Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 180 of 199
Found at i:52327070 original size:20 final size:20
Alignment explanation
Indices: 52327025--52327074 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
52327015 TTACGCTTTT
52327025 CAAAAAAGTTAATTATTTGA
1 CAAAAAAGTTAATTATTTGA
*
52327045 CCAAAAAAGTTAATTATATTTA
1 -CAAAAAAGTTAATTAT-TTGA
52327067 -AAAAAAGT
1 CAAAAAAGT
52327075 AAAAAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.30
21 16 0.59
22 3 0.11
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (20 bp):
CAAAAAAGTTAATTATTTGA
Found at i:52327281 original size:69 final size:69
Alignment explanation
Indices: 52327188--52327326 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
52327178 AAAAAACAAC
52327188 TTATTTTCCTAAATAAAATTAAAAAATCTAAATGTCTAATTAAAAAAATTGACATATAAACCTTA
1 TTATTTTCCTAAATAAAATTAAAAAATCTAAATGTCTAATTAAAAAAATTGACATATAAACCTTA
52327253 TTTA
66 TTTA
52327257 TTATTTTCCTAAATAAAATTAAAAAATCTAAATGTCTAATTAAAAAAATTGACATATAAACCTTA
1 TTATTTTCCTAAATAAAATTAAAAAATCTAAATGTCTAATTAAAAAAATTGACATATAAACCTTA
52327322 TTTA
66 TTTA
52327326 T
1 T
52327327 CCTTAAGTTC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (69 bp):
TTATTTTCCTAAATAAAATTAAAAAATCTAAATGTCTAATTAAAAAAATTGACATATAAACCTTA
TTTA
Found at i:52347405 original size:18 final size:18
Alignment explanation
Indices: 52347382--52347459 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
52347372 ACCATTATAA
52347382 TATATTTTATATAATATT
1 TATATTTTATATAATATT
* * *
52347400 TATATTTTGTAT-GTAAT
1 TATATTTTATATAATATT
* *
52347417 TAT-TTTTCTATTAAAATT
1 TATATTTTATA-TAATATT
52347435 TAT-TTTATATATAATA-T
1 TATATTT-TATATAATATT
52347452 TATATTTT
1 TATATTTT
52347460 TAAATTTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
16 6 0.13
17 12 0.26
18 26 0.55
19 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (18 bp):
TATATTTTATATAATATT
Found at i:52348656 original size:20 final size:20
Alignment explanation
Indices: 52348631--52348678 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
52348621 TTTCAAATCG
52348631 AGTTGAGTGAAATAAATTCA
1 AGTTGAGTGAAATAAATTCA
*
52348651 AGTTGAGTGAAATAAATTCG
1 AGTTGAGTGAAATAAATTCA
52348671 AGTTGAGT
1 AGTTGAGT
52348679 TGAATCGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (20 bp):
AGTTGAGTGAAATAAATTCA
Found at i:52354479 original size:18 final size:18
Alignment explanation
Indices: 52354456--52354498 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
52354446 TGAATCGTGG
* *
52354456 ATCTTCTTCTTCTTCATC
1 ATCTTCTCCTCCTTCATC
*
52354474 ATCTTCACCTCCTTCATC
1 ATCTTCTCCTCCTTCATC
*
52354492 GTCTTCT
1 ATCTTCT
52354499 AGTTTAATTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.37, G:0.02, T:0.49
Consensus pattern (18 bp):
ATCTTCTCCTCCTTCATC
Found at i:52356350 original size:20 final size:21
Alignment explanation
Indices: 52356325--52356371 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
52356315 GAAAATATAA
52356325 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
52356345 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
52356365 ATTTTGA
1 ATTTTGA
52356372 TTTTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:52356356 original size:19 final size:20
Alignment explanation
Indices: 52356325--52356376 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
52356315 GAAAATATAA
52356325 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
52356345 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
52356365 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
52356377 TTTTGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:52358271 original size:11 final size:11
Alignment explanation
Indices: 52358257--52358285 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
52358247 TTTTTCTGTA
52358257 TATTTTTAAAT
1 TATTTTTAAAT
52358268 TA-TTTTAAAT
1 TATTTTTAAAT
52358278 TATTTTTA
1 TATTTTTA
52358286 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:52358275 original size:10 final size:10
Alignment explanation
Indices: 52358260--52358313 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
52358250 TTCTGTATAT
52358260 TTTTAAATTA
1 TTTTAAATTA
52358270 TTTTAAATTA
1 TTTTAAATTA
*
52358280 TTTT-TATT-
1 TTTTAAATTA
52358288 TTTTAAA--A
1 TTTTAAATTA
52358296 TTTTAAA-TA
1 TTTTAAATTA
*
52358305 GTTTAAATT
1 TTTTAAATT
52358314 GTTCACATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 11 0.30
9 11 0.30
10 15 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTTAAATTA
Found at i:52359215 original size:25 final size:25
Alignment explanation
Indices: 52359161--52359227 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
52359151 CTCTCATAAC
* **
52359161 AAAAATTTTAAAAATAAAATATTTAT
1 AAAAATTATAAAAAT-TTATATTTAT
* *
52359187 AAAAATT-TCAAAATTTATATTTTT
1 AAAAATTATAAAAATTTATATTTAT
52359211 CAAAAATTATAAAAATT
1 -AAAAATTATAAAAATT
52359228 CTAAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.21
25 13 0.38
26 14 0.41
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATTATAAAAATTTATATTTAT
Found at i:52359225 original size:26 final size:25
Alignment explanation
Indices: 52359160--52359227 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
52359150 TCTCTCATAA
*
52359160 CAAAAATTTTAAAAATAAAATATTTAT
1 CAAAAA-TTTAAAAAT-TAATATTTAT
* * *
52359187 -AAAAATTTCAAAATTTATATTTTT
1 CAAAAATTTAAAAATTAATATTTAT
52359211 CAAAAATTATAAAAATT
1 CAAAAATT-TAAAAATT
52359228 CTAAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 7 0.21
25 15 0.44
26 12 0.35
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
CAAAAATTTAAAAATTAATATTTAT
Found at i:52362222 original size:21 final size:21
Alignment explanation
Indices: 52362198--52362241 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
52362188 AAACTAGCCA
* *
52362198 TGATGGTTTAGATGCTAGGGT
1 TGATGGGTTAGAGGCTAGGGT
*
52362219 TGATGGGTTAGAGGCTGGGGT
1 TGATGGGTTAGAGGCTAGGGT
52362240 TG
1 TG
52362242 CTAGGATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.45, T:0.34
Consensus pattern (21 bp):
TGATGGGTTAGAGGCTAGGGT
Found at i:52362933 original size:4 final size:4
Alignment explanation
Indices: 52362924--52362953 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
52362914 TAAGGACAAG
*
52362924 TAAA TAAA TAAA TACA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
52362954 TAGAGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:52363075 original size:19 final size:19
Alignment explanation
Indices: 52363034--52363075 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52363024 AATTTGTAAT
*
52363034 AAAATAGATAATAATAGAT
1 AAAATAGATAATAATAGAA
*
52363053 AAAATA-ATAATAGTGAGAA
1 AAAATAGATAATAAT-AGAA
52363072 AAAA
1 AAAA
52363076 ACAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (19 bp):
AAAATAGATAATAATAGAA
Found at i:52363126 original size:4 final size:4
Alignment explanation
Indices: 52363091--52363133 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
52363081 AATAAAAAGG
* ** *
52363091 AAAT AAAT AGAT AAAT GTAT AAAT ATAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
52363134 AAGGGAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:52368608 original size:25 final size:27
Alignment explanation
Indices: 52368509--52368620 Score: 89
Period size: 24 Copynumber: 4.4 Consensus size: 27
52368499 AATCATCTCA
52368509 CGGGAAGCTCAT-A-AGAGCC--TTAAT
1 CGGGAAGCTCATGAGAGAGCCAATT-AT
* *
52368533 CGGAAAGCTCAT-A-CGAGCCAA-TAT
1 CGGGAAGCTCATGAGAGAGCCAATTAT
* * **
52368557 CAGGAAACTCATGAGAGAGCCTTTTAT
1 CGGGAAGCTCATGAGAGAGCCAATTAT
52368584 CGGGAAGCTC-TG-GAGAGCCAATTAT
1 CGGGAAGCTCATGAGAGAGCCAATTAT
*
52368609 TGGGAAGCTCAT
1 CGGGAAGCTCAT
52368621 ATGAACCATA
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
24 28 0.41
25 22 0.32
26 8 0.12
27 11 0.16
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
CGGGAAGCTCATGAGAGAGCCAATTAT
Found at i:52370615 original size:23 final size:22
Alignment explanation
Indices: 52370572--52370615 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52370562 TTCTAAGTCG
52370572 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
52370595 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52370616 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:52370724 original size:45 final size:45
Alignment explanation
Indices: 52370660--52370753 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
52370650 AACAGGTACT
* *
52370660 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
52370705 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
52370750 CGGT
1 CGGT
52370754 TCACATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:52370815 original size:51 final size:51
Alignment explanation
Indices: 52370755--52370931 Score: 184
Period size: 51 Copynumber: 3.5 Consensus size: 51
52370745 ATGTTCGGTT
* *
52370755 CACATAGTACTACACATGTGACCATTACCATCCGATATACGTAGTAGCCTA
1 CACATAGTACTACACACGTGACCATTACCATCCGATATACGTAGTAGCCTG
* * * * *
52370806 CACATAGTACTACACACGTGATCGA-AACTATTCG--GTACGTATAGTAGCCTG
1 CACATAGTACTACACACGTGA-CCATTACCATCCGATATACG--TAGTAGCCTG
* * * *
52370857 CACATAGTACTACACATGCGA-C-TTATCATTCCGATAAACGTAGTAGCCTG
1 CACATAGTACTACACACGTGACCATTACCA-TCCGATATACGTAGTAGCCTG
52370907 CACATAGTACTACACACGTGACCAT
1 CACATAGTACTACACACGTGACCAT
52370932 CACTTTCACT
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
49 6 0.06
50 32 0.32
51 55 0.56
52 6 0.06
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
CACATAGTACTACACACGTGACCATTACCATCCGATATACGTAGTAGCCTG
Found at i:52374570 original size:21 final size:21
Alignment explanation
Indices: 52374546--52374596 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
52374536 CACACGGGAC
* *
52374546 GCCTGATACGACATACAAGGT
1 GCCTGATACGACACACAAAGT
*
52374567 GCCTGAAATACGACACATAAAGT
1 GCCTG--ATACGACACACAAAGT
52374590 GCCTGAT
1 GCCTGAT
52374597 CAGAAAAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
GCCTGATACGACACACAAAGT
Found at i:52374579 original size:23 final size:23
Alignment explanation
Indices: 52374551--52374595 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52374541 GGGACGCCTG
* *
52374551 ATACGACATACAAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
52374574 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
52374596 TCAGAAAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:52375608 original size:6 final size:6
Alignment explanation
Indices: 52375592--52375631 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
52375582 AAAACCCTAG
*
52375592 TTTTTC CTTTTC TTTTTC TTTTTC -TTTTC TTCTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTT
52375632 CCCCTATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:52375615 original size:18 final size:18
Alignment explanation
Indices: 52375592--52375631 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
52375582 AAAACCCTAG
52375592 TTTTTCCTTTTCTT-TTTC
1 TTTTT-CTTTTCTTCTTTC
52375610 TTTTTCTTTTCTTCTTTC
1 TTTTTCTTTTCTTCTTTC
52375628 TTTT
1 TTTT
52375632 CCCCTATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTCTTCTTTC
Found at i:52375677 original size:21 final size:21
Alignment explanation
Indices: 52375653--52375707 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
52375643 AATTGCTCTC
*
52375653 TGTTTCTTTTCTTCTTTGTTT
1 TGTTTCTTTTCTTCTTTCTTT
*
52375674 TGTTTC-TTTCTTTTTTCTTT
1 TGTTTCTTTTCTTCTTTCTTT
52375694 T-TTTCTTTTACTTC
1 TGTTTCTTTT-CTTC
52375708 ATTATATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
20 16 0.55
21 9 0.31
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.76
Consensus pattern (21 bp):
TGTTTCTTTTCTTCTTTCTTT
Found at i:52375748 original size:9 final size:8
Alignment explanation
Indices: 52375734--52375797 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
52375724 TTAGTTAACA
52375734 ATAATAAT
1 ATAATAAT
52375742 GATAATAAT
1 -ATAATAAT
52375751 ATAAT-AT
1 ATAATAAT
52375758 A-ATATAAT
1 ATA-ATAAT
52375766 ATAAT-AT
1 ATAATAAT
52375773 A-ATATAAT
1 ATA-ATAAT
52375781 ATAATATAAT
1 AT-A-ATAAT
52375791 ATAATAA
1 ATAATAA
52375798 ATATCTATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
6 2 0.04
7 10 0.21
8 17 0.35
9 10 0.21
10 9 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
ATAATAAT
Found at i:52375756 original size:5 final size:5
Alignment explanation
Indices: 52375746--52375801 Score: 105
Period size: 5 Copynumber: 11.4 Consensus size: 5
52375736 AATAATGATA
52375746 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
52375796 A-AAT AT
1 ATAAT AT
52375802 CTATTTACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.08
5 46 0.92
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:52382098 original size:25 final size:25
Alignment explanation
Indices: 52382070--52382265 Score: 96
Period size: 25 Copynumber: 7.8 Consensus size: 25
52382060 AATCTCTTTC
*
52382070 GAGCCATATAACGGGAAGCTCAAGT
1 GAGCCATATAACGGGAAGCTCAAGA
* * *
52382095 GAGCCATGTAATGGGAAGCTTATA-A
1 GAGCCATATAACGGGAAGCTCA-AGA
* * *
52382120 GAGCCATA-ATCGGGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCAAGA
* **
52382144 GAGCCA-ATATCGAAAAGCTCATGAGA
1 GAGCCATATAACGGGAAGCTCA--AGA
* * ** * *
52382170 GAGCCTTTTATTGAGAAGCTTAAGA
1 GAGCCATATAACGGGAAGCTCAAGA
* * *
52382195 GAGCTAT-TAATCGCGAAGCTCATGA
1 GAGCCATATAA-CGGGAAGCTCAAGA
* *
52382220 GAGCCATATAAAGGGATGCTCATA-A
1 GAGCCATATAACGGGAAGCTCA-AGA
* * *
52382245 GAGCTAAATAACGGGATGCTC
1 GAGCCATATAACGGGAAGCTC
52382266 TTGCGAGCTA
Statistics
Matches: 128, Mismatches: 34, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
23 1 0.01
24 29 0.23
25 77 0.60
26 10 0.08
27 11 0.09
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCAAGA
Found at i:52382147 original size:24 final size:25
Alignment explanation
Indices: 52382069--52382166 Score: 85
Period size: 24 Copynumber: 4.0 Consensus size: 25
52382059 GAATCTCTTT
* *
52382069 CGAGCCATATAACGGGAAGCTCAAG
1 CGAGCCATATATCGGGAAGCTCATG
* * * *
52382094 TGAGCCATGTAAT-GGGAAGCTTATA
1 CGAGCCATAT-ATCGGGAAGCTCATG
*
52382119 AGAGCCATA-ATCGGGAAGCTCATG
1 CGAGCCATATATCGGGAAGCTCATG
**
52382143 CGAGCCA-ATATCGAAAAGCTCATG
1 CGAGCCATATATCGGGAAGCTCATG
52382167 AGAGAGCCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
23 3 0.05
24 29 0.51
25 24 0.42
26 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
CGAGCCATATATCGGGAAGCTCATG
Found at i:52393133 original size:21 final size:21
Alignment explanation
Indices: 52393109--52393150 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52393099 TCTATCAAAC
*
52393109 TTCAGGTTTTTCCTGTAAAAA
1 TTCAAGTTTTTCCTGTAAAAA
*
52393130 TTCAAGTTTTTCCTTTAAAAA
1 TTCAAGTTTTTCCTGTAAAAA
52393151 CCTAAGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (21 bp):
TTCAAGTTTTTCCTGTAAAAA
Found at i:52393157 original size:21 final size:21
Alignment explanation
Indices: 52393105--52393151 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52393095 TTTTTCTATC
*
52393105 AAACTTCAGGTTTTTCCTGTAA
1 AAAC-TCAAGTTTTTCCTGTAA
* *
52393127 AAATTCAAGTTTTTCCTTTAA
1 AAACTCAAGTTTTTCCTGTAA
52393148 AAAC
1 AAAC
52393152 CTAAGTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (21 bp):
AAACTCAAGTTTTTCCTGTAA
Found at i:52395072 original size:3 final size:3
Alignment explanation
Indices: 52395064--52395092 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52395054 GCTATATTTG
52395064 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
52395093 TGCATGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52407088 original size:20 final size:20
Alignment explanation
Indices: 52407051--52407152 Score: 75
Period size: 20 Copynumber: 5.1 Consensus size: 20
52407041 GTAATGTTAT
**
52407051 ACAGAGGCATCGTAGTGCAA
1 ACAGAGGCATAATAGTGCAA
* *
52407071 ACAGAGGCATAATTGTGCAG
1 ACAGAGGCATAATAGTGCAA
*
52407091 TCAGAGGCATTAA-AGTGCAA
1 ACAGAGGCA-TAATAGTGCAA
* **
52407111 ACAGAGACACTAA-AGTGTGA
1 ACAGAGGCA-TAATAGTGCAA
*
52407131 ACAGAGGCACCAA-AGTGCAA
1 ACAGAGGCA-TAATAGTGCAA
52407151 AC
1 AC
52407153 CCGTACAAGT
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
20 62 0.95
21 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (20 bp):
ACAGAGGCATAATAGTGCAA
Found at i:52413358 original size:16 final size:18
Alignment explanation
Indices: 52413325--52413358 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
52413315 TATTAATAGG
52413325 GTGAATTTTGTGTTAATT
1 GTGAATTTTGTGTTAATT
52413343 GTGAA-TTTGT-TTAATT
1 GTGAATTTTGTGTTAATT
52413359 TTACATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (18 bp):
GTGAATTTTGTGTTAATT
Found at i:52415498 original size:28 final size:28
Alignment explanation
Indices: 52415460--52415557 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
52415450 AAAAATAAAA
*
52415460 ATTTATCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
* *
52415488 ATTTACGAAAATATTGCAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
52415516 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
52415544 ATTTACCAAAATAT
1 ATTTACCAAAATAT
52415558 ATCAAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 63 0.98
29 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:52415660 original size:27 final size:27
Alignment explanation
Indices: 52415622--52415699 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
52415612 CAATGGTATT
* *
52415622 ATTGGCGGCACCAAAGGTGCCAAA-TAA
1 ATTGGTGGCACCAATGGTGCCAAAGT-A
* * *
52415649 ATTGGTGGCACCATTGTTGCCAAAGTC
1 ATTGGTGGCACCAATGGTGCCAAAGTA
52415676 ATTGGTGGCACC-ATGGTGCCAAAG
1 ATTGGTGGCACCAATGGTGCCAAAG
52415700 GGAAAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 10 0.23
27 32 0.74
28 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (27 bp):
ATTGGTGGCACCAATGGTGCCAAAGTA
Found at i:52415810 original size:18 final size:18
Alignment explanation
Indices: 52415773--52415848 Score: 98
Period size: 19 Copynumber: 4.1 Consensus size: 18
52415763 TCAACTCATT
* *
52415773 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAA-ACTA
52415792 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
* *
52415810 TTCTCATTTAATAAATCTA
1 TTTTAATTTAATAAA-CTA
52415829 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
52415847 TT
1 TT
52415849 AAGTAATACT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
18 21 0.42
19 29 0.58
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATTTAATAAACTA
Found at i:52415823 original size:37 final size:37
Alignment explanation
Indices: 52415778--52415848 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
52415768 TCATTTTTTT
*
52415778 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAAATCTATTTTAATTTAATAAACTATTCTC
52415815 ATTTAATAAATCTATTTTAATTTAATAAACTATT
1 ATTTAATAAATCTATTTTAATTTAATAAACTATT
52415849 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAAATCTATTTTAATTTAATAAACTATTCTC
Found at i:52416904 original size:20 final size:20
Alignment explanation
Indices: 52416837--52416918 Score: 60
Period size: 19 Copynumber: 4.0 Consensus size: 20
52416827 TCTCAAATTT
*
52416837 ATTATGTTAGAAATTTTTAAA
1 ATTAT-TTAGAATTTTTTAAA
* * * *
52416858 TTTTTTTA-ACTTTCTTTATAT
1 ATTATTTAGAATTT-TTTA-AA
52416879 ATTATTTAGAATTTTTTAAA
1 ATTATTTAGAATTTTTTAAA
* *
52416899 ATTA-TTATAATTGTTTAAA
1 ATTATTTAGAATTTTTTAAA
52416918 A
1 A
52416919 GATATATAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.36
20 12 0.26
21 14 0.30
22 4 0.09
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTATTTAGAATTTTTTAAA
Found at i:52418409 original size:13 final size:13
Alignment explanation
Indices: 52418359--52418419 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
52418349 ACACTCAAAT
*
52418359 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
*
52418372 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
52418385 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
52418398 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
52418411 -TTTCAAAAG
1 TTTTCAAAAG
52418420 TATTGCCAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
12 8 0.21
13 31 0.79
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:52423782 original size:13 final size:13
Alignment explanation
Indices: 52423764--52423788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52423754 AAAAGCACTG
52423764 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
52423777 TTTTTCTTTTTT
1 TTTTTCTTTTTT
52423789 TAAAAAGACT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:52429138 original size:13 final size:14
Alignment explanation
Indices: 52429114--52429146 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52429104 TCATTTGGGA
52429114 TTAAAAATATATCT
1 TTAAAAATATATCT
*
52429128 TTAAAAA-ATATTT
1 TTAAAAATATATCT
52429141 TTAAAA
1 TTAAAA
52429147 TAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAAATATATCT
Found at i:52430209 original size:15 final size:16
Alignment explanation
Indices: 52430160--52430209 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
52430150 TCAACGTTAC
52430160 TATT-TTAATAATAAA
1 TATTATTAATAATAAA
*
52430175 TATTTATTAAAATTATAAA
1 TA-TTATT--AATAATAAA
52430194 TA-TATTAATAATAAA
1 TATTATTAATAATAAA
52430209 T
1 T
52430210 GTTTTGTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 6 0.21
19 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTATTAATAATAAA
Found at i:52432233 original size:34 final size:35
Alignment explanation
Indices: 52432178--52432244 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
52432168 CAAACACCAG
*
52432178 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
52432213 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
52432245 TATTTTACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:52432656 original size:27 final size:26
Alignment explanation
Indices: 52432617--52432667 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
52432607 TACAAGGACT
52432617 TATGACATATTTTAACTTAGTATAAAAA
1 TATGACATATTTTAA-TTA-TATAAAAA
52432645 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
52432668 TATGAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 3 0.13
27 9 0.39
28 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TATGACATATTTTAATTATATAAAAA
Found at i:52436598 original size:24 final size:24
Alignment explanation
Indices: 52436571--52436637 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
52436561 AATTTAATCT
52436571 TTGAAGTTTATATTTTTTA-TTAAA
1 TTGAAGTTTA-ATTTTTTAGTTAAA
**
52436595 TTGATTTTTAATTTTTTAGTTAAA
1 TTGAAGTTTAATTTTTTAGTTAAA
*
52436619 TTTAA-TAATTAATTTTTTA
1 TTGAAGT--TTAATTTTTTA
52436638 ATAAGAGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.25
24 16 0.44
25 11 0.31
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTGAAGTTTAATTTTTTAGTTAAA
Found at i:52442979 original size:8 final size:8
Alignment explanation
Indices: 52442968--52443019 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
52442958 TAAAATGAAT
52442968 AAAATATA
1 AAAATATA
*
52442976 AAAATGTA
1 AAAATATA
*
52442984 AAAAGATA
1 AAAATATA
* *
52442992 TATATATA
1 AAAATATA
*
52443000 AAATTAT-
1 AAAATATA
52443007 AAAATATA
1 AAAATATA
52443015 AAAAT
1 AAAAT
52443020 TATATTTATG
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (8 bp):
AAAATATA
Found at i:52443011 original size:31 final size:31
Alignment explanation
Indices: 52442966--52443060 Score: 86
Period size: 31 Copynumber: 3.0 Consensus size: 31
52442956 AATAAAATGA
52442966 ATAAAA-TATAAAAATGTAAAAAGATATATAT
1 ATAAAATTAT-AAAATGTAAAAAGATATATAT
* * *
52442997 ATAAAATTATAAAATATAAAAA-TTATATTT
1 ATAAAATTATAAAATGTAAAAAGATATATAT
* ** *
52443027 ATGAAAATTAAAAAAATGTGTATAGATATATAT
1 AT-AAAATT-ATAAAATGTAAAAAGATATATAT
52443060 A
1 A
52443061 AAGATACGCA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
30 8 0.16
31 23 0.46
32 12 0.24
33 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (31 bp):
ATAAAATTATAAAATGTAAAAAGATATATAT
Found at i:52443307 original size:32 final size:32
Alignment explanation
Indices: 52443271--52443358 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
52443261 TTAAATAGAT
* **
52443271 AAATAATAATAATAAAATAATAGTAGTAGTAA
1 AAATAATAATAATAAAAAAATAACAGTAGTAA
* * *
52443303 AAATAAAAAAAATAAAAAAATAACAGTATTAA
1 AAATAATAATAATAAAAAAATAACAGTAGTAA
* * *
52443335 ACATAATAATTATAGTAAAAATAA
1 AAATAATAATAATA-AAAAAATAA
52443359 TGATAACATT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
32 36 0.82
33 8 0.18
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (32 bp):
AAATAATAATAATAAAAAAATAACAGTAGTAA
Found at i:52456263 original size:20 final size:21
Alignment explanation
Indices: 52456226--52456268 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
52456216 AGAGTGGTGT
52456226 TGGAAGAATTGTTAAGAGAAG
1 TGGAAGAATTGTTAAGAGAAG
52456247 TGGAAGAATTG-TAAGAGAAG
1 TGGAAGAATTGTTAAGAGAAG
52456267 TG
1 TG
52456269 AAGGTAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (21 bp):
TGGAAGAATTGTTAAGAGAAG
Found at i:52457751 original size:12 final size:13
Alignment explanation
Indices: 52457728--52457752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52457718 TTGTCTTAAG
52457728 TTTTATGTTTTTT
1 TTTTATGTTTTTT
52457741 TTTTATGTTTTT
1 TTTTATGTTTTT
52457753 CCATTGTTTC
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTATGTTTTTT
Found at i:52457815 original size:23 final size:23
Alignment explanation
Indices: 52457766--52457816 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
52457756 TTGTTTCATA
*
52457766 AGTCTTTTCTTTTAGAAATTTTT
1 AGTCTTGTCTTTTAGAAATTTTT
* *
52457789 -GTCTTGTCTTTTATAGATTTTT
1 AGTCTTGTCTTTTAGAAATTTTT
52457811 AGTCTT
1 AGTCTT
52457817 ACTTTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.61
Consensus pattern (23 bp):
AGTCTTGTCTTTTAGAAATTTTT
Found at i:52457821 original size:22 final size:22
Alignment explanation
Indices: 52457774--52457822 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
52457764 TAAGTCTTTT
*
52457774 CTTTTAGAAATTTTTGTCTTGT
1 CTTTTAGAAATTTTTGTCTTGA
* *
52457796 CTTTTATAGATTTTTAGTCTT-A
1 CTTTTAGAAATTTTT-GTCTTGA
52457818 CTTTT
1 CTTTT
52457823 GCAAGTGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.61
Consensus pattern (22 bp):
CTTTTAGAAATTTTTGTCTTGA
Found at i:52458761 original size:12 final size:12
Alignment explanation
Indices: 52458744--52458768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52458734 TGAGAACAAG
52458744 AATCAAGTATTT
1 AATCAAGTATTT
52458756 AATCAAGTATTT
1 AATCAAGTATTT
52458768 A
1 A
52458769 TCATGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AATCAAGTATTT
Found at i:52460041 original size:21 final size:21
Alignment explanation
Indices: 52460015--52460058 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
52460005 GTATTTTTCT
*
52460015 ACTCTGAACCTTGAATGTCAA
1 ACTCTGAACCTTGAATCTCAA
*
52460036 ACTCTGAACCTTGGATCTCAA
1 ACTCTGAACCTTGAATCTCAA
52460057 AC
1 AC
52460059 CTCAAACCTC
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:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (21 bp):
ACTCTGAACCTTGAATCTCAA
Found at i:52460064 original size:7 final size:7
Alignment explanation
Indices: 52460052--52460109 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
52460042 AACCTTGGAT
52460052 CTCAAAC
1 CTCAAAC
52460059 CTCAAAC
1 CTCAAAC
52460066 CTCAAAC
1 CTCAAAC
52460073 CTCAAAC
1 CTCAAAC
*
52460080 CTTAAAC
1 CTCAAAC
*
52460087 ATCAAAC
1 CTCAAAC
*
52460094 C-CGAAC
1 CTCAAAC
*
52460100 CCCAAAC
1 CTCAAAC
52460107 CTC
1 CTC
52460110 GAATCCCAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
6 5 0.12
7 38 0.88
ACGTcount: A:0.41, C:0.43, G:0.02, T:0.14
Consensus pattern (7 bp):
CTCAAAC
Found at i:52485887 original size:30 final size:32
Alignment explanation
Indices: 52485827--52485890 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
52485817 CACTTATTTT
52485827 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
52485860 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
52485891 ATATACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:52486154 original size:41 final size:41
Alignment explanation
Indices: 52486109--52486263 Score: 276
Period size: 41 Copynumber: 3.8 Consensus size: 41
52486099 ACCGGCTCTT
*
52486109 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
52486150 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
52486191 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
* *
52486232 AGCCTGCTAGAC-TATAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
52486264 TAACGATAAA
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
40 18 0.16
41 93 0.84
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:52490647 original size:22 final size:21
Alignment explanation
Indices: 52490614--52490655 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52490604 TAAAAATTCA
52490614 AAAAATTCAAAAAAATTATTTC
1 AAAAATTC-AAAAAATTATTTC
52490636 AAAAATAT-AAAAAATTATTT
1 AAAAAT-TCAAAAAATTATTT
52490656 TTAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 6 0.32
23 1 0.05
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATTCAAAAAATTATTTC
Found at i:52491482 original size:26 final size:26
Alignment explanation
Indices: 52491453--52491534 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
52491443 GTCGAGTCGG
52491453 TTTAAATTCAATTTAAATAATAAAAA
1 TTTAAATTCAATTTAAATAATAAAAA
* *
52491479 TTTAAATTTAAATTT-AATTATAAAATA
1 TTTAAA-TTCAATTTAAATAATAAAA-A
* *
52491506 TATAAATATCAA-TTAAA-AATAAAAT
1 TTTAAAT-TCAATTTAAATAATAAAAA
52491531 TTTA
1 TTTA
52491535 TTATTTTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.07
26 24 0.53
27 18 0.40
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TTTAAATTCAATTTAAATAATAAAAA
Found at i:52492562 original size:24 final size:24
Alignment explanation
Indices: 52492528--52492607 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 24
52492518 AAGAACTTTG
52492528 AAAATATTTTAACTATTT-TAAATAA
1 AAAATA-TTTAA-TATTTATAAATAA
52492553 AAAATATTTAAT-TTTATATAATAA
1 AAAATATTTAATATTTATA-AATAA
*
52492577 AAATAAATATTAATTATTTATGAAATAA
1 AAA-ATAT-TTAA-TATTTAT-AAATAA
52492605 AAA
1 AAA
52492608 TAGAATTCGA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
22 3 0.06
23 3 0.06
24 13 0.28
25 9 0.19
26 4 0.09
27 1 0.02
28 13 0.28
29 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (24 bp):
AAAATATTTAATATTTATAAATAA
Found at i:52494808 original size:50 final size:51
Alignment explanation
Indices: 52494753--52494877 Score: 150
Period size: 50 Copynumber: 2.5 Consensus size: 51
52494743 TATCCCAAAT
** * * *
52494753 ATGGTCTTACATGA-GAGTTCTCATATTGGTGCCCATGCAATGTCCCAGAC
1 ATGGTCTTACATGAGGACCTCTCATATCGGTGCCAACGCAATGTCCCAGAC
* *
52494803 ATGGTCTT--ATGGAGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACAT-GAGGACCTCTCATATCGGTGCCAACGCAATGTCCCAGAC
52494853 ATGGTCTTACATG-GGACCTCTCATA
1 ATGGTCTTACATGAGGACCTCTCATA
52494878 ACCTCAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
48 2 0.03
49 2 0.03
50 56 0.89
51 1 0.02
52 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (51 bp):
ATGGTCTTACATGAGGACCTCTCATATCGGTGCCAACGCAATGTCCCAGAC
Found at i:52502279 original size:5 final size:5
Alignment explanation
Indices: 52502271--52502295 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52502261 TTAAAATTTA
52502271 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
52502296 TGACTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:52503379 original size:41 final size:41
Alignment explanation
Indices: 52503316--52503417 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
52503306 GTTAGAGCTA
* *
52503316 TAGCGGCGTTTATGACAAAAACGCTGCAAAAGGTCAAGCAT
1 TAGCGGCGCTTATGAAAAAAACGCTGCAAAAGGTCAAGCAT
* * * *
52503357 TAGCGGCGCTTAT-AAAACAAACGTTGCTATAGGTCTAGCAT
1 TAGCGGCGCTTATGAAAA-AAACGCTGCAAAAGGTCAAGCAT
* *
52503398 TAGCGACGCTTTTTGAAAAA
1 TAGCGGCGC-TTATGAAAAA
52503418 CGCCGCTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 3 0.06
41 39 0.78
42 4 0.08
43 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (41 bp):
TAGCGGCGCTTATGAAAAAAACGCTGCAAAAGGTCAAGCAT
Found at i:52503604 original size:41 final size:39
Alignment explanation
Indices: 52503501--52503629 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 39
52503491 AGCTTTAGTG
* * * *
52503501 GCATTAGCGGCGCTTTTTAAAAAACGCCACAATTGATCGA
1 GCATTAGCGGCGC-TTTTGAAAAACGCCGCTATAGATCGA
* *
52503541 GCATTAACGGCGATATTTGAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGCT-TTTGAAAAACGCCGCTATAGATCGA
* * *
52503581 GCATTAGCGGTGCTTTATCGAAAAACGTCGCTATAGATTGA
1 GCATTAGCGGCGCTTT-T-GAAAAACGCCGCTATAGATCGA
52503622 GCATTAGC
1 GCATTAGC
52503630 AGTTCTTTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
39 3 0.04
40 44 0.59
41 28 0.37
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (39 bp):
GCATTAGCGGCGCTTTTGAAAAACGCCGCTATAGATCGA
Found at i:52504012 original size:14 final size:14
Alignment explanation
Indices: 52503991--52504032 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
52503981 TAGAGTTTTG
52503991 AGTTTAGGGTTTAT
1 AGTTTAGGGTTTAT
* *
52504005 GGTTTAGGATTTAT
1 AGTTTAGGGTTTAT
*
52504019 AGTTTGGGGTTTAT
1 AGTTTAGGGTTTAT
52504033 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (14 bp):
AGTTTAGGGTTTAT
Found at i:52505156 original size:38 final size:40
Alignment explanation
Indices: 52505113--52505197 Score: 102
Period size: 43 Copynumber: 2.1 Consensus size: 40
52505103 TGCAATAGCA
*
52505113 ATTTGACTTAAACGGC-GTC-ATTTTCTTCCCCAAATTAG
1 ATTTGACTTAAACGCCAGTCTATTTTCTTCCCCAAATTAG
* *
52505151 ATTTGATTTAAACGCCAAAATTCTATTTTCTTCCCCAAATTAG
1 ATTTGACTTAAACGCC---AGTCTATTTTCTTCCCCAAATTAG
52505194 ATTT
1 ATTT
52505198 CCCCGAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
38 14 0.36
42 2 0.05
43 23 0.59
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (40 bp):
ATTTGACTTAAACGCCAGTCTATTTTCTTCCCCAAATTAG
Found at i:52509245 original size:43 final size:43
Alignment explanation
Indices: 52509181--52509471 Score: 207
Period size: 43 Copynumber: 6.7 Consensus size: 43
52509171 TTTGATAAAT
* *
52509181 GCCGCTAAAGA--ATGGTATTTTTAGCAGCGTTTGTGATAAAAGT
1 GCCGCTAAAGATCAT-GT-TTTTTAGCGGCGTTTGTGATAAAAGC
* * * **
52509224 GCTGCTAAAGATCATATTTTTTTAGCGACGTTTGTGA-AAAAAA
1 GCCGCTAAAGATCAT-GTTTTTTAGCGGCGTTTGTGATAAAAGC
* * * *
52509267 GCCGTTAAA-AGTCAT-TCTCTATATCGGCGTTTGTGATAAAAGC
1 GCCGCTAAAGA-TCATGT-TTTTTAGCGGCGTTTGTGATAAAAGC
* * * *
52509310 ACAGCTAAAGGTCATGTTTTTCAGCGGCGTTTGTGATAAAAGC
1 GCCGCTAAAGATCATGTTTTTTAGCGGCGTTTGTGATAAAAGC
* * * *
52509353 GCCGCTAAAGATCATGTTCTTTAGTGGTGTTTGTGGGT-AAAGC
1 GCCGCTAAAGATCATGTTTTTTAGCGGCGTTTGT-GATAAAAGC
* * ** * * *
52509396 GCCGCTAAAGGTCATGTTCTTTAGCAACGTTTTTTTATAAAAGT
1 GCCGCTAAAGATCATGTTTTTTAGCGGCG-TTTGTGATAAAAGC
* * * *
52509440 GCCACTAAAGGTCATGTTCTATAGCGGCGTTT
1 GCCGCTAAAGATCATGTTTTTTAGCGGCGTTT
52509472 TTCACATAAA
Statistics
Matches: 194, Mismatches: 44, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.01
42 16 0.08
43 121 0.62
44 53 0.27
45 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
GCCGCTAAAGATCATGTTTTTTAGCGGCGTTTGTGATAAAAGC
Found at i:52509385 original size:86 final size:85
Alignment explanation
Indices: 52509207--52509471 Score: 234
Period size: 86 Copynumber: 3.1 Consensus size: 85
52509197 ATTTTTAGCA
* * * * *
52509207 GCGTTTGTGATAAAAGTGCTGCTAAAGATCATATTTTTTTAGCGACGTTTGTGA-AAAAAAGCCG
1 GCGTTTGTGATAAAAGCGCAGCTAAAGGTC--ATGTTTTTAGCGACGTTTGTGATAAAAGAGCCG
*
52509271 TTAAA-AGTCAT-TCTCTATATCG
64 CTAAAGA-TCATGT-TCTATATCG
* * *
52509293 GCGTTTGTGATAAAAGCACAGCTAAAGGTCATGTTTTTCAGCGGCGTTTGTGATAAAAGCGCCGC
1 GCGTTTGTGATAAAAGCGCAGCTAAAGGTCATGTTTTT-AGCGACGTTTGTGATAAAAGAGCCGC
*
52509358 TAAAGATCATGTTCTTTAGT-G
65 TAAAGATCATGTTCTATA-TCG
* * * * * * *
52509379 GTGTTTGTGGGT-AAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACGTTTTTTTATAAAAGTGCC
1 GCGTTTGT-GATAAAAGCGCAGCTAAAGGTCATGTT-TTTAGCGACG-TTTGTGATAAAAGAGCC
* * *
52509443 ACTAAAGGTCATGTTCTATAGCG
63 GCTAAAGATCATGTTCTATATCG
52509466 GCGTTT
1 GCGTTT
52509472 TTCACATAAA
Statistics
Matches: 146, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
84 7 0.05
85 13 0.09
86 81 0.55
87 45 0.31
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (85 bp):
GCGTTTGTGATAAAAGCGCAGCTAAAGGTCATGTTTTTAGCGACGTTTGTGATAAAAGAGCCGCT
AAAGATCATGTTCTATATCG
Found at i:52510909 original size:19 final size:20
Alignment explanation
Indices: 52510872--52510909 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52510862 TATAGGAATA
52510872 ATATTTAAATATGATTTTTG
1 ATATTTAAATATGATTTTTG
*
52510892 ATATTTAAA-ATTATTTTT
1 ATATTTAAATATGATTTTT
52510910 AATTGTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATATTTAAATATGATTTTTG
Found at i:52515113 original size:42 final size:42
Alignment explanation
Indices: 52515049--52515128 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
52515039 GTTTTCAAAT
* *
52515049 AAAAGCGCCGCTAAAGACCATGTTCTTTACCGGCGCTTAGGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTACCGGCGCTTAGGA
*
52515091 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTACCGGCGCTT
52515129 TAAAAAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTACCGGCGCTTAGGA
Found at i:52515161 original size:43 final size:43
Alignment explanation
Indices: 52515049--52515173 Score: 132
Period size: 42 Copynumber: 2.9 Consensus size: 43
52515039 GTTTTCAAAT
* * * *
52515049 AAAAGCGCCGCTAAAGACCATGTTCTTTACCGGCGC-TTAGGA
1 AAAAACGCCGCTAAAGACAATGTTCTTTAGCGGCGCTTTAGAA
52515091 AAAAACGCCGCTAAAGA-ACATGTTCTTTAGCGGCGCTTTA-AA
1 AAAAACGCCGCTAAAGACA-ATGTTCTTTAGCGGCGCTTTAGAA
* * *
52515133 AAGAAATGCTGCTAAAGACAATGCTCTTTTAGCGGCG-TTTA
1 AA-AAACGCCGCTAAAGACAATGTTC-TTTAGCGGCGCTTTA
52515174 TTCTTAAGCG
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
42 35 0.49
43 25 0.35
44 11 0.15
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACAATGTTCTTTAGCGGCGCTTTAGAA
Found at i:52515559 original size:21 final size:21
Alignment explanation
Indices: 52515535--52515588 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
52515525 GCCTACTCTG
* *
52515535 CTTCTCTTGGTGCAGCTTCTA
1 CTTCTCTCGCTGCAGCTTCTA
* *
52515556 CTTCTCTCGCTGTAGCTTCTG
1 CTTCTCTCGCTGCAGCTTCTA
*
52515577 CTTCTCGCGCTG
1 CTTCTCTCGCTG
52515589 TCGCCTCTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.33, G:0.20, T:0.41
Consensus pattern (21 bp):
CTTCTCTCGCTGCAGCTTCTA
Found at i:52515589 original size:21 final size:21
Alignment explanation
Indices: 52515548--52515600 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
52515538 CTCTTGGTGC
*
52515548 AGCTTCTACTTCTCTCGCTGT
1 AGCTTCTACTTCTCGCGCTGT
*
52515569 AGCTTCTGCTTCTCGCGCTGT
1 AGCTTCTACTTCTCGCGCTGT
* *
52515590 CGCCTCTACTT
1 AGCTTCTACTT
52515601 TAAGTTGTTG
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:0.08, C:0.36, G:0.17, T:0.40
Consensus pattern (21 bp):
AGCTTCTACTTCTCGCGCTGT
Found at i:52518897 original size:12 final size:11
Alignment explanation
Indices: 52518855--52518932 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 11
52518845 TCAATTTTAA
52518855 AATAATATATT
1 AATAATATATT
*
52518866 AATAAGTCAT-GT
1 AATAA-T-ATATT
52518878 AA-AATATACTT
1 AATAATATA-TT
52518889 AATAATATATT
1 AATAATATATT
*
52518900 AATAAGTCAT-GT
1 AATAA-T-ATATT
52518912 AA-AATATACTT
1 AATAATATA-TT
52518923 AATAATATAT
1 AATAATATAT
52518933 ATTTAAGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
9 4 0.08
10 2 0.04
11 23 0.43
12 20 0.38
13 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (11 bp):
AATAATATATT
Found at i:52518897 original size:34 final size:34
Alignment explanation
Indices: 52518855--52519214 Score: 219
Period size: 34 Copynumber: 10.3 Consensus size: 34
52518845 TCAATTTTAA
52518855 AATAATATATTAATAAGTCATGTAAAATATACTT
1 AATAATATATTAATAAGTCATGTAAAATATACTT
52518889 AATAATATATTAATAAGTCATGTAAAATATACTT
1 AATAATATATTAATAAGTCATGTAAAATATACTT
* * *
52518923 AATAATATA-TATTTAAGTAATGTAAGATAT-C--
1 AATAATATATTA-ATAAGTCATGTAAAATATACTT
*
52518954 --------ATTAATAAGTCGTGTAAAATATACTT
1 AATAATATATTAATAAGTCATGTAAAATATACTT
* * * *
52518980 AATAATATA-TATTTAAGTAATGTAAGATATCAATTTT
1 AATAATATATTA-ATAAGTCATGTAAAATAT--A-CTT
*
52519017 AAAATATATATTCATTAATAAGTCGTGTAAAATATACTT
1 --AATA-ATA-T-ATTAATAAGTCATGTAAAATATACTT
* * * *
52519056 AATAATATA-TATTTAAGTAATGTAAGATATCAATTTT
1 AATAATATATTA-ATAAGTCATGTAAAATAT--A-CTT
52519093 AAAATAATATATTAATAAGTCATGTAAAATATACTT
1 --AATAATATATTAATAAGTCATGTAAAATATACTT
* * * *
52519129 AATAATATA-TATTTAAGTAATGTAAGATATCAATTTT
1 AATAATATATTA-ATAAGTCATGTAAAATAT--A-CTT
**
52519166 AAAATATATATTCATTAATAAGTGGTGTAAAATATACTT
1 --AATA-ATA-T-ATTAATAAGTCATGTAAAATATACTT
52519205 AATAATATAT
1 AATAATATAT
52519215 ATTTAAGTAA
Statistics
Matches: 251, Mismatches: 35, Indels: 80
0.69 0.10 0.22
Matches are distributed among these distances:
23 15 0.06
24 3 0.01
33 9 0.04
34 114 0.45
35 2 0.01
36 11 0.04
37 15 0.06
39 36 0.14
40 10 0.04
41 2 0.01
42 30 0.12
43 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (34 bp):
AATAATATATTAATAAGTCATGTAAAATATACTT
Found at i:52518958 original size:57 final size:57
Alignment explanation
Indices: 52518893--52519011 Score: 222
Period size: 57 Copynumber: 2.1 Consensus size: 57
52518883 ATACTTAATA
52518893 ATAT-ATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
*
52518949 ATATCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
52519006 ATATCA
1 ATATCA
52519012 ATTTTAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 4 0.07
57 57 0.93
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (57 bp):
ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
Found at i:52519024 original size:91 final size:90
Alignment explanation
Indices: 52518859--52519025 Score: 230
Period size: 91 Copynumber: 1.8 Consensus size: 90
52518849 TTTTAAAATA
* *
52518859 ATATATTAATAAGTCATGTAAAATATACTTAATAATATATTAATAAGTCATGTAAAATATACTTA
1 ATATATTAATAAGTCATGTAAAATATACTTAATAATATATTAATAAGTAATGTAAAATATAATTA
*
52518924 ATAATATATATTTAAGTAATGTAAG
66 ATAAAATATATTTAAGTAATGTAAG
* * *
52518949 ATATCATTAATAAGTCGTGTAAAATATACTTAATAATATA-TATTTAAGTAATGTAAGATATCAA
1 ATAT-ATTAATAAGTCATGTAAAATATACTTAATAATATATTA-ATAAGTAATGTAAAATAT-AA
*
52519013 TT-TTAAAATATAT
63 TTAATAAAATATAT
52519026 ATTCATTAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
90 6 0.09
91 58 0.87
92 3 0.04
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (90 bp):
ATATATTAATAAGTCATGTAAAATATACTTAATAATATATTAATAAGTAATGTAAAATATAATTA
ATAAAATATATTTAAGTAATGTAAG
Found at i:52519039 original size:76 final size:76
Alignment explanation
Indices: 52518952--52519264 Score: 587
Period size: 76 Copynumber: 4.2 Consensus size: 76
52518942 ATGTAAGATA
52518952 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
52519017 AAAATATATAT
66 AAAATATATAT
52519028 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
52519093 AAAATA-ATA-
66 AAAATATATAT
*
52519102 T-ATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
52519166 AAAATATATAT
66 AAAATATATAT
*
52519177 TCATTAATAAGTGGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
52519242 AAAATATATAT
66 AAAATATATAT
52519253 TCATTAATAAGT
1 TCATTAATAAGT
52519265 TAAATGAAAT
Statistics
Matches: 231, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
73 68 0.29
74 4 0.02
75 4 0.02
76 155 0.67
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (76 bp):
TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
AAAATATATAT
Found at i:52519129 original size:149 final size:151
Alignment explanation
Indices: 52518949--52519264 Score: 591
Period size: 149 Copynumber: 2.1 Consensus size: 151
52518939 GTAATGTAAG
*
52518949 ATATCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
52519014 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGT
66 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGT
52519079 AAGATATCAATTTTAAAATA-
131 AAGATATCAATTTTAAAATAT
52519099 ATAT-ATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
*
52519163 TTTAAAATATATATTCATTAATAAGTGGTGTAAAATATACTTAATAATATATATTTAAGTAATGT
66 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGT
52519228 AAGATATCAATTTTAAAATAT
131 AAGATATCAATTTTAAAATAT
52519249 ATATTCATTAATAAGT
1 ATA-TCATTAATAAGT
52519265 TAAATGAAAT
Statistics
Matches: 161, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
149 143 0.89
150 7 0.04
151 1 0.01
152 10 0.06
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (151 bp):
ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGT
AAGATATCAATTTTAAAATAT
Found at i:52519461 original size:67 final size:67
Alignment explanation
Indices: 52519389--52519527 Score: 235
Period size: 67 Copynumber: 2.1 Consensus size: 67
52519379 TTTGTTGAGA
* *
52519389 ATTCATTATATAACGAATTTATTAAACATTCAATCAATTA-ACTAACCAAAATTGATACTTCATT
1 ATTCATTATATAACGAATTTATAAAACATTCAATCAATTACA-TAACCAAAATTGATAATTCATT
52519453 GAC
65 GAC
*
52519456 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
1 ATTCATTATATAACGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
52519521 AC
66 AC
52519523 ATTCA
1 ATTCA
52519528 ATCAATTAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 67 0.99
68 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (67 bp):
ATTCATTATATAACGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
AC
Found at i:52519608 original size:16 final size:16
Alignment explanation
Indices: 52519587--52519622 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
52519577 ATTAATTGAA
*
52519587 ATAAAATTGTAAATCG
1 ATAAAATTGCAAATCG
52519603 ATAAAATTGCAAATCG
1 ATAAAATTGCAAATCG
52519619 ATAA
1 ATAA
52519623 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGCAAATCG
Found at i:52522248 original size:7 final size:7
Alignment explanation
Indices: 52522236--52522310 Score: 89
Period size: 7 Copynumber: 10.7 Consensus size: 7
52522226 ACCTTAAAAA
52522236 CTAAACC
1 CTAAACC
*
52522243 CCAAACC
1 CTAAACC
*
52522250 CTAATCC
1 CTAAACC
52522257 CTAAACC
1 CTAAACC
52522264 CTAAACC
1 CTAAACC
*
52522271 CCAAATCC
1 CTAAA-CC
52522279 C-AAACC
1 CTAAACC
*
52522285 CTAAAGC
1 CTAAACC
*
52522292 CTAAAAC
1 CTAAACC
52522299 CTAAACC
1 CTAAACC
52522306 CTAAA
1 CTAAA
52522311 ACCCCAAGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 3 0.05
7 52 0.90
8 3 0.05
ACGTcount: A:0.44, C:0.41, G:0.01, T:0.13
Consensus pattern (7 bp):
CTAAACC
Found at i:52523571 original size:114 final size:114
Alignment explanation
Indices: 52523382--52523803 Score: 763
Period size: 114 Copynumber: 3.7 Consensus size: 114
52523372 CCGCTAATAC
* *
52523382 TATACTTCAGCGGCGTTTTTAACCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
52523447 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAATGCCGCTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
52523496 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
* *
52523561 CGTTTTGGTTAAGATGATTTGCGGCGCATCAGACAAACGCCACTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
*
52523610 TATACTTTAGCGGCGTTTTCAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
52523675 CGTTTTGGTTAAGATGATTTGCGGCGCATTCGACAAACGCCGCTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
*
52523724 TATACTTTAGCGGCGTTTTTTATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
52523789 TGTTTTGGTTAAGAT
66 CGTTTTGGTTAAGAT
52523804 ATCTGGAGGC
Statistics
Matches: 296, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 296 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (114 bp):
TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
Found at i:52523869 original size:114 final size:113
Alignment explanation
Indices: 52523382--52523875 Score: 688
Period size: 114 Copynumber: 4.3 Consensus size: 113
52523372 CCGCTAATAC
* * * *
52523382 TATACTTCAGCGGCGTTTTTAACCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCG-TTTTCATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
52523447 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAATGCCGCTGATGA
65 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
* *
52523496 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCG-TTTTCATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
* *
52523561 CGTTTTGGTTAAGATGATTTGCGGCGCATCAGACAAACGCCACTGATGA
65 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
*
52523610 TATACTTTAGCGGCGTTTTCAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTC-ATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
52523675 CGTTTTGGTTAAGATGATTTGCGGCGCATTCGACAAACGCCGCTGATGA
65 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
* *
52523724 TATACTTTAGCGGCGTTTTTTATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCG-TTTTCATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
* * * * * * *
52523789 TGTTTTGGTTAAGAT-ATCTGGAGGCGCTTCCCACCAAACGCTGCT-ATAA
65 CGTTTTGGTTAAGATGAT-TTGCGGCGCATCCGA-CAAACGCCGCTGATGA
* * *
52523838 CTATCCTTTA-CTGGCGTTTTCCTTAAACGCCACTAATT
1 -TATACTTTAGC-GGCGTTTTCATCAAACGCCACTAATT
52523876 ATAGTATACA
Statistics
Matches: 351, Mismatches: 23, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
113 6 0.02
114 319 0.91
115 26 0.07
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (113 bp):
TATACTTTAGCGGCGTTTTCATCAAACGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTGC
GTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
Found at i:52524011 original size:116 final size:112
Alignment explanation
Indices: 52523865--52524123 Score: 272
Period size: 113 Copynumber: 2.3 Consensus size: 112
52523855 TTTCCTTAAA
** * * *
52523865 CGCCACTAATTATAGTATACATCAAGACCAAAATGGAGCGTTTTGATTAGGATATC-TTGCGGCG
1 CGCCACTAATTGCAATATACATCAAGACCAAAAT-CAGCGTTTTGATTA--ACATCGTTGCGGCG
* ** * * *
52523929 TTTAATGC-TATGCGCCGCTAATACTATACATTAGCGGCATTTTATTTATAAG
63 CTT--CCCATAAGCGCCGCTAATACTATACATTACCGGCATTTT-TTCATAAG
* * *
52523981 CGCCACTAATTGCAATATACATCAAGACCAAACTCTGCGTTTTGGTTAACATCGTTTGCGGCGCT
1 CGCCACTAATTGCAATATACATCAAGACCAAAATCAGCGTTTTGATTAACATCG-TTGCGGCGCT
* *
52524046 TCCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCGTAAG
65 TCCCATAAGCGCCGCTAATACTATACATTACCGGCATTTTTTCATAAG
*
52524094 CGCCAC-AAATGCCAATATACATCAAGACCA
1 CGCCACTAATTG-CAATATACATCAAGACCA
52524124 GAACGCTGCG
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
112 4 0.03
113 35 0.29
114 32 0.26
115 21 0.17
116 30 0.25
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (112 bp):
CGCCACTAATTGCAATATACATCAAGACCAAAATCAGCGTTTTGATTAACATCGTTGCGGCGCTT
CCCATAAGCGCCGCTAATACTATACATTACCGGCATTTTTTCATAAG
Found at i:52525372 original size:18 final size:18
Alignment explanation
Indices: 52525349--52525396 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
52525339 TATATTTTTT
*
52525349 AAAAAATTAAAAATTTAA
1 AAAAAATTAAAAATATAA
*
52525367 AAAAAATTAAAAATATAT
1 AAAAAATTAAAAATATAA
*
52525385 ATAAAATTAAAA
1 AAAAAATTAAAA
52525397 TAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAAATTAAAAATATAA
Found at i:52530263 original size:22 final size:22
Alignment explanation
Indices: 52530221--52530263 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
52530211 TGAAAATTTT
*
52530221 TATTTTAATATTAAAGTATAAA
1 TATTTTAATATTAAAGAATAAA
*
52530243 TATTTTAAATTTTAAA-AATAA
1 TATTTT-AATATTAAAGAATAA
52530264 TATACAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTTTAATATTAAAGAATAAA
Found at i:52536997 original size:12 final size:12
Alignment explanation
Indices: 52536980--52537012 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
52536970 CGACCCACCC
52536980 ATATTATTTTTT
1 ATATTATTTTTT
52536992 ATATTA-TTTTT
1 ATATTATTTTTT
*
52537003 ATATAATTTT
1 ATATTATTTT
52537013 AAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:52537137 original size:30 final size:30
Alignment explanation
Indices: 52537101--52537163 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
52537091 GCTTAACAAG
*
52537101 CAAATGTCTCTAAAATAATAGCAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
52537131 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
52537161 CAA
1 CAA
52537164 TAAATAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:52548820 original size:12 final size:12
Alignment explanation
Indices: 52548803--52548828 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52548793 GAGTTATTCG
52548803 TATTATTCGAGT
1 TATTATTCGAGT
52548815 TATTATTCGAGT
1 TATTATTCGAGT
52548827 TA
1 TA
52548829 ACTCGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (12 bp):
TATTATTCGAGT
Found at i:52549003 original size:20 final size:20
Alignment explanation
Indices: 52548969--52549057 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 20
52548959 AAAAATTACA
52548969 AAAACAATT-AAAATAATTTT
1 AAAA-AATTCAAAATAATTTT
*
52548989 CAAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
*
52549009 AAAAAAATCAAAATTTATATTTT
1 AAAAAATTCAAAA--TA-ATTTT
* *
52549032 TAAAAATTCTAAAAT-TTTTT
1 AAAAAATTC-AAAATAATTTT
52549052 AAAAAA
1 AAAAAA
52549058 ATTGAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
19 8 0.15
20 29 0.53
22 2 0.04
23 8 0.15
24 8 0.15
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:52549066 original size:43 final size:44
Alignment explanation
Indices: 52548983--52549076 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
52548973 CAATTAAAAT
*
52548983 AATTTTCAAAAATTCAAAATATTTATAAAAAAATCAAAA-TTTA
1 AATTTTTAAAAATTCAAAATATTTATAAAAAAATCAAAATTTTA
* * **
52549026 TATTTTTAAAAATTCTAAAAT-TTTTTAAAAAAATTGAAATTTTA
1 AATTTTTAAAAATTC-AAAATATTTATAAAAAAATCAAAATTTTA
52549070 AATTTTT
1 AATTTTT
52549077 TCTAAAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
43 28 0.65
44 15 0.35
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (44 bp):
AATTTTTAAAAATTCAAAATATTTATAAAAAAATCAAAATTTTA
Found at i:52553217 original size:46 final size:46
Alignment explanation
Indices: 52553168--52553406 Score: 211
Period size: 46 Copynumber: 4.9 Consensus size: 46
52553158 TGGTAGCTTT
52553168 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTC
1 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAG---TA---TC
* * *
52553220 GGCTATACTTATCTGATCAAGTGATAAAGT-GATAAGTGAT-AGCT-TC
1 AGCTACACTTATCTGATCAAGTGA-CAAGTGGA-AAGTGATAAG-TATC
* *
52553266 GGCTATACTTATCTGATCAAGTGACAAAGT-GATAAGTGAT-AGCT-TC
1 AGCTACACTTATCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TATC
52553312 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTC
1 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAA--G-TA---TC
* *
52553364 GGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
1 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGT
52553407 GATAGCTTCG
Statistics
Matches: 166, Mismatches: 10, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
45 11 0.07
46 72 0.43
48 2 0.01
49 1 0.01
50 2 0.01
52 67 0.40
53 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTATC
Found at i:52553218 original size:52 final size:51
Alignment explanation
Indices: 52553147--52553453 Score: 418
Period size: 52 Copynumber: 6.1 Consensus size: 51
52553137 ATCAAGTGAT
* **
52553147 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
52553199 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
52553245 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
52553291 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
52553343 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
52553394 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
52553447 ATAAGTG
1 A-AAGTG
52553454 GCTACACTTA
Statistics
Matches: 233, Mismatches: 11, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
46 87 0.37
48 1 0.00
49 1 0.00
51 1 0.00
52 133 0.57
53 10 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:52553253 original size:98 final size:97
Alignment explanation
Indices: 52553133--52553453 Score: 454
Period size: 98 Copynumber: 3.3 Consensus size: 97
52553123 TTTGAGTACT
* **
52553133 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-
*
52553198 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
52553231 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
52553291 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
52553323 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
52553388 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
52553427 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTG
52553454 GCTACACTTA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.21
95 1 0.01
96 1 0.01
98 114 0.57
101 1 0.01
104 41 0.21
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:52553463 original size:37 final size:37
Alignment explanation
Indices: 52553416--52553525 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
52553406 TGATAGCTTC
*
52553416 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
52553453 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
52553490 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
52553525 G
1 G
52553526 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:52554839 original size:49 final size:49
Alignment explanation
Indices: 52554778--52554919 Score: 221
Period size: 49 Copynumber: 2.9 Consensus size: 49
52554768 ATGTGAACAT
*
52554778 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
52554828 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
52554877 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCAT
52554920 TGAGAAAACG
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
49 82 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:52558132 original size:46 final size:46
Alignment explanation
Indices: 52558083--52558321 Score: 211
Period size: 46 Copynumber: 4.9 Consensus size: 46
52558073 TGGTAGCTTT
52558083 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTC
1 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAG---TA---TC
* * *
52558135 GGCTATACTTATCTGATCAAGTGATAAAGT-GATAAGTGAT-AGCT-TC
1 AGCTACACTTATCTGATCAAGTGA-CAAGTGGA-AAGTGATAAG-TATC
* *
52558181 GGCTATACTTATCTGATCAAGTGACAAAGT-GATAAGTGAT-AGCT-TC
1 AGCTACACTTATCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TATC
52558227 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTC
1 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAA--G-TA---TC
* *
52558279 GGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
1 AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGT
52558322 GATAGCTTCG
Statistics
Matches: 166, Mismatches: 10, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
45 11 0.07
46 72 0.43
48 2 0.01
49 1 0.01
50 2 0.01
52 67 0.40
53 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
AGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTATC
Found at i:52558133 original size:52 final size:51
Alignment explanation
Indices: 52558062--52558368 Score: 418
Period size: 52 Copynumber: 6.1 Consensus size: 51
52558052 ATCAAGTGAT
* **
52558062 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
52558114 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
52558160 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
52558206 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
52558258 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
52558309 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
52558362 ATAAGTG
1 A-AAGTG
52558369 GCTACACTTA
Statistics
Matches: 233, Mismatches: 11, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
46 87 0.37
48 1 0.00
49 1 0.00
51 1 0.00
52 133 0.57
53 10 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:52558168 original size:98 final size:97
Alignment explanation
Indices: 52558048--52558368 Score: 454
Period size: 98 Copynumber: 3.3 Consensus size: 97
52558038 TTTGAGTACT
* **
52558048 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-
*
52558113 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
52558146 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
52558206 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
52558238 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
52558303 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
52558342 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTG
52558369 GCTACACTTA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.21
95 1 0.01
96 1 0.01
98 114 0.57
101 1 0.01
104 41 0.21
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:52558378 original size:37 final size:37
Alignment explanation
Indices: 52558331--52558440 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
52558321 TGATAGCTTC
*
52558331 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
52558368 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
52558405 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
52558440 G
1 G
52558441 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:52561282 original size:28 final size:28
Alignment explanation
Indices: 52561222--52561288 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
52561212 TTAGGGCTTG
* * *
52561222 AGGTTCAGTGTTTGAGATTTAAGGGTTA
1 AGGTTCGGGGTTTGAGATTTAAAGGTTA
* * *
52561250 AGGTTTGGGGTTTGTGATTTAAAGTTTA
1 AGGTTCGGGGTTTGAGATTTAAAGGTTA
*
52561278 GGGTTCGGGGT
1 AGGTTCGGGGT
52561289 AACAAAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.19, C:0.03, G:0.37, T:0.40
Consensus pattern (28 bp):
AGGTTCGGGGTTTGAGATTTAAAGGTTA
Found at i:52566009 original size:51 final size:51
Alignment explanation
Indices: 52565951--52566137 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 51
52565941 TTGGTTCACA
* * * *
52565951 TAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT-AGCTATCTGGTACATG
* * * *
52566002 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGGTACGTA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATAGCTATCTGGTACATG
* * * *
52566053 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATAGCTATCTGGTACATG
*
52566103 TAGTAACCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
52566138 CACTTTCACT
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
50 43 0.38
51 68 0.60
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATAGCTATCTGGTACATG
Found at i:52566130 original size:101 final size:101
Alignment explanation
Indices: 52565950--52566133 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
52565940 ATTGGTTCAC
* *
52565950 ATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCCTGCAC
1 ATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCTGATACACGTAGTAACCTGCAC
52566015 ATAGTACTACACACGTGATCGAAGCTATCCGGTACGT
65 ATAGTACTACACACGTGATCGAAGCTATCCGGTACGT
* * * *
52566052 ATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACATGTAGTAACCTGCAC
1 ATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCTGATACACGTAGTAACCTGCAC
52566116 ATAGTACTACACACGTGA
65 ATAGTACTACACACGTGA
52566134 CCATCACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 1 0.01
101 42 0.56
102 32 0.43
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (101 bp):
ATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCTGATACACGTAGTAACCTGCACA
TAGTACTACACACGTGATCGAAGCTATCCGGTACGT
Found at i:52566157 original size:101 final size:100
Alignment explanation
Indices: 52565944--52566167 Score: 258
Period size: 101 Copynumber: 2.2 Consensus size: 100
52565934 AATGATATTG
* *
52565944 GTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCTGATACACGTAGTAAC
*
52566009 CTGCACATAGTACTACACACGTGATCGAAGCTATCC
65 CTGCACATAGTACTACACACGTGATCCAAGCTATCC
* * * * *
52566045 GGT-ACGTATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACATGTAGTA
1 GTTCAC--ATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCTGATACACGTAGTA
*
52566108 ACCTGCACATAGTACTACACACGTGA-CCATCA-CTTTCAC
63 ACCTGCACATAGTACTACACACGTGATCCA--AGCTATC-C
* *
52566147 TTTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTACACA
52566168 CAGTCTGTGC
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
100 5 0.05
101 61 0.59
102 35 0.34
103 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (100 bp):
GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCTGATACACGTAGTAACC
TGCACATAGTACTACACACGTGATCCAAGCTATCC
Found at i:52574873 original size:22 final size:22
Alignment explanation
Indices: 52574847--52574965 Score: 58
Period size: 21 Copynumber: 5.5 Consensus size: 22
52574837 TTGAAATATT
52574847 TAAAATTATTAATATATTAATA
1 TAAAATTATTAATATATTAATA
52574869 TAAAA-TATT-ATCAT-TT--TA
1 TAAAATTATTAAT-ATATTAATA
* * *
52574887 -AATATTATTAA-ACATTCATA
1 TAAAATTATTAATATATTAATA
** *
52574907 TTTAATTATTTATAT-TTAATCATA
1 TAAAATTATTAATATATT-A--ATA
52574931 TAATAAATTATTAATATAATTAATA
1 T-A-AAATTATTAATAT-ATTAATA
52574956 T-AAATTATTA
1 TAAAATTATTA
52574966 TTTTAATAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 30
0.63 0.10 0.27
Matches are distributed among these distances:
17 4 0.06
18 8 0.11
19 1 0.01
20 6 0.08
21 15 0.21
22 15 0.21
24 4 0.06
25 4 0.06
26 11 0.15
27 1 0.01
28 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATTATTAATATATTAATA
Found at i:52574972 original size:22 final size:24
Alignment explanation
Indices: 52574910--52574972 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 24
52574900 ATTCATATTT
52574910 AATTATTTATATTTAATCATATAATA
1 AATTA-TTAT-TTTAATCATATAATA
* * *
52574936 AATTATTAATATAATTA-AT-ATA
1 AATTATTATTTTAATCATATAATA
52574958 AATTATTATTTTAAT
1 AATTATTATTTTAAT
52574973 AAATTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 16 0.50
23 2 0.06
24 6 0.19
25 3 0.09
26 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTATTATTTTAATCATATAATA
Found at i:52574973 original size:18 final size:17
Alignment explanation
Indices: 52574953--52575011 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
52574943 AATATAATTA
52574953 ATATAAATTATTATTTT
1 ATATAAATTATTATTTT
**
52574970 A-ATAAATTATT-TAAT
1 ATATAAATTATTATTTT
*
52574985 ATTTAAATT-TTATTTT
1 ATATAAATTATTATTTT
52575001 AATAATAAATT
1 -AT-ATAAATT
52575012 TAAAAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.16
16 18 0.56
17 3 0.09
18 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATAAATTATTATTTT
Found at i:52574976 original size:16 final size:16
Alignment explanation
Indices: 52574955--52575005 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
52574945 TATAATTAAT
52574955 ATAAATTATTATTTTA
1 ATAAATTATTATTTTA
*
52574971 ATAAATTATTTAATATT-
1 ATAAATTA-TT-ATTTTA
52574988 -TAAATT-TTATTTTA
1 ATAAATTATTATTTTA
52575002 ATAA
1 ATAA
52575006 TAAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 3 0.10
16 14 0.48
17 2 0.07
18 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAAATTATTATTTTA
Found at i:52575021 original size:15 final size:15
Alignment explanation
Indices: 52575001--52575030 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52574991 ATTTTATTTT
52575001 AATAATAAATTTAAA
1 AATAATAAATTTAAA
*
52575016 AATAATAATTTTAAA
1 AATAATAAATTTAAA
52575031 TGATATTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAATAAATTTAAA
Found at i:52575218 original size:32 final size:32
Alignment explanation
Indices: 52575182--52575244 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
52575172 TTTTGGAATC
* *
52575182 TAGTCCCTATGCTTTTATTTTTAAGAATTTAT
1 TAGTCCCTATACTTTTATTTTCAAGAATTTAT
*
52575214 TAGTCCCTGTACTTTTATTTTCAAGAATTTA
1 TAGTCCCTATACTTTTATTTTCAAGAATTTA
52575245 GACCCTCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (32 bp):
TAGTCCCTATACTTTTATTTTCAAGAATTTAT
Found at i:52575258 original size:29 final size:31
Alignment explanation
Indices: 52575193--52575258 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 31
52575183 AGTCCCTATG
* * *
52575193 CTTTTATTTTTAAGAATTTATTAGTCCCTGTA
1 CTTTTATTTTCAAGAA-TTATTAGACCCTCTA
52575225 CTTTTATTTTCAAGAA-T-TTAGACCCTCTA
1 CTTTTATTTTCAAGAATTATTAGACCCTCTA
*
52575254 GTTTT
1 CTTTT
52575259 TAAATTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
32 15 0.50
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (31 bp):
CTTTTATTTTCAAGAATTATTAGACCCTCTA
Found at i:52577229 original size:18 final size:18
Alignment explanation
Indices: 52577206--52577243 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
52577196 TGCATCACAT
52577206 ATAAAAATTAATATTTTA
1 ATAAAAATTAATATTTTA
52577224 ATAAAAATTAATATTTTA
1 ATAAAAATTAATATTTTA
52577242 AT
1 AT
52577244 TTAAAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAAATTAATATTTTA
Found at i:52580186 original size:27 final size:27
Alignment explanation
Indices: 52580156--52580232 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
52580146 GGCCAATCAC
* *
52580156 ATTGGTGGCACCAAAGGTGCCAATGTA
1 ATTGGCGGCACCAATGGTGCCAATGTA
*
52580183 ATTGGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTA
52580210 ATTGGCGGCACCAATGGTGCCAA
1 ATTGGCGGCACCAATGGTGCCAA
52580233 AGGACTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATGTA
Found at i:52580565 original size:19 final size:19
Alignment explanation
Indices: 52580541--52580604 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
52580531 ATTAAAATAG
52580541 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
52580560 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
52580578 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
52580597 TTTAATTT
1 TTTAATTT
52580605 TAAAAATTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:52580782 original size:82 final size:82
Alignment explanation
Indices: 52580680--52580844 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
52580670 AAAAGGAAAA
52580680 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
52580745 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
*
52580762 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
52580827 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
52580844 A
1 A
52580845 TTTTAATTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (82 bp):
AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:52580952 original size:18 final size:19
Alignment explanation
Indices: 52580913--52581008 Score: 117
Period size: 19 Copynumber: 5.2 Consensus size: 19
52580903 ATTTTATATT
52580913 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
52580932 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
52580950 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
*
52580969 TTAAAT-AAGAATAG-TTTA
1 TTAAATGAA-AATAGAGTTA
*
52580987 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
52581006 TTA
1 TTA
52581009 CTTAATTAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
18 31 0.47
19 35 0.53
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:52580954 original size:37 final size:37
Alignment explanation
Indices: 52580913--52581008 Score: 174
Period size: 37 Copynumber: 2.6 Consensus size: 37
52580903 ATTTTATATT
* *
52580913 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATAAGAATAGTTTA
52580950 TTAAATTAAAATAGAGTTATTAAATAAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATAAGAATAGTTTA
52580987 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
52581009 CTTAATTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATAAGAATAGTTTA
Found at i:52581013 original size:18 final size:18
Alignment explanation
Indices: 52580920--52581013 Score: 84
Period size: 18 Copynumber: 5.1 Consensus size: 18
52580910 ATTTTAAATG
*
52580920 AAAATAGAGTTATTAAATG
1 AAAATAGAGTTATT-AATT
* *
52580939 AGAATAG-TTTATTAAATT
1 AAAATAGAGTTATT-AATT
*
52580957 AAAATAGAGTTATTAAAT
1 AAAATAGAGTTATTAATT
*
52580975 AAGAATAG-TTTATTAAATT
1 AA-AATAGAGTTATT-AATT
*
52580994 AAAATAGAGTTATTACTT
1 AAAATAGAGTTATTAATT
52581012 AA
1 AA
52581014 TTAGAATTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
18 35 0.57
19 26 0.43
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (18 bp):
AAAATAGAGTTATTAATT
Found at i:52581844 original size:7 final size:7
Alignment explanation
Indices: 52581832--52581865 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
52581822 TTATTTCTTT
52581832 TCTTTTA
1 TCTTTTA
52581839 TCTTTTA
1 TCTTTTA
52581846 TCTTTTA
1 TCTTTTA
52581853 TCTTTTA
1 TCTTTTA
*
52581860 CCTTTT
1 TCTTTT
52581866 TAAAGTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (7 bp):
TCTTTTA
Done.