Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 172 of 190
Found at i:28381215 original size:14 final size:14
Alignment explanation
Indices: 28381196--28381246 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
28381186 TTTAGTATTA
28381196 AATATTAATATTTT
1 AATATTAATATTTT
* *
28381210 AATATTATTATATT
1 AATATTAATATTTT
28381224 AATAAATTAATA-TTT
1 AAT--ATTAATATTTT
28381239 AATATTAA
1 AATATTAA
28381247 ATGCTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 15 0.48
15 5 0.16
16 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:28381223 original size:29 final size:30
Alignment explanation
Indices: 28381183--28381245 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
28381173 AAAATATAAC
*
28381183 TATT-TTAGTATTAA-ATATTAATATTTTAA
1 TATTATTAGTATTAATAAATTAATA-TTTAA
28381212 TATTATTA-TATTAATAAATTAATATTTAA
1 TATTATTAGTATTAATAAATTAATATTTAA
28381241 TATTA
1 TATTA
28381246 AATGCTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TATTATTAGTATTAATAAATTAATATTTAA
Found at i:28381309 original size:21 final size:23
Alignment explanation
Indices: 28381283--28381330 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
28381273 TAACATTAAT
28381283 AAATA-TAGTAATAAATAATTTC
1 AAATATTAGTAATAAATAATTTC
*
28381305 AATATATTATTAATAAATAATTTC
1 AA-ATATTAGTAATAAATAATTTC
28381329 AA
1 AA
28381331 TAATTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 3 0.13
24 18 0.78
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATATTAGTAATAAATAATTTC
Found at i:28381342 original size:24 final size:24
Alignment explanation
Indices: 28381291--28381342 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28381281 ATAAATATAG
*
28381291 TAATAAATAATTTCAATATATTAT
1 TAATAAATAATTTCAATATATTAA
28381315 TAATAAATAATTTCAATA-ATTTAA
1 TAATAAATAATTTCAATATA-TTAA
28381339 TAAT
1 TAAT
28381343 TATATGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAAATAATTTCAATATATTAA
Found at i:28395950 original size:8 final size:8
Alignment explanation
Indices: 28395933--28395979 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
28395923 TTTAATTTTT
28395933 TATTTATA
1 TATTTATA
28395941 TATATT-TA
1 TAT-TTATA
28395949 TATTTATA
1 TATTTATA
*
28395957 TAATTATA
1 TATTTATA
*
28395965 TATTTAAA
1 TATTTATA
28395973 TATTTAT
1 TATTTAT
28395980 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 2 0.06
8 29 0.88
9 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:28398382 original size:20 final size:21
Alignment explanation
Indices: 28398346--28398397 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28398336 TTCGAAATTA
28398346 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
28398368 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
28398389 AT-AAATATT
1 ATAAAATATT
28398398 TTAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:28398388 original size:21 final size:22
Alignment explanation
Indices: 28398346--28398397 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
28398336 TTCGAAATTA
28398346 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
28398368 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
28398389 AT-AAATATT
1 ATAAAATATT
28398398 TTAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:28404620 original size:16 final size:18
Alignment explanation
Indices: 28404601--28404637 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28404591 AATTATTTTT
28404601 TTTAAAGT-TT-ATATAA
1 TTTAAAGTATTGATATAA
*
28404617 TTTAAATTATTGATATAA
1 TTTAAAGTATTGATATAA
28404635 TTT
1 TTT
28404638 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAAGTATTGATATAA
Found at i:28405092 original size:18 final size:18
Alignment explanation
Indices: 28405071--28405106 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28405061 CATATATCTT
28405071 TAAAAAA-TATATTAAAAA
1 TAAAAAATTA-ATTAAAAA
28405089 TAAAAAATTAATTAAAAA
1 TAAAAAATTAATTAAAAA
28405107 AAGACAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAATTAATTAAAAA
Found at i:28406048 original size:39 final size:39
Alignment explanation
Indices: 28406005--28406091 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
28405995 ATAGAAAATT
28406005 AGTTTTGTTGTTCATTTCCATTTCCACGAGTTTATATTC
1 AGTTTTGTTGTTCATTTCCATTTCCACGAGTTTATATTC
*
28406044 AGTTTTGTTGTTCATTTCCATTTCCAGGAGTTTATATTC
1 AGTTTTGTTGTTCATTTCCATTTCCACGAGTTTATATTC
28406083 AGTTTTGTT
1 AGTTTTGTT
28406092 ATATTCATGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (39 bp):
AGTTTTGTTGTTCATTTCCATTTCCACGAGTTTATATTC
Found at i:28410217 original size:143 final size:143
Alignment explanation
Indices: 28409959--28410245 Score: 574
Period size: 143 Copynumber: 2.0 Consensus size: 143
28409949 AGAAAGGCGA
28409959 ATGCACAGTGATTCATTACCTCTTTTCATTTTATAATATAAAATAAGTCATTCTAATATTTATCA
1 ATGCACAGTGATTCATTACCTCTTTTCATTTTATAATATAAAATAAGTCATTCTAATATTTATCA
28410024 TCCAAATGCTCATGCAGGTTCCTTCTCTCGCTCAGCAGTAAATTACATGGCTGGATGCCATACAG
66 TCCAAATGCTCATGCAGGTTCCTTCTCTCGCTCAGCAGTAAATTACATGGCTGGATGCCATACAG
28410089 CTGTGTCTAATAT
131 CTGTGTCTAATAT
28410102 ATGCACAGTGATTCATTACCTCTTTTCATTTTATAATATAAAATAAGTCATTCTAATATTTATCA
1 ATGCACAGTGATTCATTACCTCTTTTCATTTTATAATATAAAATAAGTCATTCTAATATTTATCA
28410167 TCCAAATGCTCATGCAGGTTCCTTCTCTCGCTCAGCAGTAAATTACATGGCTGGATGCCATACAG
66 TCCAAATGCTCATGCAGGTTCCTTCTCTCGCTCAGCAGTAAATTACATGGCTGGATGCCATACAG
28410232 CTGTGTCTAATAT
131 CTGTGTCTAATAT
28410245 A
1 A
28410246 GTGATGTCCT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 144 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (143 bp):
ATGCACAGTGATTCATTACCTCTTTTCATTTTATAATATAAAATAAGTCATTCTAATATTTATCA
TCCAAATGCTCATGCAGGTTCCTTCTCTCGCTCAGCAGTAAATTACATGGCTGGATGCCATACAG
CTGTGTCTAATAT
Found at i:28416395 original size:20 final size:19
Alignment explanation
Indices: 28416359--28416402 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
28416349 AATTATAATA
*
28416359 AAATATTTAATATATATTT
1 AAATTTTTAATATATATTT
28416378 AAATTTTTAATATAATATTT
1 AAATTTTTAATAT-ATATTT
28416398 AAATT
1 AAATT
28416403 ATAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTTTTAATATATATTT
Found at i:28416395 original size:31 final size:28
Alignment explanation
Indices: 28416354--28416422 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 28
28416344 TTTTGAATTA
*
28416354 TAATAAAATATTTAATATATATTTAAATTT-T
1 TAATATAATATTTAA-AT-TA--TAAATTTAT
28416385 TAATATAATATTTAAATTATAAATTTAT
1 TAATATAATATTTAAATTATAAATTTAT
28416413 TAAT-TAATAT
1 TAATATAATAT
28416423 AATATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 13 0.36
28 5 0.14
29 2 0.06
30 2 0.06
31 14 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TAATATAATATTTAAATTATAAATTTAT
Found at i:28417337 original size:20 final size:20
Alignment explanation
Indices: 28417289--28417330 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
28417279 ATTCTAATAG
28417289 TTAAAATTTTTAAATTTTAAT
1 TTAAAATTTTTAAA-TTTAAT
28417310 TTAAAATTTTTAAA-TTAAT
1 TTAAAATTTTTAAATTTAAT
28417329 TT
1 TT
28417331 TGAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAAATTTTTAAATTTAAT
Found at i:28418439 original size:24 final size:25
Alignment explanation
Indices: 28418412--28418458 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
28418402 TGTGAAATTT
28418412 TTTTAA-AAAATAATTT-AATAAAAG
1 TTTTAATAAAA-AATTTAAATAAAAG
*
28418436 TTTTAATTAAAAATTTAAATAAA
1 TTTTAATAAAAAATTTAAATAAA
28418459 TAAATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTTTAATAAAAAATTTAAATAAAAG
Found at i:28418505 original size:12 final size:12
Alignment explanation
Indices: 28418488--28418512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28418478 GTGAAAATTG
28418488 TAAAAATATTAT
1 TAAAAATATTAT
28418500 TAAAAATATTAT
1 TAAAAATATTAT
28418512 T
1 T
28418513 TATAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:28418680 original size:13 final size:13
Alignment explanation
Indices: 28418657--28418692 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
28418647 TAATAAAATT
28418657 TTTTAATTTATCAA
1 TTTTAA-TTATCAA
*
28418671 TTTTAATTATTAA
1 TTTTAATTATCAA
28418684 TTTTAATTA
1 TTTTAATTA
28418693 AAAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTAATTATCAA
Found at i:28420285 original size:13 final size:13
Alignment explanation
Indices: 28420267--28420291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28420257 TAATAATAAA
28420267 ATATTAAAAATAT
1 ATATTAAAAATAT
28420280 ATATTAAAAATA
1 ATATTAAAAATA
28420292 AAAAACTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATTAAAAATAT
Found at i:28421520 original size:13 final size:13
Alignment explanation
Indices: 28421487--28421527 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
28421477 ATTAATAAAA
*
28421487 TTAATATATATTT
1 TTAATAAATATTT
28421500 TTAGATAAATATTT
1 TTA-ATAAATATTT
*
28421514 TTAATAAAAATTT
1 TTAATAAATATTT
28421527 T
1 T
28421528 GACAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TTAATAAATATTT
Found at i:28422058 original size:4 final size:4
Alignment explanation
Indices: 28422043--28422072 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
28422033 AAAAAGTTAA
28422043 AATT ACATT AATT AATT AATT AATT AATT A
1 AATT A-ATT AATT AATT AATT AATT AATT A
28422073 TTTTTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:28422247 original size:23 final size:22
Alignment explanation
Indices: 28422215--28422261 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
28422205 ACGCATCCAA
* * *
28422215 ATGTGTTTTATTTTTATTTTAG
1 ATGTGTTTTACTTCTACTTTAG
28422237 ATGTGCTTTTACTTCTACTTTAG
1 ATGTG-TTTTACTTCTACTTTAG
28422260 AT
1 AT
28422262 ATTTTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.60
Consensus pattern (22 bp):
ATGTGTTTTACTTCTACTTTAG
Found at i:28422422 original size:97 final size:97
Alignment explanation
Indices: 28422305--28422492 Score: 281
Period size: 97 Copynumber: 1.9 Consensus size: 97
28422295 GGTAAAAATT
* * **
28422305 AAGAAAACACCATAATTTATGATTTTGAAGTTTTTATTTCATTCTCTT-AAAAGTATATTTTATT
1 AAGAAAACACAATAACTTATGATTTCAAAGTTTTTATTTCATTCTCTTAAAAAGTATATTTTA-T
28422369 TTTCTTATTT-TGACTAAAAATATTATAACAATA
65 TTTCTTATTTGTGA-TAAAAATATTATAACAATA
* *
28422402 AAGAAAACACAATAACTTATGATTTCAAAGTTTTTATTTTATTCTTTTAAAAAGTATATTTTATT
1 AAGAAAACACAATAACTTATGATTTCAAAGTTTTTATTTCATTCTCTTAAAAAGTATATTTTATT
*
28422467 TTCTTATTTGTTATAAAAATATTATA
66 TTCTTATTTGTGATAAAAATATTATA
28422493 TAACAATTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
97 66 0.80
98 16 0.20
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (97 bp):
AAGAAAACACAATAACTTATGATTTCAAAGTTTTTATTTCATTCTCTTAAAAAGTATATTTTATT
TTCTTATTTGTGATAAAAATATTATAACAATA
Found at i:28423717 original size:15 final size:17
Alignment explanation
Indices: 28423697--28423729 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
28423687 ATACTTGAAT
28423697 TTAAATTT-T-ATTAAA
1 TTAAATTTATAATTAAA
28423712 TTAAATTTATAATTAAA
1 TTAAATTTATAATTAAA
28423729 T
1 T
28423730 AATTATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTTATAATTAAA
Found at i:28423845 original size:27 final size:27
Alignment explanation
Indices: 28423795--28423849 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
28423785 GATTGATTCA
**
28423795 TTGATTATTTAAAAATATTTAATTAAT
1 TTGATTATTTAAAAATATAAAATTAAT
28423822 TTGATTATTTATAAAATA-AAAATTAAT
1 TTGATTATTTA-AAAATATAAAATTAAT
28423849 T
1 T
28423850 AAATTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTGATTATTTAAAAATATAAAATTAAT
Found at i:28423855 original size:27 final size:27
Alignment explanation
Indices: 28423798--28423855 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
28423788 TGATTCATTG
** **
28423798 ATTATTTAAAAATATTTAATTAATTTG
1 ATTATTTAAAAATATAAAATTAATTAA
28423825 ATTATTTATAAAATA-AAAATTAATTAA
1 ATTATTTA-AAAATATAAAATTAATTAA
28423852 ATTA
1 ATTA
28423856 ATATTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTATTTAAAAATATAAAATTAATTAA
Found at i:28427556 original size:23 final size:23
Alignment explanation
Indices: 28427492--28427559 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
28427482 TGATATTGTA
* *
28427492 TAAAAATAAATTT--TAAAATTT
1 TAAAAATATATTTAATATAATTT
** *
28427513 TAAAAA-ATAAATACATTTAATTT
1 TAAAAATATATTTA-ATATAATTT
28427536 TAAAAATATATTTAATATAATTT
1 TAAAAATATATTTAATATAATTT
28427559 T
1 T
28427560 TTGTGAGAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 3 0.09
21 6 0.17
23 21 0.60
24 5 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAATATATTTAATATAATTT
Found at i:28431375 original size:7 final size:7
Alignment explanation
Indices: 28431363--28431389 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28431353 AATGAGAGAA
28431363 GCAAAAG
1 GCAAAAG
28431370 GCAAAAG
1 GCAAAAG
28431377 GCAAAAG
1 GCAAAAG
28431384 GCAAAA
1 GCAAAA
28431390 CGCGTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (7 bp):
GCAAAAG
Found at i:28437333 original size:18 final size:18
Alignment explanation
Indices: 28437312--28437365 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
28437302 TTTATATTTT
28437312 TTATTATATTTTTAAAAA
1 TTATTATATTTTTAAAAA
*
28437330 TTA-TATATAATTT--AAA
1 TTATTATAT-TTTTAAAAA
*
28437346 TTATATAAATTTTTAAAAA
1 TTAT-TATATTTTTAAAAA
28437365 T
1 T
28437366 AATTTTAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 10 0.36
19 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATTATATTTTTAAAAA
Found at i:28437348 original size:16 final size:15
Alignment explanation
Indices: 28437327--28437357 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28437317 ATATTTTTAA
28437327 AAATTATATATAATTT
1 AAATTATATA-AATTT
28437343 AAATTATATAAATTT
1 AAATTATATAAATTT
28437358 TTAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTATATAAATTT
Found at i:28437448 original size:15 final size:14
Alignment explanation
Indices: 28437430--28437473 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
28437420 TAATATAAAA
28437430 TAATATTATTTAATT
1 TAATATTATTT-ATT
28437445 TAATATTATTTA--
1 TAATATTATTTATT
28437457 TAATATTATTTGATT
1 TAATATTATTT-ATT
28437472 TA
1 TA
28437474 TAAATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.42
13 1 0.04
14 1 0.04
15 13 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TAATATTATTTATT
Found at i:28437460 original size:12 final size:13
Alignment explanation
Indices: 28437428--28437467 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
28437418 TATAATATAA
28437428 AATAATATTATTT
1 AATAATATTATTT
28437441 AATTTAATATTATTT
1 AA--TAATATTATTT
28437456 -ATAATATTATTT
1 AATAATATTATTT
28437468 GATTTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 1 0.04
15 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATAATATTATTT
Found at i:28438552 original size:55 final size:55
Alignment explanation
Indices: 28438459--28438571 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
28438449 AGTCCTTTTT
*
28438459 TGTCTAGACAATGCCTTAATTGCATCAAATTTGCAAACCAGAGAAGCTATGTGGC
1 TGTCAAGACAATGCCTTAATTGCATCAAATTTGCAAACCAGAGAAGCTATGTGGC
* *
28438514 TGTCAAGACAATGCCTTAATTGCATCACATTTGGAAACCAGAGAAGCTATGTGGC
1 TGTCAAGACAATGCCTTAATTGCATCAAATTTGCAAACCAGAGAAGCTATGTGGC
28438569 TGT
1 TGT
28438572 GAGGCCTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (55 bp):
TGTCAAGACAATGCCTTAATTGCATCAAATTTGCAAACCAGAGAAGCTATGTGGC
Found at i:28439654 original size:13 final size:13
Alignment explanation
Indices: 28439636--28439660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28439626 TGCATCAGGT
28439636 TTTTTATTTTTTA
1 TTTTTATTTTTTA
28439649 TTTTTATTTTTT
1 TTTTTATTTTTT
28439661 GTGTACAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:28445849 original size:30 final size:32
Alignment explanation
Indices: 28445813--28445882 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
28445803 CGAAATTAAT
* * *
28445813 AAAATATTATTTTTTAAATATA-A-ATATTTA
1 AAAATATTATTATATAAATATATATATAATTA
*
28445843 AAAATATCATTATATAAATATATATATAATTA
1 AAAATATTATTATATAAATATATATATAATTA
28445875 AAAA-ATTA
1 AAAATATTA
28445883 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 19 0.58
31 4 0.12
32 10 0.30
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATATTATTATATAAATATATATATAATTA
Found at i:28461707 original size:22 final size:23
Alignment explanation
Indices: 28461661--28461709 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
28461651 GATTCGATTC
* *
28461661 ATTTCAATTCGAATTATATTAAA
1 ATTTCAATTCGAATTAAAATAAA
*
28461684 ATTT-AATTCGAATTAAAATCAA
1 ATTTCAATTCGAATTAAAATAAA
28461706 ATTT
1 ATTT
28461710 TAAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTTCAATTCGAATTAAAATAAA
Found at i:28462030 original size:53 final size:53
Alignment explanation
Indices: 28461970--28462073 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
28461960 TGATTTGAGA
** * *
28461970 ATATATAAAAAATGTATTTTTTATTGTTTATTTAATTATATATTAAATTAAGT
1 ATATATAAAAAACATATTTTTTATTCTATATTTAATTATATATTAAATTAAGT
*
28462023 ATATATAAAAAACATATTTTTTATTCTATATTTAATTATATATTATATTAA
1 ATATATAAAAAACATATTTTTTATTCTATATTTAATTATATATTAAATTAA
28462074 AAAATTACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (53 bp):
ATATATAAAAAACATATTTTTTATTCTATATTTAATTATATATTAAATTAAGT
Found at i:28462099 original size:13 final size:14
Alignment explanation
Indices: 28462083--28462117 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
28462073 AAAAATTACT
28462083 ATTTAATAAT-TTA
1 ATTTAATAATATTA
28462096 ATTTAA-AATATTA
1 ATTTAATAATATTA
28462109 ATTTAATAA
1 ATTTAATAA
28462118 AAATATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 15 0.75
14 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAATAATATTA
Found at i:28462112 original size:18 final size:17
Alignment explanation
Indices: 28462089--28462131 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
28462079 TACTATTTAA
*
28462089 TAATTTAATTTAAAATAT
1 TAATTTAA-TAAAAATAT
28462107 TAATTTAATAAAAATAT
1 TAATTTAATAAAAATAT
28462124 TATATTTA
1 TA-ATTTA
28462132 TGTATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTAATAAAAATAT
Found at i:28469319 original size:13 final size:13
Alignment explanation
Indices: 28469301--28469332 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28469291 CTAATAATAG
28469301 GTAGTGAAGTATA
1 GTAGTGAAGTATA
28469314 GTAGTGAAGTATA
1 GTAGTGAAGTATA
*
28469327 GCAGTG
1 GTAGTG
28469333 TCAATGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.28
Consensus pattern (13 bp):
GTAGTGAAGTATA
Found at i:28474852 original size:18 final size:19
Alignment explanation
Indices: 28474829--28474870 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
28474819 CCCGAAATTA
28474829 ATAAAATATT-TTTTAAAT
1 ATAAAATATTATTTTAAAT
*
28474847 ATAAAATATTATTTTTAAT
1 ATAAAATATTATTTTAAAT
28474866 ATAAA
1 ATAAA
28474871 TATAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAAATATTATTTTAAAT
Found at i:28474871 original size:18 final size:17
Alignment explanation
Indices: 28474826--28474873 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
28474816 TAACCCGAAA
28474826 TTAATA-AAATATTTTT
1 TTAATATAAATATTTTT
*
28474842 TAAATATAAAATATTATTT
1 TTAATAT-AAATATT-TTT
28474861 TTAATATAAATAT
1 TTAATATAAATAT
28474874 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
18 13 0.48
19 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATAAATATTTTT
Found at i:28474903 original size:24 final size:25
Alignment explanation
Indices: 28474862--28474917 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
28474852 ATATTATTTT
*
28474862 TAATATAA-ATATAAAATTAAATATA
1 TAATA-AACATATAAAATTAAATAAA
*
28474887 T-ATAAACATATATAATTAAATAAA
1 TAATAAACATATAAAATTAAATAAA
28474911 TAATAAA
1 TAATAAA
28474918 TAATAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 19 0.70
25 6 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TAATAAACATATAAAATTAAATAAA
Found at i:28489954 original size:19 final size:19
Alignment explanation
Indices: 28489908--28489962 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
28489898 TCCTCAACAA
*
28489908 ATAAATATAATATTAATATAT
1 ATAAA-ATAA-ATAAATATAT
* *
28489929 ATTAAATAAATAAATATTT
1 ATAAAATAAATAAATATAT
28489948 ATAAAATGAAATAAA
1 ATAAAAT-AAATAAA
28489963 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 11 0.38
21 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAATAAATAAATATAT
Found at i:28489964 original size:25 final size:25
Alignment explanation
Indices: 28489906--28489967 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
28489896 ACTCCTCAAC
* *
28489906 AAATAAATATAATATTAATATATATT
1 AAATAAATA-AATATTAATATAAATG
*
28489932 AAATAAATAAATATTTATA-AAATG
1 AAATAAATAAATATTAATATAAATG
28489956 AAATAAAATAAA
1 AAAT-AAATAAA
28489968 ATAAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.22
25 16 0.50
26 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATAAATAAATATTAATATAAATG
Found at i:28490354 original size:17 final size:17
Alignment explanation
Indices: 28490319--28490351 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28490309 AAAATAGTTT
28490319 TTATATAATAATATAAA
1 TTATATAATAATATAAA
*
28490336 TTATTTAATAAT-TAAA
1 TTATATAATAATATAAA
28490352 ATTGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATATAATAATATAAA
Found at i:28491448 original size:61 final size:61
Alignment explanation
Indices: 28491353--28491474 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
28491343 AAAACACCTC
*
28491353 TCTTCTTATTCAAAACCTAAACCACTTCAGAGATTCAGCCCCAAATCAAACTCCAATCTTG
1 TCTTCTTATTCAAAACCTAAACCACTTCAGAGATTCAGCCCCAAATCAAACTCCAACCTTG
* * * * * * *
28491414 TCTTCTTATTCAGAACCTTAACCCCTTTAGAGATTTAGTCCCAAATCAAATTCCAACCTTG
1 TCTTCTTATTCAAAACCTAAACCACTTCAGAGATTCAGCCCCAAATCAAACTCCAACCTTG
28491475 ATTTTGATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.31
Consensus pattern (61 bp):
TCTTCTTATTCAAAACCTAAACCACTTCAGAGATTCAGCCCCAAATCAAACTCCAACCTTG
Found at i:28492911 original size:13 final size:13
Alignment explanation
Indices: 28492893--28492917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28492883 ATATTAAAAA
28492893 TAATTAAATTAAT
1 TAATTAAATTAAT
28492906 TAATTAAATTAA
1 TAATTAAATTAA
28492918 AATTTAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:28493202 original size:11 final size:11
Alignment explanation
Indices: 28493181--28493211 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
28493171 AAAGCTTTCA
28493181 TTTTCATAGTAT
1 TTTTCA-AGTAT
28493193 TTTTCAAGTAT
1 TTTTCAAGTAT
28493204 TTTTCAAG
1 TTTTCAAG
28493212 CATAAACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (11 bp):
TTTTCAAGTAT
Found at i:28493561 original size:16 final size:16
Alignment explanation
Indices: 28493527--28493568 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
28493517 TTTAAAAAAT
*
28493527 AAATGATACAATATAA
1 AAATGATAAAATATAA
28493543 AAATGATATAAATA-AA
1 AAATGATA-AAATATAA
28493559 AAAT-ATAAAA
1 AAATGATAAAA
28493569 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 3 0.12
16 14 0.58
17 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (16 bp):
AAATGATAAAATATAA
Found at i:28493641 original size:20 final size:18
Alignment explanation
Indices: 28493613--28493653 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28493603 TGATATAAAT
* *
28493613 TATAATATATAATTTTTA
1 TATAAAATATAATATTTA
28493631 TATAAAATATAATATTTA
1 TATAAAATATAATATTTA
28493649 TATAA
1 TATAA
28493654 TAACTCGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAAAATATAATATTTA
Found at i:28496397 original size:5 final size:5
Alignment explanation
Indices: 28496389--28496414 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28496379 AGTAGAGTAC
28496389 TCTAG TCTAG TCTAG TCTAG TCTAG T
1 TCTAG TCTAG TCTAG TCTAG TCTAG T
28496415 GAGGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TCTAG
Found at i:28498609 original size:31 final size:30
Alignment explanation
Indices: 28498573--28498700 Score: 109
Period size: 30 Copynumber: 4.3 Consensus size: 30
28498563 TATGTTAAAG
*
28498573 GCTTATTTAGCTACAAATTAAAAGTTTAAGA
1 GCTTATTTAGATACAAATT-AAAGTTTAAGA
* * *
28498604 GCTTATTTAAATACAAATTAAAGGTTAAGT
1 GCTTATTTAGATACAAATTAAAGTTTAAGA
* * * * *
28498634 GCTTATTTGGGTTCAAATTAAAGATTATG-
1 GCTTATTTAGATACAAATTAAAGTTTAAGA
* * *
28498663 GCTTATTT-GAATGC-AATAAAAGTATAAGA
1 GCTTATTTAG-ATACAAATTAAAGTTTAAGA
28498692 GCTTATTTA
1 GCTTATTTA
28498701 AGTAAAGTTG
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 11 0.14
29 18 0.23
30 32 0.41
31 17 0.22
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (30 bp):
GCTTATTTAGATACAAATTAAAGTTTAAGA
Found at i:28509566 original size:26 final size:26
Alignment explanation
Indices: 28509507--28509576 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
28509497 ATCACACAAT
* *
28509507 CACGATCATTCATCTACAAATATAAT
1 CACGATCAATCATCTACAAATATAAA
28509533 CACGATCAATCATCTACAGAA-ATAAA
1 CACGATCAATCATCTACA-AATATAAA
*
28509559 CA-GCATCAA-CAGCTACAA
1 CACG-ATCAATCATCTACAA
28509577 CATCAACATG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 1 0.03
25 8 0.21
26 28 0.72
27 2 0.05
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.21
Consensus pattern (26 bp):
CACGATCAATCATCTACAAATATAAA
Found at i:28513937 original size:22 final size:22
Alignment explanation
Indices: 28513909--28513958 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28513899 GAATAACCCT
* * *
28513909 AATAATGGGCAAAAATGCCTTG
1 AATAATGAGCAAAAATACATTG
*
28513931 AATAATGAGTAAAAATACATTG
1 AATAATGAGCAAAAATACATTG
28513953 AATAAT
1 AATAAT
28513959 CTCAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (22 bp):
AATAATGAGCAAAAATACATTG
Found at i:28514823 original size:14 final size:15
Alignment explanation
Indices: 28514781--28514814 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28514771 TAAACAACTA
28514781 TTTGTCAAATGTTTT
1 TTTGTCAAATGTTTT
28514796 TTTGTCAAATGTTTT
1 TTTGTCAAATGTTTT
28514811 TTTG
1 TTTG
28514815 CTTATGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (15 bp):
TTTGTCAAATGTTTT
Found at i:28520923 original size:162 final size:161
Alignment explanation
Indices: 28520657--28521349 Score: 569
Period size: 162 Copynumber: 4.3 Consensus size: 161
28520647 AGCATAGTTT
** * * * * *
28520657 ATATGTGT-AAAAAGGTTGTCGTTTATGT-TTATTTATGA-TTTTTTATGCTGTTAAAAGGCTAA
1 ATATGTGTGAAAAA-GTTACCGTTTATATCTT-TTTAGGACTTTGTTATGCCGTTAAAAGGCCAA
* *
28520719 AATGTAAATTTGCATTTATTATTT-TGTTTTAACACTTTAGATAGTTTCAATATATAATATTAAA
64 AATGTAAATTTGCATTTATT-TTTATGTTTTAACAC-TTAGATAGCTTCAATACATAATATTAAA
*
28520783 CTTGTCCGAATAATTAAACTTGGTTTCTA-AGATTG
127 CTTGTCCGAATAATTAAACTTGGTTTCCACA-ATTG
* * * * **
28520818 ATATGTGTAAAAAAGTTATCGTTTATGTCTTTTTAGGACTTTGGTATGCCGTT-AAAGGGTAAAA
1 ATATGTGTGAAAAAGTTACCGTTTATATCTTTTTAGGACTTTGTTATGCCGTTAAAAGGCCAAAA
* * * * *
28520882 TTGTCATTTTGCATTTATTTTTATGTTTTAATAGCTTAGATAGCTTAAATACATTATATTAAACG
66 -TGTAAATTTGCATTTATTTTTATGTTTTAACA-CTTAGATAGCTTCAATACATAATATTAAAC-
** * * * * *
28520947 TT-TTTGAATGATTGAATTTGGTTTTCACAAATG
128 TTGTCCGAATAATTAAACTTGGTTTCCACAATTG
* * * *
28520980 ATATATGTGAAAAGGTTACCGTTTATAT-TTGTTTAGCACTTT-TTCATGCCGTTAAAATGCCAA
1 ATATGTGTGAAAAAGTTACCGTTTATATCTT-TTTAGGACTTTGTT-ATGCCGTTAAAAGGCCAA
* ** * * * * * * *
28521043 AATGCAAATTTGTGTTTATTATTCTGTTTTGACAGTTTAGATAGCTTGAATACATGATATTAAAT
64 AATGTAAATTTGCATTTATTTTTATGTTTTAACA-CTTAGATAGCTTCAATACATAATATTAAAC
* *
28521108 TTATCCGAATAATTGATTAGACTTGGTTTCCACAGTTG
128 TTGTCCGAATAATT-A--A-ACTTGGTTTCCACAATTG
* * * * * *
28521146 ATATATGTGAAAATGTTACCGTTTATATCTTTTTAGGATTTTGTTATGTCGTTAAAGGGCAAAAA
1 ATATGTGTGAAAAAGTTACCGTTTATATCTTTTTAGGACTTTGTTATGCCGTTAAAAGGCCAAAA
* * * * * * * * *
28521211 TATAATTTTACAGTTATATTTATATTTTGACATTTAGATAACTTCAATACATAATATTAAACTTG
66 TGTAAATTTGCATTTATTTTTATGTTTTAACACTTAGATAGCTTCAATACATAATATTAAACTTG
** * *
28521276 TCTAAATAATTGAATTTGGTTTCCACAATTTG
131 TCCGAATAATTAAACTTGGTTTCCACAA-TTG
* * *
28521308 ATATGTATGAATAAGTTA-CGATTTATATCTGTTTAGGACTTT
1 ATATGTGTGAAAAAGTTACCG-TTTATATCTTTTTAGGACTTT
28521350 TTGTAACATT
Statistics
Matches: 426, Mismatches: 86, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
161 60 0.14
162 225 0.53
163 12 0.03
165 38 0.09
166 87 0.20
167 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (161 bp):
ATATGTGTGAAAAAGTTACCGTTTATATCTTTTTAGGACTTTGTTATGCCGTTAAAAGGCCAAAA
TGTAAATTTGCATTTATTTTTATGTTTTAACACTTAGATAGCTTCAATACATAATATTAAACTTG
TCCGAATAATTAAACTTGGTTTCCACAATTG
Found at i:28521335 original size:328 final size:324
Alignment explanation
Indices: 28520695--28521351 Score: 766
Period size: 328 Copynumber: 2.0 Consensus size: 324
28520685 TTATTTATGA
* * * * *
28520695 TTTTTTATGCTGTTAAAAGGCTAAAATGTAAATTTGCATTTATTATTTTGTTTTAACACTTTAGA
1 TTTTTCATGCCGTTAAAAGGCCAAAATGCAAATTTGCATTTATTATTCTGTTTTAACACTTTAGA
* * * * *
28520760 TAGTTTCAATATATAATATTAAACTTGTCCGAATAATTAAACTTGGTTTCTAAGATTGATATGTG
66 TAGCTTCAATACATAATATTAAACTTATCCGAATAATTAAACTTGGTTTCCAAGATTGATATATG
* * * * * *
28520825 TAAAAAAGTTATCGTTTATGTCTTTTTAGGACTTTGGTATGCCGTTAAAGGGTAAAATTGTCATT
131 TAAAAAAGTTACCGTTTATATCTTTTTAGGACTTTGGTATGCCGTTAAAGGGCAAAAATATAATT
* * * * * * * * *
28520890 TTGCATTTATTTTTATGTTTTAATAGCTTAGATAGCTTAAATACATTATATTAAACGTTTTTGAA
196 TTACAGTTATATTTATATTTTAACAGCTTAGATAACTTAAATACATAATATTAAACGTTTCTAAA
* * * *
28520955 TGATTGAATTTGGTTTTCACAAATGATATATGTGAAAAGGTTACCGTTTATATTTGTTTAGCAC
261 TAATTGAATTTGGTTTCCACAAATGATATATATGAAAAGGTTACCGTTTATATCTGTTTAGCAC
* ** * *
28521019 TTTTTCATGCCGTTAAAATGCCAAAATGCAAATTTGTGTTTATTATTCTGTTTTGACAGTTTAGA
1 TTTTTCATGCCGTTAAAAGGCCAAAATGCAAATTTGCATTTATTATTCTGTTTTAACACTTTAGA
* * *
28521084 TAGCTTGAATACATGATATTAAATTTATCCGAATAATTGATTAGACTTGGTTTCCACAG-TTGAT
66 TAGCTTCAATACATAATATTAAACTTATCCGAATAATT-A--A-ACTTGGTTTCCA-AGATTGAT
* * * * *
28521148 ATATGTGAAAATGTTACCGTTTATATCTTTTTAGGATTTTGTTATGTCGTTAAAGGGCAAAAATA
126 ATATGTAAAAAAGTTACCGTTTATATCTTTTTAGGACTTTGGTATGCCGTTAAAGGGCAAAAATA
* * *
28521213 TAATTTTACAGTTATATTTATATTTTGACA-TTTAGATAACTTCAATACATAATATTAAAC-TTG
191 TAATTTTACAGTTATATTTATATTTTAACAGCTTAGATAACTTAAATACATAATATTAAACGTT-
* *
28521276 TCTAAATAATTGAATTTGGTTTCCACAATTTGATATGTATGAATAA-GTTA-CGATTTATATCTG
255 TCTAAATAATTGAATTTGGTTTCCACAA-ATGATATATATGAA-AAGGTTACCG-TTTATATCTG
*
28521339 TTTAGGAC
317 TTTAGCAC
28521347 TTTTT
1 TTTTT
28521352 GTAACATTAA
Statistics
Matches: 276, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
324 87 0.32
325 1 0.00
326 2 0.01
327 53 0.19
328 129 0.47
329 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (324 bp):
TTTTTCATGCCGTTAAAAGGCCAAAATGCAAATTTGCATTTATTATTCTGTTTTAACACTTTAGA
TAGCTTCAATACATAATATTAAACTTATCCGAATAATTAAACTTGGTTTCCAAGATTGATATATG
TAAAAAAGTTACCGTTTATATCTTTTTAGGACTTTGGTATGCCGTTAAAGGGCAAAAATATAATT
TTACAGTTATATTTATATTTTAACAGCTTAGATAACTTAAATACATAATATTAAACGTTTCTAAA
TAATTGAATTTGGTTTCCACAAATGATATATATGAAAAGGTTACCGTTTATATCTGTTTAGCAC
Found at i:28522878 original size:21 final size:21
Alignment explanation
Indices: 28522852--28522908 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28522842 GAGTTTAGCG
*
28522852 TGTTAAAATGGATGAGAAGCA
1 TGTTAAAATGGATGAGAAACA
* *
28522873 TGTTAAAGTGGATGAGAAACG
1 TGTTAAAATGGATGAGAAACA
*
28522894 TGCTAAAATGGATGA
1 TGTTAAAATGGATGA
28522909 AGAGCGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (21 bp):
TGTTAAAATGGATGAGAAACA
Found at i:28524506 original size:19 final size:19
Alignment explanation
Indices: 28524482--28524537 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
28524472 ATATTTTTAT
28524482 TAAATATAATATATATAAA
1 TAAATATAATATATATAAA
*
28524501 TAAATAGT-GTATA-ATAAAA
1 TAAATA-TAATATATAT-AAA
*
28524520 TAAATAATAAAATATATA
1 TAAAT-ATAATATATATA
28524538 TTCTTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 6 0.21
21 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
TAAATATAATATATATAAA
Found at i:28525299 original size:18 final size:18
Alignment explanation
Indices: 28525278--28525320 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28525268 ATAAAATATG
*
28525278 TAAATTTTAAAAAAATTA
1 TAAATTTTAAAAAAATGA
*
28525296 TAAACTTTAAAAAAATGA
1 TAAATTTTAAAAAAATGA
28525314 -AAATTTT
1 TAAATTTT
28525321 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAATTTTAAAAAAATGA
Found at i:28525366 original size:19 final size:20
Alignment explanation
Indices: 28525343--28525391 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
28525333 TTTACAATTT
28525343 AAATTTTTATATATTTTTT-
1 AAATTTTTATATATTTTTTA
* * *
28525362 GAATTTTTAAATTTTTTTTA
1 AAATTTTTATATATTTTTTA
28525382 AAATTTTTAT
1 AAATTTTTAT
28525392 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AAATTTTTATATATTTTTTA
Found at i:28525379 original size:11 final size:11
Alignment explanation
Indices: 28525365--28525400 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
28525355 ATTTTTTGAA
28525365 TTTTTAAATTT
1 TTTTTAAATTT
28525376 TTTTTAAAATTT
1 TTTTT-AAATTT
*
28525388 TTATTAAATTT
1 TTTTTAAATTT
28525399 TT
1 TT
28525401 ATGTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAAATTT
Found at i:28525803 original size:19 final size:18
Alignment explanation
Indices: 28525768--28525806 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28525758 ATTTTGTGAT
*
28525768 AATTTTTTGAAAGTTTAA
1 AATTTTTTGAAAATTTAA
*
28525786 AATTTTTTATAAAATTTAA
1 AATTTTTT-GAAAATTTAA
28525805 AA
1 AA
28525807 AGATTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTTTTTGAAAATTTAA
Found at i:28525892 original size:9 final size:9
Alignment explanation
Indices: 28525870--28525939 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
28525860 ATTATTTTAT
*
28525870 TTTTTTGAAG
1 TTTTTT-AAA
28525880 TTTTTTAAA
1 TTTTTTAAA
28525889 TTTTTTAGTAA
1 TTTTTTA--AA
*
28525900 TTTTTACAAA
1 TTTTT-TAAA
* *
28525910 ATTTTAAAA
1 TTTTTTAAA
28525919 TGTTTTTAAA
1 T-TTTTTAAA
*
28525929 TTTTTTTAA
1 TTTTTTAAA
28525938 TT
1 TT
28525940 ATGTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 21 0.43
10 20 0.41
11 7 0.14
12 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:28525970 original size:19 final size:19
Alignment explanation
Indices: 28525946--28525983 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28525936 AATTATGTAT
* *
28525946 TTTTAAGAATTTTTTAAAA
1 TTTTAAAAAGTTTTTAAAA
28525965 TTTTAAAAAGTTTTTAAAA
1 TTTTAAAAAGTTTTTAAAA
28525984 ATTTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTAAAAAGTTTTTAAAA
Found at i:28525984 original size:11 final size:10
Alignment explanation
Indices: 28525944--28525987 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
28525934 TTAATTATGT
*
28525944 ATTTTTAAGA
1 ATTTTTAAAA
*
28525954 ATTTTTTAAA
1 ATTTTTAAAA
28525964 A-TTTTAAAA
1 ATTTTTAAAA
28525973 AGTTTTTAAAA
1 A-TTTTTAAAA
28525984 ATTT
1 ATTT
28525988 CTTTTTATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.28
10 12 0.41
11 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (10 bp):
ATTTTTAAAA
Found at i:28526513 original size:20 final size:20
Alignment explanation
Indices: 28526488--28526527 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28526478 TTGTATATCC
28526488 AAAATTAAAATTTCATCATT
1 AAAATTAAAATTTCATCATT
* *
28526508 AAAATTAAATTTTTATCATT
1 AAAATTAAAATTTCATCATT
28526528 TTATTAACAG
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:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTAAAATTTCATCATT
Found at i:28528163 original size:20 final size:21
Alignment explanation
Indices: 28528125--28528163 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28528115 TCTATAATCT
28528125 AAATTTTATTATCAAACAAAA
1 AAATTTTATTATCAAACAAAA
28528146 AAATATTTATT-T-AAACAA
1 AAAT-TTTATTATCAAACAA
28528164 TTATTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTTATTATCAAACAAAA
Found at i:28529420 original size:31 final size:32
Alignment explanation
Indices: 28529372--28529454 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 32
28529362 TATCATATAA
*
28529372 AATATTAAAATTAATATATTTATAATATAT-TT
1 AATATAAAAATTAATATA-TTATAATATATATT
* *
28529404 TATATAAAAATT-ATATATTATAATTTATATT
1 AATATAAAAATTAATATATTATAATATATATT
*
28529435 AATATAAAAATATAAAATAT
1 AATATAAAAAT-TAATATAT
28529455 ATTTTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 10 0.23
31 17 0.40
32 11 0.26
33 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATATAAAAATTAATATATTATAATATATATT
Found at i:28529527 original size:20 final size:20
Alignment explanation
Indices: 28529502--28529574 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
28529492 AAAATTTTAA
*
28529502 ATTATATTTATTTATATTTT
1 ATTATATTTATTTATATATT
*
28529522 ATTATA-TAATTTATTATATT
1 ATTATATTTATTTA-TATATT
* *
28529542 ATCATATCTTATTT-TAAATT
1 ATTATAT-TTATTTATATATT
*
28529562 ATTAAATTTATTT
1 ATTATATTTATTT
28529575 GTAGTTATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 12 0.28
20 26 0.60
22 5 0.12
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATATTTATTTATATATT
Found at i:28529542 original size:53 final size:54
Alignment explanation
Indices: 28529428--28529543 Score: 121
Period size: 52 Copynumber: 2.2 Consensus size: 54
28529418 ATATTATAAT
*
28529428 TTATATTAATATAAAAATATAAAATATATTTTTTAAATTTTATTAAATTCATATA
1 TTATATT-ATATAAAAATATAAAATATATTTTTTAAATTTTATTAAATTAATATA
* * * * * * *
28529483 AT-TATTAT-TAAAATTTTAAATTATATTTATTTATATTTTATTATA-TAATTTA
1 TTATATTATATAAAAATATAAAATATATTT-TTTAAATTTTATTAAATTAATATA
28529535 TTATATTAT
1 TTATATTAT
28529544 CATATCTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
52 23 0.46
53 22 0.44
54 4 0.08
55 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (54 bp):
TTATATTATATAAAAATATAAAATATATTTTTTAAATTTTATTAAATTAATATA
Found at i:28539010 original size:45 final size:45
Alignment explanation
Indices: 28538946--28539034 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
28538936 TAAGTCATAG
*
28538946 TCATAACGAAAGGCCTTA-TTGAAATAAATTTGAAAACGTTATATC
1 TCATAACGAAAGACCTTATTTG-AATAAATTTGAAAACGTTATATC
*
28538991 TCATAACGAAAGATCTTATTTGAATAAATTTGAAAACGTTATAT
1 TCATAACGAAAGACCTTATTTGAATAAATTTGAAAACGTTATAT
28539035 TTTACATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 38 0.93
46 3 0.07
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (45 bp):
TCATAACGAAAGACCTTATTTGAATAAATTTGAAAACGTTATATC
Found at i:28540310 original size:17 final size:18
Alignment explanation
Indices: 28540278--28540311 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28540268 TATTATAAGT
28540278 AATATATTTCAAATATTA
1 AATATATTTCAAATATTA
*
28540296 AATAT-TTTGAAATATT
1 AATATATTTCAAATATT
28540312 TTGATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATATTTCAAATATTA
Found at i:28544316 original size:16 final size:16
Alignment explanation
Indices: 28544292--28544322 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28544282 GTACACAAAA
*
28544292 GTTTTGGTTTGTATTT
1 GTTTAGGTTTGTATTT
28544308 GTTTAGGTTTGTATT
1 GTTTAGGTTTGTATT
28544323 CCTTATAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.65
Consensus pattern (16 bp):
GTTTAGGTTTGTATTT
Found at i:28544478 original size:16 final size:16
Alignment explanation
Indices: 28544459--28544491 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28544449 GGGTTTGAGA
28544459 TTGTGTTTGTTTAAGT
1 TTGTGTTTGTTTAAGT
*
28544475 TTGTGTTTGTTTTAGT
1 TTGTGTTTGTTTAAGT
28544491 T
1 T
28544492 GAGAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.24, T:0.67
Consensus pattern (16 bp):
TTGTGTTTGTTTAAGT
Found at i:28545688 original size:28 final size:29
Alignment explanation
Indices: 28545656--28545711 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
28545646 ATTAAAATTC
* * *
28545656 TTTTGATATTTC-AATTTTAAATATTTTA
1 TTTTGATATTACAAAATATAAATATTTTA
28545684 TTTTGATATTACAAAATATAAATATTTT
1 TTTTGATATTACAAAATATAAATATTTT
28545712 TAATAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (29 bp):
TTTTGATATTACAAAATATAAATATTTTA
Found at i:28545806 original size:42 final size:42
Alignment explanation
Indices: 28545713--28545817 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
28545703 AAATATTTTT
*
28545713 AATAATA-AATAGTATTATATTATTATTTTAATAATAAATAAGA
1 AATAATATAATAATATT-T-TTATTATTTTAATAATAAATAAGA
* ***
28545756 ACAT-ATATAATAATATTTTTATTATTTTAATAATTAATGTTA
1 A-ATAATATAATAATATTTTTATTATTTTAATAATAAATAAGA
*
28545798 AATAATATACTAATATTTTT
1 AATAATATAATAATATTTTT
28545818 TTAATATGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
41 2 0.04
42 36 0.68
43 5 0.09
44 10 0.19
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (42 bp):
AATAATATAATAATATTTTTATTATTTTAATAATAAATAAGA
Found at i:28545975 original size:21 final size:20
Alignment explanation
Indices: 28545949--28546009 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
28545939 TAATAGATAC
28545949 TTTTAATATGAAATATAAATA
1 TTTTAATAT-AAATATAAATA
* * *
28545970 TTTTAATAATATATATTATTA
1 TTTTAAT-ATAAATATAAATA
*
28545991 TTTTAATATTAATA-AAATA
1 TTTTAATATAAATATAAATA
28546010 ATATTTTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 22 0.69
22 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTAATATAAATATAAATA
Found at i:28546035 original size:42 final size:43
Alignment explanation
Indices: 28545966--28546065 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 43
28545956 ATGAAATATA
* *
28545966 AATATTTTAATAATATATATTATTATTTTAA-TATTAATAAAAT
1 AATATTTTAAGAATATATATTACTATTTTAAGTATT-ATAAAAT
*
28546009 AATATTTTAAGAATAGTA-A-TACTATTTTAAGTATTTTAAAAT
1 AATATTTTAAGAATA-TATATTACTATTTTAAGTATTATAAAAT
* * *
28546051 ATTAATATAAGAATA
1 AATATTTTAAGAATA
28546066 ATAAATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 28 0.57
43 19 0.39
44 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (43 bp):
AATATTTTAAGAATATATATTACTATTTTAAGTATTATAAAAT
Found at i:28550107 original size:18 final size:19
Alignment explanation
Indices: 28550086--28550121 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28550076 AAAATATAAA
*
28550086 TAAT-ATAATTAAAATTTC
1 TAATCATAATAAAAATTTC
28550104 TAATCATAATAAAAATTT
1 TAATCATAATAAAAATTT
28550122 ACAAAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATCATAATAAAAATTTC
Found at i:28552259 original size:14 final size:14
Alignment explanation
Indices: 28552236--28552270 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28552226 TTAGATAATT
*
28552236 TAATTTTTTTTAAA
1 TAATTTTTTATAAA
28552250 TATATTTTTTATAAA
1 TA-ATTTTTTATAAA
28552265 TAATTT
1 TAATTT
28552271 AAAATCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATTTTTTATAAA
Found at i:28553498 original size:2 final size:2
Alignment explanation
Indices: 28553481--28553516 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
28553471 GTATATTGTA
28553481 AT AT A- AT AT A- 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
28553517 GATGTGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28577977 original size:25 final size:24
Alignment explanation
Indices: 28577948--28577994 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28577938 AGATATAGTG
*
28577948 ATAAACATGAAAAAAATATAAAAAA
1 ATAAAAAT-AAAAAAATATAAAAAA
* *
28577973 ATAAAAATAAAACAATTTAAAA
1 ATAAAAATAAAAAAATATAAAA
28577995 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (24 bp):
ATAAAAATAAAAAAATATAAAAAA
Found at i:28590242 original size:3 final size:3
Alignment explanation
Indices: 28590228--28590278 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
28590218 TATTTTCAAC
* * * * *
28590228 ATA ATA ACA ATA ATA ATA ATA ACA ATA ACA ATA ACA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28590276 ATA
1 ATA
28590279 TCTTACAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (3 bp):
ATA
Found at i:28590248 original size:15 final size:15
Alignment explanation
Indices: 28590228--28590278 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
28590218 TATTTTCAAC
28590228 ATAATAACAATAATA
1 ATAATAACAATAATA
*
28590243 ATAATAACAATAACA
1 ATAATAACAATAATA
*
28590258 ATAACAACAATAATA
1 ATAATAACAATAATA
28590273 ATAATA
1 ATAATA
28590279 TCTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAATAACAATAATA
Found at i:28595577 original size:18 final size:18
Alignment explanation
Indices: 28595495--28595617 Score: 71
Period size: 17 Copynumber: 6.9 Consensus size: 18
28595485 ACAAAATCAA
**
28595495 ATTT-TTAATTTTTAATT
1 ATTTATTAATTTAAAATT
28595512 ATTTATTAA--TAAAATT
1 ATTTATTAATTTAAAATT
* * *
28595528 A-TTATTTGATATAAAAATA
1 ATTTA-TTAAT-TTAAAATT
* *
28595547 ATTTAAT-ATTTTAAATT
1 ATTTATTAATTTAAAATT
28595564 ATTTATTAATTTTATAAA-T
1 ATTTATTAA-TTTA-AAATT
* *
28595583 ATTAAATAATTTAAAATT
1 ATTTATTAATTTAAAATT
28595601 -TTTATTATATTTAAAAT
1 ATTTATTA-ATTTAAAAT
28595618 ATAATATAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
15 3 0.04
16 9 0.11
17 23 0.29
18 21 0.26
19 18 0.22
20 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
ATTTATTAATTTAAAATT
Found at i:28595596 original size:36 final size:35
Alignment explanation
Indices: 28595541--28595627 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 35
28595531 ATTTGATATA
* *
28595541 AAAATAATTTAAT-ATTTTAAATTATTTATTA-ATTTT
1 AAAAT-ATTAAATAATTTAAAATT-TTTATTATA-TTT
28595577 ATAAATATTAAATAATTTAAAATTTTTATTATATTT
1 A-AAATATTAAATAATTTAAAATTTTTATTATATTT
28595613 AAAATA-TAATATAAT
1 AAAATATTAA-ATAAT
28595628 CCACTTTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
34 3 0.07
35 10 0.22
36 18 0.40
37 14 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
AAAATATTAAATAATTTAAAATTTTTATTATATTT
Found at i:28595689 original size:21 final size:21
Alignment explanation
Indices: 28595673--28595722 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
28595663 GTATATCTCT
28595673 ATTATTAAT-TTTAATATCACC
1 ATTA-TAATATTTAATATCACC
* * *
28595694 ATTATAATATTTAATTTTATC
1 ATTATAATATTTAATATCACC
28595715 ATTATAAT
1 ATTATAAT
28595723 GATTAATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATAATATTTAATATCACC
Found at i:28596210 original size:19 final size:19
Alignment explanation
Indices: 28596183--28596220 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28596173 CTTATATAGT
*
28596183 CATTGACTTAATGATGTGG
1 CATTAACTTAATGATGTGG
*
28596202 CATTAACTTATTGATGTGG
1 CATTAACTTAATGATGTGG
28596221 TAATTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (19 bp):
CATTAACTTAATGATGTGG
Found at i:28596339 original size:29 final size:29
Alignment explanation
Indices: 28596276--28596344 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
28596266 TTATACTCAT
** *
28596276 AAAAAATTTGAAATTTAATCCATGTACTC
1 AAAAAATTTGAAATTTAATCCATCAAATC
*
28596305 ACAAAAATTT-AAATTTAATCCCTCAAATAC
1 A-AAAAATTTGAAATTTAATCCATCAAAT-C
28596335 AAAAATATTT
1 AAAAA-ATTT
28596345 TGAATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAAATTTGAAATTTAATCCATCAAATC
Found at i:28596382 original size:17 final size:18
Alignment explanation
Indices: 28596347--28596393 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
28596337 AAATATTTTG
*
28596347 AATTTTTAAAAAATTATT
1 AATTTTTAAAAAATCATT
*
28596365 AATTTTTTAAAAA-CATT
1 AATTTTTAAAAAATCATT
**
28596382 AAACTTTAAAAA
1 AATTTTTAAAAA
28596394 TTGCTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTTTAAAAAATCATT
Found at i:28596416 original size:13 final size:13
Alignment explanation
Indices: 28596398--28596431 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28596388 TAAAAATTGC
*
28596398 TATAATATTCTCT
1 TATAATATTCTAT
28596411 TATAATATTCTAT
1 TATAATATTCTAT
*
28596424 CATAATAT
1 TATAATAT
28596432 GAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAATATTCTAT
Found at i:28597252 original size:16 final size:14
Alignment explanation
Indices: 28597217--28597258 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
28597207 AAGTTTGATA
28597217 TATTAAT-TTAAAT
1 TATTAATATTAAAT
28597230 TATTAATATTATAAT
1 TATTAATATTA-AAT
28597245 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
28597259 GATAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 6 0.23
16 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:28597834 original size:27 final size:26
Alignment explanation
Indices: 28597783--28597834 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
28597773 CTAATTCTAG
*
28597783 TTAAAATTAATAATAAATAATTTTAT
1 TTAAAATTAATAATAAATAAATTTAT
*
28597809 TTAAAATTTAAT-ATGAATAGAATTTA
1 TTAAAA-TTAATAATAAATA-AATTTA
28597835 ATGAAGCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAAAATTAATAATAAATAAATTTAT
Found at i:28602245 original size:11 final size:11
Alignment explanation
Indices: 28602229--28602254 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28602219 CAATTGATAA
28602229 AAATATTAAAT
1 AAATATTAAAT
28602240 AAATATTAAAT
1 AAATATTAAAT
28602251 AAAT
1 AAAT
28602255 TAGTTGGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATTAAAT
Found at i:28609592 original size:2 final size:2
Alignment explanation
Indices: 28609585--28609615 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28609575 AAATTAAAAT
*
28609585 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28609616 CTTTTCCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28614515 original size:3 final size:3
Alignment explanation
Indices: 28614507--28614532 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28614497 CTACCTCCGG
28614507 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28614533 TTTAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28614751 original size:323 final size:318
Alignment explanation
Indices: 28614080--28615032 Score: 1423
Period size: 323 Copynumber: 3.0 Consensus size: 318
28614070 TCATGATATG
*
28614080 AGACAAAAAAGCTCCATG----GTTAAGATCATGACATACGACACGAATCACGTCGCATCATCGT
1 AGACAAAAAAGCTCCATGTAATGTTAAGATCATGACATACGACACGTATCACGTCGCATCATCGT
* **
28614141 ATAATGAAAGCATTGATAAGTTGATTCACCACTTCAAATCACTACCTCCTCCCATTATTATTATT
66 ATAATGAAAGCATTGACAAGTTGATTCACCACTTCAAATCACTACCT-C-CGGATTATTATTATT
* * *
28614206 A--ATTTTTTTTGAATTTCTCTTTTGACTTTTGGTCTGACTGCTATTTCATTTATAG--AAAAAG
129 ATTATTTTTTTTTAATTTCTCTTTTGACTTTTGGTCTGACTCCTATTTCATTTATAGAAAAAAAA
*
28614267 AAAA-AAAAA-TTCCATGTTTAATTTCCATAAATAATATTCTCGAATGCTTTACACTTTTTTTTT
194 AAAACAAAAATTTCCATTTTTAATTTCCATAAATAATATTCTCGAATGCTTTACAC-TTTTTTTT
* * *
28614330 TGGATCAATATCTATCTT-TGCATTTCACATTACCTACGTTACACATTATACGTTACTAATA
258 CGGATCAATATCTAT-TTATGCATTTCACACTACCTACGTTACACATTATACATTACTAATA
*
28614391 AGACAAAAAAGCTCAATGTAATGTTAAGATCATGACATACGACACGTATCACGTCGCATCATCGT
1 AGACAAAAAAGCTCCATGTAATGTTAAGATCATGACATACGACACGTATCACGTCGCATCATCGT
*
28614456 ATAATGAAGGCATTGACAAGTTGATTCACCACTTCAAATCACTACCTCCGGTTATTATTATTATT
66 ATAATGAAAGCATTGACAAGTTGATTCACCACTTCAAATCACTACCTCCGG--ATTATTATTATT
28614521 ATTATTATTATTTTTAATTTCTCTTTTGACTTTTGGTCTGACTCCTATTTCATTTATAGAAAAAA
129 ATTATT-TT-TTTTTAATTTCTCTTTTGACTTTTGGTCTGACTCCTATTTCATTTATAGAAAAAA
* * * *
28614586 ACAAAAACAAAAATTTCCATTTTTAATTTTCATAAATAATATTCTCTAATGCCTTACACTTTCTT
192 A-AAAAACAAAAATTTCCATTTTTAATTTCCATAAATAATATTCTCGAATGCTTTACACTTTTTT
*
28614651 TTCGGATCAATATCTATTTATGCATTTCACACTACTTACGTTACACATTATACATTACTAATA
256 TTCGGATCAATATCTATTTATGCATTTCACACTACCTACGTTACACATTATACATTACTAATA
* * *
28614714 AGATAAAAAAGCTCCATGTAATGTTAAGATCATGACATACAACACGTATCATGTCGCATCATCGT
1 AGACAAAAAAGCTCCATGTAATGTTAAGATCATGACATACGACACGTATCACGTCGCATCATCGT
* * *
28614779 ATAATGAAAGCATTGACAAGTTGATTCACCATTTCAAATCACTATCTTCGG----TTATTATTAT
66 ATAATGAAAGCATTGACAAGTTGATTCACCACTTCAAATCACTACCTCCGGATTATTATTATTAT
*
28614840 TATTTTTTTTTAATTTCTCTTTTGACTTATGGTCTGACTCCTATTTCATTTATAGAAAAAGAAAA
131 TATTTTTTTTTAATTTCTCTTTTGACTTTTGGTCTGACTCCTATTTCATTTATAG--AAA-AAAA
*
28614905 AGAAAACAAAATTTTCCATTTTTAATTTCCATAAATAATATTCTCGAATGCTTTACACTTTTTTT
193 A-AAAACAAAAATTTCCATTTTTAATTTCCATAAATAATATTCTCGAATGCTTTACACTTTTTTT
* * *
28614970 TCGGATCAATATCTATCTATGCATTTTACACTACCTACGTTATACATTATACATTACTAATA
257 TCGGATCAATATCTATTTATGCATTTCACACTACCTACGTTACACATTATACATTACTAATA
28615032 A
1 A
28615033 ACATGTGGTT
Statistics
Matches: 586, Mismatches: 36, Indels: 33
0.89 0.05 0.05
Matches are distributed among these distances:
311 17 0.03
313 1 0.00
314 1 0.00
315 148 0.25
316 2 0.00
317 21 0.04
318 123 0.21
319 47 0.08
321 5 0.01
322 6 0.01
323 174 0.30
324 41 0.07
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (318 bp):
AGACAAAAAAGCTCCATGTAATGTTAAGATCATGACATACGACACGTATCACGTCGCATCATCGT
ATAATGAAAGCATTGACAAGTTGATTCACCACTTCAAATCACTACCTCCGGATTATTATTATTAT
TATTTTTTTTTAATTTCTCTTTTGACTTTTGGTCTGACTCCTATTTCATTTATAGAAAAAAAAAA
AACAAAAATTTCCATTTTTAATTTCCATAAATAATATTCTCGAATGCTTTACACTTTTTTTTCGG
ATCAATATCTATTTATGCATTTCACACTACCTACGTTACACATTATACATTACTAATA
Found at i:28616433 original size:32 final size:34
Alignment explanation
Indices: 28616393--28616457 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 34
28616383 ATAAATAAGA
* *
28616393 ATATATATTTTATTACT-AATTTA-ATTTAATTT
1 ATATATATTATATTAATAAATTTATATTTAATTT
28616425 ATATATATTATATTAATAAATTTATTATTTAAT
1 ATATATATTATATTAATAAATTTA-TATTTAAT
28616458 ACATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.54
33 6 0.21
35 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (34 bp):
ATATATATTATATTAATAAATTTATATTTAATTT
Found at i:28616789 original size:23 final size:23
Alignment explanation
Indices: 28616777--28616818 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28616767 TTTTATTTAC
28616777 TTTTAAT-TTTTTCAATTATCTA
1 TTTTAATATTTTTCAATTATCTA
28616799 TTTTAATATTTTT-AATTATC
1 TTTTAATATTTTTCAATTATC
28616819 CTTAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTAATATTTTTCAATTATCTA
Found at i:28618517 original size:19 final size:21
Alignment explanation
Indices: 28618474--28618518 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
28618464 AGTAAAGATG
* *
28618474 AAAAGAAAACAACAATCTTTT
1 AAAAGAAAACAACAACCTATT
28618495 AAAAGAAAA-AA-AACCTATT
1 AAAAGAAAACAACAACCTATT
28618514 AAAAG
1 AAAAG
28618519 GTACCCGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 9 0.41
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAGAAAACAACAACCTATT
Found at i:28626013 original size:17 final size:17
Alignment explanation
Indices: 28625991--28626033 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28625981 AAACTTAAGT
*
28625991 TTAAAATATTTTATCA-A
1 TTAAAATATTTAAT-ATA
*
28626008 TTAAAATACTTAATATA
1 TTAAAATATTTAATATA
28626025 TTAAAATAT
1 TTAAAATAT
28626034 AAAAATTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATATTTAATATA
Found at i:28633376 original size:15 final size:15
Alignment explanation
Indices: 28633309--28633369 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
28633299 GCATTGACAA
28633309 AATATA-AAATTTAT
1 AATATATAAATTTAT
* * **
28633323 ATTATATATATAAAT
1 AATATATAAATTTAT
* *
28633338 AGTATACAAAATTTAT
1 AATATA-TAAATTTAT
28633354 AATATATAAATTTAT
1 AATATATAAATTTAT
28633369 A
1 A
28633370 TATTATATGC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
14 5 0.15
15 19 0.56
16 10 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATATAAATTTAT
Found at i:28634169 original size:92 final size:92
Alignment explanation
Indices: 28634073--28634254 Score: 301
Period size: 92 Copynumber: 2.0 Consensus size: 92
28634063 GTACATCTTA
* **
28634073 ATAGGTCGGTGTAATTTAATAATTGTGTAGATCTTTAATTTGATAAACATTTAATGAGAAGGTTA
1 ATAGGTCGGTGTAATTTAATAATTGTGTAGACCTTTAATTTGATAAACATTTAATGAGAAAATTA
28634138 TTAAAATTATTTAAATAATGAGTTAAG
66 TTAAAATTATTTAAATAATGAGTTAAG
*
28634165 ATAGGTTGGTGTAATTTAATAATTGTGTAGACCTTTAATTTGATAAACATTTAATGAGAAAATTA
1 ATAGGTCGGTGTAATTTAATAATTGTGTAGACCTTTAATTTGATAAACATTTAATGAGAAAATTA
***
28634230 TTAGGGTTATTTAAATAATGAGTTA
66 TTAAAATTATTTAAATAATGAGTTA
28634255 CGATCCTCTT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 83 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (92 bp):
ATAGGTCGGTGTAATTTAATAATTGTGTAGACCTTTAATTTGATAAACATTTAATGAGAAAATTA
TTAAAATTATTTAAATAATGAGTTAAG
Found at i:28637322 original size:27 final size:26
Alignment explanation
Indices: 28637290--28637340 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
28637280 ATAATTTAGT
28637290 TTTAATTAAATTAATCAATCGAATTGA
1 TTTAATTAAATTAATCAATC-AATTGA
**
28637317 TTTAATTTTATTAATCAATCAATT
1 TTTAATTAAATTAATCAATCAATT
28637341 ATCGAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTAATTAAATTAATCAATCAATTGA
Found at i:28643265 original size:64 final size:60
Alignment explanation
Indices: 28643187--28643313 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
28643177 ATTATCTAAG
*
28643187 AATAGTTCATAAAAACACTAAAATAGCATTTGACAAACTAAGTTACGTGTGGTATAATCTTTTT
1 AATAGTTCAT-AAAA-A-T-AAATAGCATTTGACAAACTAAGTTACGTATGGTATAATCTTTTT
** *
28643251 AATAGTTCATAAAAATACCTAGTATTTGACAAACTAAGTTACGTATGGTATAATCTTTTT
1 AATAGTTCATAAAAATAAATAGCATTTGACAAACTAAGTTACGTATGGTATAATCTTTTT
28643311 AAT
1 AAT
28643314 GTATAAGAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
60 43 0.73
61 1 0.02
62 1 0.02
63 4 0.07
64 10 0.17
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (60 bp):
AATAGTTCATAAAAATAAATAGCATTTGACAAACTAAGTTACGTATGGTATAATCTTTTT
Found at i:28644011 original size:17 final size:18
Alignment explanation
Indices: 28643976--28644034 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
28643966 GTGGATCTGT
* *
28643976 ACATGTCAGGCCAACCTA
1 ACATGTTAGGTCAACCTA
28643994 ACATGTTAGGTC-ACCTA
1 ACATGTTAGGTCAACCTA
*
28644011 ACATGTTAGGTCAACCTG
1 ACATGTTAGGTCAACCTA
28644029 ACATGT
1 ACATGT
28644035 CAAGTCGGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 17 0.46
18 20 0.54
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (18 bp):
ACATGTTAGGTCAACCTA
Found at i:28648388 original size:43 final size:43
Alignment explanation
Indices: 28648340--28648428 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
28648330 TACCATGCAA
** *
28648340 ATAAATCACATGAATAAATATATTAATAATCATGCAAATATAT
1 ATAAATCACACAAATAAATATATTAATAATCATGCAAATAAAT
*
28648383 ATAAATCACACAAATAAATTTATTAATAATCATGCAAATAAAT
1 ATAAATCACACAAATAAATATATTAATAATCATGCAAATAAAT
28648426 ATA
1 ATA
28648429 TTAATAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.31
Consensus pattern (43 bp):
ATAAATCACACAAATAAATATATTAATAATCATGCAAATAAAT
Found at i:28648445 original size:31 final size:30
Alignment explanation
Indices: 28648410--28648496 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
28648400 ATTTATTAAT
28648410 AATCATGCAAATAAATATATTAATAACATG
1 AATCATGCAAATAAATATATTAATAACATG
*
28648440 CAATCACGCACAA-AAATATA-T--TAA-AT-
1 -AATCATGCA-AATAAATATATTAATAACATG
*
28648466 AATCATACAAATAAATATATTAATAATCATG
1 AATCATGCAAATAAATATATTAATAA-CATG
28648497 TAATTAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
24 2 0.04
25 14 0.31
26 1 0.02
27 2 0.04
28 6 0.13
30 3 0.07
31 15 0.33
32 2 0.04
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.29
Consensus pattern (30 bp):
AATCATGCAAATAAATATATTAATAACATG
Found at i:28648523 original size:21 final size:20
Alignment explanation
Indices: 28648484--28648523 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28648474 AAATAAATAT
*
28648484 ATTAATAATCATGTAATTAA
1 ATTAATAATCATGCAATTAA
*
28648504 ATTAATAAATCATGCGATTA
1 ATTAAT-AATCATGCAATTA
28648524 CACACGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (20 bp):
ATTAATAATCATGCAATTAA
Found at i:28648558 original size:78 final size:77
Alignment explanation
Indices: 28648395--28648664 Score: 344
Period size: 78 Copynumber: 3.4 Consensus size: 77
28648385 AAATCACACA
* * * * * * * *
28648395 AATAAATTTATTAATAATCATGCAAATAAATATATTAATAACATGCAATCACGCACAAAAATATA
1 AATAAATATATTAATAATCATGTAATTAAAT-TAATAA-ATCATGCAATTACACACATAAATATA
* **
28648460 TTAAATAATCATACA
64 TTAGATAATCAT-GT
* *
28648475 AATAAATATATTAATAATCATGTAATTAAATTAATAAATCATGCGATTACACACGTAAATATATT
1 AATAAATATATTAATAATCATGTAATTAAATTAATAAATCATGCAATTACACACATAAATATATT
28648540 AGATAATCATGT
66 AGATAATCATGT
*
28648552 GAATAAATATATTAATAAACATAG-AATTAAATTAATAAATCATGCAATTACACACATAAATATA
1 -AATAAATATATTAATAATCAT-GTAATTAAATTAATAAATCATGCAATTACACACATAAATATA
*
28648616 TTAGGTAATCATGCT
64 TTAGATAATCATG-T
28648631 AATAAATATATTAATAATCATGTAATTAAATTAA
1 AATAAATATATTAATAATCATGTAATTAAATTAA
28648665 ATTCATACAA
Statistics
Matches: 168, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
77 1 0.01
78 132 0.79
79 7 0.04
80 28 0.17
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (77 bp):
AATAAATATATTAATAATCATGTAATTAAATTAATAAATCATGCAATTACACACATAAATATATT
AGATAATCATGT
Found at i:28648582 original size:24 final size:25
Alignment explanation
Indices: 28648530--28648583 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
28648520 ATTACACACG
* *
28648530 TAAATATATTAGATAATCATGTGAA
1 TAAATATATTAGATAAACATGAGAA
28648555 TAAATATATTA-ATAAACAT-AGAA
1 TAAATATATTAGATAAACATGAGAA
28648578 TTAAAT
1 -TAAAT
28648584 TAATAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 12 0.46
25 11 0.42
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (25 bp):
TAAATATATTAGATAAACATGAGAA
Found at i:28648660 original size:24 final size:25
Alignment explanation
Indices: 28648607--28648661 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
28648597 AATTACACAC
*
28648607 ATAAATATATTAGGTAATCATGCTA
1 ATAAATATATTAGATAATCATGCTA
28648632 ATAAATATATTA-ATAATCATG-TA
1 ATAAATATATTAGATAATCATGCTA
28648655 ATTAAAT
1 A-TAAAT
28648662 TAAATTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 3 0.11
24 13 0.46
25 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.38
Consensus pattern (25 bp):
ATAAATATATTAGATAATCATGCTA
Found at i:28648704 original size:16 final size:17
Alignment explanation
Indices: 28648645--28648729 Score: 73
Period size: 17 Copynumber: 4.8 Consensus size: 17
28648635 AATATATTAA
* *
28648645 TAATCATGTAATTAAAT
1 TAATCATGCAAATAAAT
* *
28648662 TAAATTCATACAAATATAT
1 T-AA-TCATGCAAATAAAT
*
28648681 TGATCATGCAAATAAAT
1 TAATCATGCAAATAAAT
28648698 T-ATCATGCAAATATGATAT
1 TAATCATGCAAATA--A-AT
28648717 TAATCATGCAAAT
1 TAATCATGCAAAT
28648730 TCATGCAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 12 0.22
17 14 0.25
18 4 0.07
19 14 0.25
20 11 0.20
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (17 bp):
TAATCATGCAAATAAAT
Found at i:28648724 original size:20 final size:17
Alignment explanation
Indices: 28648667--28648729 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 17
28648657 TAAATTAAAT
*
28648667 TCATACAAAT-ATATTGA
1 TCATGCAAATAATATT-A
28648684 TCATGCAAATAA-ATTA
1 TCATGCAAATAATATTA
28648700 TCATGCAAATATGATATTAA
1 TCATGCAAATA--ATATT-A
28648720 TCATGCAAAT
1 TCATGCAAAT
28648730 TCATGCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 12 0.30
17 12 0.30
18 2 0.05
19 3 0.08
20 11 0.28
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (17 bp):
TCATGCAAATAATATTA
Found at i:28649357 original size:17 final size:18
Alignment explanation
Indices: 28649329--28649362 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28649319 CCAAAAATTA
28649329 AAATTAAAAACCAAAATC
1 AAATTAAAAACCAAAATC
28649347 AAATT-AAAACCAAAAT
1 AAATTAAAAACCAAAAT
28649363 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (18 bp):
AAATTAAAAACCAAAATC
Found at i:28649368 original size:18 final size:19
Alignment explanation
Indices: 28649322--28649369 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
28649312 TTTTTGACCA
28649322 AAAATTAAAATTAAAAACC
1 AAAATTAAAATTAAAAACC
*
28649341 AAAA-TCAAATT-AAAACC
1 AAAATTAAAATTAAAAACC
28649358 AAAATTAAAATT
1 AAAATTAAAATT
28649370 TTTGGACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATTAAAATTAAAAACC
Found at i:28653021 original size:15 final size:15
Alignment explanation
Indices: 28652985--28653026 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
28652975 TGTCACTTAC
28652985 GCCTATTTTCAACAT
1 GCCTATTTTCAACAT
28653000 ---T-TTTTCAACAT
1 GCCTATTTTCAACAT
28653011 GCCTATTTTCAACAT
1 GCCTATTTTCAACAT
28653026 G
1 G
28653027 GTGGCATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
14 1 0.04
15 11 0.48
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (15 bp):
GCCTATTTTCAACAT
Found at i:28656692 original size:16 final size:16
Alignment explanation
Indices: 28656671--28656705 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28656661 TCATTCTAAA
28656671 ATTAT-AATTATTTTAT
1 ATTATAAATT-TTTTAT
28656687 ATTATAAATTTTTTAT
1 ATTATAAATTTTTTAT
28656703 ATT
1 ATT
28656706 TTCAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATAAATTTTTTAT
Found at i:28657598 original size:3 final size:3
Alignment explanation
Indices: 28657590--28657618 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28657580 ATTATTTATC
28657590 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28657619 TTAGGAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.