Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold938
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: 109306
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5499 original size:124 final size:127
Alignment explanation
Indices: 5328--5575 Score: 430
Period size: 125 Copynumber: 2.0 Consensus size: 127
5318 TTATGATCTG
*
5328 AACAAAAGTTGATGCCAAAAAGGACCATTCCTGCTAGTTAAGGTTGACAA-TTTTTTAGTTATAA
1 AACAAAAGTTGATGCCAAAAAGGACCATTCCTGCTAGTTAAGATTGACAATTTTTTTAGTTATAA
5392 ATTTGTCATATTCTTCAATGTCATCACAGTTATTTTAATTCATTGTCTAGTTGCCTTAATTT
66 ATTTGTCATATTCTTCAATGTCATCACAGTTATTTTAATTCATTGTCTAGTTGCCTTAATTT
*
5454 AACAAAAGTTGATGCC-AAAAGG-CCATTGCTGCTAGTTAAGATTGACAATTTTTTTAGTTATAA
1 AACAAAAGTTGATGCCAAAAAGGACCATTCCTGCTAGTTAAGATTGACAATTTTTTTAGTTATAA
* * *
5517 ATTTGTCATATTCTTCAATGTCATCGCCGTTATTTTAATTCATTGTCTAGTTTCCTTAA
66 ATTTGTCATATTCTTCAATGTCATCACAGTTATTTTAATTCATTGTCTAGTTGCCTTAA
5576 CATCTTACTG
Statistics
Matches: 116, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
124 24 0.21
125 76 0.66
126 16 0.14
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (127 bp):
AACAAAAGTTGATGCCAAAAAGGACCATTCCTGCTAGTTAAGATTGACAATTTTTTTAGTTATAA
ATTTGTCATATTCTTCAATGTCATCACAGTTATTTTAATTCATTGTCTAGTTGCCTTAATTT
Found at i:7823 original size:1 final size:1
Alignment explanation
Indices: 7819--7844 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
7809 TTTTTTGTTT
7819 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
7845 AGTGATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:8183 original size:27 final size:29
Alignment explanation
Indices: 8144--8214 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
8134 TATTTTTAAT
8144 TTTTTTAATTAAAAA-T-AAAA-TATTTA
1 TTTTTTAATTAAAAATTAAAAATTATTTA
*
8170 TTTTTTATTATAAAAATTAAAAATTATTTA
1 TTTTTTAAT-TAAAAATTAAAAATTATTTA
** *
8200 TAATTTAAATAAAAA
1 TTTTTTAATTAAAAA
8215 ATCAGTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 8 0.22
27 6 0.17
28 1 0.03
29 10 0.28
30 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTTTAATTAAAAATTAAAAATTATTTA
Found at i:13926 original size:10 final size:10
Alignment explanation
Indices: 13897--13933 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
13887 GATACATTAC
*
13897 TGTTCATCAC
1 TGTTCATCAT
*
13907 TATTCATCAT
1 TGTTCATCAT
13917 TGTTCATCAT
1 TGTTCATCAT
13927 TGTTCAT
1 TGTTCAT
13934 GTATCGATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (10 bp):
TGTTCATCAT
Found at i:14047 original size:20 final size:20
Alignment explanation
Indices: 14004--14040 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13994 TTCAAATGCA
*
14004 TGTATCGATACATTATGAAT
1 TGTATCGATACATTAGGAAT
14024 TGTATCGATACA-TAGGA
1 TGTATCGATACATTAGGA
14041 GTGTGTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTAGGAAT
Found at i:16076 original size:21 final size:21
Alignment explanation
Indices: 16026--16069 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16016 TAATATTTTT
* *
16026 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
16047 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
16068 GA
1 GA
16070 GGAGAAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:19364 original size:13 final size:13
Alignment explanation
Indices: 19346--19373 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19336 CATTATTCAA
19346 TGTATCAATACAT
1 TGTATCAATACAT
19359 TGTATCAATACAT
1 TGTATCAATACAT
19372 TG
1 TG
19374 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:23047 original size:21 final size:21
Alignment explanation
Indices: 22995--23055 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
22985 CAGATGTATC
* *
22995 GATACATTGTATCGAAACAT-
1 GATAAATTGTATCGATACATG
* *
23015 GTTCAA-TGTATCGATACATG
1 GATAAATTGTATCGATACATG
23035 GATAAATTGTATCGATACATG
1 GATAAATTGTATCGATACATG
23056 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 12 0.36
20 7 0.21
21 14 0.42
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (21 bp):
GATAAATTGTATCGATACATG
Found at i:23121 original size:13 final size:13
Alignment explanation
Indices: 23100--23130 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23090 CGGTACATGG
*
23100 TACAATGTATCGA
1 TACATTGTATCGA
23113 TACATTGTATCGA
1 TACATTGTATCGA
23126 TACAT
1 TACAT
23131 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:23130 original size:33 final size:32
Alignment explanation
Indices: 23084--23150 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
23074 CTATCACTAT
*
23084 TTGTATCGGTACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
23117 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
23150 T
1 T
23151 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:29302 original size:13 final size:13
Alignment explanation
Indices: 29284--29312 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29274 ACAACATTTT
29284 TTGTATCGATACA
1 TTGTATCGATACA
29297 TTGTATCGATACA
1 TTGTATCGATACA
29310 TTG
1 TTG
29313 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:31212 original size:13 final size:13
Alignment explanation
Indices: 31194--31219 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31184 CACACCCAGA
31194 TGTATCGATACAT
1 TGTATCGATACAT
31207 TGTATCGATACAT
1 TGTATCGATACAT
31220 GTTCAATATA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31233 original size:19 final size:21
Alignment explanation
Indices: 31209--31260 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
31199 CGATACATTG
**
31209 TATCGATACATGTTC-AA-TA
1 TATCGATACATGGACAAATTA
31228 TATCGATACATGGACAAATTA
1 TATCGATACATGGACAAATTA
31249 TATCGATACATG
1 TATCGATACATG
31261 AAATTGGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 2 0.07
21 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
TATCGATACATGGACAAATTA
Found at i:31326 original size:13 final size:13
Alignment explanation
Indices: 31305--31335 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31295 CGATACATGG
*
31305 TACAATGTATCGA
1 TACATTGTATCGA
31318 TACATTGTATCGA
1 TACATTGTATCGA
31331 TACAT
1 TACAT
31336 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:31331 original size:33 final size:32
Alignment explanation
Indices: 31289--31355 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
31279 CTATCACTAT
31289 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
31322 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
31355 T
1 T
31356 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:32434 original size:27 final size:27
Alignment explanation
Indices: 32396--32466 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
32386 GATTGAAAAC
32396 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGGAGGAAT
32423 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGGAGGAAT
32450 GGGGTTGGAGTGTCCCC
1 GGGGTTGGAGTGTCCCC
32467 GATGAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.13, C:0.20, G:0.45, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCGGAGGAAT
Found at i:34646 original size:52 final size:51
Alignment explanation
Indices: 34568--34716 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
34558 CGAAATATGA
34568 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
34620 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
34672 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
34717 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:34723 original size:13 final size:13
Alignment explanation
Indices: 34705--34729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34695 CAAAGATCAG
34705 TGTATCGATACAA
1 TGTATCGATACAA
34718 TGTATCGATACA
1 TGTATCGATACA
34730 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34796 original size:19 final size:18
Alignment explanation
Indices: 34768--34834 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
34758 GCAGTAGCTT
34768 AAATTGTATCGATACAAA
1 AAATTGTATCGATACAAA
34786 AAATATGTATCGATAC---
1 AAAT-TGTATCGATACAAA
34802 --ATTGTATCGATACAAA
1 AAATTGTATCGATACAAA
34818 AAATATGTATCGATACA
1 AAAT-TGTATCGATACA
34835 TTGTATCGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.26
14 2 0.05
18 6 0.14
19 23 0.55
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (18 bp):
AAATTGTATCGATACAAA
Found at i:34809 original size:13 final size:13
Alignment explanation
Indices: 34791--34847 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
34781 ACAAAAAATA
34791 TGTATCGATACAT
1 TGTATCGATACAT
34804 TGTATCGATACAAAAAAT
1 TGTATCGATAC-----AT
34822 ATGTATCGATACAT
1 -TGTATCGATACAT
34836 TGTATCGATACA
1 TGTATCGATACA
34848 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 2 0.05
18 2 0.05
19 11 0.29
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:34811 original size:32 final size:32
Alignment explanation
Indices: 34770--34867 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
34760 AGTAGCTTAA
34770 ATTGTATCGATACAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAATATGTATCGATAC
34802 ATTGTATCGATACAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAATATGTATCGATAC
***
34834 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAA-AAAATATGTATCGATAC
34867 A
1 A
34868 AATCATTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 47 0.76
33 15 0.24
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (32 bp):
ATTGTATCGATACAAAAAATATGTATCGATAC
Found at i:36680 original size:21 final size:24
Alignment explanation
Indices: 36656--36707 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 24
36646 ATATGTCAAT
36656 ATGCATGGAACAT-GGC-A-TAAA
1 ATGCATGGAACATAGGCTACTAAA
*
36677 ATGCAT-AAACATAGGCTACTAAA
1 ATGCATGGAACATAGGCTACTAAA
36700 ATG-ATGGA
1 ATGCATGGA
36708 GATGAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 3 0.12
23 8 0.32
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (24 bp):
ATGCATGGAACATAGGCTACTAAA
Found at i:37658 original size:30 final size:31
Alignment explanation
Indices: 37602--37669 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
37592 AAAATGTGTC
*
37602 GATACATTTGGGTCAAAAACCCAGAATGTATT
1 GATACATTTGGATC-AAAACCCAGAATGTATT
*
37634 GATACATTTGGATC-AAACCTAGAATGTATT
1 GATACATTTGGATCAAAACCCAGAATGTATT
37664 GATACA
1 GATACA
37670 ATAAAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 21 0.62
32 13 0.38
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (31 bp):
GATACATTTGGATCAAAACCCAGAATGTATT
Found at i:38791 original size:97 final size:94
Alignment explanation
Indices: 38566--38801 Score: 229
Period size: 97 Copynumber: 2.5 Consensus size: 94
38556 AAAATGAGGC
* *** * *
38566 TGGAGTATCCCCTCTGCGGAATGAGGTTGGAGTATCCTCGATGATGACAATTTAAGCAAAAATAA
1 TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTATCC-CAATGATGACAATTTAAGCAAAAATAA
* *
38631 GAATTATCCTGACAAGTTTAAAAATGGGGT
65 GAATTATCCTGAAAAGTTTAAAAACGGGGT
* * * * * * *
38661 TGGAGTATCCCCTCGGAATATTGGGGTTCGAGTATACCCAATGATGATAATTTAAGCAAAATTAA
1 TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTAT-CCCAATGATGACAATTTAAGCAAAAATAA
** * *
38726 GGTTTAAATCTTGAAAATTTTAAAAACGGGGT
65 GAATT--ATCCTGAAAAGTTTAAAAACGGGGT
* * *
38758 TGGAGTTTCTCCTTAGAAAAATGAGGTTAGAGTATCCCCAATGA
1 TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTAT-CCCAATGA
38802 AGGAAATTTT
Statistics
Matches: 113, Mismatches: 25, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
95 55 0.49
96 2 0.02
97 56 0.50
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (94 bp):
TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTATCCCAATGATGACAATTTAAGCAAAAATAAG
AATTATCCTGAAAAGTTTAAAAACGGGGT
Found at i:38810 original size:97 final size:95
Alignment explanation
Indices: 38566--38801 Score: 238
Period size: 95 Copynumber: 2.5 Consensus size: 95
38556 AAAATGAGGC
* *** * * *
38566 TGGAGTATCCCCTCTGCGGAATGAGGTTGGAGTATCCTCGATGATGACAATTTAAGCAAAAATAA
1 TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTATCCCCAATGATGACAATTTAAGCAAAAATAA
* *
38631 GAATTATCCTGACAAGTTTAAAAATGGGGT
66 GAATTATCCTGAAAAGTTTAAAAACGGGGT
* * * * * * * *
38661 TGGAGTATCCCCTCGGAATATTGGGGTTCGAGTATACCCAATGATGATAATTTAAGCAAAATTAA
1 TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTATCCCCAATGATGACAATTTAAGCAAAAATAA
** * *
38726 GGTTTAAATCTTGAAAATTTTAAAAACGGGGT
66 GAATT--ATCCTGAAAAGTTTAAAAACGGGGT
* * *
38758 TGGAGTTTCTCCTTAGAAAAATGAGGTTAGAGTATCCCCAATGA
1 TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTATCCCCAATGA
38802 AGGAAATTTT
Statistics
Matches: 112, Mismatches: 27, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
95 56 0.50
97 56 0.50
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (95 bp):
TGGAGTATCCCCTCAGAAAAATGAGGTTAGAGTATCCCCAATGATGACAATTTAAGCAAAAATAA
GAATTATCCTGAAAAGTTTAAAAACGGGGT
Found at i:41170 original size:39 final size:39
Alignment explanation
Indices: 41127--41201 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
41117 TTGCCTGCAT
*
41127 GTATCGATACATTGA-AGAATGTATCGATACATTTGGTAC
1 GTATCGATACAATGAGA-AATGTATCGATACATTTGGTAC
* *
41166 GTATCGGTATAATGAGAAATGTATCGATACATTTGG
1 GTATCGATACAATGAGAAATGTATCGATACATTTGG
41202 GTCAAAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 31 0.97
40 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (39 bp):
GTATCGATACAATGAGAAATGTATCGATACATTTGGTAC
Found at i:41322 original size:21 final size:20
Alignment explanation
Indices: 41295--41370 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 20
41285 GCATGGTGGT
41295 TTTGTATCGATACATTTCAGGC
1 TTTGTATCGATACATTTCA--C
* *
41317 -TTGTATTGATATA-TTCAC
1 TTTGTATCGATACATTTCAC
41335 TTATGTATCGATACATTT-AC
1 TT-TGTATCGATACATTTCAC
*
41355 TGTTTGTATCAATACA
1 --TTTGTATCGATACA
41371 AATTGTAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 16 0.36
21 24 0.55
22 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (20 bp):
TTTGTATCGATACATTTCAC
Found at i:45067 original size:20 final size:20
Alignment explanation
Indices: 45042--45143 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 20
45032 AAAAAGATAA
45042 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAG
*
45062 AATGTATCGATACATTCATA-
1 AATGTATCGATACATTGA-AG
*
45082 CATGTATCGATACATCTAGGTAAAAG
1 AATGTATCGATACAT-T--G---AAG
* * *
45108 ACAAGTATCGATAAATTGAAA
1 A-ATGTATCGATACATTGAAG
45129 AATGTATCGATACAT
1 AATGTATCGATACAT
45144 CTGGATAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
20 43 0.67
21 5 0.08
24 1 0.02
25 1 0.02
26 2 0.03
27 12 0.19
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATTGAAG
Found at i:47363 original size:20 final size:20
Alignment explanation
Indices: 47338--47397 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
47328 TTTTACCCAG
*
47338 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
47358 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
*
47378 ATGTATCAATACATTCTATC
1 ATGTATCGATACATT-TATC
47398 TTTTTACCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:48627 original size:13 final size:13
Alignment explanation
Indices: 48609--48634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48599 TACACCAAGT
48609 ATGTATCGATACA
1 ATGTATCGATACA
48622 ATGTATCGATACA
1 ATGTATCGATACA
48635 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:48632 original size:32 final size:33
Alignment explanation
Indices: 48591--48654 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
48581 TAGCCAAACT
* **
48591 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
48623 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
48655 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:50892 original size:21 final size:21
Alignment explanation
Indices: 50854--50903 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
50844 TTGCAAGTTG
*
50854 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
50876 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
50897 AAATAAA
1 AAATAAA
50904 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 9 0.38
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:52719 original size:15 final size:15
Alignment explanation
Indices: 52701--52731 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52691 TAAAAATGTC
*
52701 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
52716 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
52731 C
1 C
52732 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:54823 original size:13 final size:13
Alignment explanation
Indices: 54805--54842 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
54795 CATTTTTCTT
54805 TGTATCGATACAA
1 TGTATCGATACAA
*
54818 TGTATCGATACAC
1 TGTATCGATACAA
*
54831 TATATCGATACA
1 TGTATCGATACA
54843 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:61536 original size:30 final size:30
Alignment explanation
Indices: 61467--61814 Score: 234
Period size: 30 Copynumber: 11.6 Consensus size: 30
61457 TTCATCACCC
* *
61467 TTCAAAAGTCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
**
61497 TTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
*
61526 TTCAAAAGCCCACAAGTCAGTGGCA-AC-C
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
* **
61554 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
** *
61583 TTCCGAAGCCCACAAGTCGGTGGCAT-CTT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
* * * * *
61612 TTCCAAAGTCCACAACTCCGTGACACT-CTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TAC-TT
** * * *
61643 TTCTTTTGTAAGCTCACAACTCTA-TAGCACT-CTTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCA-TAC-TT
*** *
61678 TTCTTTTTCAGCCCACAAGTCAGTGGCA-ACCT
1 TTC---AAAAGCCCACAAGTCAGTGGCATACTT
* **
61710 TT-AAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
*
61739 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
*
61769 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
1 TTCAAAAGCCCACAAGTCAGTGGCATACTT
61798 TT-AAAAGCCCACAAGTC
1 TTCAAAAGCCCACAAGTC
61815 GATGGCAACC
Statistics
Matches: 261, Mismatches: 42, Indels: 32
0.78 0.13 0.10
Matches are distributed among these distances:
27 20 0.08
28 37 0.14
29 61 0.23
30 92 0.35
31 5 0.02
32 3 0.01
33 2 0.01
34 18 0.07
35 23 0.09
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATACTT
Found at i:61585 original size:57 final size:59
Alignment explanation
Indices: 61467--61608 Score: 180
Period size: 57 Copynumber: 2.4 Consensus size: 59
61457 TTCATCACCC
* ** * ***
61467 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCACCCTT
61526 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTCAAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCACCCTT
** *
61583 TTCCGAAGCCCACAAGTCGGTGGCAT
1 TTCAAAAGCCCACAAGTCAGTGGCAT
61609 CTTTTCCAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
57 47 0.65
58 1 0.01
59 24 0.33
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCACCCTT
Found at i:61720 original size:28 final size:29
Alignment explanation
Indices: 61687--61840 Score: 197
Period size: 30 Copynumber: 5.3 Consensus size: 29
61677 TTTCTTTTTC
61687 AGCCCACAAGTCAGTGGCAACCTTT-AAA
1 AGCCCACAAGTCAGTGGCAACCTTTCAAA
* *
61715 AGCCCACAAGTTAGTGGCACCCTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACC-TTTCAAA
**
61745 AGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTCAGTGGCA-ACCTTTCAAA
61775 AGCCCACAAGTCAGTGGCAACCTTT-AAA
1 AGCCCACAAGTCAGTGGCAACCTTTCAAA
* *
61803 AGCCCACAAGTC-GATGGCAACCCTCTCTAA
1 AGCCCACAAGTCAG-TGGCAA-CCTTTCAAA
61833 AGCCCACA
1 AGCCCACA
61841 CAAGTTGGTG
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.01
28 41 0.37
29 11 0.10
30 57 0.52
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (29 bp):
AGCCCACAAGTCAGTGGCAACCTTTCAAA
Found at i:61835 original size:58 final size:56
Alignment explanation
Indices: 61687--61899 Score: 189
Period size: 58 Copynumber: 3.6 Consensus size: 56
61677 TTTCTTTTTC
*
61687 AGCCCACAAGTCAGTGGCAACCTT-TAAAAGCCCACAAGTTAGTGGCACCCTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACCTTCT-AAAGCCCACAAGTTAGTGGCAACC-TTT-AAA
** * *
61745 AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAA
1 AGCCCACAAGTCAGTGGCA-A-CCTTCTAAAGCCCACAAGTTAGTGGCAACCTTTAAA
* ** *
61803 AGCCCACAAGTC-GATGGCAACCCTCTCTAAAGCCCACACAAGTTGGTGGCAACCCCCTCAA
1 AGCCCACAAGTCAG-TGGCAA-CCT-TCTAAAG-CC-CACAAGTTAGTGGCAA-CCTTTAAA
*
61864 AGCCCACACAAGTCGGTGGCAACCCTTCT-AAGCCCA
1 AG-CC-CACAAGTCAGTGGCAA-CCTTCTAAAGCCCA
61900 ATGTAGCTGG
Statistics
Matches: 130, Mismatches: 14, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
57 3 0.02
58 45 0.35
59 8 0.06
60 40 0.31
61 10 0.08
62 5 0.04
63 18 0.14
64 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.18
Consensus pattern (56 bp):
AGCCCACAAGTCAGTGGCAACCTTCTAAAGCCCACAAGTTAGTGGCAACCTTTAAA
Found at i:61853 original size:32 final size:32
Alignment explanation
Indices: 61779--61899 Score: 141
Period size: 31 Copynumber: 4.0 Consensus size: 32
61769 TTCAAAAGCC
*
61779 CACAAGTCAGTGGCAA-CCT-T-TAAAAG-CC-
1 CACAAGTCGGTGGCAACCCTCTCT-AAAGCCCA
*
61807 CACAAGTCGATGGCAACCCTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTCTCTAAAGCCCA
* *
61839 CACAAGTTGGTGGCAACCCCCTC-AAAGCCCA
1 CACAAGTCGGTGGCAACCCTCTCTAAAGCCCA
61870 CACAAGTCGGTGGCAACCCT-TCT-AAGCCCA
1 CACAAGTCGGTGGCAACCCTCTCTAAAGCCCA
61900 ATGTAGCTGG
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
28 14 0.17
29 3 0.04
30 14 0.17
31 29 0.36
32 20 0.25
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCTCTCTAAAGCCCA
Found at i:61954 original size:49 final size:49
Alignment explanation
Indices: 61892--62126 Score: 353
Period size: 49 Copynumber: 4.7 Consensus size: 49
61882 GCAACCCTTC
* * *
61892 TAAGCCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
61941 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
61990 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
62039 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
62091 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
62127 ACATCATTTT
Statistics
Matches: 169, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
49 130 0.77
51 2 0.01
52 37 0.22
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:62172 original size:56 final size:53
Alignment explanation
Indices: 61892--62174 Score: 214
Period size: 49 Copynumber: 5.5 Consensus size: 53
61882 GCAACCCTTC
* * * * * *
61892 TAAGCCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACC--TT-T-ATCTT
1 TAAGTCCAATATAGTTGGCCTTGAATCAGCACATCGACACCTTTTCTCATCTT
* * * * *
61941 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCATCTT
1 TAAGTCCAATATAGTTGGCCTTGAATCAGCACATCGACACCTTTTCTCATCTT
* * * * *
61990 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCATCTT
1 TAAGTCCAATATAGTTGGCCTTGAATCAGCACATCGACACCTTTTCTCATCTT
* *
62039 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATCGGCACCTTTTC-CATCTT
1 TAAGTCCAATATAGTTGGCCTTGAATCAGCACATCGACACCTTTTCTCATCTT
* * * * *
62091 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCATTTTTCATCATCTT
1 TAAGTCCAATATAGTTGGCCTTGAATCAGCACATCGACA-C-CTTTTC-TCATCTT
* * *
62147 TAAGCCCAATATTGTTGGCCATGAATCA
1 TAAGTCCAATATAGTTGGCCTTGAATCA
62175 ACATATTGGC
Statistics
Matches: 204, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
48 2 0.01
49 128 0.63
52 40 0.20
53 1 0.00
54 5 0.02
56 28 0.14
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (53 bp):
TAAGTCCAATATAGTTGGCCTTGAATCAGCACATCGACACCTTTTCTCATCTT
Found at i:62854 original size:10 final size:10
Alignment explanation
Indices: 62836--62887 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
62826 TGGGGACGAA
62836 TTTTATAACT
1 TTTTATAACT
*
62846 TTTTGTAACT
1 TTTTATAACT
62856 TTTTATAACT
1 TTTTATAACT
*
62866 TTTTA-GA-T
1 TTTTATAACT
62874 TTTTATAACT
1 TTTTATAACT
62884 TTTT
1 TTTT
62888 GTTAAGCCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 6 0.17
9 2 0.06
10 28 0.78
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (10 bp):
TTTTATAACT
Found at i:62878 original size:18 final size:19
Alignment explanation
Indices: 62836--62888 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
62826 TGGGGACGAA
62836 TTTTATAACTTTTTGTAACT
1 TTTTATAACTTTTTG-AACT
62856 TTTTATAACTTTTT-AGA-T
1 TTTTATAACTTTTTGA-ACT
62874 TTTTATAACTTTTTG
1 TTTTATAACTTTTTG
62889 TTAAGCCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 16 0.52
19 1 0.03
20 14 0.45
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (19 bp):
TTTTATAACTTTTTGAACT
Found at i:63084 original size:33 final size:33
Alignment explanation
Indices: 63047--63113 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
63037 TTCAACGATT
63047 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
63080 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
63113 T
1 T
63114 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:63085 original size:13 final size:13
Alignment explanation
Indices: 63067--63091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63057 CATAAAATGT
63067 TGTATCGATACAA
1 TGTATCGATACAA
63080 TGTATCGATACA
1 TGTATCGATACA
63092 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:63172 original size:13 final size:13
Alignment explanation
Indices: 63154--63178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63144 ATTACTCAAA
63154 TGTATCGATACAT
1 TGTATCGATACAT
63167 TGTATCGATACA
1 TGTATCGATACA
63179 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:63242 original size:51 final size:51
Alignment explanation
Indices: 63187--63310 Score: 194
Period size: 52 Copynumber: 2.4 Consensus size: 51
63177 CACTGATCTT
*
63187 TGTATCGATACATGCAGGCAATTTACCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTACCCAGATGTATCGATACACTATAAAA
* * *
63238 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGC-AATTTACCCAGATGTATCGATACACTATAAAA
*
63290 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
63311 CTTTTCATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 20 0.30
52 46 0.70
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTACCCAGATGTATCGATACACTATAAAA
Found at i:68794 original size:15 final size:15
Alignment explanation
Indices: 68774--68818 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
68764 ATTTCTCCAA
68774 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
68789 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
68804 ACCCACCACAAAATC
1 ATCCACCACAAAATC
68819 GTTGATACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:74666 original size:28 final size:28
Alignment explanation
Indices: 74635--74788 Score: 152
Period size: 28 Copynumber: 5.5 Consensus size: 28
74625 CGCAAGCAAG
74635 TGGCACCCTTTTTAAGCCCACAAGTCGA
1 TGGCACCCTTTTTAAGCCCACAAGTCGA
* * *
74663 TGGCACCCTTCTAAAGCCCACAAG-CAA
1 TGGCACCCTTTTTAAGCCCACAAGTCGA
* *
74690 GTGACACCCTTTTTAAGCCCACAAGTCGG
1 -TGGCACCCTTTTTAAGCCCACAAGTCGA
*** * *
74719 TGGCACCCTTCAAAAGCCCATAAGT-AA
1 TGGCACCCTTTTTAAGCCCACAAGTCGA
* *
74746 GTGGCACCCTTTTGAAGCCCACAAGTTGA
1 -TGGCACCCTTTTTAAGCCCACAAGTCGA
*
74775 TGACA-CCTTTTTAA
1 TGGCACCCTTTTTAA
74789 AGACCACAGG
Statistics
Matches: 100, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
27 10 0.10
28 88 0.88
29 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TGGCACCCTTTTTAAGCCCACAAGTCGA
Found at i:74698 original size:56 final size:56
Alignment explanation
Indices: 74627--74796 Score: 241
Period size: 56 Copynumber: 3.0 Consensus size: 56
74617 TCAAAGCTCG
74627 CAAGCAAGTGGCACCCTTTTTAAGCCCACAAGTCGATGGCACCCTTCTAAAGCCCA
1 CAAGCAAGTGGCACCCTTTTTAAGCCCACAAGTCGATGGCACCCTTCTAAAGCCCA
* * *
74683 CAAGCAAGTGACACCCTTTTTAAGCCCACAAGTCGGTGGCACCCTTCAAAAGCCCA
1 CAAGCAAGTGGCACCCTTTTTAAGCCCACAAGTCGATGGCACCCTTCTAAAGCCCA
* * * * * * * *
74739 TAAGTAAGTGGCACCCTTTTGAAGCCCACAAGTTGATGACACCTTTTTAAAGACCA
1 CAAGCAAGTGGCACCCTTTTTAAGCCCACAAGTCGATGGCACCCTTCTAAAGCCCA
74795 CA
1 CA
74797 GGTCAGCGGA
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 99 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (56 bp):
CAAGCAAGTGGCACCCTTTTTAAGCCCACAAGTCGATGGCACCCTTCTAAAGCCCA
Found at i:74860 original size:31 final size:31
Alignment explanation
Indices: 74807--74895 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 31
74797 GGTCAGCGGA
* *
74807 AACCTCTTTTCAAAGTCTACACAAGCCGATGGC
1 AACCT-TTTTC-AAGCCCACACAAGCCGATGGC
* *
74840 AACCTTTTTCAAGCCCACACAAGTCGGTGGC
1 AACCTTTTTCAAGCCCACACAAGCCGATGGC
*
74871 -ACTTCTTTTTAAAGGCCCACACAAG
1 AAC--CTTTTTCAA-GCCCACACAAG
74896 TCAGTGGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 2 0.04
31 17 0.35
32 13 0.27
33 16 0.33
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (31 bp):
AACCTTTTTCAAGCCCACACAAGCCGATGGC
Found at i:74879 original size:32 final size:33
Alignment explanation
Indices: 74843--74904 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
74833 CGATGGCAAC
* *
74843 CTTTTTCAA-GCCCACACAAGTCGGTGGCACTT
1 CTTTTTAAAGGCCCACACAAGTCAGTGGCACTT
74875 CTTTTTAAAGGCCCACACAAGTCAGTGGCA
1 CTTTTTAAAGGCCCACACAAGTCAGTGGCA
74905 ATCATTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (33 bp):
CTTTTTAAAGGCCCACACAAGTCAGTGGCACTT
Found at i:79641 original size:20 final size:20
Alignment explanation
Indices: 79607--79657 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
79597 AATAATTTGC
79607 ATCGATACAATAAGTGAAGGT
1 ATCGATAC-ATAAGTGAAGGT
*
79628 ATCGATACATAAGTGAATGT
1 ATCGATACATAAGTGAAGGT
*
79648 ATCAATACAT
1 ATCGATACAT
79658 GTCTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGATACATAAGTGAAGGT
Found at i:81077 original size:13 final size:13
Alignment explanation
Indices: 81059--81083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81049 ATTTTGCTTA
81059 GTATCGATACATT
1 GTATCGATACATT
81072 GTATCGATACAT
1 GTATCGATACAT
81084 AAAACTGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:82354 original size:45 final size:45
Alignment explanation
Indices: 82291--82381 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
82281 TTTGTGTCAA
* * *
82291 AACTTTGAGTGGTGTGATCAACGGGCTATTTCATCATCCCAAACT
1 AACTTTGAGTGATATGATCAACGGGCTATTTCAACATCCCAAACT
* *
82336 AACTTTGAGTGATATGATCAACGGGCTGTTTCAACGTCCCAAACT
1 AACTTTGAGTGATATGATCAACGGGCTATTTCAACATCCCAAACT
82381 A
1 A
82382 CTCTGAGGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (45 bp):
AACTTTGAGTGATATGATCAACGGGCTATTTCAACATCCCAAACT
Found at i:89608 original size:33 final size:32
Alignment explanation
Indices: 89566--89807 Score: 148
Period size: 29 Copynumber: 7.8 Consensus size: 32
89556 TCAATCCCCA
*
89566 TAAAGTCCACAACTTCATGGCACCCTCTTTTTT
1 TAAAGTCCACAACTTTATGGCA-CCTCTTTTTT
*
89599 TAAAGTCCACAACTTTGTGGCACCTC---TTT
1 TAAAGTCCACAACTTTATGGCACCTCTTTTTT
* * *
89628 TAAAGTCCACAATTTTATAGCAACTTCTTTTTT
1 TAAAGTCCACAACTTTATGGC-ACCTCTTTTTT
* * *
89661 TAAAGTCCACAACTCTGTGGCA-CTC-TTTTC
1 TAAAGTCCACAACTTTATGGCACCTCTTTTTT
* * *
89691 AAAAGCCCACAAC-TCAGTGGCATCC-C--TTTT
1 TAAAGTCCACAACTTTA-TGGCA-CCTCTTTTTT
* * * *
89721 TAAAGTTCACAACTCTGTGGCA--TC-ATTTT
1 TAAAGTCCACAACTTTATGGCACCTCTTTTTT
*** * *
89750 TAAAGTCCACAACTCCGTGGCACATTTTTTTT
1 TAAAGTCCACAACTTTATGGCACCTCTTTTTT
* *
89782 TCAAAAGTCCATAACTCTATGGCACC
1 T--AAAGTCCACAACTTTATGGCACC
89808 CTTCTAAAGC
Statistics
Matches: 162, Mismatches: 32, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
28 1 0.01
29 45 0.28
30 42 0.26
31 4 0.02
32 11 0.07
33 40 0.25
34 19 0.12
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (32 bp):
TAAAGTCCACAACTTTATGGCACCTCTTTTTT
Found at i:89634 original size:29 final size:29
Alignment explanation
Indices: 89596--90005 Score: 162
Period size: 28 Copynumber: 13.9 Consensus size: 29
89586 CACCCTCTTT
*
89596 TTTTAAAGTCCACAACTTTGTGGCACCTC
1 TTTTAAAGTCCACAACTCTGTGGCACCTC
* * * * *
89625 TTTTAAAGTCCACAATTTTATAGCAACTTCTTT
1 TTTTAAAGTCCACAACTCTGTGGC-AC--C-TC
89658 TTTTAAAGTCCACAACTCTGTGGCA-CTC
1 TTTTAAAGTCCACAACTCTGTGGCACCTC
* *
89686 TTTTCAAAAGCCCACAACTCAGTGGCATCC-C
1 TTTT--AAAGTCCACAACTCTGTGGCA-CCTC
* *
89717 TTTTTAAAGTTCACAACTCTGTGGCATCAT-
1 -TTTTAAAGTCCACAACTCTGTGGCA-CCTC
* * *
89747 TTTTAAAGTCCACAACTCCGTGGCACATTTTT
1 TTTTAAAGTCCACAACTCTGTGGCAC---CTC
* *
89779 TTTTCAAAAGTCCATAACTCTATGGCACC-C
1 TTTT--AAAGTCCACAACTCTGTGGCACCTC
* * * * *
89809 TTCTAAAGCCCACAAGT-TAGTGGTATCTCC
1 TTTTAAAGTCCACAACTCT-GTGGCACCT-C
* * *
89839 TTTTAAAGCCCACAAGTCAGTGGCACCT-
1 TTTTAAAGTCCACAACTCTGTGGCACCTC
* * * *
89867 TTTCAAAG-CCTACAAGTCAGTGGCACC-A
1 TTTTAAAGTCC-ACAACTCTGTGGCACCTC
* * *
89895 TTTTAAAGCCCATAAGT-TGGTGGCACGCTC
1 TTTTAAAGTCCACAACTCT-GTGGCAC-CTC
* * * *
89925 --TTAAAGCCCATAAGT-TAGTGGCATCCCC
1 TTTTAAAGTCCACAACTCT-GTGGCA-CCTC
* * * *
89953 TTTCAAAGCCCACAAGTCAGTGGCACC-C
1 TTTTAAAGTCCACAACTCTGTGGCACCTC
* * * *
89981 TTTTTAGGTCCACAAGTCAGTGGCA
1 TTTTAAAGTCCACAACTCTGTGGCA
90006 ACATCTCAAA
Statistics
Matches: 303, Mismatches: 48, Indels: 61
0.74 0.12 0.15
Matches are distributed among these distances:
27 3 0.01
28 109 0.36
29 51 0.17
30 87 0.29
31 2 0.01
32 11 0.04
33 21 0.07
34 19 0.06
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (29 bp):
TTTTAAAGTCCACAACTCTGTGGCACCTC
Found at i:89663 original size:62 final size:61
Alignment explanation
Indices: 89566--89823 Score: 222
Period size: 62 Copynumber: 4.2 Consensus size: 61
89556 TCAATCCCCA
* * *
89566 TAAAGTCCACAACTTCATGGCACCCTCTTTTTTTAAAGTCCACAACTTTGTGGCACCTCTTT
1 TAAAGTCCACAACTTCATAGCAACCTCTTTTTTTAAAGTCCACAACTCTGTGGCA-CTCTTT
* * *
89628 TAAAGTCCACAATTTTATAGCAACTTCTTTTTTTAAAGTCCACAACTCTGTGGCACTCTTT
1 TAAAGTCCACAACTTCATAGCAACCTCTTTTTTTAAAGTCCACAACTCTGTGGCACTCTTT
* * * *
89689 TCAAAAGCCCACAAC-TCAGTGGCATCC-C--TTTTTAAAGTTCACAACTCTGTGGCA-TCATTT
1 T--AAAGTCCACAACTTCA-TAGCAACCTCTTTTTTTAAAGTCCACAACTCTGTGGCACTC--TT
89749 T
61 T
* * * * * * * * *
89750 TAAAGTCCACAACTCCGTGGC-ACATTTTTTTTTCAAAAGTCCATAACTCTATGGCACCCTTC
1 TAAAGTCCACAACTTCATAGCAACCTCTTTTTTT--AAAGTCCACAACTCTGTGGCACTCTTT
*
89812 TAAAGCCCACAA
1 TAAAGTCCACAA
89824 GTTAGTGGTA
Statistics
Matches: 159, Mismatches: 25, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
58 1 0.01
59 17 0.11
60 26 0.16
61 16 0.10
62 65 0.41
63 33 0.21
64 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (61 bp):
TAAAGTCCACAACTTCATAGCAACCTCTTTTTTTAAAGTCCACAACTCTGTGGCACTCTTT
Found at i:89703 original size:30 final size:30
Alignment explanation
Indices: 89594--89906 Score: 139
Period size: 30 Copynumber: 10.5 Consensus size: 30
89584 GGCACCCTCT
* * *
89594 TTTTTTAAAGTCCACAACTTTGTGGCAC-C
1 TTTTCTAAAGCCCACAACTCTGTGGCACTC
* * * * *
89623 TCTTT-TAAAGTCCACAATTTTATAGCAACTTC
1 T-TTTCTAAAGCCCACAACTCTGTGGC-AC-TC
* *
89655 TTTTTTTAAAGTCCACAACTCTGTGGCACTC
1 -TTTTCTAAAGCCCACAACTCTGTGGCACTC
* * *
89686 TTTTCAAAAGCCCACAACTCAGTGGCATCCC
1 TTTTCTAAAGCCCACAACTCTGTGGCA-CTC
**
89717 TTTT-TAAAGTTCACAACTCTGTGGCA-TC
1 TTTTCTAAAGCCCACAACTCTGTGGCACTC
* * *
89745 ATTTT-TAAAGTCCACAACTCCGTGGCACATTTTT
1 -TTTTCTAAAGCCCACAACTCTGTGGCAC----TC
* * * *
89779 TTTTCAAAAGTCCATAACTCTATGGCAC-C
1 TTTTCTAAAGCCCACAACTCTGTGGCACTC
* * *
89808 -CTTCTAAAGCCCACAAGT-TAGTGGTATCTC
1 TTTTCTAAAGCCCACAACTCT-GTGGCA-CTC
* * *
89838 CTTT-TAAAGCCCACAAGTCAGTGGCAC-C
1 TTTTCTAAAGCCCACAACTCTGTGGCACTC
* * *
89866 TTTTC-AAAGCCTACAAGTCAGTGGCAC-C
1 TTTTCTAAAGCCCACAACTCTGTGGCACTC
*
89894 ATTT-TAAAGCCCA
1 TTTTCTAAAGCCCA
89907 TAAGTTGGTG
Statistics
Matches: 224, Mismatches: 39, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.00
28 54 0.24
29 45 0.20
30 66 0.29
31 10 0.04
32 6 0.03
33 22 0.10
34 20 0.09
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (30 bp):
TTTTCTAAAGCCCACAACTCTGTGGCACTC
Found at i:89876 original size:28 final size:28
Alignment explanation
Indices: 89657--90119 Score: 211
Period size: 28 Copynumber: 15.9 Consensus size: 28
89647 GCAACTTCTT
* * * *
89657 TTTTTAAAGTCCACAACTCTGTGGCACTC
1 TTTTCAAAGCCCACAAGTCAGTGGCAC-C
*
89686 TTTTCAAAAGCCCACAACTCAGTGGCATCCC
1 TTTTC-AAAGCCCACAAGTCAGTGGCA--CC
* ** * * *
89717 TTTTTAAAGTTCACAACTCTGTGGCATCA
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * * *
89746 TTTTTAAAGTCCACAACTCCGTGGCACATTTTT
1 TTTTCAAAGCCCACAAGTCAGTGGCAC-----C
* * *
89779 TTTTCAAAAGTCCATAACTCTA-TGGCACC
1 TTTTC-AAAGCCCACAAGTC-AGTGGCACC
* * *
89808 -CTTCTAAAGCCCACAAGTTAGTGGTATCTCC
1 TTTTC-AAAGCCCACAAGTCAGTGG---CACC
89839 TTTT-AAAGCCCACAAGTCAGTGGCACC
1 TTTTCAAAGCCCACAAGTCAGTGGCACC
*
89866 TTTTCAAAGCCTACAAGTCAGTGGCACC
1 TTTTCAAAGCCCACAAGTCAGTGGCACC
* **
89894 ATTTT-AAAGCCCATAAGTTGGTGGCACGC
1 -TTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * *
89923 TCTT-AAAGCCCATAAGTTAGTGGCATCCC
1 TTTTCAAAGCCCACAAGTCAGTGGCA--CC
*
89952 CTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
89981 TTTT-TAGGTCCACAAGTCAGTGGCAAC
1 TTTTCAAAGCCCACAAGTCAGTGGCACC
* *
90008 ATCTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
90037 TCTT-AGAGCCCATAAGTTAGTGGCATCCC
1 TTTTCAAAGCCCACAAGTCAGTGGCA--CC
* ** * *
90066 CTTTCAAAGCTTACAAATCAATGGCATCTC
1 TTTTCAAAGCCCACAAGTCAGTGGCA-C-C
* * *
90096 CTTTCAAAGCCCACGAGTTAGTGG
1 TTTTCAAAGCCCACAAGTCAGTGG
90120 TGTACCTTTT
Statistics
Matches: 338, Mismatches: 70, Indels: 51
0.74 0.15 0.11
Matches are distributed among these distances:
27 11 0.03
28 134 0.40
29 51 0.15
30 108 0.32
31 8 0.02
32 3 0.01
33 4 0.01
34 19 0.06
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (28 bp):
TTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:89912 original size:86 final size:83
Alignment explanation
Indices: 89801--90075 Score: 266
Period size: 86 Copynumber: 3.2 Consensus size: 83
89791 CATAACTCTA
* *
89801 TGGCACCCTTCTAAAGCCCACAAGTTAGTGGTATCTCCTTTTAAAGCCCACAAGTCAGTGGCACC
1 TGGCACCCTTTTAAAGCCCACAAGTTAGTGGCA-CT-C-TTTAAAGCCCACAAGTCAGTGGCACC
* *
89866 TTTTCAAAGCCTACAAGTCAG
63 CTTTCAAAGCCCACAAGTCAG
* * * * * *
89887 TGGCACCATTTTAAAGCCCATAAGTTGGTGGCACGCTCTTAAAGCCCATAAGTTAGTGGCATCCC
1 TGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACTCT-TTAAAGCCCACAAGTCAGTGGCA--CC
89952 CTTTCAAAGCCCACAAGTCAG
63 CTTTCAAAGCCCACAAGTCAG
* * * * *
89973 TGGCACCCTTTTTAGGTCCACAAGTCAGTGGCAACATC-TCAAAGCCCACAAGTCAGTGGCACCC
1 TGGCACCCTTTTAAAGCCCACAAGTTAGTGGC-AC-TCTTTAAAGCCCACAAGTCAGTGGCACCC
* * *
90037 TCTT-AGAGCCCATAAGTTAG
64 T-TTCAAAGCCCACAAGTCAG
*
90057 TGGCATCCCCTTTCAAAGC
1 TGGCA--CCCTTTTAAAGC
90076 TTACAAATCA
Statistics
Matches: 153, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
83 1 0.01
84 44 0.29
85 3 0.02
86 102 0.67
87 2 0.01
88 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (83 bp):
TGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACTCTTTAAAGCCCACAAGTCAGTGGCACCCTT
TCAAAGCCCACAAGTCAG
Found at i:90091 original size:114 final size:114
Alignment explanation
Indices: 89801--90075 Score: 376
Period size: 114 Copynumber: 2.4 Consensus size: 114
89791 CATAACTCTA
* * * *
89801 TGGCACCCT-TCTAAAGCCCACAAGTTAGTGGTATCTCCTTTTAAAGCCCACAAGTCAGTGGCAC
1 TGGCACCCTCT-TAAAGCCCATAAGTTAGTGGCATCCCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * **
89865 CTTTTCAAAGCCTACAAGTCAGTGGCACCATTTTAAAGCCCATAAGTTGG
65 CTTTTCAAAGCCTACAAGTCAGTGGCAACATCTCAAAGCCCACAAGTCAG
*
89915 TGGCACGCTCTTAAAGCCCATAAGTTAGTGGCATCCCCTTTCAAAGCCCACAAGTCAGTGGCACC
1 TGGCACCCTCTTAAAGCCCATAAGTTAGTGGCATCCCCTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
89980 CTTTT-TAGGTCC-ACAAGTCAGTGGCAACATCTCAAAGCCCACAAGTCAG
65 CTTTTCAAAG-CCTACAAGTCAGTGGCAACATCTCAAAGCCCACAAGTCAG
*
90029 TGGCACCCTCTTAGAGCCCATAAGTTAGTGGCATCCCCTTTCAAAGC
1 TGGCACCCTCTTAAAGCCCATAAGTTAGTGGCATCCCCTTTCAAAGC
90076 TTACAAATCA
Statistics
Matches: 143, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
114 134 0.94
115 9 0.06
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (114 bp):
TGGCACCCTCTTAAAGCCCATAAGTTAGTGGCATCCCCTTTCAAAGCCCACAAGTCAGTGGCACC
TTTTCAAAGCCTACAAGTCAGTGGCAACATCTCAAAGCCCACAAGTCAG
Found at i:90182 original size:28 final size:28
Alignment explanation
Indices: 90142--90272 Score: 120
Period size: 30 Copynumber: 4.6 Consensus size: 28
90132 TTAGTGGCAT
90142 ACCTTTTTAAAGCCCACAAGTCAGTAGC
1 ACCTTTTTAAAGCCCACAAGTCAGTAGC
*
90170 ACCTTTTTAAAGCCCACAAGTCAGTAGT
1 ACCTTTTTAAAGCCCACAAGTCAGTAGC
* * * * *
90198 ATCTCCTTTTAAAACCCACAAGTTAATGGC
1 A-C-CTTTTTAAAGCCCACAAGTCAGTAGC
* ** *
90228 ATACCTTTTTAAAGCCTATGAGTCAGTGGC
1 --ACCTTTTTAAAGCCCACAAGTCAGTAGC
*
90258 ACC-TTTTAATGCCCA
1 ACCTTTTTAAAGCCCA
90273 TACTAGCTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
27 10 0.12
28 31 0.37
29 1 0.01
30 39 0.47
31 1 0.01
32 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (28 bp):
ACCTTTTTAAAGCCCACAAGTCAGTAGC
Found at i:90210 original size:30 final size:28
Alignment explanation
Indices: 90146--90220 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
90136 TGGCATACCT
*
90146 TTTTAAAGCCCACAAGTCAGTAGCACCT
1 TTTTAAAGCCCACAAGTCAGTAGCACCC
*
90174 TTTTAAAGCCCACAAGTCAGTAGTATCTCC
1 TTTTAAAGCCCACAAGTCAGTAGCA-C-CC
*
90204 TTTTAAAACCCACAAGT
1 TTTTAAAGCCCACAAGT
90221 TAATGGCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 24 0.57
29 1 0.02
30 17 0.40
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
TTTTAAAGCCCACAAGTCAGTAGCACCC
Found at i:90258 original size:30 final size:30
Alignment explanation
Indices: 90134--90258 Score: 130
Period size: 30 Copynumber: 4.2 Consensus size: 30
90124 CCTTTTTATT
90134 AGTGGCATACCTTTTTAAAGCCCACAAGTC
1 AGTGGCATACCTTTTTAAAGCCCACAAGTC
*
90164 AGTAGC--ACCTTTTTAAAGCCCACAAGTC
1 AGTGGCATACCTTTTTAAAGCCCACAAGTC
* * * * *
90192 AGTAGTAT-CTCCTTTTAAAACCCACAAGTT
1 AGTGGCATAC-CTTTTTAAAGCCCACAAGTC
* * **
90222 AATGGCATACCTTTTTAAAGCCTATGAGTC
1 AGTGGCATACCTTTTTAAAGCCCACAAGTC
90252 AGTGGCA
1 AGTGGCA
90259 CCTTTTAATG
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 27 0.36
29 1 0.01
30 47 0.62
31 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (30 bp):
AGTGGCATACCTTTTTAAAGCCCACAAGTC
Found at i:92612 original size:79 final size:79
Alignment explanation
Indices: 92513--92699 Score: 187
Period size: 79 Copynumber: 2.4 Consensus size: 79
92503 GAGTGTTCTT
* * * * * * * *
92513 GAAAATAACGAGGCTAGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAAAATCGAGA
1 GAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTTAGAAAAAAAAACCGAGA
92577 TTGGAGTATCCCCTC
65 TTGGAGTATCCCCTC
* * * ** * * * *
92592 GAAAATAACGGGGTTGGAGTATCCCCAATTATTAAAAATCAATATTTTGGGAATAAAGCCGGGGT
1 GAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTAGAAAAAAAAACCGAGAT
92657 TGGAGTATCCCCTC
66 TGGAGTATCCCCTC
* *
92671 GGAAGTAACGGGGTTGGAGTATCCCCGAT
1 GAAAATAACGGGGTTGGAGTATCCCCGAT
92700 GAAATAACGA
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 1 0.01
79 86 0.99
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (79 bp):
GAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTAGAAAAAAAAACCGAGAT
TGGAGTATCCCCTC
Found at i:92707 original size:28 final size:28
Alignment explanation
Indices: 92651--92727 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
92641 GGAATAAAGC
*** *
92651 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
92679 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * *
92707 CGAGGTTGAAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
92728 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:92774 original size:52 final size:51
Alignment explanation
Indices: 92710--92932 Score: 225
Period size: 52 Copynumber: 4.3 Consensus size: 51
92700 GAAATAACGA
* * * * *
92710 GGTTGAAGTATCCTCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAG-AAATAAAACCGG
* * * * *
92762 AGTTGGAGTATCCCCGATTAAAG-GGAAAATTGGTGTTTT-GAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTATTTTAG-AAATAAAACCGG
*
92815 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTATTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTAGAAATAAAACCGG
* * * * **
92867 GGTTGGAGTATCCCCGATTATAAAAAATCAATATTTTAGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAACCGG
92918 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
92933 TCAGAAATAA
Statistics
Matches: 145, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
50 1 0.01
51 39 0.27
52 59 0.41
53 31 0.21
54 14 0.10
55 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAACCGG
Found at i:93050 original size:51 final size:52
Alignment explanation
Indices: 92951--93069 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 52
92941 AACGGGGTTG
* * * *
92951 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAATTAAAATCGGAGTTT
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAG-TT
93005 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTT
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTT
*
93055 GAAATATCCCCGATT
1 G-AGTATCCCCGATT
93070 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
50 3 0.05
51 30 0.52
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (52 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTT
Found at i:93063 original size:133 final size:131
Alignment explanation
Indices: 92814--93065 Score: 319
Period size: 133 Copynumber: 1.9 Consensus size: 131
92804 AATAAAACCA
*
92814 GGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTATTTTAGCAATAAAACCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTATTTTAGCAATAAAACCGGAGTTGGAGTATC
* * * *
92879 CCCGATTATAAAAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTCAGAAATAAC
66 CCCGATTATAAAAAATCAATATTTTAGAAATAAAATCGGAGTTGAAATATCCCCTCAGAAATAAC
92944 G
131 G
* * * * * *
92945 GGGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAATTAAAATCGGAGTTTGAGT
1 GGGTTGGAGTATCCCCGATTGTGGAA-AAATTAGT-ATTTTAGCAA-TAAAACCGGAGTTGGAGT
* * * *
93009 ATCCCCGATTATAGAAAATTAGTGTTTT-GAAAATAAAATCGGAGTTGAAATATCCCC
63 ATCCCCGATTATAAAAAATCAATATTTTAG-AAATAAAATCGGAGTTGAAATATCCCC
93066 GATTGTGGAG
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
130 3 0.03
131 29 0.28
132 8 0.08
133 62 0.61
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (131 bp):
GGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTATTTTAGCAATAAAACCGGAGTTGGAGTATC
CCCGATTATAAAAAATCAATATTTTAGAAATAAAATCGGAGTTGAAATATCCCCTCAGAAATAAC
G
Found at i:95450 original size:13 final size:13
Alignment explanation
Indices: 95432--95457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95422 ACAAAGATCC
95432 ATGTATCGATACA
1 ATGTATCGATACA
95445 ATGTATCGATACA
1 ATGTATCGATACA
95458 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:95453 original size:33 final size:33
Alignment explanation
Indices: 95411--95477 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
95401 AAAATTTCCA
***
95411 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
95444 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
95477 A
1 A
95478 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:95521 original size:19 final size:18
Alignment explanation
Indices: 95497--95564 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
95487 CAGTAGCTAA
95497 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
95516 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
95531 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
95548 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
95565 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:95537 original size:13 final size:13
Alignment explanation
Indices: 95519--95543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95509 ACAATACTTA
95519 TGTATCGATACAT
1 TGTATCGATACAT
95532 TGTATCGATACA
1 TGTATCGATACA
95544 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:95541 original size:32 final size:32
Alignment explanation
Indices: 95500--95562 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
95490 TAGCTAATTA
*
95500 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
95532 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
95563 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:101492 original size:21 final size:21
Alignment explanation
Indices: 101460--101512 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
101450 AAAACTCAAA
* *
101460 ATGTATCAATACATTGCAAGC
1 ATGTATCGATACATTACAAGC
* *
101481 ATGTGTCGATACATTATAAGC
1 ATGTATCGATACATTACAAGC
101502 ATGTATCGATA
1 ATGTATCGATA
101513 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTACAAGC
Found at i:102392 original size:3 final size:3
Alignment explanation
Indices: 102386--102426 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
102376 AAAAAAAAAA
102386 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
102427 ACAAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:109206 original size:21 final size:19
Alignment explanation
Indices: 109181--109230 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 19
109171 ACTCTATCTT
*
109181 TTTAAATATTTATTAATTTA
1 TTTAAATATTTATT-ATATA
109201 TATTAAATAAATTTATTATATA
1 T-TTAAAT--ATTTATTATATA
109223 TTTAAATA
1 TTTAAATA
109231 GGATGCCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 12 0.46
22 5 0.19
23 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAATATTTATTATATA
Found at i:109210 original size:96 final size:101
Alignment explanation
Indices: 108977--109210 Score: 236
Period size: 96 Copynumber: 2.3 Consensus size: 101
108967 TTAGACTTTA
108977 TTTTT-AATATTTAGTTGATTTGAT-TTAAATAAATTAATAAAAATTACATATTTAAATAGAAAA
1 TTTTTAAATATTTA-TT-ATTT-ATATTAAAT-AATTAATAAAAATTACA-ATTTAAATAGAAAA
* *
109040 AAGTTTATTAATTTTAAATTCATTTAATATCATGTAAACTAT
61 AAG-TTATTAATATTAAATACATTTAATATCATGTAAACTAT
* *
109082 TTTTAAAAATATTTATTATTTAAATTTAAATAATTAATAAAAA-TAC-ATTTAAATA-AAAAAA-
1 TTTT-TAAATATTTATTATTTATA-TTAAATAATTAATAAAAATTACAATTTAAATAGAAAAAAG
* **
109143 TT-TTAATATTAAATAGA-TT-ATATC-TGTGACTCTAT
64 TTATTAATATTAAATACATTTAATATCATGT-AAACTAT
109178 CTTTTTAAATATTTATTAATTTATATTAAATAA
1 -TTTTTAAATATTTATT-ATTTATATTAAATAA
109211 ATTTATTATA
Statistics
Matches: 113, Mismatches: 9, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
95 3 0.03
96 29 0.26
97 12 0.11
98 12 0.11
99 2 0.02
101 6 0.05
102 9 0.08
104 4 0.04
105 20 0.18
106 8 0.07
107 8 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (101 bp):
TTTTTAAATATTTATTATTTATATTAAATAATTAATAAAAATTACAATTTAAATAGAAAAAAGTT
ATTAATATTAAATACATTTAATATCATGTAAACTAT
Done.