Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 168 of 203
Found at i:53205498 original size:13 final size:14
Alignment explanation
Indices: 53205444--53205498 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 14
53205434 ATATATTAGT
53205444 TAATAATATTAATAA
1 TAATAAT-TTAATAA
53205459 TAATACATTATAATAA
1 TAATA-ATT-TAATAA
*
53205475 T-ATAATATAATAA
1 TAATAATTTAATAA
53205488 TAAT-ATTTAAT
1 TAATAATTTAAT
53205499 TCATAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 13 0.37
14 4 0.11
15 9 0.26
16 9 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATAATTTAATAA
Found at i:53208271 original size:137 final size:138
Alignment explanation
Indices: 53208075--53208491 Score: 694
Period size: 138 Copynumber: 3.0 Consensus size: 138
53208065 ACATAGATAA
* *
53208075 AATTAATATATGTATTTGATTCATACAAAATACTAATTGTATATATTTTATCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTATCAAATTTATTAATA
* *
53208140 TAAACAGTTATATTAATTAATTTCAGTCAAATTATAAAAGACATTAAAATTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATTAAAATTAATATTCTTTTGGA
53208205 AAGAATAT
131 AAGAATAT
* *
53208213 AATTAATATATAAATTTGATTCATACAAAATA-TAATTTTATATATTTTATCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTATCAAATTTATTAATA
* *
53208277 TAAACAGTTATATTAATTAATTTTGGTCAAAATATAACAGACATGT-AAATTAATATTCTTTTGG
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACAT-TAAAATTAATATTCTTTTGG
53208341 AAAGAATAT
130 AAAGAATAT
*
53208350 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTATCAAATTTATTAATA
* * * *
53208415 TAAACAGTTATATTAATTAATTTCGGTCAAAATATACAATACATGAAAATTAATATTATTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATTAAAATTAATATTCTTTTGGA
53208480 AAGAATAT
131 AAGAATAT
53208488 AATT
1 AATT
53208492 CTTTTTTCTA
Statistics
Matches: 260, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
137 128 0.49
138 132 0.51
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATACTAATTGTATATATTTTATCAAATTTATTAATA
TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATTAAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:53210053 original size:22 final size:22
Alignment explanation
Indices: 53210025--53210084 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
53210015 ACCCAAATCA
*
53210025 ACTGTTTTGTTGTTATTTTGCT
1 ACTGTTTTGTTGTTATTTTACT
* *
53210047 ACTGTTTCGTTGTTGTTTTACT
1 ACTGTTTTGTTGTTATTTTACT
* *
53210069 ACTATTTTGTTATTAT
1 ACTGTTTTGTTGTTAT
53210085 ATTGTTATTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.13, C:0.10, G:0.15, T:0.62
Consensus pattern (22 bp):
ACTGTTTTGTTGTTATTTTACT
Found at i:53216543 original size:13 final size:13
Alignment explanation
Indices: 53216525--53216549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53216515 TTTTATTTGT
53216525 TTATTCCCACCGA
1 TTATTCCCACCGA
53216538 TTATTCCCACCG
1 TTATTCCCACCG
53216550 GCCGAATGTT
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:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:53216790 original size:68 final size:68
Alignment explanation
Indices: 53216716--53216844 Score: 213
Period size: 68 Copynumber: 1.9 Consensus size: 68
53216706 CTCTCTCCCT
*
53216716 TTTCCCTGTTCTCTTTCTCTATTAGTTCTATCTATAATTCTATTTATCTTCTTATTGACACAGAT
1 TTTCCCTGTTCTCTTTCTCTATTAGTTCTATCTATAATTATATTTATCTTCTTATTGACACAGAT
53216781 GTC
66 GTC
* * **
53216784 TTTCCCTGTTTTCTTTTTCTATTCTTTCTATCTATAATTATATTTATCTTCTTATTGACAC
1 TTTCCCTGTTCTCTTTCTCTATTAGTTCTATCTATAATTATATTTATCTTCTTATTGACAC
53216845 GGATATAGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (68 bp):
TTTCCCTGTTCTCTTTCTCTATTAGTTCTATCTATAATTATATTTATCTTCTTATTGACACAGAT
GTC
Found at i:53225831 original size:9 final size:9
Alignment explanation
Indices: 53225817--53225853 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53225807 TATAGTTTGA
53225817 TATTCGAAT
1 TATTCGAAT
53225826 TATTCGAAT
1 TATTCGAAT
*
53225835 TATTCGAGT
1 TATTCGAAT
*
53225844 TATTTGAAT
1 TATTCGAAT
53225853 T
1 T
53225854 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53230096 original size:48 final size:47
Alignment explanation
Indices: 53230037--53230129 Score: 168
Period size: 48 Copynumber: 2.0 Consensus size: 47
53230027 TTTGGGGGGA
53230037 GGGGGGGAGTCAAGAATAAAATGGTAACAAACTAGAGATCGATCTGG
1 GGGGGGGAGTCAAGAATAAAATGGTAACAAACTAGAGATCGATCTGG
*
53230084 GGGGGGGAAGTCAAGAATAAAATGGTAACAAACTAGAGTTCGATCT
1 GGGGGGG-AGTCAAGAATAAAATGGTAACAAACTAGAGATCGATCT
53230130 TTACAAGGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 7 0.16
48 37 0.84
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.18
Consensus pattern (47 bp):
GGGGGGGAGTCAAGAATAAAATGGTAACAAACTAGAGATCGATCTGG
Found at i:53238627 original size:243 final size:243
Alignment explanation
Indices: 53238186--53238668 Score: 804
Period size: 243 Copynumber: 2.0 Consensus size: 243
53238176 TCACCTATCA
* * * *
53238186 AACTTTAAAGTCACAACACCCAAGCTTTAGTGACGTGACATTCGTGAAAGTGTGCACGAGCTTGA
1 AACTTCAAAGTCACAACACCCAAGCTTTAGTGACATGACACTCGTGAAAGTGGGCACGAGCTTGA
*
53238251 CTTGGGGGCACTTGGTGTCGCGACACAACCTTGCCGGTGTTGTAACCTCAATGATAATAGCCATT
66 CTTAGGGGCACTTGGTGTCGCGACACAACCTTGCCGGTGTTGTAACCTCAATGATAATAGCCATT
* * *
53238316 AGGTTTCTTCATTTCAAAAATTTTCTTGGATTTGCTACCTCGAGGGTTTGTAGTTGTGAATTTGA
131 AGGTTTCTTCATTTCAAAAATTTTCTTGGATTTACGACCTCAAGGGTTTGTAGTTGTGAATTTGA
* **
53238381 GGATCGGTGTCGTGACATAACATGCTTAGTGTTGCGACTTCAACGGCT
196 GGATCGGTGTCATGACATAACATGCTTAGTGTCACGACTTCAACGGCT
* * *
53238429 AACTTCAAAGTCGCAACACCCAAGCTTTAGTGTCATGACACTCTTGAAAGTGGGCACGAGCTTGA
1 AACTTCAAAGTCACAACACCCAAGCTTTAGTGACATGACACTCGTGAAAGTGGGCACGAGCTTGA
* *
53238494 CTTAGGGGCACTTGGTGTCGCGACACAACCTTGCTGGTGTTGTAACCTCGATGATAATAGCCATT
66 CTTAGGGGCACTTGGTGTCGCGACACAACCTTGCCGGTGTTGTAACCTCAATGATAATAGCCATT
* *
53238559 AGGTTTCTTCATTTCAAAAATTTTCTTGGATTTACGACTTCAAGGGTTTGTAGTTGTGACTTTGA
131 AGGTTTCTTCATTTCAAAAATTTTCTTGGATTTACGACCTCAAGGGTTTGTAGTTGTGAATTTGA
53238624 GGATCGGTGTCATGACATAACATGCTTAGTGTCACGACTTCAACG
196 GGATCGGTGTCATGACATAACATGCTTAGTGTCACGACTTCAACG
53238669 ATAGGTTGCT
Statistics
Matches: 222, Mismatches: 18, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
243 222 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (243 bp):
AACTTCAAAGTCACAACACCCAAGCTTTAGTGACATGACACTCGTGAAAGTGGGCACGAGCTTGA
CTTAGGGGCACTTGGTGTCGCGACACAACCTTGCCGGTGTTGTAACCTCAATGATAATAGCCATT
AGGTTTCTTCATTTCAAAAATTTTCTTGGATTTACGACCTCAAGGGTTTGTAGTTGTGAATTTGA
GGATCGGTGTCATGACATAACATGCTTAGTGTCACGACTTCAACGGCT
Found at i:53239761 original size:3 final size:3
Alignment explanation
Indices: 53239753--53239788 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53239743 ACTTAATGGC
53239753 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
53239789 ACTCCACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:53243299 original size:31 final size:30
Alignment explanation
Indices: 53243207--53243306 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
53243197 TCAAAATGAC
*
53243207 TTGTAAATTTGCTAATAGTCAAGTGACCAAA
1 TTGTAAATTTACTAATA-TCAAGTGACCAAA
* * * * *
53243238 TTATAATTTTACTAATATTTAATTGTCCAAA
1 TTGTAAATTTACTAATA-TCAAGTGACCAAA
53243269 TTGTAAATTTACTAATA-CAAGAGTGACCAAA
1 TTGTAAATTTACTAATATC-A-AGTGACCAAA
*
53243300 GTGTAAA
1 TTGTAAA
53243307 CTGACTCATC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (30 bp):
TTGTAAATTTACTAATATCAAGTGACCAAA
Found at i:53243763 original size:12 final size:12
Alignment explanation
Indices: 53243713--53243766 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 12
53243703 TTTTTTATAT
53243713 AAAA-ATTA-AA
1 AAAATATTACAA
*
53243723 AAATATAATACAA
1 AAA-ATATTACAA
53243736 AAAATA-TACAA
1 AAAATATTACAA
53243747 AAAATATTA-AA
1 AAAATATTACAA
53243758 ATAAATATT
1 A-AAATATT
53243767 TTCCTATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 15 0.39
12 15 0.39
13 5 0.13
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATATTACAA
Found at i:53246410 original size:29 final size:31
Alignment explanation
Indices: 53246353--53246411 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
53246343 TTATTTTTGC
*
53246353 AAATTAAAAATTATAAAAAAATATTTTAATA
1 AAATTAAAAATTATAAAAAAATATATTAATA
53246384 AAATT-AAAATT-TAAAAAAAT-TAATTAAT
1 AAATTAAAAATTATAAAAAAATAT-ATTAAT
53246412 TATTAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 14 0.54
30 6 0.23
31 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAATTAAAAATTATAAAAAAATATATTAATA
Found at i:53251846 original size:29 final size:29
Alignment explanation
Indices: 53251800--53251857 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
53251790 CCATCCCGCT
53251800 CTACTTTAATTAAAATTTT-AAAATTTTG
1 CTACTTTAATTAAAATTTTCAAAATTTTG
* * *
53251828 CTACTTATATTTAATATTTTCAATATTTTG
1 CTACTT-TAATTAAAATTTTCAAAATTTTG
53251858 AAGTCAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 11 0.44
30 8 0.32
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (29 bp):
CTACTTTAATTAAAATTTTCAAAATTTTG
Found at i:53253703 original size:39 final size:41
Alignment explanation
Indices: 53253644--53253731 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 41
53253634 ACCCACACAA
*
53253644 ATATATTATACATATAACACCCATGCA-CTTAAATATATATT
1 ATATATTATA-ATATAACACCCATGCAGCATAAATATATATT
* *
53253685 ATATATTAT-ATATGACACCCATGCATGCATATATATATATT
1 ATATATTATAATATAACACCCATGCA-GCATAAATATATATT
53253726 ATATAT
1 ATATAT
53253732 AAATAACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 15 0.36
41 27 0.64
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.39
Consensus pattern (41 bp):
ATATATTATAATATAACACCCATGCAGCATAAATATATATT
Found at i:53260505 original size:7 final size:7
Alignment explanation
Indices: 53260493--53260520 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
53260483 TGCACGTAAA
53260493 TATATAT
1 TATATAT
53260500 TATATAT
1 TATATAT
53260507 TATATAT
1 TATATAT
53260514 TATATAT
1 TATATAT
53260521 AAGACCCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:53263924 original size:22 final size:22
Alignment explanation
Indices: 53263898--53263942 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53263888 TAATACATAT
53263898 AACTTCTTATTTACAATTTTTC
1 AACTTCTTATTTACAATTTTTC
53263920 AACTTCTTATTTACAATTTTTC
1 AACTTCTTATTTACAATTTTTC
53263942 A
1 A
53263943 TTTTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (22 bp):
AACTTCTTATTTACAATTTTTC
Found at i:53266609 original size:17 final size:17
Alignment explanation
Indices: 53266587--53266631 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
53266577 TAAGTTGTCT
53266587 TTCTCACAATGTAAACG
1 TTCTCACAATGTAAACG
53266604 TTCTCACAATGTAAACG
1 TTCTCACAATGTAAACG
*
53266621 TTCTTACAATG
1 TTCTCACAATG
53266632 CCACTTGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (17 bp):
TTCTCACAATGTAAACG
Found at i:53267813 original size:60 final size:59
Alignment explanation
Indices: 53267718--53267889 Score: 202
Period size: 60 Copynumber: 2.9 Consensus size: 59
53267708 AAAATTTTTA
* * * *
53267718 TGGCAAGCACTGAATGAAAAAGATGTCTTCGTGGCAAAACTCTAGAAAGGAAAACCTTTG
1 TGGCAAGTACTGAATGAAAAAGATGCCTTTGTGGCAAAACCCT-GAAAGGAAAACCTTTG
* * * *
53267778 TGGCAAGTACTGAATGAAAATGATGCCTTTATGGCAAAACCCTGTAAGGAAAGCCTTTG
1 TGGCAAGTACTGAATGAAAAAGATGCCTTTGTGGCAAAACCCTGAAAGGAAAACCTTTG
** * *
53267837 TGGTGAGTATTGAATGAAAAAAGATGCCTTTGTGGC-AAACCACTGAAAAGAAA
1 TGGCAAGTACTGAATG-AAAAAGATGCCTTTGTGGCAAAACC-CTGAAAGGAAA
53267890 TTCCTCAGTG
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 32 0.34
60 63 0.66
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (59 bp):
TGGCAAGTACTGAATGAAAAAGATGCCTTTGTGGCAAAACCCTGAAAGGAAAACCTTTG
Found at i:53272373 original size:23 final size:23
Alignment explanation
Indices: 53272347--53272391 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
53272337 ATATTTTAAT
53272347 GACTCTAATGACTTAGTAAATAC
1 GACTCTAATGACTTAGTAAATAC
*
53272370 GACTCTAATGACTTCGTAAATA
1 GACTCTAATGACTTAGTAAATA
53272392 TTCTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
GACTCTAATGACTTAGTAAATAC
Found at i:53277665 original size:42 final size:42
Alignment explanation
Indices: 53277606--53277694 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
53277596 GTCTCAGCCT
*
53277606 GTGTCTCTACCCGTGTAACTCACTGGCTTGAGG-CACACGGTC
1 GTGTCTCTACCCGTGTAACTCACTGACTTG-GGTCACACGGTC
* * *
53277648 GTGTCTCTGCCCGTGTAACTCGCTGACTTGGGTCACACGGTT
1 GTGTCTCTACCCGTGTAACTCACTGACTTGGGTCACACGGTC
53277690 GTGTC
1 GTGTC
53277695 GTAGGCCGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.13, C:0.29, G:0.28, T:0.29
Consensus pattern (42 bp):
GTGTCTCTACCCGTGTAACTCACTGACTTGGGTCACACGGTC
Found at i:53278625 original size:50 final size:50
Alignment explanation
Indices: 53278505--53278699 Score: 193
Period size: 50 Copynumber: 3.9 Consensus size: 50
53278495 TCATTGACGT
** * *
53278505 TATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGA
1 TATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * * *
53278555 GATGAGAGGTCTCCCA--TAAGACCATGTCTAGGACATGGCATGGGCACCGA
1 TATGAGA--ACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * *
53278605 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--G-
1 TATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * *
53278652 TACAGAAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TA-TGAGAAC-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53278700 TGTTATTATC
Statistics
Matches: 119, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
47 2 0.02
48 12 0.10
49 33 0.28
50 67 0.56
52 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:53286623 original size:26 final size:26
Alignment explanation
Indices: 53286587--53286638 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53286577 TGTTTGGATA
53286587 CCGTAAGGGTGTTGGAGTTCCAAATT
1 CCGTAAGGGTGTTGGAGTTCCAAATT
53286613 CCGTAAGGGTGTTGGAGTTCCAAATT
1 CCGTAAGGGTGTTGGAGTTCCAAATT
53286639 AACTGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (26 bp):
CCGTAAGGGTGTTGGAGTTCCAAATT
Found at i:53292341 original size:14 final size:14
Alignment explanation
Indices: 53292303--53292357 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
53292293 AATTTGGTTC
53292303 ATTTATTTTTTTATTT
1 ATTTA-TTTTTTA-TT
*
53292319 AATTAATTTTTTATT
1 -ATTTATTTTTTATT
* *
53292334 CTTTATTTTTTGTT
1 ATTTATTTTTTATT
53292348 ATTTATTTTT
1 ATTTATTTTT
53292358 AGGTGTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 20 0.61
15 2 0.06
16 7 0.21
17 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (14 bp):
ATTTATTTTTTATT
Found at i:53295391 original size:6 final size:6
Alignment explanation
Indices: 53295375--53295417 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
53295365 CCCAAAAGAA
* *
53295375 AATTTT CATTTT AATTTT AATTTT -ATTTCC AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT AATTT-T AATTTT AATTTT A
53295418 TTATTTTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 23 0.74
7 4 0.13
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:53296867 original size:19 final size:19
Alignment explanation
Indices: 53296843--53296882 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
53296833 ATCTCATCTC
53296843 ATTCA-TTGCATTTAGATTA
1 ATTCATTTGCATTTAG-TTA
53296862 ATTCATTTGCATTTAGTTA
1 ATTCATTTGCATTTAGTTA
53296881 AT
1 AT
53296883 AATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTCATTTGCATTTAGTTA
Found at i:53302512 original size:24 final size:26
Alignment explanation
Indices: 53302483--53302532 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
53302473 TGTTAAAACT
53302483 ATTTC-TAAAG-AAAACTCAAGAGAA
1 ATTTCTTAAAGAAAAACTCAAGAGAA
**
53302507 ATTTCTTGGAGAAAAACTCAAGAGAA
1 ATTTCTTAAAGAAAAACTCAAGAGAA
53302533 TTTGCAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 3 0.14
26 14 0.64
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (26 bp):
ATTTCTTAAAGAAAAACTCAAGAGAA
Found at i:53303748 original size:14 final size:14
Alignment explanation
Indices: 53303729--53303762 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
53303719 ATTCCCCAAA
*
53303729 AGCGCGTCCACGTC
1 AGCGCGTCCACATC
53303743 AGCGCGTCCACATC
1 AGCGCGTCCACATC
53303757 AGCGCG
1 AGCGCG
53303763 ATGTCAGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.41, G:0.29, T:0.12
Consensus pattern (14 bp):
AGCGCGTCCACATC
Found at i:53304024 original size:22 final size:21
Alignment explanation
Indices: 53303996--53304088 Score: 116
Period size: 22 Copynumber: 4.2 Consensus size: 21
53303986 AACTAAATCC
*
53303996 TTTCTCTCAATTTCTCTCTAA
1 TTTCTCTCAATTTCTCTCAAA
53304017 TATTCTCTCAAATTTCTCTCAAA
1 T-TTCTCTC-AATTTCTCTCAAA
*
53304040 TTTCTCTCAATTTCCTCTC-GA
1 TTTCTCTCAATTT-CTCTCAAA
53304061 TTTCCTCTCAATTTCCTCTCAAA
1 TTT-CTCTCAATTT-CTCTCAAA
53304084 TTTCT
1 TTTCT
53304089 ATTTAAAATA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.16
22 37 0.58
23 17 0.27
ACGTcount: A:0.20, C:0.30, G:0.01, T:0.48
Consensus pattern (21 bp):
TTTCTCTCAATTTCTCTCAAA
Found at i:53304035 original size:11 final size:10
Alignment explanation
Indices: 53303996--53304088 Score: 105
Period size: 11 Copynumber: 8.5 Consensus size: 10
53303986 AACTAAATCC
53303996 TTTCTCTCAA
1 TTTCTCTCAA
53304006 TTTCTCTCTAA
1 TTTCTCTC-AA
53304017 TATTCTCTCAAA
1 T-TTCTCTC-AA
53304029 TTTCTCTCAAA
1 TTTCTCTC-AA
53304040 TTTCTCTCAA
1 TTTCTCTCAA
*
53304050 TTTCCTCTCGA
1 TTT-CTCTCAA
53304061 TTTCCTCTCAA
1 TTT-CTCTCAA
53304072 TTTCCTCTCAAA
1 TTT-CTCTC-AA
53304084 TTTCT
1 TTTCT
53304089 ATTTAAAATA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
10 13 0.17
11 48 0.63
12 15 0.20
ACGTcount: A:0.20, C:0.30, G:0.01, T:0.48
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:53304069 original size:44 final size:44
Alignment explanation
Indices: 53303996--53304088 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 44
53303986 AACTAAATCC
53303996 TTTCTCTCAATTTCTCTCTAATATTCTCTCAAATTT-CTCTCAAA
1 TTTCTCTCAATTTCTCTCTAATATTCTCTC-AATTTCCTCTCAAA
*
53304040 TTTCTCTCAATTTC-CTCTCGAT-TTCCTCTCAATTTCCTCTCAAA
1 TTTCTCTCAATTTCTCTCT-AATATT-CTCTCAATTTCCTCTCAAA
53304084 TTTCT
1 TTTCT
53304089 ATTTAAAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
43 11 0.24
44 34 0.76
ACGTcount: A:0.20, C:0.30, G:0.01, T:0.48
Consensus pattern (44 bp):
TTTCTCTCAATTTCTCTCTAATATTCTCTCAATTTCCTCTCAAA
Found at i:53308469 original size:21 final size:21
Alignment explanation
Indices: 53308445--53308499 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
53308435 CACCGACAAG
* * * *
53308445 CAGATTCCCTACCGGAGGAAC
1 CAGAATCCCCACCAGAGCAAC
53308466 CAGAATCCCCACCAGAGCAAC
1 CAGAATCCCCACCAGAGCAAC
* *
53308487 CACAACCCCCACC
1 CAGAATCCCCACC
53308500 GAAGGCTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.45, G:0.15, T:0.07
Consensus pattern (21 bp):
CAGAATCCCCACCAGAGCAAC
Found at i:53308654 original size:34 final size:33
Alignment explanation
Indices: 53308614--53308712 Score: 98
Period size: 34 Copynumber: 3.0 Consensus size: 33
53308604 GAATATTTTG
53308614 ATATTATTTGATGTAATAAAATAGAAATTCTTCT
1 ATATTATTT-ATGTAATAAAATAGAAATTCTTCT
* * *
53308648 ATATTATTCCATGTACTAAAATAGAAATT-TACT
1 ATATTATT-TATGTAATAAAATAGAAATTCTTCT
* *
53308681 -TATACATTT-T-TAATATAATAGAAATTCTTCT
1 ATAT-TATTTATGTAATAAAATAGAAATTCTTCT
53308712 A
1 A
53308713 ATAAGGCAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 14 0.26
31 4 0.08
32 3 0.06
33 6 0.11
34 26 0.49
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
ATATTATTTATGTAATAAAATAGAAATTCTTCT
Found at i:53311944 original size:126 final size:126
Alignment explanation
Indices: 53311713--53312129 Score: 690
Period size: 126 Copynumber: 3.3 Consensus size: 126
53311703 CCAAACATGT
* * *
53311713 GCTATTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGGCAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* *
53311778 GCTTAAAGCGTTTTTGACACTATTTGCTTAAAAACCTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAGGA
*
53311839 GCTACTGTAGCAAAAGCCCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
53311904 ACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAGGA
*
53311965 GCTACTGTAGCAAAAGCGCGTCCACGTGGTAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
53312030 GCTTAAAGTGTTTTTGACACTATTTGCTCAAAAATGTCTACTCGAAATTATCTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAGGA
* * *
53312091 GCTACTATAGCAAGAGTGCGTCCACGTGGGAGCTTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
53312130 AAATTAACAA
Statistics
Matches: 270, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 270 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
GCTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAGGA
Found at i:53312310 original size:96 final size:96
Alignment explanation
Indices: 53312168--53312443 Score: 326
Period size: 96 Copynumber: 2.9 Consensus size: 96
53312158 CCTAAACCCC
*
53312168 AAACCCTAATTTATTTGAGTTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAATTTTATA
1 AAACCCTAATTTATTT-AATTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAATTTT-TA
53312233 AA-AATTTATAATTAATTTACTCAAGTAA-CTCT
64 AATAATTTATAATTAATTTACTCAAGTAACCT-T
* * * * * * * *
53312265 GAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTTAACTCTAAACTCTTATCTGATTTTTAAA
1 AAACCCTAATTTATTTAATTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAATTTTTAAA
*
53312330 TAATTTTTAATTAATTTACTCAAGTAACCTT
66 TAATTTATAATTAATTTACTCAAGTAACCTT
* * * * * *
53312361 AAACCCTAATTTAATTAATTTTTTCTTAAAAAAACAATAAACACGAAA-CCTAATCCAATTTTGA
1 AAACCCTAATTTATTTAATTTTTACTT--AAAAACACTAAACACTAAACCCTAATCTAATTTTTA
*
53312425 AA-ATTTTATAATTAATTTA
64 AATAATTTATAATTAATTTA
53312444 ATTGACAAAC
Statistics
Matches: 150, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
95 4 0.03
96 102 0.68
97 30 0.20
98 14 0.09
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (96 bp):
AAACCCTAATTTATTTAATTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAATTTTTAAA
TAATTTATAATTAATTTACTCAAGTAACCTT
Found at i:53313585 original size:5 final size:5
Alignment explanation
Indices: 53313577--53313608 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
53313567 AAAGAAAAGA
53313577 AAATC AAATC AAATC AAATC AAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AAATC AA
53313609 GCAGATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:53314659 original size:5 final size:6
Alignment explanation
Indices: 53314647--53314675 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53314637 TATAATATAA
53314647 TTATTT TTATTT TTATTT TTATTT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTATT
53314676 CATATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:53325635 original size:18 final size:17
Alignment explanation
Indices: 53325576--53325636 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
53325566 GCACTCTTTC
*
53325576 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
53325595 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
53325612 TGTTTCTTTTTCGATTTCT
1 T-TTTCTTTTTCAATTT-T
53325631 TTTTCT
1 TTTTCT
53325637 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:53326597 original size:14 final size:15
Alignment explanation
Indices: 53326577--53326619 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
53326567 TTTTCATGAA
53326577 AATTTTTTTTTCACG
1 AATTTTTTTTTCACG
53326592 AATTTTTTTTTCACG
1 AATTTTTTTTTCACG
53326607 AATTTTTTTTTCA
1 AATTTTTTTTTCA
53326620 ACTTGATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.63
Consensus pattern (15 bp):
AATTTTTTTTTCACG
Found at i:53326676 original size:12 final size:11
Alignment explanation
Indices: 53326657--53326704 Score: 78
Period size: 12 Copynumber: 4.2 Consensus size: 11
53326647 ATGGAAACCA
53326657 AATTTTTTTTG
1 AATTTTTTTTG
53326668 AATTTTTTTTTG
1 AA-TTTTTTTTG
53326680 AATTTTTTTTG
1 AATTTTTTTTG
53326691 AAATTTTTTTTG
1 -AATTTTTTTTG
53326703 AA
1 AA
53326705 GAAACTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 13 0.37
12 22 0.63
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:53326687 original size:23 final size:23
Alignment explanation
Indices: 53326657--53326704 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
53326647 ATGGAAACCA
*
53326657 AATTTTTTTTGAATTTTTTTTTG
1 AATTTTTTTTGAAATTTTTTTTG
53326680 AATTTTTTTTGAAATTTTTTTTG
1 AATTTTTTTTGAAATTTTTTTTG
53326703 AA
1 AA
53326705 GAAACTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (23 bp):
AATTTTTTTTGAAATTTTTTTTG
Found at i:53331250 original size:43 final size:43
Alignment explanation
Indices: 53331170--53331301 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 43
53331160 AATATTTTTT
* **
53331170 TAAAAATCATG-TTTTTAGCGGCGTTTGTGGTAGAAGCGTTGC
1 TAAAAATCATGATTTTTAGCGGCGTTTGTAGTAGAAGCGCCGC
* * * *
53331212 TAAAAATCATGATTTTTAGTGGCGCTTATAGTATAAGCGCCGC
1 TAAAAATCATGATTTTTAGCGGCGTTTGTAGTAGAAGCGCCGC
* * *
53331255 TAAAAGTCATGATCTTTAGCGGCGTTTGTAGTAGAAGCGACGC
1 TAAAAATCATGATTTTTAGCGGCGTTTGTAGTAGAAGCGCCGC
53331298 TAAA
1 TAAA
53331302 GTTAGCGACG
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 11 0.15
43 64 0.85
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (43 bp):
TAAAAATCATGATTTTTAGCGGCGTTTGTAGTAGAAGCGCCGC
Found at i:53332480 original size:169 final size:169
Alignment explanation
Indices: 53332201--53332537 Score: 620
Period size: 169 Copynumber: 2.0 Consensus size: 169
53332191 CAAGAACAAA
*
53332201 ACCCATGTTTGTATCATTTTCTGTCATTCCTTCCCTTGTTTTTTGTTTTCCTTTAAATGTTGTAT
1 ACCCATGTTTGTATCATTTTCTGTCATTCCTTCCCTTGTTTTTTGTTTTCCTTCAAATGTTGTAT
* *
53332266 TGGATCATAAACACTTGCAATGGATTGTTTCAAGGATAATGAATCAAAGCAGACAAATTCCCATG
66 TGGATCATAAACACTTGCAATGGATTATTTCAAGGACAATGAATCAAAGCAGACAAATTCCCATG
53332331 AAAAAGGTAATAGCACTGAACACTCACATGATCTAAGCG
131 AAAAAGGTAATAGCACTGAACACTCACATGATCTAAGCG
53332370 ACCCATGTTTGTATCATTTTCTGTCATTCCTTCCCTTGTTTTTTGTTTTCCTTCAAATGTTGTAT
1 ACCCATGTTTGTATCATTTTCTGTCATTCCTTCCCTTGTTTTTTGTTTTCCTTCAAATGTTGTAT
* *
53332435 TGGATCATAAACACTTGCAATGGATTATTTCAGGGACAATGAATCAAAGTAGACAAATTCCCATG
66 TGGATCATAAACACTTGCAATGGATTATTTCAAGGACAATGAATCAAAGCAGACAAATTCCCATG
*
53332500 AAGAAGGTAATAGCACTGAACACTCACATGATCTAAGC
131 AAAAAGGTAATAGCACTGAACACTCACATGATCTAAGC
53332538 CTTAACTCGG
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 162 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (169 bp):
ACCCATGTTTGTATCATTTTCTGTCATTCCTTCCCTTGTTTTTTGTTTTCCTTCAAATGTTGTAT
TGGATCATAAACACTTGCAATGGATTATTTCAAGGACAATGAATCAAAGCAGACAAATTCCCATG
AAAAAGGTAATAGCACTGAACACTCACATGATCTAAGCG
Found at i:53332978 original size:35 final size:35
Alignment explanation
Indices: 53332926--53333005 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
53332916 GAAAAAAAAT
* *
53332926 TTGCCTTAGACGTGTCTATCCCAA-TCTTTTGAAGG
1 TTGCCTTAAACGGGTCTATCCCAACT-TTTTGAAGG
* * *
53332961 TTGCCTTAAACGGGTCTATTCTAACTTTTTTAAGG
1 TTGCCTTAAACGGGTCTATCCCAACTTTTTGAAGG
53332996 TTGCCTTAAA
1 TTGCCTTAAA
53333006 ACCTATCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (35 bp):
TTGCCTTAAACGGGTCTATCCCAACTTTTTGAAGG
Found at i:53333027 original size:36 final size:35
Alignment explanation
Indices: 53332940--53333028 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
53332930 CTTAGACGTG
* * * * *
53332940 TCTATCCCAATCTTTTGAAGGTTGCCTTAAACGGG
1 TCTATCCTAAACTTTTTAAGGTTGCCTTAAACCGA
* *
53332975 TCTATTCT-AACTTTTTTAAGGTTGCCTTAAAACCTA
1 TCTATCCTAAAC-TTTTTAAGGTTGCCTT-AAACCGA
53333011 TCTATCCTAAACTTTTTA
1 TCTATCCTAAACTTTTTA
53333029 GCGTCACATT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
34 2 0.05
35 21 0.49
36 17 0.40
37 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (35 bp):
TCTATCCTAAACTTTTTAAGGTTGCCTTAAACCGA
Found at i:53335672 original size:20 final size:20
Alignment explanation
Indices: 53335649--53335731 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
53335639 TATATGCTTA
53335649 TATATTATTTTTAATAATTT
1 TATATTATTTTTAATAATTT
53335669 TATAATTA-TTTTACA-AATTT
1 TAT-ATTATTTTTA-ATAATTT
53335689 TATGA-T-TTTTTAAT-ATTT
1 TAT-ATTATTTTTAATAATTT
* * *
53335707 T-TACTATTTTTCATTATTT
1 TATATTATTTTTAATAATTT
53335726 TATATT
1 TATATT
53335732 TAAAAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
16 1 0.02
17 2 0.04
18 13 0.25
19 11 0.21
20 20 0.38
21 5 0.10
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (20 bp):
TATATTATTTTTAATAATTT
Found at i:53338700 original size:75 final size:75
Alignment explanation
Indices: 53338578--53338724 Score: 179
Period size: 75 Copynumber: 2.0 Consensus size: 75
53338568 TATGAAAAAC
** * * ** *
53338578 ACATAATGCAGGTCTTAAAGGATGCTAATGTATTAATGTAATGCATTAACTAAAGACGCATTCAA
1 ACATAATGCACATCTTAAAAGATGCTAATGTATTAATGCAAAACATTAAATAAAGACGCATTCAA
*
53338643 TAAACAAGAA
66 CAAACAAGAA
* * *
53338653 ACATAATGCACATTTTAAAAGATG-TAGATGTATTAATGCAAAACATTAAATAAAGATGCATTTA
1 ACATAATGCACATCTTAAAAGATGCTA-ATGTATTAATGCAAAACATTAAATAAAGACGCATTCA
53338717 ACAAACAA
65 ACAAACAA
53338725 AACACTTCAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 2 0.03
75 58 0.97
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (75 bp):
ACATAATGCACATCTTAAAAGATGCTAATGTATTAATGCAAAACATTAAATAAAGACGCATTCAA
CAAACAAGAA
Found at i:53339699 original size:25 final size:24
Alignment explanation
Indices: 53339656--53339709 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
53339646 GTATTGAAAT
*
53339656 TTAAAAATTTAAAAAAATATAAAGA
1 TTAAAAATATAAAAAAATATAAA-A
* * *
53339681 TTAAAAATATCAAATAATATCAAA
1 TTAAAAATATAAAAAAATATAAAA
53339705 TTAAA
1 TTAAA
53339710 TAACAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAAAAATATAAAAAAATATAAAA
Found at i:53341263 original size:116 final size:117
Alignment explanation
Indices: 53340916--53341569 Score: 411
Period size: 116 Copynumber: 5.6 Consensus size: 117
53340906 CATATGTTTA
** *** * * *
53340916 ATTGTACATTTCACATTGTT-CATCTATTGACCAGAGTGAGTTTTTTGGG-TTTCCTTTTCATTG
1 ATTGTACATTTTGCATT-TTCCATCTATTGAATGGACTGAGTTTTTCGGGTTTTCCATTTCATTG
* * * *
53340979 CTTTCAAGTATCTGGTCTTTA-AGA-GTTTCGATTGTGTTTTTTTTTCCTTCCATTTC
65 CTTTCAAGTGTCTGGTCTTTATA-ATGTTCCG-TTGTG-TTTTCTGT--TTCCATTTC
* * * *
53341035 A-TGTACATTTTCATTTTCATTTTCCATC-AGTTCAGTGGAGC-GAGTTTTTCAGGTTTTCCATT
1 ATTGTACA---T--TTTGCATTTTCCATCTA-TTGAATGGA-CTGAGTTTTTCGGGTTTTCCATT
** ** ** * * * *
53341097 TTGTTAATTTCAAGCATCTGGTC-CTATGA-GTTCTGTTCATGTTTTCTGTTTCCATTTC
59 TCATTGCTTTCAAGTGTCTGGTCTTTATAATGTTCCGTT-GTGTTTTCTGTTTCCATTTC
*
53341155 ATTGTACATTTTGCATTTTCCATCTATTGAATGGACTGA-TGTTTTCGGG-TTTCCATTTCATTT
1 ATTGTACATTTTGCATTTTCCATCTATTGAATGGACTGAGT-TTTTCGGGTTTTCCATTTCATTG
* * *
53341218 CTTTCAAGTGTCTGGTCTTTATAATG-TCCGATCGTATCTTCTGTTTCCATTTC
65 CTTTCAAGTGTCTGGTCTTTATAATGTTCCG-TTGTGTTTTCTGTTTCCATTTC
* ** * *** * * * * * *
53341271 ATTTTACGCTTTGTATTTTCCATGGGTTGAATGAAGTGACTTTTCCAGG-TTTCCATTTCACTGC
1 ATTGTACATTTTGCATTTTCCATCTATTGAATGGACTGAGTTTTTCGGGTTTTCCATTTCATTGC
*
53341335 TTTCAAGTGTCTGGCCTTTATAA-GTTCCGTTGTTGTTTTCTGTTT-C----C
66 TTTCAAGTGTCTGGTCTTTATAATGTTCCGTTG-TGTTTTCTGTTTCCATTTC
* * * * * * *
53341382 ATT-T-CATTTTGCATTTTCCATCCACTAAATGGAGTGAGTTTTTTGGGTTTTCTAGTTCATTGC
1 ATTGTACATTTTGCATTTTCCATCTATTGAATGGACTGAGTTTTTCGGGTTTTCCATTTCATTGC
* * * * * *
53341445 TTTCAAATATCTGCTCTTTGT-ATGTTCTGTTTGTGTTTTCTGATTCCATTTC
66 TTTCAAGTGTCTGGTCTTTATAATGTTCCG-TTGTGTTTTCTGTTTCCATTTC
* * * *
53341497 ATTGTACATTTTGCATTTTCTAT-TCATTGACTGGAGC-GAGTTTTTTGGGTTTTCCAATTCATT
1 ATTGTACATTTTGCATTTTCCATCT-ATTGAATGGA-CTGAGTTTTTCGGGTTTTCCATTTCATT
53341560 GCTTTCAAGT
64 GCTTTCAAGT
53341570 ACTCTTCATA
Statistics
Matches: 414, Mismatches: 88, Indels: 68
0.73 0.15 0.12
Matches are distributed among these distances:
109 31 0.07
110 45 0.11
111 8 0.02
115 35 0.08
116 140 0.34
117 60 0.14
118 7 0.02
119 1 0.00
120 10 0.02
121 7 0.02
122 11 0.03
123 34 0.08
124 25 0.06
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.49
Consensus pattern (117 bp):
ATTGTACATTTTGCATTTTCCATCTATTGAATGGACTGAGTTTTTCGGGTTTTCCATTTCATTGC
TTTCAAGTGTCTGGTCTTTATAATGTTCCGTTGTGTTTTCTGTTTCCATTTC
Found at i:53348378 original size:30 final size:31
Alignment explanation
Indices: 53348310--53348379 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
53348300 TTAATATGCT
* *
53348310 ATTTGGTACCTGAGTTTCACTTTAATGTTCA
1 ATTTGGTACCTGAGTTTCACTTCAATATTCA
**
53348341 ATTTGGTACCTGAGTTTGGCTTCAATATT-A
1 ATTTGGTACCTGAGTTTCACTTCAATATTCA
*
53348371 TTTTGGTAC
1 ATTTGGTAC
53348380 TTGATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTGAGTTTCACTTCAATATTCA
Found at i:53349539 original size:7 final size:8
Alignment explanation
Indices: 53349522--53349546 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53349512 ATAATAAATA
53349522 TTTATTTT
1 TTTATTTT
53349530 TTTATTTT
1 TTTATTTT
53349538 TTTATTTT
1 TTTATTTT
53349546 T
1 T
53349547 AAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:53349570 original size:12 final size:11
Alignment explanation
Indices: 53349540--53349568 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
53349530 TTTATTTTTT
53349540 TATTTTTAAAA
1 TATTTTTAAAA
53349551 TATTTTTAAAA
1 TATTTTTAAAA
53349562 TATTTTT
1 TATTTTT
53349569 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:53349587 original size:19 final size:18
Alignment explanation
Indices: 53349551--53349588 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53349541 ATTTTTAAAA
*
53349551 TATTTTTAAAATATTTTT
1 TATTTTTAAAATAATTTT
53349569 TATTTTTAAAATAAATTTT
1 TATTTTTAAAAT-AATTTT
53349588 T
1 T
53349589 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTTAAAATAATTTT
Found at i:53351829 original size:101 final size:102
Alignment explanation
Indices: 53351713--53351897 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
53351703 AAAGTGATGG
* * ** **
53351713 TCACGTGTGTAGTACTATGTGTAGGGTATTACGTGTACCAGA-A-TGATAGGTCGTATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
*
53351776 ACTATGTGCTGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* *
53351814 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
53351879 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
53351898 TGAACCAATA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 36 0.49
102 33 0.45
103 4 0.05
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:53351833 original size:51 final size:50
Alignment explanation
Indices: 53351767--53351897 Score: 165
Period size: 51 Copynumber: 2.6 Consensus size: 50
53351757 GATAGGTCGT
*
53351767 ATGTGTAGTACTATGTGCTGGCTACTATGCGTACCGGATAGCT-TCGATCAC
1 ATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GATCAC
* * * * * *
53351818 GTGTGTAGTACTATGTGCAGGCTACCACGTGTATCGGATAGTGATGGTCAC
1 ATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGATCAC
53351869 ATGTGTAGTACTATGTGCAGGCTACTATG
1 ATGTGTAGTACTATGTGCAGGCTACTATG
53351898 TGAACCAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.01
51 66 0.97
52 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (50 bp):
ATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGATCAC
Found at i:53351899 original size:26 final size:25
Alignment explanation
Indices: 53351819--53351899 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 25
53351809 TTCGATCACG
53351819 TGTGTAGTACTATGTGCAGGCTACCA
1 TGTGTAGTACTATGTGCAGGCTA-CA
* *
53351845 CGTGTA-T-CGGATAGTG-ATGG-TCACA
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACA
53351870 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTAC-A
53351896 TGTG
1 TGTG
53351900 AACCAATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 19 0.45
26 21 0.50
27 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (25 bp):
TGTGTAGTACTATGTGCAGGCTACA
Found at i:53352144 original size:16 final size:16
Alignment explanation
Indices: 53352123--53352154 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53352113 TGATTGAAAG
*
53352123 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
53352139 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
53352155 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:53354377 original size:22 final size:21
Alignment explanation
Indices: 53354349--53354402 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
53354339 GTTCGTGTAA
53354349 TTAAATTGTATATTTATATGTT
1 TTAAATTGTATA-TTATATGTT
*
53354371 TTAAATTG-A-ATTATTTGTT
1 TTAAATTGTATATTATATGTT
*
53354390 TGTGAATTGTATA
1 T-TAAATTGTATA
53354403 ATTTCCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
21 2 0.07
22 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (21 bp):
TTAAATTGTATATTATATGTT
Found at i:53358071 original size:51 final size:49
Alignment explanation
Indices: 53358013--53358139 Score: 125
Period size: 50 Copynumber: 2.6 Consensus size: 49
53358003 ATGAGTTACT
*
53358013 TAATGCATGACTTTATTTAAGATGCAAACTTTAACTATCATG-GTAGTTAAA
1 TAATGCAT-ACTTTATTTAAGATGCAAAC-TTAACTAACATGAG-AGTTAAA
* * * * **
53358064 TAATGCATATCATAATTTATGATGCAATCTTAACTAACATGAGAGTTTCA
1 TAATGCATA-CTTTATTTAAGATGCAAACTTAACTAACATGAGAGTTAAA
53358114 TAATGCATAACTTTA-TTAA-ATGCAAA
1 TAATGCAT-ACTTTATTTAAGATGCAAA
53358140 ACACATAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
48 6 0.10
49 3 0.05
50 28 0.45
51 25 0.40
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (49 bp):
TAATGCATACTTTATTTAAGATGCAAACTTAACTAACATGAGAGTTAAA
Found at i:53376116 original size:53 final size:53
Alignment explanation
Indices: 53375958--53376097 Score: 217
Period size: 53 Copynumber: 2.6 Consensus size: 53
53375948 ATTAGTTTTC
* * *
53375958 CCATATAATGTCATAACCCACCAATTATGGTCTTACACGATATGATCTTCTTT
1 CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
* * * *
53376011 CTATATGATGCCATAACCCACCAGTTACGGTTTTACATGATATGATCTTCTTT
1 CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
53376064 CCATATGATGTCATAACCCACCAGTTACGGTCTT
1 CCATATGATGTCATAACCCACCAGTTACGGTCTT
53376098 GCAGGACATG
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 77 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (53 bp):
CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
Found at i:53377911 original size:41 final size:40
Alignment explanation
Indices: 53377847--53378045 Score: 159
Period size: 41 Copynumber: 4.9 Consensus size: 40
53377837 TACCTAATAT
* * *
53377847 AATACACTGGCACAAAGCCTGCTAGGCTTAAAACCTGATAC
1 AATACAC-GACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
* * * *
53377888 GATACATCGACACGAAGCTTGCTAGGCTCAATGCCTGATAC
1 AATACA-CGACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
* * *
53377929 AATACACTGGCACGAAGCCTGCTAGGCATAAAGCTTGA-AC
1 AATACAC-GACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
* * **
53377969 AATACACCGACACTAAGCCTACTAGGCACAAAGCCTGA-ATC
1 AATACA-CGACACGAAGCCTGCTAGGCTTAAAGCCTGATA-C
* * * **
53378010 AATACACTAGCACTAAGCCTACTAGGCACAAAGCCT
1 AATACACGA-CACGAAGCCTGCTAGGCTTAAAGCCT
53378046 ACTAGGCACA
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
40 37 0.28
41 95 0.71
42 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (40 bp):
AATACACGACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
Found at i:53378013 original size:81 final size:82
Alignment explanation
Indices: 53377847--53378045 Score: 240
Period size: 81 Copynumber: 2.4 Consensus size: 82
53377837 TACCTAATAT
* * * * * *
53377847 AATACACTGGCACAAAGCCTGCTAGGCTTAAAACCTGATACGATACATCGACACGAAGCTTGCTA
1 AATACACTGGCACAAAGCCTGCTAGGCATAAAGCCTGATACAATACACCGACACGAAGCCTACTA
* *
53377912 GGCTCAATGCCTGATAC
66 GGCACAAAGCCTGATAC
* * *
53377929 AATACACTGGCACGAAGCCTGCTAGGCATAAAGCTTGA-ACAATACACCGACACTAAGCCTACTA
1 AATACACTGGCACAAAGCCTGCTAGGCATAAAGCCTGATACAATACACCGACACGAAGCCTACTA
53377993 GGCACAAAGCCTGA-ATC
66 GGCACAAAGCCTGATA-C
* * * *
53378010 AATACACTAGCACTAAGCCTACTAGGCACAAAGCCT
1 AATACACTGGCACAAAGCCTGCTAGGCATAAAGCCT
53378046 ACTAGGCACA
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 65 0.65
82 34 0.34
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (82 bp):
AATACACTGGCACAAAGCCTGCTAGGCATAAAGCCTGATACAATACACCGACACGAAGCCTACTA
GGCACAAAGCCTGATAC
Found at i:53378043 original size:16 final size:16
Alignment explanation
Indices: 53378015--53378061 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
53378005 GAATCAATAC
*
53378015 ACTA-GCACTAAGCCT
1 ACTAGGCACAAAGCCT
53378030 ACTAGGCACAAAGCCT
1 ACTAGGCACAAAGCCT
53378046 ACTAGGCACAAAGCCT
1 ACTAGGCACAAAGCCT
53378062 GAATCAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 4 0.13
16 26 0.87
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.15
Consensus pattern (16 bp):
ACTAGGCACAAAGCCT
Found at i:53378051 original size:57 final size:57
Alignment explanation
Indices: 53377983--53378090 Score: 207
Period size: 57 Copynumber: 1.9 Consensus size: 57
53377973 CACCGACACT
*
53377983 AAGCCTACTAGGCACAAAGCCTGAATCAATACACTAGCACTAAGCCTACTAGGCACA
1 AAGCCTACTAGGCACAAAGCCTGAATCAATACACAAGCACTAAGCCTACTAGGCACA
53378040 AAGCCTACTAGGCACAAAGCCTGAATCAATACACAAGCACTAAGCCTACTA
1 AAGCCTACTAGGCACAAAGCCTGAATCAATACACAAGCACTAAGCCTACTA
53378091 AGCATAAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.16
Consensus pattern (57 bp):
AAGCCTACTAGGCACAAAGCCTGAATCAATACACAAGCACTAAGCCTACTAGGCACA
Found at i:53378085 original size:41 final size:41
Alignment explanation
Indices: 53378035--53378121 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
53378025 AGCCTACTAG
* *
53378035 GCACAAAGCCTACTAGGCACAAAGCCTGAATCAATACACAA
1 GCACTAAGCCTACTAAGCACAAAGCCTGAATCAATACACAA
* * *
53378076 GCACTAAGCCTACTAAGCATAAATCCTGAATCAATACACCA
1 GCACTAAGCCTACTAAGCACAAAGCCTGAATCAATACACAA
53378117 GCACT
1 GCACT
53378122 CCGGCGAGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.30, G:0.13, T:0.16
Consensus pattern (41 bp):
GCACTAAGCCTACTAAGCACAAAGCCTGAATCAATACACAA
Found at i:53378105 original size:98 final size:97
Alignment explanation
Indices: 53377937--53378121 Score: 264
Period size: 98 Copynumber: 1.9 Consensus size: 97
53377927 ACAATACACT
* * * * * *
53377937 GGCACGAAGCCTGCTAGGCATAAAGCTTGAACAATACACCGACACTAAGCCTACTAGGCACAAAG
1 GGCACAAAGCCTACTAGGCACAAAGCCTGAACAATACACAGACACTAAGCCTACTAAGCACAAAG
*
53378002 CCTGAATCAATACACTAGCACTAAGCCTACTA
66 CCTGAATCAATACACCAGCACTAAGCCTACTA
*
53378034 GGCACAAAGCCTACTAGGCACAAAGCCTGAATCAATACACA-AGCACTAAGCCTACTAAGCATAA
1 GGCACAAAGCCTACTAGGCACAAAGCCTGAA-CAATACACAGA-CACTAAGCCTACTAAGCACAA
*
53378098 ATCCTGAATCAATACACCAGCACT
64 AGCCTGAATCAATACACCAGCACT
53378122 CCGGCGAGAC
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 28 0.36
98 49 0.64
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (97 bp):
GGCACAAAGCCTACTAGGCACAAAGCCTGAACAATACACAGACACTAAGCCTACTAAGCACAAAG
CCTGAATCAATACACCAGCACTAAGCCTACTA
Found at i:53378646 original size:41 final size:40
Alignment explanation
Indices: 53378573--53378695 Score: 138
Period size: 41 Copynumber: 3.0 Consensus size: 40
53378563 AGTACAAGTT
* * *
53378573 ACCTGATACAATACACCGGCACAAAGCCTGCTAGGCTTAAA
1 ACCTGATACAATACA-CGGCACGAAGCTTGCTAGGCTCAAA
* * * *
53378614 ACCTGATACGATACATCGACACGAAGCTTGCTAAGCTCAAG
1 ACCTGATACAATACA-CGGCACGAAGCTTGCTAGGCTCAAA
* *
53378655 GCCTGATACAATACACTGGCACGAAGCTTGCTAGGCACAAA
1 ACCTGATACAATACAC-GGCACGAAGCTTGCTAGGCTCAAA
53378696 GCTTGAATCA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 66 0.99
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.18
Consensus pattern (40 bp):
ACCTGATACAATACACGGCACGAAGCTTGCTAGGCTCAAA
Found at i:53378708 original size:41 final size:41
Alignment explanation
Indices: 53378637--53378869 Score: 240
Period size: 41 Copynumber: 5.7 Consensus size: 41
53378627 CATCGACACG
* * * * *
53378637 AAGCTTGCTAAGCTCAAGGCCTG-ATACAATACACTGGCACG
1 AAGCTTGCTAGGCACAAAGCCTGAAT-CAATACACTAGCACT
* *
53378678 AAGCTTGCTAGGCACAAAGCTTGAATCAATACAC-CGACACT
1 AAGCTTGCTAGGCACAAAGCCTGAATCAATACACTAG-CACT
*** *
53378719 AAGCCCACTAGGCACAAAGCCTGAATCAATACACAAGCACT
1 AAGCTTGCTAGGCACAAAGCCTGAATCAATACACTAGCACT
53378760 AAG-TCTGCTAGAG-ACAAAGCCTGAATCAATACACTAGCACT
1 AAGCT-TGCTAG-GCACAAAGCCTGAATCAATACACTAGCACT
* *
53378801 AAGCCTACTAGGCACAAAGCCTGAATCAATACACTAGCACT
1 AAGCTTGCTAGGCACAAAGCCTGAATCAATACACTAGCACT
* * * * *
53378842 GAGCCTACTAAGTACAAAGCCTGAATCA
1 AAGCTTGCTAGGCACAAAGCCTGAATCA
53378870 TTATTTCCAA
Statistics
Matches: 165, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.01
41 159 0.96
42 4 0.02
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (41 bp):
AAGCTTGCTAGGCACAAAGCCTGAATCAATACACTAGCACT
Found at i:53378716 original size:82 final size:82
Alignment explanation
Indices: 53378574--53378869 Score: 219
Period size: 82 Copynumber: 3.6 Consensus size: 82
53378564 GTACAAGTTA
* * ** * * *
53378574 CCTGATACAATACACCGGCACAAAGCCTGCTAGGCTTAAAACCTG-ATACGATACATCGACACGA
1 CCTGATACAATACACAGGCACAAAGCTTGCTAGGCACAAAGCCTGAAT-CAATACACCGACACGA
*** * *
53378638 AGCTTGCTAAGCTCAAGG
65 AGCCCACTAAGCACAAAG
* * * *
53378656 CCTGATACAATACACTGGCACGAAGCTTGCTAGGCACAAAGCTTGAATCAATACACCGACACTAA
1 CCTGATACAATACACAGGCACAAAGCTTGCTAGGCACAAAGCCTGAATCAATACACCGACACGAA
*
53378721 GCCCACTAGGCACAAAG
66 GCCCACTAAGCACAAAG
* * *
53378738 CCTGA-ATCAATACACAAGCACTAAG-TCTGCTAGAG-ACAAAGCCTGAATCAATACA-CTAGCA
1 CCTGATA-CAATACACAGGCACAAAGCT-TGCTAG-GCACAAAGCCTGAATCAATACACCGA-CA
* * *
53378799 CTAAGCCTACTAGGCACAAAG
62 CGAAGCCCACTAAGCACAAAG
** * * * *
53378820 CCTGA-ATCAATACACTA-GCACTGAGCCTACTAAGTACAAAGCCTGAATCA
1 CCTGATA-CAATACAC-AGGCACAAAGCTTGCTAGGCACAAAGCCTGAATCA
53378870 TTATTTCCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
81 5 0.03
82 171 0.95
83 4 0.02
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (82 bp):
CCTGATACAATACACAGGCACAAAGCTTGCTAGGCACAAAGCCTGAATCAATACACCGACACGAA
GCCCACTAAGCACAAAG
Found at i:53381390 original size:22 final size:25
Alignment explanation
Indices: 53381344--53381390 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
53381334 TTTCTCACCA
*
53381344 TTTTCAACATATACCTATAATCCCT
1 TTTTCAACATATACCTATAAGCCCT
53381369 TTTTC-ACATATA-C-ATAAGCCCT
1 TTTTCAACATATACCTATAAGCCCT
53381391 CAAAAGGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 1 0.05
24 7 0.33
25 5 0.24
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (25 bp):
TTTTCAACATATACCTATAAGCCCT
Found at i:53388195 original size:5 final size:5
Alignment explanation
Indices: 53388185--53388230 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
53388175 TAAGTTTGAC
53388185 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
53388231 CACGAAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:53392862 original size:119 final size:119
Alignment explanation
Indices: 53392651--53392898 Score: 381
Period size: 119 Copynumber: 2.1 Consensus size: 119
53392641 TTAGAAACAG
* * * *
53392651 GGGTCACACAGCTGTATGGTCAGGCCGTGTGACATAGCCCAAATTGTGTGAGCATTCGAAGTATG
1 GGGTCACACGGCTGTATGGCCAGGCCGTGTGACATAGCCCAAACTGTGTGAGCATTCGAAGTATA
*
53392716 GGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAGTGTGGGTATTCGAAATA
66 GGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
*
53392770 GGGTCACACGGCTGTATGGCCAGGTCGTGTGACATAGCCCAAACCT-TGTGAGCATTCGAAGTAT
1 GGGTCACACGGCTGTATGGCCAGGCCGTGTGACATAGCCCAAA-CTGTGTGAGCATTCGAAGTAT
* ** *
53392834 AGGACACATGGCTGTGTTGCAGCCCGTGTGTCTGCCAATGTGGGTATTTGAAATA
65 AGGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
*
53392889 GGGTCGCACG
1 GGGTCACACG
53392899 ATTGTGTCGC
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 116 0.99
120 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (119 bp):
GGGTCACACGGCTGTATGGCCAGGCCGTGTGACATAGCCCAAACTGTGTGAGCATTCGAAGTATA
GGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
Found at i:53402765 original size:21 final size:21
Alignment explanation
Indices: 53402736--53402781 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
53402726 TCTCTCTCGC
*
53402736 TTTCCTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
* *
53402757 TTTCATTTTCTCCTTTTTCTT
1 TTTCATTTTCGCCTTTTTCAT
53402778 TTTC
1 TTTC
53402782 CTCACTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:53425403 original size:14 final size:13
Alignment explanation
Indices: 53425381--53425411 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
53425371 TCAAGTCCCC
53425381 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
53425394 AAAAACAAAAAAGA
1 AAAAA-AAAAAAGA
53425408 AAAA
1 AAAA
53425412 GTAACAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:53432197 original size:18 final size:19
Alignment explanation
Indices: 53432176--53432237 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
53432166 ATTATTTATA
53432176 TTTTATAATAATTTT-ATT
1 TTTTATAATAATTTTAATT
* * *
53432194 TTTTATTATAAATTTTTGACT
1 TTTTATAAT-AA-TTTTAATT
*
53432215 TTTTATAA-ATTTTTAATT
1 TTTTATAATAATTTTAATT
53432233 TTTTA
1 TTTTA
53432238 GAATGTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 19 0.54
19 3 0.09
20 4 0.11
21 9 0.26
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATAATAATTTTAATT
Found at i:53432209 original size:19 final size:18
Alignment explanation
Indices: 53432170--53432209 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53432160 TTTTAAATTA
53432170 TTTATATTTTATAATAAT
1 TTTATATTTTATAATAAT
* *
53432188 TTTATTTTTTATTATAAAT
1 TTTATATTTTATAAT-AAT
53432207 TTT
1 TTT
53432210 TGACTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATTTTATAATAAT
Found at i:53432284 original size:21 final size:21
Alignment explanation
Indices: 53432243--53432286 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
53432233 TTTTAGAATG
* *
53432243 TCAAAATATTTTTTTTATTTT
1 TCAAAAAATTTTATTTATTTT
*
53432264 TCAAAAAATTTTGATTTTTTTT
1 TCAAAAAATTTT-ATTTATTTT
53432286 T
1 T
53432287 ATTTTTTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TCAAAAAATTTTATTTATTTT
Found at i:53442403 original size:40 final size:40
Alignment explanation
Indices: 53442362--53442718 Score: 477
Period size: 40 Copynumber: 8.9 Consensus size: 40
53442352 ACACAGACAA
* *
53442362 AAGCTCATAAGAGCTAATCCAATCGAAACACGCCAAACAA
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
* *
53442402 AAGCTCATAAGAGCTGATCCAA-CTGAAACATGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAATC-GAAACACGCCAAACAG
* *
53442442 AAGCTCATAAGAGTTGATCCAATCGAAACA-GACCAAATAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACG-CCAAACAG
* * *
53442482 AAGCTCATAAGAGCTGATCCAACCAAAACACGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
** * *
53442522 AAGCTCATAATCGCTGATCCAGTCGAAACACGCCACACAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
* * *
53442562 AAGCTCACAAGAGCTGATCCAATCGAAACACACCAAACAA
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
* *
53442602 AAGCTCATAAGAGCTGATCC-AGCTGAAACACGTCAAACAG
1 AAGCTCATAAGAGCTGATCCAATC-GAAACACGCCAAACAG
* *
53442642 AAGCTCATAAGAGCTTATCCAATCGAAACACGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
*
53442682 AAGCTCATAAGAGCTTATCCAATCGAAACACGCCAAA
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAA
53442719 AGAGAGTATA
Statistics
Matches: 280, Mismatches: 31, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
39 4 0.01
40 272 0.97
41 4 0.01
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.15
Consensus pattern (40 bp):
AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
Found at i:53443307 original size:20 final size:20
Alignment explanation
Indices: 53443279--53443323 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
53443269 TAATGTGTCT
*
53443279 TGTCCTAACCAAATTAATTG
1 TGTCTTAACCAAATTAATTG
**
53443299 TGTCTTAACTTAATTAATTG
1 TGTCTTAACCAAATTAATTG
53443319 TGTCT
1 TGTCT
53443324 AGTTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (20 bp):
TGTCTTAACCAAATTAATTG
Found at i:53452170 original size:20 final size:20
Alignment explanation
Indices: 53452147--53452222 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
53452137 TGCATGCAGT
*
53452147 CAGGAGCACCGAAGTGCAAA
1 CAGGGGCACCGAAGTGCAAA
* * **
53452167 CAGGGGCACAGATGTGTGAA
1 CAGGGGCACCGAAGTGCAAA
* *
53452187 TAGGGGCACCAAAGTGCAAA
1 CAGGGGCACCGAAGTGCAAA
* *
53452207 CAGGGACATCGAAGTG
1 CAGGGGCACCGAAGTG
53452223 TAGTCAGGGG
Statistics
Matches: 41, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.34, T:0.11
Consensus pattern (20 bp):
CAGGGGCACCGAAGTGCAAA
Found at i:53452232 original size:40 final size:41
Alignment explanation
Indices: 53452144--53452235 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
53452134 ACATGCATGC
* * * *
53452144 AGTCAGGAGCACCGAAGTGCAAACAGGGGCACAGATGTGTG
1 AGTCAGGGGCACCAAAGTGCAAACAGGGACACAGAAGTGTG
*
53452185 AAT-AGGGGCACCAAAGTGCAAACAGGGACATC-GAAGTGT-
1 AGTCAGGGGCACCAAAGTGCAAACAGGGACA-CAGAAGTGTG
53452224 AGTCAGGGGCAC
1 AGTCAGGGGCAC
53452236 AGTTGCTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.05
40 38 0.88
41 3 0.07
ACGTcount: A:0.34, C:0.20, G:0.35, T:0.12
Consensus pattern (41 bp):
AGTCAGGGGCACCAAAGTGCAAACAGGGACACAGAAGTGTG
Found at i:53458550 original size:101 final size:101
Alignment explanation
Indices: 53458375--53458571 Score: 340
Period size: 101 Copynumber: 2.0 Consensus size: 101
53458365 AAAGAACGTG
*
53458375 TTTTTTTGGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTATAGAAGTGCT
1 TTTTTTTGGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCT
**
53458440 AATCCTGACCTTGCCCGAATCTGGAAAGGAAAGTGT
66 AATCCTGACCTTGCCCGAATCAAGAAAGGAAAGTGT
*
53458476 TTTTTTTGGGATAATCAGTGTTTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCT
1 TTTTTTTGGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCT
* *
53458541 GATCCTGACCTTGCTCGAATCAAGAAAGGAA
66 AATCCTGACCTTGCCCGAATCAAGAAAGGAA
53458572 TTTATGGTAT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (101 bp):
TTTTTTTGGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCT
AATCCTGACCTTGCCCGAATCAAGAAAGGAAAGTGT
Found at i:53460330 original size:21 final size:20
Alignment explanation
Indices: 53460301--53460342 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
53460291 CGAAATGCAG
53460301 TCAAACTAACA-TGAATTAAAT
1 TCAAACTAA-ATTG-ATTAAAT
*
53460322 TCAAGCTAAATTGATTAAAT
1 TCAAACTAAATTGATTAAAT
53460342 T
1 T
53460343 AACCATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (20 bp):
TCAAACTAAATTGATTAAAT
Found at i:53468586 original size:27 final size:27
Alignment explanation
Indices: 53468548--53468600 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
53468538 GATAGATTTT
*
53468548 CCCTATGGAACCTTTGGTGAACTTGTG
1 CCCTATGGAACCCTTGGTGAACTTGTG
*
53468575 CCCTATGGAACCCTTGGTTAACTTGT
1 CCCTATGGAACCCTTGGTGAACTTGT
53468601 AACCAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
CCCTATGGAACCCTTGGTGAACTTGTG
Found at i:53469144 original size:31 final size:31
Alignment explanation
Indices: 53469106--53469166 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
53469096 TAAATTTGTA
53469106 GCAACAAAGTCTTGGACAAAAACATTCATCC
1 GCAACAAAGTCTTGGACAAAAACATTCATCC
*
53469137 GCAACAAAGTCTTGGACAAAAGCATTCATC
1 GCAACAAAGTCTTGGACAAAAACATTCATC
53469167 TTTGATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.20
Consensus pattern (31 bp):
GCAACAAAGTCTTGGACAAAAACATTCATCC
Found at i:53469719 original size:17 final size:17
Alignment explanation
Indices: 53469697--53469731 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53469687 CAATTTCAAA
53469697 ATGAGTAAAACTTGTGG
1 ATGAGTAAAACTTGTGG
53469714 ATGAGTAAAACTTGTGG
1 ATGAGTAAAACTTGTGG
53469731 A
1 A
53469732 AGAATGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
ATGAGTAAAACTTGTGG
Found at i:53474504 original size:44 final size:42
Alignment explanation
Indices: 53474438--53474555 Score: 182
Period size: 43 Copynumber: 2.7 Consensus size: 42
53474428 GAGAGGTAGG
53474438 CAACTTTTTTTTGCGCTCTTTGCTTTTTTTTTAAGATTTTTCT
1 CAACTTTTTTTTGCGCTCTTTGCTTTTTTTTT-AGATTTTTCT
* *
53474481 CAACTCTTTTTTTGCGCTGTTTGCTTTATTTTTAGATTTTTCT
1 CAACT-TTTTTTTGCGCTCTTTGCTTTTTTTTTAGATTTTTCT
*
53474524 CAACTTTTTTTTTGCGCTTTTTGCTTTTTTTT
1 CAAC-TTTTTTTTGCGCTCTTTGCTTTTTTTT
53474556 ATTAACTAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
43 43 0.62
44 26 0.38
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.64
Consensus pattern (42 bp):
CAACTTTTTTTTGCGCTCTTTGCTTTTTTTTTAGATTTTTCT
Found at i:53475178 original size:31 final size:31
Alignment explanation
Indices: 53475085--53475180 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
53475075 GGCAAATTAC
*
53475085 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53475116 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
53475148 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53475179 AA
1 AA
53475181 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:53484970 original size:43 final size:43
Alignment explanation
Indices: 53484904--53484988 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
53484894 GGGAAAAAAC
53484904 TGGCATTTATAGGAAGTGGTATAACCACATTGGACTAGAATAA
1 TGGCATTTATAGGAAGTGGTATAACCACATTGGACTAGAATAA
*
53484947 TGGCATTTATAGGAAGTGTTATAACCACATTGGACTAGAATA
1 TGGCATTTATAGGAAGTGGTATAACCACATTGGACTAGAATA
53484989 CGTTACAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (43 bp):
TGGCATTTATAGGAAGTGGTATAACCACATTGGACTAGAATAA
Found at i:53487098 original size:26 final size:26
Alignment explanation
Indices: 53487069--53487118 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53487059 AATAAAAGAA
*
53487069 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGATTAATTAG
53487095 AACATTCAATATTTCAGATTAATT
1 AACATTCAATATTTCAGATTAATT
53487119 TGCATTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGATTAATTAG
Found at i:53491261 original size:26 final size:26
Alignment explanation
Indices: 53491231--53491280 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53491221 AATAAAAGAA
*
53491231 AACATTCAATATTTCAGTTTAATTAG
1 AACATGCAATATTTCAGTTTAATTAG
53491257 AACATGCAATATTTCAGTTTAATT
1 AACATGCAATATTTCAGTTTAATT
53491281 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATGCAATATTTCAGTTTAATTAG
Found at i:53495491 original size:26 final size:26
Alignment explanation
Indices: 53495462--53495511 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53495452 AATAAAAGAA
*
53495462 AACATTCAATATTTCAGTTTAATTAG
1 AACATGCAATATTTCAGTTTAATTAG
53495488 AACATGCAATATTTCAGTTTAATT
1 AACATGCAATATTTCAGTTTAATT
53495512 TGCATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATGCAATATTTCAGTTTAATTAG
Found at i:53497610 original size:26 final size:26
Alignment explanation
Indices: 53497581--53497630 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53497571 AATAAAAGAA
*
53497581 AACATTCAATATTTCAGTTTAATTAG
1 AACATGCAATATTTCAGTTTAATTAG
53497607 AACATGCAATATTTCAGTTTAATT
1 AACATGCAATATTTCAGTTTAATT
53497631 TGCATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATGCAATATTTCAGTTTAATTAG
Found at i:53499729 original size:26 final size:26
Alignment explanation
Indices: 53499700--53499749 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53499690 AATAAAAGAA
*
53499700 AACATTCAATATTTCAGTTTAATTAG
1 AACATGCAATATTTCAGTTTAATTAG
53499726 AACATGCAATATTTCAGTTTAATT
1 AACATGCAATATTTCAGTTTAATT
53499750 TGCATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATGCAATATTTCAGTTTAATTAG
Found at i:53501848 original size:26 final size:26
Alignment explanation
Indices: 53501819--53501868 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53501809 AATAAAAGAA
*
53501819 AACATTCAATATTTCAGTTTAATTAG
1 AACATGCAATATTTCAGTTTAATTAG
53501845 AACATGCAATATTTCAGTTTAATT
1 AACATGCAATATTTCAGTTTAATT
53501869 TGCATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATGCAATATTTCAGTTTAATTAG
Found at i:53504331 original size:26 final size:26
Alignment explanation
Indices: 53504302--53504351 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53504292 AATGAAAGAA
53504302 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
*
53504328 AACATTCACTATTTCAGTTTAATT
1 AACATTCAATATTTCAGTTTAATT
53504352 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:53506451 original size:26 final size:26
Alignment explanation
Indices: 53506422--53506473 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
53506412 AATAAAAGAA
* *
53506422 AACATTTAGTATTTCAATTTAATTTG
1 AACATTCAATATTTCAATTTAATTTG
*
53506448 AACATTCAATATTTCAGTTTAATTTG
1 AACATTCAATATTTCAATTTAATTTG
53506474 CATTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTTG
Found at i:53509691 original size:5 final size:5
Alignment explanation
Indices: 53509681--53509728 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
53509671 TCCAAATAAG
* *
53509681 TAAAA TAAAA TAAAA TAAAA TAAAG TGATAAA TAAAG TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA T-A-AAA TAAAA T-AAAA TAAAA
53509729 ATTGGGTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 27 0.75
6 6 0.17
7 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:53511063 original size:22 final size:22
Alignment explanation
Indices: 53511035--53511108 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
53511025 TTTCACATTC
53511035 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** * *
53511057 ATCACATATACACTTTCA--CATT
1 ATCACATCGGC-CATT-AGGCCTT
53511079 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
53511102 ATCACAT
1 ATCACAT
53511109 ATACACTTTC
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:53511089 original size:45 final size:45
Alignment explanation
Indices: 53511025--53511130 Score: 203
Period size: 45 Copynumber: 2.4 Consensus size: 45
53511015 NNNNNNNNNN
53511025 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACAC
53511070 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACAC
*
53511115 TTTCACATTCAACACA
1 TTTCACATTCATCACA
53511131 AGCTGTTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (45 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACAC
Found at i:53511447 original size:72 final size:72
Alignment explanation
Indices: 53511361--53511504 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
53511351 CTCATTTTAC
53511361 TGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAATAATAT
1 TGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAATAATAT
53511426 AAATTTT
66 AAATTTT
*
53511433 TGAATTCAAAATGTGTTTTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAATAATAT
1 TGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAATAATAT
53511498 AAATTTT
66 AAATTTT
53511505 ATCTTATAAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (72 bp):
TGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAATAATAT
AAATTTT
Found at i:53513992 original size:27 final size:27
Alignment explanation
Indices: 53513962--53514138 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
53513952 AAATTGTACA
* *
53513962 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
* ** *
53513989 GCACTCAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
53514016 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
53514043 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
53514071 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
53514098 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
53514125 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
53514139 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:53514075 original size:82 final size:81
Alignment explanation
Indices: 53513962--53514117 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
53513952 AAATTGTACA
* * * *
53513962 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
53514026 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
53514043 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
53514108 TGCGAGTTGA
65 TGCGAATTGA
53514118 TTATATAGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.77
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:53514129 original size:82 final size:81
Alignment explanation
Indices: 53513958--53514138 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 81
53513948 GATTAAATTG
* * * * *
53513958 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
53514023 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
53514039 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
53514103 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
53514121 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
53514139 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:53514707 original size:98 final size:98
Alignment explanation
Indices: 53514538--53514735 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 98
53514528 TGTGATAATG
*
53514538 TTGTTGATGGATGGTAGTGCATTGCTTATGACTTACTGAGTTATAAACTCACTCGATGTTTCCTT
1 TTGTTGATAGATGGTAGTGCATTGCTTATGACTTACTGAGTTATAAACTCACTCGATGTTTCCTT
53514603 GTCACCCACTATAGGTTGCTTGGACTCATCTAT
66 GTCACCCACTATAGGTTGCTTGGACTCATCTAT
53514636 TTGTTGATAGATGGTAGTGCATTGCTTATGACTTACTGAGTTATAAACTCACTCGATGTTTCCTT
1 TTGTTGATAGATGGTAGTGCATTGCTTATGACTTACTGAGTTATAAACTCACTCGATGTTTCCTT
53514701 GTCACCCACTATAGGTTGCTTGGACTCATCTAT
66 GTCACCCACTATAGGTTGCTTGGACTCATCTAT
53514734 TT
1 TT
53514736 TTGCGGGGTC
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (98 bp):
TTGTTGATAGATGGTAGTGCATTGCTTATGACTTACTGAGTTATAAACTCACTCGATGTTTCCTT
GTCACCCACTATAGGTTGCTTGGACTCATCTAT
Found at i:53521410 original size:14 final size:15
Alignment explanation
Indices: 53521374--53521411 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53521364 AATTTAAATT
*
53521374 TTTTTTAAATAACGA
1 TTTTTTAAATAACCA
*
53521389 TATTTTAAAT-ACCA
1 TTTTTTAAATAACCA
53521403 TTTTTTAAA
1 TTTTTTAAA
53521412 AAAACTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTTTTAAATAACCA
Found at i:53523582 original size:3 final size:3
Alignment explanation
Indices: 53523576--53523620 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
53523566 TTTTAAGTGA
*
53523576 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AAG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
53523621 CACTTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:53524197 original size:26 final size:26
Alignment explanation
Indices: 53524149--53524198 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
53524139 TATTTACATT
*
53524149 TATATAATTTATTTTATAAAAATAAA
1 TATATAATTTATTTAATAAAAATAAA
*
53524175 TATATAA-TTATTATAATATAAATA
1 TATATAATTTATT-TAATAAAAATA
53524199 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATAATTTATTTAATAAAAATAAA
Found at i:53527403 original size:45 final size:47
Alignment explanation
Indices: 53527303--53527425 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 47
53527293 AAGCTCCTCC
* * ***
53527303 TGAGCTGATAAACAGTAAGCTCTATTGAGCTAAAAATGGTAAGCTCTGT
1 TGAGCTG--AAACAATAAGCTCTTTTGAGCTAAAAATGGTAAGCTCCAA
* *
53527352 TGAGCTG-AGCAATAAGCTCTTTTGAGCT-AAATTGGTAAGCTCCAA
1 TGAGCTGAAACAATAAGCTCTTTTGAGCTAAAAATGGTAAGCTCCAA
* *
53527397 TGAGCTGAAACAGTAAGCTCTTATGAGCT
1 TGAGCTGAAACAATAAGCTCTTTTGAGCT
53527426 GTGGTGAGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
45 20 0.32
46 36 0.57
49 7 0.11
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (47 bp):
TGAGCTGAAACAATAAGCTCTTTTGAGCTAAAAATGGTAAGCTCCAA
Found at i:53529262 original size:10 final size:10
Alignment explanation
Indices: 53529244--53529292 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
53529234 TAAAAGAAAA
*
53529244 GAAATGAGCT
1 GAAACGAGCT
53529254 GAAACGAGCT
1 GAAACGAGCT
53529264 -AAAGTCGAGCT
1 GAAA--CGAGCT
*
53529275 CAAACGAGCT
1 GAAACGAGCT
53529285 GAAACGAG
1 GAAACGAG
53529293 TTCAAGTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.18, G:0.29, T:0.12
Consensus pattern (10 bp):
GAAACGAGCT
Found at i:53531838 original size:152 final size:152
Alignment explanation
Indices: 53531562--53531865 Score: 590
Period size: 152 Copynumber: 2.0 Consensus size: 152
53531552 TGTGAGTAAA
*
53531562 TGCTTGTGTGATAGTTTCATACTTCAATTTGGTCAGTGTATGTGAAAATTATTAGTAGGGACTTA
1 TGCTTGTGTGATAGTTTCATACTTCAATTTGGTCAGTGTATGTGAAAATTAATAGTAGGGACTTA
53531627 TGTGAGACAATGTAGAAATATGCTAGGCAAGTGCTAAAGTGGCCTATTAGTATATGTGGGAAAGT
66 TGTGAGACAATGTAGAAATATGCTAGGCAAGTGCTAAAGTGGCCTATTAGTATATGTGGGAAAGT
53531692 GCTTGTCCTTGCATGTCAAATT
131 GCTTGTCCTTGCATGTCAAATT
53531714 TGCTTGTGTGATAGTTTCATACTTCAATTTGGTCAGTGTATGTGAAAATTAATAGTAGGGACTTA
1 TGCTTGTGTGATAGTTTCATACTTCAATTTGGTCAGTGTATGTGAAAATTAATAGTAGGGACTTA
*
53531779 TGTGAGACAATTTAGAAATATGCTAGGCAAGTGCTAAAGTGGCCTATTAGTATATGTGGGAAAGT
66 TGTGAGACAATGTAGAAATATGCTAGGCAAGTGCTAAAGTGGCCTATTAGTATATGTGGGAAAGT
53531844 GCTTGTCCTTGCATGTCAAATT
131 GCTTGTCCTTGCATGTCAAATT
53531866 AGCCAAACTA
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (152 bp):
TGCTTGTGTGATAGTTTCATACTTCAATTTGGTCAGTGTATGTGAAAATTAATAGTAGGGACTTA
TGTGAGACAATGTAGAAATATGCTAGGCAAGTGCTAAAGTGGCCTATTAGTATATGTGGGAAAGT
GCTTGTCCTTGCATGTCAAATT
Found at i:53534302 original size:47 final size:47
Alignment explanation
Indices: 53534239--53534665 Score: 701
Period size: 47 Copynumber: 9.1 Consensus size: 47
53534229 GAAATGATAG
* *
53534239 TAAGGACTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
53534286 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
53534333 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53534380 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
53534427 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53534474 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53534521 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53534568 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * * *
53534615 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAATGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53534662 TAAG
1 TAAG
53534666 TCCCGAAGGG
Statistics
Matches: 360, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 360 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:53534840 original size:37 final size:37
Alignment explanation
Indices: 53534784--53534862 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
53534774 CCGAGCTCTA
* *
53534784 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
53534821 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53534858 AAGAC
1 AAGAC
53534863 TTCATAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53537443 original size:38 final size:38
Alignment explanation
Indices: 53537392--53537467 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
53537382 GTCAAGTTTC
53537392 CATGGTTCGATTACCTTAAACAACAGTATAGAATGATG
1 CATGGTTCGATTACCTTAAACAACAGTATAGAATGATG
*
53537430 CATGGTTCGATTACCTTAAACAGCAGTATAGAATGATG
1 CATGGTTCGATTACCTTAAACAACAGTATAGAATGATG
53537468 TTCACCGGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (38 bp):
CATGGTTCGATTACCTTAAACAACAGTATAGAATGATG
Found at i:53538767 original size:12 final size:12
Alignment explanation
Indices: 53538752--53538791 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
53538742 CATGTTCATG
53538752 TTCATTTTCTTT
1 TTCATTTTCTTT
*
53538764 TTCAATTTCTTT
1 TTCATTTTCTTT
**
53538776 TTGTTTTTCTTT
1 TTCATTTTCTTT
53538788 TTCA
1 TTCA
53538792 CATGTTGTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (12 bp):
TTCATTTTCTTT
Found at i:53542439 original size:16 final size:16
Alignment explanation
Indices: 53542418--53542448 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53542408 GAAAAAAATC
*
53542418 AAAAAAAATTGATTGA
1 AAAAAAAATTAATTGA
53542434 AAAAAAAATTAATTG
1 AAAAAAAATTAATTG
53542449 TAATTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AAAAAAAATTAATTGA
Found at i:53543404 original size:6 final size:6
Alignment explanation
Indices: 53543395--53543491 Score: 86
Period size: 6 Copynumber: 16.2 Consensus size: 6
53543385 AATGAAAAAT
** * *
53543395 AAGAAA AAGAAA AAGAAA GTGAAG AAGAAA AAGAAA ATGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * ** ** *
53543443 AAGAAA TTGCAA AAGAAA AAGAAA TCGAAA AAGTGA GAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
53543491 A
1 A
53543492 CGAAGAAAAG
Statistics
Matches: 67, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:53543517 original size:18 final size:18
Alignment explanation
Indices: 53543397--53543566 Score: 118
Period size: 18 Copynumber: 9.6 Consensus size: 18
53543387 TGAAAAATAA
*
53543397 GAAAAAGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAATT
* *
53543415 GAAGAAGAAAAAGAAAAT
1 GAAAAAGAAAAAGAAATT
53543433 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
* *
53543451 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATT
** * **
53543469 GAAAAAGTGAGAGAAAAA
1 GAAAAAGAAAAAGAAATT
*
53543487 GAAAACGAAGAAAAGGAAATT
1 G-AAA--AAGAAAAAGAAATT
** *
53543508 GAAAAAGAAATTGAGATT
1 GAAAAAGAAAAAGAAATT
53543526 G----AG-AAAA-AAATT
1 GAAAAAGAAAAAGAAATT
**
53543538 GAAAAAGAAAAAGATGTT
1 GAAAAAGAAAAAGAAATT
*
53543556 GAAAAATAAAA
1 GAAAAAGAAAA
53543567 GAGAGAAAAT
Statistics
Matches: 116, Mismatches: 27, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
12 5 0.04
13 2 0.02
14 2 0.02
16 2 0.02
17 4 0.03
18 86 0.74
19 3 0.03
20 3 0.03
21 9 0.08
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.11
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:53547412 original size:10 final size:10
Alignment explanation
Indices: 53547397--53547458 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
53547387 TTTGAACCAT
*
53547397 TACCAATTCG
1 TACCAATTCA
*
53547407 TACCAAATACCA
1 TACC-AAT-TCA
*
53547419 TACCATTTCA
1 TACCAATTCA
53547429 TACCAATTCCA
1 TACCAATT-CA
* *
53547440 TACCATTTCG
1 TACCAATTCA
53547450 TACCAATTC
1 TACCAATTC
53547459 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:53547442 original size:21 final size:21
Alignment explanation
Indices: 53547397--53547459 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
53547387 TTTGAACCAT
* *
53547397 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
53547419 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
53547440 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
53547460 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:53548642 original size:10 final size:11
Alignment explanation
Indices: 53548620--53548655 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
53548610 GAAGAAGAGG
53548620 AAATTCGAAAAA
1 AAATTC-AAAAA
53548632 AAA-TCAAAAA
1 AAATTCAAAAA
53548642 AAATTCAAAAA
1 AAATTCAAAAA
53548653 AAA
1 AAA
53548656 AAGTGTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.35
11 12 0.52
12 3 0.13
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Done.