Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold157
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: 491920
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.25
Warning! 108800 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:254319 original size:15 final size:15
Alignment explanation
Indices: 254299--254327 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
254289 TACATTTAAA
254299 TTTTTTTTTTTCAAT
1 TTTTTTTTTTTCAAT
254314 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
254328 ACACTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTTTCAAT
Found at i:257132 original size:20 final size:20
Alignment explanation
Indices: 257106--257186 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 20
257096 AATGTCCAAA
257106 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* * *
257126 GTGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACA--T-G--TTTCT
*
257151 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
257171 TTGTATCGATACATGT
1 ATGTATCGATACATGT
257187 ATCGATACAG
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
20 29 0.62
22 1 0.02
23 2 0.04
25 15 0.32
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:257360 original size:20 final size:20
Alignment explanation
Indices: 257317--257362 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
257307 AAATCTTTTG
257317 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
257338 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
257358 CAAAA
1 CAAAA
257363 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:259768 original size:13 final size:13
Alignment explanation
Indices: 259750--259775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
259740 TACACCAAGT
259750 ATGTATCGATACA
1 ATGTATCGATACA
259763 ATGTATCGATACA
1 ATGTATCGATACA
259776 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:259773 original size:32 final size:33
Alignment explanation
Indices: 259732--259795 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
259722 TAGCCAAACT
**
259732 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
259764 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
259796 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:266477 original size:13 final size:13
Alignment explanation
Indices: 266459--266486 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
266449 ATACAAAGAT
266459 CAATGTATCGATA
1 CAATGTATCGATA
266472 CAATGTATCGATA
1 CAATGTATCGATA
266485 CA
1 CA
266487 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:268050 original size:12 final size:12
Alignment explanation
Indices: 268033--268058 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
268023 GTTGTGCATA
268033 AATTTGGTTTAT
1 AATTTGGTTTAT
268045 AATTTGGTTTAT
1 AATTTGGTTTAT
268057 AA
1 AA
268059 CACATAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
AATTTGGTTTAT
Found at i:268726 original size:22 final size:22
Alignment explanation
Indices: 268701--268743 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
268691 GACAAGTCTA
268701 AATGTTTTTC-AAGTAATAAATT
1 AATGTTTTTCAAAGTAA-AAATT
268723 AATGTTTTTCAAAGTAAAAAT
1 AATGTTTTTCAAAGTAAAAAT
268744 ACTTACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (22 bp):
AATGTTTTTCAAAGTAAAAATT
Found at i:268882 original size:33 final size:33
Alignment explanation
Indices: 268844--268907 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
268834 CACCCAGATT
*
268844 TATCAATATAAATTGCTAAGTATCGATACACTG
1 TATCAATACAAATTGCTAAGTATCGATACACTG
**
268877 TATCAATACAAATTGCTTTGTATCGATACAC
1 TATCAATACAAATTGCTAAGTATCGATACAC
268908 CATGAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (33 bp):
TATCAATACAAATTGCTAAGTATCGATACACTG
Found at i:269479 original size:34 final size:34
Alignment explanation
Indices: 269418--269483 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
269408 TAATTCTTGG
* *
269418 AGTGATTGAAAGGTTCTATCTTAGCCTTGAAAGAT
1 AGTGATTGAAAGGTTATACCTTAGCCTT-AAAGAT
* *
269453 AGTG-TTGTAAGGTTATACCTTTGCCTTAAAG
1 AGTGATTGAAAGGTTATACCTTAGCCTTAAAG
269484 GTAATTGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 4 0.15
34 19 0.70
35 4 0.15
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (34 bp):
AGTGATTGAAAGGTTATACCTTAGCCTTAAAGAT
Found at i:270595 original size:78 final size:78
Alignment explanation
Indices: 270461--270663 Score: 210
Period size: 78 Copynumber: 2.6 Consensus size: 78
270451 GAGATAATAA
* * * * *** * *
270461 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCTGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
*
270526 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* *
270539 CGGGATTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
* * * *
270604 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* * *
270618 CGGGGTTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
270664 GATGAAATAA
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
77 1 0.01
78 52 0.51
79 49 0.48
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:270680 original size:28 final size:28
Alignment explanation
Indices: 270621--270689 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
270611 ATAAAGCCGG
** * * *
270621 GGTTGGAGTATCCCCTCGGAAGTAATGG
1 GGTTGGAGTATCCCCGAGGAAATAACGA
*
270649 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
270677 GGTTGGAGTATCC
1 GGTTGGAGTATCC
270690 TTGATTGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:270830 original size:52 final size:52
Alignment explanation
Indices: 270677--271334 Score: 407
Period size: 52 Copynumber: 12.5 Consensus size: 52
270667 GAAATAACGA
** * *
270677 GGTTGGAGTATCCTTGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGT-GTTTTGGAAATAAAATCGG
* * * * *
270729 AGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
* * * * * *
270782 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
*** * *
270834 GGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
* * *** * *
270885 GGTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGG
*
270940 GGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAA-AAATTGGTG--TTTTGGAAATAAAATCGG
* * * * * *
270994 AGTTGGAGTATCCCCGATTAAAGGGAGAATTGGTTTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
* * * * *
271047 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
*** * *
271099 GGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
* * *** * *
271150 GGTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGG
*
271205 GGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAA-AAATTGGTG--TTTTGGAAATAAAATCGG
* * * *
271259 AGTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGTG-TTTTGGAAATAAAATCGG
* * *
271311 AGTTGGAATATCCCCGATTGTGGA
1 GGTTGGAGTATCCCCGATTATGGA
271335 GAATTGAGAA
Statistics
Matches: 464, Mismatches: 98, Indels: 87
0.71 0.15 0.13
Matches are distributed among these distances:
48 10 0.02
49 4 0.01
51 76 0.16
52 146 0.31
53 94 0.20
54 60 0.13
55 48 0.10
56 8 0.02
57 4 0.01
58 12 0.03
59 2 0.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTTGGAAATAAAATCGG
Found at i:270945 original size:27 final size:28
Alignment explanation
Indices: 270882--270957 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
270872 GAAATAAAGT
***
270882 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
270910 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
270937 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
270958 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:271076 original size:265 final size:265
Alignment explanation
Indices: 270570--271334 Score: 1313
Period size: 265 Copynumber: 2.9 Consensus size: 265
270560 AAAATAACGA
* * * *
270570 GGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
* * * * **
270635 CTCGGAAGTAATGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTTGATTGTGA
66 CTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTGTGA
*
270700 A-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGT
130 AGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGT
* * *
270763 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAA
195 TTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
270828 AACCGG
260 AACCGG
270834 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
270899 CTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAA
66 CTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAA
*
270964 GAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAGAATTGGTT
131 GAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTT
271029 TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
196 TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
271094 ACCGG
261 ACCGG
271099 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
271164 CTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAA
66 CTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAA
* *
271229 GAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA--GAAAATTAGTG
131 GAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGT-
* *
271292 TTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
195 TTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGA
271335 GAATTGAGAA
Statistics
Matches: 478, Mismatches: 20, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
263 36 0.08
264 141 0.29
265 301 0.63
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (265 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
CTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAA
GAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTT
TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
ACCGG
Found at i:271210 original size:27 final size:28
Alignment explanation
Indices: 271147--271222 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
271137 GAAATAAAGT
***
271147 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
271175 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
271202 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
271223 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:273717 original size:13 final size:13
Alignment explanation
Indices: 273699--273758 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
273689 CAAAGAATAG
273699 ATGTATCGATACA
1 ATGTATCGATACA
*
273712 ATGTATTGATACA
1 ATGTATCGATACA
* *
273725 AAG-A---ATA-G
1 ATGTATCGATACA
273733 ATGTATCGATACA
1 ATGTATCGATACA
273746 ATGTATCGATACA
1 ATGTATCGATACA
273759 CAGAAAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.05
9 4 0.11
12 4 0.11
13 27 0.73
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:273723 original size:34 final size:34
Alignment explanation
Indices: 273678--273778 Score: 168
Period size: 34 Copynumber: 3.0 Consensus size: 34
273668 AACTTCCTAG
273678 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAATAGATGTATCGATACA
*
273712 ATGTATTGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAATAGATGTATCGATACA
* *
273746 ATGTATCGATACACAGAA-AAATGTATCGATACA
1 ATGTATCGATACAAAGAATAGATGTATCGATACA
273779 TTCCCTTGGC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 14 0.22
34 49 0.78
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (34 bp):
ATGTATCGATACAAAGAATAGATGTATCGATACA
Found at i:273822 original size:19 final size:17
Alignment explanation
Indices: 273796--273930 Score: 114
Period size: 19 Copynumber: 8.2 Consensus size: 17
273786 GGCAGTAGCT
273796 AATTATGTATCGATACA
1 AATTATGTATCGATACA
273813 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
273831 -A-T-TGTATCGATACA
1 AATTATGTATCGATACA
273845 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
273863 -A-T-TGTATCGATACA
1 AATTATGTATCGATACA
273877 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
273895 -A-T-TGTATCGATACA
1 AATTATGTATCGATACA
273909 ACATTTATGTATCGATACA
1 A-A-TTATGTATCGATACA
273928 AAT
1 AAT
273931 CGCTGAAATT
Statistics
Matches: 98, Mismatches: 0, Indels: 40
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.34
14 3 0.03
16 6 0.06
17 2 0.02
18 5 0.05
19 49 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (17 bp):
AATTATGTATCGATACA
Found at i:273838 original size:13 final size:13
Alignment explanation
Indices: 273820--273908 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
273810 ACAATACTTA
273820 TGTATCGATACAT
1 TGTATCGATACAT
273833 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
273851 ATGTATCGATACAT
1 -TGTATCGATACAT
273865 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
273883 ATGTATCGATACAT
1 -TGTATCGATACAT
273897 TGTATCGATACA
1 TGTATCGATACA
273909 ACATTTATGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
14 2 0.03
16 4 0.06
18 2 0.03
19 22 0.34
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:273842 original size:32 final size:32
Alignment explanation
Indices: 273801--273927 Score: 236
Period size: 32 Copynumber: 4.0 Consensus size: 32
273791 TAGCTAATTA
273801 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
273833 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
273865 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
* *
273897 TGTATCGATACAACATTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
273928 AATCGCTGAA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 93 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:282913 original size:61 final size:61
Alignment explanation
Indices: 282803--283070 Score: 233
Period size: 61 Copynumber: 4.4 Consensus size: 61
282793 AACCACCCTT
* *
282803 CTTGACTATATTC-GATCAAGACCTTCCTCATTTGATTGTATTCGGTCAAATTTCACCCTCG
1 CTTGACTATATTCAG-TCAAGACCTTCCTCATTTGAATGTATTCGATCAAATTTCACCCTCG
* * * * * *
282864 CTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTCGATCAAATCTT-ACCC-CT
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGAATGTATTCGATCAAAT-TTCACCCTCG
* ** *
282924 CTTGACTGTATTTGGTCAAGACCTTCCTCATTTGACTGTATTC-AGTCAAATTTCACCCTCG
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGAATGTATTCGA-TCAAATTTCACCCTCG
* * * * * * * * *
282985 CTTGACTGTATTCAGTCAAGTCTTTCTTCGTTTGACTGTACTC-AGTCAAATTTTACCC-CT
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGAATGTATTCGA-TCAAATTTCACCCTCG
* * * *
283045 CTTCATTGTATTCGGTCAAGACCTTC
1 CTTGACTATATTCAGTCAAGACCTTC
283071 ATCAGTATTC
Statistics
Matches: 170, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
59 3 0.02
60 67 0.39
61 97 0.57
62 3 0.02
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (61 bp):
CTTGACTATATTCAGTCAAGACCTTCCTCATTTGAATGTATTCGATCAAATTTCACCCTCG
Found at i:282972 original size:30 final size:30
Alignment explanation
Indices: 282804--283033 Score: 107
Period size: 30 Copynumber: 7.6 Consensus size: 30
282794 ACCACCCTTC
* *
282804 TTGACTATATTC-GATCAAGACCTTCCTCAT
1 TTGACTGTATTCAG-TCAAGACTTTCCTCAT
* * **
282834 TTGATTGTATTCGGTCAA-A-TTTCACCCTCGC
1 TTGACTGTATTCAGTCAAGACTTT---CCTCAT
* * *
282865 TTGACTATATTCAGTCAAGTCTTTCCTCAA
1 TTGACTGTATTCAGTCAAGACTTTCCTCAT
* * * * *
282895 TTAAATGTACTC-GATCAA-ATCTTACC-CCT
1 TTGACTGTATTCAG-TCAAGA-CTTTCCTCAT
** *
282924 CTTGACTGTATTTGGTCAAGACCTTCCTCAT
1 -TTGACTGTATTCAGTCAAGACTTTCCTCAT
**
282955 TTGACTGTATTCAGTCAA-A-TTTCACCCTCGC
1 TTGACTGTATTCAGTCAAGACTTT---CCTCAT
* * *
282986 TTGACTGTATTCAGTCAAGTCTTTCTTCGT
1 TTGACTGTATTCAGTCAAGACTTTCCTCAT
*
283016 TTGACTGTACTCAGTCAA
1 TTGACTGTATTCAGTCAA
283034 ATTTTACCCC
Statistics
Matches: 148, Mismatches: 35, Indels: 34
0.68 0.16 0.16
Matches are distributed among these distances:
28 4 0.03
29 4 0.03
30 88 0.59
31 46 0.31
33 6 0.04
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (30 bp):
TTGACTGTATTCAGTCAAGACTTTCCTCAT
Found at i:283025 original size:121 final size:121
Alignment explanation
Indices: 282797--283070 Score: 397
Period size: 121 Copynumber: 2.3 Consensus size: 121
282787 ACCGAAAACC
* * * * *
282797 ACCCTTCTTGACTATATTCGATCAAGACCTTCCTCATTTGATTGTATTCGGTCAAATTTCACCCT
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCT
282862 CGCTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTC-GATCAAATCTT
66 CGCTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTCAG-TCAAATCTT
*
282918 ACCCCTCTTGACTGTATTTGGTCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCT
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCT
* * ** * * *
282983 CGCTTGACTGTATTCAGTCAAGTCTTTCTTCGTTTGACTGTACTCAGTCAAATTTT
66 CGCTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTCAGTCAAATCTT
* *
283039 ACCCCTCTTCATTGTATTCGGTCAAGACCTTC
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTC
283071 ATCAGTATTC
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
121 135 0.99
122 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (121 bp):
ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCT
CGCTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTCAGTCAAATCTT
Found at i:283080 original size:23 final size:23
Alignment explanation
Indices: 283052--283097 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
283042 CCTCTTCATT
283052 GTATTCGGTCAAGACCTTCATCA
1 GTATTCGGTCAAGACCTTCATCA
283075 GTATTCGGTCAAGACCTTCATCA
1 GTATTCGGTCAAGACCTTCATCA
283098 TTGGATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
GTATTCGGTCAAGACCTTCATCA
Found at i:283215 original size:30 final size:28
Alignment explanation
Indices: 283179--283288 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 28
283169 CTTGACCCCT
*
283179 TTTGACTGTATTCGGTCAATTCCTTTCTCG
1 TTTGACTGTACTCGGTCAA-T-CTTTCTCG
* * * *
283209 TTTGACTGTACTAGGTCGAATCTTGCCCCC
1 TTTGACTGTACTCGGTC-AATCTT-TCTCG
* * *
283239 TCTTAACTGTATTCAGTCAAGTCTTTCCTCG
1 T-TTGACTGTACTCGGTCAA-TCTTT-CTCG
283270 TTTGACTGTACTCGGTCAA
1 TTTGACTGTACTCGGTCAA
283289 AATTTATCGC
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
29 3 0.05
30 36 0.60
31 21 0.35
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (28 bp):
TTTGACTGTACTCGGTCAATCTTTCTCG
Found at i:283270 original size:61 final size:61
Alignment explanation
Indices: 283169--283286 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 61
283159 TTTGACTGTA
* * * *
283169 CTTGACCCCTTTTGACTGTATTCGGTCAATTCCTTTCTCGTTTGACTGTACTAGGTCGAAT
1 CTTGACCCCTCTTAACTGTATTCAGTCAAGTCCTTTCTCGTTTGACTGTACTAGGTCGAAT
* *
283230 CTTGCCCCCTCTTAACTGTATTCAGTCAAGT-CTTTCCTCGTTTGACTGTACTCGGTC
1 CTTGACCCCTCTTAACTGTATTCAGTCAAGTCCTTT-CTCGTTTGACTGTACTAGGTC
283287 AAAATTTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 4 0.08
61 46 0.92
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (61 bp):
CTTGACCCCTCTTAACTGTATTCAGTCAAGTCCTTTCTCGTTTGACTGTACTAGGTCGAAT
Found at i:283408 original size:120 final size:118
Alignment explanation
Indices: 283182--283516 Score: 325
Period size: 120 Copynumber: 2.8 Consensus size: 118
283172 GACCCCTTTT
* ** * * * * * * *
283182 GACTGTATTCGGTCAATTCCTTTCTCGTTTGACTGTACTAGGTCGAATCTTGCCCCCTCTTAACT
1 GACTGTATTCGGACAAAACCTTCCTCATTTGACTGTATTCGATCAAAT-TT-CACCCTCTTAA-T
** * *
283247 GTATTCAGTCAAGTCTTTCCTCGTTTGACTGTACTCGGTCAAAAT-TTATCGCTCTC
63 GTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTCAGTC-AAATCTTATCCCTCTC
* *
283303 GACTGTATTC-TATTAAAACCTTCCTCATTTGACTGTATTC-AGTCAAATTTCACCCTCGCTTAA
1 GACTGTATTCGGA-CAAAACCTTCCTCATTTGACTGTATTCGA-TCAAATTTCACCCT--CTTAA
* * * * *
283366 TGTATTTAGTCAAGTCTTTCCTTATTTGATTGTTCTCAGTCAAATCTTATCCCTTTT
62 TGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTCAGTCAAATCTTATCCCTCTC
* * * *
283423 GACTGTATTCGGACAAAACCTTCCTCTTTTGACTGTATTCGATCAAATTTTACCCTATTCGACTG
1 GACTGTATTCGGACAAAACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCTCTT--AATG
*
283488 TATTCAGTCAAGTCTTTCTTTATTTGACT
64 TATTCAGTCAAGTCTTTCCTTATTTGACT
283517 ACACTTGATC
Statistics
Matches: 175, Mismatches: 30, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
118 2 0.01
119 9 0.05
120 122 0.70
121 42 0.24
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (118 bp):
GACTGTATTCGGACAAAACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCTCTTAATGTA
TTCAGTCAAGTCTTTCCTTATTTGACTGTACTCAGTCAAATCTTATCCCTCTC
Found at i:283430 original size:60 final size:60
Alignment explanation
Indices: 283244--283565 Score: 166
Period size: 60 Copynumber: 5.4 Consensus size: 60
283234 CCCCCTCTTA
** * * * *
283244 ACTGTATTCAGTCAAGTCTTTCCTCGTTTGACTGTACTCGGTCAAAAT-TTATCGCT-CTCG
1 ACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTATTCGATC-AAATCTTA-CCCTATTCG
* ** * * *
283304 ACTGTATTCTA-TTAAAACCTTCCTCATTTGACTGTATTC-AGTCAAAT-TTCACCCTCGCTT--
1 ACTGTATTC-AGTCAAGTCTTTCCTTATTTGACTGTATTCGA-TCAAATCTT-ACCCT--ATTCG
* * * *
283364 AATGTATTTAGTCAAGTCTTTCCTTATTTGATTGT-TCTC-AGTCAAATCTTATCCCT-TTTG
1 ACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTAT-TCGA-TCAAATCTTA-CCCTATTCG
* * ** * *
283424 ACTGTATTCGGACAAAACCTTCCTCT-TTTGACTGTATTCGATCAAATTTTACCCTATTCG
1 ACTGTATTCAGTCAAGTCTTTCCT-TATTTGACTGTATTCGATCAAATCTTACCCTATTCG
* ** * **
283484 ACTGTATTCAGTCAAGTCTTTCTTTATTTGACTACACTT-GATCAAATCTTGCCTCGCTT-G
1 ACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTA-TTCGATCAAATCTTACC-CTATTCG
* *
283544 ATTGTATTCAGTCAAGCCTTTC
1 ACTGTATTCAGTCAAGTCTTTC
283566 TTCACCTGCC
Statistics
Matches: 202, Mismatches: 41, Indels: 38
0.72 0.15 0.14
Matches are distributed among these distances:
58 2 0.01
59 16 0.08
60 168 0.83
61 15 0.07
62 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (60 bp):
ACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTATTCGATCAAATCTTACCCTATTCG
Found at i:285087 original size:20 final size:20
Alignment explanation
Indices: 285062--285128 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
285052 GCCAGTTTCA
285062 TGTATCGATACAATTGAGTG
1 TGTATCGATACAATTGAGTG
285082 TGTATCGATAC-A---A---
1 TGTATCGATACAATTGAGTG
285095 TGTATCGATACAATTGAGTG
1 TGTATCGATACAATTGAGTG
285115 TGTATCGATACAAT
1 TGTATCGATACAAT
285129 GTATCGATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 25 0.62
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAATTGAGTG
Found at i:285100 original size:13 final size:13
Alignment explanation
Indices: 285082--285108 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
285072 CAATTGAGTG
285082 TGTATCGATACAA
1 TGTATCGATACAA
285095 TGTATCGATACAA
1 TGTATCGATACAA
285108 T
1 T
285109 TGAGTGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:285103 original size:33 final size:33
Alignment explanation
Indices: 285061--285139 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
285051 TGCCAGTTTC
285061 ATGTATCGATACAATTGAGTGTGTATCGATACA
1 ATGTATCGATACAATTGAGTGTGTATCGATACA
285094 ATGTATCGATACAATTGAGTGTGTATCGATACA
1 ATGTATCGATACAATTGAGTGTGTATCGATACA
285127 ATGTATCGATACA
1 ATGTATCGATACA
285140 GAGCATAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAATTGAGTGTGTATCGATACA
Found at i:285133 original size:13 final size:13
Alignment explanation
Indices: 285115--285139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
285105 CAATTGAGTG
285115 TGTATCGATACAA
1 TGTATCGATACAA
285128 TGTATCGATACA
1 TGTATCGATACA
285140 GAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:285921 original size:13 final size:13
Alignment explanation
Indices: 285903--285959 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
285893 CATAAAGTGT
285903 TGTATCGATACAA
1 TGTATCGATACAA
285916 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
285931 GTGTTGTATTGATACAA
1 ----TGTATCGATACAA
285948 TGTATCGATACA
1 TGTATCGATACA
285960 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:285938 original size:32 final size:32
Alignment explanation
Indices: 285883--285983 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
285873 TTCAACGATT
285883 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
285916 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
285948 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
285980 TGTA
1 TGTA
285984 AGCTACTACC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 52 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:285972 original size:19 final size:18
Alignment explanation
Indices: 285881--285978 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
285871 ATTTCAACGA
285881 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
285900 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
285916 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
285932 TGTTGTATTGATAC--AA-
1 T-TTGTATCGATACATAAG
285948 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
285964 TTTTGTATCGATACA
1 -TTTGTATCGATACA
285979 ATGTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 23 0.36
20 12 0.19
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:286004 original size:65 final size:65
Alignment explanation
Indices: 285883--286011 Score: 147
Period size: 65 Copynumber: 2.0 Consensus size: 65
285873 TTCAACGATT
* *** *
285883 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTAGCGATACATAAGAAATGTATCGATACAA
* *
285948 TGTATCGATACAT-AAGTTTTGTATCGATACAATGTAAGCTACTACCA-AA-AAATGTATCGATA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGT-AGCGA-TA-CATAAGAAATGTATCGATA
286010 CA
63 CA
286012 CTACACAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
64 21 0.39
65 27 0.50
66 4 0.07
67 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (65 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAATGTAGCGATACATAAGAAATGTATCGATACAA
Found at i:286182 original size:52 final size:52
Alignment explanation
Indices: 286055--286183 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
286045 CACTAATCTT
* * *
286055 TGTATCGATACATGTAGGTAAATCTGCCCAGAAGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATAAAA
* * * * *
286107 TGTATTGATACATACAGACAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATAAAA
286159 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
286184 TCATATTTCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATAAAA
Found at i:295763 original size:33 final size:33
Alignment explanation
Indices: 295720--295786 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
295710 CTGGGCATAA
* *
295720 TGTATAGATACAATT-CTTCATGTATCAATACAT
1 TGTATAGATAC-ATTGCTCCATGCATCAATACAT
* *
295753 TGTATCGATACATTGCTCCATGCATCGATACAT
1 TGTATAGATACATTGCTCCATGCATCAATACAT
295786 T
1 T
295787 TCACTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (33 bp):
TGTATAGATACATTGCTCCATGCATCAATACAT
Found at i:295852 original size:13 final size:13
Alignment explanation
Indices: 295834--295893 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
295824 ACAATTGAGT
295834 ATGTATCGATACA
1 ATGTATCGATACA
295847 ATGTATCGATACA
1 ATGTATCGATACA
*
295860 A---AGCG-T--A
1 ATGTATCGATACA
295867 ATGTATCGATACA
1 ATGTATCGATACA
295880 ATGTATCGATACA
1 ATGTATCGATACA
295893 A
1 A
295894 AGCATAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
9 1 0.03
10 6 0.15
11 1 0.03
13 29 0.74
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:295856 original size:33 final size:33
Alignment explanation
Indices: 295814--295912 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
295804 TGCCACTTTC
*
295814 ATGTATCGATACAATTGAGT-ATGTATCGATACA
1 ATGTATCGATACAA-AGAGTAATGTATCGATACA
*
295847 ATGTATCGATACAAAGCGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
295880 ATGTATCGATACAAAGCA-TAATGTATCGATACA
1 ATGTATCGATACAAAG-AGTAATGTATCGATACA
295913 TCTGGGTGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
32 3 0.05
33 58 0.95
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:295871 original size:20 final size:19
Alignment explanation
Indices: 295846--295912 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
295836 GTATCGATAC
295846 AATGTATCGATACAAAGCGT
1 AATGTATCGATACAAAGC-T
295866 AATGTATCGAT----A-C-
1 AATGTATCGATACAAAGCT
295879 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGC-T
295899 AATGTATCGATACA
1 AATGTATCGATACA
295913 TCTGGGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 25 0.62
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAAAGCT
Found at i:298710 original size:28 final size:28
Alignment explanation
Indices: 298678--298740 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
298668 AAGCAAGATC
* *
298678 AAGGAAATGAAATCAA-CAAGAAATATGA
1 AAGGAAACGAAAT-AAGCAAGAAATATCA
*
298706 AAGGAAACGAAATAAGCAAGAAATTTCA
1 AAGGAAACGAAATAAGCAAGAAATATCA
298734 AAGGAAA
1 AAGGAAA
298741 AAAATCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.60, C:0.08, G:0.19, T:0.13
Consensus pattern (28 bp):
AAGGAAACGAAATAAGCAAGAAATATCA
Found at i:298914 original size:2 final size:2
Alignment explanation
Indices: 298907--298932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
298897 GAATTCTAGA
298907 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
298933 TTTTTATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:300545 original size:28 final size:28
Alignment explanation
Indices: 300494--300560 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
300484 AAAATCAGGA
** * **
300494 TTGGAGTATCCCCTCGGAAGTAACGGGG
1 TTGGAGTATCCCCGAGGAAATAACAAGG
*
300522 TTGGAGTATCCCCGATGAAATAACAAGG
1 TTGGAGTATCCCCGAGGAAATAACAAGG
300550 TTGGAGTATCC
1 TTGGAGTATCC
300561 TCGACTGTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (28 bp):
TTGGAGTATCCCCGAGGAAATAACAAGG
Found at i:300611 original size:52 final size:51
Alignment explanation
Indices: 300548--300933 Score: 217
Period size: 52 Copynumber: 7.4 Consensus size: 51
300538 GAAATAACAA
* * * * * *
300548 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTACTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAACCGG
* * * * * * *
300600 AGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
300652 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * **
300704 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** * **** * *
300755 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT--AGTGTTTTGGA-AATAAAACCGG
* * *
300810 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAACCGG
* * * *
300864 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
300915 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
300934 TTGGAGAATT
Statistics
Matches: 256, Mismatches: 58, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 72 0.28
52 93 0.36
53 26 0.10
54 24 0.09
55 18 0.07
56 7 0.03
57 2 0.01
58 6 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:300761 original size:51 final size:52
Alignment explanation
Indices: 300640--300769 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
300630 GGTGTTTCGA
* * * *
300640 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * *
300692 CAATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
**
300743 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
300770 TCGGAAATAA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 36 0.55
52 29 0.45
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:300816 original size:27 final size:26
Alignment explanation
Indices: 300752--300827 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
300742 GAAATAAAGT
300752 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
300780 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
300807 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
300828 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:303320 original size:13 final size:13
Alignment explanation
Indices: 303302--303327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303292 ACAAAGATCC
303302 ATGTATCGATACA
1 ATGTATCGATACA
303315 ATGTATCGATACA
1 ATGTATCGATACA
303328 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:303323 original size:33 final size:33
Alignment explanation
Indices: 303281--303347 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
303271 AAAATTTCCA
***
303281 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
303314 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
303347 A
1 A
303348 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:303391 original size:19 final size:18
Alignment explanation
Indices: 303367--303434 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
303357 CAGTAGCTAA
303367 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
303386 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
303401 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
303418 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
303435 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:303407 original size:13 final size:13
Alignment explanation
Indices: 303389--303413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303379 ACAATACTTA
303389 TGTATCGATACAT
1 TGTATCGATACAT
303402 TGTATCGATACA
1 TGTATCGATACA
303414 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:303411 original size:32 final size:32
Alignment explanation
Indices: 303370--303432 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
303360 TAGCTAATTA
*
303370 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
303402 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
303433 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:304140 original size:55 final size:55
Alignment explanation
Indices: 304056--305008 Score: 1435
Period size: 55 Copynumber: 17.3 Consensus size: 55
304046 ATAAACTGTA
* * * * * *
304056 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
304111 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
304166 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
304221 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
304276 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
304331 TCCTACTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
304386 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTTTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
304441 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
304496 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
304551 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
304606 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * * *
304661 TCCTCCTCTTTAAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
304716 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
304771 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
304826 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
304881 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
304936 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
304991 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
305009 AAAAAGCAGA
Statistics
Matches: 831, Mismatches: 50, Indels: 34
0.91 0.05 0.04
Matches are distributed among these distances:
54 24 0.03
55 783 0.94
56 24 0.03
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:304220 original size:29 final size:28
Alignment explanation
Indices: 304130--304990 Score: 152
Period size: 28 Copynumber: 31.2 Consensus size: 28
304120 TTGAGGACTG
304130 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** *
304158 GAAAGGTGTCCTGC-TCTT-TG-GGGAATG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
304185 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
304213 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
304241 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
**** * * **
304268 GAAAGGTGTCC-TGTTCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
304296 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* * * *
304323 AAGAGGTGTCCTA-C-TCTT-TGAGGAC-TG
1 AA-AGGTG-CC-ACCAACTTGTGTGGGCTTT
* *
304350 GAAGGCGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
304378 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
*
304405 AAAGGTGCCACCAACTTTTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
304433 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
304461 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
304488 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
304515 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
304543 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
304571 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
304598 GAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
304626 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* * ** * *
304653 AAGAGGTGTCCTCC-TCTT-TAAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
304680 GAAGGCGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
304708 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
304735 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
304763 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
304790 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* * * **
304818 AAGAGGTGTCCTA-C-TCTT-TGAGGACTGG
1 AA-AGGTG-CC-ACCAACTTGTGTGGGCTTT
* *
304846 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
304873 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
304900 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
304928 AAGAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
304955 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
304983 AAGAGGTG
1 AA-AGGTG
304991 TCCTGCTCTT
Statistics
Matches: 553, Mismatches: 190, Indels: 178
0.60 0.21 0.19
Matches are distributed among these distances:
24 2 0.00
25 45 0.08
26 106 0.19
27 116 0.21
28 130 0.24
29 107 0.19
30 45 0.08
31 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:305995 original size:1 final size:1
Alignment explanation
Indices: 305991--306042 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
305981 CTTTTCTCTC
* * * * **
305991 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTGCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
306043 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:306015 original size:13 final size:13
Alignment explanation
Indices: 305992--306039 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
305982 TTTTCTCTCT
305992 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
*
306006 TTTTTTTGTTTTT
1 TTTTTTTGTTTTG
*
306019 TTTTTTTTTTTTG
1 TTTTTTTGTTTTG
306032 CTTTTTTT
1 -TTTTTTT
306040 TTTAAGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:306042 original size:18 final size:18
Alignment explanation
Indices: 305991--306042 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
305981 CTTTTCTCTC
* *
305991 TTTTT-CTTTGTTTTGTT
1 TTTTTGCTTTTTTTTTTT
*
306008 TTTTTGTTTTTTTTTTTT
1 TTTTTGCTTTTTTTTTTT
306026 TTTTTGCTTTTTTTTTT
1 TTTTTGCTTTTTTTTTT
306043 AAGAGAAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTTT
Found at i:318548 original size:80 final size:79
Alignment explanation
Indices: 318430--318637 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 79
318420 GAGATAATAA
* * * * * * *
318430 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
318495 -TTAGAAAAAAAAAAT
65 TTTAG-AAAAAAAAAC
* *
318510 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
318575 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
318589 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
318638 GAAATAACAA
Statistics
Matches: 108, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 51 0.47
80 57 0.53
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:318645 original size:28 final size:28
Alignment explanation
Indices: 318589--318660 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
318579 GGAATAAAGC
** *
318589 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
318617 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
318645 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
318661 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:318713 original size:52 final size:51
Alignment explanation
Indices: 318648--319033 Score: 217
Period size: 52 Copynumber: 7.4 Consensus size: 51
318638 GAAATAACAA
* * * * * *
318648 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAACCGG
* * * * * * *
318700 AGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
318752 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * **
318804 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** * **** * *
318855 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT--AGTGTTTTGGA-AATAAAACCGG
* * *
318910 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAACCGG
* * * *
318964 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
319015 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
319034 GTGGAGAATT
Statistics
Matches: 256, Mismatches: 58, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 72 0.28
52 93 0.36
53 26 0.10
54 24 0.09
55 18 0.07
56 7 0.03
57 2 0.01
58 6 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:318861 original size:51 final size:52
Alignment explanation
Indices: 318740--318869 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
318730 GGTGTTTCGA
* * * *
318740 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * *
318792 CAATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
**
318843 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
318870 TCGGAAATAA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 36 0.55
52 29 0.45
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:318875 original size:263 final size:263
Alignment explanation
Indices: 318538--319038 Score: 776
Period size: 263 Copynumber: 1.9 Consensus size: 263
318528 TCGAAAATAA
* * * *
318538 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* *
318603 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG--ATCAACAAGGTTGGAGTATCCCCGACT
*
318667 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTAAAGGAAAATT
129 GTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATT
* * *
318730 GGTGT-TTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCA
193 AGTGTCTT-GAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCA
318794 ATAAAAC
257 ATAAAAC
* *
318801 CGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
** *
318866 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACGGGGTTGGAGTATCCCCGATTGT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGT
* *
318931 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGT
131 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
*
318996 GTCTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
196 GTCTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
319039 GAATTGAGAA
Statistics
Matches: 216, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 148 0.69
264 41 0.19
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (263 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGT
GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
GTCTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAC
Found at i:318916 original size:27 final size:26
Alignment explanation
Indices: 318852--318927 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
318842 GAAATAAAGT
318852 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
318880 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
318907 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
318928 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:321488 original size:19 final size:18
Alignment explanation
Indices: 321464--321531 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
321454 CAGTAGCTAA
321464 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
321483 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
321498 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
321515 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
321532 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:321504 original size:13 final size:13
Alignment explanation
Indices: 321486--321510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
321476 ACAATACTTA
321486 TGTATCGATACAT
1 TGTATCGATACAT
321499 TGTATCGATACA
1 TGTATCGATACA
321511 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:321508 original size:32 final size:32
Alignment explanation
Indices: 321467--321529 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
321457 TAGCTAATTA
*
321467 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
321499 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
321530 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:321595 original size:21 final size:21
Alignment explanation
Indices: 321569--321644 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
321559 TGGGACCCTA
321569 TATCGATACATTTGTAGAATG
1 TATCGATACATTTGTAGAATG
321590 TATCGATACATTTGT-GAATG
1 TATCGATACATTTGTAGAATG
* *
321610 TATCGATACA-TTCTACAAATG
1 TATCGATACATTTGTA-GAATG
321631 TATCGATACATTTG
1 TATCGATACATTTG
321645 GAATTTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.06
20 15 0.31
21 29 0.59
22 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (21 bp):
TATCGATACATTTGTAGAATG
Found at i:321631 original size:41 final size:40
Alignment explanation
Indices: 321569--321648 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
321559 TGGGACCCTA
* *
321569 TATCGATACATTTGTAGAATGTATCGATACATTTGTGAATG
1 TATCGATACATTTCTAAAATGTATCGATACATTTG-GAATG
321610 TATCGATACA-TTCTACAAATGTATCGATACATTTGGAAT
1 TATCGATACATTTCTA-AAATGTATCGATACATTTGGAAT
321649 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (40 bp):
TATCGATACATTTCTAAAATGTATCGATACATTTGGAATG
Found at i:321929 original size:58 final size:59
Alignment explanation
Indices: 321824--321941 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 59
321814 AACAATAAGC
* * **
321824 CCATAAATATATGCAAATTGGGCTCCACTCTTCTTGGATATGTGAA-TTGAGCTCCAAG
1 CCATAAATATATGCAAATTAGGCTCCACTCTTCTTGGACATACGAATTTGAGCTCCAAG
* * * * *
321882 CCATGAATATATGGAAATTAGGCTTCACTCTTTTTGGACATACGAATTTGGGCTCCAAG
1 CCATAAATATATGCAAATTAGGCTCCACTCTTCTTGGACATACGAATTTGAGCTCCAAG
321941 C
1 C
321942 TTTATTCTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
58 38 0.76
59 12 0.24
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (59 bp):
CCATAAATATATGCAAATTAGGCTCCACTCTTCTTGGACATACGAATTTGAGCTCCAAG
Found at i:322283 original size:50 final size:50
Alignment explanation
Indices: 322208--322467 Score: 405
Period size: 50 Copynumber: 5.2 Consensus size: 50
322198 AGGTATTGCC
* * *
322208 ATTGTTGACTATTCTTCACCAACCTTTGGCAATCGAGAGAGGTGGACATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
** *
322258 ATTGTTGACTATTCTTTGCCAACCTTTGACAATCAAGAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
*
322308 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
* * *
322358 ATTATTGA-TGATTCTTCACCAACCTTTGACAATTGAGAGAGGTGGCCATA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
*
322408 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
322458 ATTGTTGACT
1 ATTGTTGACT
322468 CTAAGCAACT
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 189 0.99
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
Found at i:326204 original size:28 final size:28
Alignment explanation
Indices: 326137--326219 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
326127 TTTTAGAGAT
* *
326137 AATAACGGGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
*
326165 AGTAACTGAGGTTGGAGTATCCCCGATGA
1 AATAAC-GAGGTTGGAGTATCCCCGATGA
*
326194 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
326220 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
27 1 0.02
28 29 0.62
29 17 0.36
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:326263 original size:52 final size:51
Alignment explanation
Indices: 326202--326372 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
326192 GAAATAACGA
* *
326202 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAATCGG
* * * * * * *
326254 TGTTGGAGTATCCCCTGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCC-GATT-ATGAAAAATTAGTATTTTGGAAATAAAATCGG
* * *
326307 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGG
326358 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
326373 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 38 0.39
52 17 0.17
53 34 0.35
54 9 0.09
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGG
Found at i:326392 original size:28 final size:27
Alignment explanation
Indices: 326357--326453 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 27
326347 AATAAAGTCG
326357 GGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGTTGGAGTATCCCCTCGGAAATAAC
* *
326384 AGGGTTGGAGTATTCCCTCGGAAGTAAC
1 -GGGTTGGAGTATCCCCTCGGAAATAAC
* ***
326412 GGGGTTGGAGTATGCCCGATGAAATAAC
1 -GGGTTGGAGTATCCCCTCGGAAATAAC
326440 GAGGTTGGAGTATC
1 G-GGTTGGAGTATC
326454 TTCGATTGTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 1 0.02
28 58 0.98
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCGGAAATAAC
Found at i:326505 original size:52 final size:51
Alignment explanation
Indices: 326443--326577 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 51
326433 AAATAACGAG
** * * * *
326443 GTTGGAGTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGC
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGCA-TTTTGAAAATAAAACCGGC
** * *
326495 GTTGGAGTATCCCCGATTAAAGGAAAATTAGCATTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTAGCATTTTGAAAATAAAACCGGC
326547 GTTGGAGTATCCCCGATTGTGGAAAAATTAG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTAG
326578 TGCTTTAGCG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
52 59 0.87
53 9 0.13
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGCATTTTGAAAATAAAACCGGC
Found at i:326574 original size:240 final size:240
Alignment explanation
Indices: 326137--326670 Score: 785
Period size: 240 Copynumber: 2.2 Consensus size: 240
326127 TTTTAGAGAT
* *
326137 AATAACGGGGTTGGAGTGTTCCCTCAGAAGTAACTGAGGTTGGAGTATCCCCGATGAAATAACGA
1 AATAACGGGGTTGGAGTATTCCCTCAGAAGTAAC-GGGGTTGGAGTATCCCCGATGAAATAACGA
*
326202 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCC
65 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGCGTTGGAGTATCC
* **
326267 CCTGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAA
130 CCTGATTAAAGGAAAATTAGCATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAA
* *
326332 AATCAAT-ATTTTG-GAAATAAAGTCGGGGTTGGAGTATCCC-CTCGGA
195 AATCAATGATTTAGCGAAA-AAACT-GGGGTTGGAGTA-CCCTCTCGGA
* * *
326378 AATAACAGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATGCCCGATGAAATAACGAG
1 AATAACGGGGTTGGAGTATTCCCTCAGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* *
326443 GTTGGAGTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGCGTTGGAGTATCCC
66 GTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGCGTTGGAGTATCCC
*
326508 C-GATTAAAGGAAAATTAGCATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAA
131 CTGATTAAAGGAAAATTAGCATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAT-GAAA
* * * *
326572 AATTAGTGCTTTAGCGATAAAACTGGGGTTGGAGTACCCTCTCGGA
195 AATCAATGATTTAGCGAAAAAACTGGGGTTGGAGTACCCTCTCGGA
*
326618 AATAACGGGGTTGGAGTA-TCCC-CA-ATGATTAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATTCCCTCAGA--AGTAACGGGGTTGGAGTATCCCCGAT
326671 TGTGAAGAAA
Statistics
Matches: 265, Mismatches: 22, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
237 1 0.00
238 1 0.00
239 85 0.32
240 136 0.51
241 39 0.15
242 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (240 bp):
AATAACGGGGTTGGAGTATTCCCTCAGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGCGTTGGAGTATCCC
CTGATTAAAGGAAAATTAGCATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAA
ATCAATGATTTAGCGAAAAAACTGGGGTTGGAGTACCCTCTCGGA
Found at i:326753 original size:52 final size:54
Alignment explanation
Indices: 326654--326777 Score: 182
Period size: 52 Copynumber: 2.3 Consensus size: 54
326644 GATTAACGGG
* * *
326654 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTTGAAAATAAAATCGGA
326708 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTTGAAAATAAAATCGGA
*
326760 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
326778 GTGGAGAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
52 38 0.58
53 8 0.12
54 19 0.29
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (54 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTTGAAAATAAAATCGGA
Found at i:326754 original size:213 final size:212
Alignment explanation
Indices: 326385--326782 Score: 595
Period size: 213 Copynumber: 1.9 Consensus size: 212
326375 GGAAATAACA
* * * *
326385 GGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATGCCCGATGAAATAACGAGGTTGGAG
1 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAG
** *
326450 TATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGCGTTGGAGTATCCCCGATTAA
66 TATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
* *
326515 AGGAAAATTAGCATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTG
131 AGGAAAATTAGCATTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTG
326580 CTTTAGCGATAAAACTG
196 CTTTAGCGATAAAACTG
* *
326597 GGGTTGGAGTA-CCCTCTCGGAAATAACGGGGTTGGAGTATCCCCAATG-ATTAACGGGGTTGGA
1 GGGTTGGAGTATCCC-CTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGA
*
326660 GTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
65 GTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
* ** *
326725 TATA-GAAAATTAGTGTTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
128 TAAAGGAAAATTAG-CATTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
326783 GAATTGAGAA
Statistics
Matches: 166, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
211 30 0.18
212 58 0.35
213 78 0.47
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (212 bp):
GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAG
TATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
AGGAAAATTAGCATTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTG
CTTTAGCGATAAAACTG
Found at i:334148 original size:42 final size:42
Alignment explanation
Indices: 334092--334210 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
334082 TTCTTCTCTC
* * *
334092 CTCCTTCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
334134 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
334176 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
334211 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:334151 original size:12 final size:11
Alignment explanation
Indices: 334125--334200 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
334115 TCTATTATCT
*
334125 CTCCTGTCTCTC
1 CTCCTATCTC-C
334137 CTCCTATCATCC
1 CTCCTATC-TCC
334149 CTCCTATCT--
1 CTCCTATCTCC
*
334158 CTACTATCT--
1 CTCCTATCTCC
*
334167 CTCCTGTCTCTC
1 CTCCTATCTC-C
334179 CTCCTATCATCC
1 CTCCTATC-TCC
*
334191 CTCCTCTCTC
1 CTCCTATCTC
334201 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:334152 original size:24 final size:24
Alignment explanation
Indices: 334116--334201 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
334106 CCTCCTCTCT
* *
334116 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
334140 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
334161 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
334182 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
334202 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:334176 original size:18 final size:18
Alignment explanation
Indices: 334107--334177 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
334097 TCTGTCATCC
* *
334107 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
334125 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
334147 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
334167 CTCCTGTCTCT
1 CTCCTGTCTCT
334178 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:335883 original size:13 final size:13
Alignment explanation
Indices: 335865--335890 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
335855 ACAAAGATCC
335865 ATGTATCGATACA
1 ATGTATCGATACA
335878 ATGTATCGATACA
1 ATGTATCGATACA
335891 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:335886 original size:33 final size:33
Alignment explanation
Indices: 335844--335910 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
335834 AAAATTTCCA
***
335844 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
335877 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
335910 A
1 A
335911 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:335954 original size:19 final size:18
Alignment explanation
Indices: 335930--335997 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
335920 CAGTAGCTAA
335930 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
335949 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
335964 TT-T-TATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
335981 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
335998 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.21
14 1 0.02
15 2 0.05
16 2 0.05
17 2 0.05
18 4 0.09
19 23 0.53
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:335976 original size:32 final size:32
Alignment explanation
Indices: 335935--335995 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
335925 GCTAATTATG
*
335935 TATCGATACAATACTTATGTATCGATACATTT
1 TATCGATACAAAACTTATGTATCGATACATTT
335967 TATCGATACAAAACTTATGTATCGATACA
1 TATCGATACAAAACTTATGTATCGATACA
335996 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTT
Found at i:336878 original size:55 final size:55
Alignment explanation
Indices: 336794--337295 Score: 621
Period size: 55 Copynumber: 9.0 Consensus size: 55
336784 ATAAAGTGTA
* * * *
336794 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGGGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGGG
*
336849 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
** *
336904 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
* * *
336959 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
*
337014 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
* *
337069 TCCTGCTCTTTGGGGACTGAAGAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
** * * *
337124 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAAATTGTGTGGGCTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
** * ** * *
337184 TCCCACTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
* * * *
337243 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
337296 AAAAGGCATC
Statistics
Matches: 403, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
55 298 0.74
56 5 0.01
59 55 0.14
60 45 0.11
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (55 bp):
TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
Found at i:338311 original size:1 final size:1
Alignment explanation
Indices: 338307--338363 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
338297 CTTTTCTCTC
* * * * * **
338307 TTTTTCTTTTTTTGTTTTTTGTTTTTTTTTCTTTTTTTTCTTTTGCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
338364 AAAGAGAAGG
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:338324 original size:31 final size:30
Alignment explanation
Indices: 338289--338363 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
338279 GCTTAAGTAG
338289 GTTTTTTTCTTTTCTCTCTTTTTCTTT-TTTT
1 GTTTTTTT-TTTTCTCTCTTTTT-TTTCTTTT
* *
338320 GTTTTTTGTTTTTTTTTCTTTTTTTTCTTTT
1 GTTTTTT-TTTTTCTCTCTTTTTTTTCTTTT
338351 GCTTTTTTTTTTT
1 G-TTTTTTTTTTT
338364 AAAGAGAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 3 0.08
31 29 0.74
32 7 0.18
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (30 bp):
GTTTTTTTTTTTCTCTCTTTTTTTTCTTTT
Found at i:338325 original size:15 final size:14
Alignment explanation
Indices: 338307--338363 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 14
338297 CTTTTCTCTC
*
338307 TTTTTCTTTTTTTG
1 TTTTTTTTTTTTTG
*
338321 TTTTTTGTTTTTTTT
1 TTTTTT-TTTTTTTG
338336 TCTTTTTTTTCTTTTG
1 T-TTTTTTTT-TTTTG
338352 CTTTTTTTTTTT
1 -TTTTTTTTTTT
338364 AAAGAGAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 13 0.36
16 17 0.47
17 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:338356 original size:25 final size:25
Alignment explanation
Indices: 338290--338361 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
338280 CTTAAGTAGG
* *
338290 TTTTTTTCTTTT-CTCTCTTTTTCT
1 TTTTTTTCTTTTGCTTTTTTTTTCT
*
338314 TTTTTTGTTTTTTG-TTTTTTTTTCT
1 TTTTTT-TCTTTTGCTTTTTTTTTCT
338339 TTTTTTTCTTTTGCTTTTTTTTT
1 TTTTTTTCTTTTGCTTTTTTTTT
338362 TTAAAGAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 12 0.29
25 29 0.71
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (25 bp):
TTTTTTTCTTTTGCTTTTTTTTTCT
Found at i:352036 original size:42 final size:42
Alignment explanation
Indices: 351978--352096 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
351968 TTCTTCTCTC
* * * *
351978 CTCCTCCTGTCGTCCCTCCTCTCTTTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
352020 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
352062 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
352097 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:352037 original size:12 final size:11
Alignment explanation
Indices: 352011--352086 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
352001 TTTATTATCT
*
352011 CTCCTGTCTCTC
1 CTCCTATCTC-C
352023 CTCCTATCATCC
1 CTCCTATC-TCC
352035 CTCCTATCT--
1 CTCCTATCTCC
*
352044 CTACTATCT--
1 CTCCTATCTCC
*
352053 CTCCTGTCTCTC
1 CTCCTATCTC-C
352065 CTCCTATCATCC
1 CTCCTATC-TCC
*
352077 CTCCTCTCTC
1 CTCCTATCTC
352087 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:357484 original size:28 final size:28
Alignment explanation
Indices: 357423--357504 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
357413 TTTTGGAGAT
*
357423 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
357451 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
357479 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
357505 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:357642 original size:51 final size:51
Alignment explanation
Indices: 357487--357656 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 51
357477 GAAATAACGA
* *
357487 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGG
* * * * * *
357539 TGTTGGAGCATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGG
*** *
357591 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
357642 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
357657 TCGGAAATAA
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
51 39 0.39
52 50 0.51
53 10 0.10
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:357674 original size:28 final size:28
Alignment explanation
Indices: 357639--357737 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
357629 GAAATAAAGT
357639 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
* *
357667 CGGGGTTGGAGTATTCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
***
357695 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
*
357723 CGAGGTTGGAGTATC
1 CGGGGTTGGAGTATC
357738 TTCGATTGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAA
Found at i:357789 original size:52 final size:51
Alignment explanation
Indices: 357727--358063 Score: 184
Period size: 52 Copynumber: 6.4 Consensus size: 51
357717 AAATAACGAG
** * * *
357727 GTTGGAGTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCGGA
** * * *
357779 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCGGA
* * * ** *
357831 GTTGGAGTATCCCCGATTGTGAAAAAATTAGTGCTTT-AGCGATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTG-AAAAATTGGAGTTTTGA-AAATAAAACCGGA
* ** ** * *
357883 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGAGT-T--TTGAAAATAAAACCGGA
* * *
357938 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGAG--TTTTGAAAATAAAACCGGA
* * * * *
357992 GTTAGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGAGTTTTGAAAATAAAACCGGA
*
358043 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
358064 GAGAATTGAG
Statistics
Matches: 220, Mismatches: 42, Indels: 46
0.71 0.14 0.15
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 2 0.01
51 37 0.17
52 89 0.40
53 25 0.11
54 27 0.12
55 20 0.09
56 2 0.01
57 5 0.02
58 6 0.03
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCGGA
Found at i:357841 original size:104 final size:103
Alignment explanation
Indices: 357721--358063 Score: 293
Period size: 104 Copynumber: 3.3 Consensus size: 103
357711 CCGATGAAAT
* **
357721 AACGAGGTTGGAGTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
*
357786 TATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAA
66 TATCCCCGATTAAAGGAAAATTGGAGTTTTGAAAATAA
* ** * * *
357824 AACCGGGGTTGGAGTATCCCCGATTGTGAAAAAATTAGTGCTTTAGCG--ATAAAACCGGGGTTG
1 AA-CGGGGTTGGAGTATCCCCGATTGTG-AAAAATTGGTATTTTTG-GAAATAAAATCGGAGTTG
* * ** ** ** *
357887 GAGTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT-T
63 GAGTAT-CCC-C-G-ATTAAAGGAAAATTGGAGT-T--TTGAAAATAA
* *
357932 AACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAG
1 AACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGG
* * *
357997 AGTATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAA
64 AGTATCCCCGATTAAAGGAAAATTGGAGTTTTGAAAATAA
* *
358036 AATCGGAGTTGGAATATCCCCGATTGTG
1 AA-CGGGGTTGGAGTATCCCCGATTGTG
358064 GAGAATTGAG
Statistics
Matches: 182, Mismatches: 40, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.24
105 43 0.24
106 16 0.09
107 36 0.20
108 15 0.08
109 22 0.12
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (103 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
TATCCCCGATTAAAGGAAAATTGGAGTTTTGAAAATAA
Found at i:357842 original size:239 final size:240
Alignment explanation
Indices: 357423--357954 Score: 865
Period size: 239 Copynumber: 2.2 Consensus size: 240
357413 TTTTGGAGAT
*
357423 AATAACGGGGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
*
357488 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGCATCCC
66 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGCATCCC
* *
357553 CGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATG-AAAA
131 CGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAA
* * **
357617 ATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGA
196 ATCAATACTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
357662 AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* *
357727 GTTGGAGTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
66 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGCATCCC
*
357792 CGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAA
131 CGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAA
* * * **
357857 ATTAGTGCTTTAGCGATAAAACCGGGGTTGGAGTATCCCCTCGGA
196 ATCAATACTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
*
357902 AATAACGGGGTTGGAGTA-TCCC-C-GATGATTAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATTCCCTCGGA--AGTAACGGGGTTGGAGTATCCCCGAT
357955 TGTGAAGAAA
Statistics
Matches: 273, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
237 2 0.01
238 1 0.00
239 212 0.78
240 58 0.21
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (240 bp):
AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGCATCCC
CGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAA
ATCAATACTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
Found at i:357942 original size:27 final size:28
Alignment explanation
Indices: 357879--357954 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
357869 GCGATAAAAC
***
357879 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
357907 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
357934 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
357955 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:358034 original size:212 final size:212
Alignment explanation
Indices: 357667--358063 Score: 636
Period size: 212 Copynumber: 1.9 Consensus size: 212
357657 TCGGAAATAA
* *
357667 CGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
** *
357732 AGTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
66 AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATT
* * *
357797 AAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAAATTAG
131 AAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGAAAAAATTAG
357862 TGCTTTAGCGATAAAAC
196 TGCTTTAGCGATAAAAC
* *
357879 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
*
357943 AGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGA
66 AGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGA
* * *
358008 TTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTG
129 TTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTG
358064 GAGAATTGAG
Statistics
Matches: 169, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
211 28 0.17
212 102 0.60
213 39 0.23
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (212 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATT
AAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGAAAAAATTAG
TGCTTTAGCGATAAAAC
Found at i:358038 original size:51 final size:53
Alignment explanation
Indices: 357942--358060 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
357932 AACGGGGTTG
* * *
357942 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
357996 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
358047 GAATATCCCCGATT
1 GAGTATCCCCGATT
358061 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:360449 original size:13 final size:13
Alignment explanation
Indices: 360431--360456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
360421 ACAAAGATCC
360431 ATGTATCGATACA
1 ATGTATCGATACA
360444 ATGTATCGATACA
1 ATGTATCGATACA
360457 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:360452 original size:33 final size:33
Alignment explanation
Indices: 360410--360476 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
360400 AAAATTTCCA
***
360410 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
360443 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
360476 A
1 A
360477 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:360520 original size:19 final size:18
Alignment explanation
Indices: 360496--360563 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
360486 CAGTAGCTAA
360496 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
360515 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
360530 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
360547 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
360564 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:360536 original size:13 final size:13
Alignment explanation
Indices: 360518--360542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
360508 ACAATACTTA
360518 TGTATCGATACAT
1 TGTATCGATACAT
360531 TGTATCGATACA
1 TGTATCGATACA
360543 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:360540 original size:32 final size:32
Alignment explanation
Indices: 360499--360561 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
360489 TAGCTAATTA
*
360499 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
360531 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
360562 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:360625 original size:21 final size:21
Alignment explanation
Indices: 360599--360675 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
360589 GTTGGGACCC
360599 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
*
360620 TGTATCGATACATTCCATAAA
1 TGTATCGATACATTCCACAAA
* *
360641 TGTATCAATACATTCTACAAA
1 TGTATCGATACATTCCACAAA
360662 TGTATCGATACATT
1 TGTATCGATACATT
360676 TGGATAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCCACAAA
Found at i:362670 original size:50 final size:50
Alignment explanation
Indices: 362545--362802 Score: 302
Period size: 50 Copynumber: 5.1 Consensus size: 50
362535 AGGTGTTGCC
* * *
362545 ATTGTTGACCATTCTTCACCAACCTTTGACAATCGAGAGAGGGTGACTGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGA-GGTGGCCGTA
* * * *
362596 ATTGTTAACTATTCTTCACTAACCTTTGACAATCAAAAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
* * *
362646 ATTGTTGACTATTTTTCACCAACCTTTGACAATCGAGAGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
* * * *
362696 ATTGTTGACGATTCTTCACCAATCTTTGATAATTGAGAGAGGTGGTCC-TA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGG-CCGTA
* * * * * *
362746 ATTGTTGACTATTTTTCACAAACTTTTGACAATAGAAAGAAGTGGCCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGG-CCGTA
362797 ATTGTT
1 ATTGTT
362803 AACTCTAAAC
Statistics
Matches: 175, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
50 130 0.74
51 45 0.26
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
Found at i:363040 original size:17 final size:17
Alignment explanation
Indices: 363018--363051 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
363008 TTTACCCATC
363018 AATGCACTAACATATAT
1 AATGCACTAACATATAT
* *
363035 AATGCATTAATATATAT
1 AATGCACTAACATATAT
363052 TTTATAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (17 bp):
AATGCACTAACATATAT
Found at i:366740 original size:51 final size:50
Alignment explanation
Indices: 366683--366850 Score: 196
Period size: 51 Copynumber: 3.3 Consensus size: 50
366673 ATGAAATAAC
*
366683 GGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCG
1 GGGTTGGAGTATCCCCGATT-TGAAAAATTGGTATTTTGGAAATAAAATCG
* ** * *
366734 GTGTTGGAGCCTCCCCGA-TTAAAGGAAATTGGTGTTTT-GAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTTGAA--AAATTGGTATTTTGGAAATAAAATCG
*** *
366784 GGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCG
1 GGGTTGGAGTATCCCCGATT-TGAAAAATTGGTATTTTGGAAATAAAATCG
366835 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
366851 TCGAAATAAC
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
49 3 0.03
50 37 0.38
51 54 0.56
52 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTTGAAAAATTGGTATTTTGGAAATAAAATCG
Found at i:366889 original size:28 final size:27
Alignment explanation
Indices: 366833--366928 Score: 126
Period size: 28 Copynumber: 3.6 Consensus size: 27
366823 GAAATAAAGT
366833 CGGGGTTGGAGTATCCCCTCGAAATAA
1 CGGGGTTGGAGTATCCCCTCGAAATAA
* *
366860 CGGGGTTGGAGTATTCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCTC-GAAATAA
366888 CGGGGTTGGAGTATCCCCGAT-GAAATAA
1 CGGGGTTGGAGTATCCCC--TCGAAATAA
366916 C-GGGTTGG-GTATC
1 CGGGGTTGGAGTATC
366929 TTCGATTGTG
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
26 5 0.08
27 26 0.42
28 30 0.48
30 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCTCGAAATAA
Found at i:367030 original size:50 final size:51
Alignment explanation
Indices: 366952--367082 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
366942 AATTGGTATT
* * *
366952 TTTGGAAATAAAATCGGAGTTGG-G-ATCCCCGATTAAAGAAAATT-G-GC
1 TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGAAAATTAGTGC
***
366999 GTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGC
1 -TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGAAAATTAGTGC
**
367051 TTT-AGCGATAAAACCGGGGTTGGAGTATCCCC
1 TTTGA-AAATAAAACCGGGGTTGGAGTATCCCC
367083 TCGGAAATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
48 20 0.29
49 1 0.01
50 18 0.26
51 29 0.41
52 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (51 bp):
TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGAAAATTAGTGC
Found at i:367071 original size:232 final size:235
Alignment explanation
Indices: 366624--367140 Score: 741
Period size: 232 Copynumber: 2.2 Consensus size: 235
366614 TTTTGGAGAT
* *
366624 AATAACGGTG-TGGAGTGTTCCCTCGGAAGTAACGGGG--GGAGTATCCCCGATGAAATAACGGG
1 AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
* *
366686 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGTGTTGGAGCCTCCCCG
66 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGAGTTGGAGCATCCCCG
* * *
366751 ATTAAAGGAAATTGGTGTTTTGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAAAAATCAA
131 ATTAAAGAAAATTGGCGTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAA
* * **
366816 TATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTC-GA
196 TACTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
366855 AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
1 AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
*
366920 TTGG-GTATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGG-G-ATCCCC
66 TTGGAGTATCCTCGATTGTGAAAAATTGGTA-TTTTGGAAATAAAATCGGAGTTGGAGCATCCCC
* * *
366982 GATTAAAGAAAATTGGCG-TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATT
130 GATTAAAGAAAATTGGCGTTTTG-AAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATC
* * **
367046 AGTGCTTTAGCGATAAAACCGGGGTTGGAGTATCCCCTCGGA
194 AATACTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
*
367088 AATAACGGGGTTGGAGTA-TCCC-C-GATGATTAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATTCCCTCGGA--AGTAACGGGGTTGGAGTATCCCCGAT
367141 TGTGAAGAAT
Statistics
Matches: 258, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
230 2 0.01
231 14 0.05
232 144 0.56
233 46 0.18
234 52 0.20
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (235 bp):
AATAACGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGGG
TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGAGTTGGAGCATCCCCG
ATTAAAGAAAATTGGCGTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAA
TACTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
Found at i:367128 original size:27 final size:28
Alignment explanation
Indices: 367065--367140 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
367055 GCGATAAAAC
***
367065 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
367093 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
367120 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
367141 TGTGAAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:367240 original size:205 final size:205
Alignment explanation
Indices: 366860--367250 Score: 558
Period size: 205 Copynumber: 1.9 Consensus size: 205
366850 CTCGAAATAA
* *
366860 CGGGGTTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGGGTTGGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGGGTTGGG
**
366925 TATCTTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGGATCCCCGATTAAAG
66 TATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGGATCCCCGATTAAAG
* * *
366990 AAAATTGGCGTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGCTTTA
131 AAAATTAGCGTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTAGTGCTTTA
367055 GCGATAAAAC
196 GCGATAAAAC
*
367065 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAAC-GGGTTGG
* * * *
367129 AGTATCCCCGATTGTGAAGAATTGGTGTTTTTTGAAA-AAAATCGGAGTTAGAGTATCCCCGATT
65 -GTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTT-G-GGATCCCCGATT
* * * *
367193 ATAG-AAATTAGTGTTTTGAAAAT-AAATCGGAGTTGGAATAT-CCCGATTGTGGAGAATT
127 AAAGAAAATTAGCG-TTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATT
367251 GAATGAAACT
Statistics
Matches: 165, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
204 5 0.03
205 83 0.50
206 54 0.33
207 23 0.14
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (205 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGGGTTGGG
TATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGGATCCCCGATTAAAG
AAAATTAGCGTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTAGTGCTTTA
GCGATAAAAC
Found at i:369028 original size:17 final size:17
Alignment explanation
Indices: 369006--369040 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
368996 AAATGGAATA
369006 GGTTTTTCTTTGTTTTT
1 GGTTTTTCTTTGTTTTT
* *
369023 GGTTTTTTTTTTTTTTT
1 GGTTTTTCTTTGTTTTT
369040 G
1 G
369041 CTAAAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (17 bp):
GGTTTTTCTTTGTTTTT
Found at i:369581 original size:13 final size:13
Alignment explanation
Indices: 369563--369588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
369553 ACAAAGATCC
369563 ATGTATCGATACA
1 ATGTATCGATACA
369576 ATGTATCGATACA
1 ATGTATCGATACA
369589 CGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:369650 original size:18 final size:17
Alignment explanation
Indices: 369627--369691 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 17
369617 CAGTAGCTAA
369627 TTATGTATCGATACATAC
1 TTATGTATCGATACA-AC
369645 TTATGTATCGATAC-A-
1 TTATGTATCGATACAAC
*
369660 -T-TGTATCGATAAAAAC
1 TTATGTATCGAT-ACAAC
369676 TTATGTATCGATACAA
1 TTATGTATCGATACAA
369692 ATTGTTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 9 0.22
14 2 0.05
15 1 0.03
16 1 0.03
17 4 0.10
18 23 0.57
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (17 bp):
TTATGTATCGATACAAC
Found at i:369668 original size:31 final size:31
Alignment explanation
Indices: 369630--369690 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
369620 TAGCTAATTA
* *
369630 TGTATCGATACATACTTATGTATCGATACAT
1 TGTATCGATAAAAACTTATGTATCGATACAT
369661 TGTATCGATAAAAACTTATGTATCGATACA
1 TGTATCGATAAAAACTTATGTATCGATACA
369691 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
TGTATCGATAAAAACTTATGTATCGATACAT
Done.