Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 103 of 332
Found at i:33362285 original size:6 final size:6
Alignment explanation
Indices: 33362253--33362360 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
33362243 AAAGAAATTG
* * ** *
33362253 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
33362300 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
33362351 AAAGAA AAAG
1 AAAGAA AAAG
33362361 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:33362340 original size:14 final size:13
Alignment explanation
Indices: 33362321--33362358 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
33362311 AAAAGTGAGA
33362321 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
33362333 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
33362348 GAAAAAGAAAA
1 GAAAAAGAAAA
33362359 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:33362372 original size:21 final size:21
Alignment explanation
Indices: 33362322--33362372 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
33362312 AAAGTGAGAG
*
33362322 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
33362343 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
33362364 AAAAAGAAA
1 AAAAAGAAA
33362373 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:33362412 original size:33 final size:33
Alignment explanation
Indices: 33362375--33362437 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33362365 AAAAGAAATT
33362375 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
33362408 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
33362438 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:33368353 original size:20 final size:20
Alignment explanation
Indices: 33368300--33368356 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
33368290 GAGCTGGAGT
* * *
33368300 TGAGCTGGATGTGAACTTGT
1 TGAGCTGGATCTGAGCTTGC
*
33368320 TGAGCTGGAACTGAGCTTGC
1 TGAGCTGGATCTGAGCTTGC
*
33368340 TGAGCTGGTTCTGAGCT
1 TGAGCTGGATCTGAGCT
33368357 GGTCGAGCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.32
Consensus pattern (20 bp):
TGAGCTGGATCTGAGCTTGC
Found at i:33374213 original size:45 final size:45
Alignment explanation
Indices: 33374164--33374427 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
33374154 TCGGCCATGG
* * * * *
33374164 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33374209 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33374254 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33374299 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33374344 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
33374389 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
33374428 TCCACCTCTT
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 203 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:33375073 original size:18 final size:18
Alignment explanation
Indices: 33375047--33375087 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
33375037 CATTAAACAC
*
33375047 TTTTTTTTTC-AGATTTT
1 TTTTTTTTTCGAAATTTT
33375064 TTTTTCTTTTCGAAATTTT
1 TTTTT-TTTTCGAAATTTT
33375083 TTTTT
1 TTTTT
33375088 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTCGAAATTTT
Found at i:33375086 original size:13 final size:13
Alignment explanation
Indices: 33375065--33375111 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
33375055 TCAGATTTTT
33375065 TTTTCTTTTCGAAA
1 TTTT-TTTTCGAAA
* *
33375079 TTTTTTTTTGAAT
1 TTTTTTTTCGAAA
33375092 TTTTTTTTCG-AA
1 TTTTTTTTCGAAA
33375104 TTTTTTTT
1 TTTTTTTT
33375112 GACTTGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 9 0.31
13 16 0.55
14 4 0.14
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCGAAA
Found at i:33376820 original size:30 final size:30
Alignment explanation
Indices: 33376786--33376882 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33376776 TAAACTAAAA
33376786 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33376816 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
33376846 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
33376876 TGAGCTA
1 TGAGCTA
33376883 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33377112 original size:20 final size:20
Alignment explanation
Indices: 33377087--33377129 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
33377077 TATTGAAGTC
33377087 AAGTGTTTA-GTGTGTTTAAT
1 AAGTG-TTACGTGTGTTTAAT
*
33377107 AAGTGTTACTTGTGTTTAAT
1 AAGTGTTACGTGTGTTTAAT
33377127 AAG
1 AAG
33377130 CTCATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (20 bp):
AAGTGTTACGTGTGTTTAAT
Found at i:33380713 original size:20 final size:20
Alignment explanation
Indices: 33380690--33380735 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
33380680 TAAGCTCGGT
33380690 TGAGCTCAAATAAGCTGAAA
1 TGAGCTCAAATAAGCTGAAA
* *
33380710 TGAGCTCAAATGAGCTGAAT
1 TGAGCTCAAATAAGCTGAAA
33380730 TGAGCT
1 TGAGCT
33380736 GGACGAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (20 bp):
TGAGCTCAAATAAGCTGAAA
Found at i:33380736 original size:10 final size:10
Alignment explanation
Indices: 33380690--33380736 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
33380680 TAAGCTCGGT
*
33380690 TGAGCTCAAA
1 TGAGCTGAAA
*
33380700 TAAGCTGAAA
1 TGAGCTGAAA
*
33380710 TGAGCTCAAA
1 TGAGCTGAAA
*
33380720 TGAGCTGAAT
1 TGAGCTGAAA
33380730 TGAGCTG
1 TGAGCTG
33380737 GACGAATCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (10 bp):
TGAGCTGAAA
Found at i:33383945 original size:20 final size:20
Alignment explanation
Indices: 33383922--33383968 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33383912 GGGTTAAGAT
*
33383922 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33383942 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33383962 TGAGCTG
1 TGAGCTG
33383969 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33385692 original size:48 final size:48
Alignment explanation
Indices: 33385637--33385742 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
33385627 TTGTCTTTTC
*
33385637 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33385685 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33385733 TTTCTTTTTC
1 TTTCTTTTTC
33385743 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33386821 original size:11 final size:12
Alignment explanation
Indices: 33386762--33386827 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 12
33386752 CTCGCAAGAC
33386762 TTTTCACTTTTT
1 TTTTCACTTTTT
33386774 TTTT--CTTCTTT
1 TTTTCACTT-TTT
*
33386785 TTTTAACTCGATTTT
1 TTTTCACT---TTTT
33386800 TTTGTCACTTTTT
1 TTT-TCACTTTTT
33386813 TTTTC-CTTTTT
1 TTTTCACTTTTT
33386824 TTTT
1 TTTT
33386828 GAAATTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 15
0.74 0.02 0.24
Matches are distributed among these distances:
10 3 0.07
11 17 0.37
12 6 0.13
13 9 0.20
15 6 0.13
16 5 0.11
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTCACTTTTT
Found at i:33388261 original size:20 final size:20
Alignment explanation
Indices: 33388238--33388284 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33388228 GGGTTAAGAT
*
33388238 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33388258 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33388278 TGAGCTG
1 TGAGCTG
33388285 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33404511 original size:23 final size:22
Alignment explanation
Indices: 33404459--33404511 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33404449 TCCACGTCTT
*
33404459 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33404481 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33404504 TTTCTTTT
1 TTTCTTTT
33404512 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33406988 original size:30 final size:30
Alignment explanation
Indices: 33406893--33406989 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
33406883 AGCTCACTCC
** * *
33406893 TAGCTCATTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTCAGCTCACGAGCTAAAGCT
* * **
33406923 TAGCTCAACTTCAGCTTAGGA-CTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAAG-CT
*
33406953 CAGCTCAACGTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAAC-TTCAGCTCACGAGCTAAAGCT
33406983 TAGCTCA
1 TAGCTCA
33406990 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 3 0.06
30 41 0.82
31 6 0.12
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAAGCT
Found at i:33414134 original size:427 final size:428
Alignment explanation
Indices: 33413355--33414195 Score: 1393
Period size: 428 Copynumber: 2.0 Consensus size: 428
33413345 GTTGCGCGCG
33413355 GACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACAAACAGATCTGAA
1 GACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACAAACAGATCTGAA
* **
33413420 ATCAAACAAATATTAAGATTAAACGAATCAATTTGAATTTAAAATTCCAAATTCAATTAAAAGAG
66 ATCAAACAAAGAACAAGATTAAACGAATCAATTTGAATTTAAAATTCCAAATTCAATTAAAAGAG
33413485 CAGCAAGAAGAAAAGAAATAGAATCGATGAATCAAACGAATTGAAAGAAAGAAAAGATGCGAATC
131 CAGC-A-AAG-AAAGAAATAGAATCGATGAATCAAACGAATTGAAAGAAAGAAAAGATGCGAATC
33413550 TGCAAGGAATTGATTCGGCCAAGAATGCCCAATTCCAGCAATCAATTTGATTCCCGAATTGAAAG
193 TGCAAGGAATTGATTCGGCCAAGAATGCCCAATTCCAGCAATCAATTTGATTCCCGAATTGAAAG
33413615 AATCCAATCGGCCAAACCTAGGAATGGGGATTTTTGGGTTCGAATGGGTGTGCCAATAGGAGAAC
258 AATCCAATCGGCCAAACCTAGGAATGGGGATTTTTGGGTTCGAATGGGTGTGCCAATAGGAGAAC
33413680 AACTTAAACGATGAGATCTTGAGTTTAATCAATGC-GGAAAACAAACAAGAACAGCAAAATATTA
323 AACTTAAACGATGAGATCTTGAGTTTAATCAATGCTGGAAAACAAACAAGAACAGCAAAATATTA
33413744 GATG-GAAATC-GCACAAGTATAATGATACGGAGGCGCACC
388 GATGAGAAATCGGCACAAGTATAATGATACGGAGGCGCACC
* * *
33413783 GACCAAGATCGAGTTGCCAAGTCACGAGAAATTCCTATGAAAGCT-CTAGACAAATCAGATCTGA
1 GACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACAAA-CAGATCTGA
33413847 AATCAAAACAAAGAACAAGATTAAACCGAATCAGATTTGAATTTAAAATTCCCAAATTCAATT-A
65 AATC-AAACAAAGAACAAGATTAAA-CGAATCA-ATTTGAATTTAAAATT-CCAAATTCAATTAA
33413911 AA-AGCAGC-AAG-AAG-AA-AGAA-CGATGAATCAAACGAAATTGAGAAGAAAGAAAAGATGCG
126 AAGAGCAGCAAAGAAAGAAATAGAATCGATGAATCAAACG-AATTGA-AAGAAAGAAAAGATGCG
33413970 AATCTGCCAAGGAATTGATTCGGCCAAGAATGCCCAATTTCCAGCAATCAA-TTGATTCCCGAAT
189 AATCTG-CAAGGAATTGATTCGGCCAAGAATGCCCAA-TTCCAGCAATCAATTTGATTCCCGAAT
*
33414034 TGAAAGAAATCCAATCGGCCAAACCCTAGGAATTGGGA-TTTTGGGTTCGAATGGGTGCTGCCAA
252 TGAAAG-AATCCAATCGGCCAAA-CCTAGGAATGGGGATTTTTGGGTTCGAATGGGTG-TGCCAA
33414098 TAGGAGAACAACTTAAACGATGAGATCTTGAGTTTAATCAATGCTGGAAAACAAACAAGAACAGC
314 TAGGAGAACAACTTAAACGATGAGATCTTGAGTTTAATCAATGCTGGAAAACAAACAAGAACAGC
33414163 AAAATATTAGATGAGAAATCGGCACAAGTATAA
379 AAAATATTAGATGAGAAATCGGCACAAGTATAA
33414196 GCAAAGAAAA
Statistics
Matches: 391, Mismatches: 7, Indels: 28
0.92 0.02 0.07
Matches are distributed among these distances:
422 14 0.04
423 10 0.03
424 25 0.06
425 52 0.13
426 48 0.12
427 75 0.19
428 88 0.23
429 23 0.06
430 25 0.06
431 19 0.05
432 12 0.03
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.21
Consensus pattern (428 bp):
GACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACAAACAGATCTGAA
ATCAAACAAAGAACAAGATTAAACGAATCAATTTGAATTTAAAATTCCAAATTCAATTAAAAGAG
CAGCAAAGAAAGAAATAGAATCGATGAATCAAACGAATTGAAAGAAAGAAAAGATGCGAATCTGC
AAGGAATTGATTCGGCCAAGAATGCCCAATTCCAGCAATCAATTTGATTCCCGAATTGAAAGAAT
CCAATCGGCCAAACCTAGGAATGGGGATTTTTGGGTTCGAATGGGTGTGCCAATAGGAGAACAAC
TTAAACGATGAGATCTTGAGTTTAATCAATGCTGGAAAACAAACAAGAACAGCAAAATATTAGAT
GAGAAATCGGCACAAGTATAATGATACGGAGGCGCACC
Found at i:33416111 original size:23 final size:22
Alignment explanation
Indices: 33416060--33416111 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
33416050 CCTCGTCTTT
*
33416060 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33416082 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33416105 TTCTTTT
1 TTCTTTT
33416112 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33416186 original size:18 final size:18
Alignment explanation
Indices: 33416105--33416187 Score: 53
Period size: 19 Copynumber: 4.4 Consensus size: 18
33416095 TTTCTTCAAC
*
33416105 TTCTTTTTCAATTTTC-TT
1 TTCTTTTTC-ATTCTCTTT
*
33416123 TTCTGTTTCACATTC-CTTT
1 TTCT-TTT-TCATTCTCTTT
** * *
33416142 TTCACTCTCAATCTCTTTT
1 TTCTTTTTCATTCTC-TTT
33416161 TCTCTTTTTCATTCTCTTT
1 T-TCTTTTTCATTCTCTTT
33416180 TTCTTTTT
1 TTCTTTTT
33416188 TCCTCACTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
17 4 0.08
18 14 0.29
19 19 0.40
20 11 0.23
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.65
Consensus pattern (18 bp):
TTCTTTTTCATTCTCTTT
Found at i:33426398 original size:11 final size:11
Alignment explanation
Indices: 33426382--33426431 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
33426372 ATAAATCACT
33426382 TTTTTTTCGAA
1 TTTTTTTCGAA
*
33426393 TTTTTTT-TAA
1 TTTTTTTCGAA
*
33426403 TTTTTTTTCGAT
1 -TTTTTTTCGAA
*
33426415 TTTTTTTTG-A
1 TTTTTTTCGAA
33426425 TTTTTTT
1 TTTTTTT
33426432 AAACTTGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 9 0.28
11 22 0.69
12 1 0.03
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:33426407 original size:22 final size:22
Alignment explanation
Indices: 33426381--33426431 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
33426371 CATAAATCAC
33426381 TTTTTTTTCGAATTTTTTTTAA
1 TTTTTTTTCGAATTTTTTTTAA
* *
33426403 TTTTTTTTCGATTTTTTTTTGA
1 TTTTTTTTCGAATTTTTTTTAA
33426425 TTTTTTT
1 TTTTTTT
33426432 AAACTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (22 bp):
TTTTTTTTCGAATTTTTTTTAA
Found at i:33434852 original size:30 final size:30
Alignment explanation
Indices: 33434754--33434854 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
33434744 AGTTTAAACT
*
33434754 AAAATGAGCTAAGCTTTAGCTCGTGAGCT-
1 AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
* * * * * * *
33434783 AAAGTTGAGCTGAGGCTAAACTCCTAAGCTG
1 AAA-ATGAGCTAAGGTTTAGCTCGTGAGCTG
** *
33434814 AAGTTGAGCTAAGGTTTAGCTCGTGAGTTG
1 AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
33434844 AAAATGAGCTA
1 AAAATGAGCTA
33434855 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 18, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
29 3 0.06
30 47 0.90
31 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (30 bp):
AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
Found at i:33436382 original size:20 final size:20
Alignment explanation
Indices: 33436336--33436382 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33436326 AGCTTGTTTC
*
33436336 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
33436356 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33436376 CAGCTCA
1 CAGCTCA
33436383 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33442450 original size:12 final size:13
Alignment explanation
Indices: 33442419--33442449 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
33442409 ATACAAGTTA
33442419 AAAAAATCCAAAT
1 AAAAAATCCAAAT
33442432 AAAAAATCCAAAT
1 AAAAAATCCAAAT
33442445 AAAAA
1 AAAAA
33442450 TTGAAGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATCCAAAT
Found at i:33446011 original size:11 final size:11
Alignment explanation
Indices: 33445995--33446024 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
33445985 TTGTAGATTC
33445995 AAAAAAAATCG
1 AAAAAAAATCG
*
33446006 AAAAAAAATTG
1 AAAAAAAATCG
33446017 AAAAAAAA
1 AAAAAAAA
33446025 ATTTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:33446012 original size:12 final size:12
Alignment explanation
Indices: 33445995--33446041 Score: 69
Period size: 13 Copynumber: 3.9 Consensus size: 12
33445985 TTGTAGATTC
*
33445995 AAAAAAAATCG-
1 AAAAAAAATTGA
33446006 AAAAAAAATTGA
1 AAAAAAAATTGA
33446018 AAAAAAAATTTGA
1 AAAAAAAA-TTGA
33446031 AAAAAAAATTG
1 AAAAAAAATTG
33446042 CATACGGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 10 0.30
12 11 0.33
13 12 0.36
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:33446033 original size:11 final size:11
Alignment explanation
Indices: 33445995--33446037 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
33445985 TTGTAGATTC
*
33445995 AAAAAAAATCG
1 AAAAAAAATTG
33446006 AAAAAAAATTG
1 AAAAAAAATTG
33446017 AAAAAAAAATTTG
1 -AAAAAAAA-TTG
33446030 AAAAAAAA
1 AAAAAAAA
33446038 ATTGCATACG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 10 0.34
12 16 0.55
13 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:33448311 original size:17 final size:18
Alignment explanation
Indices: 33448272--33448313 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
33448262 AAGAAGAAAA
33448272 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
33448289 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
33448306 TCAAAAGA
1 ACAAAAGA
33448314 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:33455450 original size:71 final size:73
Alignment explanation
Indices: 33455338--33455484 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 73
33455328 TTTAATGCTA
* * *
33455338 TCCCAAGTCCCATGCACACACTAAATTCGGCTGGTTGGG-AAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCTTGGGAAAAATACAACAGCCAACTTT-GCTT
33455401 TAAATGCCG
65 TAAATGCCG
* * * * * *
33455410 TCCCAAGTCCCATG-ACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
33455474 AAATGCCG
66 AAATGCCG
33455482 TCC
1 TCC
33455485 ATGTACCTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 19 0.30
72 39 0.61
73 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:33456619 original size:30 final size:29
Alignment explanation
Indices: 33456574--33456659 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
33456564 TTCTTTTGTT
*
33456574 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TTCTTTTTCAATC
33456604 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATT-TCTTTTTCAATC
* *
33456634 TCATTTTCTTTTTCTTTTTCTTTTTC
1 TCAATTTCTTTTTC-ATTTCTTTTTC
33456660 TTTTTGCTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.12
30 35 0.71
31 8 0.16
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTCAATC
Found at i:33456630 original size:12 final size:12
Alignment explanation
Indices: 33456613--33456664 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
33456603 CTCAAATTTC
33456613 TTTTCATTCTCT
1 TTTTCATTCTCT
* *
33456625 TTTTCAATCTCA
1 TTTTCATTCTCT
* *
33456637 TTTTCTTTTTCT
1 TTTTCATTCTCT
* *
33456649 TTTTCTTTTTCT
1 TTTTCATTCTCT
33456661 TTTT
1 TTTT
33456665 GCTTTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTCATTCTCT
Found at i:33456648 original size:6 final size:6
Alignment explanation
Indices: 33456637--33456670 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
33456627 TTCAATCTCA
33456637 TTTTCT TTTTCT TTTTCT TTTTCT TTTTGCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TTT
33456671 CAAAGGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:33456682 original size:12 final size:12
Alignment explanation
Indices: 33456667--33456697 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
33456657 TTCTTTTTGC
33456667 TTTTCAAAGGCT
1 TTTTCAAAGGCT
33456679 TTTTCAAAGGCT
1 TTTTCAAAGGCT
33456691 TTTTCAA
1 TTTTCAA
33456698 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:33456755 original size:5 final size:5
Alignment explanation
Indices: 33456745--33456801 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33456735 CTCTTGCCTC
*
33456745 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
33456792 TCTTT TCTTT
1 TCTTT TCTTT
33456802 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:33456785 original size:15 final size:14
Alignment explanation
Indices: 33456745--33456801 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
33456735 CTCTTGCCTC
*
33456745 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
33456760 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
33456775 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
33456792 TCTTTTCTTT
1 TCTTTTCTTT
33456802 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:33456802 original size:21 final size:21
Alignment explanation
Indices: 33456745--33456812 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
33456735 CTCTTGCCTC
* *
33456745 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
33456766 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
33456787 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
33456807 CTCTTT
1 -TCTTT
33456813 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:33457729 original size:12 final size:12
Alignment explanation
Indices: 33457712--33457752 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
33457702 TAAAACACCC
*
33457712 TTTTTTTCAGAT
1 TTTTTTTCAAAT
33457724 TTTTTTTCAAA-
1 TTTTTTTCAAAT
*
33457735 TTTTTTTCGAAT
1 TTTTTTTCAAAT
33457747 TTTTTT
1 TTTTTT
33457753 AACTTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:33457738 original size:10 final size:11
Alignment explanation
Indices: 33457712--33457752 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
33457702 TAAAACACCC
*
33457712 TTTTTTTCAGAT
1 TTTTTTTCA-AA
33457724 TTTTTTTCAAA
1 TTTTTTTCAAA
*
33457735 TTTTTTTCGAA
1 TTTTTTTCAAA
33457746 TTTTTTT
1 TTTTTTT
33457753 AACTTGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:33461028 original size:30 final size:30
Alignment explanation
Indices: 33460934--33461030 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
33460924 TAAACTAAAA
* *
33460934 TGAGCTAAGCTTTAGCTCGTGTGCT-AAAG
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAG
* * * * * **
33460963 TTGAGCTAAGGCTAAACTCCTAAGCTGAATT
1 -TGAGCTAAGGTTTAGCTCGTGAGCTGAAAG
*
33460994 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAG
33461024 TGAGCTA
1 TGAGCTA
33461031 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
30 47 0.96
31 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAAG
Found at i:33463359 original size:15 final size:15
Alignment explanation
Indices: 33463339--33463386 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
33463329 TCAAAGATGG
33463339 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
33463354 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
33463368 GTTTATGGATATAAA
1 GTTTATGGATATGAA
33463383 GTTT
1 GTTT
33463387 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:33463373 original size:14 final size:14
Alignment explanation
Indices: 33463333--33463376 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33463323 AAGGATTCAA
33463333 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
33463347 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
33463362 AGATGGGTTTATGG
1 AGATGGGTTTATGG
33463376 A
1 A
33463377 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:33463402 original size:29 final size:29
Alignment explanation
Indices: 33463333--33463392 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
33463323 AAGGATTCAA
*
33463333 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
33463362 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
33463391 AG
1 AG
33463393 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:33467499 original size:20 final size:20
Alignment explanation
Indices: 33467474--33467528 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
33467464 TGTGGTTCAA
*
33467474 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
33467494 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
33467514 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
33467529 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:33473264 original size:14 final size:14
Alignment explanation
Indices: 33473236--33473277 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
33473226 CTTTTCTTTC
*
33473236 TTTTCTTTTCACTCT
1 TTTTCTTTT-TCTCT
*
33473251 TTTTGTTTTTCTCT
1 TTTTCTTTTTCTCT
33473265 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
33473278 GATCAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:33473669 original size:17 final size:18
Alignment explanation
Indices: 33473649--33473686 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
33473639 TCGAAGAACA
*
33473649 TTTTTTT-TTACTC-TTT
1 TTTTTTTATTTCTCATTT
33473665 TTTTTTTATTTCTCATTT
1 TTTTTTTATTTCTCATTT
33473683 TTTT
1 TTTT
33473687 CACACAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTATTTCTCATTT
Found at i:33473759 original size:13 final size:13
Alignment explanation
Indices: 33473741--33473783 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
33473731 TGAATACAAA
33473741 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
33473754 TTTTTTTATGAAT
1 TTTTTTTTTGAAT
33473767 ATTTTTTTTTGAAT
1 -TTTTTTTTTGAAT
33473781 TTT
1 TTT
33473784 AATTTTTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:33473790 original size:14 final size:12
Alignment explanation
Indices: 33473739--33473783 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 12
33473729 ATTGAATACA
33473739 AATTTTTTTTTG
1 AATTTTTTTTTG
33473751 AATTTTTTTTATG
1 AATTTTTTTT-TG
33473764 AATATTTTTTTTTG
1 -A-ATTTTTTTTTG
33473778 AATTTT
1 AATTTT
33473784 AATTTTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 15 0.50
13 3 0.10
14 3 0.10
15 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:33484631 original size:11 final size:12
Alignment explanation
Indices: 33484608--33484644 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
33484598 AAAAAAATCG
33484608 AAATTCAAAAAA
1 AAATTCAAAAAA
33484620 AAATTCAAAAAA
1 AAATTCAAAAAA
* *
33484632 AAAGTGAAAAAA
1 AAATTCAAAAAA
33484644 A
1 A
33484645 TCGAGCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:33484656 original size:27 final size:27
Alignment explanation
Indices: 33484626--33484703 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
33484616 AAAAAAATTC
33484626 AAAAAAAAAGTGAAAAAAA-TCGAGCAA
1 AAAAAAAAAGTGAAAAAAAGT-GAGCAA
*
33484653 AAAAAAAGAA-AGAAAAAAAGTGAGCAA
1 AAAAAAA-AAGTGAAAAAAAGTGAGCAA
** *
33484680 AAAAATCAAGTTAAAAAAAAGTGA
1 AAAAAAAAAG-TGAAAAAAAGTGA
33484704 AAAGTCTTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.05
27 26 0.62
28 14 0.33
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (27 bp):
AAAAAAAAAGTGAAAAAAAGTGAGCAA
Found at i:33485705 original size:6 final size:6
Alignment explanation
Indices: 33485696--33485815 Score: 69
Period size: 6 Copynumber: 19.2 Consensus size: 6
33485686 GAAAGAGATT
** * * **
33485696 GAAAAA GAAATT GAAAGAA AAAAAAA GAAAAC GAAAAA GAAAAA GAAATT
1 GAAAAA GAAAAA GAAA-AA GAA-AAA GAAAAA GAAAAA GAAAAA GAAAAA
* ** ** * *
33485746 GCAAAA GAAAAA GAAATC GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA
*
33485796 GAAAATT GAAAAA GAAAAA G
1 GAAAA-A GAAAAA GAAAAA G
33485816 CGAAAAAAGA
Statistics
Matches: 81, Mismatches: 28, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
6 63 0.78
7 13 0.16
8 5 0.06
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:33485733 original size:7 final size:6
Alignment explanation
Indices: 33485709--33485815 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
33485699 AAAGAAATTG
* ** *
33485709 AAAG-A AAA-AA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
33485755 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
33485806 AAAGAA AAAG
1 AAAGAA AAAG
33485816 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
5 7 0.09
6 57 0.76
7 7 0.09
8 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:33485770 original size:18 final size:18
Alignment explanation
Indices: 33485696--33485770 Score: 87
Period size: 18 Copynumber: 4.1 Consensus size: 18
33485686 GAAAGAGATT
*
33485696 GAAAAAGAAATTGAAAGAAA
1 GAAAAAGAAATCG-AA-AAA
* *
33485716 AAAAAAGAAAACGAAAAA
1 GAAAAAGAAATCGAAAAA
* *
33485734 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
33485752 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
33485770 G
1 G
33485771 TGAGAGAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
18 34 0.74
19 2 0.04
20 10 0.22
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:33485797 original size:14 final size:13
Alignment explanation
Indices: 33485776--33485813 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
33485766 AAAAGTGAGA
33485776 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
33485788 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
33485803 GAAAAAGAAAA
1 GAAAAAGAAAA
33485814 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:33485827 original size:21 final size:21
Alignment explanation
Indices: 33485777--33485827 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
33485767 AAAGTGAGAG
*
33485777 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
33485798 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
33485819 AAAAAGAAA
1 AAAAAGAAA
33485828 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:33485867 original size:33 final size:33
Alignment explanation
Indices: 33485830--33485892 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33485820 AAAAGAAATT
33485830 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
33485863 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
33485893 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:33487620 original size:20 final size:20
Alignment explanation
Indices: 33487597--33487650 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33487587 AGTTTTCCCC
*
33487597 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33487617 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33487637 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33487651 TAATTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33487632 original size:30 final size:30
Alignment explanation
Indices: 33487597--33487670 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
33487587 AGTTTTCCCC
33487597 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
*
33487627 AGCTCGTTTGAGCTCAATTTAGCTTAATTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33487657 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33487671 TGGCTTAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33494912 original size:30 final size:30
Alignment explanation
Indices: 33494827--33494923 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33494817 TAAACTAAAA
* *
33494827 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
33494857 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
33494887 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
33494916 ATGAGCTA
1 -TGAGCTA
33494924 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:33497183 original size:30 final size:30
Alignment explanation
Indices: 33497138--33497212 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
33497128 GTTTCTTTTG
33497138 TTTCAATTTCTTTTTCA-TCTTCTTTTTCAC
1 TTTCAATTTCTTTTTCATTC-TCTTTTTCAC
* *
33497168 TTTCAAATTTC-TTTTCGTTCTCTTTTTCAA
1 TTTC-AATTTCTTTTTCATTCTCTTTTTCAC
* *
33497198 TCTCATTTTCTTTTT
1 TTTCAATTTCTTTTT
33497213 GCTTTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 5 0.13
30 25 0.66
31 8 0.21
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.64
Consensus pattern (30 bp):
TTTCAATTTCTTTTTCATTCTCTTTTTCAC
Found at i:33497321 original size:15 final size:14
Alignment explanation
Indices: 33497281--33497326 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
33497271 CTCTTGCCTC
*
33497281 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
33497296 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
33497311 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
33497326 T
1 T
33497327 TTCTTCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:33497328 original size:20 final size:20
Alignment explanation
Indices: 33497299--33497348 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
33497289 TTTTATTTCA
33497299 TTTTCTTTTTCTTCT-TTTGCT
1 TTTTC-TTTTCTTCTCTTTG-T
33497320 TTTTCTTTTCTTCTCTTTGT
1 TTTTCTTTTCTTCTCTTTGT
33497340 TTTCTCTTT
1 TTT-TCTTT
33497349 ACAAGAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTCTTCTCTTTGT
Found at i:33498128 original size:20 final size:20
Alignment explanation
Indices: 33498082--33498128 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33498072 AGCTCGTTTC
*
33498082 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33498102 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33498122 CAGCTCA
1 CAGCTCA
33498129 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33499545 original size:14 final size:14
Alignment explanation
Indices: 33499526--33499572 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
33499516 AAAAAAATAT
33499526 AAAAAAATTCGAAA
1 AAAAAAATTCGAAA
*
33499540 AAAAAAATTTGAAA
1 AAAAAAATTCGAAA
33499554 AAAAAAATTC-AAA
1 AAAAAAATTCGAAA
33499567 AAAAAA
1 AAAAAA
33499573 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:33499661 original size:28 final size:27
Alignment explanation
Indices: 33499618--33499684 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
33499608 GTATTGAAGG
* *
33499618 AAAAAAAAGAAGAAAAAAATTCAGAATT
1 AAAAAAAA-AAGAAAAAAAATCAAAATT
33499646 AAAAAAAAAAGAAAAAAAATCAAAATT
1 AAAAAAAAAAGAAAAAAAATCAAAATT
*
33499673 GAAAAAAAAAGA
1 AAAAAAAAAAGA
33499685 GTGATTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 28 0.78
28 8 0.22
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.10
Consensus pattern (27 bp):
AAAAAAAAAAGAAAAAAAATCAAAATT
Found at i:33500515 original size:21 final size:20
Alignment explanation
Indices: 33500490--33500534 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
33500480 AATCTTGAAT
*
33500490 GAAATTGAGAGA-AGAAAAAA
1 GAAAATGAGAGAGAG-AAAAA
*
33500510 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAGAAAAA
33500530 GAAAA
1 GAAAA
33500535 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAGAAAAA
Found at i:33500550 original size:6 final size:6
Alignment explanation
Indices: 33500541--33500576 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
33500531 AAAAAAGAAT
* *
33500541 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
33500577 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:33500551 original size:27 final size:27
Alignment explanation
Indices: 33500487--33500552 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
33500477 ACGAATCTTG
* *
33500487 AATGAAATTGAG-AGAAGAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAGAA
*
33500513 AATGAGAGTGAGAAAAAGAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAGAA
**
33500540 TTTGAGATTGAGA
1 AATGAGATTGAGA
33500553 TTGAGATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (27 bp):
AATGAGATTGAGAAAAAGAAAAAAGAA
Found at i:33504444 original size:30 final size:30
Alignment explanation
Indices: 33504410--33504506 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
33504400 TAAACTAAAA
*
33504410 TGAGCTAAACTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33504440 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
33504470 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
33504500 TGAGCTA
1 TGAGCTA
33504507 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.86
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33508911 original size:20 final size:20
Alignment explanation
Indices: 33508865--33508911 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33508855 AGCTCGTTTC
*
33508865 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33508885 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33508905 CAGCTCA
1 CAGCTCA
33508912 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33510701 original size:22 final size:22
Alignment explanation
Indices: 33510673--33510716 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33510663 TTTTGAACCA
33510673 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33510695 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33510717 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33513329 original size:20 final size:20
Alignment explanation
Indices: 33513304--33513346 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
33513294 AAAAGAAAAG
33513304 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
33513324 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
33513344 AAA
1 AAA
33513347 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:33515687 original size:22 final size:22
Alignment explanation
Indices: 33515659--33515702 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33515649 TTTTGAACCA
33515659 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33515681 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33515703 AAATACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33520508 original size:23 final size:23
Alignment explanation
Indices: 33520481--33520526 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
33520471 TAAAGGGCTG
*
33520481 CACATTCATGGATATTTATGATT
1 CACATTCATGGATATTCATGATT
33520504 CACATTCATGGATATTCATGATT
1 CACATTCATGGATATTCATGATT
33520527 TTTCTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (23 bp):
CACATTCATGGATATTCATGATT
Found at i:33524499 original size:21 final size:21
Alignment explanation
Indices: 33524475--33524544 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
33524465 CACATACATC
33524475 ATGAACTCAGACCATAACTCA
1 ATGAACTCAGACCATAACTCA
*
33524496 ATG-ACTTCATATGCCACATATA-TC-
1 ATGAAC-TC--A-GAC-CATA-ACTCA
33524520 ATGAACTCAGACCATAACTCA
1 ATGAACTCAGACCATAACTCA
33524541 ATGA
1 ATGA
33524545 GTTCAGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 1 0.03
20 8 0.21
21 11 0.29
22 1 0.03
23 1 0.03
24 7 0.18
25 8 0.21
26 1 0.03
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (21 bp):
ATGAACTCAGACCATAACTCA
Found at i:33530063 original size:56 final size:54
Alignment explanation
Indices: 33529956--33530114 Score: 178
Period size: 56 Copynumber: 2.9 Consensus size: 54
33529946 TTTGATGACA
* * *
33529956 TGATACATGCTAGGTCCGAGAGCTTGTGTAGCCCCGTTGAGAGGCAT-GTAATTATG
1 TGATACATGCTAGGTCCGAGAGCTTATGTAGCCCTGTTGAGAGGCGTGGT-A--ATG
* * *
33530012 TGGTACACGCTAGGTCCGGGAGCTTATGTA-CCCTGTTGAGAGGCGTGGTAATG
1 TGATACATGCTAGGTCCGAGAGCTTATGTAGCCCTGTTGAGAGGCGTGGTAATG
* * *
33530065 TGATGCATGCTAGGTCTGAGTGCTCATATGTAGCCCTGTTGAGAGGCGTG
1 TGATACATGCTAGGTCCGAGAGCT--TATGTAGCCCTGTTGAGAGGCGTG
33530115 CTATTTCATG
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
53 21 0.24
55 21 0.24
56 45 0.52
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (54 bp):
TGATACATGCTAGGTCCGAGAGCTTATGTAGCCCTGTTGAGAGGCGTGGTAATG
Found at i:33536882 original size:55 final size:53
Alignment explanation
Indices: 33536796--33536943 Score: 145
Period size: 55 Copynumber: 2.7 Consensus size: 53
33536786 CATGATACAT
* * * *
33536796 GCTAGGTTCAGGAGCTTGTGTAGCCCCGTTGAGAGGCAT-GTAATTATGTGGTCCAC
1 GCTAGG-TCAGGAGCTTATGTAGCCCTGTTGAGAGGCATGGT-A--ATGTGATCCAA
* * *
33536852 GCTAGGTCCGGAGCTTATGTAGCCCTGTTGAGAGGCGTGGTAATGTGATGCAA
1 GCTAGGTCAGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATGTGATCCAA
* *
33536905 GCTAGGTCTGAGTGCTCATATGTAGCCCTGTTGAGAGGC
1 GCTAGGTCAG-GAGCT--TATGTAGCCCTGTTGAGAGGC
33536944 GTGTTATGTC
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
53 17 0.22
54 4 0.05
55 29 0.37
56 29 0.37
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.28
Consensus pattern (53 bp):
GCTAGGTCAGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATGTGATCCAA
Found at i:33538323 original size:34 final size:31
Alignment explanation
Indices: 33538259--33538323 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
33538249 AATGTTGAAG
*
33538259 AGTCTTCCAATGTGAACAAGGTGAACCGAAT
1 AGTCTTCCAATGTGAACAAGGTGAAACGAAT
33538290 AGTCTTGCC-ATGTGAACATAGGTGTGAAACGAAT
1 AGTCTT-CCAATGTGAACA-A-G-GTGAAACGAAT
33538324 TAAGGAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 15 0.52
32 3 0.10
33 1 0.03
34 10 0.34
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (31 bp):
AGTCTTCCAATGTGAACAAGGTGAAACGAAT
Found at i:33540869 original size:22 final size:22
Alignment explanation
Indices: 33540841--33540884 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33540831 TTTTGAACCA
33540841 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33540863 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33540885 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33543356 original size:19 final size:18
Alignment explanation
Indices: 33543310--33543375 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
33543300 CAAATGAGAG
33543310 AAAAAGAAAAGAGCGAAAATA
1 AAAAAGAAAAGA---AAAATA
*
33543331 CAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAAT-A
*
33543350 AAAAAGAAAAGAAAATTCA
1 AAAAAGAAAAGAAAAAT-A
33543369 AAAAAGA
1 AAAAAGA
33543376 GAATGAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.12
19 24 0.60
21 11 0.28
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATA
Found at i:33547673 original size:22 final size:22
Alignment explanation
Indices: 33547645--33547688 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33547635 TTTTGAACCA
33547645 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33547667 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33547689 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33548293 original size:22 final size:21
Alignment explanation
Indices: 33548268--33548309 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
33548258 TATGTCTAAA
*
33548268 TTTAATTATTACTTTTAAATTG
1 TTTAATTATTA-ATTTAAATTG
*
33548290 TTTAGTTATTAATTTAAATT
1 TTTAATTATTAATTTAAATT
33548310 ATGATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTAATTATTAATTTAAATTG
Found at i:33552665 original size:12 final size:12
Alignment explanation
Indices: 33552650--33552680 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
33552640 TTCTTTTTGC
33552650 TTTTCAAAGGCT
1 TTTTCAAAGGCT
33552662 TTTTCAAAGGCT
1 TTTTCAAAGGCT
33552674 TTTTCAA
1 TTTTCAA
33552681 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:33552738 original size:5 final size:5
Alignment explanation
Indices: 33552728--33552796 Score: 61
Period size: 5 Copynumber: 13.0 Consensus size: 5
33552718 CTCTTGCCTC
*
33552728 TCTTT TCTTT T-TATT TCGTTT TCTTTT TCTTTT TCTTT T-TCT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TC-TTT TCTTT TCTTT TCTTT
33552775 TGCTTTT TCTTT TCTTT TCTTT
1 T-C-TTT TCTTT TCTTT TCTTT
33552797 GTTTTCTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.07
5 29 0.53
6 17 0.31
7 5 0.09
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:33552750 original size:6 final size:6
Alignment explanation
Indices: 33552741--33552796 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
33552731 TTTCTTTTTA
*
33552741 TTTCGT TTTCTT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTTC-T TTTC-T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT
33552790 TTTCTT T
1 TTTCTT T
33552797 GTTTTCTCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 10 0.22
6 24 0.53
7 5 0.11
8 5 0.11
9 1 0.02
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:33552754 original size:21 final size:20
Alignment explanation
Indices: 33552728--33552796 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 20
33552718 CTCTTGCCTC
33552728 TCTTTTCTTTTTATTTCGTTT
1 TCTTTTCTTTTTATTTC-TTT
*
33552749 TCTTTTTCTTTTTCTTT-TTCT
1 TC-TTTTCTTTTTATTTCTT-T
*
33552770 TCTTTTGCTTTTTCTTTTCTTT
1 TCTTTT-CTTTTT-ATTTCTTT
33552792 TCTTT
1 TCTTT
33552797 GTTTTCTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 6 0.15
21 11 0.27
22 22 0.54
23 2 0.05
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (20 bp):
TCTTTTCTTTTTATTTCTTT
Found at i:33552760 original size:27 final size:26
Alignment explanation
Indices: 33552728--33552792 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 26
33552718 CTCTTGCCTC
*
33552728 TCTTTTCTTTTTATTTCGTTTT-CTTTT
1 TCTTTTCTTTTT-CTTC-TTTTGCTTTT
33552755 TCTTTTTCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTTTTTCTTCTTTTGCTTTT
33552782 TCTTTTCTTTT
1 TCTTTTCTTTT
33552793 CTTTGTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 13 0.37
27 12 0.34
28 10 0.29
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (26 bp):
TCTTTTCTTTTTCTTCTTTTGCTTTT
Found at i:33552797 original size:21 final size:22
Alignment explanation
Indices: 33552728--33552796 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 22
33552718 CTCTTGCCTC
*
33552728 TCTTTT-CTTTTT-ATTTCGTTT
1 TCTTTTGCTTTTTCTTTTC-TTT
* *
33552749 TCTTTTTCTTTTTCTTTT-TCT
1 TCTTTTGCTTTTTCTTTTCTTT
33552770 TCTTTTGCTTTTTCTTTTCTTT
1 TCTTTTGCTTTTTCTTTTCTTT
33552792 TCTTT
1 TCTTT
33552797 GTTTTCTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 25 0.61
22 13 0.32
23 3 0.07
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (22 bp):
TCTTTTGCTTTTTCTTTTCTTT
Found at i:33552807 original size:27 final size:25
Alignment explanation
Indices: 33552728--33552807 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 25
33552718 CTCTTGCCTC
33552728 TCTTTTCTTTTTATT-TCGTTTTCTTTT
1 TCTTTTCTTTTT-TTGT--TTTTCTTTT
* *
33552755 TCTTTTTCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTTTTT-TTGTTTTTCTTTT
33552782 TCTTTTCTTTTCTTTGTTTTCTCTTT
1 TCTTTTCTTTT-TTTGTTTT-TCTTT
33552808 ACAAGAATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 15 0.33
27 17 0.38
28 12 0.27
29 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.78
Consensus pattern (25 bp):
TCTTTTCTTTTTTTGTTTTTCTTTT
Found at i:33570729 original size:20 final size:20
Alignment explanation
Indices: 33570683--33570729 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33570673 AGCTTGTTTC
*
33570683 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
33570703 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33570723 CAGCTCA
1 CAGCTCA
33570730 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33572461 original size:19 final size:19
Alignment explanation
Indices: 33572437--33572476 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33572427 AGCTCCCATG
*
33572437 TAGCTCCATACCAGCTCAT
1 TAGCTCCAGACCAGCTCAT
**
33572456 TAGCTCGGGACCAGCTCAT
1 TAGCTCCAGACCAGCTCAT
33572475 TA
1 TA
33572477 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (19 bp):
TAGCTCCAGACCAGCTCAT
Found at i:33572605 original size:12 final size:12
Alignment explanation
Indices: 33572573--33572606 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
33572563 TATTGACTTT
33572573 TTAATTAATAAG
1 TTAATTAATAAG
33572585 TTCAA-TAATAAG
1 TT-AATTAATAAG
33572597 TTAATTAATA
1 TTAATTAATA
33572607 TCCTACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (12 bp):
TTAATTAATAAG
Found at i:33573753 original size:14 final size:14
Alignment explanation
Indices: 33573730--33573773 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33573720 TTGTTCATAT
*
33573730 CCTTTTATTCCTAC
1 CCTTTCATTCCTAC
33573744 CCTTTCATTCCTAC
1 CCTTTCATTCCTAC
* * *
33573758 CATTCCATTCGTAC
1 CCTTTCATTCCTAC
33573772 CC
1 CC
33573774 CTCTTTTCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.16, C:0.41, G:0.02, T:0.41
Consensus pattern (14 bp):
CCTTTCATTCCTAC
Found at i:33574628 original size:20 final size:20
Alignment explanation
Indices: 33574582--33574628 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33574572 TAGCTGTTTC
*
33574582 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
33574602 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33574622 CAGCTCA
1 CAGCTCA
33574629 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33576153 original size:10 final size:9
Alignment explanation
Indices: 33576118--33576152 Score: 54
Period size: 8 Copynumber: 3.9 Consensus size: 9
33576108 AAAAGTGAGC
33576118 AAAAAAAAG
1 AAAAAAAAG
33576127 -AAAAAAAG
1 AAAAAAAAG
33576135 TAAAAAAAAG
1 -AAAAAAAAG
33576145 AAAAAAAA
1 AAAAAAAA
33576153 AAGTGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 8 0.33
10 8 0.33
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:33577254 original size:48 final size:47
Alignment explanation
Indices: 33577175--33577280 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
33577165 GAGTGTCATG
*
33577175 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
33577223 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
33577271 GAAAAAGAAA
1 GAAAAAGAAA
33577281 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:33578970 original size:20 final size:20
Alignment explanation
Indices: 33578924--33578970 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33578914 AGCTCGTTTC
*
33578924 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33578944 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33578964 CAGCTCA
1 CAGCTCA
33578971 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33582632 original size:12 final size:12
Alignment explanation
Indices: 33582611--33582704 Score: 63
Period size: 12 Copynumber: 7.6 Consensus size: 12
33582601 AGAAAAGGAG
*
33582611 AAAGAGATTGAA
1 AAAGAAATTGAA
33582623 AAAGAAATTGAA
1 AAAGAAATTGAA
33582635 AAAG--A--GAA
1 AAAGAAATTGAA
*
33582643 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
33582657 AAAGAAAATTGAA
1 AAAG-AAATTGAA
33582670 AAAGAAATGAGAATGAA
1 AAAGAAAT-----TGAA
33582687 AAA-AAATTGAA
1 AAAGAAATTGAA
33582698 AAAGAAA
1 AAAGAAA
33582705 AAGCGAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 26
0.71 0.02 0.27
Matches are distributed among these distances:
8 7 0.10
10 2 0.03
11 7 0.10
12 23 0.34
13 6 0.09
14 6 0.09
15 5 0.07
16 4 0.06
17 7 0.10
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:33582645 original size:20 final size:20
Alignment explanation
Indices: 33582620--33582664 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
33582610 GAAAGAGATT
*
33582620 GAAAAAGAAATTGAA-AAAGA
1 GAAAAAGAAAATGAAGAAA-A
33582640 GAAAAAGAAAATGAAGAAAA
1 GAAAAAGAAAATGAAGAAAA
33582660 GAAAA
1 GAAAA
33582665 TTGAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
GAAAAAGAAAATGAAGAAAA
Found at i:33582672 original size:28 final size:28
Alignment explanation
Indices: 33582640--33582705 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
33582630 TTGAAAAAGA
33582640 GAAAAAGAAAAT-GAA-GAAAAGAAAATT
1 GAAAAAGAAAATAGAATGAAAA-AAAATT
33582667 GAAAAAG-AAATGAGAATGAAAAAAAATT
1 GAAAAAGAAAAT-AGAATGAAAAAAAATT
33582695 GAAAAAGAAAA
1 GAAAAAGAAAA
33582706 AGCGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 4 0.11
27 7 0.20
28 16 0.46
29 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (28 bp):
GAAAAAGAAAATAGAATGAAAAAAAATT
Found at i:33582676 original size:18 final size:17
Alignment explanation
Indices: 33582622--33582707 Score: 54
Period size: 17 Copynumber: 5.0 Consensus size: 17
33582612 AAGAGATTGA
*
33582622 AAAAGAAATTGAAAAAGAG
1 AAAAGAAAATG-AAAA-AG
33582641 AAAAAGAAAATG---AAG
1 -AAAAGAAAATGAAAAAG
33582656 AAAAGAAAATTGAAAAAG
1 AAAAGAAAA-TGAAAAAG
* *
33582674 AAATGAGAATGAAAAA-
1 AAAAGAAAATGAAAAAG
* *
33582690 AAATTGAAAAAGAAAAAG
1 AAA-AGAAAATGAAAAAG
33582708 CGAAAAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
14 9 0.16
15 4 0.07
16 4 0.07
17 18 0.33
18 10 0.18
20 10 0.18
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (17 bp):
AAAAGAAAATGAAAAAG
Found at i:33582688 original size:17 final size:18
Alignment explanation
Indices: 33582660--33582707 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
33582650 ATGAAGAAAA
33582660 GAAAATTGAAAAAGAAA-T
1 GAAAA-TGAAAAAGAAATT
*
33582678 GAGAATGAAAAA-AAATT
1 GAAAATGAAAAAGAAATT
*
33582695 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
33582708 CGAAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 18 0.72
18 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:33582715 original size:27 final size:26
Alignment explanation
Indices: 33582640--33582725 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
33582630 TTGAAAAAGA
*
33582640 GAAAAAGAAAATGA-AGAAAAGAAAATT
1 GAAAAAGAAAA-GAGA-AAAAAAAAATT
*
33582667 GAAAAAGAAATGAGAATGAAAAAAAATT
1 GAAAAAGAAAAGAGAA--AAAAAAAATT
* *
33582695 GAAAAAGAAAAAGCGAAAAAAGAAATT
1 GAAAAAG-AAAAGAGAAAAAAAAAATT
33582722 GAAA
1 GAAA
33582726 GAGAGCTTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 3 0.06
27 24 0.48
28 16 0.32
29 7 0.14
ACGTcount: A:0.70, C:0.01, G:0.19, T:0.10
Consensus pattern (26 bp):
GAAAAAGAAAAGAGAAAAAAAAAATT
Found at i:33582759 original size:33 final size:33
Alignment explanation
Indices: 33582722--33582784 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33582712 AAAAGAAATT
33582722 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
33582755 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
33582785 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:33592312 original size:30 final size:30
Alignment explanation
Indices: 33592278--33592374 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33592268 AGCTCACTCC
33592278 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
33592308 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
33592338 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
33592368 TAGCTCA
1 TAGCTCA
33592375 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:33593617 original size:14 final size:14
Alignment explanation
Indices: 33593595--33593642 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
33593585 ACCTAAACCG
* *
33593595 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
33593609 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
33593623 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
33593637 ACCATT
1 ACCATT
33593643 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:33600966 original size:13 final size:13
Alignment explanation
Indices: 33600950--33600982 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
33600940 AAAAAAATAT
33600950 AAAAAAATTCAAA
1 AAAAAAATTCAAA
33600963 AAAAAAATTCAAA
1 AAAAAAATTCAAA
33600976 AAAAAAA
1 AAAAAAA
33600983 GTTTGTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:33601073 original size:21 final size:20
Alignment explanation
Indices: 33601049--33601087 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33601039 CGGAATTAAA
33601049 AAAAAAGAAGAAAAAAAAATC
1 AAAAAAGAA-AAAAAAAAATC
**
33601070 AAAATTGAAAAAAAAAAA
1 AAAAAAGAAAAAAAAAAA
33601088 GTGATTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAAATC
Found at i:33602004 original size:21 final size:20
Alignment explanation
Indices: 33601975--33602020 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
33601965 AATCTTGAAT
*
33601975 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
33601996 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
33602016 GAAAA
1 GAAAA
33602021 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:33602047 original size:12 final size:12
Alignment explanation
Indices: 33602027--33602062 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
33602017 AAAAAAGAAT
*
33602027 TTGAGATTGAGA
1 TTGATATTGAGA
*
33602039 TTGATATTGATA
1 TTGATATTGAGA
33602051 TTGATATTGAGA
1 TTGATATTGAGA
33602063 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:33609073 original size:23 final size:22
Alignment explanation
Indices: 33609021--33609073 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33609011 TCCACGTCTT
*
33609021 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33609043 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33609066 TTTCTTTT
1 TTTCTTTT
33609074 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33612097 original size:17 final size:17
Alignment explanation
Indices: 33612077--33612118 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
33612067 TCCACCGATT
*
33612077 CATGCATCTTGAG-TGTC
1 CATGCACCTT-AGCTGTC
33612094 CATGCACCTTAGCTGTC
1 CATGCACCTTAGCTGTC
33612111 CATGCACC
1 CATGCACC
33612119 CTCCAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (17 bp):
CATGCACCTTAGCTGTC
Found at i:33614430 original size:20 final size:19
Alignment explanation
Indices: 33614407--33614471 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
33614397 AAGCTCAAAC
33614407 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
33614427 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
33614447 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
33614467 GAGCT
1 GAGCT
33614472 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:33615432 original size:21 final size:22
Alignment explanation
Indices: 33615393--33615436 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
33615383 ATGAATACTC
33615393 CTTCAAGCTTAAATCAGCTCAA
1 CTTCAAGCTTAAATCAGCTCAA
* *
33615415 CTTCAA-CTTAACTTAGCTCAA
1 CTTCAAGCTTAAATCAGCTCAA
33615436 C
1 C
33615437 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
CTTCAAGCTTAAATCAGCTCAA
Found at i:33617170 original size:12 final size:11
Alignment explanation
Indices: 33617153--33617182 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
33617143 ACAAGTTTGA
33617153 AAAAAAATTCCG
1 AAAAAAATT-CG
33617165 AAAAAAATTCG
1 AAAAAAATTCG
33617176 AAAAAAA
1 AAAAAAA
33617183 AGTGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.13
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:33617183 original size:12 final size:13
Alignment explanation
Indices: 33617151--33617183 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
33617141 ATACAAGTTT
33617151 GAAAAAAAATTCC
1 GAAAAAAAATTCC
33617164 G-AAAAAAATT-C
1 GAAAAAAAATTCC
33617175 GAAAAAAAA
1 GAAAAAAAA
33617184 GTGATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.84
13 1 0.05
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (13 bp):
GAAAAAAAATTCC
Found at i:33617546 original size:19 final size:19
Alignment explanation
Indices: 33617524--33617563 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
33617514 CTTTTCGAGA
33617524 GATTGTGAGGTTTTGTGGT
1 GATTGTGAGGTTTTGTGGT
33617543 GATTGTGAGGTTTTGTGGT
1 GATTGTGAGGTTTTGTGGT
33617562 GA
1 GA
33617564 GGTTTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.45
Consensus pattern (19 bp):
GATTGTGAGGTTTTGTGGT
Found at i:33621600 original size:12 final size:12
Alignment explanation
Indices: 33621583--33621619 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
33621573 AAAAGAGAAT
33621583 AAATTCAGAAAA
1 AAATTCAGAAAA
33621595 AAATTCA-AAAA
1 AAATTCAGAAAA
*
33621606 AAAATC-GAAAA
1 AAATTCAGAAAA
33621617 AAA
1 AAA
33621620 AGAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.73, C:0.08, G:0.05, T:0.14
Consensus pattern (12 bp):
AAATTCAGAAAA
Found at i:33621628 original size:24 final size:25
Alignment explanation
Indices: 33621601--33621676 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
33621591 AAAAAAATTC
33621601 AAAAAA-AAATCGA-AAAAAAAGAAA
1 AAAAAAGAAAT-GAGAAAAAAAGAAA
* *
33621625 AAAAAAGAAGTGAGCAAAAAAGAAA
1 AAAAAAGAAATGAGAAAAAAAGAAA
* *
33621650 AAAAAAGTAA--A-AAAAGAAGAAA
1 AAAAAAGAAATGAGAAAAAAAGAAA
33621672 AAAAA
1 AAAAA
33621677 GTGAAAAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 14 0.32
23 1 0.02
24 8 0.18
25 21 0.48
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.04
Consensus pattern (25 bp):
AAAAAAGAAATGAGAAAAAAAGAAA
Done.