Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 32 of 335
Found at i:11715180 original size:3 final size:3
Alignment explanation
Indices: 11715172--11715208 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
11715162 TGGTTTAACC
11715172 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11715209 TGAATTCGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11715678 original size:39 final size:39
Alignment explanation
Indices: 11715624--11715702 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
11715614 TGTGCACGGA
11715624 AACAAACCGTACGCTAAGTATACACCCAGTGGTATTTCT
1 AACAAACCGTACGCTAAGTATACACCCAGTGGTATTTCT
11715663 AACAAACCGTACGCTAAGTATACACCCAGTGGTATTTCT
1 AACAAACCGTACGCTAAGTATACACCCAGTGGTATTTCT
11715702 A
1 A
11715703 TAATTCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (39 bp):
AACAAACCGTACGCTAAGTATACACCCAGTGGTATTTCT
Found at i:11717116 original size:46 final size:46
Alignment explanation
Indices: 11717066--11717240 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
11717056 TGGTTGAGCA
11717066 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
11717112 TCCGAACTCGTTGAGTTGAGTCCGAGTT--GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
11717156 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
11717204 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11717241 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
44 3 0.03
45 2 0.02
46 88 0.81
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:11717220 original size:92 final size:92
Alignment explanation
Indices: 11717063--11717231 Score: 304
Period size: 92 Copynumber: 1.8 Consensus size: 92
11717053 GGATGGTTGA
*
11717063 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
11717128 TGAGTCCGAGTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTGTGAGATGTAACTAG
*
11717155 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
11717219 TTGAGTCCGAGTT
65 TTGAGTCCGAGTT
11717232 CGCTTATGGG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 2 0.03
92 72 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTGTGAGATGTAACTAG
Found at i:11718629 original size:13 final size:14
Alignment explanation
Indices: 11718605--11718637 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
11718595 TAAAATCATT
11718605 ATTTCATATATTTC
1 ATTTCATATATTTC
11718619 ATTTC-TATATTTC
1 ATTTCATATATTTC
*
11718632 AATTCA
1 ATTTCA
11718638 ATAACTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTCATATATTTC
Found at i:11719949 original size:5 final size:5
Alignment explanation
Indices: 11719936--11719990 Score: 55
Period size: 5 Copynumber: 11.6 Consensus size: 5
11719926 TTTACTTTAC
* *
11719936 TATATA TATAA TAT-A -ATAA TATAA TATAA AAT-A TATAA TAAAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
11719984 TA-AA TAT
1 TATAA TAT
11719991 CTTTATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
3 2 0.05
4 9 0.22
5 26 0.63
6 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:11719962 original size:22 final size:20
Alignment explanation
Indices: 11719937--11719990 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
11719927 TTACTTTACT
*
11719937 ATATATATAATATAATAATATA
1 ATATA-ATAATAT-ATAATAAA
11719959 ATATAA-AATATATAATAAA
1 ATATAATAATATATAATAAA
11719978 ATATAATAA-ATAT
1 ATATAATAATATAT
11719991 CTTTATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 17 0.57
20 7 0.23
21 1 0.03
22 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAATAATATATAATAAA
Found at i:11728389 original size:1 final size:1
Alignment explanation
Indices: 11728383--11728413 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
11728373 CTCATTAACC
11728383 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11728414 CAGCTACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11731015 original size:8 final size:7
Alignment explanation
Indices: 11730986--11731017 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
11730976 AGGATGGAAA
11730986 TTAAATT
1 TTAAATT
11730993 TTAAATT
1 TTAAATT
11731000 TTAAATT
1 TTAAATT
*
11731007 TTAAAAT
1 TTAAATT
11731014 TTAA
1 TTAA
11731018 TAATTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TTAAATT
Found at i:11731093 original size:30 final size:30
Alignment explanation
Indices: 11731025--11731101 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
11731015 TAATAATTAT
* * *
11731025 TATTTTTA-TAATTTAAAAGAAATAAATTA
1 TATTTTTATTATTTTTAAAGAAATAAAATA
*
11731054 -ATTTTTTATTATTTTTAAAGAGATAAAATA
1 TA-TTTTTATTATTTTTAAAGAAATAAAATA
11731084 TATTTTTATT-TTTATTAA
1 TATTTTTATTATTT-TTAA
11731102 TTTAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 9 0.22
30 29 0.73
31 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
TATTTTTATTATTTTTAAAGAAATAAAATA
Found at i:11733247 original size:2 final size:2
Alignment explanation
Indices: 11733240--11733264 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11733230 AGGATTTACA
11733240 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11733265 CGGTTTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11747998 original size:13 final size:13
Alignment explanation
Indices: 11747980--11748006 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11747970 TTTTACCTAA
11747980 ATTTTCAATTTTT
1 ATTTTCAATTTTT
11747993 ATTTTCAATTTTT
1 ATTTTCAATTTTT
11748006 A
1 A
11748007 CCGATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTCAATTTTT
Found at i:11757585 original size:3 final size:3
Alignment explanation
Indices: 11757577--11757629 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
11757567 AGGTTGTTAA
11757577 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
11757625 TTC TT
1 TTC TT
11757630 TTTAAAGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:11774701 original size:12 final size:13
Alignment explanation
Indices: 11774684--11774712 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11774674 AGGTTTTGAA
11774684 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
11774696 AAAAATAAAAAAT
1 AAAAATAAAAAAT
11774709 AAAA
1 AAAA
11774713 TTTACAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:11775849 original size:17 final size:17
Alignment explanation
Indices: 11775800--11775854 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
11775790 TTTAGCGTTG
*
11775800 ATTATATTACAAAATTTT
1 ATTAT-TTATAAAATTTT
*
11775818 -CTATTT-TAAATATTTT
1 ATTATTTATAAA-ATTTT
11775834 ATTATTTATAAAA-TTT
1 ATTATTTATAAAATTTT
11775850 ATTAT
1 ATTAT
11775855 GTTTATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.10
16 15 0.48
17 9 0.29
18 4 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTTATAAAATTTT
Found at i:11777269 original size:29 final size:26
Alignment explanation
Indices: 11777217--11777270 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
11777207 TTAATTAGGT
*
11777217 ATTTGAAATTTTAATTTTTTATTAAA
1 ATTTGAAATTTTAAATTTTTATTAAA
11777243 ATTTGATAATTTTTATAATTTTTATTAA
1 ATTTGA-AA-TTTTA-AATTTTTATTAA
11777271 TTTTTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 5 0.21
29 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
ATTTGAAATTTTAAATTTTTATTAAA
Found at i:11777271 original size:10 final size:10
Alignment explanation
Indices: 11777227--11777278 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
11777217 ATTTGAAATT
11777227 TTAATTTTTTA
1 TTAA-TTTTTA
* *
11777238 TTAAAATTTGA
1 TT-AATTTTTA
11777249 -TAATTTTTA
1 TTAATTTTTA
11777258 -TAATTTTTA
1 TTAATTTTTA
11777267 TTAATTTTTA
1 TTAATTTTTA
11777277 TT
1 TT
11777279 GTTATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 15 0.43
10 12 0.34
11 6 0.17
12 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TTAATTTTTA
Found at i:11777294 original size:14 final size:15
Alignment explanation
Indices: 11777268--11777298 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11777258 TAATTTTTAT
11777268 TAATTTTTATTGTTA
1 TAATTTTTATTGTTA
11777283 TAATTTTT-TTGTTA
1 TAATTTTTATTGTTA
11777297 TA
1 TA
11777299 TATCACATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TAATTTTTATTGTTA
Found at i:11783440 original size:6 final size:6
Alignment explanation
Indices: 11783426--11783460 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
11783416 GTAGTTGTTG
* *
11783426 TCATGA TCATTA TCATTA TCATTA TAATTA TCATT
1 TCATTA TCATTA TCATTA TCATTA TCATTA TCATT
11783461 TAGCCCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (6 bp):
TCATTA
Found at i:11794399 original size:23 final size:24
Alignment explanation
Indices: 11794373--11794419 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
11794363 AAAAGCTAAC
*
11794373 TACAAAATTAAATC-TCTAAGATT
1 TACAAAATCAAATCTTCTAAGATT
*
11794396 TACAGAATCAAATCTTCTAAGATT
1 TACAAAATCAAATCTTCTAAGATT
11794420 ATAAATCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (24 bp):
TACAAAATCAAATCTTCTAAGATT
Found at i:11797007 original size:29 final size:30
Alignment explanation
Indices: 11796951--11797013 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
11796941 GATTAGACTA
** *
11796951 AAATTTTTAAATTTAAAAAGTAGGAGGATT
1 AAATTTTTAAATTTAAAAAGTAAAAGGATC
* *
11796981 AAATTTTTAACTTT-TAAAGTAAAAGGATC
1 AAATTTTTAAATTTAAAAAGTAAAAGGATC
11797010 AAAT
1 AAAT
11797014 CTAAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.37
Consensus pattern (30 bp):
AAATTTTTAAATTTAAAAAGTAAAAGGATC
Found at i:11800631 original size:5 final size:6
Alignment explanation
Indices: 11800617--11800642 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11800607 TTTTGGTTTA
11800617 TTTTGT TTTTGT TTTTGT TTTTGT TT
1 TTTTGT TTTTGT TTTTGT TTTTGT TT
11800643 AATTAAATAG
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:11802958 original size:15 final size:15
Alignment explanation
Indices: 11802938--11802979 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11802928 AATTGATTTA
11802938 TTAATTATTTAAATT
1 TTAATTATTTAAATT
*
11802953 TTAATT-TGTAAATT
1 TTAATTATTTAAATT
11802967 TATAA-TATTTAAA
1 T-TAATTATTTAAA
11802980 ATTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAATTATTTAAATT
Found at i:11806267 original size:2 final size:2
Alignment explanation
Indices: 11806260--11806285 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11806250 AATTAAAACT
11806260 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
11806286 ACTACCATTC
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):
TA
Found at i:11806829 original size:21 final size:21
Alignment explanation
Indices: 11806797--11806837 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11806787 TCATAAAGTT
11806797 TGTTTATATTTTAATTAATCA
1 TGTTTATATTTTAATTAATCA
11806818 TGTTT-TAGTTTTAATTAATC
1 TGTTTATA-TTTTAATTAATC
11806838 TTAATTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (21 bp):
TGTTTATATTTTAATTAATCA
Found at i:11806845 original size:21 final size:20
Alignment explanation
Indices: 11806803--11806862 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
11806793 AGTTTGTTTA
* **
11806803 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
11806823 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
11806844 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
11806863 GTTTTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:11826870 original size:39 final size:39
Alignment explanation
Indices: 11826825--11826907 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
11826815 ATTATTAAAT
11826825 TGACATTAAAAATAATTTATTATATTACTAATCACTATG
1 TGACATTAAAAATAATTTATTATATTACTAATCACTATG
11826864 TGACATTAAAAATAATTTATTATATTACTAATCACTATG
1 TGACATTAAAAATAATTTATTATATTACTAATCACTATG
11826903 TGACA
1 TGACA
11826908 ATAATTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (39 bp):
TGACATTAAAAATAATTTATTATATTACTAATCACTATG
Found at i:11829744 original size:11 final size:11
Alignment explanation
Indices: 11829730--11829765 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
11829720 TTCAGCTGAT
11829730 GAAAATGAAGA
1 GAAAATGAAGA
11829741 GAAAATGAAGA
1 GAAAATGAAGA
11829752 GAAAATGAAGA
1 GAAAATGAAGA
11829763 GAA
1 GAA
11829766 TTCTAGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:11830091 original size:147 final size:144
Alignment explanation
Indices: 11829874--11830168 Score: 394
Period size: 147 Copynumber: 2.0 Consensus size: 144
11829864 TTGCTGCTTA
* * * *
11829874 AAATATCTATTTTGGGATTATTTTCACTTTAGGTCCTTCATCATTTGACAATTGAGCTATTTAAT
1 AAATATCTACTTTGGGATTATTTACACTTTAGGTCCTTCATCATTTGAAAATTGAGCTATTCAAT
* * *
11829939 CCTTCTAGCAACTTTTACACCTTTTTTTTTAATTTAGTCTTTTTTATTTAATTAATCACCCGAAC
66 CCTTCTAGCAACTTTTACA-C--TTTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAAC
11830004 GTCAAAATTTTCTAACG
128 GTCAAAATTTTCTAACG
* * * * *
11830021 AAATATCTCCTTTGGGCTTATTTACCCTTTAGGTTCTTTC-TCATTTGAAAATTGAGCTATTCGA
1 AAATATCTACTTTGGGATTATTTACACTTTAGG-TCCTTCATCATTTGAAAATTGAGCTATTCAA
* * * *
11830085 TTCTTCTATCAGCTTTTACACTTTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACTT
65 TCCTTCTAGCAACTTTTACACTTTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACGT
*
11830150 CAAAATTTTCTAAGG
130 CAAAATTTTCTAACG
11830165 AAAT
1 AAAT
11830169 TTTAATACTA
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
144 58 0.45
146 1 0.01
147 66 0.51
148 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.46
Consensus pattern (144 bp):
AAATATCTACTTTGGGATTATTTACACTTTAGGTCCTTCATCATTTGAAAATTGAGCTATTCAAT
CCTTCTAGCAACTTTTACACTTTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACGTC
AAAATTTTCTAACG
Found at i:11831118 original size:2 final size:2
Alignment explanation
Indices: 11831111--11831136 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11831101 AATTTGTTTG
11831111 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
11831137 TGAATTATTA
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:11833552 original size:7 final size:7
Alignment explanation
Indices: 11833540--11833575 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
11833530 CAATCTTCTT
11833540 ACACTTC
1 ACACTTC
11833547 ACACTTC
1 ACACTTC
11833554 ACACTTC
1 ACACTTC
11833561 ACACTTC
1 ACACTTC
11833568 ACACTTC
1 ACACTTC
11833575 A
1 A
11833576 TGATTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.28
Consensus pattern (7 bp):
ACACTTC
Found at i:11848613 original size:14 final size:14
Alignment explanation
Indices: 11848594--11848623 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11848584 TTATATCGAG
11848594 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
11848608 ACCAATCCAATTCA
1 ACCAATCCAAATCA
11848622 AC
1 AC
11848624 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:11850333 original size:30 final size:30
Alignment explanation
Indices: 11850297--11850387 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
11850287 TATGAGAAAC
11850297 TAGACTCAATAAGCTTTAATTCCATATTTT
1 TAGACTCAATAAGCTTTAATTCCATATTTT
11850327 TAGACTCAATAAGCTTTAATTCCATATTTT
1 TAGACTCAATAAGCTTTAATTCCATATTTT
*
11850357 TAGACTCAATAAGCTTTAATTCTATATTTT
1 TAGACTCAATAAGCTTTAATTCCATATTTT
11850387 T
1 T
11850388 TTCATCTTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (30 bp):
TAGACTCAATAAGCTTTAATTCCATATTTT
Found at i:11851991 original size:131 final size:132
Alignment explanation
Indices: 11851841--11852445 Score: 442
Period size: 131 Copynumber: 4.6 Consensus size: 132
11851831 GACAAGATTT
11851841 GATATTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
1 GATATTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
* * * * *
11851906 TAATCGAATATCATTTCAAAATTTCACTCATGTCTTTTAAAAATCCCTTA-AACGAAGGCGAT-G
66 TAATCGAATATCACTTCAAAATTTCACTCAGGTCTTCTAAAAATCCCTTAGAACGAAGGCAATAC
11851969 TGC
131 T-C
* * *
11851972 GATATTTGGCAATTCGCGGAATCGTACCCTAACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAA
1 GATATTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
* * *
11852037 TAATCAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAGAACGAAGGCAATAC
66 TAATCGAATATCACTTCAAAATTTCACTCAGGTCTTCTAAAAATCCCTTAGAACGAAGGCAATAC
11852102 TC
131 TC
* * * * ** ** **
11852104 GGTGTTTGACAATTTG-GGAATCATGCCCTATTGTGCTGGGTTGTGATTTCTTGTTTGCTCAAAA
1 GATATTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
* * * *** * * * * *
11852168 CAATTGAATATTC-CTTTAGGTTTTCACTCATGT-TTATTAAAAA-CCTTTCAAAACAAAGG--A
66 TAATCGAATA-TCACTTCAAAATTTCACTCAGGTCTT-CTAAAAATCCCTT-AGAACGAAGGCAA
**
11852228 TGTTC
128 TACTC
** *** * * * ** ** * * *
11852233 GAGGTTTGGTGATTTG-AGAATCGTGCCCTATCGTGCTGGGTTGCGCTTTTTCATTTGTTCTAAA
1 GATATTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
** * * * ** * * * * *
11852297 CGATCCAAGATCCCTTCGTAATTTCACTCACGTTTTCTAAAAA-CCCTTTAAAACGAAAGAAATA
66 TAATCGAATATCACTTCAAAATTTCACTCAGGTCTTCTAAAAATCCC-TTAGAACGAAGGCAATA
*
11852361 TTC
130 CTC
* * * * * *
11852364 AATGTTTGACAATTCAG-GGAATAGTACCCTATCGTGCTGGGTTGCAATTTTC-CGTTTGTTCAA
1 GATATTTGACAATTC-GCGGAATCGTGCCCTAACGTGCTGGGTTGCAA-TTTCGCGTTTGCTCAA
*
11852427 AATAATCGAATATCTCTTC
64 AATAATCGAATATCACTTC
11852446 GGAGTTTCAC
Statistics
Matches: 376, Mismatches: 86, Indels: 23
0.78 0.18 0.05
Matches are distributed among these distances:
128 2 0.01
129 89 0.24
130 11 0.03
131 195 0.52
132 75 0.20
133 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (132 bp):
GATATTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAA
TAATCGAATATCACTTCAAAATTTCACTCAGGTCTTCTAAAAATCCCTTAGAACGAAGGCAATAC
TC
Found at i:11858907 original size:48 final size:48
Alignment explanation
Indices: 11858849--11858945 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
11858839 CTAAAAAGAA
11858849 AGAATATTCAAACCTTGAAAAAGAATAGACAAACTTAAAAGGTTACCG
1 AGAATATTCAAACCTTGAAAAAGAATAGACAAACTTAAAAGGTTACCG
11858897 AGAATATTCAAACCTTGAAAAAGAATAGACAAACTTAAAAGGTTACCG
1 AGAATATTCAAACCTTGAAAAAGAATAGACAAACTTAAAAGGTTACCG
11858945 A
1 A
11858946 TTAAATCAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (48 bp):
AGAATATTCAAACCTTGAAAAAGAATAGACAAACTTAAAAGGTTACCG
Found at i:11866009 original size:72 final size:73
Alignment explanation
Indices: 11865919--11866060 Score: 191
Period size: 72 Copynumber: 2.0 Consensus size: 73
11865909 TATTTAAGTT
* ** * *
11865919 TTTTTTACTAAATTAATATTTAAATGTTATTTTGTGTTAATTTA-CTAAATTAAAT-TAAAAATA
1 TTTTTTACCAAATTAATATTTAAATACTATTTTATATTAATTTATC-AAATT-AATCTAAAAATA
11865982 TTATCAAATA
64 TTATCAAATA
*
11865992 TTTTTTACCAAA-TAATATTTAGATACTATTTTATATTAATTTATCAAATTAATCTAAAAATATT
1 TTTTTTACCAAATTAATATTTAAATACTATTTTATATTAATTTATCAAATTAATCTAAAAATATT
11866056 ATCAA
66 ATCAA
11866061 TTTTGATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 3 0.05
72 46 0.75
73 12 0.20
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (73 bp):
TTTTTTACCAAATTAATATTTAAATACTATTTTATATTAATTTATCAAATTAATCTAAAAATATT
ATCAAATA
Found at i:11869354 original size:15 final size:16
Alignment explanation
Indices: 11869336--11869367 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11869326 AATATCGTGA
11869336 TTTTTAATA-AATATT
1 TTTTTAATATAATATT
11869351 TTTTTAATATAATATT
1 TTTTTAATATAATATT
11869367 T
1 T
11869368 AAAATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAATATAATATT
Found at i:11874938 original size:12 final size:12
Alignment explanation
Indices: 11874921--11874946 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11874911 TCGTATTTCC
11874921 TTTTAAATTAAT
1 TTTTAAATTAAT
11874933 TTTTAAATTAAT
1 TTTTAAATTAAT
11874945 TT
1 TT
11874947 ATGAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAAATTAAT
Found at i:11880769 original size:33 final size:33
Alignment explanation
Indices: 11880727--11880792 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
11880717 TTTATGTTAC
11880727 GCCATGTTTGGTTGGGGGGAATGGAATAACATT
1 GCCATGTTTGGTTGGGGGGAATGGAATAACATT
11880760 GCCATGTTTGGTTGGGGGGAATGGAATAACATT
1 GCCATGTTTGGTTGGGGGGAATGGAATAACATT
11880793 CTCCTCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.36, T:0.30
Consensus pattern (33 bp):
GCCATGTTTGGTTGGGGGGAATGGAATAACATT
Found at i:11882407 original size:18 final size:19
Alignment explanation
Indices: 11882369--11882409 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
11882359 TGGTTCGTGT
11882369 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
11882388 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
11882406 TTTC
1 TTTC
11882410 TCATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:11882599 original size:39 final size:38
Alignment explanation
Indices: 11882532--11882665 Score: 99
Period size: 39 Copynumber: 3.4 Consensus size: 38
11882522 ACCAATATGG
* * *
11882532 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
11882571 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
11882609 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
11882650 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
11882666 AACTCGAGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:11882932 original size:18 final size:19
Alignment explanation
Indices: 11882906--11882944 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
11882896 TTTCAATTCA
11882906 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
11882925 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
11882943 AT
1 AT
11882945 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:11884260 original size:5 final size:5
Alignment explanation
Indices: 11884250--11884286 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
11884240 TTATGTTTAT
11884250 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
11884287 TAAAACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:11885180 original size:27 final size:27
Alignment explanation
Indices: 11885142--11885202 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
11885132 ACGCCTGCTA
11885142 GGCACGAAGGCCAGAATACACATCACC
1 GGCACGAAGGCCAGAATACACATCACC
*
11885169 GGCACGAAGGCCCGAATACACATCACC
1 GGCACGAAGGCCAGAATACACATCACC
11885196 GGCACGA
1 GGCACGA
11885203 TGCCTGCTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.34, G:0.25, T:0.07
Consensus pattern (27 bp):
GGCACGAAGGCCAGAATACACATCACC
Found at i:11885230 original size:43 final size:43
Alignment explanation
Indices: 11885169--11885284 Score: 182
Period size: 43 Copynumber: 2.7 Consensus size: 43
11885159 ACACATCACC
* *
11885169 GGCACGAAGGCCCGAATACACATCACCGGCACGATGCCTGCTA
1 GGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGCTA
*
11885212 GGCACGAAGGCCCGAATACACATCACCAGCACGAAGCTTGCTA
1 GGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGCTA
*
11885255 GGCACGAAGGCCCGAATATA-AT-ACCAGCAC
1 GGCACGAAGGCCCGAATACACATCACCAGCAC
11885285 TAGGCCTACG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 8 0.12
42 2 0.03
43 59 0.86
ACGTcount: A:0.32, C:0.33, G:0.24, T:0.11
Consensus pattern (43 bp):
GGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGCTA
Found at i:11885315 original size:38 final size:38
Alignment explanation
Indices: 11885265--11885388 Score: 158
Period size: 38 Copynumber: 3.2 Consensus size: 38
11885255 GGCACGAAGG
* * * *
11885265 CCCGAATATAATACCAGCACTAGGCCTACGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
*
11885303 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
** *
11885341 CCCGGATATTTTACCAGCACGAAGCCTACGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTACGGG-ATTTAA
11885380 GCCCGGATA
1 -CCCGGATA
11885389 CACATCAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
38 62 0.83
39 5 0.07
40 8 0.11
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
Found at i:11886359 original size:2 final size:2
Alignment explanation
Indices: 11886347--11886379 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11886337 CACTTTCAAA
11886347 AT AT A- 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
11886380 TCAACTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11888256 original size:30 final size:30
Alignment explanation
Indices: 11888222--11888283 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
11888212 ACAATAAGAT
11888222 AAATG-CTTCCAAAATAATAAAAAAATTAAC
1 AAATGCCTT-CAAAATAATAAAAAAATTAAC
* *
11888252 AAATGCCTTTAAAATAATAAGAAAATTAAC
1 AAATGCCTTCAAAATAATAAAAAAATTAAC
11888282 AA
1 AA
11888284 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATGCCTTCAAAATAATAAAAAAATTAAC
Found at i:11888779 original size:26 final size:27
Alignment explanation
Indices: 11888748--11888833 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 27
11888738 GTTAAGAATG
*
11888748 TTATTAAATTTTATTTAATAGTAATTA
1 TTATTAAATTATATTTAATAGTAATTA
* * * *
11888775 -TATTAAAATATAATTAA-ATTATTTA
1 TTATTAAATTATATTTAATAGTAATTA
* *
11888800 TTATTAAATTATATTTAATAAT-ATTC
1 TTATTAAATTATATTTAATAGTAATTA
11888826 TTATTAAA
1 TTATTAAA
11888834 ATTTAGTAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
25 6 0.13
26 39 0.83
27 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAGTAATTA
Found at i:11890570 original size:17 final size:16
Alignment explanation
Indices: 11890528--11890570 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
11890518 TTGATCTGTC
11890528 AAATTGAAAATATGCTT
1 AAATT-AAAATATGCTT
11890545 AAATATAAAATATGCTAT
1 AAAT-TAAAATATGCT-T
*
11890563 GAATTAAA
1 AAATTAAA
11890571 TAATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (16 bp):
AAATTAAAATATGCTT
Found at i:11910492 original size:35 final size:35
Alignment explanation
Indices: 11910446--11910515 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
11910436 TATAGAACCA
11910446 AAACCAAACCCTTTTCTCCTAGTTTTACCAAACTT
1 AAACCAAACCCTTTTCTCCTAGTTTTACCAAACTT
11910481 AAACCAAACCCTTTTCTCCTAGTTTTACCAAACTT
1 AAACCAAACCCTTTTCTCCTAGTTTTACCAAACTT
11910516 CTACGAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.34
Consensus pattern (35 bp):
AAACCAAACCCTTTTCTCCTAGTTTTACCAAACTT
Found at i:11920762 original size:18 final size:18
Alignment explanation
Indices: 11920741--11920777 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11920731 AACAATTAGG
11920741 AACTTGATAAAAATTTAA
1 AACTTGATAAAAATTTAA
11920759 AACTTGATAAAAATTTAA
1 AACTTGATAAAAATTTAA
11920777 A
1 A
11920778 CATTTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AACTTGATAAAAATTTAA
Found at i:11924374 original size:232 final size:235
Alignment explanation
Indices: 11923923--11924405 Score: 839
Period size: 232 Copynumber: 2.1 Consensus size: 235
11923913 CCATATCAAT
* *
11923923 AATAC-AAAAGTTCATCTATGAGAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACAGAA
1 AATACTAAAACTTAATCTATGAGAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACAGAA
11923987 AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTT
66 AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTT
11924052 TCACTAAATATTTTTTTTCTTAAAAATCGGGAAAGGGGAGAACTTCCAGCGATGTGCAGAAAATC
131 TCACTAAATATTTTTTTTCTTAAAAATCGGGAAAGGGGAGAACTTCCAGCGATGTGCAGAAAATC
11924117 TTCAGATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
196 TTCAGATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
* * *
11924157 AATACTAAAATTTAATCTATGAGAATTAGCTAGAGTACAGTAATAGATAAAAACTAATTACATAA
1 AATACTAAAACTTAATCTATGAGAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACAGAA
11924222 AAATCAGTCTAAAAG-A-AGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTT
66 AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTT
* * * * *
11924285 TCACTAAATA-TTTTTTTCTTAAATATGGGGGAAGGGGAGGACTTCCAGCGATGTGTAGAAAATC
131 TCACTAAATATTTTTTTTCTTAAAAATCGGGAAAGGGGAGAACTTCCAGCGATGTGCAGAAAATC
*
11924349 TTCAGATGTTGCTACTGCCGACAAGTTCTTCCAATATGTA
196 TTCAGATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
11924389 AATACTAAAACTTAATC
1 AATACTAAAACTTAATC
11924406 GTGAAGTATA
Statistics
Matches: 237, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
232 104 0.44
233 57 0.24
234 6 0.03
235 70 0.30
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (235 bp):
AATACTAAAACTTAATCTATGAGAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACAGAA
AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTT
TCACTAAATATTTTTTTTCTTAAAAATCGGGAAAGGGGAGAACTTCCAGCGATGTGCAGAAAATC
TTCAGATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
Found at i:11928209 original size:68 final size:70
Alignment explanation
Indices: 11928122--11928251 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 70
11928112 TAAAAATATT
* *
11928122 AAATTTTATATAAACTTACAAAAA-ATATGTATAAAA-TCAT-AACAACTTATAAATATTATAAA
1 AAATTTTATATAAACTTACAAAAATA-AT-AAAAAAATTCATCAA-AACTTATAAATATTATAAA
11928184 CCCTATAA
63 CCCTATAA
*
11928192 AAATTTTA-ATAAA-TTACAAAAATAATAAAAAAATTCATCAAAATTTATAAATATTATAAA
1 AAATTTTATATAAACTTACAAAAATAATAAAAAAATTCATCAAAACTTATAAATATTATAAA
11928252 AACTTATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
67 5 0.09
68 33 0.61
69 8 0.15
70 8 0.15
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (70 bp):
AAATTTTATATAAACTTACAAAAATAATAAAAAAATTCATCAAAACTTATAAATATTATAAACCC
TATAA
Found at i:11928260 original size:10 final size:9
Alignment explanation
Indices: 11928154--11928261 Score: 54
Period size: 9 Copynumber: 11.2 Consensus size: 9
11928144 AAATATGTAT
*
11928154 AAAATCATA
1 AAAATTATA
*
11928163 ACAACTTATA
1 A-AAATTATA
*
11928173 AATATTATA
1 AAAATTATA
***
11928182 AACCCTATA
1 AAAATTATA
*
11928191 AAAATTTTA
1 AAAATTATA
*
11928200 ATAAATTACA
1 A-AAATTATA
*
11928210 AAAATAATAAA
1 AAAAT--TATA
11928221 AAAATTCATCA
1 AAAATT-AT-A
*
11928232 AAATTTATA
1 AAAATTATA
*
11928241 AATATTATA
1 AAAATTATA
11928250 AAAACTTATA
1 AAAA-TTATA
11928260 AA
1 AA
11928262 TATAAAAAAA
Statistics
Matches: 73, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
9 35 0.48
10 24 0.33
11 14 0.19
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:11928271 original size:19 final size:19
Alignment explanation
Indices: 11928231--11928272 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11928221 AAAATTCATC
* * *
11928231 AAAATTTATAAATATTATA
1 AAAACTTATAAATATAAAA
11928250 AAAACTTATAAATATAAAA
1 AAAACTTATAAATATAAAA
11928269 AAAA
1 AAAA
11928273 TCATACTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAACTTATAAATATAAAA
Found at i:11929943 original size:29 final size:30
Alignment explanation
Indices: 11929877--11929943 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
11929867 TCAAAATTAT
*
11929877 ATATGAATTTTAATTTAATGTGCAACTATAT
1 ATATGAATTTTAATTTAA-GTGCAACTATAC
* *
11929908 ATATGAATTTTAATTTGA-TGCAATTATAC
1 ATATGAATTTTAATTTAAGTGCAACTATAC
*
11929937 ATGTGAA
1 ATATGAA
11929944 ACTCTAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
31 17 0.53
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (30 bp):
ATATGAATTTTAATTTAAGTGCAACTATAC
Found at i:11930162 original size:30 final size:30
Alignment explanation
Indices: 11930126--11930193 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
11930116 GAAATGGATC
11930126 AAAACAAAATTTTATGTATAAAATTGTACA
1 AAAACAAAATTTTATGTATAAAATTGTACA
11930156 AAAACAAAATTTTATGTATAAAATTGTACA
1 AAAACAAAATTTTATGTATAAAATTGTACA
*
11930186 AAATCAAA
1 AAAACAAA
11930194 GTTCATGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAACAAAATTTTATGTATAAAATTGTACA
Found at i:11930202 original size:29 final size:30
Alignment explanation
Indices: 11930126--11930209 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
11930116 GAAATGGATC
* *
11930126 AAAACAAAATTTTATGTATAAAATTGTACA
1 AAAACAAAAGTTCATGTATAAAATTGTACA
* *
11930156 AAAACAAAATTTTATGTATAAAATTGTACA
1 AAAACAAAAGTTCATGTATAAAATTGTACA
* *
11930186 AAATC-AAAGTTCATGTATACAATT
1 AAAACAAAAGTTCATGTATAAAATT
11930210 ACACACAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAACAAAAGTTCATGTATAAAATTGTACA
Found at i:11943143 original size:21 final size:21
Alignment explanation
Indices: 11943102--11943143 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11943092 CTTCCTCCAT
*
11943102 CTCCTCTTCATCAATTTCTTC
1 CTCCTCTTCATCAATTACTTC
11943123 CTCCTCTTCATC-ATATACTTC
1 CTCCTCTTCATCAAT-TACTTC
11943144 TTCTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCTTCATCAATTACTTC
Found at i:11944596 original size:322 final size:322
Alignment explanation
Indices: 11944003--11944645 Score: 1045
Period size: 322 Copynumber: 2.0 Consensus size: 322
11943993 AAATATTAAT
* **
11944003 TAATTTTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAGTTTAATAAAA
1 TAATTCTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAACTTAATAAAA
*
11944068 AATATTAAAATAAACGACAATAGAAAATTTTATTAAATAAAAGGTTGAATAACACCTTATTAATT
66 AATATTAAAATAAACGACAATAAAAAATTTTATTAAATAAAAGGTTGAATAACACCTTATTAATT
* * *
11944133 TTATCATATATCAAAGGTACACACGAAATGTAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
131 CTATCATATATCAAAGGGACACACGAAATATAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
* * *
11944198 GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAACTTGGAAAAGGAAAACAGT
196 GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
* *
11944263 TGATGGATATAA-AAAGAAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTTC
261 TAATAGATATAAGAAA-AAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTTC
* *
11944325 TAATTCTTAATCTCAACGTTTATGTAGTAAACATTAAATTGCGAAATGTAAACAACTTAATAAAA
1 TAATTCTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAACTTAATAAAA
* *
11944390 AATATTGAAATAAACGACAATAAAAAATTTTATTAAATAAAAGGTTGAATAACATCTTATTAATT
66 AATATTAAAATAAACGACAATAAAAAATTTTATTAAATAAAAGGTTGAATAACACCTTATTAATT
* * *
11944455 CTATCATATATCAAAGGGACACACGAAATATAGAATAAAATTTCGAGTTAAGGTTATTGTACTTT
131 CTATCATATATCAAAGGGACACACGAAATATAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
** *
11944520 GTGATAGCAGGGGAATTCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
196 GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
* * *
11944585 TAATAGATATAAGAAAAAATTTGATTAAATGAGGAAGTTTTTACTTACCGGAATTAAGGTT
261 TAATAGATATAAGAAAAAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTT
11944646 GGCGCGGCAT
Statistics
Matches: 295, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
322 292 0.99
323 3 0.01
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (322 bp):
TAATTCTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAACTTAATAAAA
AATATTAAAATAAACGACAATAAAAAATTTTATTAAATAAAAGGTTGAATAACACCTTATTAATT
CTATCATATATCAAAGGGACACACGAAATATAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
TAATAGATATAAGAAAAAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTTC
Found at i:11946201 original size:91 final size:90
Alignment explanation
Indices: 11946046--11946224 Score: 331
Period size: 91 Copynumber: 2.0 Consensus size: 90
11946036 ATCTCAACCG
*
11946046 GGACGTCTTGTCGTAGATACAATTGAAGTCCCCAATGTGTTTTAGACGGAACAGCTTCAGTTCAC
1 GGACGTCCTGTCGTAGATACAATTGAAGTCCCCAATGTGTTTTAGACGGAACAGCTTCAGTTCAC
11946111 TTTTTTTATTTAAATTATCATTCTCT
66 -TTTTTTATTTAAATTATCATTCTCT
*
11946137 GGACGTCCTGTCGTAGATATAATTGAAGTCCCCAATGTGTTTTAGACGGAACAGCTTCAGTTCAC
1 GGACGTCCTGTCGTAGATACAATTGAAGTCCCCAATGTGTTTTAGACGGAACAGCTTCAGTTCAC
11946202 TTTTTTATTTAAATTATCATTCT
66 TTTTTTATTTAAATTATCATTCT
11946225 TTTAAGAGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 23 0.27
91 63 0.73
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (90 bp):
GGACGTCCTGTCGTAGATACAATTGAAGTCCCCAATGTGTTTTAGACGGAACAGCTTCAGTTCAC
TTTTTTATTTAAATTATCATTCTCT
Found at i:11948192 original size:21 final size:21
Alignment explanation
Indices: 11948166--11948210 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
11948156 TCAAGTACAC
11948166 CATTCACAAGAGGCTCCTCAT
1 CATTCACAAGAGGCTCCTCAT
*
11948187 CATTCATAAGAGGCTCCTCAT
1 CATTCACAAGAGGCTCCTCAT
11948208 CAT
1 CAT
11948211 CAATTTGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (21 bp):
CATTCACAAGAGGCTCCTCAT
Found at i:11959644 original size:30 final size:29
Alignment explanation
Indices: 11959581--11959654 Score: 104
Period size: 25 Copynumber: 2.7 Consensus size: 29
11959571 TAAATACAGC
11959581 TAAAAT-ATAACAAAATTAACAAATTCCT
1 TAAAATAATAACAAAATTAACAAATTCCT
11959609 T----TAATAACAAAATTAACAAATTCCTT
1 TAAAATAATAACAAAATTAACAAATTCC-T
11959635 TAAAATAATAACAAAATTAA
1 TAAAATAATAACAAAATTAA
11959655 TAATAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
24 1 0.03
25 21 0.52
26 2 0.05
28 1 0.03
30 15 0.38
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (29 bp):
TAAAATAATAACAAAATTAACAAATTCCT
Found at i:11959707 original size:14 final size:14
Alignment explanation
Indices: 11959688--11959718 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11959678 ATCCAAACAA
11959688 TAACAACAAAATAG
1 TAACAACAAAATAG
*
11959702 TAACAACATAATAG
1 TAACAACAAAATAG
11959716 TAA
1 TAA
11959719 TATGGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:11961260 original size:5 final size:5
Alignment explanation
Indices: 11961248--11961283 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
11961238 GTGATAATGA
*
11961248 CTTTCT CTTCT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTT-T CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
11961284 TTTGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 25 0.89
6 3 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (5 bp):
CTTTT
Found at i:11963236 original size:19 final size:19
Alignment explanation
Indices: 11963212--11963248 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11963202 AACTATTCAA
11963212 TTTTTTTTG-CGTAATGTTT
1 TTTTTTTTGTC-TAATGTTT
11963231 TTTTTTTTGTCTAATGTT
1 TTTTTTTTGTCTAATGTT
11963249 ACATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.11, C:0.05, G:0.14, T:0.70
Consensus pattern (19 bp):
TTTTTTTTGTCTAATGTTT
Found at i:11969560 original size:16 final size:16
Alignment explanation
Indices: 11969541--11969589 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
11969531 ATAGAAGTAA
*
11969541 AAAATCAAAATAAAAC
1 AAAATTAAAATAAAAC
*
11969557 AAAATTAAAATTTAAA-
1 AAAATTAAAA-TAAAAC
*
11969573 AAAATTAAAAAAAAAC
1 AAAATTAAAATAAAAC
11969589 A
1 A
11969590 TAAAGTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 3 0.11
16 20 0.74
17 4 0.15
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATTAAAATAAAAC
Found at i:11970521 original size:14 final size:15
Alignment explanation
Indices: 11970496--11970524 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11970486 GCAAGCCCTT
11970496 TTAATAATAAAAATA
1 TTAATAATAAAAATA
11970511 TTAAT-ATAAAAATA
1 TTAATAATAAAAATA
11970525 AAATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATAATAAAAATA
Found at i:11971042 original size:19 final size:20
Alignment explanation
Indices: 11971004--11971043 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11970994 TTTTATTTTA
*
11971004 TGTTAACATAAATAATAAAT
1 TGTTAACATAAATAAAAAAT
*
11971024 TGTTAA-ATATATAAAAAAT
1 TGTTAACATAAATAAAAAAT
11971043 T
1 T
11971044 TAAACACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
TGTTAACATAAATAAAAAAT
Found at i:11979954 original size:24 final size:23
Alignment explanation
Indices: 11979914--11979959 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
11979904 AATTAAATAT
*
11979914 AAAATATTTTAGTAATATGAAAAA
1 AAAATATTTTAGAAATAT-AAAAA
11979938 AAAATCATTTTA-AAATATAAAA
1 AAAAT-ATTTTAGAAATATAAAA
11979960 GTAACTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATATTTTAGAAATATAAAAA
Found at i:11980737 original size:27 final size:27
Alignment explanation
Indices: 11980682--11980739 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
11980672 AATTTGATTA
* * *
11980682 AAAATTAAGAAATAGAAATAGAAATAG
1 AAAATTAAGAAATAGAAAAAAAAAAAG
11980709 AAAATTAA-AAATAGAGAAAAAAAAAAG
1 AAAATTAAGAAATAGA-AAAAAAAAAAG
11980736 AAAA
1 AAAA
11980740 AATTGCCTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (27 bp):
AAAATTAAGAAATAGAAAAAAAAAAAG
Found at i:11982134 original size:108 final size:108
Alignment explanation
Indices: 11982016--11982233 Score: 436
Period size: 108 Copynumber: 2.0 Consensus size: 108
11982006 TTTAACGCAG
11982016 TTAATTTTTTTATCTAAAAAGTATAACCTAGTAATAGTTTAGATAGAAACAAACTTTTAAATATC
1 TTAATTTTTTTATCTAAAAAGTATAACCTAGTAATAGTTTAGATAGAAACAAACTTTTAAATATC
11982081 AAAATGATAAAATATAGTTGAAGATAAAACCTTGTGTAATTCT
66 AAAATGATAAAATATAGTTGAAGATAAAACCTTGTGTAATTCT
11982124 TTAATTTTTTTATCTAAAAAGTATAACCTAGTAATAGTTTAGATAGAAACAAACTTTTAAATATC
1 TTAATTTTTTTATCTAAAAAGTATAACCTAGTAATAGTTTAGATAGAAACAAACTTTTAAATATC
11982189 AAAATGATAAAATATAGTTGAAGATAAAACCTTGTGTAATTCT
66 AAAATGATAAAATATAGTTGAAGATAAAACCTTGTGTAATTCT
11982232 TT
1 TT
11982234 TCTGAAGTAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (108 bp):
TTAATTTTTTTATCTAAAAAGTATAACCTAGTAATAGTTTAGATAGAAACAAACTTTTAAATATC
AAAATGATAAAATATAGTTGAAGATAAAACCTTGTGTAATTCT
Found at i:11984668 original size:30 final size:31
Alignment explanation
Indices: 11984642--11984700 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
11984632 GTAAATACTC
*
11984642 AAAATTT-AAGGGGTTAA-AGTGTAAATATGA
1 AAAATTTGAA-GGGCTAATAGTGTAAATATGA
11984672 AAAATTTGAAGGGCTAATAGTGTAAATAT
1 AAAATTTGAAGGGCTAATAGTGTAAATAT
11984701 TTTAAAGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.31
Consensus pattern (31 bp):
AAAATTTGAAGGGCTAATAGTGTAAATATGA
Found at i:11984931 original size:28 final size:28
Alignment explanation
Indices: 11984899--11984953 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
11984889 GATGTTGATG
11984899 ATATT-TTATAAT-TATTTAATTAAGATAA
1 ATATTATTATAATAT-TTTAATT-AGATAA
*
11984927 ATATTATTTTAATATTTTAATTAGATA
1 ATATTATTATAATATTTTAATTAGATA
11984954 TTTTACTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 10 0.42
29 13 0.54
30 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (28 bp):
ATATTATTATAATATTTTAATTAGATAA
Found at i:11986722 original size:40 final size:40
Alignment explanation
Indices: 11986637--11986774 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 40
11986627 CTCGAGAATA
* ** *
11986637 TAAAGTGGATAGGATTCGTTAC-TAATTCACTATAATACCT
1 TAAAGTGGATAGGATTTGTT-CTTAATTCACTATGGTAACT
* * *
11986677 CAAAGTGGATAGGATTTGTTCTTGATTCACTATGGTAATT
1 TAAAGTGGATAGGATTTGTTCTTAATTCACTATGGTAACT
** *
11986717 TAAAGTAAATAGGATTTATTCTTAATTCACTATGGTAACT
1 TAAAGTGGATAGGATTTGTTCTTAATTCACTATGGTAACT
* *
11986757 TAAGGCGGATAGGATTTG
1 TAAAGTGGATAGGATTTG
11986775 ACCTGAAAAG
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 78 0.99
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTGTTCTTAATTCACTATGGTAACT
Found at i:11987167 original size:21 final size:21
Alignment explanation
Indices: 11987141--11987180 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11987131 CGAATATGCT
11987141 AACAGAAGCTCGTAAGAGCAG
1 AACAGAAGCTCGTAAGAGCAG
*
11987162 AACAGAAGTTCGTAAGAGC
1 AACAGAAGCTCGTAAGAGC
11987181 TAATCCACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.12
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCAG
Found at i:11999020 original size:3 final size:3
Alignment explanation
Indices: 11999012--11999038 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11999002 AACGGATTGC
11999012 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
11999039 AACAGTAGCT
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12001133 original size:13 final size:13
Alignment explanation
Indices: 12001115--12001140 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12001105 TATCGTTGGT
12001115 TCTGAGATTGAGA
1 TCTGAGATTGAGA
12001128 TCTGAGATTGAGA
1 TCTGAGATTGAGA
12001141 CACCAATGAT
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:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
TCTGAGATTGAGA
Found at i:12007752 original size:15 final size:16
Alignment explanation
Indices: 12007732--12007765 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
12007722 AGTTGAACAT
12007732 TAAAGTTAATTGC-CC
1 TAAAGTTAATTGCACC
12007747 TAAAGTTAATTGCACC
1 TAAAGTTAATTGCACC
12007763 TAA
1 TAA
12007766 TTTTTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (16 bp):
TAAAGTTAATTGCACC
Found at i:12007897 original size:27 final size:27
Alignment explanation
Indices: 12007865--12007925 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
12007855 TTAAATTTTA
*
12007865 ATAAAAAAGTAAAATA-TATAAAAATC
1 ATAAAAAAGTAAAAAATTATAAAAATC
*
12007891 ATAAAAATGTAAAAAATTATAAAAATC
1 ATAAAAAAGTAAAAAATTATAAAAATC
12007918 ATAAAAAA
1 ATAAAAAA
12007926 AATTATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (27 bp):
ATAAAAAAGTAAAAAATTATAAAAATC
Found at i:12007903 original size:8 final size:8
Alignment explanation
Indices: 12007865--12007924 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 8
12007855 TTAAATTTTA
12007865 ATAAAAA-
1 ATAAAAAT
12007872 AGTAAAATAT
1 A-TAAAA-AT
12007882 ATAAAAAT
1 ATAAAAAT
12007890 CATAAAAAT
1 -ATAAAAAT
*
12007899 GTAAAAAATT
1 AT-AAAAA-T
12007909 ATAAAAAT
1 ATAAAAAT
12007917 CATAAAAA
1 -ATAAAAA
12007925 AAATTATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
7 1 0.02
8 9 0.20
9 31 0.70
10 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (8 bp):
ATAAAAAT
Found at i:12007935 original size:9 final size:9
Alignment explanation
Indices: 12007875--12007924 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
12007865 ATAAAAAAGT
12007875 AAAATATATA
1 AAAAT-TATA
*
12007885 AAAATCATA
1 AAAATTATA
12007894 AAAATGTA-A
1 AAAAT-TATA
12007903 AAAATTATA
1 AAAATTATA
*
12007912 AAAATCATA
1 AAAATTATA
12007921 AAAA
1 AAAA
12007925 AAATTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 2 0.06
9 27 0.77
10 6 0.17
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (9 bp):
AAAATTATA
Found at i:12009218 original size:53 final size:53
Alignment explanation
Indices: 12009137--12009287 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
12009127 CTTACACGGT
* *
12009137 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
12009192 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
12009245 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
12009288 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:12010950 original size:57 final size:54
Alignment explanation
Indices: 12010854--12010977 Score: 126
Period size: 57 Copynumber: 2.2 Consensus size: 54
12010844 TTTTACTTTT
* * *
12010854 TTTATAATTTTCTTACGACTTTATAAAAGTTTATAATTTTTTCTATATTTCTATATA
1 TTTATAATTTT-TTACAACTTTATAAAAGTTTATAATTTTTT-AATATTTAT-TATA
* * *
12010911 TTTATAATTTTTTACAACTTTTGTAAAA-TATTACT-ATTTTTTAATCTTTATTGTA
1 TTTATAATTTTTTACAAC-TTTATAAAAGT-TTA-TAATTTTTTAATATTTATTATA
12010966 TTTATAATTTTT
1 TTTATAATTTTT
12010978 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
55 15 0.26
56 13 0.22
57 29 0.50
58 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (54 bp):
TTTATAATTTTTTACAACTTTATAAAAGTTTATAATTTTTTAATATTTATTATA
Found at i:12011025 original size:29 final size:28
Alignment explanation
Indices: 12010966--12011036 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
12010956 CTTTATTGTA
* *
12010966 TTTATAATTTTTAATAAAAAATAAAATTT
1 TTTATATTTTTTATTAAAAAATAAAA-TT
* *
12010995 TTTATATTTTTTATTAAAAATTATTAA-T
1 TTTATATTTTTTATTAAAAAATA-AAATT
12011023 TTTAT-TTTTTTATT
1 TTTATATTTTTTATT
12011037 TTTTATCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.24
28 6 0.16
29 20 0.54
30 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATATTTTTTATTAAAAAATAAAATT
Found at i:12011039 original size:9 final size:9
Alignment explanation
Indices: 12011022--12011067 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
12011012 AAATTATTAA
12011022 TTTTAT-TT
1 TTTTATCTT
12011030 TTTTA--TT
1 TTTTATCTT
12011037 TTTTATCTT
1 TTTTATCTT
12011046 TTTTATCTT
1 TTTTATCTT
12011055 TTTTATCTT
1 TTTTATCTT
12011064 TTTT
1 TTTT
12011068 GCCACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.19
8 5 0.14
9 24 0.67
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATCTT
Found at i:12011929 original size:15 final size:15
Alignment explanation
Indices: 12011903--12011943 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12011893 CAAAGAATTC
12011903 AAAATTTAAAATAAAAT
1 AAAA-TTAAAAT-AAAT
12011920 AAAA-TAAAATAAAT
1 AAAATTAAAATAAAT
12011934 AAAATTAAAA
1 AAAATTAAAA
12011944 CTAATCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.35
15 11 0.48
17 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTAAAATAAAT
Found at i:12011935 original size:4 final size:5
Alignment explanation
Indices: 12011909--12011943 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
12011899 ATTCAAAATT
12011909 TAAAA TAAAA TAAAA TAAAA T-AAA TAAAA TTAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -TAAAA
12011944 CTAATCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:12021574 original size:16 final size:16
Alignment explanation
Indices: 12021553--12021587 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12021543 AAACCAAACG
12021553 GGTCCATTTAATTTTT
1 GGTCCATTTAATTTTT
12021569 GGTCCATTTAATTTTT
1 GGTCCATTTAATTTTT
12021585 GGT
1 GGT
12021588 TTTTTCGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (16 bp):
GGTCCATTTAATTTTT
Found at i:12023977 original size:2 final size:2
Alignment explanation
Indices: 12023970--12024005 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12023960 GGGACAAAGA
12023970 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
12024006 TTCATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12035809 original size:21 final size:21
Alignment explanation
Indices: 12035783--12035822 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12035773 GTCTTAACTG
12035783 CTGATGTGGCAAGTTAACTAA
1 CTGATGTGGCAAGTTAACTAA
*
12035804 CTGATGTGGCCAGTTAACT
1 CTGATGTGGCAAGTTAACT
12035823 TGCCACATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (21 bp):
CTGATGTGGCAAGTTAACTAA
Found at i:12035881 original size:3 final size:3
Alignment explanation
Indices: 12035873--12035914 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12035863 TTAATAACAG
12035873 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12035915 GAAAGTGCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12036281 original size:13 final size:13
Alignment explanation
Indices: 12036265--12036299 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
12036255 TGCTGTGGAA
12036265 AAGTACTTTTGAG
1 AAGTACTTTTGAG
*
12036278 AAGTACTTTTGAT
1 AAGTACTTTTGAG
*
12036291 AAGTGCTTT
1 AAGTACTTT
12036300 GGAAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:12036590 original size:21 final size:19
Alignment explanation
Indices: 12036534--12036601 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
12036524 TAATTATTTA
12036534 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
12036553 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
12036572 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
12036593 TTATAATTA
1 TTA-AATTA
12036602 GATATTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.39
20 7 0.17
21 15 0.37
22 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:12038000 original size:8 final size:8
Alignment explanation
Indices: 12037989--12038018 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12037979 CCTTTTATTC
12037989 TTTTTCTT
1 TTTTTCTT
12037997 TTTTTCTT
1 TTTTTCTT
12038005 CTTTTTCTT
1 -TTTTTCTT
12038014 TTTTT
1 TTTTT
12038019 AAACCCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:12038006 original size:17 final size:17
Alignment explanation
Indices: 12037981--12038019 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12037971 CTCCTTCCCC
12037981 TTTTATTCTTTTTCTTT
1 TTTTATTCTTTTTCTTT
*
12037998 TTTTCTTCTTTTTCTTT
1 TTTTATTCTTTTTCTTT
12038015 TTTTA
1 TTTTA
12038020 AACCCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTCTTTTTCTTT
Found at i:12046702 original size:19 final size:19
Alignment explanation
Indices: 12046678--12046718 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
12046668 CGCAGACCCA
12046678 TTGTTTTGTTGTCTTGAAG
1 TTGTTTTGTTGTCTTGAAG
12046697 TTGTTTTGTTGTCTTGAAG
1 TTGTTTTGTTGTCTTGAAG
12046716 TTG
1 TTG
12046719 GGTGAAGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.05, G:0.27, T:0.59
Consensus pattern (19 bp):
TTGTTTTGTTGTCTTGAAG
Found at i:12049648 original size:22 final size:22
Alignment explanation
Indices: 12049609--12049667 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
12049599 GTTTTAAGAA
*
12049609 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
12049630 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
12049652 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
12049668 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:12049684 original size:26 final size:24
Alignment explanation
Indices: 12049638--12049697 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
12049628 ATTTGTTTTA
*
12049638 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
12049662 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
12049688 TTTTTTATTT
1 ATATTTATTT
12049698 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:12057069 original size:11 final size:11
Alignment explanation
Indices: 12057039--12057133 Score: 57
Period size: 11 Copynumber: 8.4 Consensus size: 11
12057029 GCAAATATTT
* *
12057039 TAAAATAGTAG
1 TAAAATAATAA
12057050 TAAAA-AATAA
1 TAAAATAATAA
12057060 TAAAATAATAA
1 TAAAATAATAA
* * *
12057071 TTATATAATAT
1 TAAAATAATAA
12057082 TCAAACAATAATACA
1 T--AA-AATAATA-A
*
12057097 AAAAATAATAA
1 TAAAATAATAA
* *
12057108 TAATATAATAG
1 TAAAATAATAA
* *
12057119 TGAAATGATAA
1 TAAAATAATAA
12057130 TAAA
1 TAAA
12057134 TAGTAGCAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
10 8 0.13
11 38 0.61
12 7 0.11
13 3 0.05
14 6 0.10
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.28
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:12058040 original size:23 final size:23
Alignment explanation
Indices: 12057997--12058040 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12057987 ACTAGAATTT
* *
12057997 ATGATTATGCTTTGAATTTATTA
1 ATGATTATCCTTTGAAATTATTA
12058020 ATGATTTATCCTTT-AAATTAT
1 ATGA-TTATCCTTTGAAATTAT
12058041 ATCATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (23 bp):
ATGATTATCCTTTGAAATTATTA
Found at i:12063478 original size:74 final size:75
Alignment explanation
Indices: 12063330--12063495 Score: 204
Period size: 74 Copynumber: 2.3 Consensus size: 75
12063320 GCAAAGTGTG
** *
12063330 AAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCCATA
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
* **
12063390 CTGAGCTGTG
66 CCGAGCTGAA
12063400 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AAAAATGTAGGTATGGCATT-TCCCAT
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTAT-CCAT
*
12063463 ACCGAGTTGAA
65 ACCGAGCTGAA
12063474 AAATGTAGGTATGGTATT-TCAA
1 AAATGTAGGTATGGTATTATCAA
12063496 TGAGGAAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
70 14 0.17
73 9 0.11
74 46 0.55
75 14 0.17
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
CCGAGCTGAA
Found at i:12063493 original size:35 final size:35
Alignment explanation
Indices: 12063330--12063493 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
12063320 GCAAAGTGTG
* **
12063330 AAATGTAGGTATGGTATCAT-CCATACTGAGTTGTG
1 AAATGTAGGTATGGTAT-TTCCCATACTGAGTTGAA
* **
12063365 AAATGTAGGTATGGTATTAT-CCATACTGAGCTGTG
1 AAATGTAGGTATGGTATT-TCCCATACTGAGTTGAA
12063400 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AA
1 AAATGTAGGTATGGTATT-TC----CCATACTGAGTTGAA
* *
12063439 AAATGTAGGTATGGCATTTCCCATACCGAGTTGAA
1 AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
12063474 AAATGTAGGTATGGTATTTC
1 AAATGTAGGTATGGTATTTC
12063494 AATGAGGAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
34 11 0.10
35 73 0.64
38 2 0.02
39 17 0.15
40 11 0.10
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (35 bp):
AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
Found at i:12064715 original size:8 final size:8
Alignment explanation
Indices: 12064702--12064731 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
12064692 AATTAAGGGA
12064702 AAAATTGC
1 AAAATTGC
12064710 AAAATTGC
1 AAAATTGC
12064718 AAAATTGC
1 AAAATTGC
12064726 AAAATT
1 AAAATT
12064732 TACTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (8 bp):
AAAATTGC
Found at i:12067821 original size:5 final size:5
Alignment explanation
Indices: 12067813--12067854 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
12067803 TCTTTAGTTT
12067813 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
12067855 TAAAACATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:12067890 original size:8 final size:8
Alignment explanation
Indices: 12067877--12067902 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12067867 TATCTTTATT
12067877 ATATAATA
1 ATATAATA
12067885 ATATAATA
1 ATATAATA
12067893 ATATAATA
1 ATATAATA
12067901 AT
1 AT
12067903 GTACTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:12071944 original size:22 final size:22
Alignment explanation
Indices: 12071914--12071967 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
12071904 ATTAATAATG
*
12071914 ATATAATTTTCTT-AATAAAAAT
1 ATATTATTTTCTTCAA-AAAAAT
*
12071936 ATATTATTTTTTTTCAAAAAAAT
1 ATATTA-TTTTCTTCAAAAAAAT
12071959 ATATATATT
1 ATAT-TATT
12071968 AGTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 18 0.67
24 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTATTTTCTTCAAAAAAAT
Found at i:12071977 original size:23 final size:23
Alignment explanation
Indices: 12071925--12071977 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
12071915 TATAATTTTC
* **
12071925 TTAATAAAAATATATTATTTTTT
1 TTAAAAAAAATATATTATTTAGT
*
12071948 TTCAAAAAAATATA-TATATTAGT
1 TTAAAAAAAATATATTAT-TTAGT
12071971 TTAAAAA
1 TTAAAAA
12071978 TCTAAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAAAAAAAATATATTATTTAGT
Found at i:12072576 original size:18 final size:18
Alignment explanation
Indices: 12072555--12072593 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12072545 GTGAATAGTA
* *
12072555 AAATTAAACTTAAATATT
1 AAATTAAACATAAAAATT
12072573 AAATTAAACATAAAAATT
1 AAATTAAACATAAAAATT
12072591 AAA
1 AAA
12072594 CTCACACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTAAACATAAAAATT
Found at i:12077369 original size:18 final size:18
Alignment explanation
Indices: 12077346--12077383 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12077336 CCCAAAGTCT
12077346 GATATAATATTGGGATAG
1 GATATAATATTGGGATAG
12077364 GATATAATATTGGGATAG
1 GATATAATATTGGGATAG
12077382 GA
1 GA
12077384 GATGGAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (18 bp):
GATATAATATTGGGATAG
Found at i:12077517 original size:12 final size:11
Alignment explanation
Indices: 12077500--12077541 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
12077490 AAGTCATATT
12077500 TAATTTTTATA
1 TAATTTTTATA
*
12077511 TATATTTTAATA
1 TA-ATTTTTATA
12077523 -AATTTATTATA
1 TAATTT-TTATA
12077534 TAATTTTT
1 TAATTTTT
12077542 TCACCTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.15
11 9 0.35
12 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:12077766 original size:17 final size:17
Alignment explanation
Indices: 12077744--12077778 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12077734 ATTTTTGGAC
12077744 TAAGAAAAACAACTTAA
1 TAAGAAAAACAACTTAA
12077761 TAAGAAAAACAACTTAA
1 TAAGAAAAACAACTTAA
12077778 T
1 T
12077779 TCTTTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (17 bp):
TAAGAAAAACAACTTAA
Found at i:12083752 original size:17 final size:17
Alignment explanation
Indices: 12083730--12083763 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12083720 GAGGCTCATA
*
12083730 TCCGTCATTGCTCTGTT
1 TCCGTCATTGCTATGTT
*
12083747 TCCGTCCTTGCTATGTT
1 TCCGTCATTGCTATGTT
12083764 CCTCTAGCAT
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:0.06, C:0.29, G:0.18, T:0.47
Consensus pattern (17 bp):
TCCGTCATTGCTATGTT
Found at i:12090204 original size:30 final size:30
Alignment explanation
Indices: 12090136--12090206 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
12090126 TTGATTGAAT
* *
12090136 TAAAATTAAAGTTTCGTGTATATATTTAAAC
1 TAAAATTAAAGTTTCGTGTATAAATGT-AAC
12090167 TAAAATTAAAGTTTCATGTGTATAAATGT-AC
1 TAAAATTAAAGTTTC--GTGTATAAATGTAAC
12090198 -AAAATTAAA
1 TAAAATTAAA
12090207 ATTCATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 9 0.25
31 17 0.47
33 10 0.28
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (30 bp):
TAAAATTAAAGTTTCGTGTATAAATGTAAC
Found at i:12112630 original size:36 final size:36
Alignment explanation
Indices: 12112583--12112654 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12112573 ACCCTAAGCC
12112583 TAGATTTTAACTTTTCTTTTTGACCTTTTTACAAAA
1 TAGATTTTAACTTTTCTTTTTGACCTTTTTACAAAA
12112619 TAGATTTTAACTTTTCTTTTTGACCTTTTTACAAAA
1 TAGATTTTAACTTTTCTTTTTGACCTTTTTACAAAA
12112655 ATCATGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.53
Consensus pattern (36 bp):
TAGATTTTAACTTTTCTTTTTGACCTTTTTACAAAA
Found at i:12112938 original size:41 final size:41
Alignment explanation
Indices: 12112881--12112962 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
12112871 TGACAATGAT
*
12112881 TACTTTGATTATTATCAATCTCAAATAGATATTTGGAATAA
1 TACTTTGATTATTATCAATCTCAAATAGATACTTGGAATAA
12112922 TACTTTGATTATTATCAATCTCAAATAGATACTTGGAATAA
1 TACTTTGATTATTATCAATCTCAAATAGATACTTGGAATAA
12112963 CCATACTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (41 bp):
TACTTTGATTATTATCAATCTCAAATAGATACTTGGAATAA
Found at i:12114212 original size:2 final size:2
Alignment explanation
Indices: 12114205--12114239 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12114195 GTTTTCTTAA
12114205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12114240 AGAATCACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12125388 original size:17 final size:16
Alignment explanation
Indices: 12125363--12125399 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12125353 ATTAATAAGT
*
12125363 TTATTATTATTTAATTA
1 TTATGATTATTT-ATTA
12125380 TTATGATTATTTATTA
1 TTATGATTATTTATTA
12125396 TTAT
1 TTAT
12125400 ATTTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATGATTATTTATTA
Found at i:12126513 original size:22 final size:21
Alignment explanation
Indices: 12126449--12126513 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
12126439 TTTTTTTAAG
12126449 AAAATAAAGATAACAAAATAAA
1 AAAATAAAGA-AACAAAATAAA
* * **
12126471 AAGATAAAGGAAATACTATAAA
1 AAAATAAA-GAAACAAAATAAA
*
12126493 ATAAATAAAGAAAGAAAATAA
1 A-AAATAAAGAAACAAAATAA
12126514 TTCAAAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.15
Consensus pattern (21 bp):
AAAATAAAGAAACAAAATAAA
Done.