Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 28 of 182
Found at i:11302249 original size:6 final size:6
Alignment explanation
Indices: 11302238--11302271 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
11302228 AGAAGAAGCA
11302238 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAG
11302272 GAGAGCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:11305231 original size:19 final size:20
Alignment explanation
Indices: 11305209--11305247 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11305199 TTCTTATTTT
11305209 TACAAT-TTAAAAATATTAA
1 TACAATATTAAAAATATTAA
*
11305228 TACAATCATTAATAATATTA
1 TACAAT-ATTAAAAATATTA
11305248 TTTTTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
TACAATATTAAAAATATTAA
Found at i:11312109 original size:17 final size:16
Alignment explanation
Indices: 11312069--11312110 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11312059 CGACATTTTA
*
11312069 AAATTTAAAAATAATT
1 AAATTTGAAAATAATT
11312085 AACA-TTGAAAATAATGT
1 AA-ATTTGAAAATAAT-T
11312102 AAATTTGAA
1 AAATTTGAA
11312111 CTCGTCGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (16 bp):
AAATTTGAAAATAATT
Found at i:11312969 original size:28 final size:29
Alignment explanation
Indices: 11312922--11312980 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
11312912 TTTTAATATT
11312922 AATAATAAAATTATATTTTAA-CTTTTAA
1 AATAATAAAATTATATTTTAATCTTTTAA
11312950 AATAATAAAAATT-TGA-TTTAATCTTTTAA
1 AATAAT-AAAATTAT-ATTTTAATCTTTTAA
11312979 AA
1 AA
11312981 ATTATAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
AATAATAAAATTATATTTTAATCTTTTAA
Found at i:11315748 original size:22 final size:23
Alignment explanation
Indices: 11315700--11315750 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
11315690 ATTAAATCGT
*
11315700 AATTTTTACAATAATAAAAGTAT
1 AATTTTTACAATAATAAAAGTAA
* * *
11315723 AATTTTTA-AATGATTAAATTAA
1 AATTTTTACAATAATAAAAGTAA
11315745 AATTTT
1 AATTTT
11315751 ATTATTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
AATTTTTACAATAATAAAAGTAA
Found at i:11316178 original size:20 final size:20
Alignment explanation
Indices: 11316153--11316233 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
11316143 ATTATATTGT
11316153 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
*
11316173 TGTTTTGGTTGTTGTTTTT--
1 TGTTTTGG-TGTTTTTTTTAC
* * *
11316192 TG--CT--TCTTCTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
*
11316208 TATTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
11316228 TGTTTT
1 TGTTTT
11316234 AATTTTATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
14 8 0.18
16 1 0.02
17 1 0.02
18 1 0.02
19 2 0.04
20 23 0.51
21 9 0.20
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.70
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:11316190 original size:21 final size:20
Alignment explanation
Indices: 11316153--11316191 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11316143 ATTATATTGT
*
11316153 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTGTTTTTAC
11316173 TGTTTTGGTTGTTGTTTTT
1 TGTTTTGG-TGTTGTTTTT
11316192 TGCTTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.03, C:0.03, G:0.23, T:0.72
Consensus pattern (20 bp):
TGTTTTGGTGTTGTTTTTAC
Found at i:11316267 original size:23 final size:24
Alignment explanation
Indices: 11316241--11316291 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
11316231 TTTAATTTTA
* *
11316241 TTTTCGTGTTGTTTTTGCTG-TAT
1 TTTTAGTGCTGTTTTTGCTGCTAT
* *
11316264 TTTTATTGCTGTTTTTGTTGCTAT
1 TTTTAGTGCTGTTTTTGCTGCTAT
11316288 TTTT
1 TTTT
11316292 GTTATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.06, C:0.08, G:0.18, T:0.69
Consensus pattern (24 bp):
TTTTAGTGCTGTTTTTGCTGCTAT
Found at i:11316284 original size:12 final size:12
Alignment explanation
Indices: 11316252--11316294 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
11316242 TTTCGTGTTG
*
11316252 TTTTTGCTG-TA
1 TTTTTGTTGCTA
* *
11316263 TTTTTATTGCTG
1 TTTTTGTTGCTA
11316275 TTTTTGTTGCTA
1 TTTTTGTTGCTA
11316287 TTTTTGTT
1 TTTTTGTT
11316295 ATTTTTAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.07, C:0.07, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGCTA
Found at i:11319992 original size:22 final size:23
Alignment explanation
Indices: 11319949--11319993 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11319939 ATACTATAGG
* *
11319949 TGAAAAAAACTCAAGTATTAATT
1 TGAAAAAAAATCAAGTACTAATT
*
11319972 TGAAAAAAAAT-AATTACTAATT
1 TGAAAAAAAATCAAGTACTAATT
11319994 AAATATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (23 bp):
TGAAAAAAAATCAAGTACTAATT
Found at i:11333296 original size:30 final size:29
Alignment explanation
Indices: 11333252--11333332 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 29
11333242 AAATTTTAAA
* *
11333252 TTAATAAA-GATAAAATTATATTTTAATTTT
1 TTAA-AAATGATAAAATTATAATTTAA-ATT
11333282 TTAAAAATGATAAAAATT-TAAATTTAAATT
1 TTAAAAATGAT-AAAATTAT-AATTTAAATT
* *
11333312 TTAAAAATTATAAAAATATAA
1 TTAAAAATGATAAAATTATAA
11333333 ATCATTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 10 0.23
30 21 0.49
31 12 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAAAAATGATAAAATTATAATTTAAATT
Found at i:11333719 original size:2 final size:2
Alignment explanation
Indices: 11333712--11333745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11333702 TTTAAAAATG
11333712 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
11333746 CCGATTACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11333915 original size:3 final size:3
Alignment explanation
Indices: 11333907--11333931 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11333897 ATTTATCTCA
11333907 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
11333932 TCCCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11336738 original size:87 final size:87
Alignment explanation
Indices: 11336587--11336755 Score: 311
Period size: 87 Copynumber: 1.9 Consensus size: 87
11336577 TGCTGCCCCT
*
11336587 GGTTGAGTCAAGTTAAAGTTGATTGGTTTGCAAACCACCAACTGTATGATTTGATAATAAAATGC
1 GGTTAAGTCAAGTTAAAGTTGATTGGTTTGCAAACCACCAACTGTATGATTTGATAATAAAATGC
*
11336652 TAGAATACGGTTAACTGCGCCG
66 AAGAATACGGTTAACTGCGCCG
11336674 GGTTAAGTCAAGTTAAAGTTGATTGGTTTGCAAACCACCAACTGTATGATTTGATAATAAAATGC
1 GGTTAAGTCAAGTTAAAGTTGATTGGTTTGCAAACCACCAACTGTATGATTTGATAATAAAATGC
*
11336739 AAGAATATGGTTAACTG
66 AAGAATACGGTTAACTG
11336756 TGGAAAGAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (87 bp):
GGTTAAGTCAAGTTAAAGTTGATTGGTTTGCAAACCACCAACTGTATGATTTGATAATAAAATGC
AAGAATACGGTTAACTGCGCCG
Found at i:11338100 original size:15 final size:15
Alignment explanation
Indices: 11338076--11338107 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11338066 ACCACCAAGG
*
11338076 CCACCGCCATACATT
1 CCACCACCATACATT
11338091 CCACCACCATACATT
1 CCACCACCATACATT
11338106 CC
1 CC
11338108 GGAGTTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.50, G:0.03, T:0.19
Consensus pattern (15 bp):
CCACCACCATACATT
Found at i:11339755 original size:17 final size:16
Alignment explanation
Indices: 11339732--11339772 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11339722 ATAGTAAAAA
11339732 TATAATTTTAT-TATT
1 TATAATTTTATATATT
11339747 T-TAATAATTTATATATT
1 TATAAT--TTTATATATT
11339764 TATAATTTT
1 TATAATTTT
11339773 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.18
15 1 0.05
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:11340202 original size:30 final size:31
Alignment explanation
Indices: 11340159--11340219 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
11340149 ACTTACTGAC
* *
11340159 TTAAATAAAAATTTTCGAATAATTCAATAAT
1 TTAAATAAAAATTTTCAAACAATTCAATAAT
*
11340190 TTAAAT-AAAATTTTCAAACAATTTAATAAT
1 TTAAATAAAAATTTTCAAACAATTCAATAAT
11340220 CATTTTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (31 bp):
TTAAATAAAAATTTTCAAACAATTCAATAAT
Found at i:11341795 original size:17 final size:17
Alignment explanation
Indices: 11341773--11341811 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11341763 TTTATTAAAT
** *
11341773 AATTTAAATTTATTTTA
1 AATTTAAACATATATTA
11341790 AATTTAAACATATATTA
1 AATTTAAACATATATTA
11341807 AATTT
1 AATTT
11341812 TGAGATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAAACATATATTA
Found at i:11341904 original size:21 final size:23
Alignment explanation
Indices: 11341864--11341911 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
11341854 ATAAATAGAT
*
11341864 TAAATTACACGTTTTGTTAAGAA
1 TAAATTACACGTTTTATTAAGAA
*
11341887 TAAATTA-AC-TTTTATTAATAA
1 TAAATTACACGTTTTATTAAGAA
11341908 TAAA
1 TAAA
11341912 GATTATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
TAAATTACACGTTTTATTAAGAA
Found at i:11344361 original size:19 final size:17
Alignment explanation
Indices: 11344327--11344363 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
11344317 ATATATCAAA
11344327 ATTAAAATTTTAAAAAT
1 ATTAAAATTTTAAAAAT
11344344 ATTAATAATTTATAAAAAT
1 ATTAA-AATTT-TAAAAAT
11344363 A
1 A
11344364 ACTAACTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAAATTTTAAAAAT
Found at i:11345215 original size:2 final size:2
Alignment explanation
Indices: 11345208--11345266 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
11345198 ATCACTGTTT
11345208 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11345250 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
11345267 ATATATATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11345271 original size:2 final size:2
Alignment explanation
Indices: 11345266--11345297 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11345256 TCTCTCTCTC
11345266 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11345298 ATTAGCTTTT
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):
TA
Found at i:11350167 original size:26 final size:26
Alignment explanation
Indices: 11350116--11350167 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11350106 ATTCAATTAT
* *
11350116 GAATAAGAGATATATTTTTTCCTAAA
1 GAATAAGAAATATATTTTATCCTAAA
* *
11350142 GAATAAGAAATATCTTTTATCGTAAA
1 GAATAAGAAATATATTTTATCCTAAA
11350168 AATTTCCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (26 bp):
GAATAAGAAATATATTTTATCCTAAA
Found at i:11351811 original size:22 final size:21
Alignment explanation
Indices: 11351785--11351838 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
11351775 AATCTTGTTG
11351785 TTTTGTTGTTATTTTCTCACTA
1 TTTTGTTGTTATTTT-TCACTA
* *
11351807 TTTTGTTATCA--TTTCACTA
1 TTTTGTTGTTATTTTTCACTA
*
11351826 TTATGTTGTTATT
1 TTTTGTTGTTATT
11351839 GTTTAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
19 14 0.56
20 2 0.08
22 9 0.36
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTGTTGTTATTTTTCACTA
Found at i:11355345 original size:22 final size:22
Alignment explanation
Indices: 11355320--11355371 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
11355310 TTGTTCTTAA
*
11355320 TTATTATTTATTAT-AATACTAC
1 TTATT-TTAATTATAAATACTAC
* *
11355342 TTATTTTAATTCTAAATACTAT
1 TTATTTTAATTATAAATACTAC
11355364 TTATTTTA
1 TTATTTTA
11355372 CTTCCTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTTTAATTATAAATACTAC
Found at i:11357650 original size:8 final size:9
Alignment explanation
Indices: 11357637--11357716 Score: 61
Period size: 10 Copynumber: 8.1 Consensus size: 9
11357627 TCTATATTAC
11357637 TATATATTTT
1 TATA-ATTTT
11357647 TATAATTTTT
1 TATAA-TTTT
*
11357657 TACAATTTTT
1 TATAA-TTTT
11357667 TATAAATTCTT
1 TAT-AATT-TT
*
11357678 TACTATTTTTT
1 TA-TA-ATTTT
11357689 TATAATTTT
1 TATAATTTT
* *
11357698 TGTGATTTT
1 TATAATTTT
11357707 TATAATTTT
1 TATAATTTT
11357716 T
1 T
11357717 CTTTCTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
9 20 0.35
10 23 0.40
11 11 0.19
12 3 0.05
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (9 bp):
TATAATTTT
Found at i:11357650 original size:10 final size:10
Alignment explanation
Indices: 11357623--11357749 Score: 50
Period size: 9 Copynumber: 12.6 Consensus size: 10
11357613 ATTATAATTT
*
11357623 TTTTTCTATA
1 TTTTTATATA
**
11357633 TTACTATATA
1 TTTTTATATA
11357643 TTTTTATA-A
1 TTTTTATATA
*
11357652 TTTTT-TACAA
1 TTTTTATA-TA
*
11357662 TTTTTTATAAA
1 -TTTTTATATA
*
11357673 TTCTTTACTATT
1 TT-TTTA-TATA
11357685 TTTTTATA-A
1 TTTTTATATA
* *
11357694 TTTTTGT-GA
1 TTTTTATATA
11357703 TTTTTATA-A
1 TTTTTATATA
* *
11357712 TTTTTCTTTCTA
1 -TTTT-TATATA
11357724 TTTTTA-ATA
1 TTTTTATATA
*
11357733 TTTTTCTATA
1 TTTTTATATA
11357743 CTTTTTA
1 -TTTTTA
11357750 AAATAAGTTT
Statistics
Matches: 88, Mismatches: 16, Indels: 25
0.68 0.12 0.19
Matches are distributed among these distances:
8 2 0.02
9 27 0.31
10 26 0.30
11 26 0.30
12 7 0.08
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTTATATA
Found at i:11357667 original size:21 final size:20
Alignment explanation
Indices: 11357643--11357698 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
11357633 TTACTATATA
11357643 TTTTTATAATTTTTTACAAT
1 TTTTTATAATTTTTTACAAT
* *
11357663 TTTTTATAAATTCTTTACTATT
1 TTTTTAT-AATTTTTTAC-AAT
11357685 TTTTTATAATTTTT
1 TTTTTATAATTTTT
11357699 GTGATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 15 0.48
22 9 0.29
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATAATTTTTTACAAT
Found at i:11357748 original size:21 final size:21
Alignment explanation
Indices: 11357641--11357748 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
11357631 TATTACTATA
11357641 TATTTTTATAA-TTTT-TTAC
1 TATTTTTATAATTTTTCTTAC
* * *
11357660 AATTTTTTATAAATTCT-TTAC
1 TA-TTTTTATAATTTTTCTTAC
*
11357681 TATTTTTTTATAATTTTT-GT--
1 TA--TTTTTATAATTTTTCTTAC
* *
11357701 GATTTTTATAATTTTTCTTTC
1 TATTTTTATAATTTTTCTTAC
11357722 TATTTTTA-ATATTTTTCTATAC
1 TATTTTTATA-ATTTTTCT-TAC
11357744 T-TTTT
1 TATTTT
11357749 AAAATAAGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
18 14 0.20
19 2 0.03
20 11 0.15
21 27 0.38
22 17 0.24
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTTTTATAATTTTTCTTAC
Found at i:11361484 original size:16 final size:16
Alignment explanation
Indices: 11361459--11361496 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11361449 TCAATTAATT
*
11361459 AAAAAA-ATTTCTATC
1 AAAAAATATTTCTATA
*
11361474 AAAAAATATTTTTATA
1 AAAAAATATTTCTATA
11361490 AAAAAAT
1 AAAAAAT
11361497 TAATTCCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAAATATTTCTATA
Found at i:11363477 original size:17 final size:19
Alignment explanation
Indices: 11363436--11363478 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
11363426 AGTCCAATAA
11363436 AAATAATAGAAAATATATT
1 AAATAATAGAAAATATATT
* *
11363455 ATATAATA-AAACTATA-T
1 AAATAATAGAAAATATATT
11363472 AAATAAT
1 AAATAAT
11363479 CAGATTATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 7 0.33
19 7 0.33
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATAATAGAAAATATATT
Found at i:11368537 original size:133 final size:133
Alignment explanation
Indices: 11368368--11368747 Score: 627
Period size: 133 Copynumber: 2.9 Consensus size: 133
11368358 GCAACCACTG
* * * * * *
11368368 TAGAAATCTTCATCTAAGATGAGGAGGGCTAGCCAAAAGCTATTTTTGGGATTCCAAATTGCCTT
1 TAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGGATTTCAAATTACATT
* *
11368433 ACATTGAACATGCATATGGAATAGGG-CATATTGAGCTCATCACTCTCAGTCATCACTTTCATCC
66 ACATTGAACATGCATATGTAAT-GGGACATGTTGAGCTCATCACTCTCAGTCATCACTTTCATCC
11368497 ACCC
130 ACCC
*
11368501 TAGAAATCTACATCTAGGATGAGGAGGGCTAACCAAAAGCTGTTTTTGGGATTTCAAATTACATT
1 TAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGGATTTCAAATTACATT
* *
11368566 ACATTGAACATGCATATGTTATGGGACATGTTGAGCTCATCACTCTCAGTCATCACTTTCATCCG
66 ACATTGAACATGCATATGTAATGGGACATGTTGAGCTCATCACTCTCAGTCATCACTTTCATCCA
11368631 CCC
131 CCC
11368634 TAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGGATTTCAAATTACATT
1 TAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGGATTTCAAATTACATT
* *
11368699 ACATTGAACATGCATATGTCATGGGACATGTTGAGCTTATCACTCTCAG
66 ACATTGAACATGCATATGTAATGGGACATGTTGAGCTCATCACTCTCAG
11368748 CCATTTCCAC
Statistics
Matches: 232, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
132 3 0.01
133 229 0.99
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (133 bp):
TAGAAATCTACATCTAGGATGAGGAGGGCTAGCCAAAAGCTGTTTTTGGGATTTCAAATTACATT
ACATTGAACATGCATATGTAATGGGACATGTTGAGCTCATCACTCTCAGTCATCACTTTCATCCA
CCC
Found at i:11370936 original size:48 final size:48
Alignment explanation
Indices: 11370840--11370940 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
11370830 GAGGCAACAA
* *
11370840 AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGGAGGCGTGAAGTAGAG
1 AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGAAGGCGTGAAGAAGAG
* * *
11370888 AGGGAAAGGGAGGA-GAAGGAGAGAGAACAAAGAAGGCTTG-AGAAAGAG
1 AGGGAAAGAGAAGAGGAA-GAGAGAGAACAAAGAAGGCGTGAAG-AAGAG
11370936 AGGGA
1 AGGGA
11370941 GCGAATTAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 5 0.11
48 41 0.89
ACGTcount: A:0.48, C:0.04, G:0.45, T:0.04
Consensus pattern (48 bp):
AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGAAGGCGTGAAGAAGAG
Found at i:11377173 original size:24 final size:23
Alignment explanation
Indices: 11377146--11377191 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
11377136 TTGAAGCTAT
*
11377146 TTCTCAATTCAGCAATAATAGTTC
1 TTCTCAATTAAGCAAT-ATAGTTC
* *
11377170 TTCTCCATTAAGCTATATAGTT
1 TTCTCAATTAAGCAATATAGTT
11377192 GATCAAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (23 bp):
TTCTCAATTAAGCAATATAGTTC
Found at i:11377222 original size:2 final size:2
Alignment explanation
Indices: 11377215--11377295 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
11377205 TATATTCGTG
11377215 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11377257 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11377296 TTTATCGAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11377889 original size:17 final size:17
Alignment explanation
Indices: 11377867--11377903 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11377857 AAAAAATATT
* *
11377867 AATTTCACTATATAAAA
1 AATTTCAATAAATAAAA
11377884 AATTTCAATAAATAAAA
1 AATTTCAATAAATAAAA
11377901 AAT
1 AAT
11377904 GTATAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTTCAATAAATAAAA
Found at i:11390141 original size:26 final size:25
Alignment explanation
Indices: 11390112--11390224 Score: 77
Period size: 26 Copynumber: 4.3 Consensus size: 25
11390102 TCTAAATTTT
*
11390112 TTTTTTTAATTTTTAAGGGGCTTAAA
1 TTTTTTTAATTTTTAA-GGGCTCAAA
*
11390138 TTTTTTTAAAATTTTTATA-GG-TCAATTT
1 TTTTTTT--AATTTTTA-AGGGCTCAA--A
* *
11390166 TTTTTATTAACTTTTAAGGGCCTCAAG
1 TTTTT-TTAATTTTTAAGGG-CTCAAA
* * *
11390193 TTTTTTTAGTTTTTAAGGGTTTAAA
1 TTTTTTTAATTTTTAAGGGCTCAAA
11390218 TTTTTTT
1 TTTTTTT
11390225 TTTACCAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
25 10 0.14
26 23 0.33
27 16 0.23
28 13 0.19
29 7 0.10
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (25 bp):
TTTTTTTAATTTTTAAGGGCTCAAA
Found at i:11390220 original size:55 final size:54
Alignment explanation
Indices: 11390104--11390225 Score: 131
Period size: 55 Copynumber: 2.2 Consensus size: 54
11390094 TAAAAGGATC
* * * *
11390104 TAAATTTTTTTTTTTAATTTTTAAGGGGCTTAAATTTTTTTAAAATTTTTATAGG
1 TAAATTTTTTTTATTAACTTTTAAGGGCCTCAAATTTTTTT-AAATTTTTATAGG
* * *
11390159 TCAATTTTTTTTATTAACTTTTAAGGGCCTCAAGTTTTTTT-AGTTTTTA-AGGG
1 TAAATTTTTTTTATTAACTTTTAAGGGCCTCAAATTTTTTTAAATTTTTATA-GG
11390212 TTTAAATTTTTTTT
1 --TAAATTTTTTTT
11390226 TTACCAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
52 1 0.02
53 9 0.16
55 46 0.82
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.58
Consensus pattern (54 bp):
TAAATTTTTTTTATTAACTTTTAAGGGCCTCAAATTTTTTTAAATTTTTATAGG
Found at i:11391944 original size:24 final size:23
Alignment explanation
Indices: 11391912--11391957 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
11391902 CATTGATAAT
*
11391912 GAAGACAATAAGTGATAAGAGAA
1 GAAGACAATAAGTCATAAGAGAA
*
11391935 GAAGAACAATAAGTCATAGGAGA
1 GAAG-ACAATAAGTCATAAGAGA
11391958 GATGAACGGT
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:0.54, C:0.07, G:0.26, T:0.13
Consensus pattern (23 bp):
GAAGACAATAAGTCATAAGAGAA
Found at i:11400506 original size:16 final size:15
Alignment explanation
Indices: 11400487--11400555 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 15
11400477 TGAATAAGAC
11400487 TGTAATGAAATAGAAT
1 TGTAATGAAATA-AAT
11400503 TGTAATGAAATAGAAT
1 TGTAATGAAATA-AAT
11400519 TGTAATGTAAA-AAAT
1 TGTAATG-AAATAAAT
11400534 TGTAATGAAATAAATT
1 TGTAATGAAATAAA-T
11400550 TGTAAT
1 TGTAAT
11400556 CAATAATTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.06
15 13 0.26
16 31 0.62
17 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (15 bp):
TGTAATGAAATAAAT
Found at i:11400553 original size:31 final size:32
Alignment explanation
Indices: 11400487--11400555 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
11400477 TGAATAAGAC
11400487 TGTAATGAAATAGAATTGTAATGAAATAGAAT
1 TGTAATGAAATAGAATTGTAATGAAATAGAAT
11400519 TGTAATGTAAA-A-AATTGTAATGAAATA-AATT
1 TGTAATG-AAATAGAATTGTAATGAAATAGAA-T
11400550 TGTAAT
1 TGTAAT
11400556 CAATAATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 2 0.06
31 22 0.63
32 8 0.23
33 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTAATGAAATAGAATTGTAATGAAATAGAAT
Found at i:11401959 original size:25 final size:26
Alignment explanation
Indices: 11401905--11401965 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
11401895 TAAACTAAAT
*
11401905 TTAATAATT-ATATTAATAGTATTTTA
1 TTAAT-ATTAATATTAATAGTATTATA
*
11401931 TTAAT-TTAATATTAA-AGTGATTATC
1 TTAATATTAATATTAATAGT-ATTATA
11401956 TTAATATTAA
1 TTAATATTAA
11401966 ATATAACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 5 0.17
25 16 0.53
26 9 0.30
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (26 bp):
TTAATATTAATATTAATAGTATTATA
Found at i:11401977 original size:17 final size:20
Alignment explanation
Indices: 11401930--11401980 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
11401920 ATAGTATTTT
*
11401930 ATTAATTTAATATTAAAGTG
1 ATTAACTTAATATTAAAGTG
*
11401950 ATTATCTTAATATTAAA-T-
1 ATTAACTTAATATTAAAGTG
11401968 A-TAACTTAATATT
1 ATTAACTTAATATT
11401981 TATCTTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.39
18 1 0.04
19 1 0.04
20 15 0.54
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
ATTAACTTAATATTAAAGTG
Found at i:11417196 original size:5 final size:5
Alignment explanation
Indices: 11417186--11417213 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11417176 GAAATCGAGA
11417186 GGAAG GGAAG GGAAG GGAAG GGAAG GGA
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGA
11417214 GGAGGGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:11419103 original size:16 final size:16
Alignment explanation
Indices: 11419084--11419133 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
11419074 ATAAAGAATT
11419084 TAATTTATTATTTTAA
1 TAATTTATTATTTTAA
*
11419100 TAATTTATT-TTAT-A
1 TAATTTATTATTTTAA
*
11419114 TTATATTA-TATTTTAA
1 TAAT-TTATTATTTTAA
11419130 TAAT
1 TAAT
11419134 AAAATTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 5 0.19
15 9 0.33
16 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTATTATTTTAA
Found at i:11423542 original size:16 final size:16
Alignment explanation
Indices: 11423509--11423544 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11423499 ACTTGAATTC
*
11423509 AAGAGAAAATTGTATA
1 AAGAGAAAATTCTATA
*
11423525 AAGAGAAAATTCTTTA
1 AAGAGAAAATTCTATA
11423541 AAGA
1 AAGA
11423545 TATTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.17, T:0.25
Consensus pattern (16 bp):
AAGAGAAAATTCTATA
Found at i:11424599 original size:26 final size:28
Alignment explanation
Indices: 11424547--11424604 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
11424537 ATAGATGAAG
*
11424547 TTTGATTTAATAATTATACACATGAAA-T
1 TTTGATTT-ATAATTATACACAAGAAACT
* *
11424575 TTTGATTT-TAATTGTACATAAGAAACT
1 TTTGATTTATAATTATACACAAGAAACT
11424602 TTT
1 TTT
11424605 ATTATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 4 0.15
28 8 0.31
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (28 bp):
TTTGATTTATAATTATACACAAGAAACT
Found at i:11436829 original size:38 final size:38
Alignment explanation
Indices: 11436758--11436868 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 38
11436748 TCAAGGATCA
* * ** *
11436758 CATCTTA-TGGACCAAAAGTCACATTGACCGCTATTCC
1 CATCTTATTGGATCAAAGGTCACATCAATCGCTATTCC
* **
11436795 CATCTTATTGGATCAAAGGTCACATCAATTGCTATTTT
1 CATCTTATTGGATCAAAGGTCACATCAATCGCTATTCC
* *
11436833 TATCTTATTGGATCAAGGGTCACATCAATCGCTATT
1 CATCTTATTGGATCAAAGGTCACATCAATCGCTATT
11436869 TCATCATATT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
37 7 0.11
38 55 0.89
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (38 bp):
CATCTTATTGGATCAAAGGTCACATCAATCGCTATTCC
Found at i:11436869 original size:38 final size:38
Alignment explanation
Indices: 11436796--11436869 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
11436786 CGCTATTCCC
*
11436796 ATCTTATTGGATCAAAGGTCACATCAATTGCTATTTTT
1 ATCTTATTGGATCAAAGGTCACATCAATCGCTATTTTT
*
11436834 ATCTTATTGGATCAAGGGTCACATCAATCGCTATTT
1 ATCTTATTGGATCAAAGGTCACATCAATCGCTATTT
11436870 CATCATATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (38 bp):
ATCTTATTGGATCAAAGGTCACATCAATCGCTATTTTT
Found at i:11438069 original size:14 final size:15
Alignment explanation
Indices: 11438050--11438079 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11438040 AAATTGTGTT
11438050 TTTAATA-TTTATTA
1 TTTAATATTTTATTA
11438064 TTTAATATTTTATTA
1 TTTAATATTTTATTA
11438079 T
1 T
11438080 ACTCTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTAATATTTTATTA
Found at i:11446100 original size:22 final size:22
Alignment explanation
Indices: 11446048--11446116 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
11446038 ATTTTGAGTT
* * *
11446048 TTTTTAAAAAAAAAAATATTTTAA
1 TTTTTAAAATAATAAA-ATTAT-A
11446072 TTCTTTAAAATAATAAAATTATA
1 TT-TTTAAAATAATAAAATTATA
** *
11446095 TTTTTATTATAATAAAAATATA
1 TTTTTAAAATAATAAAATTATA
11446117 CAATTTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 17 0.45
23 3 0.08
24 6 0.16
25 12 0.32
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTTAAAATAATAAAATTATA
Found at i:11447763 original size:15 final size:17
Alignment explanation
Indices: 11447733--11447771 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
11447723 GTTCACAATC
*
11447733 GGGTACTCGTAA-TTTT
1 GGGTATTCGTAATTTTT
11447749 GGGTATTCG-AATTTTT
1 GGGTATTCGTAATTTTT
11447765 GGGTATT
1 GGGTATT
11447772 AAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.18, C:0.08, G:0.28, T:0.46
Consensus pattern (17 bp):
GGGTATTCGTAATTTTT
Found at i:11448012 original size:21 final size:21
Alignment explanation
Indices: 11447962--11448012 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
11447952 ATGATAGTAT
11447962 AATCCAAATATAAAATTTAAA
1 AATCCAAATATAAAATTTAAA
** * *
11447983 AATTTAAATATAAAGTTTATA
1 AATCCAAATATAAAATTTAAA
11448004 AATCCAAAT
1 AATCCAAAT
11448013 TACATAATTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAAA
Found at i:11449436 original size:6 final size:6
Alignment explanation
Indices: 11449425--11449473 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
11449415 CAATTCACAC
11449425 CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG
1 CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG
11449473 C
1 C
11449474 TGCTCCACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.16, T:0.33
Consensus pattern (6 bp):
CCTCTG
Found at i:11458099 original size:18 final size:17
Alignment explanation
Indices: 11458072--11458109 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11458062 TCAGATCACT
11458072 AATTTTCGAT-TCGATCA
1 AATTTTCGATAT-GATCA
11458089 AATTGTTCGATATGATCA
1 AATT-TTCGATATGATCA
11458107 AAT
1 AAT
11458110 AAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 14 0.74
19 1 0.05
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (17 bp):
AATTTTCGATATGATCA
Found at i:11458133 original size:10 final size:9
Alignment explanation
Indices: 11458115--11458145 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
11458105 CAAATAAATT
11458115 ATTAAAAAA
1 ATTAAAAAA
11458124 ATTAAAAAA
1 ATTAAAAAA
11458133 ATTAAACAAA
1 ATTAAA-AAA
11458143 ATT
1 ATT
11458146 TGTTCAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:11464832 original size:6 final size:6
Alignment explanation
Indices: 11464821--11464846 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11464811 CACACACCTC
11464821 TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TC
11464847 TTCCTTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:11465715 original size:31 final size:31
Alignment explanation
Indices: 11465680--11465739 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
11465670 AAATGGTTAA
11465680 TGAACTATTCGAAA-GTTTTTATGTAAGTCGC
1 TGAACTATTC-AAATGTTTTTATGTAAGTCGC
*
11465711 TGAACTATTCAAATGTTTTTATTTAAGTC
1 TGAACTATTCAAATGTTTTTATGTAAGTC
11465740 ATTGCGTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (31 bp):
TGAACTATTCAAATGTTTTTATGTAAGTCGC
Found at i:11466595 original size:25 final size:26
Alignment explanation
Indices: 11466538--11466595 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
11466528 AAAAAATTTA
*
11466538 AAAATATT-TATAAATATCAAATGGAT
1 AAAATATTACATAAATATCAAAT-GAT
11466564 -AAA-ATTACATAAATATCAAAT-AT
1 AAAATATTACATAAATATCAAATGAT
11466587 AAAATATTA
1 AAAATATTA
11466596 ATCAATTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 20 0.71
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAATATTACATAAATATCAAATGAT
Found at i:11468552 original size:38 final size:38
Alignment explanation
Indices: 11468509--11468592 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
11468499 AACAAATTTA
* * * *
11468509 AAAATATATATAATATATCAAATACACTTAAAA-ACATT
1 AAAATAAATATAAAAAAT-AAATAAACTTAAAATACATT
*
11468547 AAAATAAATATAAAAAATAAATAAATTTAAAATACATT
1 AAAATAAATATAAAAAATAAATAAACTTAAAATACATT
11468585 AAAA-AAAT
1 AAAATAAAT
11468593 CTATATTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 16 0.40
38 24 0.60
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (38 bp):
AAAATAAATATAAAAAATAAATAAACTTAAAATACATT
Found at i:11468735 original size:12 final size:12
Alignment explanation
Indices: 11468718--11468813 Score: 65
Period size: 12 Copynumber: 8.3 Consensus size: 12
11468708 ATAACATCTA
11468718 AACAACAAAAAT
1 AACAACAAAAAT
*
11468730 AACAACCAAAAT
1 AACAACAAAAAT
* **
11468742 AGCAGTAAAAAT
1 AACAACAAAAAT
*
11468754 AACAGC-AAAAT
1 AACAACAAAAAT
**
11468765 AAC-A-TTAAA-
1 AACAACAAAAAT
*
11468774 AACAACAAAAAG
1 AACAACAAAAAT
*
11468786 AGCAACAAAAAT
1 AACAACAAAAAT
* *
11468798 AACAGCAAAAAC
1 AACAACAAAAAT
11468810 AACA
1 AACA
11468814 CGAAAACAGC
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
9 3 0.05
10 4 0.06
11 11 0.17
12 46 0.72
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:11468751 original size:24 final size:24
Alignment explanation
Indices: 11468724--11468781 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
11468714 TCTAAACAAC
*
11468724 AAAAATAACAACCAAAATAGCAGT
1 AAAAATAACAACCAAAATAACAGT
* *
11468748 AAAAATAAC-AGCAAAATAACATT
1 AAAAATAACAACCAAAATAACAGT
*
11468771 AAAAACAACAA
1 AAAAATAACAA
11468782 AAAGAGCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.12
Consensus pattern (24 bp):
AAAAATAACAACCAAAATAACAGT
Found at i:11468756 original size:44 final size:44
Alignment explanation
Indices: 11468702--11468813 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
11468692 GTAAAAACGC
* * * *
11468702 ATAAAAATAACATCTAAACAACA-AAAATAACAACCAAAATAGCA
1 ATAAAAATAACAGCAAAACAACATAAAA-AACAACAAAAAGAGCA
* * *
11468746 GTAAAAATAACAGCAAAATAACATTAAAAACAACAAAAAGAGCA
1 ATAAAAATAACAGCAAAACAACATAAAAAACAACAAAAAGAGCA
*
11468790 ACAAAAATAACAGCAAAAACAACA
1 ATAAAAATAACAGC-AAAACAACA
11468814 CGAAAACAGC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
44 45 0.80
45 11 0.20
ACGTcount: A:0.67, C:0.17, G:0.05, T:0.11
Consensus pattern (44 bp):
ATAAAAATAACAGCAAAACAACATAAAAAACAACAAAAAGAGCA
Found at i:11468782 original size:56 final size:55
Alignment explanation
Indices: 11468705--11468813 Score: 139
Period size: 56 Copynumber: 2.0 Consensus size: 55
11468695 AAAACGCATA
* * * * *
11468705 AAAATAACATCTAAACAACAAAAATAACAACCAAAATAGCAGTAAAAATAACAGC
1 AAAATAACATCTAAACAACAAAAAGAACAACAAAAATAACAGCAAAAACAACAGC
*
11468760 AAAATAACAT-TAAAAACAACAAAAAGAGCAACAAAAATAACAGCAAAAACAACA
1 AAAATAACATCT--AAACAACAAAAAGAACAACAAAAATAACAGCAAAAACAACA
11468814 CGAAAACAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 1 0.02
55 10 0.22
56 35 0.76
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (55 bp):
AAAATAACATCTAAACAACAAAAAGAACAACAAAAATAACAGCAAAAACAACAGC
Found at i:11468808 original size:33 final size:35
Alignment explanation
Indices: 11468760--11468831 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
11468750 AAATAACAGC
** *
11468760 AAAATAACATTAAAAACAACA-AAAAGAGCAA-CA
1 AAAATAACAGCAAAAACAACACAAAACAGCAATCA
11468793 AAAATAACAGCAAAAACAACACGAAAACAGCAATCA
1 AAAATAACAGCAAAAACAACAC-AAAACAGCAATCA
11468829 AAA
1 AAA
11468832 CAGTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 19 0.58
35 9 0.27
36 5 0.15
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (35 bp):
AAAATAACAGCAAAAACAACACAAAACAGCAATCA
Found at i:11468832 original size:56 final size:56
Alignment explanation
Indices: 11468717--11468833 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 56
11468707 AATAACATCT
* * * * * * *
11468717 AAACAACAAAAATAACAACCAAAATAGCAGTAAAAATAACAGCAAAATAACATTAA
1 AAACAACAAAAAGAACAACAAAAATAACAGCAAAAACAACAGCAAAACAACAATAA
* * *
11468773 AAACAACAAAAAGAGCAACAAAAATAACAGCAAAAACAACA-CGAAAACAGCAATCA
1 AAACAACAAAAAGAACAACAAAAATAACAGCAAAAACAACAGC-AAAACAACAATAA
11468829 AAACA
1 AAACA
11468834 GTAAAAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 1 0.02
56 49 0.98
ACGTcount: A:0.67, C:0.19, G:0.07, T:0.08
Consensus pattern (56 bp):
AAACAACAAAAAGAACAACAAAAATAACAGCAAAAACAACAGCAAAACAACAATAA
Found at i:11468861 original size:19 final size:20
Alignment explanation
Indices: 11468825--11468900 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 20
11468815 GAAAACAGCA
11468825 ATCAAAACAGTAAAAAAAAT
1 ATCAAAACAGTAAAAAAAAT
*
11468845 ATCAAAACTGT-AAAAAAAT
1 ATCAAAACAGTAAAAAAAAT
* * *
11468864 A--AAAATAGCAAAAAAAGT
1 ATCAAAACAGTAAAAAAAAT
*
11468882 AACCAAAACAGTAAAAAAA
1 -ATCAAAACAGTAAAAAAA
11468901 CAGCACCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.11
18 7 0.16
19 10 0.22
20 10 0.22
21 13 0.29
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.13
Consensus pattern (20 bp):
ATCAAAACAGTAAAAAAAAT
Found at i:11470240 original size:12 final size:13
Alignment explanation
Indices: 11470213--11470245 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
11470203 TAACACAATT
11470213 TTTTAATTAATAA
1 TTTTAATTAATAA
*
11470226 TTTTAATT-TTAA
1 TTTTAATTAATAA
11470238 TTTTAATT
1 TTTTAATT
11470246 GTTTTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAATTAATAA
Found at i:11471388 original size:68 final size:67
Alignment explanation
Indices: 11471298--11471426 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 67
11471288 ATTTTAAGGC
* *
11471298 TTAATTTTGATTATATATGATCTCAATATTGTATTTATTAAATTTTCATATTTTCTTGTATTTTA
1 TTAAATTTGATTATATATGATCTCAATATTGTATTTATTAAATTTT-ATATTTT-TTATATTTTA
11471363 AAAT
64 AAAT
*
11471367 TTAAATTT-ATTATATATGATCTCAATATTGTATTTATTAAGTTTTATATTTTTTATATTT
1 TTAAATTTGATTATATATGATCTCAATATTGTATTTATTAAATTTTATATTTTTTATATTT
11471427 ATTTATTTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
66 7 0.12
67 7 0.12
68 36 0.63
69 7 0.12
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (67 bp):
TTAAATTTGATTATATATGATCTCAATATTGTATTTATTAAATTTTATATTTTTTATATTTTAAA
AT
Found at i:11473703 original size:19 final size:18
Alignment explanation
Indices: 11473679--11473728 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
11473669 AAATTGGCAT
11473679 AAACTTATCAAAATTATAA
1 AAACTTAT-AAAATTATAA
*
11473698 AAACTTATAGATATTATAA
1 AAACTTATA-AAATTATAA
*
11473717 AAAATTATAAAA
1 AAACTTATAAAA
11473729 AAATTGGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 3 0.11
19 24 0.89
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (18 bp):
AAACTTATAAAATTATAA
Found at i:11473733 original size:11 final size:10
Alignment explanation
Indices: 11473688--11473730 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
11473678 TAAACTTATC
11473688 AAAATTATAA
1 AAAATTATAA
*
11473698 AAACTTAT-A
1 AAAATTATAA
* *
11473707 GATATTATAA
1 AAAATTATAA
11473717 AAAATTATAA
1 AAAATTATAA
11473727 AAAA
1 AAAA
11473731 ATTGGTGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 6 0.23
10 20 0.77
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATTATAA
Found at i:11473813 original size:20 final size:20
Alignment explanation
Indices: 11473772--11473814 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
11473762 AAATATATTT
*
11473772 AAAACATTTAAAATTTTATA
1 AAAACATTTAAAATTCTATA
*
11473792 AAAACATATTAGAATTCT-TA
1 AAAACAT-TTAAAATTCTATA
11473812 AAA
1 AAA
11473815 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAACATTTAAAATTCTATA
Found at i:11473859 original size:18 final size:17
Alignment explanation
Indices: 11473831--11473888 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
11473821 AAATTGTAAA
11473831 AAAATTATAAAAACTATT
1 AAAATTATAAAAA-TATT
11473849 AAAATGT-TAAAAATATGT
1 AAAAT-TATAAAAATAT-T
*
11473867 AAACTTATAAAAATTATT
1 AAAATTATAAAAA-TATT
11473885 AAAA
1 AAAA
11473889 AATCATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.12
18 26 0.76
19 4 0.12
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATATT
Found at i:11473878 original size:47 final size:48
Alignment explanation
Indices: 11473787--11473879 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 48
11473777 ATTTAAAATT
* * *
11473787 TTATAAAAACATATTAGAATTCTTAAAATATAAAAAATTGTAAAAAAA
1 TTATAAAAACATATTAAAATTCTAAAAATATAAAAAATTATAAAAAAA
** *
11473835 TTATAAAAAC-TATTAAAATGT-TAAAAATATGTAAACTTATAAAAA
1 TTATAAAAACATATTAAAAT-TCTAAAAATATAAAAAATTATAAAAA
11473880 TTATTAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
47 27 0.71
48 11 0.29
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (48 bp):
TTATAAAAACATATTAAAATTCTAAAAATATAAAAAATTATAAAAAAA
Found at i:11474476 original size:31 final size:31
Alignment explanation
Indices: 11474438--11474514 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
11474428 TTACAAATTG
* **
11474438 ATCACTAAACTATTTGAAAATTTTTATTTAA
1 ATCACTAAACTATTTAAAAAGATTTATTTAA
* * **
11474469 ATTACTAAATTATGCAAAAAGATTTATTTAA
1 ATCACTAAACTATTTAAAAAGATTTATTTAA
*
11474500 ATCATTAAACTATTT
1 ATCACTAAACTATTT
11474515 TGTTAATAAA
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (31 bp):
ATCACTAAACTATTTAAAAAGATTTATTTAA
Found at i:11476274 original size:3 final size:3
Alignment explanation
Indices: 11476268--11476294 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11476258 TAATGACAAC
11476268 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
11476295 AATAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:11491955 original size:25 final size:25
Alignment explanation
Indices: 11491898--11491956 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
11491888 ATTTTATTAT
* *
11491898 TTAAATAATTTATATTTTTATAATTT
1 TTAAA-AAATTATATTTTTATAATTG
* *
11491924 TTTAAAAATTATATTTTTATCATTG
1 TTAAAAAATTATATTTTTATAATTG
11491949 TTAAAAAA
1 TTAAAAAA
11491957 ATAAAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAAAATTATATTTTTATAATTG
Found at i:11491956 original size:26 final size:25
Alignment explanation
Indices: 11491889--11491958 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
11491879 AAAAATGTAA
* * *
11491889 TTTTATTA-TTTAAATAATTTATAT
1 TTTTATAATTTTAAAAAAATTATAT
**
11491913 TTTTATAATTTTTTAAAAATTATAT
1 TTTTATAATTTTAAAAAAATTATAT
*
11491938 TTTTATCATTGTTAAAAAAAT
1 TTTTATAATT-TTAAAAAAAT
11491959 AAAATATAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 7 0.19
25 21 0.58
26 8 0.22
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (25 bp):
TTTTATAATTTTAAAAAAATTATAT
Found at i:11492001 original size:17 final size:19
Alignment explanation
Indices: 11491981--11492020 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
11491971 TATTTTTATT
*
11491981 AATTTAAA-ATTTTAAA-A
1 AATTTAAATAATTTAAATA
11491998 AA-TTAAATAATTTAAATA
1 AATTTAAATAATTTAAATA
11492016 AATTT
1 AATTT
11492021 TTTCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 3 0.16
19 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTAAATAATTTAAATA
Found at i:11493114 original size:2 final size:2
Alignment explanation
Indices: 11493107--11493146 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11493097 ACAAAAGATA
11493107 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
11493147 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11494458 original size:32 final size:31
Alignment explanation
Indices: 11494422--11494490 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 31
11494412 CCATTATACC
*
11494422 GTTAACGACA-ATTAATGAATAGTGACTAAAAT
1 GTTAACGACATA-TAACGAA-AGTGACTAAAAT
*
11494454 GTTAA-AACATGATAACGAAAGTGACTAAAAT
1 GTTAACGACAT-ATAACGAAAGTGACTAAAAT
11494485 G-TAACG
1 GTTAACG
11494491 TTTCAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
30 3 0.10
31 16 0.52
32 11 0.35
33 1 0.03
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (31 bp):
GTTAACGACATATAACGAAAGTGACTAAAAT
Found at i:11496315 original size:9 final size:9
Alignment explanation
Indices: 11496297--11496352 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
11496287 GTCAACAAAT
11496297 AATT-TTAA
1 AATTATTAA
11496305 AATTATTAA
1 AATTATTAA
11496314 AATTATT--
1 AATTATTAA
11496321 --TT-TTAA
1 AATTATTAA
11496327 AA-TA-TAA
1 AATTATTAA
11496334 AATTATTAA
1 AATTATTAA
11496343 AATTATTAA
1 AATTATTAA
11496352 A
1 A
11496353 TAATTTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.15
8 6 0.15
9 24 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTATTAA
Found at i:11496357 original size:20 final size:19
Alignment explanation
Indices: 11496293--11496359 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
11496283 CTACGTCAAC
11496293 AAATAATTTTAAAATTATT
1 AAATAATTTTAAAATTATT
*
11496312 AAAATTATTTTTTAAAA-TA-T
1 -AAA-TA-ATTTTAAAATTATT
11496332 -AA-AATTATTAAAATTATT
1 AAATAATT-TTAAAATTATT
11496350 AAATAATTTT
1 AAATAATTTT
11496360 CAATTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
15 2 0.05
16 7 0.18
17 2 0.05
18 3 0.08
19 4 0.11
20 8 0.21
21 4 0.11
22 8 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATAATTTTAAAATTATT
Found at i:11497383 original size:16 final size:17
Alignment explanation
Indices: 11497350--11497382 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11497340 ATTTAATAAT
11497350 TTTATAATTTAAAAAAA
1 TTTATAATTTAAAAAAA
*
11497367 TTTATATTTTAAAAAA
1 TTTATAATTTAAAAAA
11497383 TAATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATAATTTAAAAAAA
Found at i:11500436 original size:25 final size:24
Alignment explanation
Indices: 11500398--11500450 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
11500388 TGAACTTCAC
11500398 ACTTTTTCTTAATTTAGTACCTAA
1 ACTTTTTCTTAATTTAGTACCTAA
* * *
11500422 ACTTTTTTTTCAATTTGGTACGTAA
1 ACTTTTTCTT-AATTTAGTACCTAA
11500447 ACTT
1 ACTT
11500451 GACACTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (24 bp):
ACTTTTTCTTAATTTAGTACCTAA
Found at i:11500469 original size:31 final size:31
Alignment explanation
Indices: 11500433--11500512 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
11500423 CTTTTTTTTC
* *
11500433 AATTTGGTACGTAAACTTGACACTTTTAAC-T
1 AATTTGGTACCTAAACTTCACACTTTT-ACTT
* *
11500464 AATTTGGCACCTAAACTTCACACTTTTTCTT
1 AATTTGGTACCTAAACTTCACACTTTTACTT
* *
11500495 AAGTTGGTACTTAAACTT
1 AATTTGGTACCTAAACTT
11500513 TTGGAGGATC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTCACACTTTTACTT
Found at i:11501110 original size:58 final size:60
Alignment explanation
Indices: 11500974--11501115 Score: 164
Period size: 58 Copynumber: 2.4 Consensus size: 60
11500964 AAAAAGCTTA
* * * ** *
11500974 ATCAAATTAGGAAAAAAATGTCAAGTTCAGGTATCAAATTGGGCCCAAAAAAAGTTTAGGT
1 ATCAAATTAAG-AAAAAATGTCAAGTTAAGGTACCAAATTGGGCAAAAAAAAAGTTTAGAT
* * *
11501035 ACCAAATTAAGAGAAAATGTCAAGTTAAGGTACCGAATT-GG-AAAAAAAAATGTTT-GAT
1 ATCAAATTAAGAAAAAATGTCAAGTTAAGGTACCAAATTGGGCAAAAAAAAA-GTTTAGAT
11501093 ATCAAATTAAGAAAAAATGTCAA
1 ATCAAATTAAGAAAAAATGTCAA
11501116 ATTTATGTAC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 30 0.43
59 6 0.09
60 24 0.35
61 9 0.13
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.24
Consensus pattern (60 bp):
ATCAAATTAAGAAAAAATGTCAAGTTAAGGTACCAAATTGGGCAAAAAAAAAGTTTAGAT
Found at i:11501202 original size:10 final size:9
Alignment explanation
Indices: 11501187--11501258 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 9
11501177 CATGTGAGTG
11501187 AAAAATAAT
1 AAAAATAAT
11501196 -AAAA-AAT
1 AAAAATAAT
11501203 AAATAA-AAT
1 AAA-AATAAT
*
11501212 -AAAA-AGT
1 AAAAATAAT
11501219 AAAAATAAT
1 AAAAATAAT
*
11501228 AAAAATTATT
1 AAAAA-TAAT
*
11501238 CAAAAT-AT
1 AAAAATAAT
11501246 AAAAA-AAT
1 AAAAATAAT
11501254 AAAAA
1 AAAAA
11501259 ATTATGAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
7 7 0.14
8 24 0.47
9 13 0.25
10 7 0.14
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:11501214 original size:16 final size:16
Alignment explanation
Indices: 11501187--11501232 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
11501177 CATGTGAGTG
11501187 AAAAATAATAAAAAAT
1 AAAAATAATAAAAAAT
*
11501203 AAATAA-AATAAAAAGT
1 AAA-AATAATAAAAAAT
11501219 AAAAATAATAAAAA
1 AAAAATAATAAAAA
11501233 TTATTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAATAATAAAAAAT
Found at i:11501243 original size:32 final size:33
Alignment explanation
Indices: 11501187--11501249 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
11501177 CATGTGAGTG
11501187 AAAAATAATAAAAAATAAATAAAATA-AAAAGT
1 AAAAATAATAAAAAATAAATAAAATATAAAAGT
* *
11501219 AAAAATAAT-AAAAATTATTCAAAATATAAAA
1 AAAAATAATAAAAAATAAAT-AAAATATAAAA
11501250 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 8 0.30
32 15 0.56
33 4 0.15
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (33 bp):
AAAAATAATAAAAAATAAATAAAATATAAAAGT
Found at i:11502293 original size:16 final size:17
Alignment explanation
Indices: 11502272--11502304 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11502262 TAAGCGTAAA
11502272 TTAAAT-TATAATTATT
1 TTAAATATATAATTATT
*
11502288 TTAAATATGTAATTATT
1 TTAAATATATAATTATT
11502305 AGAATTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAAATATATAATTATT
Found at i:11506412 original size:173 final size:173
Alignment explanation
Indices: 11506123--11506454 Score: 637
Period size: 173 Copynumber: 1.9 Consensus size: 173
11506113 TGTTGGGCCG
*
11506123 GATTAAAATTGGTCTCTACACTATTTTTAACACAATTTTTAGAATTATCTATAGCTTTTCCTCAA
1 GATTAAAATTGGTCTCTACACTATTTTTAACACAATTTCTAGAATTATCTATAGCTTTTCCTCAA
* *
11506188 CCCATAAATAAGAGGATCATTTCGACACACTCAAATCTATGCCCTTCTGTGTTGACGATAATGCC
66 CCCATAAATAAGAGGATCATTTCGACACACTCAAATCTATGCCCTTCTGTGTTGACGACAACGCC
11506253 CATGTTTATCGAGTTAAGACTCAGTTAACACAATTTTTAACAC
131 CATGTTTATCGAGTTAAGACTCAGTTAACACAATTTTTAACAC
11506296 GATTAAAATTGGTCTCTACACTATTTTTAACACAATTTCTAGAATTATCTATAGCTTTTCCTCAA
1 GATTAAAATTGGTCTCTACACTATTTTTAACACAATTTCTAGAATTATCTATAGCTTTTCCTCAA
11506361 CCCATAAATAAGAGGATCATTTCGACACACTCAAATCTATGCCCTTCTGTGTTGACGACAACGCC
66 CCCATAAATAAGAGGATCATTTCGACACACTCAAATCTATGCCCTTCTGTGTTGACGACAACGCC
11506426 CATGTTTATCGAGTTAAGACTCAGTTAAC
131 CATGTTTATCGAGTTAAGACTCAGTTAAC
11506455 TTCAACATCA
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 156 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (173 bp):
GATTAAAATTGGTCTCTACACTATTTTTAACACAATTTCTAGAATTATCTATAGCTTTTCCTCAA
CCCATAAATAAGAGGATCATTTCGACACACTCAAATCTATGCCCTTCTGTGTTGACGACAACGCC
CATGTTTATCGAGTTAAGACTCAGTTAACACAATTTTTAACAC
Found at i:11508204 original size:19 final size:20
Alignment explanation
Indices: 11508180--11508222 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11508170 ATCTTTAATC
11508180 ATTTTAATAAGTT-TCTATA
1 ATTTTAATAAGTTGTCTATA
* *
11508199 ATTTTATTAATTTGTCTATA
1 ATTTTAATAAGTTGTCTATA
11508219 ATTT
1 ATTT
11508223 CTAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTAATAAGTTGTCTATA
Found at i:11508230 original size:20 final size:20
Alignment explanation
Indices: 11508193--11508231 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11508183 TTAATAAGTT
*
11508193 TCTATAATTTTATTAATTTG
1 TCTATAATTTTATAAATTTG
11508213 TCTATAATTTCTA-AAATTT
1 TCTATAATTT-TATAAATTT
11508232 TTATAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
TCTATAATTTTATAAATTTG
Found at i:11521531 original size:15 final size:15
Alignment explanation
Indices: 11521513--11521545 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11521503 AATAAGATTT
11521513 TTATAAAACCAAACA
1 TTATAAAACCAAACA
11521528 TTATAAAACCAAACA
1 TTATAAAACCAAACA
11521543 TTA
1 TTA
11521546 ACGTGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (15 bp):
TTATAAAACCAAACA
Found at i:11524335 original size:19 final size:18
Alignment explanation
Indices: 11524313--11524348 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11524303 ATTAATATTA
*
11524313 ATATTTTATATTATTTTAG
1 ATATTTTAGA-TATTTTAG
11524332 ATATTTTAGATATTTTA
1 ATATTTTAGATATTTTA
11524349 TCTAGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
ATATTTTAGATATTTTAG
Found at i:11524338 original size:9 final size:9
Alignment explanation
Indices: 11524313--11524348 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
11524303 ATTAATATTA
*
11524313 ATATTTTAT
1 ATATTTTAG
11524322 ATTATTTTAG
1 A-TATTTTAG
11524332 ATATTTTAG
1 ATATTTTAG
11524341 ATATTTTA
1 ATATTTTA
11524349 TCTAGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (9 bp):
ATATTTTAG
Found at i:11534830 original size:6 final size:6
Alignment explanation
Indices: 11534821--11534872 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
11534811 TTATTTAATC
* *
11534821 TTAAAT TTAAAT TCAAA- TTAAAT TTAAAC TT-AAT TTAAAT TTAAACT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T
11534868 TTAAA
1 TTAAA
11534873 GGAAAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
5 8 0.21
6 25 0.64
7 6 0.15
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:11534843 original size:17 final size:17
Alignment explanation
Indices: 11534821--11534868 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
11534811 TTATTTAATC
11534821 TTAAATTTAAA-TTCAAA
1 TTAAATTTAAACTT-AAA
*
11534838 TTAAATTTAAACTTAAT
1 TTAAATTTAAACTTAAA
11534855 TTAAATTTAAACTT
1 TTAAATTTAAACTT
11534869 TAAAGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAACTTAAA
Found at i:11534905 original size:17 final size:18
Alignment explanation
Indices: 11534821--11534907 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 18
11534811 TTATTTAATC
11534821 TTAAATTTAAA-TTCAAA-
1 TTAAATTTAAACTT-AAAG
*
11534838 TTAAATTTAAACTT-AAT
1 TTAAATTTAAACTTAAAG
11534855 TTAAATTTAAACTTTAAAGG
1 TTAAATTTAAAC-TTAAA-G
**
11534875 AAAAAAAGTTTAAACTT-AAG
1 --TTAAA-TTTAAACTTAAAG
11534895 TTAAATTTAAACT
1 TTAAATTTAAACT
11534908 CAAAATAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.04
17 31 0.54
18 7 0.12
19 2 0.04
20 1 0.02
21 2 0.04
22 5 0.09
23 7 0.12
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.39
Consensus pattern (18 bp):
TTAAATTTAAACTTAAAG
Found at i:11536449 original size:25 final size:28
Alignment explanation
Indices: 11536391--11536459 Score: 108
Period size: 25 Copynumber: 2.6 Consensus size: 28
11536381 TTTTCACATA
11536391 AAAAATTTCATCCATTTTATTGTCTATT
1 AAAAATTTCATCCATTTTATTGTCTATT
11536419 AAAAATTTCATCCATTTT-TT-T-TATT
1 AAAAATTTCATCCATTTTATTGTCTATT
*
11536444 AAAAATTTCATTCATT
1 AAAAATTTCATCCATT
11536460 ATACTTGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
25 19 0.47
26 1 0.03
27 2 0.05
28 18 0.45
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (28 bp):
AAAAATTTCATCCATTTTATTGTCTATT
Found at i:11537175 original size:28 final size:30
Alignment explanation
Indices: 11537121--11537177 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
11537111 TATTTTGAGA
***
11537121 TTTTCTGATATTTTTTTGCTTTCTATTTAG
1 TTTTCTGATATTTTTTTAAATTCTATTTAG
11537151 TTTTCTGAT-TTTTTTTAAATT-TATTTA
1 TTTTCTGATATTTTTTTAAATTCTATTTA
11537178 AAGAAATAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (30 bp):
TTTTCTGATATTTTTTTAAATTCTATTTAG
Found at i:11538248 original size:25 final size:25
Alignment explanation
Indices: 11538220--11538270 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11538210 TGAGTTGGGG
11538220 AGGGGAGAGATTATAAGTACTTCTA
1 AGGGGAGAGATTATAAGTACTTCTA
11538245 AGGGGAGAGATTATAAGTACTTCTA
1 AGGGGAGAGATTATAAGTACTTCTA
11538270 A
1 A
11538271 CCATTAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.27
Consensus pattern (25 bp):
AGGGGAGAGATTATAAGTACTTCTA
Found at i:11538906 original size:25 final size:26
Alignment explanation
Indices: 11538867--11538915 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
11538857 ACAAAATTGA
*
11538867 TAAAAAAAATTAT-AAATTTTAAAGG
1 TAAAAAAAATCATAAAATTTTAAAGG
*
11538892 TAAAAAAAGTCATAAAATTTTAAA
1 TAAAAAAAATCATAAAATTTTAAA
11538916 ATCCGATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (26 bp):
TAAAAAAAATCATAAAATTTTAAAGG
Found at i:11541100 original size:18 final size:19
Alignment explanation
Indices: 11541067--11541102 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11541057 TAACCTTCAT
11541067 TTTTAAAATATTCATTTTC
1 TTTTAAAATATTCATTTTC
*
11541086 TTTTAAACT-TTCATTTT
1 TTTTAAAATATTCATTTT
11541103 AAATTATGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAAATATTCATTTTC
Found at i:11541923 original size:13 final size:13
Alignment explanation
Indices: 11541907--11541932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11541897 TTTAAAAATT
11541907 TTATTTAATTAAA
1 TTATTTAATTAAA
11541920 TTATTTAATTAAA
1 TTATTTAATTAAA
11541933 GATTTATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTAATTAAA
Found at i:11544338 original size:16 final size:16
Alignment explanation
Indices: 11544317--11544349 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11544307 TACTAACTTG
11544317 AGAAGTTGACTCTGTT
1 AGAAGTTGACTCTGTT
11544333 AGAAGTTGACTCTGTT
1 AGAAGTTGACTCTGTT
11544349 A
1 A
11544350 TAGATACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (16 bp):
AGAAGTTGACTCTGTT
Found at i:11551608 original size:6 final size:6
Alignment explanation
Indices: 11551597--11551657 Score: 50
Period size: 6 Copynumber: 9.3 Consensus size: 6
11551587 CTCCTACATA
* * *
11551597 TATTTT TATTTT TATTTT ATATTGTT TCAAGTTT TACTTT TATTTT TAATTAT
1 TATTTT TATTTT TATTTT -TATT-TT T--ATTTT TATTTT TATTTT T-ATTTT
11551650 TATTTT TA
1 TATTTT TA
11551658 ACATGTTAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
6 28 0.62
7 10 0.22
8 5 0.11
9 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (6 bp):
TATTTT
Found at i:11564102 original size:2 final size:2
Alignment explanation
Indices: 11564097--11564153 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
11564087 TACATTATAA
11564097 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11564139 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
11564154 CAACTTATTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:11567716 original size:2 final size:2
Alignment explanation
Indices: 11567709--11567734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11567699 CAAAGCATAA
11567709 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
11567735 TATTGTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11571678 original size:20 final size:20
Alignment explanation
Indices: 11571653--11571690 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11571643 ATAGTCAATT
11571653 AGAAAAGAAAAAGAAACAAA
1 AGAAAAGAAAAAGAAACAAA
11571673 AGAAAAGAAAAAGAAACA
1 AGAAAAGAAAAAGAAACA
11571691 TACTCATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAAGAAACAAA
Found at i:11581838 original size:17 final size:18
Alignment explanation
Indices: 11581812--11581851 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
11581802 ACTTTACATG
*
11581812 TAATATATAATATTTTAA
1 TAATAAATAATATTTTAA
*
11581830 -AATAAATAATTTTTTAA
1 TAATAAATAATATTTTAA
11581847 TAATA
1 TAATA
11581852 TATTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAAATAATATTTTAA
Found at i:11582018 original size:24 final size:24
Alignment explanation
Indices: 11581986--11582035 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
11581976 TTTTTAGTAA
11581986 AACTCTTAAATTCCATCAAACAAT
1 AACTCTTAAATTCCATCAAACAAT
11582010 AACTCTTAAATTCCATCAAACAAT
1 AACTCTTAAATTCCATCAAACAAT
11582034 AA
1 AA
11582036 TTATAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (24 bp):
AACTCTTAAATTCCATCAAACAAT
Found at i:11583469 original size:17 final size:17
Alignment explanation
Indices: 11583439--11583472 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11583429 AATTTTATCA
**
11583439 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
11583456 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
11583473 AAAATTATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:11583520 original size:31 final size:29
Alignment explanation
Indices: 11583459--11583520 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
11583449 TAAAAATTTT
*
11583459 AAATTAATAAAAATAAAATTATGTTTTAA
1 AAATTAATAAAAATAAAATTATATTTTAA
* *
11583488 AAATTAATAAAAATCTAATTTAATATTTTAA
1 AAATTAATAAAAAT-AAAATT-ATATTTTAA
11583519 AA
1 AA
11583521 CTATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.50
30 4 0.14
31 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
AAATTAATAAAAATAAAATTATATTTTAA
Found at i:11585824 original size:27 final size:27
Alignment explanation
Indices: 11585789--11585851 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
11585779 AGTAAAAATA
*
11585789 TATAGAAATATTTAT-AAATTCAAAATTT
1 TATA-AAATATTTATAAAATT-AAAATGT
*
11585817 TATAAAAT-CTTATAAAATTAAAATGT
1 TATAAAATATTTATAAAATTAAAATGT
11585843 T-TAAAATAT
1 TATAAAATAT
11585852 AGAAATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 6 0.20
26 11 0.37
27 9 0.30
28 4 0.13
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (27 bp):
TATAAAATATTTATAAAATTAAAATGT
Found at i:11607840 original size:37 final size:37
Alignment explanation
Indices: 11607790--11607861 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
11607780 AAGATTATTA
*
11607790 GGAGAAAGTAGAAATCTGTGGAAATACCTGTGGATTT
1 GGAGAAAGTAGAAATCCGTGGAAATACCTGTGGATTT
*
11607827 GGAGAAAGTAGAAATCCGTGGAAATACTTGTGGAT
1 GGAGAAAGTAGAAATCCGTGGAAATACCTGTGGAT
11607862 ATTTTCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.25
Consensus pattern (37 bp):
GGAGAAAGTAGAAATCCGTGGAAATACCTGTGGATTT
Found at i:11608476 original size:17 final size:17
Alignment explanation
Indices: 11608456--11608488 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11608446 TTTATACAAA
11608456 ATTTGTTATT-ATATTTT
1 ATTT-TTATTGATATTTT
11608473 ATTTTTATTGATATTT
1 ATTTTTATTGATATTT
11608489 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
ATTTTTATTGATATTTT
Found at i:11614845 original size:79 final size:79
Alignment explanation
Indices: 11614714--11614867 Score: 290
Period size: 79 Copynumber: 1.9 Consensus size: 79
11614704 GAGTAAACCC
*
11614714 ATGGATAGAAAGATAAGTTTTCAATTGAACCATTTGAGATATAAATCCTAATAAACTCAATTAAT
1 ATGGATAGAAAGATAAGTTTCCAATTGAACCATTTGAGATATAAATCCTAATAAACTCAATTAAT
11614779 GTCTCTAATCACCG
66 GTCTCTAATCACCG
*
11614793 ATGGATAGAAAGATAAGTTTCCAATTGAATCATTTGAGATATAAATCCTAATAAACTCAATTAAT
1 ATGGATAGAAAGATAAGTTTCCAATTGAACCATTTGAGATATAAATCCTAATAAACTCAATTAAT
11614858 GTCTCTAATC
66 GTCTCTAATC
11614868 TACCATCCAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (79 bp):
ATGGATAGAAAGATAAGTTTCCAATTGAACCATTTGAGATATAAATCCTAATAAACTCAATTAAT
GTCTCTAATCACCG
Found at i:11616418 original size:18 final size:20
Alignment explanation
Indices: 11616382--11616425 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
11616372 TAATAGTTGG
11616382 TATATAATATACTACTATTA
1 TATATAATATACTACTATTA
*
11616402 TATATAAT-TATTA-TATTA
1 TATATAATATACTACTATTA
11616420 TA-ATAA
1 TATATAA
11616426 AAATATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 4 0.17
20 8 0.35
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAATATACTACTATTA
Done.