Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 48 of 105
Found at i:9235936 original size:30 final size:30
Alignment explanation
Indices: 9235898--9235962 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
9235888 ATTATAATCA
9235898 TTTTTCCTTTCCTTTTT-TT-TTTTTTG-TTC
1 TTTTTCCTTT--TTTTTATTCTTTTTTGTTTC
9235927 TTTTCTCCTTTTTTTTATTCTTTTTTGTTTC
1 TTTT-TCCTTTTTTTTATTCTTTTTTGTTTC
9235958 TTTTT
1 TTTTT
9235963 GACATATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
28 5 0.16
29 6 0.19
30 14 0.44
31 7 0.22
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (30 bp):
TTTTTCCTTTTTTTTATTCTTTTTTGTTTC
Found at i:9240027 original size:15 final size:14
Alignment explanation
Indices: 9240004--9240038 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
9239994 AAGAGAACTC
9240004 TTTTGTTCTTTTTCT
1 TTTTGTTCTTTTT-T
*
9240019 TTTTTTTCTTTTTT
1 TTTTGTTCTTTTTT
9240033 TTTTGT
1 TTTTGT
9240039 CGATGATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.86
Consensus pattern (14 bp):
TTTTGTTCTTTTTT
Found at i:9241794 original size:20 final size:20
Alignment explanation
Indices: 9241771--9241863 Score: 66
Period size: 19 Copynumber: 4.7 Consensus size: 20
9241761 TTTGAACTAT
9241771 GGTTTTAGGGTTTCACTTAG
1 GGTTTTAGGGTTTCACTTAG
* * *
9241791 GG-TTTAGGGTTTTACCTAT
1 GGTTTTAGGGTTTCACTTAG
* * *
9241810 GG-CTTAGAGTTTTACACATAG
1 GGTTTTAG-GGTTT-CACTTAG
* *
9241831 GGTTTTAAGGTTT-ACCTAAG
1 GGTTTTAGGGTTTCA-CTTAG
9241851 GGTTTTAGGGTTT
1 GGTTTTAGGGTTT
9241864 AGGTCTCACA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
19 21 0.38
20 21 0.38
21 10 0.18
22 3 0.05
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (20 bp):
GGTTTTAGGGTTTCACTTAG
Found at i:9241915 original size:13 final size:14
Alignment explanation
Indices: 9241884--9241921 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
9241874 TAGGGCTTTG
*
9241884 TTTTAAAGTTTACA
1 TTTTAAGGTTTACA
9241898 TTTTAAGGTTTA-A
1 TTTTAAGGTTTACA
9241911 TTTTAAGGTTT
1 TTTTAAGGTTT
9241922 TGATTTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (14 bp):
TTTTAAGGTTTACA
Found at i:9252592 original size:3 final size:3
Alignment explanation
Indices: 9252584--9252698 Score: 62
Period size: 3 Copynumber: 39.7 Consensus size: 3
9252574 ATTTTCTTTG
* * * * *
9252584 TTA TTA TTA CTA TTA TTA TTT TTA -TA GTA -TA GTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
9252630 TTC TTA -TA GTA -TA GTA -TA TTG TATA TTA TCA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
*
9252673 -TA TTA TTA TTTC TTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TT
9252699 GTTTCCTTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
2 12 0.14
3 71 0.82
4 4 0.05
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:9252619 original size:28 final size:28
Alignment explanation
Indices: 9252588--9252646 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
9252578 TCTTTGTTAT
* *
9252588 TATTACTATTATTATTTTTATAGTATAG
1 TATTACTATTAGTATTCTTATAGTATAG
*
9252616 TATTATTATTAGTATTCTTATAGTATAG
1 TATTACTATTAGTATTCTTATAGTATAG
9252644 TAT
1 TAT
9252647 ATTGTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (28 bp):
TATTACTATTAGTATTCTTATAGTATAG
Found at i:9252674 original size:27 final size:24
Alignment explanation
Indices: 9252576--9252697 Score: 77
Period size: 27 Copynumber: 4.7 Consensus size: 24
9252566 CGAGATCAAT
*
9252576 TTTCTTTGTTATTATTACTATTATTA
1 TTTCTTAG-TATTATTA-TATTATTA
* *
9252602 TTTTTATAGTA-TAGTATTATTATTA
1 TTTCT-TAGTATTATTA-TATTATTA
* *
9252627 GTATTCTTA-TAGTATAGTATATTGTATA
1 -T-TTCTTAGTA-T-TATTATATTAT-TA
9252655 TTATCATTAGTATTATTATATTATTA
1 TT-TC-TTAGTATTATTATATTATTA
*
9252681 TTTCTTATTATTATTAT
1 TTTCTTAGTATTATTAT
9252698 TGTTTCCTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
24 12 0.16
25 16 0.21
26 14 0.18
27 22 0.29
28 11 0.14
29 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (24 bp):
TTTCTTAGTATTATTATATTATTA
Found at i:9253040 original size:20 final size:21
Alignment explanation
Indices: 9253004--9253046 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
9252994 AGGTTTTGGG
9253004 GATTCTAGGATTCTGGGATTA
1 GATTCTAGGATTCTGGGATTA
*
9253025 GATT-TAGG-TTCATGGGGTTA
1 GATTCTAGGATTC-TGGGATTA
9253045 GA
1 GA
9253047 ATTAAGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.23, C:0.07, G:0.33, T:0.37
Consensus pattern (21 bp):
GATTCTAGGATTCTGGGATTA
Found at i:9253452 original size:15 final size:15
Alignment explanation
Indices: 9253432--9253503 Score: 67
Period size: 15 Copynumber: 4.6 Consensus size: 15
9253422 ATCGTAGATT
9253432 TTTATTTTATTTTTA
1 TTTATTTTATTTTTA
9253447 TTTATTTTATATTTTAAA
1 TTTATTTTAT-TTTT--A
*
9253465 TTT-TTTTAATTTTAA
1 TTTATTTT-ATTTTTA
*
9253480 TTTAATTTT-TTATTA
1 TTT-ATTTTATTTTTA
9253495 TTTATTTTA
1 TTTATTTTA
9253504 CTAACTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
14 5 0.11
15 21 0.45
16 4 0.09
17 11 0.23
18 6 0.13
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:9253461 original size:22 final size:24
Alignment explanation
Indices: 9253435--9253521 Score: 74
Period size: 24 Copynumber: 3.6 Consensus size: 24
9253425 GTAGATTTTT
9253435 ATTTTATTTTTATTTATTTTA-T-
1 ATTTTATTTTTATTTATTTTATTA
*
9253457 ATTTTAAATTTTT-TTAATTTTAATTTA
1 ATTTT--ATTTTTATTTATTTT-A-TTA
* *
9253484 ATTTT-TTATTATTTATTTTACTA
1 ATTTTATTTTTATTTATTTTATTA
9253507 ACTTTTATTTTTATT
1 A-TTTTATTTTTATT
9253522 GAGAAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
22 5 0.10
23 10 0.20
24 16 0.31
25 14 0.27
26 1 0.02
27 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTATTTTTATTTATTTTATTA
Found at i:9253609 original size:15 final size:17
Alignment explanation
Indices: 9253591--9253626 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9253581 AAAACAAAAG
9253591 AAAAC-AAA-AAATATA
1 AAAACTAAATAAATATA
9253606 AAAACTAAATAAATATA
1 AAAACTAAATAAATATA
9253623 AAAA
1 AAAA
9253627 AATCTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 3 0.16
17 11 0.58
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAACTAAATAAATATA
Found at i:9259352 original size:20 final size:21
Alignment explanation
Indices: 9259324--9259362 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
9259314 ACTTGAAATC
*
9259324 TTGTGAATCTTTCGGAAACCT
1 TTGTGAATCTTTAGGAAACCT
9259345 TTGT-AATCTTTAGGAAAC
1 TTGTGAATCTTTAGGAAAC
9259363 TTGGAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (21 bp):
TTGTGAATCTTTAGGAAACCT
Found at i:9259838 original size:55 final size:55
Alignment explanation
Indices: 9259579--9259907 Score: 245
Period size: 55 Copynumber: 5.9 Consensus size: 55
9259569 ATTTTTTTCG
** * * * *
9259579 ACTTGTGGTTTCATCTTGGTCA-TCTGAACTTGGCTTAATCTAGATCATTTTTCAA
1 ACTTGTGGTTTCATCTCAGTCATTC-GATCTTAGCTCAATCTAGATCATTTTCCAA
** * * * *
9259634 ACTTGTGGTTTTGTCT-TGATCA-TCTGATCTTAGCTCAGTCCAAATCATTTTCCAA
1 ACTTGTGGTTTCATCTCAG-TCATTC-GATCTTAGCTCAATCTAGATCATTTTCCAA
* * * * * * * *
9259689 ACTTATGGTTTCATCTGTCTCAATCTTTCAATCTTAGCTCAGTCCAGATCATTTT-TAG
1 ACTTGTGGTTTCA----TCTCAGTCATTCGATCTTAGCTCAATCTAGATCATTTTCCAA
* * * * *
9259747 ATTTGTAGTTTCGT-TCCAGTCATTCGATCTTAGCTCAGTCTCGATCATTTTCCAA
1 ACTTGTGGTTTCATCT-CAGTCATTCGATCTTAGCTCAATCTAGATCATTTTCCAA
* * *
9259802 ACTTATGGTTTCATCTCAGTCATTCGATCTTGGCTCAATCTAGATCATTTTCCAG
1 ACTTGTGGTTTCATCTCAGTCATTCGATCTTAGCTCAATCTAGATCATTTTCCAA
* ** * * *
9259857 ACTTGTGATTTTGTCTCAGTCAATCAATCTTTGCTCAATCTAGATCATTTT
1 ACTTGTGGTTTCATCTCAGTCATTCGATCTTAGCTCAATCTAGATCATTTT
9259908 ATTTATCACC
Statistics
Matches: 218, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
53 1 0.00
54 32 0.15
55 143 0.66
56 1 0.00
58 10 0.05
59 29 0.13
60 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (55 bp):
ACTTGTGGTTTCATCTCAGTCATTCGATCTTAGCTCAATCTAGATCATTTTCCAA
Found at i:9260150 original size:28 final size:28
Alignment explanation
Indices: 9260118--9260172 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
9260108 TCTTTGTTAT
*
9260118 TATTACTATAATTATT-TTGATAGTATAA
1 TATTACTATAAGTATTATT-ATAGTATAA
* *
9260146 TATTAGTATTAGTATTATTATAGTATA
1 TATTACTATAAGTATTATTATAGTATA
9260173 GTATATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (28 bp):
TATTACTATAAGTATTATTATAGTATAA
Found at i:9260157 original size:6 final size:6
Alignment explanation
Indices: 9260146--9260225 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
9260136 GATAGTATAA
* *
9260146 TATTAG TATTAG TATTAT TA-TAG TA-TAG TATATAG TA-TAG TATATTG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TAT-TAG TATTAG TAT-TAG
* * * * *
9260193 TA-TAT TATTAT TATTAT TATTAT TATTAT TATT
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATT
9260226 TTCTTTCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
5 17 0.27
6 38 0.59
7 9 0.14
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (6 bp):
TATTAG
Found at i:9260158 original size:17 final size:18
Alignment explanation
Indices: 9260138--9260188 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
9260128 ATTATTTTGA
9260138 TAGTATAATAT-TAGTAT
1 TAGTATAATATATAGTAT
*
9260155 TAGTATTAT-TATAGTA-
1 TAGTATAATATATAGTAT
9260171 TAGTAT-ATAGTATAGTAT
1 TAGTATAATA-TATAGTAT
9260189 ATTGTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.07
16 7 0.24
17 20 0.69
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (18 bp):
TAGTATAATATATAGTAT
Found at i:9260179 original size:12 final size:12
Alignment explanation
Indices: 9260137--9260196 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
9260127 AATTATTTTG
9260137 ATAGTATA-A-T
1 ATAGTATATAGT
9260147 ATTAGTAT-TAGT
1 A-TAGTATATAGT
9260159 AT--TATTATAGT
1 ATAGTA-TATAGT
9260170 ATAGTATATAGT
1 ATAGTATATAGT
*
9260182 ATAGTATATTGT
1 ATAGTATATAGT
9260194 ATA
1 ATA
9260197 TTATTATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 14 0.33
12 22 0.52
13 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (12 bp):
ATAGTATATAGT
Found at i:9260203 original size:3 final size:3
Alignment explanation
Indices: 9260195--9260225 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9260185 GTATATTGTA
9260195 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9260226 TTCTTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9260578 original size:21 final size:23
Alignment explanation
Indices: 9260554--9260602 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
9260544 TGGAGATTCT
**
9260554 GGGTTTA-GATTCGGGTTCTTG-
1 GGGTTTATGATTAAGGTTCTTGA
9260575 GGG-TTATGATTAAGGTTCTTGA
1 GGGTTTATGATTAAGGTTCTTGA
9260597 GGGTTT
1 GGGTTT
9260603 CTACAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.13
21 15 0.65
22 3 0.13
23 2 0.09
ACGTcount: A:0.14, C:0.06, G:0.37, T:0.43
Consensus pattern (23 bp):
GGGTTTATGATTAAGGTTCTTGA
Found at i:9261000 original size:9 final size:9
Alignment explanation
Indices: 9260988--9261069 Score: 67
Period size: 9 Copynumber: 8.8 Consensus size: 9
9260978 TTCCATTTTA
9260988 TTTTTA-TT
1 TTTTTATTT
9260996 TTTTTATTT
1 TTTTTATTT
9261005 TTTTTATTT
1 TTTTTATTT
* *
9261014 ATTTTATAT
1 TTTTTATTT
**
9261023 TTTGAATTT
1 TTTTTATTT
*
9261032 TTTTAATTT
1 TTTTTATTT
9261041 TATTTTGAATTT
1 T-TTTT--ATTT
9261053 TTTATTATTT
1 TTT-TTATTT
*
9261063 ATTTTAT
1 TTTTTAT
9261070 CGACTTTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
8 6 0.10
9 36 0.60
10 9 0.15
11 2 0.03
12 7 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTTATTT
Found at i:9261006 original size:28 final size:28
Alignment explanation
Indices: 9260982--9261058 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
9260972 TCTTTTTTCC
*
9260982 ATTTTATTTTTATTTTTTTATTTTTTTT
1 ATTTTATTTTTATTTTTTTATTTTTTTA
**
9261010 A-TTTA-TTTTATATTTTGAATTTTTTTA
1 ATTTTATTTTTAT-TTTTTTATTTTTTTA
* *
9261037 ATTTTATTTTGAATTTTTTATT
1 ATTTTATTTTTATTTTTTTATT
9261059 ATTTATTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
26 6 0.15
27 17 0.44
28 12 0.31
29 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (28 bp):
ATTTTATTTTTATTTTTTTATTTTTTTA
Found at i:9261046 original size:21 final size:22
Alignment explanation
Indices: 9261006--9261064 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
9260996 TTTTTATTTT
*
9261006 TTTTATTTATTTTATATTTTGAA
1 TTTT-TTTAATTTATATTTTGAA
9261029 TTTTTTTAATTT-TATTTTGAA
1 TTTTTTTAATTTATATTTTGAA
*
9261050 TTTTTTATTATTTAT
1 TTTTTT-TAATTTAT
9261065 TTTATCGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 15 0.47
22 12 0.38
23 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (22 bp):
TTTTTTTAATTTATATTTTGAA
Found at i:9261084 original size:7 final size:7
Alignment explanation
Indices: 9260983--9261067 Score: 59
Period size: 7 Copynumber: 12.3 Consensus size: 7
9260973 CTTTTTTCCA
9260983 TTTTA-T
1 TTTTATT
9260989 TTTTATTT
1 TTTTA-TT
9260997 TTTTATT
1 TTTTATT
9261004 TTTT-TT
1 TTTTATT
*
9261010 ATTTATT
1 TTTTATT
*
9261017 TTATATT
1 TTTTATT
**
9261024 TTGAATT
1 TTTTATT
*
9261031 TTTT-TAA
1 TTTTAT-T
9261038 TTTTATT
1 TTTTATT
**
9261045 TTGAATT
1 TTTTATT
9261052 TTTTATT
1 TTTTATT
*
9261059 ATTTATT
1 TTTTATT
9261066 TT
1 TT
9261068 ATCGACTTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
6 11 0.19
7 41 0.69
8 7 0.12
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTATT
Found at i:9261177 original size:15 final size:17
Alignment explanation
Indices: 9261147--9261179 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
9261137 AAAAGGACAC
9261147 AAATAAAAGAAAACAAA
1 AAATAAAAGAAAACAAA
9261164 AAAT-AAAG-AAACAAA
1 AAATAAAAGAAAACAAA
9261179 A
1 A
9261180 TAAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (17 bp):
AAATAAAAGAAAACAAA
Found at i:9264298 original size:16 final size:16
Alignment explanation
Indices: 9264279--9264313 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9264269 AAATTATTAA
*
9264279 ATTAATAAATATATTT
1 ATTAATAAATAAATTT
*
9264295 ATTAATAAGTAAATTT
1 ATTAATAAATAAATTT
9264311 ATT
1 ATT
9264314 TTTATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
ATTAATAAATAAATTT
Found at i:9264500 original size:15 final size:16
Alignment explanation
Indices: 9264480--9264509 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9264470 TTAGTTTAAA
9264480 AATATAAAA-AATTAT
1 AATATAAAATAATTAT
9264495 AATATAAAATAATTA
1 AATATAAAATAATTA
9264510 CAATTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:9268428 original size:18 final size:17
Alignment explanation
Indices: 9268405--9268451 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
9268395 TATATTTTGA
9268405 CTTTTCTTTCTTTCTTT
1 CTTTTCTTTCTTTCTTT
9268422 CCTTTTCCTTT-TTTCTTT
1 -CTTTT-CTTTCTTTCTTT
9268440 CTTATTCTTTCT
1 CTT-TTCTTTCT
9268452 CTCCTCCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (17 bp):
CTTTTCTTTCTTTCTTT
Found at i:9268496 original size:2 final size:2
Alignment explanation
Indices: 9268489--9268514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9268479 TGCTATGAAA
9268489 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
9268515 CTCCAAACAT
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:9268874 original size:13 final size:13
Alignment explanation
Indices: 9268841--9268880 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9268831 ATGATACATC
9268841 ATCACATCATTGTT
1 ATCACATCATT-TT
9268855 ATCACATCATTTT
1 ATCACATCATTTT
* *
9268868 GTCACATCCTTTT
1 ATCACATCATTTT
9268881 CAATAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (13 bp):
ATCACATCATTTT
Found at i:9269262 original size:6 final size:6
Alignment explanation
Indices: 9269251--9269289 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
9269241 TTTTGCATAG
* *
9269251 ATATAA ATATAA ATATAAA ATATAA ATGTAA ATGTAA AT
1 ATATAA ATATAA ATAT-AA ATATAA ATATAA ATATAA AT
9269290 TTCTAGCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:9269275 original size:19 final size:19
Alignment explanation
Indices: 9269251--9269288 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9269241 TTTTGCATAG
9269251 ATATAAATATAAATATAAA
1 ATATAAATATAAATATAAA
* *
9269270 ATATAAATGTAAATGTAAA
1 ATATAAATATAAATATAAA
9269289 TTTCTAGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
ATATAAATATAAATATAAA
Found at i:9271256 original size:16 final size:16
Alignment explanation
Indices: 9271232--9271268 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
9271222 AATTACACCT
* *
9271232 AAAATATAAATAATAG
1 AAAAGATAAATAAAAG
9271248 AAAAGATAAATAAAAG
1 AAAAGATAAATAAAAG
9271264 AAAAG
1 AAAAG
9271269 GAAGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (16 bp):
AAAAGATAAATAAAAG
Found at i:9273170 original size:15 final size:15
Alignment explanation
Indices: 9273145--9273184 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
9273135 AAATTTTTTA
*
9273145 AAAAATAAAAAATTT
1 AAAATTAAAAAATTT
*
9273160 AGAATTAAAAAATTT
1 AAAATTAAAAAATTT
9273175 AAAATTAAAA
1 AAAATTAAAA
9273185 TTAATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATTAAAAAATTT
Found at i:9273455 original size:2 final size:2
Alignment explanation
Indices: 9273450--9273475 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9273440 AAAATGTCTG
9273450 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
9273476 ATAAATAAGA
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:9273813 original size:27 final size:27
Alignment explanation
Indices: 9273774--9273828 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
9273764 AGCGAACGTG
*
9273774 AAAGGAGGGGAAG-AGAAGCAGAAAAA
1 AAAGGAGGCGAAGAAGAAGCAGAAAAA
**
9273800 AAAGAGAGGCGAAGAAGAAGTGGAAAAA
1 AAAG-GAGGCGAAGAAGAAGCAGAAAAA
9273828 A
1 A
9273829 CACATAGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 8 0.33
28 12 0.50
ACGTcount: A:0.58, C:0.04, G:0.36, T:0.02
Consensus pattern (27 bp):
AAAGGAGGCGAAGAAGAAGCAGAAAAA
Found at i:9276106 original size:29 final size:29
Alignment explanation
Indices: 9276073--9276132 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
9276063 TGAAAAACAG
* *
9276073 AAAAAGCAAAAAAT-AAGAAAATCTTCTC
1 AAAAAACAAAAAATAAAAAAAATCTTCTC
* *
9276101 AAAAAATAAAAAATAAAAAAAATCTTTTC
1 AAAAAACAAAAAATAAAAAAAATCTTCTC
9276130 AAA
1 AAA
9276133 CAAGTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (29 bp):
AAAAAACAAAAAATAAAAAAAATCTTCTC
Found at i:9276473 original size:14 final size:14
Alignment explanation
Indices: 9276451--9276486 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
9276441 ATTTTAAGAC
* *
9276451 TAATTTTTAATTTT
1 TAATATTTAATATT
9276465 TAATATTTAATATT
1 TAATATTTAATATT
9276479 TAATATTT
1 TAATATTT
9276487 TGATAAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATATTTAATATT
Found at i:9276755 original size:3 final size:3
Alignment explanation
Indices: 9276747--9276815 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
9276737 AGTTAAAGAT
9276747 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
9276794 ATA GTA GT- ATA ATA AAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
9276816 GTTTAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 3 0.05
3 57 0.95
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9277016 original size:22 final size:22
Alignment explanation
Indices: 9276986--9277033 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
9276976 TATAGAATAT
9276986 TAAGAAAT-ATAAAAATAAATAAA
1 TAAGAAATAAT-AAAATAAA-AAA
9277009 TAAG-AATAATAAAATAAAAAA
1 TAAGAAATAATAAAATAAAAAA
9277030 TAAG
1 TAAG
9277034 GAAAAAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.29
22 11 0.46
23 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (22 bp):
TAAGAAATAATAAAATAAAAAA
Found at i:9277492 original size:13 final size:13
Alignment explanation
Indices: 9277470--9277513 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
9277460 TTTGTGAAAC
*
9277470 AAAACTCTAAAAT
1 AAAACCCTAAAAT
*
9277483 AAAACCCTAAAGT
1 AAAACCCTAAAAT
* *
9277496 AAAACCTTAAAAC
1 AAAACCCTAAAAT
9277509 AAAAC
1 AAAAC
9277514 TTTAAATCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAACCCTAAAAT
Found at i:9277644 original size:13 final size:13
Alignment explanation
Indices: 9277628--9277653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9277618 TAATGTGAAA
9277628 CCTAAAATAAAAC
1 CCTAAAATAAAAC
9277641 CCTAAAATAAAAC
1 CCTAAAATAAAAC
9277654 TTTAGTCGAA
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:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
CCTAAAATAAAAC
Found at i:9283460 original size:18 final size:18
Alignment explanation
Indices: 9283416--9283461 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
9283406 AAAATGCCTT
9283416 AAAGAAAAAAAAGTGAAA
1 AAAGAAAAAAAAGTGAAA
9283434 AAA-ATAAAAAAAGAT-AAA
1 AAAGA-AAAAAAAG-TGAAA
9283452 AAAGAAAAAA
1 AAAGAAAAAA
9283462 GAAAGTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 22 0.88
19 2 0.08
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAGAAAAAAAAGTGAAA
Found at i:9284238 original size:9 final size:9
Alignment explanation
Indices: 9284211--9284253 Score: 54
Period size: 8 Copynumber: 4.8 Consensus size: 9
9284201 GGCATATTTA
9284211 AAAAAAATG
1 AAAAAAATG
9284220 AAAGAAAAATG
1 -AA-AAAAATG
9284231 AAAAAAATG
1 AAAAAAATG
9284240 -AAAAAA-G
1 AAAAAAATG
9284247 AAAAAAA
1 AAAAAAA
9284254 ATGGTTATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 1 0.03
8 12 0.39
9 7 0.23
10 4 0.13
11 7 0.23
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAAAAAATG
Found at i:9284254 original size:9 final size:10
Alignment explanation
Indices: 9284210--9284256 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 10
9284200 GGGCATATTT
9284210 AAAAAAAATG
1 AAAAAAAATG
9284220 AAAGAAAAATG
1 AAA-AAAAATG
9284231 -AAAAAAATG
1 AAAAAAAATG
9284240 --AAAAAA-G
1 AAAAAAAATG
9284247 AAAAAAAATG
1 AAAAAAAATG
9284257 GTTATGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 1 0.03
8 6 0.18
9 13 0.39
10 6 0.18
11 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:9284254 original size:20 final size:20
Alignment explanation
Indices: 9284210--9284254 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
9284200 GGGCATATTT
*
9284210 AAAAAAAATGAAAGAAAAAT
1 AAAAAAAATGAAAGAAAAAA
* *
9284230 GAAAAAAATGAAA-AAAGAA
1 AAAAAAAATGAAAGAAAAAA
9284249 AAAAAA
1 AAAAAA
9284255 TGGTTATGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAAAATGAAAGAAAAAA
Found at i:9284756 original size:7 final size:7
Alignment explanation
Indices: 9284746--9284815 Score: 61
Period size: 7 Copynumber: 9.4 Consensus size: 7
9284736 TTTAAAAGAA
9284746 AAAAAAG
1 AAAAAAG
*
9284753 AAAAAAA
1 AAAAAAG
9284760 AAAGAAAG
1 AAA-AAAG
*
9284768 TAAAAAG
1 AAAAAAG
9284775 AAAAAAG
1 AAAAAAG
*
9284782 AAAAAGTG
1 AAAAA-AG
9284790 AAAGAAAG
1 AAA-AAAG
9284798 AAGGAAAA-
1 AA--AAAAG
9284806 AAAAAAG
1 AAAAAAG
9284813 AAA
1 AAA
9284816 TGAATAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
6 4 0.08
7 27 0.53
8 14 0.27
9 5 0.10
10 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:9286494 original size:10 final size:9
Alignment explanation
Indices: 9286474--9286530 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
9286464 AAGAAAAAAC
*
9286474 AAAGCGAAA
1 AAAGGGAAA
9286483 AAAGGTGAAA
1 AAAGG-GAAA
* *
9286493 AAATGAAAA
1 AAAGGGAAA
9286502 AAAGGGAAA
1 AAAGGGAAA
*
9286511 AAATGGAAA
1 AAAGGGAAA
9286520 AAA-GGAAA
1 AAAGGGAAA
9286528 AAA
1 AAA
9286531 AACAAAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 8 0.20
9 25 0.61
10 8 0.20
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (9 bp):
AAAGGGAAA
Found at i:9286531 original size:18 final size:18
Alignment explanation
Indices: 9286479--9286530 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
9286469 AAAACAAAGC
9286479 GAAAAAAGGTGAAAAAATG
1 GAAAAAAGG-GAAAAAATG
*
9286498 AAAAAAAGGGAAAAAATG
1 GAAAAAAGGGAAAAAATG
9286516 GAAAAAA-GGAAAAAA
1 GAAAAAAGGGAAAAAA
9286531 AACAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.26
18 15 0.48
19 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (18 bp):
GAAAAAAGGGAAAAAATG
Found at i:9286924 original size:34 final size:32
Alignment explanation
Indices: 9286886--9286990 Score: 107
Period size: 34 Copynumber: 3.3 Consensus size: 32
9286876 TGGCCATAAA
9286886 AAAATTAATTAAAAAATTTA-AATTTTAAAATTTT
1 AAAATTAA-TAAAAAATTTAGAA-TTTAAAA-TTT
9286920 AAAATATAATAAAAAATTTAGAATTTAAAATTT
1 AAAAT-TAATAAAAAATTTAGAATTTAAAATTT
*
9286953 -AAATT--T--AAAATTTAAAATTTAAAA-TT
1 AAAATTAATAAAAAATTTAGAATTTAAAATTT
9286979 AATAATTAATAA
1 AA-AATTAATAA
9286991 TAAGAAAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
26 2 0.03
27 18 0.29
28 4 0.06
29 1 0.02
30 1 0.02
31 1 0.02
32 4 0.06
33 3 0.05
34 23 0.37
35 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
AAAATTAATAAAAAATTTAGAATTTAAAATTT
Found at i:9286956 original size:20 final size:20
Alignment explanation
Indices: 9286898--9286985 Score: 81
Period size: 20 Copynumber: 4.3 Consensus size: 20
9286888 AATTAATTAA
*
9286898 AAAATTTAAATTTTAAAATTTT
1 AAAATTTAAAATTT-AAA-TTT
* *
9286920 AAAATATAATAA--AAAATTT
1 AAAATTTAA-AATTTAAATTT
*
9286939 AGAATTTAAAATTTAAATTT
1 AAAATTTAAAATTTAAATTT
*
9286959 AAAATTTAAAATTTAAAATT
1 AAAATTTAAAATTTAAATTT
9286979 AATAATT
1 AA-AATT
9286986 AATAATAAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.04
19 10 0.19
20 29 0.54
21 4 0.07
22 8 0.15
23 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
AAAATTTAAAATTTAAATTT
Found at i:9286987 original size:27 final size:27
Alignment explanation
Indices: 9286903--9286987 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
9286893 ATTAAAAAAT
*
9286903 TTAAATTTTAAAATTTTAAAATATAATAA
1 TTAAAATTTAAAA-TTTAAAAT-TAATAA
* *
9286932 --AAAATTTAGAATTTAAAATTTAA-AT
1 TTAAAATTTAAAATTTAAAA-TTAATAA
9286957 TTAAAATTTAAAATTTAAAATTAATAA
1 TTAAAATTTAAAATTTAAAATTAATAA
9286984 TTAA
1 TTAA
9286988 TAATAAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
25 1 0.02
26 14 0.30
27 32 0.68
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
TTAAAATTTAAAATTTAAAATTAATAA
Found at i:9287005 original size:7 final size:7
Alignment explanation
Indices: 9286931--9287011 Score: 56
Period size: 7 Copynumber: 11.6 Consensus size: 7
9286921 AAATATAATA
9286931 AAAAATT
1 AAAAATT
* *
9286938 TAGAATT
1 AAAAATT
*
9286945 TAAAATT
1 AAAAATT
*
9286952 -TAAATT
1 AAAAATT
*
9286958 TAAAATT
1 AAAAATT
*
9286965 TAAAATT
1 AAAAATT
*
9286972 TAAAATT
1 AAAAATT
*
9286979 AATAATT
1 AAAAATT
* *
9286986 AATAATA
1 AAAAATT
9286993 AGAAAATT
1 A-AAAATT
9287001 AAAAATT
1 AAAAATT
9287008 AAAA
1 AAAA
9287012 CAACAAAAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.08
7 52 0.84
8 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (7 bp):
AAAAATT
Found at i:9287020 original size:22 final size:22
Alignment explanation
Indices: 9286973--9287020 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
9286963 TTTAAAATTT
* * *
9286973 AAAATTAATAATTAATAATAAG
1 AAAATTAAAAATTAATAACAAA
9286995 AAAATTAAAAATTAA-AACAACA
1 AAAATTAAAAATTAATAACAA-A
9287017 AAAA
1 AAAA
9287021 GAGCTTTGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAATTAAAAATTAATAACAAA
Found at i:9287237 original size:2 final size:2
Alignment explanation
Indices: 9287230--9287264 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9287220 AGGCAGCCAG
* *
9287230 AT AT AT AT AT AC AT AT AT AT AT GT 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
9287265 CACCCACACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:9288718 original size:12 final size:11
Alignment explanation
Indices: 9288697--9288745 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
9288687 TCAGTTAAAG
9288697 ATAAAATAATA
1 ATAAAATAATA
9288708 ATAACAATAATA
1 ATAA-AATAATA
*
9288720 ATAAGATAATA
1 ATAAAATAATA
* * *
9288731 GTATAATAAAA
1 ATAAAATAATA
9288742 ATAA
1 ATAA
9288746 TGTTTAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:9289396 original size:13 final size:13
Alignment explanation
Indices: 9289378--9289419 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
9289368 TAAATTTATG
*
9289378 AAATGAAACCTTA
1 AAATGAAACCCTA
9289391 AAATGAAACCCTA
1 AAATGAAACCCTA
* *
9289404 AAGTAAAACCCTA
1 AAATGAAACCCTA
9289417 AAA
1 AAA
9289420 CAAAACTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (13 bp):
AAATGAAACCCTA
Found at i:9289534 original size:39 final size:40
Alignment explanation
Indices: 9289459--9289548 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 40
9289449 AACCCTAGGA
* *
9289459 GAGACCCTAAACTATAAGTGGAATTTCAAAAGCTTAA-AT
1 GAGACCCTAAACTATAAGTGAAATTTCAAAACCTTAATAT
* *
9289498 GAGACCCTAAACTATAA-TCGAAATCTT-GAAACCTTAATGT
1 GAGACCCTAAACTATAAGT-GAAAT-TTCAAAACCTTAATAT
*
9289538 GAAACCCTAAA
1 GAGACCCTAAA
9289549 ATGAAACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 1 0.02
39 29 0.67
40 13 0.30
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (40 bp):
GAGACCCTAAACTATAAGTGAAATTTCAAAACCTTAATAT
Found at i:9290359 original size:17 final size:17
Alignment explanation
Indices: 9290322--9290360 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9290312 TAATGAAAGG
* *
9290322 AATTATAATTAAATTAT
1 AATTATAATTAAATCAC
9290339 AATTATAATTAAATCAC
1 AATTATAATTAAATCAC
9290356 AATTA
1 AATTA
9290361 ATTTTTTTTT
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:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATAATTAAATCAC
Found at i:9297895 original size:251 final size:252
Alignment explanation
Indices: 9297436--9297935 Score: 781
Period size: 251 Copynumber: 2.0 Consensus size: 252
9297426 TGTTTGCTAA
** * * *
9297436 AAATGCTGTTAAGAACGTCGTCTATACCTGCATTGAGAAAAATAATGGCATTTTAGGAAAAAATG
1 AAATGCTGTTAAGAACGTCACCTATACCTGAATTAAGAAAAATAATGACATTTTAGGAAAAAATG
* *
9297501 CTGCTAACTTAATGACATTTGTACTAACAAATATCGTTAAATTTAGTGGTATTTTTGGATACAAA
66 CTGCTAACTTAAAGACATTTGTACTAACAAATATCGCTAAATTTAGTGGTATTTTTGGATACAAA
* * *
9297566 TGCCATTAATTTATGTAATTTAGAGACTTTTTTTACACAAATGCTGCTAAATTTAGCGGTGTTTT
131 TGCCATTAATTTATGTAATTTAAAGACATTTTTTACACAAATGCAGCTAAATTTAGCGGTGTTTT
*
9297631 TAAATACAAATGCCACGATTTCTAAATTTAGTGATGTTTTTTCATACAAATGCCATT
196 TAAACACAAATGCCACGATTTCTAAATTTAGTGATGTTTTTTCATACAAATGCCATT
*
9297688 AAATGCTGTTAAGAAC-TCACCTATACTTGTAATTAAGAAAAATAATGACATTTTAGGAAAAAAT
1 AAATGCTGTTAAGAACGTCACCTATACCTG-AATTAAGAAAAATAATGACATTTTAGGAAAAAAT
* ** ** *
9297752 GTTGCTAACTTAACAG-TGTTTGTGTTGACAAATATCGCTAAATTTAGTGGTA-TTTTGGATACA
65 GCTGCTAACTTAA-AGACATTTGTACTAACAAATATCGCTAAATTTAGTGGTATTTTTGGATACA
9297815 AATGCCATTAATTTATGTAATTTAAAGACATTTTTTACACAAATGCAGCTAAATTTAGCGGTGTT
129 AATGCCATTAATTTATGTAATTTAAAGACATTTTTTACACAAATGCAGCTAAATTTAGCGGTGTT
* *
9297880 TTTAAACACAAATGCCACTATTTTTAAATTTAGTGATGTTTTTTCATACAAATGCC
194 TTTAAACACAAATGCCACGATTTCTAAATTTAGTGATGTTTTTTCATACAAATGCC
9297936 GCTAAATTAG
Statistics
Matches: 226, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
251 136 0.60
252 89 0.39
253 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (252 bp):
AAATGCTGTTAAGAACGTCACCTATACCTGAATTAAGAAAAATAATGACATTTTAGGAAAAAATG
CTGCTAACTTAAAGACATTTGTACTAACAAATATCGCTAAATTTAGTGGTATTTTTGGATACAAA
TGCCATTAATTTATGTAATTTAAAGACATTTTTTACACAAATGCAGCTAAATTTAGCGGTGTTTT
TAAACACAAATGCCACGATTTCTAAATTTAGTGATGTTTTTTCATACAAATGCCATT
Found at i:9298132 original size:63 final size:60
Alignment explanation
Indices: 9298048--9298239 Score: 179
Period size: 62 Copynumber: 3.1 Consensus size: 60
9298038 AATTGAATAC
* * *
9298048 TCAAGGCATTTTTTGCTAAAAACGCCTTGAATAATCTCATTCAATTTTTCGTAAAGGATTAT
1 TCAAGGCATTTTTAGCCAAAAATGCCTTGAATAATC-CATTCAATTTTT-GTAAAGGATTAT
* ** ***
9298110 TTAAGGCATTTTCTAGCCAAAAATGCCTTGAATAATCCAAAACAAAAATTG-AAAGGGATTAT
1 TCAAGGCATTTT-TAGCCAAAAATGCCTTGAATAATCC-ATTCAATTTTTGTAAA-GGATTAT
* * * * * *
9298172 TGAAGTCATTTTTGGCCAAAAATACCTTGAATAACCCCATTTAATTTTTTGTAAAGGATTAT
1 TCAAGGCATTTTTAGCCAAAAATGCCTTGAATAA-TCCATTCAA-TTTTTGTAAAGGATTAT
9298234 TCAAGG
1 TCAAGG
9298240 GGTTTTCTAA
Statistics
Matches: 102, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
61 26 0.25
62 46 0.45
63 30 0.29
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (60 bp):
TCAAGGCATTTTTAGCCAAAAATGCCTTGAATAATCCATTCAATTTTTGTAAAGGATTAT
Found at i:9309503 original size:24 final size:23
Alignment explanation
Indices: 9309476--9309525 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
9309466 TTTATATTCA
*
9309476 AATAGTTATAACTATTTATTACAT
1 AATAATTATAACTATTTA-TACAT
***
9309500 AATAATTATTTTTATTTATACAT
1 AATAATTATAACTATTTATACAT
9309523 AAT
1 AAT
9309526 TATTCAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
AATAATTATAACTATTTATACAT
Found at i:9309515 original size:20 final size:20
Alignment explanation
Indices: 9309490--9309529 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9309480 GTTATAACTA
9309490 TTTATTACATA-ATAATTATT
1 TTTATT-CATACATAATTATT
*
9309510 TTTATTTATACATAATTATT
1 TTTATTCATACATAATTATT
9309530 CAAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTCATACATAATTATT
Found at i:9311544 original size:21 final size:20
Alignment explanation
Indices: 9311507--9311545 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9311497 GTTTGTATTG
9311507 TTAATTTTTTTAGTATTAGA
1 TTAATTTTTTTAGTATTAGA
*
9311527 TTAATTTTTATTATTATTA
1 TTAATTTTT-TTAGTATTA
9311546 TTTTTGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TTAATTTTTTTAGTATTAGA
Found at i:9311732 original size:43 final size:43
Alignment explanation
Indices: 9311640--9311723 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
9311630 TTAATGTGTA
* *
9311640 AAAAATTA-AAATACTTAATAAATTACTACATTTCAAAATCAT
1 AAAAATAATAAATACTTAATAAATTACTACATTTAAAAATCAT
* ** *
9311682 AAAAATAATAAATATTTAATAGTTTATTACATTTAAAAATCA
1 AAAAATAATAAATACTTAATAAATTACTACATTTAAAAATCA
9311724 AGTAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
42 7 0.20
43 28 0.80
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.36
Consensus pattern (43 bp):
AAAAATAATAAATACTTAATAAATTACTACATTTAAAAATCAT
Found at i:9313445 original size:21 final size:19
Alignment explanation
Indices: 9313419--9313459 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
9313409 TTTAAATTGT
9313419 TAGAAAAAATAAATAATGGAA
1 TAGAAAAAATAAA-AA-GGAA
*
9313440 TAGAAATAATAAAAAGGAA
1 TAGAAAAAATAAAAAGGAA
9313459 T
1 T
9313460 TTTGGCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (19 bp):
TAGAAAAAATAAAAAGGAA
Found at i:9314391 original size:22 final size:22
Alignment explanation
Indices: 9314366--9314437 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
9314356 GGTATAACTT
* *
9314366 TATGTACATAGTACTTATAAGA
1 TATGTACATGGTACTTATAGGA
* * *
9314388 TATGTATATGGTACTAATGGGA
1 TATGTACATGGTACTTATAGGA
*
9314410 TATGTACATGGTATTTATAGGA
1 TATGTACATGGTACTTATAGGA
9314432 TATGTA
1 TATGTA
9314438 AATTTAGGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (22 bp):
TATGTACATGGTACTTATAGGA
Found at i:9314457 original size:44 final size:42
Alignment explanation
Indices: 9314354--9314462 Score: 105
Period size: 44 Copynumber: 2.5 Consensus size: 42
9314344 TATATACATC
*
9314354 TAGGTATAACTTTATGTACATAGTACTTATAAGATATGTATA
1 TAGGTATAACTATATGTACATAGTACTTATAAGATATGTATA
* * * *
9314396 T-GGTACTAA-TGGGATATGTACATGGTATTTATAGGATATGTAAATT
1 TAGGTA-TAACT---ATATGTACATAGTACTTATAAGATATGT--ATA
9314442 TAGGTATAACTATATGTACAT
1 TAGGTATAACTATATGTACAT
9314463 CTAATCATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
41 5 0.09
42 4 0.07
44 34 0.63
46 6 0.11
47 5 0.09
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (42 bp):
TAGGTATAACTATATGTACATAGTACTTATAAGATATGTATA
Found at i:9315850 original size:17 final size:19
Alignment explanation
Indices: 9315830--9315865 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
9315820 TTAGTTGAGT
9315830 TAGTTAGTT-TTT-AGTTA
1 TAGTTAGTTATTTCAGTTA
9315847 TAGTTAGTTATTTCAGTTA
1 TAGTTAGTTATTTCAGTTA
9315866 ATGCTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.56
Consensus pattern (19 bp):
TAGTTAGTTATTTCAGTTA
Found at i:9316618 original size:146 final size:146
Alignment explanation
Indices: 9316370--9316632 Score: 391
Period size: 146 Copynumber: 1.8 Consensus size: 146
9316360 AAGATAAAAC
* * * ** * *
9316370 TAAAAGGGAGTTGGCCCTCAAAGATGTATCCAAAAAATTATACTTTCTAGAAAATCAATTAAAAG
1 TAAAAGAGAGTTGACCCTCAAAGATGTATCCAAAAAATTAGACGCTATAGAAAATCAACTAAAAG
* *
9316435 TCATTAAAGCTAGGTATGATCCTAAGCCTTCTCTTGTCCATAACTTTCCAAGCCTATATGGCTTG
66 CCATTAAAGCTAGGTATGATCCTAAGCCTACTCTTGTCCATAACTTTCCAAGCCTATATGGCTTG
9316500 GTGAGAAAAACAAAGT
131 GTGAGAAAAACAAAGT
* * * * *
9316516 TAAAAGAGTGTTGACCCTTAAAGATTTATCCAAAAAATTAGACGCTATAGAAAATCAACTAGAGG
1 TAAAAGAGAGTTGACCCTCAAAGATGTATCCAAAAAATTAGACGCTATAGAAAATCAACTAAAAG
*
9316581 CCATTAAAGCTAGGTATGATCCTAAGCCTACTTTTGTCCATAACTTTCCAAG
66 CCATTAAAGCTAGGTATGATCCTAAGCCTACTCTTGTCCATAACTTTCCAAG
9316633 GTCATGTGGC
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
146 102 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (146 bp):
TAAAAGAGAGTTGACCCTCAAAGATGTATCCAAAAAATTAGACGCTATAGAAAATCAACTAAAAG
CCATTAAAGCTAGGTATGATCCTAAGCCTACTCTTGTCCATAACTTTCCAAGCCTATATGGCTTG
GTGAGAAAAACAAAGT
Found at i:9318241 original size:21 final size:21
Alignment explanation
Indices: 9318212--9318252 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9318202 CAAAGAAAAA
9318212 GAATAAAGTGG-GTAGATTTTG
1 GAATAAAGTGGTGTA-ATTTTG
*
9318233 GAATTAAGTGGTGTAATTTT
1 GAATAAAGTGGTGTAATTTT
9318253 TTAACACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (21 bp):
GAATAAAGTGGTGTAATTTTG
Found at i:9319882 original size:21 final size:21
Alignment explanation
Indices: 9319856--9319896 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9319846 AGTTGCAATC
*
9319856 AATTTG-GATTTTAATCTTTAT
1 AATTTGTGATTCT-ATCTTTAT
9319877 AATTTGTGATTCTATCTTTA
1 AATTTGTGATTCTATCTTTA
9319897 AGTCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (21 bp):
AATTTGTGATTCTATCTTTAT
Found at i:9328593 original size:284 final size:285
Alignment explanation
Indices: 9328045--9328597 Score: 849
Period size: 284 Copynumber: 1.9 Consensus size: 285
9328035 TAGCACCTTC
* * *
9328045 AAATATAGTGTTTTTACTTGCTGAAATTGGTGCTAAAGTTTTAAATTTTTGATGGATTTTGGTAC
1 AAATATAGTGTTTTTACATGCTAAAATTGGTGCTAAAGTTTTAAATCTTTGATGGATTTTGGTAC
**
9328110 ATTTAATGTTATTTTCATGATTCTAGGATTTAAGACTTGTGGACTTGATTTTCATGAAATCCATG
66 ATTTAATGTTATTTTCATGATTCTAGGATTTAAGACTTGTGGACTCAATTTTCATGAAATCCATG
* *
9328175 CATAAAAATGCATATGCGGCAATACAATGCAAGTAGGCAACCAAACCTTATAGCTTCCCATCATC
131 CATAAAAATGCATATGCGGCAATACAATACAAGTAGGCAACCAAACCCTATAGCTTCCCATCATC
* * * * *
9328240 CATCCATGTAGTAAAACAAGTGTTTGAATTGCACAAAGACATTTCCATCACCTTTCACATTCAGC
196 CATCAATGCAGGAAAACAAGTGTTTGAATTGCACAAAGACACTTCCATCACCATTCACATTCAGC
9328305 CACACCTATCCTAATGAAATTGCAA
261 CACACCTATCCTAATGAAATTGCAA
*
9328330 AAATATAGTGTTTTTACATGCTAAAATTGGTGTTAAA-TTTTAAATCTTTGATGGATTTTGGTAC
1 AAATATAGTGTTTTTACATGCTAAAATTGGTGCTAAAGTTTTAAATCTTTGATGGATTTTGGTAC
* *
9328394 ATTTAATGTTATTTTCATGATTTTAGGATTTAAGACTTGTGGACTCAATTTTCATGAAATCCATT
66 ATTTAATGTTATTTTCATGATTCTAGGATTTAAGACTTGTGGACTCAATTTTCATGAAATCCATG
* * ** * * * *
9328459 TATGAAGGTGCATATTCGGCCATGCAATACAAGGT-GGCAACCAAACCCTATAGCTTCCTATCAT
131 CATAAAAATGCATATGCGGCAATACAATACAA-GTAGGCAACCAAACCCTATAGCTTCCCATCAT
* * *
9328523 CCATCAATGCAGGAAAGCAAGTGTTTGAATTGTACAAAGACACTTCCATCACCATTCACATTTAG
195 CCATCAATGCAGGAAAACAAGTGTTTGAATTGCACAAAGACACTTCCATCACCATTCACATTCAG
9328588 CCACACCTAT
260 CCACACCTAT
9328598 TTCAAGAAAG
Statistics
Matches: 241, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
284 205 0.85
285 36 0.15
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (285 bp):
AAATATAGTGTTTTTACATGCTAAAATTGGTGCTAAAGTTTTAAATCTTTGATGGATTTTGGTAC
ATTTAATGTTATTTTCATGATTCTAGGATTTAAGACTTGTGGACTCAATTTTCATGAAATCCATG
CATAAAAATGCATATGCGGCAATACAATACAAGTAGGCAACCAAACCCTATAGCTTCCCATCATC
CATCAATGCAGGAAAACAAGTGTTTGAATTGCACAAAGACACTTCCATCACCATTCACATTCAGC
CACACCTATCCTAATGAAATTGCAA
Found at i:9328962 original size:30 final size:30
Alignment explanation
Indices: 9328928--9328991 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
9328918 TGGCCAAAAT
9328928 CTCTTCTTTAAGATCCCATTCAGCCAAGCA
1 CTCTTCTTTAAGATCCCATTCAGCCAAGCA
*
9328958 CTCTTCTTTAAGATCCTATTCAGCCAAGCA
1 CTCTTCTTTAAGATCCCATTCAGCCAAGCA
9328988 CTCT
1 CTCT
9328992 CAAGAAGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.09, T:0.33
Consensus pattern (30 bp):
CTCTTCTTTAAGATCCCATTCAGCCAAGCA
Found at i:9340610 original size:9 final size:9
Alignment explanation
Indices: 9340598--9340654 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
9340588 TAAAAATGTT
*
9340598 AAAATATTA
1 AAAATAATA
9340607 AAAA-AATA
1 AAAATAATA
9340615 AAAATAAATA
1 AAAAT-AATA
*
9340625 AAAATGATA
1 AAAATAATA
9340634 AAAATAA-A
1 AAAATAATA
* *
9340642 AAATTAAGA
1 AAAATAATA
9340651 AAAA
1 AAAA
9340655 AATGAATGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 14 0.35
9 17 0.43
10 9 0.22
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (9 bp):
AAAATAATA
Found at i:9340636 original size:27 final size:28
Alignment explanation
Indices: 9340605--9340659 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
9340595 GTTAAAATAT
*
9340605 TAAAAA-AATAAAAATAA-ATAAAAATGA
1 TAAAAATAA-AAAAATAAGAAAAAAATGA
*
9340632 TAAAAATAAAAAATTAAGAAAAAAATGA
1 TAAAAATAAAAAAATAAGAAAAAAATGA
9340660 ATGAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (28 bp):
TAAAAATAAAAAAATAAGAAAAAAATGA
Found at i:9340929 original size:19 final size:19
Alignment explanation
Indices: 9340887--9340922 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9340877 AAAATTTTAA
*
9340887 AAAAATATTTATTAAATAT
1 AAAAATATTTATTAAAAAT
9340906 AAAAATATTT-TTAAAAA
1 AAAAATATTTATTAAAAA
9340923 ATTAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATATTTATTAAAAAT
Found at i:9340931 original size:21 final size:20
Alignment explanation
Indices: 9340886--9340933 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
9340876 TAAAATTTTA
*
9340886 AAAAAATATTTATTAAATAT
1 AAAAAATATTTATTAAAAAT
9340906 -AAAAATATTT-TTAAAAAATT
1 AAAAAATATTTATT-AAAAA-T
9340926 AAAAAATA
1 AAAAAATA
9340934 AAAATAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.08
19 14 0.58
20 1 0.04
21 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATATTTATTAAAAAT
Found at i:9344030 original size:22 final size:22
Alignment explanation
Indices: 9344000--9344069 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
9343990 GCTTGAATAT
*
9344000 CACTTTATGGGGAGAATATGTA
1 CACTCTATGGGGAGAATATGTA
9344022 CACTCTATGGGGAGAATATGTA
1 CACTCTATGGGGAGAATATGTA
*
9344044 CACTCTATGGGAAGAATATGTA
1 CACTCTATGGGGAGAATATGTA
9344066 CACT
1 CACT
9344070 TGCTGCTAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (22 bp):
CACTCTATGGGGAGAATATGTA
Found at i:9345360 original size:25 final size:24
Alignment explanation
Indices: 9345323--9345373 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
9345313 TTGTAGCCAT
** *
9345323 ATATTTTCTTAAAATTTGAGTTACA
1 ATATTTTAGTAAAATTAGAG-TACA
*
9345348 ATATTTTAGTAAAGTTAGAGTACA
1 ATATTTTAGTAAAATTAGAGTACA
9345372 AT
1 AT
9345374 TGTTGATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (24 bp):
ATATTTTAGTAAAATTAGAGTACA
Found at i:9346465 original size:125 final size:125
Alignment explanation
Indices: 9346295--9346547 Score: 276
Period size: 125 Copynumber: 2.0 Consensus size: 125
9346285 ATATGCCTTC
* * * *
9346295 AATAATCCTTTTCGATTTTTATTAGGGAACTATTCAAGGTATTTTTGCCCAAAAAATACCTTGAA
1 AATAATCCTTTTCAATTTTTATGAGGGAACTATTCAAGATATTTTTGACCAAAAAATACCTTGAA
* * * * *
9346360 TAAT-CCTTATAAAAAAATTGAATGAGGTTTTTCTAGGCATTTCTAACAAAAAATATTTTG
66 TAATCCCTTA-AAAAAAATTAAATGAGGTTATTCAAGGCATTTCTAACAAAAAACATCTTG
* * * * * * **
9346420 AATAATCCTTTTCAATTTTTATGAGAGG-ATTATTTAAGATGTTTTTTATCAGAAAATGTCTTGA
1 AATAATCCTTTTCAATTTTTATGAG-GGAACTATTCAAGATATTTTTGACCAAAAAATACCTTGA
* * * * *
9346484 ATAATCCCTTACAAAAAATTAAATGGGGTTATTCAAGGTATTTCTAGCCAAAAACATCTTG
65 ATAATCCCTTAAAAAAAATTAAATGAGGTTATTCAAGGCATTTCTAACAAAAAACATCTTG
9346545 AAT
1 AAT
9346548 CTTTCCCTTT
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
125 97 0.93
126 7 0.07
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (125 bp):
AATAATCCTTTTCAATTTTTATGAGGGAACTATTCAAGATATTTTTGACCAAAAAATACCTTGAA
TAATCCCTTAAAAAAAATTAAATGAGGTTATTCAAGGCATTTCTAACAAAAAACATCTTG
Found at i:9347155 original size:40 final size:40
Alignment explanation
Indices: 9347101--9347198 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 40
9347091 AATTTATTTG
* * * *
9347101 AATGATGATTATTGAAGGCATTTTTGAGGAAAATGCCTTA
1 AATGATCATCATTGAAGGCATTTTTAAAGAAAATGCCTTA
**
9347141 AATGATCATCATTGAAGGTGTTTTTAAAGAAAATGCCTTA
1 AATGATCATCATTGAAGGCATTTTTAAAGAAAATGCCTTA
* *
9347181 AATGATCAACATTTAAGG
1 AATGATCATCATTGAAGG
9347199 TGTTTTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (40 bp):
AATGATCATCATTGAAGGCATTTTTAAAGAAAATGCCTTA
Found at i:9347199 original size:40 final size:41
Alignment explanation
Indices: 9347121--9347246 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 41
9347111 ATTGAAGGCA
* *
9347121 TTTTT-GAGGAAAATGCCTTAAATGATCATCATTGAAGGTG
1 TTTTTAGAAGAAAATGCCTTAAATGATCATCATTTAAGGTG
*
9347161 TTTTTA-AAGAAAATGCCTTAAATGATCAACATTTAAGGTG
1 TTTTTAGAAGAAAATGCCTTAAATGATCATCATTTAAGGTG
** * *
9347201 TTTTTTTAGAAGAAAACACCTTAAATAATGATCATTTAAGGTG
1 --TTTTTAGAAGAAAATGCCTTAAATGATCATCATTTAAGGTG
9347244 TTT
1 TTT
9347247 CTTCAACCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
40 36 0.49
41 3 0.04
42 6 0.08
43 29 0.39
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (41 bp):
TTTTTAGAAGAAAATGCCTTAAATGATCATCATTTAAGGTG
Found at i:9347237 original size:43 final size:42
Alignment explanation
Indices: 9347136--9347246 Score: 145
Period size: 43 Copynumber: 2.7 Consensus size: 42
9347126 GAGGAAAATG
* **
9347136 CCTTAAATGATCATCATTGAAGGTG--TTTTTAAAGAAAATG
1 CCTTAAATGATCATCATTTAAGGTGTTTTTTTAAAGAAAACA
*
9347176 CCTTAAATGATCAACATTTAAGGTGTTTTTTTAGAAGAAAACA
1 CCTTAAATGATCATCATTTAAGGTGTTTTTTTA-AAGAAAACA
* *
9347219 CCTTAAATAATGATCATTTAAGGTGTTT
1 CCTTAAATGATCATCATTTAAGGTGTTT
9347247 CTTCAACCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 23 0.38
42 6 0.10
43 32 0.52
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (42 bp):
CCTTAAATGATCATCATTTAAGGTGTTTTTTTAAAGAAAACA
Found at i:9348369 original size:52 final size:51
Alignment explanation
Indices: 9348279--9348422 Score: 180
Period size: 52 Copynumber: 2.8 Consensus size: 51
9348269 ATAACCATAT
* * * *
9348279 AAACTTACCCATTAAGAATCCTTCTTCTCTAAGCATTCTTCTCCTGTAAGTC
1 AAACTTACCTATTAAGAATCCTT-TTCTCTTAGAATTCTTCTCCTGCAAGTC
* * * *
9348331 AAACTTGCCTATTAAGAATCCTTTTCCTTTTAGAATTCTTCTCTTGCATGTC
1 AAACTTACCTATTAAGAATCCTTTT-CTCTTAGAATTCTTCTCCTGCAAGTC
*
9348383 AAATTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTT
1 AAACTTACCTATTAAGAATCCT-TTTCTCTTAGAATTCTT
9348423 TTTTTACAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.03
52 74 0.94
53 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (51 bp):
AAACTTACCTATTAAGAATCCTTTTCTCTTAGAATTCTTCTCCTGCAAGTC
Found at i:9348473 original size:11 final size:11
Alignment explanation
Indices: 9348457--9348489 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9348447 AAATAATATC
9348457 AACAAATCTCT
1 AACAAATCTCT
*
9348468 AACAAATCTCA
1 AACAAATCTCT
9348479 AACAAATCTCT
1 AACAAATCTCT
9348490 TATGGGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (11 bp):
AACAAATCTCT
Found at i:9348773 original size:25 final size:25
Alignment explanation
Indices: 9348720--9348785 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
9348710 AACCAAGCTC
* **
9348720 TTCTTATATCTCGAACTGTCAACTA
1 TTCTCATATCTCGAACCATCAACTA
* *
9348745 TTCTCATATCTCGAACCATCGACTT
1 TTCTCATATCTCGAACCATCAACTA
* *
9348770 TTCTCACATCTTGAAC
1 TTCTCATATCTCGAAC
9348786 ATTTGACTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.38
Consensus pattern (25 bp):
TTCTCATATCTCGAACCATCAACTA
Found at i:9348853 original size:31 final size:31
Alignment explanation
Indices: 9348815--9348929 Score: 160
Period size: 31 Copynumber: 3.7 Consensus size: 31
9348805 TCAAACTTTT
* *
9348815 AGCTCTGATACTACTTATTGGGAAATACCAC
1 AGCTCTGATACCATTTATTGGGAAATACCAC
*
9348846 AGCTCTGATACCATTTATTGAGG-AATACCGC
1 AGCTCTGATACCATTTATTG-GGAAATACCAC
* * *
9348877 AGCTTTGATACCATTTATTGAGAAACACCAC
1 AGCTCTGATACCATTTATTGGGAAATACCAC
9348908 AGCTCTGATACCATTTATTGGG
1 AGCTCTGATACCATTTATTGGG
9348930 CTAAAAGTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 70 0.96
32 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (31 bp):
AGCTCTGATACCATTTATTGGGAAATACCAC
Found at i:9349552 original size:52 final size:52
Alignment explanation
Indices: 9349415--9349570 Score: 144
Period size: 52 Copynumber: 3.0 Consensus size: 52
9349405 ATAACCATAT
* * * * *
9349415 AAACTTGCCCATTAAAAATCCTTC-TTCTCTTAAAATTCTTCTTCTGT--AAGTG
1 AAACTTACCTATTAAAAAT-CTTCTTTTTCTTAGAATTCTTC-TCT-TACAAGTC
*
9349467 AAACTTGCCTATTAAAAAT-TT-TTTTTCTTTTAGAATTCTTCTCTTACAAGTC
1 AAACTTACCTATTAAAAATCTTCTTTTTC--TTAGAATTCTTCTCTTACAAGTC
* *
9349519 AAACTTATCTATTAAAAATCTTCTTTTTCTTAGAAATT-TTCTTTTACAAGTC
1 AAACTTACCTATTAAAAATCTTCTTTTTCTTAG-AATTCTTCTCTTACAAGTC
9349571 TTCTTGTCCA
Statistics
Matches: 89, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
50 7 0.08
51 3 0.03
52 67 0.75
53 6 0.07
54 6 0.07
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (52 bp):
AAACTTACCTATTAAAAATCTTCTTTTTCTTAGAATTCTTCTCTTACAAGTC
Found at i:9349607 original size:11 final size:11
Alignment explanation
Indices: 9349591--9349626 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9349581 TCAAGCAATA
9349591 TCTAACAAATC
1 TCTAACAAATC
9349602 TCTAACAAATC
1 TCTAACAAATC
* *
9349613 CCAAACAAATC
1 TCTAACAAATC
9349624 TCT
1 TCT
9349627 TATGAGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:9349905 original size:25 final size:25
Alignment explanation
Indices: 9349853--9349921 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
9349843 TTAAACCAAG
**
9349853 CTCTTC-CTATATCTCGAACTGTCAA
1 CTCTTCTC-ATATCTCGAACCATCAA
*
9349878 CTCTTCTCATATCTCGAACCATCGA
1 CTCTTCTCATATCTCGAACCATCAA
* *
9349903 CTCTTCTCACATCTTGAAC
1 CTCTTCTCATATCTCGAAC
9349922 ATTTGACTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (25 bp):
CTCTTCTCATATCTCGAACCATCAA
Found at i:9350007 original size:31 final size:31
Alignment explanation
Indices: 9349965--9350032 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
9349955 CTGATTTTAC
* * *
9349965 TTGTTGGGGAACCCCATAACTTTGATACCAT
1 TTGTTGAGGAACACCATAACTCTGATACCAT
*
9349996 TTGTTGAGGAACACCATAGCTCTGATACCAT
1 TTGTTGAGGAACACCATAACTCTGATACCAT
9350027 TTGTTG
1 TTGTTG
9350033 GGCTAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (31 bp):
TTGTTGAGGAACACCATAACTCTGATACCAT
Found at i:9350610 original size:52 final size:51
Alignment explanation
Indices: 9350520--9350663 Score: 180
Period size: 52 Copynumber: 2.8 Consensus size: 51
9350510 ATAACCATAT
* * * *
9350520 AAACTTACCCATTAAGAATCCTTCTTCTCTAAGCATTCTTCTCCTGTAAGTC
1 AAACTTACCTATTAAGAATCCTT-TTCTCTTAGAATTCTTCTCCTGCAAGTC
* * * *
9350572 AAACTTGCCTATTAAGAATCCTTTTCCTTTTAGAATTCTTCTCTTGCATGTC
1 AAACTTACCTATTAAGAATCCTTTT-CTCTTAGAATTCTTCTCCTGCAAGTC
*
9350624 AAATTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTT
1 AAACTTACCTATTAAGAATCCT-TTTCTCTTAGAATTCTT
9350664 TTTTTACAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.03
52 74 0.94
53 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (51 bp):
AAACTTACCTATTAAGAATCCTTTTCTCTTAGAATTCTTCTCCTGCAAGTC
Found at i:9350714 original size:11 final size:11
Alignment explanation
Indices: 9350698--9350730 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9350688 AAATAATATC
9350698 AACAAATCTCT
1 AACAAATCTCT
*
9350709 AACAAATCTCA
1 AACAAATCTCT
9350720 AACAAATCTCT
1 AACAAATCTCT
9350731 TATGGGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (11 bp):
AACAAATCTCT
Found at i:9351015 original size:25 final size:25
Alignment explanation
Indices: 9350962--9351027 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
9350952 AACCAAGCTC
* **
9350962 TTCTTATATCTCGAACTGTCAACTA
1 TTCTCATATCTCGAACCATCAACTA
* *
9350987 TTCTCATATCTCGAACCATCGACTT
1 TTCTCATATCTCGAACCATCAACTA
* *
9351012 TTCTCACATCTTGAAC
1 TTCTCATATCTCGAAC
9351028 ATTTGACTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.38
Consensus pattern (25 bp):
TTCTCATATCTCGAACCATCAACTA
Found at i:9351095 original size:31 final size:31
Alignment explanation
Indices: 9351057--9351171 Score: 160
Period size: 31 Copynumber: 3.7 Consensus size: 31
9351047 TCAAACTTTT
* *
9351057 AGCTCTGATACTACTTATTGGGAAATACCAC
1 AGCTCTGATACCATTTATTGGGAAATACCAC
*
9351088 AGCTCTGATACCATTTATTGAGG-AATACCGC
1 AGCTCTGATACCATTTATTG-GGAAATACCAC
* * *
9351119 AGCTTTGATACCATTTATTGAGAAACACCAC
1 AGCTCTGATACCATTTATTGGGAAATACCAC
9351150 AGCTCTGATACCATTTATTGGG
1 AGCTCTGATACCATTTATTGGG
9351172 CTAAAAGTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 70 0.96
32 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (31 bp):
AGCTCTGATACCATTTATTGGGAAATACCAC
Found at i:9351795 original size:52 final size:52
Alignment explanation
Indices: 9351658--9351813 Score: 144
Period size: 52 Copynumber: 3.0 Consensus size: 52
9351648 ATAACCATAT
* * * * *
9351658 AAACTTGCCCATTAAAAATCCTTC-TTCTCTTAAAATTCTTCTTCTGT--AAGTG
1 AAACTTACCTATTAAAAAT-CTTCTTTTTCTTAGAATTCTTC-TCT-TACAAGTC
*
9351710 AAACTTGCCTATTAAAAAT-TT-TTTTTCTTTTAGAATTCTTCTCTTACAAGTC
1 AAACTTACCTATTAAAAATCTTCTTTTTC--TTAGAATTCTTCTCTTACAAGTC
* *
9351762 AAACTTATCTATTAAAAATCTTCTTTTTCTTAGAAATT-TTCTTTTACAAGTC
1 AAACTTACCTATTAAAAATCTTCTTTTTCTTAG-AATTCTTCTCTTACAAGTC
9351814 TTTTTGTCCA
Statistics
Matches: 89, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
50 7 0.08
51 3 0.03
52 67 0.75
53 6 0.07
54 6 0.07
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (52 bp):
AAACTTACCTATTAAAAATCTTCTTTTTCTTAGAATTCTTCTCTTACAAGTC
Found at i:9351850 original size:11 final size:11
Alignment explanation
Indices: 9351834--9351869 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9351824 TCAAGCAATA
9351834 TCTAACAAATC
1 TCTAACAAATC
9351845 TCTAACAAATC
1 TCTAACAAATC
* *
9351856 CCAAACAAATC
1 TCTAACAAATC
9351867 TCT
1 TCT
9351870 TATGAGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:9352148 original size:25 final size:25
Alignment explanation
Indices: 9352096--9352164 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
9352086 TTAAACCAAG
**
9352096 CTCTTC-CTATATCTCGAACTGTCAA
1 CTCTTCTC-ATATCTCGAACCATCAA
*
9352121 CTCTTCTCATATCTCGAACCATCGA
1 CTCTTCTCATATCTCGAACCATCAA
* *
9352146 CTCTTCTCACATCTTGAAC
1 CTCTTCTCATATCTCGAAC
9352165 ATTTGACTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (25 bp):
CTCTTCTCATATCTCGAACCATCAA
Found at i:9352250 original size:31 final size:31
Alignment explanation
Indices: 9352208--9352275 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
9352198 CTGATTTTAC
* * *
9352208 TTGTTGGGGAACCCCATAACTTTGATACCAT
1 TTGTTGAGGAACACCATAACTCTGATACCAT
*
9352239 TTGTTGAGGAACACCATAGCTCTGATACCAT
1 TTGTTGAGGAACACCATAACTCTGATACCAT
9352270 TTGTTG
1 TTGTTG
9352276 GGCTAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (31 bp):
TTGTTGAGGAACACCATAACTCTGATACCAT
Found at i:9352802 original size:14 final size:14
Alignment explanation
Indices: 9352783--9352816 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
9352773 ATTAAGAATC
9352783 TCTCTTAGAATTCT
1 TCTCTTAGAATTCT
9352797 TCTCTTAGAATTCT
1 TCTCTTAGAATTCT
9352811 TCTCTT
1 TCTCTT
9352817 GTAAGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (14 bp):
TCTCTTAGAATTCT
Found at i:9352864 original size:52 final size:52
Alignment explanation
Indices: 9352796--9352927 Score: 203
Period size: 52 Copynumber: 2.5 Consensus size: 52
9352786 CTTAGAATTC
* *
9352796 TTCTCTTAGAATTCTTCTCTTGTAAGTCAAACTTGCCTATTAAGAATCC-CT
1 TTCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCCTCT
*
9352847 TTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCCTCT
1 TT-CTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCCTCT
* *
9352900 TTCTCTTAGAATTCTTCTTTTTCAAGTC
1 TTCTCTTAGAATTCTTCTCTTGCAAGTC
9352928 TTCTTGTCTA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.03
52 67 0.92
53 4 0.05
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.44
Consensus pattern (52 bp):
TTCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCCTCT
Found at i:9352964 original size:11 final size:11
Alignment explanation
Indices: 9352948--9352983 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
9352938 TCAAACAATA
9352948 TCTAACAAATC
1 TCTAACAAATC
9352959 TCTAACAAATC
1 TCTAACAAATC
*
9352970 TCAAACAAATC
1 TCTAACAAATC
9352981 TCT
1 TCT
9352984 TATGAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:9354409 original size:11 final size:11
Alignment explanation
Indices: 9354395--9354425 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9354385 TCACTTTTTT
9354395 TTTTTTTTTAA
1 TTTTTTTTTAA
*
9354406 TTTTCTTTTAA
1 TTTTTTTTTAA
9354417 TTTTTTTTT
1 TTTTTTTTT
9354426 TACATAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:9355348 original size:2 final size:2
Alignment explanation
Indices: 9355341--9355369 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9355331 TATTTCCCAA
9355341 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 A
9355370 AATTGAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9360313 original size:2 final size:2
Alignment explanation
Indices: 9360306--9360342 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9360296 TGTTGTCTTA
*
9360306 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9360343 TAAGACAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:9360566 original size:18 final size:18
Alignment explanation
Indices: 9360505--9360576 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
9360495 TCATAATATT
9360505 TTAAATATATTTAAATAAAA
1 TTAAATATATTT-AA-AAAA
*
9360525 TTAAATATA---AAATAA
1 TTAAATATATTTAAAAAA
**
9360540 TTATTTATATTTAAAAAA
1 TTAAATATATTTAAAAAA
*
9360558 TTAAATATATATAAAAAA
1 TTAAATATATTTAAAAAA
9360576 T
1 T
9360577 AATAAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 10 0.24
16 2 0.05
18 21 0.50
20 9 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATATATTTAAAAAA
Found at i:9360765 original size:2 final size:2
Alignment explanation
Indices: 9360760--9360790 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9360750 TTTTTAACCT
*
9360760 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9360791 TTATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9363134 original size:12 final size:12
Alignment explanation
Indices: 9363104--9363134 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9363094 ATGAAAAAAG
*
9363104 AAAAAAATTACA
1 AAAAAAATTAAA
9363116 AAAAAAATTAAA
1 AAAAAAATTAAA
9363128 AAAAAAA
1 AAAAAAA
9363135 GAGATCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAATTAAA
Found at i:9364287 original size:29 final size:28
Alignment explanation
Indices: 9364250--9364310 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
9364240 TGGATGTCAC
*
9364250 ATGAATTTAATTAAT-TAATGTATCAAATA
1 ATGAATTT-ATTAATATAATATAT-AAATA
*
9364279 ATGATTTTATTAATATAATATATAAAT-
1 ATGAATTTATTAATATAATATATAAATA
9364306 ATGAA
1 ATGAA
9364311 ATTAAATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 4 0.14
28 10 0.36
29 14 0.50
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.43
Consensus pattern (28 bp):
ATGAATTTATTAATATAATATATAAATA
Found at i:9365237 original size:26 final size:28
Alignment explanation
Indices: 9365208--9365264 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
9365198 TAATATTTTT
*
9365208 AAATATTAAAAAAAG-AAA-AAAGGAAA
1 AAATATTAAAAAAAGTAAAGAAAAGAAA
* *
9365234 AAATATTGAAAAAGGTAAAGAAAAGAAA
1 AAATATTAAAAAAAGTAAAGAAAAGAAA
9365262 AAA
1 AAA
9365265 AAAGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 13 0.50
27 3 0.12
28 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (28 bp):
AAATATTAAAAAAAGTAAAGAAAAGAAA
Found at i:9366916 original size:42 final size:42
Alignment explanation
Indices: 9366835--9366917 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
9366825 CAAGTTATTA
** * *
9366835 TTGATTTTTTACCCTTTCATTCCCTATTGCGTCAACTACATG
1 TTGATTTTTTACAATTTCATTCCCTATTACCTCAACTACATG
* * *
9366877 TTGATTTTTTACAATTTCATTCTCTATTACCTTAGCTACAT
1 TTGATTTTTTACAATTTCATTCCCTATTACCTCAACTACAT
9366918 CTTTCACTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.48
Consensus pattern (42 bp):
TTGATTTTTTACAATTTCATTCCCTATTACCTCAACTACATG
Found at i:9367493 original size:18 final size:17
Alignment explanation
Indices: 9367470--9367526 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
9367460 CTAATTTCTA
9367470 TTATAATCTTTTACTTTG
1 TTATAA-CTTTTACTTTG
**
9367488 TTATAA-AATT--TTTG
1 TTATAACTTTTACTTTG
9367502 TTATAAGCTTTTACTTTG
1 TTATAA-CTTTTACTTTG
9367520 TTATAAC
1 TTATAAC
9367527 CATGTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 10 0.32
16 4 0.13
17 1 0.03
18 16 0.52
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (17 bp):
TTATAACTTTTACTTTG
Found at i:9367498 original size:32 final size:32
Alignment explanation
Indices: 9367448--9367525 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
9367438 TGCATGTCCC
* ** *
9367448 TTACGTTGTTATCTAATTTCTATTATAATCTT
1 TTACTTTGTTATAAAATTTCTATTATAAGCTT
* *
9367480 TTACTTTGTTATAAAATTTTTGTTATAAGCTT
1 TTACTTTGTTATAAAATTTCTATTATAAGCTT
9367512 TTACTTTGTTATAA
1 TTACTTTGTTATAA
9367526 CCATGTTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (32 bp):
TTACTTTGTTATAAAATTTCTATTATAAGCTT
Found at i:9368382 original size:42 final size:41
Alignment explanation
Indices: 9368202--9368412 Score: 161
Period size: 42 Copynumber: 5.2 Consensus size: 41
9368192 TCTAAACAAT
* *
9368202 AGAAAGCCTTAACTAT-AATTTCGAGCAATTAAGAATATCAGC
1 AGAAAACCTTAACTATAAATTT-GAGCAATTAAGAAAAT-AGC
* * *
9368244 AAAAAATCC-TAACTATAATTTTGACCAATTAAG--AAT-G-
1 AGAAAA-CCTTAACTATAAATTTGAGCAATTAAGAAAATAGC
* * * * * *
9368281 -GAAAACCCTCACTAT-TATTTCAAACAAATAAGAACAATAGC
1 AGAAAACCTTAACTATAAATTT-GAGCAATTAAGAA-AATAGC
* *
9368322 A-AAAACCTCAAATATAAATTTGAGCAATTAAGAACAATAGC
1 AGAAAACCTTAACTATAAATTTGAGCAATTAAGAA-AATAGC
* *
9368363 AGAAAACCTTAACTATAAATTTGAGCAATTAAAAATAATAAC
1 AGAAAACCTTAACTATAAATTTGAGCAATTAAGAA-AATAGC
9368405 AGAAAACC
1 AGAAAACC
9368413 ATAAATCAAA
Statistics
Matches: 132, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
35 5 0.04
36 18 0.14
38 1 0.01
39 3 0.02
40 3 0.02
41 28 0.21
42 68 0.52
43 6 0.05
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.24
Consensus pattern (41 bp):
AGAAAACCTTAACTATAAATTTGAGCAATTAAGAAAATAGC
Found at i:9370142 original size:15 final size:17
Alignment explanation
Indices: 9370122--9370153 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
9370112 ATTTATATTT
9370122 ATATTTA-AAA-AATAC
1 ATATTTATAAACAATAC
9370137 ATATTTATAAACAATAC
1 ATATTTATAAACAATAC
9370154 TTAAATGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATTTATAAACAATAC
Found at i:9371542 original size:15 final size:16
Alignment explanation
Indices: 9371522--9371552 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9371512 TTTATTGAAT
9371522 TTCTAAAG-GATAAGA
1 TTCTAAAGAGATAAGA
9371537 TTCTAAAGAGATAAGA
1 TTCTAAAGAGATAAGA
9371553 GCTTCACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
TTCTAAAGAGATAAGA
Found at i:9372383 original size:22 final size:24
Alignment explanation
Indices: 9372358--9372401 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9372348 ATTTTTGCTT
9372358 TATTTA-TTT-TTTGTTTAGCTGA
1 TATTTATTTTATTTGTTTAGCTGA
9372380 TATTTATTTTATTTGTTTAGCT
1 TATTTATTTTATTTGTTTAGCT
9372402 TGTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (24 bp):
TATTTATTTTATTTGTTTAGCTGA
Found at i:9391357 original size:8 final size:8
Alignment explanation
Indices: 9391346--9391392 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
9391336 AAAAGAAAGC
9391346 AAAAAATA
1 AAAAAATA
9391354 AAAAACA-A
1 AAAAA-ATA
9391362 AATAAAATA
1 AA-AAAATA
*
9391371 AAATAATA
1 AAAAAATA
*
9391379 AAATAATA
1 AAAAAATA
9391387 AAAAAA
1 AAAAAA
9391393 AGAAAAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:9392497 original size:51 final size:51
Alignment explanation
Indices: 9392377--9392642 Score: 312
Period size: 52 Copynumber: 5.2 Consensus size: 51
9392367 AGAGAGAAGA
9392377 AAACTAAGA-TTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTC
1 AAAC-AAGATTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTC
* * * * *
9392428 AAACAAAATTTTTTAAAAGTGTCAAAACCTCTATTTAGGGGGAGCTATTTTC
1 AAACAAGA-TTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTC
** *
9392480 AAGA-AAGATTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGTGATTTTT
1 AA-ACAAGATTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTC
*
9392531 AAGA-AAGTTTTTTTAAAAGTGTGTCAAAGCCTCTATTT-AGGGTGAGCCATTTTC
1 AA-ACAAG-ATTTTTAAAAGT-T-TCAAAGCCTCTATTTAAGGG-GAGCCATTTTC
* *
9392585 AAATAAGATTTTT-AAAGTTTCAAAGCCTCTGTTT-AGGGGAG-CATTTTC
1 AAACAAGATTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTC
9392633 AAACAAGATT
1 AAACAAGATT
9392643 CAAATCCTCT
Statistics
Matches: 188, Mismatches: 19, Indels: 19
0.83 0.08 0.08
Matches are distributed among these distances:
48 16 0.09
49 3 0.02
50 21 0.11
51 49 0.26
52 59 0.31
53 12 0.06
54 28 0.15
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (51 bp):
AAACAAGATTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTC
Found at i:9392623 original size:103 final size:103
Alignment explanation
Indices: 9392381--9392638 Score: 355
Period size: 103 Copynumber: 2.5 Consensus size: 103
9392371 AGAAGAAAAC
*
9392381 TAAGATTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAAATTTTTTAAAA
1 TAAGATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAAATTTTTTAAAA
*
9392446 GTGTCAAAACCTCTATTTAGGGGGAGCTATTTTCAAGA
66 GTGTCAAAACCTCTATTTAGGGGGAGCCATTTTCAAGA
** * **
9392484 -AAGATTTTTAAAAGTTTCAAAGCCTCTATTTAAGGGGAGTGATTTTTAAGA-AAGTTTTTTTAA
1 TAAGATTTTT-AAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAA-ACAAAATTTTTTAA
* *
9392547 AAGTGTGTCAAAGCCTCTATTTAGGGTGAGCCATTTTCAA-A
64 AA--GTGTCAAAACCTCTATTTAGGGGGAGCCATTTTCAAGA
*
9392588 TAAGATTTTTAAAGTTTCAAAGCCTCTGTTT-AGGGGAG-CATTTTCAAACAA
1 TAAGATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAA
9392639 GATTCAAATC
Statistics
Matches: 137, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
101 1 0.01
102 17 0.12
103 55 0.40
104 22 0.16
105 42 0.31
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (103 bp):
TAAGATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAAATTTTTTAAAA
GTGTCAAAACCTCTATTTAGGGGGAGCCATTTTCAAGA
Done.