724 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21357681 ACCCTAATTT
*
21357691 TTCCCTTTTTCTTTTC
1 TTCCCCTTTTCTTTTC
21357707 TTCCCCTTTTC-TTTC
1 TTCCCCTTTTCTTTTC
21357722 TTC
1 TTC
21357725 TTGTTTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TTCCCCTTTTCTTTTC
Found at i:21357767 original size:14 final size:15
Alignment explanation
Indices: 21357743--21357771 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21357733 GAATGGCTTA
21357743 TGCTATTCTTTCTTT
1 TGCTATTCTTTCTTT
21357758 TGCT-TTCTTTCTTT
1 TGCTATTCTTTCTTT
21357772 ATTTCATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.03, C:0.21, G:0.07, T:0.69
Consensus pattern (15 bp):
TGCTATTCTTTCTTT
Found at i:21359064 original size:27 final size:26
Alignment explanation
Indices: 21359024--21359138 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
21359014 AGCATGGCTG
* ** *
21359024 CCAGAACAAATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
21359050 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
21359078 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
21359105 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
21359132 CCAGAAC
1 CCAGAAC
21359139 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.06
27 57 0.73
28 16 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:21359083 original size:54 final size:54
Alignment explanation
Indices: 21359024--21359138 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
21359014 AGCATGGCTG
* *
21359024 CCAGAACAAATA-ATGTGATAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAAATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
21359078 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAAATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
21359132 CCAGAAC
1 CCAGAAC
21359139 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAAATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:21360866 original size:26 final size:26
Alignment explanation
Indices: 21360757--21360858 Score: 177
Period size: 26 Copynumber: 3.9 Consensus size: 26
21360747 CATGAAATTC
21360757 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
21360783 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
21360809 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
21360835 TTATCATGGAACATTTACCTAACC
1 TTATCATGAAACATTTACCTAACC
21360859 TTTTATCAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:21361506 original size:20 final size:19
Alignment explanation
Indices: 21361460--21361506 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
21361450 AGTCCTTTTT
*
21361460 CCTAATTTCTCTTAATTAAG
1 CCTAA-TTCACTTAATTAAG
21361480 -CTAAATTCACTTAATTAAAG
1 CCT-AATTCACTTAATT-AAG
21361500 CCTAATT
1 CCTAATT
21361507 AAACAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (19 bp):
CCTAATTCACTTAATTAAG
Found at i:21370042 original size:22 final size:22
Alignment explanation
Indices: 21370017--21370075 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
21370007 TTAGTGGCCT
21370017 AATTATTGAAATTATAAATTAA
1 AATTATTGAAATTATAAATTAA
* * *
21370039 AATTCA-AGGATTTATAAATTAA
1 AATT-ATTGAAATTATAAATTAA
21370061 AATT-TTAGAAATTAT
1 AATTATT-GAAATTAT
21370076 GATATAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (22 bp):
AATTATTGAAATTATAAATTAA
Found at i:21377195 original size:15 final size:15
Alignment explanation
Indices: 21377152--21377205 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
21377142 ATATTATAAT
21377152 TTTTATT-AATTCATA
1 TTTTATTAAATT-ATA
*
21377167 TTTTAATAATAATTATA
1 TTTT-ATTA-AATTATA
21377184 TTTTATTAAATTATA
1 TTTTATTAAATTATA
*
21377199 TATTATT
1 TTTTATT
21377206 TTATTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 17 0.52
16 5 0.15
17 7 0.21
18 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATTAAATTATA
Found at i:21377291 original size:6 final size:6
Alignment explanation
Indices: 21377280--21377320 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
21377270 ATTAAAATTT
21377280 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAA
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAA
21377321 TAAATCTACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAC
Found at i:21378516 original size:30 final size:29
Alignment explanation
Indices: 21378456--21378517 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
21378446 CTTTTATACC
*
21378456 TTAATTAAACCTTAATTAACATTACTTAA
1 TTAATTAAACCTTAATTAACATTAATTAA
* *
21378485 TTAATTAAATCTTTAATTAA-TTTAATATAA
1 TTAATTAAA-CCTTAATTAACATTAAT-TAA
21378515 TTA
1 TTA
21378518 TCATTAGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAATTAAACCTTAATTAACATTAATTAA
Found at i:21381147 original size:10 final size:10
Alignment explanation
Indices: 21381113--21381167 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
21381103 AATTTTAGCT
21381113 TTTATATTTA
1 TTTATATTTA
**
21381123 TTTATCCTTA
1 TTTATATTTA
21381133 TTTATATTTA
1 TTTATATTTA
*
21381143 ATTATATTTA
1 TTTATATTTA
21381153 TTTA-ATTGTA
1 TTTATATT-TA
21381163 TTTAT
1 TTTAT
21381168 CTTTTAGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 3 0.08
10 34 0.92
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTATATTTA
Found at i:21381147 original size:14 final size:14
Alignment explanation
Indices: 21381137--21381167 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21381127 TCCTTATTTA
21381137 TATTTAATTATATT
1 TATTTAATTATATT
*
21381151 TATTTAATTGTATT
1 TATTTAATTATATT
21381165 TAT
1 TAT
21381168 CTTTTAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TATTTAATTATATT
Found at i:21396019 original size:16 final size:16
Alignment explanation
Indices: 21395987--21396080 Score: 68
Period size: 16 Copynumber: 5.7 Consensus size: 16
21395977 GCAACCCAAC
*
21395987 TTTTATT-TTTGTTTAT
1 TTTTATTATTT-TATAT
*
21396003 TTTTCTTATTTTATAT
1 TTTTATTATTTTATAT
21396019 TTTATATTATTTATATTAT
1 TTT-TATTATTT-TA-TAT
21396038 TTATTATTTATTTTATA-
1 TT-TTA-TTATTTTATAT
* * *
21396055 ATTTA-TAATTTATAA
1 TTTTATTATTTTATAT
21396070 TTTTATTATTT
1 TTTTATTATTT
21396081 ATTACTTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 8 0.13
15 4 0.06
16 20 0.32
17 11 0.17
18 4 0.06
19 9 0.14
20 7 0.11
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (16 bp):
TTTTATTATTTTATAT
Found at i:21396021 original size:7 final size:7
Alignment explanation
Indices: 21396009--21396080 Score: 58
Period size: 7 Copynumber: 9.7 Consensus size: 7
21395999 TTATTTTTCT
21396009 TATTTTA
1 TATTTTA
21396016 TATTTTA
1 TATTTTA
21396023 TATTATTTA
1 TA-T-TTTA
21396032 TATTATT-
1 TATT-TTA
21396039 TATTATT-
1 TATT-TTA
21396046 TATTTTA
1 TATTTTA
*
21396053 TAATTTA
1 TATTTTA
*
21396060 TAATTTA
1 TATTTTA
21396067 TAATTTTA
1 T-ATTTTA
21396075 TTATTT
1 -TATTT
21396081 ATTACTTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
6 2 0.04
7 35 0.61
8 13 0.23
9 7 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TATTTTA
Found at i:21396028 original size:26 final size:24
Alignment explanation
Indices: 21395987--21396050 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
21395977 GCAACCCAAC
* * *
21395987 TTTTATTTTTGTTTATTTTTCTTA
1 TTTTATTTTTATTTATTTATATTA
21396011 TTTTATATTTTATATTATTTATATTA
1 TTTTAT-TTTTAT-TTATTTATATTA
21396037 -TTTATTATTTATTT
1 TTTTATT-TTTATTT
21396051 TATAATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 9 0.26
25 15 0.44
26 10 0.29
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATTTTTATTTATTTATATTA
Found at i:21396031 original size:9 final size:9
Alignment explanation
Indices: 21396019--21396082 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
21396009 TATTTTATAT
21396019 TTTATATTA
1 TTTATATTA
21396028 TTTATATTA
1 TTTATATTA
21396037 TTTATTATTTA
1 TTTA-TA-TTA
*
21396048 TTT-TATAA
1 TTTATATTA
21396056 TTTATA--A
1 TTTATATTA
21396063 TTTATA--A
1 TTTATATTA
21396070 TTT-TATTA
1 TTTATATTA
21396078 TTTAT
1 TTTAT
21396083 TACTTTATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
6 2 0.04
7 11 0.23
8 9 0.19
9 18 0.38
10 2 0.04
11 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATATTA
Found at i:21396050 original size:37 final size:34
Alignment explanation
Indices: 21396008--21396083 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 34
21395998 TTTATTTTTC
* *
21396008 TTATTTTATATTTTATATTATTTATATTATTTATTAT
1 TTATTTTATAATTTATA--ATTTATAAT-TTTATTAT
21396045 TTATTTTATAATTTATAATTTATAATTTTATTAT
1 TTATTTTATAATTTATAATTTATAATTTTATTAT
21396079 TTATT
1 TTATT
21396084 ACTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 13 0.35
35 8 0.22
37 16 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (34 bp):
TTATTTTATAATTTATAATTTATAATTTTATTAT
Found at i:21396081 original size:7 final size:7
Alignment explanation
Indices: 21396032--21396091 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
21396022 ATATTATTTA
21396032 TATTATT
1 TATTATT
21396039 TATTATT
1 TATTATT
21396046 TA-T-TT
1 TATTATT
*
21396051 TATAATT
1 TATTATT
*
21396058 TATAATT
1 TATTATT
*
21396065 TATAATTT
1 TATTA-TT
21396073 TATTATT
1 TATTATT
21396080 TATTACTT
1 TATTA-TT
21396088 TATT
1 TATT
21396092 TTTGGATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
5 4 0.09
6 1 0.02
7 30 0.64
8 12 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTATT
Found at i:21396089 original size:15 final size:14
Alignment explanation
Indices: 21396032--21396091 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
21396022 ATATTATTTA
21396032 TATTATTTATTATT
1 TATTATTTATTATT
*
21396046 TA-T-TTTATAATT
1 TATTATTTATTATT
* *
21396058 TATAATTTATAATTT
1 TATTATTTATTA-TT
21396073 TATTATTTATTACTT
1 TATTATTTATTA-TT
21396088 TATT
1 TATT
21396092 TTTGGATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
12 10 0.26
13 1 0.03
14 9 0.24
15 18 0.47
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTTATTATT
Found at i:21398831 original size:99 final size:99
Alignment explanation
Indices: 21398651--21398834 Score: 289
Period size: 99 Copynumber: 1.9 Consensus size: 99
21398641 AAATTATTTT
*
21398651 TTAGGAAGATGTTGGACTGAGTAACTGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAA
1 TTAGGAAGATGTTGGACTGAGTAACCGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAA
* *
21398716 AGGTTCGATATGTTCTTAAGAAAAATATAATAAA
66 AGGTTCAATATATTCTTAAGAAAAATATAATAAA
* * *
21398750 TTAGG-AGTATGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAA
1 TTAGGAAG-ATGTTGGACTGAGTAACCGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAA
*
21398814 AAGGTTCAATGTATTCTTAAG
65 AAGGTTCAATATATTCTTAAG
21398835 CAATAATAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 2 0.03
99 75 0.97
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (99 bp):
TTAGGAAGATGTTGGACTGAGTAACCGAGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAA
AGGTTCAATATATTCTTAAGAAAAATATAATAAA
Found at i:21398873 original size:8 final size:8
Alignment explanation
Indices: 21398857--21398913 Score: 78
Period size: 8 Copynumber: 6.8 Consensus size: 8
21398847 TTATAATGAT
21398857 AAAAAGAA
1 AAAAAGAA
*
21398865 AATAAGAA
1 AAAAAGAA
21398873 AAAAAGAA
1 AAAAAGAA
21398881 AAAAAGAAGA
1 AAAAAG-A-A
21398891 AAAAAGAAA
1 AAAAAG-AA
21398900 AAAAAGAA
1 AAAAAGAA
21398908 AAAAAG
1 AAAAAG
21398914 TAATGTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 28 0.62
9 8 0.18
10 9 0.20
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:21398877 original size:11 final size:10
Alignment explanation
Indices: 21398857--21398912 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
21398847 TTATAATGAT
*
21398857 AAAAAGAAAAT
1 AAAAA-AAAAG
21398868 AAGAAAAAAAG
1 AA-AAAAAAAG
21398879 --AAAAAAAG
1 AAAAAAAAAG
*
21398887 AAGAAAAAAG
1 AAAAAAAAAG
21398897 -AAAAAAAAG
1 AAAAAAAAAG
21398906 AAAAAAA
1 AAAAAAA
21398913 GTAATGTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 13 0.34
11 6 0.16
12 3 0.08
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:21398901 original size:27 final size:27
Alignment explanation
Indices: 21398860--21398913 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
21398850 TAATGATAAA
21398860 AAGAAAATAAGAAAAAAAGAAAAAAAG
1 AAGAAAATAAGAAAAAAAGAAAAAAAG
21398887 AAGAAAA-AAGAAAAAAAAGAAAAAAAG
1 AAGAAAATAAG-AAAAAAAGAAAAAAAG
21398914 TAATGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (27 bp):
AAGAAAATAAGAAAAAAAGAAAAAAAG
Found at i:21399559 original size:10 final size:10
Alignment explanation
Indices: 21399544--21399592 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
21399534 AATTTTAGCT
21399544 TTTATCTTTA
1 TTTATCTTTA
21399554 TTTATCTTTA
1 TTTATCTTTA
*
21399564 ATTATCTTTA
1 TTTATCTTTA
*
21399574 TTTAAT-TGTA
1 TTT-ATCTTTA
21399584 TTTATCTTT
1 TTTATCTTT
21399593 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:21405325 original size:27 final size:27
Alignment explanation
Indices: 21405287--21405338 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
21405277 AAAGGTGAGA
*
21405287 TCATAAAATTAATA-TTTAGTTATTAAT
1 TCATAAAATTAA-ACTTAAGTTATTAAT
*
21405314 TCATCAAATTAAACTTAAGTTATTA
1 TCATAAAATTAAACTTAAGTTATTA
21405339 TTTATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (27 bp):
TCATAAAATTAAACTTAAGTTATTAAT
Found at i:21429937 original size:13 final size:13
Alignment explanation
Indices: 21429919--21429954 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
21429909 GAAGAAATTG
21429919 AAGTCACACGGCC
1 AAGTCACACGGCC
*
21429932 AAGTCACACAGCC
1 AAGTCACACGGCC
21429945 AAGTCACACG
1 AAGTCACACG
21429955 CTCGTGTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.19, T:0.08
Consensus pattern (13 bp):
AAGTCACACGGCC
Found at i:21448973 original size:16 final size:17
Alignment explanation
Indices: 21448934--21448977 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
21448924 TTTAATCTAG
* *
21448934 TTATTTTTAAATAATAT
1 TTATTTTAAAATAACAT
21448951 TTA-TTTAAAAT-ACAT
1 TTATTTTAAAATAACAT
21448966 TTATTTTAAAAT
1 TTATTTTAAAAT
21448978 TATTATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 15 0.62
17 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTTAAAATAACAT
Found at i:21450191 original size:56 final size:56
Alignment explanation
Indices: 21450105--21450216 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
21450095 AATGTGTGTT
21450105 TATTTACATCTGAAGCAAAATTCAATTTGTCATGAAAGATTTGCAAACAATCTTTC
1 TATTTACATCTGAAGCAAAATTCAATTTGTCATGAAAGATTTGCAAACAATCTTTC
21450161 TATTTACATCTGAAGCAAAATTCAATTTGTCATGAAAGATTTGCAAACAATCTTTC
1 TATTTACATCTGAAGCAAAATTCAATTTGTCATGAAAGATTTGCAAACAATCTTTC
21450217 CTTATGAAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (56 bp):
TATTTACATCTGAAGCAAAATTCAATTTGTCATGAAAGATTTGCAAACAATCTTTC
Found at i:21455011 original size:15 final size:15
Alignment explanation
Indices: 21454963--21455013 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
21454953 TCTGTATAGG
*
21454963 TGAACCCCCTGTACA
1 TGAACCCCCTGTATA
* * *
21454978 TG-AGCCCATGTATG
1 TGAACCCCCTGTATA
*
21454992 CGAACCCCCTGTATA
1 TGAACCCCCTGTATA
21455007 TGAACCC
1 TGAACCC
21455014 TATAGACGAA
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (15 bp):
TGAACCCCCTGTATA
Found at i:21455024 original size:28 final size:29
Alignment explanation
Indices: 21454964--21455025 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
21454954 CTGTATAGGT
* *
21454964 GAACCCCCTGTACATGAGCCCATGTATGC
1 GAACCCCCTGTACATGAACCCATATATGC
*
21454993 GAACCCCCTGTATATGAACCC-TATA-GAC
1 GAACCCCCTGTACATGAACCCATATATG-C
21455021 GAACC
1 GAACC
21455026 TCTTAATGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 1 0.03
28 9 0.31
29 19 0.66
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.19
Consensus pattern (29 bp):
GAACCCCCTGTACATGAACCCATATATGC
Found at i:21455136 original size:34 final size:34
Alignment explanation
Indices: 21455091--21455205 Score: 205
Period size: 34 Copynumber: 3.4 Consensus size: 34
21455081 TTAGCATGCA
*
21455091 AACCCCAATGTTATATAGTATGAAGTAGTATGTG
1 AACCCCCATGTTATATAGTATGAAGTAGTATGTG
21455125 AACCCCCATGTTATATAGTATGAAGTAGTATGTG
1 AACCCCCATGTTATATAGTATGAAGTAGTATGTG
*
21455159 AACCCCCATGTTATATAGTATGACGTAGTATGTG
1 AACCCCCATGTTATATAGTATGAAGTAGTATGTG
21455193 AA-CCCCATGTTAT
1 AACCCCCATGTTAT
21455206 GTACTTTGTG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
33 11 0.14
34 68 0.86
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (34 bp):
AACCCCCATGTTATATAGTATGAAGTAGTATGTG
Found at i:21455242 original size:15 final size:15
Alignment explanation
Indices: 21455222--21455270 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
21455212 TGTGAATTAA
21455222 ATGTGCGAACCCTAT
1 ATGTGCGAACCCTAT
*
21455237 ATGTGCGAACCCTGT
1 ATGTGCGAACCCTAT
** *
21455252 ATGTGTAAACCCTAC
1 ATGTGCGAACCCTAT
21455267 ATGT
1 ATGT
21455271 ATAAATCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (15 bp):
ATGTGCGAACCCTAT
Found at i:21455359 original size:15 final size:15
Alignment explanation
Indices: 21455339--21455434 Score: 120
Period size: 15 Copynumber: 6.4 Consensus size: 15
21455329 AGCGTTCCTG
21455339 TATGTGCGAACCCTA
1 TATGTGCGAACCCTA
* *
21455354 TATGTGTGAACCTTA
1 TATGTGCGAACCCTA
* * * *
21455369 TATGTACGATCCTTG
1 TATGTGCGAACCCTA
21455384 TATGTGCGAACCCTA
1 TATGTGCGAACCCTA
*
21455399 TATGCGCGAACCCTA
1 TATGTGCGAACCCTA
*
21455414 TATGTGCGAACCCTT
1 TATGTGCGAACCCTA
21455429 TATGTG
1 TATGTG
21455435 AACCTATAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 68 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (15 bp):
TATGTGCGAACCCTA
Found at i:21455433 original size:45 final size:45
Alignment explanation
Indices: 21455337--21455434 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
21455327 TAAGCGTTCC
* * * *
21455337 TGTATGTGCGAACCCTATATGTGTGAACCTTATATGTACGATCCT
1 TGTATGTGCGAACCCTATATGCGCGAACCCTATATGTACGACCCT
*
21455382 TGTATGTGCGAACCCTATATGCGCGAACCCTATATGTGCGAACCCT
1 TGTATGTGCGAACCCTATATGCGCGAACCCTATATGTACG-ACCCT
21455428 T-TATGTG
1 TGTATGTG
21455435 AACCTATAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 42 0.89
46 5 0.11
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (45 bp):
TGTATGTGCGAACCCTATATGCGCGAACCCTATATGTACGACCCT
Found at i:21456952 original size:11 final size:12
Alignment explanation
Indices: 21456921--21456963 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
21456911 TTGATGATAA
*
21456921 TTATATTTTTCT
1 TTATCTTTTTCT
*
21456933 TTGTCTTTTT-T
1 TTATCTTTTTCT
21456944 TTA-CTTTTTCT
1 TTATCTTTTTCT
21456955 TTATCTTTT
1 TTATCTTTT
21456964 AATAATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.23
11 7 0.27
12 13 0.50
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (12 bp):
TTATCTTTTTCT
Found at i:21457624 original size:17 final size:17
Alignment explanation
Indices: 21457604--21457643 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
21457594 TATAAAAGCC
21457604 TATAATAATTTAAAATA
1 TATAATAATTTAAAATA
* * *
21457621 TATAAAAATTTATAGTA
1 TATAATAATTTAAAATA
21457638 TATAAT
1 TATAAT
21457644 TTATAAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TATAATAATTTAAAATA
Found at i:21461888 original size:18 final size:19
Alignment explanation
Indices: 21461865--21461902 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21461855 AAATAGTAAC
*
21461865 TAAATT-ATATTAGTTTTT
1 TAAATTGATATTAATTTTT
*
21461883 TAAATTGGTATTAATTTTT
1 TAAATTGATATTAATTTTT
21461902 T
1 T
21461903 TTGTTAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
TAAATTGATATTAATTTTT
Found at i:21463220 original size:7 final size:7
Alignment explanation
Indices: 21463204--21463243 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
21463194 TATTATATTT
*
21463204 AAATTTA
1 AAATTCA
21463211 AAATTCA
1 AAATTCA
21463218 AAATTCA
1 AAATTCA
21463225 AAATTCA
1 AAATTCA
* *
21463232 AATTTTA
1 AAATTCA
21463239 AAATT
1 AAATT
21463244 TAATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATTCA
Found at i:21463227 original size:14 final size:14
Alignment explanation
Indices: 21463204--21463243 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
21463194 TATTATATTT
21463204 AAATTTAAAATTCA
1 AAATTTAAAATTCA
*
21463218 AAATTCAAAATTCA
1 AAATTTAAAATTCA
*
21463232 AATTTTAAAATT
1 AAATTTAAAATT
21463244 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTTAAAATTCA
Found at i:21463245 original size:7 final size:7
Alignment explanation
Indices: 21463200--21463246 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
21463190 AATCTATTAT
21463200 ATTT-AA
1 ATTTAAA
21463206 ATTTAAA
1 ATTTAAA
*
21463213 ATTCAAA
1 ATTTAAA
*
21463220 ATTCAAA
1 ATTTAAA
*
21463227 ATTCAAA
1 ATTTAAA
*
21463234 TTTTAAA
1 ATTTAAA
21463241 ATTTAA
1 ATTTAA
21463247 TTTTTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 4 0.11
7 32 0.89
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (7 bp):
ATTTAAA
Found at i:21463270 original size:15 final size:15
Alignment explanation
Indices: 21463234--21463271 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
21463224 AAAATTCAAA
*
21463234 TTTTAAAAT-TTAAT
1 TTTTAATATATTAAT
21463248 TTTT-ATATATTAAT
1 TTTTAATATATTAAT
21463262 TTTTAATATA
1 TTTTAATATA
21463272 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 13 0.62
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAATATATTAAT
Found at i:21463280 original size:17 final size:17
Alignment explanation
Indices: 21463240--21463283 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 17
21463230 CAAATTTTAA
21463240 AATTTAATTTTT-ATAT
1 AATTTAATTTTTAATAT
21463256 -A-TTAATTTTTAATAT
1 AATTTAATTTTTAATAT
*
21463271 AATTTGATTTTTA
1 AATTTAATTTTTA
21463284 TATTTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 9 0.38
15 5 0.21
16 1 0.04
17 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
AATTTAATTTTTAATAT
Found at i:21467784 original size:18 final size:18
Alignment explanation
Indices: 21467761--21467795 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21467751 ATAAGAAATT
21467761 CTCCTAAGTATTATAGTC
1 CTCCTAAGTATTATAGTC
21467779 CTCCTAAGTATTATAGT
1 CTCCTAAGTATTATAGT
21467796 TTCATGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (18 bp):
CTCCTAAGTATTATAGTC
Found at i:21470638 original size:45 final size:45
Alignment explanation
Indices: 21470567--21470669 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
21470557 GTTTGCAGAC
* * * * * * *
21470567 AAGCTGGTAGTACGGTGTGGATAAACCATTTATTGGTGTAGATAA
1 AAGCTGCTAGTACGGTGTGAATAAACCACTCATTGATGCAAATAA
* *
21470612 AAGTTGCTAGTACGTTGTGAATAAACCACTCATTGATGCAAATAA
1 AAGCTGCTAGTACGGTGTGAATAAACCACTCATTGATGCAAATAA
21470657 AAGCTGCTAGTAC
1 AAGCTGCTAGTAC
21470670 ATTATGCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (45 bp):
AAGCTGCTAGTACGGTGTGAATAAACCACTCATTGATGCAAATAA
Found at i:21470760 original size:79 final size:79
Alignment explanation
Indices: 21470614--21470769 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
21470604 GTAGATAAAA
* *
21470614 GTTGCTAGTACGTTGTGAATAAACCACTCATTGATGCAAATAAAAGCTGCTAGTACATTATGCAT
1 GTTGCTAGTACGTTGTGAATAAACCACTCATTGATACAAATAAAAGCTACTAGTACATTATGCAT
*
21470679 AAACTACTCATCAG
66 AAACCACTCATCAG
* * ** * *
21470693 GTTGCTAGTATGTTGTGGATAAACCACTTGTTGATACAGATAAAAGCTACTAGTAC-GT-TGCAG
1 GTTGCTAGTACGTTGTGAATAAACCACTCATTGATACAAATAAAAGCTACTAGTACATTATGC--
21470756 ATAAACCACTCATC
64 ATAAACCACTCATC
21470770 GATGCAGAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 3 0.05
78 1 0.02
79 62 0.94
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (79 bp):
GTTGCTAGTACGTTGTGAATAAACCACTCATTGATACAAATAAAAGCTACTAGTACATTATGCAT
AAACCACTCATCAG
Found at i:21472218 original size:30 final size:30
Alignment explanation
Indices: 21472170--21472226 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
21472160 TAGACACTTC
* *
21472170 CACACGGGTAATCTACACGCCCGTGTGAGA
1 CACACGGGTAAGCCACACGCCCGTGTGAGA
* *
21472200 CACACGGGTAGGCCACACGCCTGTGTG
1 CACACGGGTAAGCCACACGCCCGTGTG
21472227 TCATGGCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.23, C:0.32, G:0.30, T:0.16
Consensus pattern (30 bp):
CACACGGGTAAGCCACACGCCCGTGTGAGA
Found at i:21485864 original size:25 final size:25
Alignment explanation
Indices: 21485830--21485933 Score: 158
Period size: 25 Copynumber: 4.2 Consensus size: 25
21485820 CAAAATGACT
21485830 TGGCACTAAGTGTGCGGAATTTATA
1 TGGCACTAAGTGTGCGGAATTTATA
*
21485855 TGGCACTAAGTGTGCGGAAATTATA
1 TGGCACTAAGTGTGCGGAATTTATA
21485880 TGGCACTAAGTGTGCGGAAATTT-TA
1 TGGCACTAAGTGTGCGG-AATTTATA
* *
21485905 TGGCACTATGTGTGC-GAATATATA
1 TGGCACTAAGTGTGCGGAATTTATA
21485929 TGGCA
1 TGGCA
21485934 TTGGTGTGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
23 4 0.05
24 8 0.11
25 57 0.78
26 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (25 bp):
TGGCACTAAGTGTGCGGAATTTATA
Found at i:21491151 original size:22 final size:23
Alignment explanation
Indices: 21491112--21491168 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
21491102 AATAATAATT
*
21491112 TTAAATAATATTCTTAATATTTTA
1 TTAAA-AATATACTTAATATTTTA
21491136 TTAAAAATATAC-TAATATTTTA
1 TTAAAAATATACTTAATATTTTA
*
21491158 ATATAAAATAT
1 TTA-AAAATAT
21491169 TTATTACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 12 0.40
23 13 0.43
24 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAAAATATACTTAATATTTTA
Found at i:21491165 original size:23 final size:22
Alignment explanation
Indices: 21491126--21491168 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
21491116 ATAATATTCT
*
21491126 TAATATTTTATTAAAAATATAC
1 TAATATTTTAATAAAAATATAC
21491148 TAATATTTTAATATAAAATAT
1 TAATATTTTAATA-AAAATAT
21491169 TTATTACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTTAATAAAAATATAC
Found at i:21491517 original size:171 final size:171
Alignment explanation
Indices: 21491232--21491574 Score: 650
Period size: 171 Copynumber: 2.0 Consensus size: 171
21491222 TAATATAACT
21491232 ATAAGTATTTGTTATCTTGCTTAATTTTATTTATCCCTTTGAACACTAATGTGACATTTTCTGCT
1 ATAAGTATTTGTTATCTTGCTTAATTTTATTTATCCCTTTGAACACTAATGTGACATTTTCTGCT
* *
21491297 TCTCATATTTATATTCATATTATTATTAATATTGAGTTAATGTTATCTCTCAATTGAGTTTCAAC
66 TCTCATAATTATATTCATATTATTATTAAGATTGAGTTAATGTTATCTCTCAATTGAGTTTCAAC
*
21491362 TTAGTTATGAAATTACTGAAATTTTATTTTTTTACTAAACA
131 TTAGTTATGAAATTACTGAAATTTCATTTTTTTACTAAACA
21491403 ATAAGTATTTGTTATCTTGCTTAATTTTATTTATCCCTTTGAACACTAATGTGACATTTTCTGCT
1 ATAAGTATTTGTTATCTTGCTTAATTTTATTTATCCCTTTGAACACTAATGTGACATTTTCTGCT
*
21491468 TCTCATAATTATATTCATATTATTATTAAGATTGAGTTAATGTTATCTCTTAATTGAGTTTCAAC
66 TCTCATAATTATATTCATATTATTATTAAGATTGAGTTAATGTTATCTCTCAATTGAGTTTCAAC
21491533 TTAGTTATGAAATTACTGAAATTTCATTTTTTTACTAAACA
131 TTAGTTATGAAATTACTGAAATTTCATTTTTTTACTAAACA
21491574 A
1 A
21491575 CAAATATTAT
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 168 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (171 bp):
ATAAGTATTTGTTATCTTGCTTAATTTTATTTATCCCTTTGAACACTAATGTGACATTTTCTGCT
TCTCATAATTATATTCATATTATTATTAAGATTGAGTTAATGTTATCTCTCAATTGAGTTTCAAC
TTAGTTATGAAATTACTGAAATTTCATTTTTTTACTAAACA
Found at i:21492584 original size:20 final size:19
Alignment explanation
Indices: 21492542--21492585 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
21492532 TTATAACATT
* * *
21492542 TTCTTTCAACTTTTTTTTG
1 TTCTTTCAACGTTTCTTTC
21492561 TTCTTTACAACGTTTCTTTC
1 TTCTTT-CAACGTTTCTTTC
21492581 TTCTT
1 TTCTT
21492586 CTTTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.11, C:0.20, G:0.05, T:0.64
Consensus pattern (19 bp):
TTCTTTCAACGTTTCTTTC
Found at i:21493360 original size:21 final size:21
Alignment explanation
Indices: 21493335--21493375 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21493325 AAACTCGAAT
*
21493335 TTGAACCCTGAACATTAAATC
1 TTGAACCATGAACATTAAATC
*
21493356 TTGAACCATGAACCTTAAAT
1 TTGAACCATGAACATTAAAT
21493376 TCCAAACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
TTGAACCATGAACATTAAATC
Found at i:21494323 original size:21 final size:22
Alignment explanation
Indices: 21494293--21494349 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
21494283 CCTTCAAAAA
*
21494293 TCTATCAAAATTC-ATTGAAATT
1 TCTATCAAAATTCTA-TCAAATT
*
21494315 T-TCTCAAAATTCTATCAAATT
1 TCTATCAAAATTCTATCAAATT
21494336 TCTATCAAAATTCT
1 TCTATCAAAATTCT
21494350 TTGTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTATCAAAATTCTATCAAATT
Found at i:21494332 original size:11 final size:11
Alignment explanation
Indices: 21494286--21494349 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
21494276 AATATTCCCT
*
21494286 TCAAAAATCTA
1 TCAAAATTCTA
21494297 TCAAAATTC-A
1 TCAAAATTCTA
** * *
21494307 TTGAAATTTTC
1 TCAAAATTCTA
21494318 TCAAAATTCTA
1 TCAAAATTCTA
*
21494329 TCAAATTTCTA
1 TCAAAATTCTA
21494340 TCAAAATTCT
1 TCAAAATTCT
21494350 TTGTTTAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 7 0.17
11 34 0.83
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (11 bp):
TCAAAATTCTA
Found at i:21494547 original size:48 final size:48
Alignment explanation
Indices: 21494487--21494593 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 48
21494477 ATAATTTTAA
* *
21494487 AATTTAAATACTATTCGATATTATT-TTAATTTATGCAAATT-TAATTA-
1 AATTTCAATACTATTCAATATT-TTATTAATTTATGC-AATTATAATTAC
* *
21494534 AATTTGCAATACTATTTAATATTTTATTCATTTATGCAATTATAATTAC
1 AATTT-CAATACTATTCAATATTTTATTAATTTATGCAATTATAATTAC
21494583 AATTTCAATAC
1 AATTTCAATAC
21494594 AGCTTTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
47 11 0.21
48 36 0.69
49 5 0.10
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (48 bp):
AATTTCAATACTATTCAATATTTTATTAATTTATGCAATTATAATTAC
Found at i:21495849 original size:25 final size:25
Alignment explanation
Indices: 21495813--21495865 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
21495803 TCCGACAACC
* *
21495813 GATTCTCGTGGCACTCGATGTGTTT
1 GATTCTCATGGCACCCGATGTGTTT
21495838 GATTCTCATGGCACCCGATGTGTTT
1 GATTCTCATGGCACCCGATGTGTTT
21495863 GAT
1 GAT
21495866 GATGAGCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (25 bp):
GATTCTCATGGCACCCGATGTGTTT
Found at i:21496248 original size:18 final size:18
Alignment explanation
Indices: 21496225--21496267 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
21496215 TGCCAGGTGC
*
21496225 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
21496243 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
21496261 GTTTCCT
1 GTATCCT
21496268 TTTCCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:21500026 original size:126 final size:126
Alignment explanation
Indices: 21499754--21500258 Score: 720
Period size: 126 Copynumber: 4.0 Consensus size: 126
21499744 TTATAGCCTC
* *
21499754 ATTTTTCTACGAACTACTGTAGCAAAATAGCGTCCACGTCG-GAGCTTTTTCCAGAAATTTTGCT
1 ATTTTTCAACGAACTACTGTAGCAAAAGAGCGTCCACGT-GAGAGCTTTTTCCAGAAATTTTGCT
* *
21499818 GACAGTGCATCCTGCTTGAA--A-CTTCGGCACTATTTGTTCAGAAATGTCTACTCAGAATT
65 GACAGTGCATCCTGCTTGAAGCATTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
*
21499877 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTG
1 ATTTTTCAACGAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTG
* * *
21499942 ACAGTGCATCTTGCTTGAAGCATTTTCGGCGCTATTTGTTGAGAAACGTCTACTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
* * *
21500003 ATTTTTCAACGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTTTTCTAGAAATTTTGCTG
1 ATTTTTCAACGAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTG
* * *
21500068 ACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTTAGAAACGTCTACTCAAAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
*
21500129 ATTTTTCTAA-GAACTACTGTAGCAAAAGAGCGTCCACGT-AGGAGCTTTTTTC-GAAAATTTTG
1 ATTTTTC-AACGAACTACTGTAGCAAAAGAGCGTCCACGTGA-GAGCTTTTTCCAG-AAATTTTG
* * * * *
21500191 CTGACAGTGCATCCTGCTTGAAGCGTTTTCTGACACTATTT-TTCCAGAAATGTCTGCTTAGAAT
63 CTGACAGTGCATCCTGCTTGAAGCATTTTC-GGCACTATTTGTT-CAGAAACGTCTACTCAGAAT
21500255 T
126 T
21500256 ATT
1 ATT
21500259 CTTGCAAAAA
Statistics
Matches: 348, Mismatches: 25, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
122 1 0.00
123 80 0.23
125 2 0.01
126 235 0.68
127 30 0.09
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (126 bp):
ATTTTTCAACGAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTG
ACAGTGCATCCTGCTTGAAGCATTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
Found at i:21500590 original size:20 final size:20
Alignment explanation
Indices: 21500565--21500637 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
21500555 TCTTGTATGT
21500565 ATCAATTAACCCTAAATTTA
1 ATCAATTAACCCTAAATTTA
* *
21500585 ATCAATTAACCCTAAACCCTAA
1 ATCAATTAACCCTAAA--TTTA
*
21500607 ATCAA-T--CCAT-AATTTA
1 ATCAATTAACCCTAAATTTA
21500623 ATCAATTAACCCTAA
1 ATCAATTAACCCTAA
21500638 TACCCTAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
16 7 0.17
17 1 0.02
18 2 0.05
19 6 0.15
20 17 0.41
21 1 0.02
22 7 0.17
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (20 bp):
ATCAATTAACCCTAAATTTA
Found at i:21505988 original size:15 final size:15
Alignment explanation
Indices: 21505952--21505988 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
21505942 ATTAAAATGT
*
21505952 TAAATATATATTTCA
1 TAAATATATATTTAA
21505967 TAAATATATATTTAA
1 TAAATATATATTTAA
*
21505982 TATATAT
1 TAAATAT
21505989 TTTTCTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATATATATTTAA
Found at i:21508648 original size:23 final size:24
Alignment explanation
Indices: 21508598--21508648 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
21508588 TATATAATTT
21508598 TTTTAAATAACTAACAAAAATGAC
1 TTTTAAATAACTAACAAAAATGAC
21508622 --TTAAATACACTAAC-AAAAT-AC
1 TTTTAAATA-ACTAACAAAAATGAC
21508643 TTTTAA
1 TTTTAA
21508649 CAGCAGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 2 0.08
22 12 0.50
23 10 0.42
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (24 bp):
TTTTAAATAACTAACAAAAATGAC
Found at i:21509579 original size:13 final size:13
Alignment explanation
Indices: 21509561--21509594 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21509551 TTAGAAGGAA
21509561 GTTAATGGTAATG
1 GTTAATGGTAATG
21509574 GTTAATGGTAATG
1 GTTAATGGTAATG
*
21509587 GTAAATGG
1 GTTAATGG
21509595 GGGTGTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (13 bp):
GTTAATGGTAATG
Found at i:21514703 original size:43 final size:43
Alignment explanation
Indices: 21514621--21514716 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 43
21514611 TGAAATTACA
** * *
21514621 TGTAAGACCATGTCTGGGACATTGAAATTTTATCCTGATTAT-G
1 TGTAAGACCATGTCTAAGACATTGAAATATTATCATGATT-TCG
**
21514664 TGTAAGACCATGTCTAAGACATTGGCATCATTAT-ATGATTTCG
1 TGTAAGACCATGTCTAAGACATTGAAAT-ATTATCATGATTTCG
21514707 TGTAAGACCA
1 TGTAAGACCA
21514717 CATCTGGGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.02
43 40 0.89
44 4 0.09
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTAAGACATTGAAATATTATCATGATTTCG
Found at i:21517711 original size:13 final size:13
Alignment explanation
Indices: 21517695--21517727 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21517685 TTTAATTAAC
*
21517695 TTAGTTAATTAGT
1 TTAGATAATTAGT
21517708 TTAGATAATTAGT
1 TTAGATAATTAGT
21517721 TTA-ATAA
1 TTAGATAA
21517728 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:21523091 original size:10 final size:9
Alignment explanation
Indices: 21523069--21523117 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
21523059 TGAATCCTCC
21523069 TATTT-TTT
1 TATTTATTT
21523077 TATTTATTCT
1 TATTTATT-T
*
21523087 TATTT-TTA
1 TATTTATTT
21523095 T-TTTATTT
1 TATTTATTT
21523103 TATTTATTTT
1 TATTTA-TTT
21523113 TATTT
1 TATTT
21523118 TTCTTTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 3 0.09
8 9 0.26
9 8 0.24
10 14 0.41
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (9 bp):
TATTTATTT
Found at i:21523100 original size:5 final size:5
Alignment explanation
Indices: 21523074--21523161 Score: 58
Period size: 5 Copynumber: 16.8 Consensus size: 5
21523064 CCTCCTATTT
*
21523074 TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA -TTTA TTTTTA TTTTTC
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA
*
21523121 TTTTGA TTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
21523162 GAAAGACATA
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
3 3 0.04
4 8 0.12
5 27 0.40
6 24 0.35
7 6 0.09
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:21523105 original size:26 final size:28
Alignment explanation
Indices: 21523073--21523135 Score: 94
Period size: 26 Copynumber: 2.3 Consensus size: 28
21523063 TCCTCCTATT
21523073 TTTTTATTTATTCTTATTTTTATTTT-A
1 TTTTTATTTATTCTTATTTTTATTTTGA
* *
21523100 -TTTTATTTATTTTTATTTTTCTTTTGA
1 TTTTTATTTATTCTTATTTTTATTTTGA
21523127 TTTTTATTT
1 TTTTTATTT
21523136 TCATTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 23 0.72
27 1 0.03
28 8 0.25
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (28 bp):
TTTTTATTTATTCTTATTTTTATTTTGA
Found at i:21523131 original size:7 final size:6
Alignment explanation
Indices: 21523069--21523141 Score: 67
Period size: 6 Copynumber: 11.8 Consensus size: 6
21523059 TGAATCCTCC
* *
21523069 TATTTT T-TTATT TATTCT TATTTT TATTTT ATTTTATT TATTTT TATTTT
1 TATTTT TATT-TT TATTTT TATTTT TATTTT -TATT-TT TATTTT TATTTT
* * *
21523119 TCTTTT GATTTT TATTTT CATTT
1 TATTTT TATTTT TATTTT TATTT
21523142 CAATTTTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 2 0.04
6 42 0.78
7 8 0.15
8 2 0.04
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:21523134 original size:44 final size:43
Alignment explanation
Indices: 21523069--21523161 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 43
21523059 TGAATCCTCC
* * *
21523069 TATTTTTTTATTTATTCTTATTTTTATTT-TATTTTATTTATTTT
1 TATTTTTTTATTGATTCTTATTTTCATTTCAATTTTA-TTA-TTT
*
21523113 TATTTTTCTT-TTGATTTTTATTTTCATTTCAATTTTATTATTT
1 TATTTTT-TTATTGATTCTTATTTTCATTTCAATTTTATTATTT
21523156 TATTTT
1 TATTTT
21523162 GAAAGACATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
43 9 0.21
44 26 0.60
45 8 0.19
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (43 bp):
TATTTTTTTATTGATTCTTATTTTCATTTCAATTTTATTATTT
Found at i:21526027 original size:13 final size:13
Alignment explanation
Indices: 21526011--21526043 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21526001 TTTAATTAAA
*
21526011 TTAGTTAATTAGT
1 TTAGATAATTAGT
21526024 TTAGATAATTAGT
1 TTAGATAATTAGT
21526037 TTA-ATAA
1 TTAGATAA
21526044 ACAAATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:21529147 original size:30 final size:30
Alignment explanation
Indices: 21529111--21529199 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
21529101 GACACGGCCT
** *
21529111 AGACACACGGGTTTGTCTACTGGTCATGTG
1 AGACACACGGGCGTGTCTACTGGGCATGTG
* *
21529141 AGACACACAGGCGTGTCTACTGGGCGTGTG
1 AGACACACGGGCGTGTCTACTGGGCATGTG
*
21529171 AGACACACGGGC-TGGC-ACATGGGCATGTG
1 AGACACACGGGCGTGTCTAC-TGGGCATGTG
21529200 GTCGGCCGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.04
29 12 0.24
30 36 0.72
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.21
Consensus pattern (30 bp):
AGACACACGGGCGTGTCTACTGGGCATGTG
Found at i:21535528 original size:33 final size:33
Alignment explanation
Indices: 21535487--21535554 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
21535477 GATGGAAAAG
* *
21535487 AGAAGAAGTTAGCATAAAGCTTATTAAGTTACA
1 AGAAGAAGTAAGCATAAAGCTTAGTAAGTTACA
21535520 AGAAGAAGTAAGCATAAAGCTTAGTAAGTTACA
1 AGAAGAAGTAAGCATAAAGCTTAGTAAGTTACA
21535553 AG
1 AG
21535555 TAAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (33 bp):
AGAAGAAGTAAGCATAAAGCTTAGTAAGTTACA
Found at i:21535947 original size:48 final size:48
Alignment explanation
Indices: 21535829--21536114 Score: 277
Period size: 48 Copynumber: 5.9 Consensus size: 48
21535819 AAAAGGCAAG
* * * * *
21535829 ATGCCGATGCCATATCCCAGACATGGTCTTACACTGGCACTCATATATCT
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAG--CTCACATATCA
* * * * *
21535879 GTGCTGATTCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCG
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
* * * * *
21535927 AGGCCGATGCCATGTCCCAAACATGGTCTTACACTAGTTCTCGTATAA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
* * * **
21535975 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCGTATATCA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
* * * * * *
21536023 AGGTCGATGCCATGTCCCAAACATGGTCTTACATTAGCTCTCGTATAA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
* * * *
21536071 ATGTCGATGCCATGTTCCAAACATGATC-TACACTGGCTCACATA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATA
21536115 CCCTTAGTAT
Statistics
Matches: 193, Mismatches: 43, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
47 12 0.06
48 151 0.78
50 30 0.16
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (48 bp):
ATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
Found at i:21536021 original size:96 final size:96
Alignment explanation
Indices: 21535831--21536114 Score: 399
Period size: 96 Copynumber: 2.9 Consensus size: 96
21535821 AAGGCAAGAT
* * * * * ** *
21535831 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCACTCATATATCTGTGCTGATTCCATGTTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTATAAATGT-C-GATGCCATGTTC
* *
21535896 CAAACATGGTCTTACACTAGCTCACATATCGAG
64 CAAACATGGTCTTACACTGGCTCACATATCAAG
*
21535929 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGTTCTCGTATAAATGTCGATGCCATGTTCCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTATAAATGTCGATGCCATGTTCCA
**
21535994 AACATGGTCTTACACTGGCTCGTATATCAAG
66 AACATGGTCTTACACTGGCTCACATATCAAG
* *
21536025 GTCGATGCCATGTCCCAAACATGGTCTTACATTAGCTCTCGTATAAATGTCGATGCCATGTTCCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTATAAATGTCGATGCCATGTTCCA
*
21536090 AACATGATC-TACACTGGCTCACATA
66 AACATGGTCTTACACTGGCTCACATA
21536115 CCCTTAGTAT
Statistics
Matches: 167, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
95 14 0.08
96 110 0.66
97 1 0.01
98 42 0.25
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTATAAATGTCGATGCCATGTTCCA
AACATGGTCTTACACTGGCTCACATATCAAG
Found at i:21536095 original size:144 final size:144
Alignment explanation
Indices: 21535833--21536104 Score: 343
Period size: 144 Copynumber: 1.9 Consensus size: 144
21535823 GGCAAGATGC
* * * *
21535833 CGATGCCATATCCCAGACATGGTCTTACACTGGCACTCATATATCTGTGCTGATTCCATGTTCCA
1 CGATGCCATATCCCAAACATGGTCTTACACTGG-ACTCATATATCGGTGCTGATGCCATGTCCCA
** *
21535898 AACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTA
65 AACATGGTCTTACACTAGCTCACATATAAAGGCCGATGCCATGTCCCAAACATGATC-TACACTA
21535963 GTTCTCGTATAAATGT
129 GTTCTCGTATAAATGT
* * *
21535979 CGATGCCATGTTCCAAACATGGTCTTACACTGG-CTCGTATATCAAGGT-C-GATGCCATGTCCC
1 CGATGCCATATCCCAAACATGGTCTTACACTGGACTCATATATC--GGTGCTGATGCCATGTCCC
* * * * * *
21536041 AAACATGGTCTTACATTAGCTCTCGTATAAATGTCGATGCCATGTTCCAAACATGATCTACACT
64 AAACATGGTCTTACACTAGCTCACATATAAAGGCCGATGCCATGTCCCAAACATGATCTACACT
21536105 GGCTCACATA
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
143 6 0.06
144 69 0.64
145 1 0.01
146 32 0.30
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (144 bp):
CGATGCCATATCCCAAACATGGTCTTACACTGGACTCATATATCGGTGCTGATGCCATGTCCCAA
ACATGGTCTTACACTAGCTCACATATAAAGGCCGATGCCATGTCCCAAACATGATCTACACTAGT
TCTCGTATAAATGT
Found at i:21540915 original size:20 final size:20
Alignment explanation
Indices: 21540890--21540931 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
21540880 AGGGTAAGTG
*
21540890 ATAAACATTCTATTTGGGCT
1 ATAAACATTCTATTTGGACT
21540910 ATAAACATTCTATTTGGACT
1 ATAAACATTCTATTTGGACT
21540930 AT
1 AT
21540932 TTTCGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (20 bp):
ATAAACATTCTATTTGGACT
Found at i:21543777 original size:42 final size:42
Alignment explanation
Indices: 21543656--21543777 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
21543646 GTTTCTGTTT
* * * **
21543656 AACCCTAATGGGTTTCCGGTTTAGCTCTTTTGAGCTTCAGTTT
1 AACCCTTATGGGTTTCC-GTTTAGCACTTATGAGCTTCAGTCC
* * * *
21543699 AACCCTTATGGGTTTCCATTCAGCACCTATAAGCTTCAGTCC
1 AACCCTTATGGGTTTCCGTTTAGCACTTATGAGCTTCAGTCC
* * *
21543741 AACCCTTACGGGTTTCTGTTTAGCACTTATGTGCTTC
1 AACCCTTATGGGTTTCCGTTTAGCACTTATGAGCTTC
21543778 TGTACAGCCT
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 47 0.75
43 16 0.25
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (42 bp):
AACCCTTATGGGTTTCCGTTTAGCACTTATGAGCTTCAGTCC
Found at i:21545196 original size:27 final size:27
Alignment explanation
Indices: 21545166--21545256 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
21545156 ATCAAAGTGC
*
21545166 GCCACAAAGGCGATCCATACAAAGTAT
1 GCCACAAAGGCGATCCATACAGAGTAT
* * * * *
21545193 GCCACAAAGGCTATCTATAGAGGGTAC
1 GCCACAAAGGCGATCCATACAGAGTAT
* * *
21545220 GCCACAAAGGTGATTCATTCAGAGTAT
1 GCCACAAAGGCGATCCATACAGAGTAT
21545247 GCCACAAAGG
1 GCCACAAAGG
21545257 TTGACAGGAT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
GCCACAAAGGCGATCCATACAGAGTAT
Found at i:21547874 original size:30 final size:30
Alignment explanation
Indices: 21547838--21547894 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
21547828 ATGGGCAGAG
* *
21547838 ACACGGGCGTGTGTCTCAGTCGTGTGTGAC
1 ACACGGGCATGTGTCACAGTCGTGTGTGAC
* *
21547868 ACACGGGCATGTTTCACGGTCGTGTGT
1 ACACGGGCATGTGTCACAGTCGTGTGT
21547895 CCCCTGGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.35, T:0.28
Consensus pattern (30 bp):
ACACGGGCATGTGTCACAGTCGTGTGTGAC
Found at i:21551619 original size:25 final size:25
Alignment explanation
Indices: 21551585--21551633 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
21551575 AGTACTTCGG
21551585 ATTGAGTCATCTCTAATTTTTTCAA
1 ATTGAGTCATCTCTAATTTTTTCAA
21551610 ATTGAGTCATCTCTAATTTTTTCA
1 ATTGAGTCATCTCTAATTTTTTCA
21551634 TATTTCCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (25 bp):
ATTGAGTCATCTCTAATTTTTTCAA
Found at i:21553020 original size:21 final size:21
Alignment explanation
Indices: 21552982--21553021 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21552972 TAGGGATTTT
* *
21552982 TTTAAGGGTTAAGTAAATTGC
1 TTTAAGGGATAAGAAAATTGC
*
21553003 TTTAAGGGATATGAAAATT
1 TTTAAGGGATAAGAAAATT
21553022 AGTAGAATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.38
Consensus pattern (21 bp):
TTTAAGGGATAAGAAAATTGC
Found at i:21557539 original size:39 final size:39
Alignment explanation
Indices: 21557483--21557659 Score: 291
Period size: 39 Copynumber: 4.5 Consensus size: 39
21557473 ACAAAGCATG
*
21557483 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
21557524 CGGGACTTAGCCCGGATATAGCACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
21557563 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
21557602 CAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
21557641 CGGGACTTAGCCCGAATAT
1 CGGGACTTAGCCCGGATAT
21557660 TTTTCCAATA
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 120 0.94
40 2 0.02
41 6 0.05
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:21559074 original size:3 final size:3
Alignment explanation
Indices: 21559066--21559096 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
21559056 TAAAAGATAC
21559066 TTA TTA TTA TTA TTA TTA TTA TTA TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
21559097 ATTGAGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21559254 original size:21 final size:21
Alignment explanation
Indices: 21559215--21559256 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21559205 ATTAGTTAAG
*
21559215 TAAATAAAATGAAATAAAGAA
1 TAAATAAAATGAAAGAAAGAA
21559236 TAAATAAAA-GAAAAGAAAGAA
1 TAAATAAAATG-AAAGAAAGAA
21559257 AAACAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (21 bp):
TAAATAAAATGAAAGAAAGAA
Found at i:21560229 original size:37 final size:38
Alignment explanation
Indices: 21560187--21560279 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 38
21560177 CGGATAGATT
*
21560187 CGATGAGGCGTTGGTCATCAC-TTTGCTTCG-GCTTAGC
1 CGATGAGGCGTTGGTCATCACTTTTGCTTCGAAC-TAGC
* * *
21560224 CGATGAGACGTTGGTCGTCACTTATTTGCTTCGAACTATC
1 CGATGAGGCGTTGGTCATCAC-T-TTTGCTTCGAACTAGC
21560264 CGATGAGGCGTTGGTC
1 CGATGAGGCGTTGGTC
21560280 GCCATTCTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 19 0.40
40 27 0.57
41 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.32
Consensus pattern (38 bp):
CGATGAGGCGTTGGTCATCACTTTTGCTTCGAACTAGC
Found at i:21567521 original size:57 final size:57
Alignment explanation
Indices: 21567433--21567547 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
21567423 TTTATAAAGG
21567433 TGTTTGATTGTTGTATTCAAGGCAAACCTCTACCAATCATCATTGCAAAATGACCTA
1 TGTTTGATTGTTGTATTCAAGGCAAACCTCTACCAATCATCATTGCAAAATGACCTA
*
21567490 TGTTTGATTGTTGTATTCAGGGCAAACCTCTACCAATCATCATTGCAAAATGACCTA
1 TGTTTGATTGTTGTATTCAAGGCAAACCTCTACCAATCATCATTGCAAAATGACCTA
21567547 T
1 T
21567548 CAAGTCTATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (57 bp):
TGTTTGATTGTTGTATTCAAGGCAAACCTCTACCAATCATCATTGCAAAATGACCTA
Found at i:21585267 original size:20 final size:22
Alignment explanation
Indices: 21585237--21585284 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
21585227 GGATATGCTG
*
21585237 TAAATTGAAAG-TTTTTGATAGA
1 TAAA-TGAAAGATTATTGATAGA
21585259 -AAATGAAAGATTATTGATAGA
1 TAAATGAAAGATTATTGATAGA
21585280 TAAAT
1 TAAAT
21585285 CACTTTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAATGAAAGATTATTGATAGA
Found at i:21586005 original size:33 final size:33
Alignment explanation
Indices: 21585968--21586208 Score: 126
Period size: 33 Copynumber: 7.6 Consensus size: 33
21585958 TACCCAAATG
**
21585968 GTACAACTTGAAAAGGTTATGTACACTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* *
21586001 GTAC-ACTTGAAAAGGAAAGGTATACTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* * * * *
21586033 ATACCA-TATGAAAATGAAAGGTATACTTTGTGT
1 GTACAACT-TGAAAAGGAAATGTACACTTTGTGT
* * *
21586066 ATACCACTTGAAAAGGAAAGGTACAC-------
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* ** * * *
21586092 -TA-TACTTGAAAAGGTTATATGCACTTTGAGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* ** *
21586123 GTACAAATTGAAAAGGGTATGTACACTTCGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* * * * * *
21586156 GTACCACTTGAAAAAGGGAATGTGCACCTCGAGT
1 GTACAACTTG-AAAAGGAAATGTACACTTTGTGT
*
21586190 GTACAACTAGAAAAGGAAA
1 GTACAACTTGAAAAGGAAA
21586209 AGTCCATCGG
Statistics
Matches: 165, Mismatches: 30, Indels: 26
0.75 0.14 0.12
Matches are distributed among these distances:
24 16 0.10
25 2 0.01
32 30 0.18
33 89 0.54
34 28 0.17
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (33 bp):
GTACAACTTGAAAAGGAAATGTACACTTTGTGT
Found at i:21586192 original size:34 final size:34
Alignment explanation
Indices: 21586119--21586203 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
21586109 TATGCACTTT
* * *
21586119 GAGTGTACAAATTG-AAAAGGGTATGTACACTTC
1 GAGTGTACAACTTGAAAAAGGGAATGTACACCTC
* * *
21586152 GTGTGTACCACTTGAAAAAGGGAATGTGCACCTC
1 GAGTGTACAACTTGAAAAAGGGAATGTACACCTC
*
21586186 GAGTGTACAACTAGAAAA
1 GAGTGTACAACTTGAAAA
21586204 GGAAAAGTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 11 0.26
34 31 0.74
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (34 bp):
GAGTGTACAACTTGAAAAAGGGAATGTACACCTC
Found at i:21593651 original size:33 final size:33
Alignment explanation
Indices: 21593614--21593861 Score: 205
Period size: 33 Copynumber: 7.6 Consensus size: 33
21593604 TACCCAAATG
**
21593614 GTACAACTTGAAAAGGTTATGTACACTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* *
21593647 GTAC-ACTTGAAAAGGAAAGGTATACTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* * * *
21593679 ATACCA-TATGAAAAGGAAAGGTATACTTTGTGT
1 GTACAACT-TGAAAAGGAAATGTACACTTTGTGT
* * * * *
21593712 ATACCACTTGAAAAGGAAAGGTACACTATATGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* ** * * *
21593745 GTAC-ACTTGAAAATGTTATATGCACTTTGAGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* ** *
21593777 GTACAAATTGAAAAGGGTATGTACACTTCGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* * * * *
21593810 GTACCACTTGAAAAGGGAATGTACACCTCGAGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
*
21593843 GTACAACTAGAAAAGGAAA
1 GTACAACTTGAAAAGGAAA
21593862 AGTCCATCGG
Statistics
Matches: 178, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
32 51 0.29
33 126 0.71
34 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (33 bp):
GTACAACTTGAAAAGGAAATGTACACTTTGTGT
Found at i:21593691 original size:65 final size:65
Alignment explanation
Indices: 21593621--21593861 Score: 209
Period size: 65 Copynumber: 3.7 Consensus size: 65
21593611 ATGGTACAAC
* * *
21593621 TTGAAAAGGTTATGTACACTTTGTGTGTAC-ACTTGAAAAGGAAAGGTATACTTTGTGTATACCA
1 TTGAAAAGGTAATGTACACTTTGAGTGTACAACTTGAAAAGGAAAGGTACACTTTGTGTATACCA
* * * * * * *
21593685 TATGAAAAGGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAAGGTACACTATATGTGTACA
1 T-TGAAAAGGTAATGTACACTTTGAGTGTACAACTTGAAAAGGAAAGGTACACT-T-TGTGTATA
21593750 -C-
63 CCA
* * * * * ** * * *
21593751 TTGAAAATGTTATATGCACTTTGAGTGTACAAATTGAAAAGGGTATGTACACTTCGTGTGTACCA
1 TTGAAAAGGTAATGTACACTTTGAGTGTACAACTTGAAAAGGAAAGGTACACTTTGTGTATACCA
* * * *
21593816 CTTGAAAAGGGAATGTACACCTCGAGTGTACAACTAGAAAAGGAAA
1 -TTGAAAAGGTAATGTACACTTTGAGTGTACAACTTGAAAAGGAAA
21593862 AGTCCATCGG
Statistics
Matches: 135, Mismatches: 35, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
63 5 0.04
64 3 0.02
65 62 0.46
66 56 0.41
67 2 0.01
68 7 0.05
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (65 bp):
TTGAAAAGGTAATGTACACTTTGAGTGTACAACTTGAAAAGGAAAGGTACACTTTGTGTATACCA
Found at i:21597649 original size:22 final size:22
Alignment explanation
Indices: 21597624--21597666 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21597614 TCTTCCTATT
21597624 TTGCTACCATTTTATTATTATA
1 TTGCTACCATTTTATTATTATA
* *
21597646 TTGCTACTATTTTGTTATTAT
1 TTGCTACCATTTTATTATTAT
21597667 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTATTATTATA
Found at i:21597732 original size:30 final size:30
Alignment explanation
Indices: 21597696--21597758 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
21597686 ACTTATTTTA
21597696 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
21597726 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
21597756 TTG
1 TTG
21597759 CTTATTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:21597888 original size:12 final size:12
Alignment explanation
Indices: 21597867--21597900 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21597857 TATATATTTT
*
21597867 AAAATTATATAA
1 AAAATAATATAA
21597879 AAAATAATATAA
1 AAAATAATATAA
*
21597891 AAATTAATAT
1 AAAATAATAT
21597901 GGTCAGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:21598708 original size:10 final size:9
Alignment explanation
Indices: 21598669--21598733 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
21598659 AATGTTAAAA
21598669 TTTT-AATT
1 TTTTAAATT
*
21598677 TTTTAACTT
1 TTTTAAATT
21598686 TCTTTATATATT
1 T-TTTA-A-ATT
21598698 TTTTAGAATTT
1 TTTTA-AA-TT
21598709 TTTTAAAATT
1 TTTT-AAATT
*
21598719 TTTAAAATT
1 TTTTAAATT
21598728 TTTTAA
1 TTTTAA
21598734 GAAATATGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
8 4 0.09
9 14 0.30
10 10 0.22
11 14 0.30
12 4 0.09
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTAAATT
Found at i:21598785 original size:20 final size:20
Alignment explanation
Indices: 21598752--21598833 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
21598742 AATTTTGGAG
* *
21598752 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTAAA
21598771 -TTTTAAAAATTTATTTTAAA
1 TTTTTAAAAA-TTATTTTAAA
*
21598791 TTTTTAAGAATTATTTTAAA
1 TTTTTAAAAATTATTTTAAA
21598811 TTTTTAAAAATTATTTTAAA
1 TTTTTAAAAATTATTTTAAA
21598831 TTT
1 TTT
21598834 CTTTTTTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
18 8 0.14
20 40 0.71
21 8 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTAAA
Found at i:21598809 original size:12 final size:11
Alignment explanation
Indices: 21598770--21598830 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 11
21598760 AATATTTTGA
21598770 ATTTTAAAAATTT
1 ATTTT-AAAA-TT
21598783 ATTTT-AAA-T
1 ATTTTAAAATT
21598792 -TTTTAAGAATT
1 ATTTTAA-AATT
21598803 ATTTT-AAATT
1 ATTTTAAAATT
*
21598813 -TTTAAAAATT
1 ATTTTAAAATT
21598823 ATTTTAAA
1 ATTTTAAA
21598831 TTTCTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
8 4 0.10
9 5 0.12
10 11 0.28
11 11 0.28
12 4 0.10
13 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:21598812 original size:10 final size:10
Alignment explanation
Indices: 21598781--21598832 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
21598771 TTTTAAAAAT
21598781 TTATTTTAAA
1 TTATTTTAAA
*
21598791 TT-TTTAAGAA
1 TTATTTTA-AA
21598801 TTATTTTAAA
1 TTATTTTAAA
*
21598811 TT-TTTAAAAA
1 TTATTT-TAAA
21598821 TTATTTTAAA
1 TTATTTTAAA
21598831 TT
1 TT
21598833 TCTTTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 7 0.21
10 20 0.59
11 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TTATTTTAAA
Found at i:21602109 original size:23 final size:23
Alignment explanation
Indices: 21602083--21602136 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
21602073 AACATTTATT
*
21602083 ATTAT-TTAAATATTTTACATATC
1 ATTATATTAAAT-TTTTAAATATC
*
21602106 ATTATATTAAATTTTTAAATATT
1 ATTATATTAAATTTTTAAATATC
21602129 ATTA-ATTA
1 ATTATATTA
21602137 TTATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 18 0.64
24 6 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTATATTAAATTTTTAAATATC
Found at i:21602142 original size:30 final size:32
Alignment explanation
Indices: 21602087--21602146 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
21602077 TTTATTATTA
21602087 TTTAAATATTTTACATATCATTATATTAAATT
1 TTTAAATATTTTACATATCATTATATTAAATT
21602119 TTTAAATATTATTA-AT-T-ATTATATTAAA
1 TTTAAATATT-TTACATATCATTATATTAAA
21602147 ATAATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 11 0.41
31 1 0.04
32 12 0.44
33 3 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
TTTAAATATTTTACATATCATTATATTAAATT
Found at i:21603798 original size:453 final size:453
Alignment explanation
Indices: 21602952--21603857 Score: 1794
Period size: 453 Copynumber: 2.0 Consensus size: 453
21602942 TATTTTGATT
21602952 TGATATACACTATCACCGATCAATCTAAAGCTTCCATGATAACAGAAACCATACAAGACATAAGA
1 TGATATACACTATCACCGATCAATCTAAAGCTTCCATGATAACAGAAACCATACAAGACATAAGA
21603017 AAATAAGGACTTCAACAAAGCTTAAACTACGCCCTTAAGATGAATCATTAATAGCACTAGCAAGG
66 AAATAAGGACTTCAACAAAGCTTAAACTACGCCCTTAAGATGAATCATTAATAGCACTAGCAAGG
*
21603082 TTTGCACAATGATTTTTACCAATTGGTTCATTTCAGATGTTGAAAACCAGCGCCTGATATGTGAC
131 TTTGCACAATGATTTTTACCAATTGATTCATTTCAGATGTTGAAAACCAGCGCCTGATATGTGAC
21603147 CATGCTCAGATTTTGGAGGCCACCGCCGGACAAAACTTGAATGCTTTTCTGGGTCATTCTATTTG
196 CATGCTCAGATTTTGGAGGCCACCGCCGGACAAAACTTGAATGCTTTTCTGGGTCATTCTATTTG
21603212 TCAAACTGAAGCCTATATGCTTGAATATATTTTGAAGATTGAATTCAAGACGTACCACTAGTGAG
261 TCAAACTGAAGCCTATATGCTTGAATATATTTTGAAGATTGAATTCAAGACGTACCACTAGTGAG
21603277 ATCATTGCCACCAAGACCCTGCCATGTGATGGTCCAGCCTCCGCATTGATAGCCCAAGTTATCAG
326 ATCATTGCCACCAAGACCCTGCCATGTGATGGTCCAGCCTCCGCATTGATAGCCCAAGTTATCAG
21603342 CATGAGTTCCGGATACTAGTATCTTAGTTGCTTTCTTGGGAAGGGGTAACAATGGCTTATCAG
391 CATGAGTTCCGGATACTAGTATCTTAGTTGCTTTCTTGGGAAGGGGTAACAATGGCTTATCAG
21603405 TGATATACACTATCACCGATCAATCTAAAGCTTCCATGATAACAGAAACCATACAAGACATAAGA
1 TGATATACACTATCACCGATCAATCTAAAGCTTCCATGATAACAGAAACCATACAAGACATAAGA
21603470 AAATAAGGACTTCAACAAAGCTTAAACTACGCCCTTAAGATGAATCATTAATAGCACTAGCAAGG
66 AAATAAGGACTTCAACAAAGCTTAAACTACGCCCTTAAGATGAATCATTAATAGCACTAGCAAGG
*
21603535 TTTGCACAATGATTTTTACCAATTGATTCATTTCAGATGTTGAAAACCAGTGCCTGATATGTGAC
131 TTTGCACAATGATTTTTACCAATTGATTCATTTCAGATGTTGAAAACCAGCGCCTGATATGTGAC
21603600 CATGCTCAGATTTTGGAGGCCACCGCCGGACAAAACTTGAATGCTTTTCTGGGTCATTCTATTTG
196 CATGCTCAGATTTTGGAGGCCACCGCCGGACAAAACTTGAATGCTTTTCTGGGTCATTCTATTTG
21603665 TCAAACTGAAGCCTATATGCTTGAATATATTTTGAAGATTGAATTCAAGACGTACCACTAGTGAG
261 TCAAACTGAAGCCTATATGCTTGAATATATTTTGAAGATTGAATTCAAGACGTACCACTAGTGAG
21603730 ATCATTGCCACCAAGACCCTGCCATGTGATGGTCCAGCCTCCGCATTGATAGCCCAAGTTATCAG
326 ATCATTGCCACCAAGACCCTGCCATGTGATGGTCCAGCCTCCGCATTGATAGCCCAAGTTATCAG
21603795 CATGAGTTCCGGATACTAGTATCTTAGTTGCTTTCTTGGGAAGGGGTAACAATGGCTTATCAG
391 CATGAGTTCCGGATACTAGTATCTTAGTTGCTTTCTTGGGAAGGGGTAACAATGGCTTATCAG
21603858 CAGATTCACC
Statistics
Matches: 451, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
453 451 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (453 bp):
TGATATACACTATCACCGATCAATCTAAAGCTTCCATGATAACAGAAACCATACAAGACATAAGA
AAATAAGGACTTCAACAAAGCTTAAACTACGCCCTTAAGATGAATCATTAATAGCACTAGCAAGG
TTTGCACAATGATTTTTACCAATTGATTCATTTCAGATGTTGAAAACCAGCGCCTGATATGTGAC
CATGCTCAGATTTTGGAGGCCACCGCCGGACAAAACTTGAATGCTTTTCTGGGTCATTCTATTTG
TCAAACTGAAGCCTATATGCTTGAATATATTTTGAAGATTGAATTCAAGACGTACCACTAGTGAG
ATCATTGCCACCAAGACCCTGCCATGTGATGGTCCAGCCTCCGCATTGATAGCCCAAGTTATCAG
CATGAGTTCCGGATACTAGTATCTTAGTTGCTTTCTTGGGAAGGGGTAACAATGGCTTATCAG
Found at i:21605299 original size:3 final size:3
Alignment explanation
Indices: 21605291--21605329 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
21605281 GTTCAACCTT
21605291 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
21605330 TGGAGGATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21607842 original size:18 final size:18
Alignment explanation
Indices: 21607815--21607907 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
21607805 TACGACCGTT
21607815 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
21607833 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
21607851 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
21607869 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
21607887 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
21607905 TAC
1 TAC
21607908 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:21614435 original size:31 final size:31
Alignment explanation
Indices: 21614397--21614473 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
21614387 AATGGATGAT
* * *
21614397 TGATTTGTCACTTTTCGATAACGTTAGTTAC
1 TGATTTGTCACTTTTCAATAACGCTAGTGAC
21614428 TGATTTGTCACTTTTCAATAACGCTAGTGAC
1 TGATTTGTCACTTTTCAATAACGCTAGTGAC
* *
21614459 TGAGTTGTTACTTTT
1 TGATTTGTCACTTTT
21614474 TTTAAAGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (31 bp):
TGATTTGTCACTTTTCAATAACGCTAGTGAC
Found at i:21618109 original size:25 final size:25
Alignment explanation
Indices: 21618081--21618138 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
21618071 ATATGTAAAC
*
21618081 AATTTAATATTATA-ATTAAAAATAT
1 AATTTAATAATATATATT-AAAATAT
* *
21618106 AATTTAGTAATATATATTATAATAT
1 AATTTAATAATATATATTAAAATAT
21618131 -ATTTAATA
1 AATTTAATA
21618139 GTACAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 7 0.25
25 18 0.64
26 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
AATTTAATAATATATATTAAAATAT
Found at i:21627783 original size:16 final size:16
Alignment explanation
Indices: 21627753--21627794 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
21627743 TTATTTATTA
21627753 AATTAA-TTT-TAATT
1 AATTAATTTTCTAATT
21627767 AATTAATTTTCTAATT
1 AATTAATTTTCTAATT
*
21627783 AAATAATTTTCT
1 AATTAATTTTCT
21627795 CAACTCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 3 0.12
16 16 0.64
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAATTTTCTAATT
Found at i:21638081 original size:18 final size:18
Alignment explanation
Indices: 21638054--21638150 Score: 115
Period size: 18 Copynumber: 5.4 Consensus size: 18
21638044 TACGACCGTT
21638054 TACAGTACTATTCACGTA
1 TACAGTACTATTCACGTA
*
21638072 TACAGCACTATTCACGTA
1 TACAGTACTATTCACGTA
*
21638090 TAC-GATACTATTCATGTA
1 TACAG-TACTATTCACGTA
** *
21638108 TATGGCACTATTCACGTA
1 TACAGTACTATTCACGTA
* *
21638126 TACGGTACTGTTCACGTA
1 TACAGTACTATTCACGTA
21638144 TACAGTA
1 TACAGTA
21638151 GTTGGGATTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
17 1 0.01
18 65 0.97
19 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (18 bp):
TACAGTACTATTCACGTA
Done.