Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 30 of 202
Found at i:8719832 original size:20 final size:20
Alignment explanation
Indices: 8719807--8719852 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
8719797 TCACTCTCAA
8719807 CAAAAATTACAAAAAAAAAAT
1 CAAAAATT-CAAAAAAAAAAT
*
8719828 CAAAAATTCAACAAAAAAAT
1 CAAAAATTCAAAAAAAAAAT
8719848 CAAAA
1 CAAAA
8719853 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (20 bp):
CAAAAATTCAAAAAAAAAAT
Found at i:8721044 original size:27 final size:27
Alignment explanation
Indices: 8720986--8721059 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
8720976 AAAAATAAAA
* *
8720986 ATTTACCAAAATACTACAAGTTTTTTTT
1 ATTTACCAAAATA-TATAAATTTTTTTT
8721014 ATTTACCAAAATATATAAATTTTTTTT
1 ATTTACCAAAATATATAAATTTTTTTT
8721041 ATTTACCAAAATATATAAA
1 ATTTACCAAAATATATAAA
8721060 AAAACCAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 31 0.70
28 13 0.30
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.45
Consensus pattern (27 bp):
ATTTACCAAAATATATAAATTTTTTTT
Found at i:8721068 original size:18 final size:16
Alignment explanation
Indices: 8721045--8721079 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
8721035 TTTTTTATTT
8721045 ACCAAAATATATAAAAAA
1 ACCAAAAT-TA-AAAAAA
8721063 ACCAAAATTAAAAAAA
1 ACCAAAATTAAAAAAA
8721079 A
1 A
8721080 AACCTGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.14
Consensus pattern (16 bp):
ACCAAAATTAAAAAAA
Found at i:8721231 original size:4 final size:4
Alignment explanation
Indices: 8721222--8721346 Score: 89
Period size: 4 Copynumber: 30.5 Consensus size: 4
8721212 GCAGAAGGAG
* *
8721222 AGAA AGAA AGAA AGAA ATGAGA GGAA AGAA AGAA AGAA AGAA AGGGGA
1 AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA AGAA AGAA AGAA A--GAA
* *
8721270 GGAA AGAA AGAAA AGGAA AG-G AGAA GAGAA A-AA AGGAA AGAA AG-A
1 AGAA AGAA AG-AA A-GAA AGAA AGAA -AGAA AGAA A-GAA AGAA AGAA
* *
8721315 AG-A AGAA A-AA AGAA AGAA GGAA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
8721347 GGAAAGGAGA
Statistics
Matches: 99, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
3 14 0.14
4 64 0.65
5 17 0.17
6 4 0.04
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:8721249 original size:22 final size:21
Alignment explanation
Indices: 8721223--8721352 Score: 103
Period size: 22 Copynumber: 6.2 Consensus size: 21
8721213 CAGAAGGAGA
*
8721223 GAAAGAAAGAAAGAAATGAGAG
1 GAAAGAAAGAAAGAAA-GAAAG
8721245 GAAAGAAAGAAAGAAAGAAAG
1 GAAAGAAAGAAAGAAAGAAAG
* *
8721266 G---GGAGGAAAGAAAGAAAAG
1 GAAAGAAAGAAAGAAAG-AAAG
*
8721285 GAAAG-GAGAAGAGAAA-AAAG
1 GAAAGAAAGAA-AGAAAGAAAG
8721305 GAAAGAAAGAAGAAGAAA-AAA-
1 GAAAGAAAG-A-AAGAAAGAAAG
* *
8721326 GAAAGAAGGAAGGAAAGAAAGG
1 GAAAGAAAGAAAGAAAGAAA-G
8721348 GAAAG
1 GAAAG
8721353 GAGAAGAGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
18 11 0.12
19 10 0.11
20 13 0.15
21 18 0.20
22 36 0.40
23 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAGAAAG
Found at i:8721253 original size:26 final size:26
Alignment explanation
Indices: 8721217--8721332 Score: 118
Period size: 26 Copynumber: 4.7 Consensus size: 26
8721207 TGGGGGCAGA
* *
8721217 AGGAGAGAAAGAAAGAAAGAAATGAG
1 AGGAAAGAAAGAAAGAAAGAAAGGAG
*
8721243 AGGAAAGAAAGAAAGAAAGAAAGGGG
1 AGGAAAGAAAGAAAGAAAGAAAGGAG
*
8721269 AGGAAAGAAAG-AA-AAGGAAAGGAG
1 AGGAAAGAAAGAAAGAAAGAAAGGAG
* *
8721293 A--AGAGAAA-AAAGGAAAGAAAGAAG
1 AGGAAAGAAAGAAA-GAAAGAAAGGAG
*
8721317 AAGAAA-AAAGAAAGAA
1 AGGAAAGAAAGAAAGAA
8721333 GGAAGGAAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
22 8 0.11
24 20 0.27
25 8 0.11
26 39 0.52
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (26 bp):
AGGAAAGAAAGAAAGAAAGAAAGGAG
Found at i:8721313 original size:29 final size:29
Alignment explanation
Indices: 8721275--8721367 Score: 89
Period size: 33 Copynumber: 3.0 Consensus size: 29
8721265 GGGGAGGAAA
8721275 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAG
1 GAAAG-AAAGGAAAGGAGAAGAGAAAAAAG
* * *
8721305 GAAAGAAA-GAAGAAGAAAAAAGAAAGAAGGAAG
1 GAAAGAAAGGAA-AGGAGAAGAG-AA-AA--AAG
8721338 GAAAGAAAGGGAAAGGAGAAGAGAAAAAAG
1 GAAAGAAA-GGAAAGGAGAAGAGAAAAAAG
8721368 AAGAAGAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
28 3 0.06
29 10 0.20
30 10 0.20
31 2 0.04
32 2 0.04
33 13 0.26
34 7 0.14
35 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (29 bp):
GAAAGAAAGGAAAGGAGAAGAGAAAAAAG
Found at i:8721343 original size:63 final size:65
Alignment explanation
Indices: 8721251--8721396 Score: 192
Period size: 63 Copynumber: 2.3 Consensus size: 65
8721241 AGAGGAAAGA
* *
8721251 AAGAAAGAAAGAAAGGGGAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGA-AAGAAAGA
1 AAGAAAGAAAGAAA-GGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAGAAG-AAGA
8721315 AG
64 AG
* *
8721317 AAGAAA-AAAGAAA-GAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAGAAGAAGAAGAAG
1 AAGAAAGAAAGAAAGGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAGAAG
* *
8721380 AAG-AGGGAAGAAAGGAA
1 AAGAAAGAAAGAAAGGAA
8721397 AAAAAAGGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
62 1 0.01
63 51 0.72
64 6 0.08
65 7 0.10
66 6 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (65 bp):
AAGAAAGAAAGAAAGGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAGAAG
Found at i:8721363 original size:22 final size:21
Alignment explanation
Indices: 8721274--8721367 Score: 88
Period size: 21 Copynumber: 4.4 Consensus size: 21
8721264 AGGGGAGGAA
*
8721274 AGAAAGAAAAGGAAAGGAGAAG
1 AGAAA-AAAGGGAAAGGAGAAG
*
8721296 AGAAAAAA-GGAAAGAAAGAAG
1 AGAAAAAAGGGAAAG-GAGAAG
*
8721317 AAGAAAAAA--GAAAGAAGGAAG
1 -AGAAAAAAGGGAAAGGA-GAAG
8721338 -GAAAGAAAGGGAAAGGAGAAG
1 AGAAA-AAAGGGAAAGGAGAAG
8721359 AGAAAAAAG
1 AGAAAAAAG
8721368 AAGAAGAAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
19 4 0.06
20 11 0.17
21 25 0.40
22 23 0.37
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
AGAAAAAAGGGAAAGGAGAAG
Found at i:8721400 original size:34 final size:41
Alignment explanation
Indices: 8721245--8721388 Score: 119
Period size: 41 Copynumber: 3.6 Consensus size: 41
8721235 GAAATGAGAG
* * *
8721245 GAAAGAAAGAAAGAAAGAAAGGGG-AGGA-AAGA-AAGAAAA
1 GAAAGAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAA-AAAA
* *
8721284 GGAAAGGA-GAAGAGAAA-AAA-GGAAAGAAAGAAGAAGAAAAAA
1 -GAAAGAAGGAAG-GAAAGAAAGGGAAAG-GAGAAG-AGAAAAAA
8721326 GAAAGAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA
1 GAAAGAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA
8721367 G-AAGAA-GAA-G-AAGAAGAGGGAA
1 GAAAGAAGGAAGGAAAGAA-AGGGAA
8721389 GAAAGGAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
37 5 0.06
38 9 0.10
39 11 0.12
40 16 0.18
41 22 0.25
42 17 0.19
43 8 0.09
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (41 bp):
GAAAGAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA
Found at i:8731068 original size:36 final size:36
Alignment explanation
Indices: 8731025--8731129 Score: 99
Period size: 26 Copynumber: 3.2 Consensus size: 36
8731015 AATAATAAAT
8731025 AAAATAATACACACTAAAATTATTAATTTTATACT-
1 AAAATAATACACACTAAAATTATTAATTTTATACTC
**
8731060 --ACGAAT--A-A-T--A-TTATTAATTTTATACTC
1 AAAATAATACACACTAAAATTATTAATTTTATACTC
*
8731087 AAAATAATACACACTAAAATTATTAA-TTT-TACTA
1 AAAATAATACACACTAAAATTATTAATTTTATACTC
8731121 AAAATAATA
1 AAAATAATA
8731130 ACTAACTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
26 16 0.29
27 1 0.02
29 5 0.09
30 1 0.02
31 2 0.04
32 1 0.02
33 5 0.09
34 13 0.24
35 4 0.07
36 7 0.13
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.37
Consensus pattern (36 bp):
AAAATAATACACACTAAAATTATTAATTTTATACTC
Found at i:8731285 original size:3 final size:3
Alignment explanation
Indices: 8731277--8731353 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
8731267 TCTTCATACT
8731277 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
8731325 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
8731354 TAATAATAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:8731358 original size:3 final size:3
Alignment explanation
Indices: 8731352--8731392 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
8731342 CAACAACAAC
*
8731352 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
8731393 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8731645 original size:27 final size:27
Alignment explanation
Indices: 8731607--8731682 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
8731597 ATAATACGAG
8731607 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
8731634 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
8731661 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
8731683 GTGACCAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:8731785 original size:28 final size:29
Alignment explanation
Indices: 8731746--8731817 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 29
8731736 TTTTTTTTTG
*
8731746 ATATATTTTGGTAAATAAAAAAAAGTT-T
1 ATATATTTTGGTAAATAAAAAAAACTTGT
8731774 ATATATTTTGGTAAATAAAAAAAACTTGT
1 ATATATTTTGGTAAATAAAAAAAACTTGT
*
8731803 A-GTATTTTGGTAAAT
1 ATATATTTTGGTAAAT
8731818 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.40
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAACTTGT
Found at i:8738051 original size:16 final size:17
Alignment explanation
Indices: 8738026--8738059 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
8738016 ATATATTTTC
8738026 ATATAATTTATA-AAAA
1 ATATAATTTATATAAAA
*
8738042 ATATATTTTATATAAAA
1 ATATAATTTATATAAAA
8738059 A
1 A
8738060 ATTATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTATATAAAA
Found at i:8738202 original size:16 final size:15
Alignment explanation
Indices: 8738181--8738210 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
8738171 TTTTTTTAGA
8738181 ATATTTTATATTTTTT
1 ATATTTT-TATTTTTT
8738197 ATATTTTTATTTTT
1 ATATTTTTATTTTT
8738211 CAGATGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
ATATTTTTATTTTTT
Found at i:8744245 original size:15 final size:15
Alignment explanation
Indices: 8744225--8744263 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
8744215 TACAAAAAAA
**
8744225 AAAAACAATGAAGTT
1 AAAAACAAAAAAGTT
8744240 AAAAACAAAAAAGTT
1 AAAAACAAAAAAGTT
8744255 AAAAACAAA
1 AAAAACAAA
8744264 GTTTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.13
Consensus pattern (15 bp):
AAAAACAAAAAAGTT
Found at i:8745625 original size:17 final size:17
Alignment explanation
Indices: 8745603--8745636 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8745593 ATAATTAAAC
*
8745603 AAATTGGAAATTAAATT
1 AAATTGAAAATTAAATT
8745620 AAATTGAAAATTAAATT
1 AAATTGAAAATTAAATT
8745637 CAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATTGAAAATTAAATT
Found at i:8749853 original size:18 final size:17
Alignment explanation
Indices: 8749830--8749865 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
8749820 TACTATGCCA
8749830 AAAGAGAAGCAAAAAAAG
1 AAAGAGAAG-AAAAAAAG
*
8749848 AAAGAGAAGAGAAAAAG
1 AAAGAGAAGAAAAAAAG
8749865 A
1 A
8749866 GACCGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAGAGAAGAAAAAAAG
Found at i:8750414 original size:17 final size:16
Alignment explanation
Indices: 8750360--8750422 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
8750350 TTTTATTTTG
8750360 AAAAATATATATAA-TA
1 AAAAATATATA-AATTA
*
8750376 TAAAAT-TATAAATTTA
1 AAAAATATATAAA-TTA
*
8750392 TGAAAATATATACAATTA
1 -AAAAATATATA-AATTA
8750410 AAAAATATATAAA
1 AAAAATATATAAA
8750423 AAAACCTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.05
15 4 0.10
16 9 0.23
17 15 0.38
18 7 0.18
19 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAAATATATAAATTA
Found at i:8754835 original size:13 final size:14
Alignment explanation
Indices: 8754807--8754836 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8754797 ATTTTTAAAA
8754807 AATTTAAAATTAAT
1 AATTTAAAATTAAT
8754821 AATTTAAAA-TAAT
1 AATTTAAAATTAAT
8754834 AAT
1 AAT
8754837 ATTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTTAAAATTAAT
Found at i:8754891 original size:20 final size:22
Alignment explanation
Indices: 8754845--8754893 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
8754835 ATATTTTTTT
8754845 TAAATTCCAAGTTTTTATAATA
1 TAAATTCCAAGTTTTTATAATA
*
8754867 TAAATTCCATGTTTTT-TAA-A
1 TAAATTCCAAGTTTTTATAATA
8754887 TAAATTC
1 TAAATTC
8754894 GAGTGGGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 15 0.58
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTCCAAGTTTTTATAATA
Found at i:8756369 original size:11 final size:10
Alignment explanation
Indices: 8756355--8756423 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 10
8756345 AAATTAAAAA
8756355 AAAAGTATTTT
1 AAAA-TATTTT
8756366 AAAATTATTTT
1 AAAA-TATTTT
***
8756377 AAAAT-TAAA
1 AAAATATTTT
8756386 AAAAGTATTTT
1 AAAA-TATTTT
8756397 AAAAATATTTTT
1 -AAAATA-TTTT
8756409 AAAATATTTT
1 AAAATATTTT
8756419 AAAAT
1 AAAAT
8756424 TAAAAAAAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.11
10 11 0.23
11 23 0.49
12 8 0.17
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
AAAATATTTT
Found at i:8756390 original size:31 final size:32
Alignment explanation
Indices: 8756336--8756413 Score: 113
Period size: 31 Copynumber: 2.4 Consensus size: 32
8756326 ACCAAAAATT
*
8756336 TATTTTTAAAAATTAAAAAAAAAGTATTTTAAAAT
1 TATTTTT-AAAATT--AAAAAAAGTATTTTAAAAA
8756371 TA-TTTTAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTTAAAATTAAAAAAAGTATTTTAAAAA
8756402 TATTTTTAAAAT
1 TATTTTTAAAAT
8756414 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 20 0.49
32 9 0.22
33 6 0.15
34 4 0.10
35 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (32 bp):
TATTTTTAAAATTAAAAAAAGTATTTTAAAAA
Found at i:8756407 original size:42 final size:43
Alignment explanation
Indices: 8756354--8756441 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 43
8756344 AAAATTAAAA
8756354 AAAAAGTA-TTTTAAAATTATTTTAAAATTAAAAAAAGTATTTT
1 AAAAAGTATTTTTAAAA-TATTTTAAAATTAAAAAAAGTATTTT
8756397 AAAAA-TATTTTTAAAATATTTTAAAATTAAAAAAAGTATTTT
1 AAAAAGTATTTTTAAAATATTTTAAAATTAAAAAAAGTATTTT
8756439 AAA
1 AAA
8756442 TATTATATCG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
42 31 0.70
43 13 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (43 bp):
AAAAAGTATTTTTAAAATATTTTAAAATTAAAAAAAGTATTTT
Found at i:8759627 original size:17 final size:17
Alignment explanation
Indices: 8759605--8759638 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8759595 ATGTCATATA
*
8759605 CTTAAAATAAAATAGTG
1 CTTAAAACAAAATAGTG
8759622 CTTAAAACAAAATAGTG
1 CTTAAAACAAAATAGTG
8759639 GAGATAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (17 bp):
CTTAAAACAAAATAGTG
Found at i:8762549 original size:176 final size:176
Alignment explanation
Indices: 8762251--8762773 Score: 751
Period size: 176 Copynumber: 3.0 Consensus size: 176
8762241 TTGAGGCATC
* * *
8762251 AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTCAAATTTGTGCGAAATATGGGGAGCAAAA
1 AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTCAAATTTGAGCAAAATATAGGGAGCAAAA
* *
8762316 CTAAAATTTAGCTATTCTTATATAATCTTTAAAAAGTTGATGGATTAGAACTGAAATTTAGCCAT
66 ATAAAATTTAGCCATTCTTATATAATCTTTAAAAAGTTGATGGATTAGAACTGAAATTTAGCCAT
* * * *
8762381 AGTTTTCTATGACAATAGAAAAGAAAAAAAGAATGGATATGTGTCT
131 AATTTTCTATGTCAAAAGAAAAGAAAAAAAGAATGGACATGTGTCT
* *
8762427 AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTCAAATTTAAGCTAAATATAGGGAGCAAAA
1 AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTCAAATTTGAGCAAAATATAGGGAGCAAAA
* * * *
8762492 ATGAAATTTAGCCATTCTTATATCATCTTTAAAAATTTGATGGATTAGAATTGAAATTTAGCCAT
66 ATAAAATTTAGCCATTCTTATATAATCTTTAAAAAGTTGATGGATTAGAACTGAAATTTAGCCAT
*
8762557 AATTTTCTATGTCAAAAGAAAAGGAAAAAAAAGAATGGCCATGTGTCT
131 AATTTTCTATGTCAAAAGAAAA-G-AAAAAAAGAATGGACATGTGTCT
* * * *
8762605 AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTTAAATTTGAGCAAAATACAGAGATCAAAA
1 AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTCAAATTTGAGCAAAATATAGGGAGCAAAA
* * * * * * *
8762670 TTAAAATTTAACCATACTTATATAATCTTAAAAAAGTAGAGGGATTAGAACTAAAATTTAGCCAC
66 ATAAAATTTAGCCATTCTTATATAATCTTTAAAAAGTTGATGGATTAGAACTGAAATTTAGCCA-
* *
8762735 TATTTTTTTATGTCAAAAGAAAAG-AAAAAAGAATGGACA
130 TAATTTTCTATGTCAAAAGAAAAGAAAAAAAGAATGGACA
8762774 AGTATAGAAA
Statistics
Matches: 309, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
176 153 0.50
177 1 0.00
178 134 0.43
179 21 0.07
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.31
Consensus pattern (176 bp):
AAATTATGTCAAAATTAAAGTATAGAGATTAAATCTCAAATTTGAGCAAAATATAGGGAGCAAAA
ATAAAATTTAGCCATTCTTATATAATCTTTAAAAAGTTGATGGATTAGAACTGAAATTTAGCCAT
AATTTTCTATGTCAAAAGAAAAGAAAAAAAGAATGGACATGTGTCT
Found at i:8770350 original size:13 final size:13
Alignment explanation
Indices: 8770332--8770405 Score: 121
Period size: 13 Copynumber: 5.7 Consensus size: 13
8770322 CTCAAATTTT
8770332 TCAAAAGCACTTC
1 TCAAAAGCACTTC
8770345 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
8770358 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
8770371 TCCACAGCACTTC
1 TCAAAAGCACTTC
8770384 TCAAAAGCACTTC
1 TCAAAAGCACTTC
8770397 TCAAAAGCA
1 TCAAAAGCA
8770406 ATGAAGAACT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 55 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:8770960 original size:32 final size:32
Alignment explanation
Indices: 8770914--8771006 Score: 177
Period size: 32 Copynumber: 2.9 Consensus size: 32
8770904 TGTCAATCAT
*
8770914 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
8770946 TTCAATATCTAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
8770978 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCTAACAAGCTTAAAACATAAT
8771007 CAATATCTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCTAACAAGCTTAAAACATAATAAA
Found at i:8771030 original size:27 final size:27
Alignment explanation
Indices: 8770915--8771033 Score: 87
Period size: 32 Copynumber: 4.0 Consensus size: 27
8770905 GTCAATCATT
* *
8770915 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
*
8770946 TTCAATATCTAACAAGCTTAAAACATAATAAA
1 -TCAATATCTAACAAGATTAAAAC---AT-AA
*
8770978 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
8771006 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
8771033 T
1 T
8771034 AATTTCAAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
26 2 0.02
27 23 0.28
28 2 0.02
29 2 0.02
32 54 0.65
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:8771041 original size:59 final size:62
Alignment explanation
Indices: 8770912--8771051 Score: 180
Period size: 59 Copynumber: 2.3 Consensus size: 62
8770902 ATTGTCAATC
*
8770912 ATTTCAATATCCAACAAGCTTAAAACATAATAAATTCAATATCTAACAAGCTTAAAACATAATA
1 ATTTCAATATCCAACAAGCTTAAAAC--AATAAATTCAATATCTAACAAGATTAAAACATAATA
* * *
8770976 AATTCAATATCTAACAAGCTTAAAAC-AT-AA-TCAATATCTAACAA-ATTCAAGACATAATA
1 ATTTCAATATCCAACAAGCTTAAAACAATAAATTCAATATCTAACAAGATT-AAAACATAATA
*
8771035 ATTTCAAAATCCAACAA
1 ATTTCAATATCCAACAA
8771052 ACTAAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
58 2 0.03
59 38 0.56
60 2 0.03
61 2 0.03
64 24 0.35
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (62 bp):
ATTTCAATATCCAACAAGCTTAAAACAATAAATTCAATATCTAACAAGATTAAAACATAATA
Found at i:8771210 original size:80 final size:80
Alignment explanation
Indices: 8771115--8771271 Score: 305
Period size: 80 Copynumber: 2.0 Consensus size: 80
8771105 TTTAAACTAA
8771115 AACATACATAACATAGAAACAATAACCCTAAGCCTAAAACCTACCTAATATTTCTAACCATATAA
1 AACATACATAACATAGAAACAATAACCCTAAGCCTAAAACCTACCTAATATTTCTAACCATATAA
8771180 TTAGTCCACATACAT
66 TTAGTCCACATACAT
*
8771195 AACATACATAACATAGAAACAATAACCCTAAGCCTTAAACCTACCTAATATTTCTAACCATATAA
1 AACATACATAACATAGAAACAATAACCCTAAGCCTAAAACCTACCTAATATTTCTAACCATATAA
8771260 TTAGTCCACATA
66 TTAGTCCACATA
8771272 GTTTGTGCAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (80 bp):
AACATACATAACATAGAAACAATAACCCTAAGCCTAAAACCTACCTAATATTTCTAACCATATAA
TTAGTCCACATACAT
Found at i:8772658 original size:41 final size:41
Alignment explanation
Indices: 8772612--8772723 Score: 157
Period size: 34 Copynumber: 2.9 Consensus size: 41
8772602 ATAATTGCAT
*
8772612 TAATAATTTTTTGATAAATTAAGCTACTTTCTTTGTAATTC
1 TAATAATTTTTTGAGAAATTAAGCTACTTTCTTTGTAATTC
*
8772653 TAATAATTTTTTGAGAAATTAAGCTA----C-TT-T-ATTT
1 TAATAATTTTTTGAGAAATTAAGCTACTTTCTTTGTAATTC
8772687 TAATAATTTTTTGAGAAATTAAGCTACTTTCTTTGTA
1 TAATAATTTTTTGAGAAATTAAGCTACTTTCTTTGTA
8772724 TCAATACTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
34 29 0.47
35 1 0.02
36 2 0.03
37 1 0.02
38 1 0.02
39 2 0.03
40 1 0.02
41 25 0.40
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (41 bp):
TAATAATTTTTTGAGAAATTAAGCTACTTTCTTTGTAATTC
Found at i:8774184 original size:6 final size:6
Alignment explanation
Indices: 8774173--8774200 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
8774163 AAAAATAATT
8774173 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
8774201 AAATAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:8781266 original size:17 final size:19
Alignment explanation
Indices: 8781244--8781281 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
8781234 TTAAAAGATT
8781244 TTTTAT-TCAAATAAA-AA
1 TTTTATCTCAAATAAATAA
*
8781261 TTTTATCTTAAATAAATAA
1 TTTTATCTCAAATAAATAA
8781280 TT
1 TT
8781282 CAACAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTATCTCAAATAAATAA
Found at i:8790963 original size:20 final size:21
Alignment explanation
Indices: 8790924--8790963 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8790914 TTCGTGATTA
8790924 AATCAATTCATGCTCGAAATC
1 AATCAATTCATGCTCGAAATC
8790945 AATC-ATTCAATGCTC-AAAT
1 AATCAATTC-ATGCTCGAAAT
8790964 TAATTCGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (21 bp):
AATCAATTCATGCTCGAAATC
Found at i:8801668 original size:13 final size:13
Alignment explanation
Indices: 8801650--8801728 Score: 88
Period size: 13 Copynumber: 6.1 Consensus size: 13
8801640 AGTTTGGCAA
8801650 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
8801663 TGCTTTTCAAAAG
1 TGCTTTTGAAAAG
* *
8801676 TG-TTGTGGAAATG
1 TGCTT-TTGAAAAG
*
8801689 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
8801702 TACTTTTGATAAG
1 TGCTTTTGAAAAG
8801715 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
8801728 T
1 T
8801729 TTGGTTTAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
12 2 0.04
13 49 0.92
14 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:8810156 original size:21 final size:21
Alignment explanation
Indices: 8810132--8810200 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
8810122 CCGAATGCTG
* *
8810132 CATAAGTGCTAAATTGAAACC
1 CATAAGAGCTGAATTGAAACC
* * * *
8810153 CATAAGGGTTGAATGGAAACT
1 CATAAGAGCTGAATTGAAACC
* *
8810174 CATAGGAGCTGAACTGAAACC
1 CATAAGAGCTGAATTGAAACC
8810195 CATAAG
1 CATAAG
8810201 GGTTAAACAG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
CATAAGAGCTGAATTGAAACC
Found at i:8810213 original size:21 final size:21
Alignment explanation
Indices: 8810147--8810233 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
8810137 GTGCTAAATT
* **
8810147 GAAACCCATAAGGGTTGAATG
1 GAAACCCATAAGGGTTAAACA
* * * *
8810168 GAAACTCAT-AGGAGCTGAACT
1 GAAACCCATAAGG-GTTAAACA
8810189 GAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGGGTTAAACA
* *
8810210 GAAACTCATATA-AGTTAAACA
1 GAAACCCATA-AGGGTTAAACA
8810231 GAA
1 GAA
8810234 GCTTGTGAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.06
21 46 0.87
22 4 0.08
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (21 bp):
GAAACCCATAAGGGTTAAACA
Found at i:8810342 original size:24 final size:24
Alignment explanation
Indices: 8810305--8810400 Score: 156
Period size: 24 Copynumber: 4.0 Consensus size: 24
8810295 TACTTGGGTA
*
8810305 ATTTGCCGTCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
8810329 ATATACCGTCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
8810353 ATTTACCATCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
8810377 ATTTACCGTCAATTCATCATTTGC
1 ATTTACCGTCAATTCATCCTTTGC
8810401 CACAGAACGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (24 bp):
ATTTACCGTCAATTCATCCTTTGC
Found at i:8813080 original size:51 final size:50
Alignment explanation
Indices: 8812997--8813187 Score: 224
Period size: 51 Copynumber: 3.8 Consensus size: 50
8812987 GTCAATGTTA
* *
8812997 TCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCAT
1 TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAA-AGC-T
* * * *
8813049 T-CGGTACACGTAGTAGCCTGCACATAATACTACACACGTGACCAAAGCT
1 TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAAGCT
8813098 TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAA-CT
1 TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-AAGCT
*** * * *
8813148 ATCTTATACTCATAGTAGCCTACACATAGTACTACACATG
1 -TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATG
8813188 AGTTCTCATG
Statistics
Matches: 120, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.02
50 43 0.36
51 74 0.62
52 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (50 bp):
TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAAGCT
Found at i:8813174 original size:101 final size:100
Alignment explanation
Indices: 8812997--8813185 Score: 274
Period size: 101 Copynumber: 1.9 Consensus size: 100
8812987 GTCAATGTTA
* *
8812997 TCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCATTCGGTACACGTAG
1 TCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCATTC-ATACACATAG
*
8813062 TAGCCTGCACATAATACTACACACGTGACCAAAGCT
65 TAGCCTACACATAATACTACACACGTGACCAAAGCT
* *
8813098 TCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAACTATC-TT-ATACTCAT
1 TCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACC--AA-TATCATTCATACACAT
*
8813161 AGTAGCCTACACATAGTACTACACA
63 AGTAGCCTACACATAATACTACACA
8813186 TGAGTTCTCA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
101 71 0.90
103 4 0.05
104 4 0.05
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (100 bp):
TCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCATTCATACACATAGT
AGCCTACACATAATACTACACACGTGACCAAAGCT
Found at i:8816088 original size:44 final size:44
Alignment explanation
Indices: 8816025--8816178 Score: 254
Period size: 44 Copynumber: 3.5 Consensus size: 44
8816015 CAGATCACAT
8816025 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
8816069 TTATCACTTGTCACTGATCAGATAAGTGTAGTTAAAGCTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
8816113 TTGTCACTTGTCACTGATCAGATAACTGTAGCTAAAGCTACCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
8816157 TTATCACTTGTTACTGATCAGA
1 TTATCACTTGTCACTGATCAGA
8816179 AGTACTCAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 101 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:8819596 original size:6 final size:6
Alignment explanation
Indices: 8819558--8819641 Score: 78
Period size: 6 Copynumber: 14.0 Consensus size: 6
8819548 GAGGCATGCT
* * * * *
8819558 CAGCAA CAGCAG CATCAG CAGCAA CAACAA CAGCAA CAGCGA CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
* * * * *
8819606 CAGCAA CAGCCA CAACAC CAGCAG CAGCAG CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
8819642 AGAGAAGGGA
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.44, C:0.36, G:0.19, T:0.01
Consensus pattern (6 bp):
CAGCAA
Found at i:8832606 original size:21 final size:22
Alignment explanation
Indices: 8832581--8832628 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8832571 TATTCAAAAA
* *
8832581 TAAAA-TAATAATTATAAAATT
1 TAAAATTAATAATAAAAAAATT
8832602 TAAAATTAATAATAAAAAAATT
1 TAAAATTAATAATAAAAAAATT
*
8832624 CAAAA
1 TAAAA
8832629 AATGAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATTAATAATAAAAAAATT
Found at i:8833429 original size:17 final size:17
Alignment explanation
Indices: 8833407--8833444 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
8833397 AAACCTTAAA
8833407 TGTAAAAGAAAAGTATG
1 TGTAAAAGAAAAGTATG
8833424 TGTAAAAGAAAAGTATG
1 TGTAAAAGAAAAGTATG
8833441 TGTA
1 TGTA
8833445 TGCCATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (17 bp):
TGTAAAAGAAAAGTATG
Found at i:8849366 original size:12 final size:10
Alignment explanation
Indices: 8849339--8849399 Score: 59
Period size: 11 Copynumber: 5.6 Consensus size: 10
8849329 CAACTAAATC
8849339 ATTTCTCTCA
1 ATTTCTCTCA
8849349 ATTTCTCTCTA
1 ATTTCTCTC-A
8849360 ATATTCTCTCAA
1 AT-TTCTCTC-A
*
8849372 ATTCCTCTCAA
1 ATTTCTCTC-A
*
8849383 ATTCCTCTCAA
1 ATTTCTCTC-A
8849394 ATTTCT
1 ATTTCT
8849400 ATTTAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.20
11 27 0.59
12 10 0.22
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTTCTCTCA
Found at i:8849381 original size:11 final size:11
Alignment explanation
Indices: 8849343--8849396 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
8849333 TAAATCATTT
*
8849343 CTCTC-AATTT
1 CTCTCAAATTC
8849353 CTCTCTAATATT-
1 CTCTC-AA-ATTC
8849365 CTCTCAAATTC
1 CTCTCAAATTC
8849376 CTCTCAAATTC
1 CTCTCAAATTC
8849387 CTCTCAAATT
1 CTCTCAAATT
8849397 TCTATTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.20
11 23 0.57
12 6 0.15
13 3 0.08
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:8849456 original size:24 final size:24
Alignment explanation
Indices: 8849425--8849471 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
8849415 AAATTTTTAA
8849425 TTATTTTTAAAATAGTTTTAAATT
1 TTATTTTTAAAATAGTTTTAAATT
* **
8849449 TTATTTTTTAAATTTTTTTAAAT
1 TTATTTTTAAAATAGTTTTAAAT
8849472 CATAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTATTTTTAAAATAGTTTTAAATT
Found at i:8850598 original size:52 final size:52
Alignment explanation
Indices: 8850537--8850706 Score: 166
Period size: 52 Copynumber: 3.2 Consensus size: 52
8850527 AATAAAATAG
8850537 ATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATAACTA
1 ATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATAACTA
* * ** * * ** * *
8850589 ATATTTCCATCATGGTCATATAGTTTGAATGGACACCGTAGTATTAAATA-A-AA-TA
1 ATATTTCCATAAT-G--AGATAG-CCGATTGG-TA-TTTAGTATTTAGTACATAACTA
8850644 GATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATAACTA
1 -ATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATAACTA
8850697 ATATTTCCAT
1 ATATTTCCAT
8850707 CATGGTCATA
Statistics
Matches: 88, Mismatches: 20, Indels: 20
0.69 0.16 0.16
Matches are distributed among these distances:
50 10 0.11
51 2 0.02
52 29 0.33
53 8 0.09
55 8 0.09
56 19 0.22
57 2 0.02
58 10 0.11
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (52 bp):
ATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATAACTA
Found at i:8850709 original size:108 final size:108
Alignment explanation
Indices: 8850520--8850736 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
8850510 CGGAAGCACA
8850520 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATA
1 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATA
8850585 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCGT
66 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCGT
8850628 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATA
1 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATA
8850693 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCGT
66 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCGT
8850736 A
1 A
8850737 CGAGGATCCA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (108 bp):
AGTATTAAATAAAATAGATATTTCCATAATGAGATAGCCGATTGGTATTTAGTATTTAGTACATA
ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCGT
Found at i:8851347 original size:18 final size:18
Alignment explanation
Indices: 8851324--8851361 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
8851314 AGATGATGCA
* *
8851324 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
8851342 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
8851360 GT
1 GT
8851362 TTCATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:8851839 original size:49 final size:49
Alignment explanation
Indices: 8851785--8852003 Score: 393
Period size: 49 Copynumber: 4.5 Consensus size: 49
8851775 GTTTATATTA
8851785 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
8851834 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
8851883 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* **
8851932 ATATAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTCC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
8851981 ATTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
8852004 AATATTCTTA
Statistics
Matches: 164, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 164 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:8855023 original size:106 final size:105
Alignment explanation
Indices: 8854834--8855042 Score: 328
Period size: 106 Copynumber: 2.0 Consensus size: 105
8854824 TGGGAGCGAT
* * **
8854834 TTCAGAAATTCTTCTGATAAAGTATCCTGCTTGAAGCATTTTTATACTATTTGCTTTGAAACGTC
1 TTCAAAAATTCTTCTGATAAAGCATCCTGCTTGAAGCATTTTTATACTATTTGCTCAGAAACGTC
8854899 AACTCAAAATTATTTTTTCAGGAACTACTGTAGCAAAAAA
66 AACTCAAAATTATTTTTTCAGGAACTACTGTAGCAAAAAA
* **
8854939 TTCAAAAATTCTTCTGATAAAGCATCCTGCTTTAAGTGTTTTTTATACTATTTGCTCAGAAACGT
1 TTCAAAAATTCTTCTGATAAAGCATCCTGCTTGAAG-CATTTTTATACTATTTGCTCAGAAACGT
* *
8855004 TAACTCAAAATTATTTTTTCAGGACCTACTGTAGCAAAA
65 CAACTCAAAATTATTTTTTCAGGAACTACTGTAGCAAAA
8855043 GCGTGTCCTT
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
105 33 0.35
106 61 0.65
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (105 bp):
TTCAAAAATTCTTCTGATAAAGCATCCTGCTTGAAGCATTTTTATACTATTTGCTCAGAAACGTC
AACTCAAAATTATTTTTTCAGGAACTACTGTAGCAAAAAA
Found at i:8855166 original size:125 final size:125
Alignment explanation
Indices: 8854939--8855191 Score: 407
Period size: 125 Copynumber: 2.0 Consensus size: 125
8854929 TAGCAAAAAA
* *
8854939 TTCAAAAATTCTTCTGATAAAGCATCCTGCTTTAAGTGTTTTTTATACTATTTGCTCAGAAACGT
1 TTCAAAAATTCTTCTGATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGT
* * * * **
8855004 TAACTCAAAATTATTTTTTCAGGACCTACTGTAGCAAAAGCGTGTCCTTGTGGAAGCGAT
66 CAACTCAAAATTATTTTTTCAGAACCTACTGTAGCAAAAACGCGTCCACGTGGAAGCGAT
* *
8855064 TTCAGAAATTCTTCTGATAAAGCATCTTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGT
1 TTCAAAAATTCTTCTGATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGT
*
8855129 CAACTCAAAATTATTTTTTCAGAACCTACTGTAGCAAAAACGCGTCCACGTGGGAGCGAT
66 CAACTCAAAATTATTTTTTCAGAACCTACTGTAGCAAAAACGCGTCCACGTGGAAGCGAT
8855189 TTC
1 TTC
8855192 CTTAATAAAT
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 117 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (125 bp):
TTCAAAAATTCTTCTGATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGT
CAACTCAAAATTATTTTTTCAGAACCTACTGTAGCAAAAACGCGTCCACGTGGAAGCGAT
Found at i:8855906 original size:16 final size:17
Alignment explanation
Indices: 8855884--8855924 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
8855874 CTTTTGTAGG
8855884 ATTAATATATTAAAATT
1 ATTAATATATTAAAATT
* *
8855901 -TTAATA-ATTATATTT
1 ATTAATATATTAAAATT
8855916 ATTAATATA
1 ATTAATATA
8855925 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.35
16 12 0.60
17 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATATATTAAAATT
Found at i:8871378 original size:18 final size:17
Alignment explanation
Indices: 8871355--8871409 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 17
8871345 GAGGGACGTG
8871355 GAGGGAGAGGACGGGGGA
1 GAGGGAGAGGA-GGGGGA
8871373 GAGGGAGAGGAAGGGGGA
1 GAGGGAGAGG-AGGGGGA
8871391 GAGGGAGAGGGAGGGGGA
1 GAGGGAGA-GGAGGGGGA
8871409 G
1 G
8871410 GTTCGGCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 32 0.91
19 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.69, T:0.00
Consensus pattern (17 bp):
GAGGGAGAGGAGGGGGA
Found at i:8871410 original size:6 final size:6
Alignment explanation
Indices: 8871355--8871409 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
8871345 GAGGGACGTG
* * *
8871355 GAGGGA GA-GGA CGGGGGA GAGGGA GAGGAA GGGGGA GAGGGA GAGGGA
1 GAGGGA GAGGGA -GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
*
8871403 GGGGGA G
1 GAGGGA G
8871410 GTTCGGCTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 3 0.08
6 34 0.85
7 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:8873075 original size:21 final size:19
Alignment explanation
Indices: 8873026--8873081 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
8873016 AATTTTCGAG
8873026 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
8873045 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
8873064 GATATATACAATCTTAGA
1 G--ATATACAATCTTAGA
8873082 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:8873300 original size:18 final size:21
Alignment explanation
Indices: 8873276--8873314 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
8873266 GGCTTACTGT
*
8873276 TTTTTTTC-TATTT-CGATTA
1 TTTTTTACTTATTTACGATTA
8873295 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
8873315 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:8873547 original size:3 final size:3
Alignment explanation
Indices: 8873539--8873581 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
8873529 ATTAATTTTG
*
8873539 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
8873582 ACCTACATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8873547 original size:15 final size:15
Alignment explanation
Indices: 8873523--8873580 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
8873513 GTTTTTAGTC
8873523 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
8873537 TGTTATTATTATTTT
1 TATTATTATTAATTT
*
8873552 TATTATTATATTATATAT
1 TATTA-T-TATTA-ATTT
8873570 TATTATTATTA
1 TATTATTATTA
8873581 TACCTACATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 3 0.09
15 13 0.37
16 6 0.17
17 6 0.17
18 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:8873955 original size:51 final size:52
Alignment explanation
Indices: 8873845--8873956 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 52
8873835 TTCCACGTTT
**
8873845 TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATATTTTA
1 TATATGTATACTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTA
* * * * *
8873896 TATGTGTATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTATTTTA
1 TATATGTATACTTATATATTTCATT-TTTTCATAAATGCATGAATATATTTTA
8873947 TATATGTATA
1 TATATGTATA
8873957 AGTTTTATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 28 0.55
52 23 0.45
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.55
Consensus pattern (52 bp):
TATATGTATACTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTA
Found at i:8878652 original size:10 final size:11
Alignment explanation
Indices: 8878632--8878683 Score: 63
Period size: 10 Copynumber: 4.8 Consensus size: 11
8878622 CAAATTTTTC
*
8878632 AAAAAAAAAAG
1 AAAAGAAAAAG
*
8878643 AAAA-AGAAAG
1 AAAAGAAAAAG
8878653 AAAAGAAAAAG
1 AAAAGAAAAAG
8878664 -AAAGAAAAAGG
1 AAAAGAAAAA-G
8878675 AAAAGAAAA
1 AAAAGAAAA
8878684 GCAAAAGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 18 0.50
11 10 0.28
12 8 0.22
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:8878658 original size:15 final size:16
Alignment explanation
Indices: 8878637--8878682 Score: 76
Period size: 15 Copynumber: 2.9 Consensus size: 16
8878627 TTTTCAAAAA
8878637 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
8878653 -AAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
*
8878668 AAAAAGGAAAAGAAA
1 AAAAAGAAAAAGAAA
8878683 AGCAAAAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:8878673 original size:6 final size:6
Alignment explanation
Indices: 8878632--8878683 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
8878622 CAAATTTTTC
8878632 AAAAA- AAAAAG AAAAAG --AAAG -AAAAG AAAAAG --AAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
8878674 GAAAAG AAAA
1 AAAAAG AAAA
8878684 GCAAAAGGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
4 8 0.20
5 9 0.22
6 23 0.57
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:8878684 original size:11 final size:11
Alignment explanation
Indices: 8878633--8878690 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
8878623 AAATTTTTCA
* *
8878633 AAAAAAAAAGA
1 AAAAGAAAAGG
8878644 AAAAG-AAA-G
1 AAAAGAAAAGG
*
8878653 AAAAGAAAAAG
1 AAAAGAAAAGG
8878664 -AAAGAAAAAGG
1 AAAAG-AAAAGG
*
8878675 AAAAGAAAAGC
1 AAAAGAAAAGG
8878686 AAAAG
1 AAAAG
8878691 GAGAGGCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.13
10 10 0.26
11 20 0.51
12 4 0.10
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGG
Found at i:8880306 original size:132 final size:131
Alignment explanation
Indices: 8879927--8880417 Score: 636
Period size: 132 Copynumber: 3.8 Consensus size: 131
8879917 TTGTCTCTCT
* * *
8879927 AAGCAGATTCAAGCCACCAAGCCTTGTCTCTCTAAGCAGCAGCGGAGTAAGTTGAAGATTGTAGA
1 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAG-AAGTTGAAGATTGTAGA
* *
8879992 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAAATCTTATCTTTTCAAGATAGT-
65 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAAGGTAAATCTTATCTTTCCAAGATAGTG
8880056 GA
130 GA
* * **
8880058 GAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGC---GAAG-T--AGGCTGTAGA
1 -AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGTTGAAGATTGTAGA
* *
8880117 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAGGTAAATCTTATCTTTCCAAGATAGTG
65 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAAGGTAAATCTTATCTTTCCAAGATAGTG
8880182 GA
130 GA
*
8880184 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAGA
1 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAA-GTTGAAGATTGTAGA
* * * *
8880249 TCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGGCAAATATTATCTTTCCAAGATAGTG
65 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAAGGTAAATCTTATCTTTCCAAGATAGTG
*
8880314 GG
130 GA
* * * * * * *
8880316 AAGCAGATTTAAGCTACCAAACCTTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAAA
1 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAG-AAGTTGAAGATTGTAGA
** * *
8880381 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
65 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAG
8880418 CCGATAATCC
Statistics
Matches: 316, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
125 109 0.34
126 2 0.01
127 1 0.00
128 6 0.02
129 2 0.01
130 1 0.00
132 175 0.55
133 20 0.06
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (131 bp):
AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGTTGAAGATTGTAGAT
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAAGGTAAATCTTATCTTTCCAAGATAGTGG
A
Found at i:8880432 original size:44 final size:43
Alignment explanation
Indices: 8880379--8880756 Score: 238
Period size: 44 Copynumber: 8.8 Consensus size: 43
8880369 GAAGATGGCA
8880379 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * * * *
8880423 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * *** *
8880466 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * *
8880507 AGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTCAGCAAG-CA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCAT
* * * *
8880551 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAT
*
8880596 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * * * *
8880640 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * * *** *
8880683 GGATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-TCGCGTC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * *
8880724 AGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
8880757 CTAAGTAAAC
Statistics
Matches: 268, Mismatches: 48, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
40 43 0.16
41 18 0.07
42 7 0.03
43 22 0.08
44 147 0.55
45 28 0.10
46 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
Found at i:8880658 original size:173 final size:173
Alignment explanation
Indices: 8880423--8880748 Score: 387
Period size: 173 Copynumber: 1.9 Consensus size: 173
8880413 TAAAGCCGAT
* * * * * *
8880423 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATGAATCCTATCTCCCTGAAGTTG
** * *
8880488 CAG-AGAGCAGATC-GCATC-TAG-TCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTCAGCAAG
66 CAGTAGAGCAGATCAAAACCTTAGATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-TC-GC--G
8880549 -CAAGTCTTATC-CTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCA
126 TCAAGTCTTATCTCT-CTGAAGTTGCAGTGAGGTAGACTGAAGATGGCA
* * *
8880596 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGAT-AATCCTATCTCCCTGAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-ATGAATCCTATCTCCCTGAAGTT
* * * *
8880660 GCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCGTCTA
65 GCAGTAGAGCAGATCAAAACCTTAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCGTCAA
8880725 GTCTTATCTCTCTGAAGTTGCAGT
130 GTCTTATCTCTCTGAAGTTGCAGT
8880749 AGAGCAGACT
Statistics
Matches: 129, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
172 1 0.01
173 80 0.62
174 13 0.10
175 4 0.03
176 10 0.08
177 21 0.16
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (173 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATGAATCCTATCTCCCTGAAGTTG
CAGTAGAGCAGATCAAAACCTTAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCGTCAAG
TCTTATCTCTCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCA
Found at i:8880743 original size:217 final size:217
Alignment explanation
Indices: 8880368--8880795 Score: 784
Period size: 217 Copynumber: 2.0 Consensus size: 217
8880358 CGGAGTAGGT
8880368 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
1 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
* * *
8880433 CCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
66 CCCTGAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTAAAGTTGCAGAGAGCAG
* *
8880498 ATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTCAGCAAGCAAGTCTTATCCTC
131 ATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAGCAAACAAGTCTTATCCTC
8880563 CTGAAGTTGCAGTGAGGTAGAC
196 CTGAAGTTGCAGTGAGGTAGAC
*
8880585 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCT
1 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
8880650 CCCTGAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTAAAGTTGCAGAGAGCAG
66 CCCTGAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTAAAGTTGCAGAGAGCAG
* *
8880715 ATCGCGTCTAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAGTAAACAAGTCTTATCCTC
131 ATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAGCAAACAAGTCTTATCCTC
8880780 CTGAAGTTGCAGTGAG
196 CTGAAGTTGCAGTGAG
8880796 ACAGACTAAA
Statistics
Matches: 203, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 203 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (217 bp):
TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
CCCTGAAGTTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTCTCTAAAGTTGCAGAGAGCAG
ATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAGCAAACAAGTCTTATCCTC
CTGAAGTTGCAGTGAGGTAGAC
Found at i:8880784 original size:44 final size:43
Alignment explanation
Indices: 8880469--8880812 Score: 171
Period size: 44 Copynumber: 8.0 Consensus size: 43
8880459 AAACCTTGGA
* * * *
8880469 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CATCTAG
1 TCTTATCTC-CTGAAGTTGCAGTAGAGCAGACTAAGTAAACAAG
* * *
8880509 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTCAGCAAGCAAG
1 TCTTATCTC-CTGAAGTTGCAGTAGAGCAGACTAAGTAAACAAG
* ** *
8880553 TCTTATCCTCCTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGGCAAA
1 TCTTAT-CTCCTGAAGTTGCAGTAGA-GCAGACT-AAGTA-AACAAG
* * *** *
8880598 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAA-
1 TCTTATCT-CCTGAAGTTGCAGTAGAGCAGACTA-AGTAAACAAG
* * * * **
8880642 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGA-TCAA--AACCTTGG
1 TCTTATCT-CCTGAAGTTGCAGTAGAGCAGACT-AAGTAAAC-AAG
* ** *
8880685 ATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-TCGCGT---CTAG
1 -TCTTATCTC-CTGAAGTTGCAGTAGAGCAGACT-AAGTAAACAAG
8880726 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTAAGTAAACAAG
1 TCTTATCTC-CTGAAGTTGCAGTAGAGCAGACTAAGTAAACAAG
*
8880770 TCTTATCCTCCTGAAGTTGCAGT-GAGACAGACTAAATAAACAA
1 TCTTAT-CTCCTGAAGTTGCAGTAGAG-CAGACTAAGTAAACAA
8880813 ATCCTGTCTC
Statistics
Matches: 245, Mismatches: 33, Indels: 48
0.75 0.10 0.15
Matches are distributed among these distances:
40 43 0.18
41 20 0.08
42 3 0.01
43 17 0.07
44 118 0.48
45 42 0.17
46 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCTGAAGTTGCAGTAGAGCAGACTAAGTAAACAAG
Found at i:8881177 original size:19 final size:19
Alignment explanation
Indices: 8881149--8881212 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
8881139 AATTTTCGAG
*
8881149 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8881168 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8881187 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
8881208 GATAT
1 GATAT
8881213 ATACAATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:8881231 original size:19 final size:21
Alignment explanation
Indices: 8881150--8881225 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
8881140 ATTTTCGAGG
8881150 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
*
8881169 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
8881190 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
8881211 ATATACAATATTAGA
1 ATATACAATCTTAGA
8881226 AGATATGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 18 0.35
21 34 0.65
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:8881690 original size:3 final size:3
Alignment explanation
Indices: 8881682--8881720 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
8881672 ATTAATTTTG
8881682 TTA TTA TTA TT- TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
8881721 ACCTACATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
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:8881696 original size:23 final size:23
Alignment explanation
Indices: 8881666--8881720 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
8881656 GTTTTTAGTC
* *
8881666 TATTTTATTAATTTTGTTAT-TAT
1 TATTTTATT-ATTATATTATATAT
8881689 TATTTTATTATTATATTATATAT
1 TATTTTATTATTATATTATATAT
8881712 TATTATTAT
1 TATT-TTAT
8881721 ACCTACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 16 0.57
24 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTTTATTATTATATTATATAT
Found at i:8881721 original size:11 final size:11
Alignment explanation
Indices: 8881682--8881720 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
8881672 ATTAATTTTG
*
8881682 TTATTATTATT
1 TTATTATTATA
8881693 TTATTATTATA
1 TTATTATTATA
8881704 TTATATATTATTA
1 TTAT-TATTA-TA
8881717 TTAT
1 TTAT
8881721 ACCTACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 5 0.20
13 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATTATA
Found at i:8891815 original size:14 final size:14
Alignment explanation
Indices: 8891792--8891829 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
8891782 TAAACGAAAC
8891792 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
8891805 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
8891819 -GAGAAA-AAAAA
1 AGAGAAAGAAAAA
8891830 TTAGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 9 0.38
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:8891822 original size:15 final size:13
Alignment explanation
Indices: 8891792--8891828 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
8891782 TAAACGAAAC
8891792 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
8891805 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
8891819 -GAGAA-AAAAA
1 AGAGAAGAAAAA
8891829 ATTAGGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 2 0.09
13 7 0.30
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:8894636 original size:33 final size:33
Alignment explanation
Indices: 8894599--8894741 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 33
8894589 ACACTATAAA
8894599 TGTAAGACCATGACAGGGCCATGGCAATGCATG
1 TGTAAGACCATGACAGGGCCATGGCAATGCATG
* * *
8894632 TGTAAGACCAT-AGCTGGGCTATGGC-ATTC-TG
1 TGTAAGACCATGA-CAGGGCCATGGCAATGCATG
* * *** * ** **
8894663 ATGATAAGACCATAACCGGGTTTTGGCATTATAAA
1 -TG-TAAGACCATGACAGGGCCATGGCAATGCATG
* *
8894698 TGTAAGACTATGGCAGGGCCATGGCAATGCATG
1 TGTAAGACCATGACAGGGCCATGGCAATGCATG
8894731 TGTAAGACCAT
1 TGTAAGACCAT
8894742 AGTTGGACTA
Statistics
Matches: 80, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
31 2 0.03
32 6 0.08
33 68 0.85
34 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (33 bp):
TGTAAGACCATGACAGGGCCATGGCAATGCATG
Found at i:8894673 original size:99 final size:99
Alignment explanation
Indices: 8894533--8894756 Score: 367
Period size: 99 Copynumber: 2.3 Consensus size: 99
8894523 AATGTTTAAA
* *
8894533 TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCGTAACTGGGTTATGACACTATAA
1 TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACCGGGTTATGACACTATAA
8894598 ATGTAAGACCATGACAGGGCCATGGCAATGCATG
66 ATGTAAGACCATGACAGGGCCATGGCAATGCATG
* * * *
8894632 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACCGGGTTTTGGCATTATAA
1 TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACCGGGTTATGACACTATAA
* *
8894697 ATGTAAGACTATGGCAGGGCCATGGCAATGCATG
66 ATGTAAGACCATGACAGGGCCATGGCAATGCATG
*
8894731 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGTTGGGCTATGGCA
8894757 CAAAAAGAAC
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 115 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (99 bp):
TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACCGGGTTATGACACTATAA
ATGTAAGACCATGACAGGGCCATGGCAATGCATG
Found at i:8900444 original size:2 final size:2
Alignment explanation
Indices: 8900437--8900468 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8900427 TTACAAGCTA
8900437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8900469 TATGGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8905199 original size:31 final size:31
Alignment explanation
Indices: 8905097--8905199 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
8905087 TATAGATAAA
* *
8905097 TTTAAAAATTAAGTT-TTAAATCATTTTTAAT
1 TTTAAAAA-TAATTTATTAAATAATTTTTAAT
*** *
8905128 TTT-AAAATAATTTTATTTTTTTCAA-TTTCAA-
1 TTTAAAAATAA-TTTA-TTAAAT-AATTTTTAAT
8905159 TTTAAAAATAATTTATTAAATAATTTTTAAT
1 TTTAAAAATAATTTATTAAATAATTTTTAAT
8905190 TTTAAAAATA
1 TTTAAAAATA
8905200 GGGTAAATTA
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
29 5 0.09
30 14 0.25
31 20 0.36
32 15 0.27
33 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTAAAAATAATTTATTAAATAATTTTTAAT
Found at i:8906200 original size:20 final size:21
Alignment explanation
Indices: 8906170--8906211 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
8906160 ATCTAACGTG
8906170 GCAAGTTAACTGGCCACATCA
1 GCAAGTTAACTGGCCACATCA
*
8906191 GCAA-TTAACTTGCCACATCA
1 GCAAGTTAACTGGCCACATCA
8906211 G
1 G
8906212 TGGTCCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
GCAAGTTAACTGGCCACATCA
Found at i:8910982 original size:2 final size:2
Alignment explanation
Indices: 8910975--8911002 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8910965 ATTATAAACC
8910975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8911003 CATTACGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8912199 original size:45 final size:44
Alignment explanation
Indices: 8912014--8912201 Score: 170
Period size: 45 Copynumber: 4.2 Consensus size: 44
8912004 ATACTCGGAT
* * *
8912014 AATCACATATATCGAACAATGCCAACGTCCCAGACGTGGTCTTACATG
1 AATCACATATATCG----ATGCCAATGTCCCAGACATGGTCTTACACG
* * * * *
8912062 CTATCTC--ATATCGATGCCACTGTCCCGGACAAGGTCTTACACG
1 -AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
*
8912105 AATCA-A-ATA-CGATGCCAATGTCCTAGACATGGTCTTACACG
1 AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
* *
8912146 TAATCACATATATCGATGCCATTGTCCCAGACGTGGTCTTACACG
1 -AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
*
8912191 AGAACACATAT
1 A-ATCACATAT
8912202 CGAAAATCCT
Statistics
Matches: 115, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
41 28 0.24
42 11 0.10
43 25 0.22
44 4 0.03
45 37 0.32
47 6 0.05
49 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (44 bp):
AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
Found at i:8914423 original size:19 final size:20
Alignment explanation
Indices: 8914386--8914423 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
8914376 CCTGAAAAAT
* *
8914386 GCATTTTAATGACACTCAAA
1 GCATGTTAATGACAATCAAA
8914406 GCATGTTAA-GACAATCAA
1 GCATGTTAATGACAATCAA
8914424 CCTAAAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
GCATGTTAATGACAATCAAA
Found at i:8917258 original size:30 final size:29
Alignment explanation
Indices: 8917178--8917251 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
8917168 ATTTCATCTC
*
8917178 GTCAAAATAATTTTTTTAGAACACATTAT
1 GTCAAAATTATTTTTTTAGAACACATTAT
* * *
8917207 GTTAAATTTATTTTTTTAGAACCCA-TATT
1 GTCAAAATTATTTTTTTAGAACACATTA-T
8917236 GTCAAAATTATTTTTT
1 GTCAAAATTATTTTTT
8917252 CCAGAACAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (29 bp):
GTCAAAATTATTTTTTTAGAACACATTAT
Found at i:8917319 original size:24 final size:23
Alignment explanation
Indices: 8917278--8917323 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
8917268 CAATTAAAAA
*
8917278 AATTAAACCCTAAAACCCTAATC
1 AATTAAAACCTAAAACCCTAATC
*
8917301 AATTAAAAACCTAATACCCTAAT
1 AATT-AAAACCTAAAACCCTAAT
8917324 TTAAATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (23 bp):
AATTAAAACCTAAAACCCTAATC
Found at i:8923217 original size:18 final size:18
Alignment explanation
Indices: 8923194--8923236 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8923184 TAAGAGGTTT
8923194 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
8923212 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
8923230 TTAATTA
1 TTAATTA
8923237 CACATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:8941064 original size:29 final size:30
Alignment explanation
Indices: 8941031--8941087 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
8941021 CCTTTTTACT
*
8941031 TTTCCCTCAAAACTTTTACTCCT-TCCCAC
1 TTTCCCCCAAAACTTTTACTCCTCTCCCAC
8941060 TTTCCCCCAAAACTTTTACTCCTCTCCC
1 TTTCCCCCAAAACTTTTACTCCTCTCCC
8941088 CTCCCAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTCCTCTCCCAC
Found at i:8943511 original size:31 final size:31
Alignment explanation
Indices: 8943473--8943536 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
8943463 GTTTGCCCAC
8943473 TTTAGTCCATAACGTTATCAAACATTCTCAA
1 TTTAGTCCATAACGTTATCAAACATTCTCAA
* * *
8943504 TTTAGTCCCTAATGTTATCAGACATTCTCAA
1 TTTAGTCCATAACGTTATCAAACATTCTCAA
8943535 TT
1 TT
8943537 CAATCCTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (31 bp):
TTTAGTCCATAACGTTATCAAACATTCTCAA
Found at i:8943644 original size:21 final size:20
Alignment explanation
Indices: 8943620--8943666 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
8943610 AAAACCCTTA
8943620 AAAATTGGAAAAAAAATTATT
1 AAAATTGGAAAAAAAATTA-T
*
8943641 AAAATAGGAAAAAAAATTAT
1 AAAATTGGAAAAAAAATTAT
8943661 AAAATT
1 AAAATT
8943667 ACAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAATTGGAAAAAAAATTAT
Found at i:8943919 original size:15 final size:16
Alignment explanation
Indices: 8943881--8943919 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
8943871 TACATAATGA
*
8943881 AAATAAT-ATTATTTC
1 AAATAATAATCATTTC
8943896 AAATAATAATCATTT-
1 AAATAATAATCATTTC
8943911 AAATAATAA
1 AAATAATAA
8943920 ATACCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAATAATCATTTC
Found at i:8945466 original size:62 final size:62
Alignment explanation
Indices: 8945369--8945498 Score: 260
Period size: 62 Copynumber: 2.1 Consensus size: 62
8945359 ATCGAAAAAG
8945369 AAAATTATATCCAGTAAGTTAGGACACAATGTCTTGAACTCCCGATGCACGAATGAATGCCA
1 AAAATTATATCCAGTAAGTTAGGACACAATGTCTTGAACTCCCGATGCACGAATGAATGCCA
8945431 AAAATTATATCCAGTAAGTTAGGACACAATGTCTTGAACTCCCGATGCACGAATGAATGCCA
1 AAAATTATATCCAGTAAGTTAGGACACAATGTCTTGAACTCCCGATGCACGAATGAATGCCA
8945493 AAAATT
1 AAAATT
8945499 TACTTATTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (62 bp):
AAAATTATATCCAGTAAGTTAGGACACAATGTCTTGAACTCCCGATGCACGAATGAATGCCA
Found at i:8946101 original size:15 final size:15
Alignment explanation
Indices: 8946081--8946133 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
8946071 ATATGTGAAT
8946081 TATAAAATATATATA
1 TATAAAATATATATA
8946096 TATAAAATATATATA
1 TATAAAATATATATA
*
8946111 TATATAATATAT-T-
1 TATAAAATATATATA
8946124 T-TAAAATATA
1 TATAAAATATA
8946134 AAGAATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 8 0.22
13 1 0.03
14 1 0.03
15 26 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAATATATATA
Found at i:8946109 original size:17 final size:17
Alignment explanation
Indices: 8946087--8946122 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
8946077 GAATTATAAA
8946087 ATATATATATATAAAAT
1 ATATATATATATAAAAT
*
8946104 ATATATATATATAATAT
1 ATATATATATATAAAAT
8946121 AT
1 AT
8946123 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATATATATAAAAT
Found at i:8946408 original size:3 final size:3
Alignment explanation
Indices: 8946400--8946453 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
8946390 AAAGATATAC
8946400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8946448 ATA ATA
1 ATA ATA
8946454 CAATATTAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8947888 original size:20 final size:20
Alignment explanation
Indices: 8947842--8947888 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
8947832 TAAATTTTAG
*
8947842 TATTTTTATAATGTTTATTG
1 TATTTTTATAATGTTTATTC
* * *
8947862 TAATTTTATAATTTTTTTTC
1 TATTTTTATAATGTTTATTC
8947882 TATTTTT
1 TATTTTT
8947889 TACAAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
TATTTTTATAATGTTTATTC
Found at i:8947906 original size:18 final size:19
Alignment explanation
Indices: 8947885--8947926 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
8947875 TTTTTTCTAT
8947885 TTTTTACAAATTTTAAA-A
1 TTTTTACAAATTTTAAATA
* *
8947903 TTTTTGCAATTTTTAAATA
1 TTTTTACAAATTTTAAATA
8947922 TTTTT
1 TTTTT
8947927 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTACAAATTTTAAATA
Found at i:8949048 original size:114 final size:113
Alignment explanation
Indices: 8948844--8949182 Score: 527
Period size: 114 Copynumber: 3.0 Consensus size: 113
8948834 TAAGATGTTT
* *
8948844 GGGCATAACATGAATCATTTGAAGATGGATAAGCAATCTAGAGAG-GATCTATTACTCAAAGTGA
1 GGGCATAACATGAATCATTTGAAGATGGATAAGTAATCTAGAGAGAGATCTATCACTCAAAGTGA
8948908 TACTATAAACATATCTCATTCGCCATGGTTAATTTGATCAATACTTTG
66 TACTATAAACATATCTCATTCGCCATGGTTAATTTGATCAATACTTTG
*
8948956 GGGCATAACATGAATCATTTAAAGATGGATAAGTAATCTAGAGAGAAGATCTATCACTCAAAGTG
1 GGGCATAACATGAATCATTTGAAGATGGATAAGTAATCTAGAGAG-AGATCTATCACTCAAAGTG
** *
8949021 ATACTATAAACATATCTCATTTTCCATGATTAATTTGATCAATACTTTG
65 ATACTATAAACATATCTCATTCGCCATGGTTAATTTGATCAATACTTTG
*** * * *
8949070 ATTCATAACATGAACCATTTGAAGATGGATAGGTAATCTAGAGAGAGGATCTATCACTCAAACTG
1 GGGCATAACATGAATCATTTGAAGATGGATAAGTAATCTAGAGAGA-GATCTATCACTCAAAGTG
* *
8949135 ATACTATAAACATATCTCATTCGCTATGGTTAATTTCATCAATACTTT
65 ATACTATAAACATATCTCATTCGCCATGGTTAATTTGATCAATACTTT
8949183 AACCAGAGCA
Statistics
Matches: 206, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
112 43 0.21
113 1 0.00
114 162 0.79
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (113 bp):
GGGCATAACATGAATCATTTGAAGATGGATAAGTAATCTAGAGAGAGATCTATCACTCAAAGTGA
TACTATAAACATATCTCATTCGCCATGGTTAATTTGATCAATACTTTG
Found at i:8950438 original size:20 final size:20
Alignment explanation
Indices: 8950413--8950452 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8950403 ATATACATTT
8950413 TACAAAATGGTTGAATATGG
1 TACAAAATGGTTGAATATGG
* *
8950433 TACAAAGTGGTTTAATATGG
1 TACAAAATGGTTGAATATGG
8950453 GCCTGTAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (20 bp):
TACAAAATGGTTGAATATGG
Found at i:8960409 original size:2 final size:2
Alignment explanation
Indices: 8960404--8960446 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
8960394 AAAAAGCTAA
8960404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8960446 A
1 A
8960447 AACGAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8962452 original size:18 final size:19
Alignment explanation
Indices: 8962418--8962478 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
8962408 TAGTTTTAAA
*
8962418 ATTTTAAAAATATTTTTAT
1 ATTTTAAAAATAATTTTAT
*
8962437 ATTTT-ATAATAATTTTA-
1 ATTTTAAAAATAATTTTAT
*
8962454 ATTTTAAAAATATATTTTTT
1 ATTTTAAAAATA-ATTTTAT
8962474 ATTTT
1 ATTTT
8962479 CTTTTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 5 0.14
18 15 0.43
19 10 0.29
20 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAAAAATAATTTTAT
Found at i:8976685 original size:108 final size:108
Alignment explanation
Indices: 8976496--8976715 Score: 431
Period size: 108 Copynumber: 2.0 Consensus size: 108
8976486 TCGAAAATTG
8976496 AGGGCCTCGAGGGTGAGCTCGTTATGTGTAGAGCTGTTGTGGGTAAAGGGATATTGGTTTCGATC
1 AGGGCCTCGAGGGTGAGCTCGTTATGTGTAGAGCTGTTGTGGGTAAAGGGATATTGGTTTCGATC
8976561 CCTAAGCAACATAAAATGGATATCCCCAAGTTGAAAGACTTTA
66 CCTAAGCAACATAAAATGGATATCCCCAAGTTGAAAGACTTTA
8976604 AGGGCCTCGAGGGTGAGCTCGTTATGTGTAGAGCTGTTGTGGGTAAAGGGATATTGGTTTCGATC
1 AGGGCCTCGAGGGTGAGCTCGTTATGTGTAGAGCTGTTGTGGGTAAAGGGATATTGGTTTCGATC
*
8976669 CCTAAGCAACGTAAAATGGATATCCCCAAGTTGAAAGACTTTA
66 CCTAAGCAACATAAAATGGATATCCCCAAGTTGAAAGACTTTA
8976712 AGGG
1 AGGG
8976716 GATGATGTCC
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 111 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (108 bp):
AGGGCCTCGAGGGTGAGCTCGTTATGTGTAGAGCTGTTGTGGGTAAAGGGATATTGGTTTCGATC
CCTAAGCAACATAAAATGGATATCCCCAAGTTGAAAGACTTTA
Found at i:8977245 original size:31 final size:33
Alignment explanation
Indices: 8977209--8977280 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 33
8977199 ATATTTTTAC
* ** *
8977209 ATTTTAAAAATAA-ATTTTATGTTTTTTTATA-
1 ATTTTAAAAATAATATTTAATAATTTTATATAT
8977240 ATTTT-AAAATAATATTTAATAATTTTATATAT
1 ATTTTAAAAATAATATTTAATAATTTTATATAT
8977272 ATTTTAAAA
1 ATTTTAAAA
8977281 TTTTGACTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 7 0.21
31 19 0.56
32 5 0.15
33 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (33 bp):
ATTTTAAAAATAATATTTAATAATTTTATATAT
Found at i:8977275 original size:19 final size:22
Alignment explanation
Indices: 8977232--8977284 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
8977222 ATTTTATGTT
*
8977232 TTTTTATAATTTTAAAATAATA
1 TTTTAATAATTTTAAAATAATA
*
8977254 -TTTAATAATTTT-ATAT-ATA
1 TTTTAATAATTTTAAAATAATA
8977273 TTTTAA-AATTTT
1 TTTTAATAATTTT
8977285 GACTGATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAATAATTTTAAAATAATA
Found at i:8981891 original size:3 final size:3
Alignment explanation
Indices: 8981885--8981919 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
8981875 TGAAAATGAT
*
8981885 GAA GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
8981920 TAGGGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:8993244 original size:36 final size:37
Alignment explanation
Indices: 8993173--8993244 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
8993163 TTAAAAGTAA
* *
8993173 TGGTGAATTTTATTTTATTTTTAAATTTAATTTAATT
1 TGGTGAATTTTATTATATTTTTAAATTTAAATTAATT
8993210 TGGT-AATTTTA-TATATTTTCTATAA-TTAAATTAAT
1 TGGTGAATTTTATTATATTTT-TA-AATTTAAATTAAT
8993245 GTTCGGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 7 0.23
36 18 0.58
37 6 0.19
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.58
Consensus pattern (37 bp):
TGGTGAATTTTATTATATTTTTAAATTTAAATTAATT
Found at i:8995665 original size:15 final size:14
Alignment explanation
Indices: 8995644--8995679 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
8995634 ATAATCCTTA
*
8995644 ATAATTATCTTAAT
1 ATAATTATCCTAAT
8995658 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
8995673 ATAATTA
1 ATAATTA
8995680 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:9000005 original size:2 final size:2
Alignment explanation
Indices: 8999998--9000022 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8999988 AAATATGCGC
8999998 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9000023 TCTTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9000348 original size:15 final size:15
Alignment explanation
Indices: 9000328--9000357 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9000318 TTTTTTTTAG
9000328 AAAATTATAAAAATA
1 AAAATTATAAAAATA
*
9000343 AAAATTATAGAAATA
1 AAAATTATAAAAATA
9000358 TTATAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAATTATAAAAATA
Found at i:9000362 original size:26 final size:25
Alignment explanation
Indices: 9000325--9000374 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
9000315 AAGTTTTTTT
9000325 TAGAAAATTATAAAAATAAAAATTA
1 TAGAAAATTATAAAAATAAAAATTA
*
9000350 TAGAAATATTATAAAAATTAAAATT
1 TAGAAA-ATTATAAAAATAAAAATT
9000375 CACTACTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (25 bp):
TAGAAAATTATAAAAATAAAAATTA
Found at i:9002584 original size:3 final size:3
Alignment explanation
Indices: 9002576--9002650 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
9002566 ACAAAGAGGA
9002576 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
9002624 AAG AAG AAG AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
9002651 GGGGGAAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9007166 original size:43 final size:43
Alignment explanation
Indices: 9007105--9007190 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
9007095 AGATGCATAG
9007105 TTTGCTTGATTATAAGTGGTCAATTGGGGTGCCTATGGGCATC
1 TTTGCTTGATTATAAGTGGTCAATTGGGGTGCCTATGGGCATC
*
9007148 TTTGCTTGATTATAAGTGGTCAATTGGGGTGCTTATGGGCATC
1 TTTGCTTGATTATAAGTGGTCAATTGGGGTGCCTATGGGCATC
9007191 ATGTTGTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (43 bp):
TTTGCTTGATTATAAGTGGTCAATTGGGGTGCCTATGGGCATC
Found at i:9013532 original size:25 final size:26
Alignment explanation
Indices: 9013480--9013533 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
9013470 GAATGGGAAA
*
9013480 GAAAAACTAAGTTAAAGATTTGGGGG
1 GAAAAACTAAGTTAAAGATTTGGAGG
**
9013506 GAAAAACTAAGTTAGGGATTT-GAGG
1 GAAAAACTAAGTTAAAGATTTGGAGG
9013531 GAA
1 GAA
9013534 TAAGGGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.43, C:0.04, G:0.31, T:0.22
Consensus pattern (26 bp):
GAAAAACTAAGTTAAAGATTTGGAGG
Found at i:9013754 original size:84 final size:84
Alignment explanation
Indices: 9013666--9013823 Score: 190
Period size: 84 Copynumber: 1.9 Consensus size: 84
9013656 ATCATTTTTA
* * ** * ** *
9013666 ACCTTTTGCGACATTTATGCAAAAACACCACTATTGCTTTACCTTTTGCGGTGTTTATGGGAAAA
1 ACCTTTAGCGACATTTAGGCAAAAACACCACTATTGCTTTACCTTTCACAGCATTTATCGGAAAA
9013731 ACGCCGCTATTTTTGTTAT
66 ACGCCGCTATTTTTGTTAT
* * * * * *
9013750 ACCTTTAGTGGCGTTTAGGGAAAAACGCCACTATTTCTTTACCTTTCACAGCATTTATCGGAAAA
1 ACCTTTAGCGACATTTAGGCAAAAACACCACTATTGCTTTACCTTTCACAGCATTTATCGGAAAA
9013815 ACGCCGCTA
66 ACGCCGCTA
9013824 ACCCTGCTCC
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 60 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (84 bp):
ACCTTTAGCGACATTTAGGCAAAAACACCACTATTGCTTTACCTTTCACAGCATTTATCGGAAAA
ACGCCGCTATTTTTGTTAT
Found at i:9014045 original size:12 final size:12
Alignment explanation
Indices: 9014028--9014053 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9014018 TTTTCGATCT
9014028 AAACGCCGCTAA
1 AAACGCCGCTAA
9014040 AAACGCCGCTAA
1 AAACGCCGCTAA
9014052 AA
1 AA
9014054 GCTTAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:9016816 original size:24 final size:24
Alignment explanation
Indices: 9016784--9016832 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
9016774 AAAATTTCTC
9016784 TTTCACTTTCATTAGAGTGTGACA
1 TTTCACTTTCATTAGAGTGTGACA
9016808 TTTCACTTTCATTAGAGTGTGACA
1 TTTCACTTTCATTAGAGTGTGACA
9016832 T
1 T
9016833 GGTCTAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (24 bp):
TTTCACTTTCATTAGAGTGTGACA
Done.