Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 39
Found at i:5181960 original size:21 final size:22
Alignment explanation
Indices: 5181920--5181960 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5181910 TTATCATATA
* *
5181920 ATTATATATATTATATATTAAT
1 ATTATATATATTACAAATTAAT
5181942 ATTAT-TATATTACAAATTA
1 ATTATATATATTACAAATTA
5181961 TTACAAGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATATATATTACAAATTAAT
Found at i:5181963 original size:3 final size:3
Alignment explanation
Indices: 5181879--5181953 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
5181869 TCCGAGCTGA
* * * * *
5181879 TAT TAT TA- TAT TGT TAT TAC TAT TAT TAC TAT TAT CA- TAT AAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5181924 TAT ATAT TAT ATAT TAA TAT TAT TA- TAT TA
1 TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TA
5181954 CAAATTATTA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
2 7 0.13
3 41 0.76
4 6 0.11
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:5183393 original size:3 final size:3
Alignment explanation
Indices: 5183385--5183416 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5183375 TATGAAATGA
5183385 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5183417 ATTTTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5186109 original size:41 final size:41
Alignment explanation
Indices: 5186062--5186150 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
5186052 TGAAAGGTAT
5186062 AGAAGAGATTAAAGAAAATGTGTTTTTAGATGAATTTCTGG
1 AGAAGAGATTAAAGAAAATGTGTTTTTAGATGAATTTCTGG
5186103 AGAAGAGATTAAAGAAAATGTGTTTTTAGATGAATTTCTGG
1 AGAAGAGATTAAAGAAAATGTGTTTTTAGATGAATTTCTGG
*
5186144 AAAAGAG
1 AGAAGAG
5186151 TTGATAAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (41 bp):
AGAAGAGATTAAAGAAAATGTGTTTTTAGATGAATTTCTGG
Found at i:5186983 original size:43 final size:41
Alignment explanation
Indices: 5186918--5186998 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
5186908 TACATGTTAT
* * **
5186918 ATGATATGAGATTAAGTGATGAAACATAGATGATATATATATG
1 ATGATATAAGAATAAGACATGAAACA-A-ATGATATATATATG
*
5186961 ATGATATAAGAATAAGACATGAATCAAATGATATATAT
1 ATGATATAAGAATAAGACATGAAACAAATGATATATAT
5186999 GTTTATGTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 11 0.33
42 1 0.03
43 21 0.64
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (41 bp):
ATGATATAAGAATAAGACATGAAACAAATGATATATATATG
Found at i:5187265 original size:22 final size:22
Alignment explanation
Indices: 5187234--5187294 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5187224 TGGTCTACGC
* *
5187234 GGTCCTTCGGGACATATACAGT-
1 GGTCCATCGGGACAAATACA-TA
5187256 GGTCCATCGGGACAAATACATA
1 GGTCCATCGGGACAAATACATA
5187278 GGT-CATTCGGGACAAAT
1 GGTCCA-TCGGGACAAAT
5187295 TTCATATGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.09
22 32 0.91
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (22 bp):
GGTCCATCGGGACAAATACATA
Found at i:5187593 original size:18 final size:17
Alignment explanation
Indices: 5187550--5187596 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
5187540 CAACATATGC
5187550 TTATATGATAAAAATGAA
1 TTAT-TGATAAAAATGAA
*
5187568 TTAGTGATAATAACATG-A
1 TTATTGATAA-AA-ATGAA
5187586 TTATTGATAAA
1 TTATTGATAAA
5187597 TATGTTCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 7 0.28
18 15 0.60
19 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (17 bp):
TTATTGATAAAAATGAA
Found at i:5188040 original size:12 final size:12
Alignment explanation
Indices: 5188006--5188064 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
5187996 TTTTAGCATT
*
5188006 TGGTACTGTAGCA
1 TGGTACTGT-TCA
*
5188019 GGGTACTGTTCA
1 TGGTACTGTTCA
*
5188031 TGGTATTGTTCA
1 TGGTACTGTTCA
5188043 ---TACTGTTCA
1 TGGTACTGTTCA
*
5188052 CGGTACTGTTCA
1 TGGTACTGTTCA
5188064 T
1 T
5188065 ACCATATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
9 8 0.22
12 21 0.57
13 8 0.22
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (12 bp):
TGGTACTGTTCA
Found at i:5188048 original size:21 final size:21
Alignment explanation
Indices: 5188022--5188066 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5188012 TGTAGCAGGG
* *
5188022 TACTGTTCATGGTATTGTTCA
1 TACTGTTCACGGTACTGTTCA
5188043 TACTGTTCACGGTACTGTTCA
1 TACTGTTCACGGTACTGTTCA
5188064 TAC
1 TAC
5188067 CATATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (21 bp):
TACTGTTCACGGTACTGTTCA
Found at i:5188835 original size:2 final size:2
Alignment explanation
Indices: 5188828--5188871 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5188818 CCATTTTGAA
5188828 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5188870 AT
1 AT
5188872 GGTACAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5195961 original size:23 final size:23
Alignment explanation
Indices: 5195917--5195963 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5195907 AACATATTAT
**
5195917 GTAGCGCTTATATAATGTAATAG
1 GTAGCGCTTATATAATAAAATAG
5195940 GTAGCGCTTATATAATAAAATAG
1 GTAGCGCTTATATAATAAAATAG
5195963 G
1 G
5195964 CATTTAACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAG
Found at i:5196009 original size:64 final size:64
Alignment explanation
Indices: 5195937--5196083 Score: 276
Period size: 64 Copynumber: 2.3 Consensus size: 64
5195927 TATAATGTAA
*
5195937 TAGGTAGCGCTTATATAATAAAATAGGCATTTAACCGGAAATATTATCAAGTACAATAACATAT
1 TAGGTAGCGCTTATATAATAAAACAGGCATTTAACCGGAAATATTATCAAGTACAATAACATAT
5196001 TAGGTAGCGCTTATATAATAAAACAGGCATTTAACCGGAAATATTATCAAGTACAATAACATAT
1 TAGGTAGCGCTTATATAATAAAACAGGCATTTAACCGGAAATATTATCAAGTACAATAACATAT
*
5196065 TAGGTAACGCTTATATAAT
1 TAGGTAGCGCTTATATAAT
5196084 GTAATATGTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (64 bp):
TAGGTAGCGCTTATATAATAAAACAGGCATTTAACCGGAAATATTATCAAGTACAATAACATAT
Found at i:5196550 original size:198 final size:197
Alignment explanation
Indices: 5196128--5196818 Score: 818
Period size: 198 Copynumber: 3.5 Consensus size: 197
5196118 AGTAAATCAA
* *
5196128 TATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* ** * * * *
5196193 TGGATCGATAAAATTTTAAATGTATAT--ACACTTTATGCGTGCACCTCGTTGGGCTTTCATTAT
66 TGGATCGAT--ACTTTTAAAAATATATCGACACTTTATGCATGCACCTCTTTGGGCATTCATTTT
* * ** *
5196256 GG-GAACAAGTATCGACGTAAACTTAAAGAGTGTCGAT-CATTAT-TTAGACCTATTTT--TCAT
129 GGACAAAAAGTATCGACACAAA-TTAAA-AGTGTCGATACATTATGTT-CACCTATTTTAAT-AT
5196316 AAAACTGG
190 AAAACTGG
*
5196324 TATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGATGTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
*
5196389 TGGATCGATACTTTTTAAAACATATATCGACACTTTATGCATGCAACC-CTTTTGGCATTCATTT
66 TGGATCGATAC-TTTTAAAA-ATATATCGACACTTTATGCATGC-ACCTCTTTGGGCATTCATTT
*
5196453 TGGACAAAAAATATCGACACAAATATAAAA-TGT-GATACATTATGTTCACCTATTTTAATATAA
128 TGGACAAAAAGTATCGACACAAAT-TAAAAGTGTCGATACATTATGTTCACCTATTTTAATATAA
*
5196516 AACCGG
192 AACTGG
* *
5196522 TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAT-TTTAT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT-T
* * * **
5196586 TGGGATCGATACTTTTAATAATTGTATCGACACTTTATGTTTGCACCTCATTTGGGCATTCATTT
65 TTGGATCGATACTTTTAA-AAATATATCGACACTTTATGCATGCACCTC-TTTGGGCATTCATTT
* * *
5196651 TGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACATTATG-GCGACCTGTTTTCTAAT
128 TGGACAAAAAGTATCGACACAAATTA-A-AAGTGTCGATACATTATGTTC-ACCT-ATTT-TAAT
5196715 -T--AACTGG
188 ATAAAACTGG
* *
5196722 TATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* *
5196787 TGGGTCGATACTTTTAGAAAATGTATCGACAC
66 TGGATCGATACTTTTA-AAAATATATCGACAC
5196819 ATATTTAGGT
Statistics
Matches: 432, Mismatches: 39, Indels: 44
0.84 0.08 0.09
Matches are distributed among these distances:
194 1 0.00
195 7 0.02
196 82 0.19
197 49 0.11
198 149 0.34
199 24 0.06
200 93 0.22
201 19 0.04
202 4 0.01
203 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
TGGATCGATACTTTTAAAAATATATCGACACTTTATGCATGCACCTCTTTGGGCATTCATTTTGG
ACAAAAAGTATCGACACAAATTAAAAGTGTCGATACATTATGTTCACCTATTTTAATATAAAACT
GG
Found at i:5198587 original size:11 final size:11
Alignment explanation
Indices: 5198571--5198633 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
5198561 TATACATAAC
5198571 AATGTTCAAAT
1 AATGTTCAAAT
5198582 AATGTTCAAAT
1 AATGTTCAAAT
* *
5198593 AATTTATACATAAC
1 AATGT-T-CA-AAT
5198607 AATGTTCAAAT
1 AATGTTCAAAT
5198618 AATGTTCAAAT
1 AATGTTCAAAT
5198629 AATGT
1 AATGT
5198634 ACCCACAACG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
11 33 0.73
12 3 0.07
13 3 0.07
14 6 0.13
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:5198601 original size:36 final size:36
Alignment explanation
Indices: 5198557--5198631 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
5198547 GTACACAATA
5198557 AATTTATACATAACAATGTTCAAATAATGTTCAAAT
1 AATTTATACATAACAATGTTCAAATAATGTTCAAAT
5198593 AATTTATACATAACAATGTTCAAATAATGTTCAAAT
1 AATTTATACATAACAATGTTCAAATAATGTTCAAAT
5198629 AAT
1 AAT
5198632 GTACCCACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (36 bp):
AATTTATACATAACAATGTTCAAATAATGTTCAAAT
Found at i:5198630 original size:25 final size:24
Alignment explanation
Indices: 5198571--5198630 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
5198561 TATACATAAC
5198571 AATGTTCAAAT--AATGTTCAAAT
1 AATGTTCAAATAAAATGTTCAAAT
5198593 AAT-TT-ATACATAACAATGTTCAAAT
1 AATGTTCA-A-ATAA-AATGTTCAAAT
5198618 AATGTTCAAATAA
1 AATGTTCAAATAA
5198631 TGTACCCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 5 0.16
25 18 0.58
26 3 0.10
27 1 0.03
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (24 bp):
AATGTTCAAATAAAATGTTCAAAT
Found at i:5199630 original size:6 final size:6
Alignment explanation
Indices: 5199621--5199675 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
5199611 AACATCATAG
* * * *
5199621 TCATAA TCATCA TCATCA TCATCA TCATCA TCTTCA TCGTCA TCTTCA
1 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA
*
5199669 TCTTCA T
1 TCATCA T
5199676 TGACCTCTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (6 bp):
TCATCA
Found at i:5199657 original size:18 final size:18
Alignment explanation
Indices: 5199621--5199675 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
5199611 AACATCATAG
* *
5199621 TCATAATCATCATCATCA
1 TCATCATCATCATCTTCA
5199639 TCATCATCATCATCTTCA
1 TCATCATCATCATCTTCA
* *
5199657 TCGTCATCTTCATCTTCA
1 TCATCATCATCATCTTCA
5199675 T
1 T
5199676 TGACCTCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (18 bp):
TCATCATCATCATCTTCA
Found at i:5200495 original size:2 final size:2
Alignment explanation
Indices: 5200488--5200537 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5200478 GTTTTCGGAG
5200488 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5200530 AT AT AT AT
1 AT AT AT AT
5200538 CATTCTCCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5201654 original size:179 final size:178
Alignment explanation
Indices: 5201352--5201919 Score: 455
Period size: 199 Copynumber: 3.1 Consensus size: 178
5201342 TTTTTAAAAA
* * * * *
5201352 GTATCGACACTTTATGCATGCAACCCTTTGGCATTCCTTTTGGACAAAAAGTATCGACACCAATT
1 GTATCGACACTTTATGCATGCAACACTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAAT
** * * *
5201417 CCACAGGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTATAATTATACCGGTTAC
66 AAAAAAGTGTCGATACATGTTGTAGACCTATTCTCACATAAAACCAGTATAATTATACCGGTTAC
** * * * * * *
5201482 ATTGTAAATTTACTTATTACATTATATTTAAGGGTTTTGATGTTTCT-G
131 ATTACAAAATCACCTATTACATTATAATTAAGAGTTTCGATGTTT-TAG
* * * *
5201530 GTATCGACACTTTATGCATTCATCATTTTGGGCATTCATTCTGGACAAAACGTATCGACACAAAA
1 GTATCGACACTTTATGCATGCAACACTTT-GGCATTCATTCTGGACAAAAAGTATCGACACAAAA
* * *
5201595 TAAAAAAGTGTCGATACAT-TATGTAGATCTATTCTCACATAAAACCGGTATATTTATACCGGTT
65 TAAAAAAGTGTCGATACATGT-TGTAGACCTATTCTCACATAAAACCAGTATAATTATACCGGTT
* *
5201659 ATATTACAAAATCACCTATTACATTATAATTATGAGTTTCGATGTTTTAG
129 ACATTACAAAATCACCTATTACATTATAATTAAGAGTTTCGATGTTTTAG
* * *
5201709 G-ATCGACACTTTGTATAAATGTATCGACACTTAGTGGTGCACCCTTTTTGAGCATTTATTATGG
1 GTATCGACAC--T-T-T--ATGCAT-G-CA---A------CA--C--TTTG-GCATTCATTCTGG
* * * * * *
5201773 ACAAAATGTATTGACACATAATGAAAAAGTATCGATATAT-TATGTAGACCTATTCTCACATAAA
44 ACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATGT-TGTAGACCTATTCTCACATAAA
* * * * * * *
5201837 ACCGGTATATTTATACCAGTTATATTGCAAAATTACCTATTACATTATAATTATG-GTTTTCGAT
108 ACCAGTATAATTATACCGGTTACATTACAAAATCACCTATTACATTATAATTAAGAG-TTTCGAT
5201901 GTTTCTAG
172 GTTT-TAG
5201909 G-ATCGACACTT
1 GTATCGACACTT
5201920 CTTATAAATG
Statistics
Matches: 320, Mismatches: 43, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
178 35 0.11
179 123 0.38
180 1 0.00
181 1 0.00
182 1 0.00
184 5 0.02
186 2 0.01
195 2 0.01
197 1 0.00
198 3 0.01
199 134 0.42
200 12 0.04
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (178 bp):
GTATCGACACTTTATGCATGCAACACTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAAT
AAAAAAGTGTCGATACATGTTGTAGACCTATTCTCACATAAAACCAGTATAATTATACCGGTTAC
ATTACAAAATCACCTATTACATTATAATTAAGAGTTTCGATGTTTTAG
Found at i:5202072 original size:200 final size:197
Alignment explanation
Indices: 5201555--5202518 Score: 1036
Period size: 200 Copynumber: 4.9 Consensus size: 197
5201545 GCATTCATCA
*
5201555 TTTTGGGCATTCATTCTGGACAAAACGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTA
1 TTTTGGGCATTCATTCTGGACAAAACGTATCGACAC-AAATTAAAAAGTGTCGATACATTATGTA
*
5201620 GATCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATT-ACAAAATCACCTATTACATT
65 GA-CTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTGACAAAATTACCTATTACATT
5201684 ATAATTATGAGTTTCGATGTTT-TAGGATCGACACTTTGTATAAATGTATCGACACTTAGTGGTG
129 ATAATTATG-GTTTCGATGTTTCTAGGATCGACACTTT-TATAAATGTATCGACACTTAGTGGTG
5201748 CACCCT
192 CACCCT
* * * * * * * *
5201754 TTTTGAGCATTTATTATGGACAAAATGTATTGACACATAATGAAAAAGTATCGATATATTATGTA
1 TTTTGGGCATTCATTCTGGACAAAACGTATCGACACA-AATTAAAAAGTGTCGATACATTATGTA
*
5201819 GACCTATTCTCACATAAAACCGGTATATTTATACCAGTTATATTG-CAAAATTACCTATTACATT
65 GA-CTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTGACAAAATTACCTATTACATT
**
5201883 ATAATTATGGTTTTCGATGTTTCTAGGATCGACACTTCTTATAAATGTATAAACACTTAGTGGTG
129 ATAATTATGG-TTTCGATGTTTCTAGGATCGACACTT-TTATAAATGTATCGACACTTAGTGGTG
5201948 CACCCT
192 CACCCT
* * *
5201954 TTTTGGGCATTCCTTCTGGACCAAAA-GTATCGATACAAATTACACAAGTGTCGATACA-TATTG
1 TTTTGGGCATTCATTCTGGA-CAAAACGTATCGACACAAATTA-AAAAGTGTCGATACATTA-TG
* * * * *
5202017 TACACATATTCTCTCATAAAACTGGTATATGTATACCGGTTACATTGAC-AAATTACCTATTACA
63 TAGAC-TATTCTCACATAAAACCGGTATATTTATACCGGTTATATTGACAAAATTACCTATTACA
* * **
5202081 TTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTGTTTATAAATGTATCGACACTTTTTG
127 TTATAATTAT-GGTTTCGATGTTTCTAGGATCGACAC-T-TTTATAAATGTATCGACACTTAGTG
5202146 TGTGCACCC-
189 -GTGCACCCT
* *
5202155 TTTTGGGCATTCCTTCTGG-----A-G-A---A-AC---------AGTGTCGATACATTATGTAT
1 TTTTGGGCATTCATTCTGGACAAAACGTATCGACACAAATTAAAAAGTGTCGATACATTATGTAG
* * * * *
5202200 ACATATTCTCTCATAAAACCGGTTTAGTTATACCGGTTACATTGA-AAAATTACCTATTACATTG
66 AC-TATTCTCACATAAAACCGGTATATTTATACCGGTTATATTGACAAAATTACCTATTACATTA
* *
5202264 TAATTATGGGTTTCGATGTTTCTGGGATCGACACTTTCAATAAATGTATCGACACATTA-TGCGT
130 TAATTAT-GGTTTCGATGTTTCTAGGATCGACACTTT-TATAAATGTATCGACAC-TTAGTG-GT
* * *
5202328 TCA-TCA
191 GCACCCT
* * * * *
5202334 TTTTGGGCATTCATTATGGACAAAATGTATTGACACATAATAAAAAAGTGTCGATATATTATGTA
1 TTTTGGGCATTCATTCTGGACAAAACGTATCGACACA-AATTAAAAAGTGTCGATACATTATGTA
* * *
5202399 GACCTATTCTCACATAAAACCGGTATATTTATACTGGTTATATT-ATAAAATTACCTATTATATT
65 GA-CTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTGACAAAATTACCTATTACATT
* * * * *
5202463 ATAATTATGGGTTTCGATATTTTTGGGATCGACACTTTTTATAAACGTTTCGACAC
129 ATAATTAT-GGTTTCGATGTTTCTAGGATCGACAC-TTTTATAAATGTATCGACAC
5202519 ATATTCTTAC
Statistics
Matches: 659, Mismatches: 63, Indels: 85
0.82 0.08 0.11
Matches are distributed among these distances:
178 3 0.00
179 40 0.06
180 109 0.17
181 2 0.00
184 1 0.00
185 1 0.00
186 1 0.00
189 1 0.00
190 4 0.01
191 1 0.00
194 1 0.00
195 2 0.00
198 2 0.00
199 143 0.22
200 286 0.43
201 53 0.08
202 9 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (197 bp):
TTTTGGGCATTCATTCTGGACAAAACGTATCGACACAAATTAAAAAGTGTCGATACATTATGTAG
ACTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTGACAAAATTACCTATTACATTAT
AATTATGGTTTCGATGTTTCTAGGATCGACACTTTTATAAATGTATCGACACTTAGTGGTGCACC
CT
Found at i:5202234 original size:180 final size:179
Alignment explanation
Indices: 5202000--5202345 Score: 525
Period size: 180 Copynumber: 1.9 Consensus size: 179
5201990 AAATTACACA
*
5202000 AGTGTCGATACATATTGTACACATATTCTCTCATAAAACTGGTATATGTATACCGGTTACATTGA
1 AGTGTCGATACATATTGTACACATATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTGA
* * **
5202065 CAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTGTTTATAAAT
66 AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGACACTT-TCAATAAAT
* * * *
5202130 GTATCGACACTTTTTGTGTGCACCCTTTTGGGCATTCCTTCTGGAGAAAC
130 GTATCGACACATTATGCGTGCACCATTTTGGGCATTCCTTCTGGAGAAAC
* *
5202180 AGTGTCGATACAT-TATGTATACATATTCTCTCATAAAACCGGTTTA-GTTATACCGGTTACATT
1 AGTGTCGATACATAT-TGTACACATATTCTCTCATAAAACCGGTATATG-TATACCGGTTACATT
*
5202243 GAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTTCTGGGATCGACACTTTCAATAAA
64 GAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGACACTTTCAATAAA
* *
5202308 TGTATCGACACATTATGCGTTCATCATTTTGGGCATTC
129 TGTATCGACACATTATGCGTGCACCATTTTGGGCATTC
5202346 ATTATGGACA
Statistics
Matches: 150, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
179 40 0.27
180 110 0.73
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (179 bp):
AGTGTCGATACATATTGTACACATATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTGA
AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGACACTTTCAATAAATG
TATCGACACATTATGCGTGCACCATTTTGGGCATTCCTTCTGGAGAAAC
Found at i:5202916 original size:19 final size:19
Alignment explanation
Indices: 5202870--5202918 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
5202860 TTACATCAAC
*
5202870 ATACAAAAGTATAAATCGT
1 ATACAAAATTATAAATCGT
5202889 ATACAAAATTATAAAT-GTT
1 ATACAAAATTATAAATCG-T
5202908 ATACAAAATTA
1 ATACAAAATTA
5202919 ACTCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:5204348 original size:18 final size:18
Alignment explanation
Indices: 5204325--5204363 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5204315 TCCTCCTCAT
5204325 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
5204343 TTCCTCCCTCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
5204361 TTC
1 TTC
5204364 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:5204639 original size:21 final size:21
Alignment explanation
Indices: 5204614--5204657 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5204604 CACCTTATGC
*
5204614 CTCTCAAGTGTCTGTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
* *
5204635 CTCTCAAGTTTCTCTTTGACT
1 CTCTCAAGTGTCTCTTCGACT
5204656 CT
1 CT
5204658 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:5205064 original size:22 final size:21
Alignment explanation
Indices: 5205036--5205090 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
5205026 AACTTACATT
5205036 TATAATAAAATTTATAATTTTA
1 TATAATAAAATTT-TAATTTTA
*
5205058 TATAATAACTATATTTTCATTTTA
1 TATAATAA--A-ATTTTAATTTTA
5205082 TATAA-AAAA
1 TATAATAAAA
5205091 CAAAAACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 8 0.28
23 2 0.07
24 13 0.45
25 4 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAATAAAATTTTAATTTTA
Found at i:5207343 original size:182 final size:181
Alignment explanation
Indices: 5207084--5207575 Score: 680
Period size: 182 Copynumber: 2.7 Consensus size: 181
5207074 TATGCGTACT
* * * *
5207084 TATTAAAGTATCGACACTTTCAAAATATCCGGTAGCGCTTTATCGGTTTTGTC-ACTTATAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTCTCAT-GACC
* * * *
5207148 TGTTTTATCATATTTTTACCTTTTATATCGTTATAGATTGATACATTTTTATAAAGTATCGACAC
65 -GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATTTTTATAAAGTATCGACAC
5207213 TTTATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCAATACTTA
129 TTTATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCAATACTTA
* * * * *
5207266 TATTAAAATATCGACACTTTCAATATATCCGGTATCTCTTTACCGGTTTTATCTTCTCCTGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTCTCATGACCG
* * * *
5207331 ATTTTGTCATATTTTTACATGTTATATCGTTGTGGATTGATACATATTTATAAAGAATCGACACT
66 -TTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATTTTTATAAAGTATCGACACT
* * *
5207396 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTA
130 TTATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCAATACTTA
* * * *
5207448 TATTCAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTCTCATGACC-
* * * * *
5207513 GTTTTGTCATATTTTTTCCTATTATATTGATGTGGATCGATATATTTTTATAAAGTATCGACA
65 GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATTTTTATAAAGTATCGACA
5207576 TAAATCAACA
Statistics
Matches: 271, Mismatches: 36, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
181 1 0.00
182 266 0.98
183 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTCTCATGACCG
TTTTGTCATATTTTTACCTATTATATCGTTGTGGATTGATACATTTTTATAAAGTATCGACACTT
TATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCAATACTTA
Found at i:5210920 original size:159 final size:158
Alignment explanation
Indices: 5210614--5211554 Score: 907
Period size: 159 Copynumber: 5.9 Consensus size: 158
5210604 CTCCACCAAC
* * * * * *
5210614 CGGTGCCTGATTTCCGTTTCCCCCTCTTCCTTTTGTAATTAGGGACCTTGGACTTGGATG-ACGA
1 CGGTGCCTGATTTTCGTTT-CCCCACTTCCTTTTGTTATTAGGGATCTTGGACTCGGACGTA-GA
* * * *
5210678 AGATA-CATCTGCATCTGGTCGAACAGAAGAGTTTGTC-GGGAGGTCATCTCCAGGAGCAAGAAC
64 AGATACCTTC-ACATCTGGTTGAACAGAAGGGTTTG-CAGGGAGGTCATCTCCAGGAGCAAGAAC
* * * ** ** *
5210741 AGTACGCTTTTTGGTAGGCATTGGCAGCTCTT
127 AGTAGGCTTTTCGGTTGGCATCAGTGGCTCCT
* * * * *
5210773 TGGTGTCTGACTTTT-GTTTCCCCCACTTCCTTTTGTTATTAGGAACCTTGGACTTGGACGTAGA
1 CGGTGCCTGA-TTTTCGTTT-CCCCACTTCCTTTTGTTATTAGGGATCTTGGACTCGGACGTAGA
* * * * *
5210837 AGATACCTTCGCATCTGGTTGAGCAGAAGCGTTTGCTGGGAGGTCATCTCCAGGAGCAAGAAGAG
64 AGATACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGGGAGGTCATCTCCAGGAGCAAGAACAG
*
5210902 TAGGCTTTTCGGTTGGCATCAGTGGCTCCC
129 TAGGCTTTTCGGTTGGCATCAGTGGCTCCT
* * * *
5210932 CGGTGCCTGATTTTCGTCTCCCCATCTTCCTTTTGTTTTTAGGGATCTTGGACTCGGACATCGAA
1 CGGTGCCTGATTTTCGTTTCCCCA-CTTCCTTTTGTTATTAGGGATCTTGGACTCGGACGTAGAA
* * * *
5210997 GGTACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGGTAGGTCATCTCCCGGAGCAATAACAGT
65 GATACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGGGAGGTCATCTCCAGGAGCAAGAACAGT
* * * * *
5211062 AGGTTTTTCAGTCGGTATCAGTGGCTCAT
130 AGGCTTTTCGGTTGGCATCAGTGGCTCCT
* * * * * *
5211091 TGGTGCCTGATTTTCGTTTCCCCATTTTCCTCTTGTTATTAGGGATGTTGGTCTCGGACATCA-A
1 CGGTGCCTGATTTTCGTTTCCCCA-CTTCCTTTTGTTATTAGGGATCTTGGACTCGGACGT-AGA
*
5211155 AGATACCTTCTCATCTGGTTGAACAGAAGGGTTTGC-GGAGAGGTCATCTCCAGGAGCAAGAACA
64 AGATACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGG-GAGGTCATCTCCAGGAGCAAGAACA
* * * *
5211219 GTAGGCTTTTCAGTTGGCATCTGGGGATCCT
128 GTAGGCTTTTCGGTTGGCATCAGTGGCTCCT
* * * * *** * *
5211250 CAGTGCCTGATTTTCCTTTCTCCA-TATCCCTTCTGTTATTACTAATCTCGGACTCAGACGTCA-
1 CGGTGCCTGATTTTCGTTTCCCCACT-T-CCTTTTGTTATTAGGGATCTTGGACTCGGACGT-AG
* * *
5211313 AAGATACCTTCACATCTGGTTGAACAGAAGGGTTGGCAAGGAGGTCATCTCCAGTAGCAAGAACA
63 AAGATACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGGGAGGTCATCTCCAGGAGCAAGAACA
* * * *
5211378 GTAGGATTTTCGGTTGGCATCGGCGGATCCT
128 GTAGGCTTTTCGGTTGGCATCAGTGGCTCCT
* * * * * * ** * * *
5211409 CAGTGCCTGATTTCCGTTTCTCCATATTCCTTCTGTTAGTACTGATCTCGGACTCAGACATCA-A
1 CGGTGCCTGATTTTCGTTTCCCCA-CTTCCTTTTGTTATTAGGGATCTTGGACTCGGACGT-AGA
* * * *
5211473 AGATACCTTCACATCTGGTTGAACTGAAGGGTTGGCAAGGAGGTCATCT---GGAGAAAGAACAG
64 AGATACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGGGAGGTCATCTCCAGGAGCAAGAACAG
5211535 TAGGCTTTTCGGTTGGCATC
129 TAGGCTTTTCGGTTGGCATC
5211555 GGCAGCTCCT
Statistics
Matches: 673, Mismatches: 96, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
156 30 0.04
157 1 0.00
158 13 0.02
159 619 0.92
160 9 0.01
161 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (158 bp):
CGGTGCCTGATTTTCGTTTCCCCACTTCCTTTTGTTATTAGGGATCTTGGACTCGGACGTAGAAG
ATACCTTCACATCTGGTTGAACAGAAGGGTTTGCAGGGAGGTCATCTCCAGGAGCAAGAACAGTA
GGCTTTTCGGTTGGCATCAGTGGCTCCT
Found at i:5211519 original size:477 final size:477
Alignment explanation
Indices: 5210615--5211521 Score: 1112
Period size: 477 Copynumber: 1.9 Consensus size: 477
5210605 TCCACCAACC
* * * * *
5210615 GGTGCCTGATTTCCGTTTCCCCCTCTTCCTTTTGTAATTAGGGACCTTGGACTTGGATGACGAAG
1 GGTGCCTGATTTCCGTTTCCCCATCTTCCTCTTGTAATTAGGGACCTTGGACTCGGATCACAAAG
5210680 ATACATCTGCATCTGGTCGAACAGAAGAGTTTGTCGGGAGGTCATCTCCAGGAGCAAGAACAGTA
66 ATACATCTGCATCTGGTCGAACAGAAGAGTTTGTCGGGAGGTCATCTCCAGGAGCAAGAACAGTA
** * * ** * * *
5210745 CGCTTTTTGGTAGGCATTGGCAGCTCTTTGGTGTCTGACTTTTGTTTCCCCCACTTCCTTTTGTT
131 CGCTTTTCAGTAGGCATTGGCAGATCCTCAGTGCCTGACTTTTCTTTCCCCCACTTCCTTCTGTT
* * ** * * * **
5210810 ATTAGGAACCTTGGACTTGGACGTAGAAGATACCTTCGCATCTGGTTGAGCAGAAGCGTTTGCTG
196 ATTACGAACCTCGGACTCAGACGTAGAAGATACCTTCACATCTGGTTGAACAGAAGCGTTGGCAA
* * * * *
5210875 GGAGGTCATCTCCAGGAGCAAGAAGAGTAGGCTTTTCGGTTGGCATCAGTGGCTCCCCGGTGCCT
261 GGAGGTCATCTCCAGGAGCAAGAACAGTAGGATTTTCGGTTGGCATCAGCGGATCCCCAGTGCCT
* * * ** * * * * *
5210940 GATTTTCGTCTCCCCATCTTCCTTTTGTTTTTAGGGATCTTGGACTCGGACATCGAAGGTACCTT
326 GATTTCCGTCTCCCCATATTCCTTCTGTTAGTACGGATCTCGGACTCAGACATCAAAGATACCTT
*
5211005 CACATCTGGTTGAACAGAAGGGTTTGCAGGTAGGTCATCTCCCGGAGCAATAACAGTAGGTTTTT
391 CACATCTGGTTGAACAGAAGGGTTGGCAGGTAGGTCATCTCCCGGAGCAATAACAGTAGGTTTTT
5211070 CAGTCGGTATCAGTGGCTCATT
456 CAGTCGGTATCAGTGGCTCATT
* * * ** *
5211092 GGTGCCTGATTTTCGTTTCCCCATTTTCCTCTTGTTATTAGGGATGTTGGTCTCGGA-CATCAAA
1 GGTGCCTGATTTCCGTTTCCCCATCTTCCTCTTGTAATTAGGGACCTTGGACTCGGATCA-CAAA
* * *
5211156 GATACCTTCT-CATCTGGTTGAACAGAAGGGTTTG-CGGAGAGGTCATCTCCAGGAGCAAGAACA
65 GATA-CATCTGCATCTGGTCGAACAGAAGAGTTTGTCGG-GAGGTCATCTCCAGGAGCAAGAACA
* * * *
5211219 GTAGGCTTTTCAGTTGGCATCTGG-GGATCCTCAGTGCCTGA-TTTTCCTTT-CTCCA-TATCCC
128 GTACGCTTTTCAGTAGGCAT-TGGCAGATCCTCAGTGCCTGACTTTT-CTTTCCCCCACT-T-CC
* * *
5211280 TTCTGTTATTACTAATCTCGGACTCAGACGTCA-AAGATACCTTCACATCTGGTTGAACAGAAGG
189 TTCTGTTATTACGAACCTCGGACTCAGACGT-AGAAGATACCTTCACATCTGGTTGAACAGAAGC
* * *
5211344 GTTGGCAAGGAGGTCATCTCCAGTAGCAAGAACAGTAGGATTTTCGGTTGGCATCGGCGGATCCT
253 GTTGGCAAGGAGGTCATCTCCAGGAGCAAGAACAGTAGGATTTTCGGTTGGCATCAGCGGATCCC
* * *
5211409 CAGTGCCTGATTTCCGTTTCTCCATATTCCTTCTGTTAGTACTGATCTCGGACTCAGACATCAAA
318 CAGTGCCTGATTTCCGTCTCCCCATATTCCTTCTGTTAGTACGGATCTCGGACTCAGACATCAAA
*
5211474 GATACCTTCACATCTGGTTGAACTGAAGGGTTGGCAAGG-AGGTCATCT
383 GATACCTTCACATCTGGTTGAACAGAAGGGTTGGC-AGGTAGGTCATCT
5211522 GGAGAAAGAA
Statistics
Matches: 359, Mismatches: 62, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
475 1 0.00
476 13 0.04
477 334 0.93
478 11 0.03
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (477 bp):
GGTGCCTGATTTCCGTTTCCCCATCTTCCTCTTGTAATTAGGGACCTTGGACTCGGATCACAAAG
ATACATCTGCATCTGGTCGAACAGAAGAGTTTGTCGGGAGGTCATCTCCAGGAGCAAGAACAGTA
CGCTTTTCAGTAGGCATTGGCAGATCCTCAGTGCCTGACTTTTCTTTCCCCCACTTCCTTCTGTT
ATTACGAACCTCGGACTCAGACGTAGAAGATACCTTCACATCTGGTTGAACAGAAGCGTTGGCAA
GGAGGTCATCTCCAGGAGCAAGAACAGTAGGATTTTCGGTTGGCATCAGCGGATCCCCAGTGCCT
GATTTCCGTCTCCCCATATTCCTTCTGTTAGTACGGATCTCGGACTCAGACATCAAAGATACCTT
CACATCTGGTTGAACAGAAGGGTTGGCAGGTAGGTCATCTCCCGGAGCAATAACAGTAGGTTTTT
CAGTCGGTATCAGTGGCTCATT
Found at i:5223782 original size:30 final size:31
Alignment explanation
Indices: 5223746--5223805 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5223736 CTTAGCTTTA
**
5223746 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
5223776 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5223806 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5224742 original size:19 final size:21
Alignment explanation
Indices: 5224718--5224769 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5224708 CGGCCAAGAG
*
5224718 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
5224737 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5224758 CATGTATTTTCA
1 CATGTATTTTCA
5224770 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5233364 original size:30 final size:31
Alignment explanation
Indices: 5233328--5233387 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5233318 CTTAGTTTTA
**
5233328 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
5233358 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5233388 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5234320 original size:19 final size:20
Alignment explanation
Indices: 5234293--5234344 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
5234283 CGGCCAAGAG
5234293 CATGTATTTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
*
5234312 CATGCATTTTCATTTTAAAAT
1 CATGTATTTTCA-TTTAAAAT
5234333 CATGTATTTTCA
1 CATGTATTTTCA
5234345 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
21 18 0.62
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:5242929 original size:12 final size:12
Alignment explanation
Indices: 5242912--5242941 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5242902 TTCATTAATC
5242912 GGAGAAGACGGA
1 GGAGAAGACGGA
5242924 GGAGAAGACGGA
1 GGAGAAGACGGA
5242936 GGAGAA
1 GGAGAA
5242942 TTAGGGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.50, T:0.00
Consensus pattern (12 bp):
GGAGAAGACGGA
Found at i:5256694 original size:20 final size:20
Alignment explanation
Indices: 5256669--5256706 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5256659 TTTGGTTTAC
5256669 AGAATGTAAGATTACCAGTG
1 AGAATGTAAGATTACCAGTG
5256689 AGAATGTAAGATTACCAG
1 AGAATGTAAGATTACCAG
5256707 GGAATAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGTAAGATTACCAGTG
Found at i:5257654 original size:43 final size:43
Alignment explanation
Indices: 5257580--5257709 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 43
5257570 TTTTTTAATA
* * *
5257580 TAGTGTATTAGTAAATTATTACTTT-AGTTGTAATATGTTAGTT
1 TAGTGCATTCGTAGATTATTACTTTGA-TTGTAATATGTTAGTT
* * * * * **
5257623 TTGTGTATTTGTTGATTGTTGTTTTGATTGTAATATGTTAGTT
1 TAGTGCATTCGTAGATTATTACTTTGATTGTAATATGTTAGTT
* *
5257666 TAGTGCATTCGTAGATTATTACTTTGGTTGTAACATGTTAGTT
1 TAGTGCATTCGTAGATTATTACTTTGATTGTAATATGTTAGTT
5257709 T
1 T
5257710 GATATATTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
43 69 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.20, T:0.53
Consensus pattern (43 bp):
TAGTGCATTCGTAGATTATTACTTTGATTGTAATATGTTAGTT
Found at i:5267358 original size:19 final size:19
Alignment explanation
Indices: 5267316--5267358 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
5267306 AATAACCAAT
* * *
5267316 AAATTCGCAACGCGATCTT
1 AAATTCGCAACACGAACTC
5267335 AAATTCGCAACACGAACTC
1 AAATTCGCAACACGAACTC
*
5267354 CAATT
1 AAATT
5267359 TTGCAACTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (19 bp):
AAATTCGCAACACGAACTC
Found at i:5267455 original size:26 final size:26
Alignment explanation
Indices: 5267417--5267466 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5267407 CGCGTTTACT
* * * *
5267417 TTCGCAACGCGAATTTTATTTTTGAA
1 TTCGAAACCCGAATATTAATTTTGAA
5267443 TTCGAAACCCGAATATTAATTTTG
1 TTCGAAACCCGAATATTAATTTTG
5267467 TAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (26 bp):
TTCGAAACCCGAATATTAATTTTGAA
Found at i:5267583 original size:23 final size:23
Alignment explanation
Indices: 5267557--5267600 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5267547 TCTCTCACTC
5267557 TCTCCGACGACATCCGTCCCCCA
1 TCTCCGACGACATCCGTCCCCCA
* *
5267580 TCTCCGGCGACATCCTTCCCC
1 TCTCCGACGACATCCGTCCCC
5267601 ATATCCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.52, G:0.14, T:0.20
Consensus pattern (23 bp):
TCTCCGACGACATCCGTCCCCCA
Found at i:5267607 original size:22 final size:23
Alignment explanation
Indices: 5267559--5267612 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
5267549 TCTCACTCTC
* *
5267559 TCCGACGACATCCGTCCCCCATC
1 TCCGGCGACATCCGTCCCCCATA
*
5267582 TCCGGCGACATCC-TTCCCCATA
1 TCCGGCGACATCCGTCCCCCATA
5267604 TCCGGCGAC
1 TCCGGCGAC
5267613 CCCCCTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.19
Consensus pattern (23 bp):
TCCGGCGACATCCGTCCCCCATA
Found at i:5268041 original size:14 final size:14
Alignment explanation
Indices: 5268024--5268061 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5268014 AGCGAATTTC
5268024 ATTTTCAAGTTACG
1 ATTTTCAAGTTACG
*
5268038 ATTTTCATGTTACG
1 ATTTTCAAGTTACG
*
5268052 AATTT-AAGTT
1 ATTTTCAAGTT
5268062 TCAAGAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTTTCAAGTTACG
Found at i:5273464 original size:24 final size:24
Alignment explanation
Indices: 5273435--5273490 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5273425 GTGAGTACTA
**
5273435 GTCAATATTCAAAATTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
** *
5273459 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
5273483 GTCAATAC
1 GTCAATAC
5273491 TCGGATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (24 bp):
GTCAATACCCAAAATTTGATCTTG
Found at i:5273495 original size:24 final size:24
Alignment explanation
Indices: 5273449--5273502 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5273439 ATATTCAAAA
5273449 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
5273473 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
5273497 TTTGAT
1 TTTGAT
5273503 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:5275945 original size:20 final size:20
Alignment explanation
Indices: 5275920--5276007 Score: 133
Period size: 20 Copynumber: 4.4 Consensus size: 20
5275910 CAACGCAGAA
5275920 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
5275940 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
5275960 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
5275980 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
5276000 ATCGCAAC
1 ATCGCAAC
5276008 AAGAGAATCG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:5276035 original size:19 final size:18
Alignment explanation
Indices: 5276013--5276158 Score: 82
Period size: 19 Copynumber: 8.4 Consensus size: 18
5276003 GCAACAAGAG
5276013 AATCGCAATGCAAAATGAA
1 AATCGCAATGC-AAATGAA
* *
5276032 AATCCCAATGCGAAATAAA
1 AATCGCAATGC-AAATGAA
* *
5276051 AATCGCAA--C-GA-GAG
1 AATCGCAATGCAAATGAA
5276065 AATCGCAATGCGAAATGAA
1 AATCGCAATGC-AAATGAA
* *
5276084 AATCGCAA--C-GA-GAG
1 AATCGCAATGCAAATGAA
5276098 AATCGCAATGCGAAATGAA
1 AATCGCAATGC-AAATGAA
* *
5276117 AATCGCAA--CGAGTG--
1 AATCGCAATGCAAATGAA
5276131 AATCGCAATGCGAAAATGAA
1 AATCGCAATGC--AAATGAA
5276151 AATCGCAA
1 AATCGCAA
5276159 CGCGAAATCG
Statistics
Matches: 94, Mismatches: 17, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
14 27 0.29
15 2 0.02
16 6 0.06
17 3 0.03
18 5 0.05
19 43 0.46
20 8 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (18 bp):
AATCGCAATGCAAATGAA
Found at i:5276070 original size:14 final size:14
Alignment explanation
Indices: 5276051--5276138 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
5276041 GCGAAATAAA
5276051 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5276065 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5276084 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5276098 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
5276117 AATCGCAACGAGTG
1 AATCGCAACGAGAG
5276131 AATCGCAA
1 AATCGCAA
5276139 TGCGAAAATG
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5276079 original size:33 final size:33
Alignment explanation
Indices: 5276032--5276168 Score: 222
Period size: 33 Copynumber: 4.2 Consensus size: 33
5276022 GCAAAATGAA
* *
5276032 AATCCCAATGCGAAATAAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
5276065 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
5276098 AATCGCAATGCGAAATGAAAATCGCAACGAGTG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
5276131 AATCGCAATGCGAAAATGAAAATCGCAACGCGA-
1 AATCGCAATGCG-AAATGAAAATCGCAACGAGAG
5276164 AATCG
1 AATCG
5276169 TTGCGATAGT
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 80 0.82
34 18 0.18
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:5276310 original size:14 final size:14
Alignment explanation
Indices: 5276291--5276327 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5276281 CATCAATTAA
5276291 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5276305 ACAAATCATCTTTT
1 ACAAATCAACATTT
5276319 ACAAATCAA
1 ACAAATCAA
5276328 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5277784 original size:42 final size:42
Alignment explanation
Indices: 5277684--5277788 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
5277674 TGTTGGGATG
* * * *
5277684 GACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGAAGGG
1 GACCTCTTGAACGATGACAGGGGCCTCTTGAACGATGG-AGGA
** *
5277727 GA-CTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGG-GGA
1 GACCTCTTGAACGATGACAGGGGCCTCTTGAACGAT-GGAGGA
5277768 GACCTCTTGAACGATGACAGG
1 GACCTCTTGAACGATGACAGG
5277789 TGAGTCGGGC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 4 0.08
42 42 0.84
43 4 0.08
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
GACCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAGGA
Found at i:5278291 original size:20 final size:20
Alignment explanation
Indices: 5278268--5278354 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
5278258 GAAACTTAAA
*
5278268 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
5278288 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
5278308 ATCGCAATGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
5278328 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
5278348 ATCGCAA
1 ATCGCAA
5278355 CGAGAGAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:5278420 original size:19 final size:19
Alignment explanation
Indices: 5278398--5278451 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
5278388 AGCAATTATA
*
5278398 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTC
*
5278417 GTTTTGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
5278436 ATTTCGCGTTGCGATT
1 GTTTCGCGTTGCGATT
5278452 CTCTAGTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:5278462 original size:14 final size:14
Alignment explanation
Indices: 5278442--5278499 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
5278432 TTTCATTTCG
5278442 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5278456 AGTTGCGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
5278475 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5278489 CGTTGCGATTC
1 CGTTGCGATTC
5278500 ATTTCGCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
16 3 0.08
17 3 0.08
19 10 0.27
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5278466 original size:33 final size:33
Alignment explanation
Indices: 5278424--5278514 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
5278414 TTGGTTTTGC
5278424 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
* *
5278457 GTTGCGATTTTCATTTCTCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
*
5278490 GTTGCGA--TTCATTTCGCGTTACGAT
1 GTTGCGATTTTCATTTCGCGTTGCGAT
5278515 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.30
33 38 0.70
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
Found at i:5278481 original size:19 final size:19
Alignment explanation
Indices: 5278399--5278484 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 19
5278389 GCAATTATAG
* **
5278399 TTTCGCGTTGCGATTTTGG
1 TTTCTCGTTGCGATTTTCA
5278418 TTT-TGCGTTGCGATTTTCA
1 TTTCT-CGTTGCGATTTTCA
*
5278437 TTTCGCGTTGCGA--TTC-
1 TTTCTCGTTGCGATTTTCA
*
5278453 --TCTAGTTGCGATTTTCA
1 TTTCTCGTTGCGATTTTCA
5278470 TTTCTCGTTGCGATT
1 TTTCTCGTTGCGATT
5278485 CTCTCGTTGC
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 3 0.06
19 38 0.72
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (19 bp):
TTTCTCGTTGCGATTTTCA
Found at i:5278775 original size:94 final size:94
Alignment explanation
Indices: 5278614--5278970 Score: 590
Period size: 94 Copynumber: 3.8 Consensus size: 94
5278604 ACTTCAACCA
* *
5278614 AAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
5278679 CAAATTTACTTTCAACCAAAAGACAAAAC
66 CAAATTTACTTTCAACCAAAAGACAAAAC
*
5278708 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGTAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
* *
5278773 CAAATTTACTTTAAACCAAAAGATAAAAC
66 CAAATTTACTTTCAACCAAAAGACAAAAC
*
5278802 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACATTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
*
5278867 TAAATTTAC-TTCAACCAAAAGACAAAAC
66 CAAATTTACTTTCAACCAAAAGACAAAAC
* ** *
5278895 AAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATGGTTTAGCAGTATTGGCAGCAACCGA
1 -AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
*
5278960 ATAAATTTACT
65 ACAAATTTACT
5278971 AAGCAATCTA
Statistics
Matches: 246, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
93 17 0.07
94 229 0.93
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
CAAATTTACTTTCAACCAAAAGACAAAAC
Found at i:5280687 original size:19 final size:19
Alignment explanation
Indices: 5280659--5280717 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
5280649 TCTTTTGGTT
5280659 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5280678 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5280697 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5280716 GA
1 GA
5280718 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5280761 original size:33 final size:33
Alignment explanation
Indices: 5280715--5280793 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
5280705 AATCGCAATG
**
5280715 CGATTTTGGTTTCGCGTTGCGATTATCTCGTTA
1 CGATTTTCATTTCGCGTTGCGATTATCTCGTTA
* *
5280748 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTATCTCGTTA
5280781 CGATTTTCATTTC
1 CGATTTTCATTTC
5280794 TCTCGTTGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTATCTCGTTA
Found at i:5280852 original size:20 final size:21
Alignment explanation
Indices: 5280770--5280869 Score: 118
Period size: 21 Copynumber: 4.9 Consensus size: 21
5280760 CGCGTTGCGA
5280770 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
5280791 TTCTCTCGTTGCGATTTGCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
5280812 TTCTCTCGTTGCAATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
5280833 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
5280853 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
5280870 AAGTTTAGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
20 29 0.42
21 40 0.58
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.51
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:5281452 original size:20 final size:20
Alignment explanation
Indices: 5281427--5281640 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
5281417 CTTTAAAAAC
5281427 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5281447 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5281467 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
5281488 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
5281508 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
5281528 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
5281548 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5281568 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
5281588 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
5281609 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
5281630 CTCGTTGCGAT
1 CGCGTTGCGAT
5281641 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
20 108 0.68
21 52 0.32
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5281662 original size:41 final size:41
Alignment explanation
Indices: 5281429--5281640 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
5281419 TTAAAAACCG
*
5281429 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
5281470 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
5281510 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
5281550 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
5281591 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
5281632 CGTTGCGAT
1 CGTTGCGAT
5281641 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 76 0.48
41 83 0.52
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:5281672 original size:20 final size:20
Alignment explanation
Indices: 5281649--5281701 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
5281639 ATAGTCAGAA
*
5281649 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
5281669 TCGCGTTGCAATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
5281689 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5281702 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:5283665 original size:37 final size:37
Alignment explanation
Indices: 5283615--5283695 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
5283605 GGACCTTTGT
5283615 TGGAGGCTAGTATGGTCCAACATCGC-TCCACCAAAAG
1 TGGAGGCTAGTATGGTCCAACATC-CTTCCACCAAAAG
5283652 TGGAGGCTAGTATGGTCCAACATCCTTCCACCAAAAG
1 TGGAGGCTAGTATGGTCCAACATCCTTCCACCAAAAG
5283689 TGGAGGC
1 TGGAGGC
5283696 ATTCATGTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (37 bp):
TGGAGGCTAGTATGGTCCAACATCCTTCCACCAAAAG
Found at i:5285136 original size:31 final size:31
Alignment explanation
Indices: 5285063--5285136 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
5285053 CAGTTACGTC
5285063 GGGGATCATATTGCAAATGGACTAAATGTTG
1 GGGGATCATATTGCAAATGGACTAAATGTTG
* *
5285094 AGGGACCATATTGCAAATGGACTAAATGTTG
1 GGGGATCATATTGCAAATGGACTAAATGTTG
*
5285125 GGGGATTATATT
1 GGGGATCATATT
5285137 ATAAGTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.30
Consensus pattern (31 bp):
GGGGATCATATTGCAAATGGACTAAATGTTG
Found at i:5289495 original size:2 final size:2
Alignment explanation
Indices: 5289490--5289570 Score: 66
Period size: 2 Copynumber: 42.0 Consensus size: 2
5289480 AAAAATAATA
* * *
5289490 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT GT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5289531 GA- ACT AT AT A- AT -T A- AGT -T AT AT AT AT AT AT AT AT AT AT
1 -AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
5289569 AT
1 AT
5289571 TATTCAAAGT
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
1 6 0.09
2 57 0.88
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5289705 original size:19 final size:18
Alignment explanation
Indices: 5289669--5289752 Score: 71
Period size: 19 Copynumber: 4.5 Consensus size: 18
5289659 TTGAGAAATT
* *
5289669 TTGAGAATATAGA-TAAA
1 TTGAGAATTTAGAGGAAA
5289686 TTGAGAATTTAGAGAGAAA
1 TTGAGAATTTAGAG-GAAA
*
5289705 TTGAGAAATTTAGAGGGAA
1 TTGAG-AATTTAGAGGAAA
* * *
5289724 TAGAAAATTTTGGAGGGAAA
1 TTGAGAA-TTTAGA-GGAAA
5289744 TTGAGAATT
1 TTGAGAATT
5289753 GAGATTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
17 12 0.23
18 2 0.04
19 21 0.40
20 18 0.34
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (18 bp):
TTGAGAATTTAGAGGAAA
Found at i:5289713 original size:27 final size:27
Alignment explanation
Indices: 5289652--5289714 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
5289642 GGGAATTTAG
* *
5289652 AGAGAAATTGAGAAATTTTGAGAATAT
1 AGAGAAATTGAGAAATTTAGAGAAAAT
*
5289679 AGATAAATTGAG-AATTTAGAGAGAAAT
1 AGAGAAATTGAGAAATTTAGAGA-AAAT
*
5289706 TGAGAAATT
1 AGAGAAATT
5289715 TAGAGGGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (27 bp):
AGAGAAATTGAGAAATTTAGAGAAAAT
Found at i:5289727 original size:46 final size:45
Alignment explanation
Indices: 5289644--5289732 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 45
5289634 TTTTATTTGG
*
5289644 GAATTTAGAGAGAAATTGAGAAATTTTGAGAATATAGATAAATTGA
1 GAATTTAGAGAGAAATTGAGAAATTTAGAGAATATAGA-AAATTGA
*
5289690 GAATTTAGAGAGAAATTGAGAAATTTAGAGGGA-ATAGAAAATT
1 GAATTTAGAGAGAAATTGAGAAATTTAGA-GAATATAGAAAATT
5289733 TTGGAGGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 5 0.12
46 33 0.82
47 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (45 bp):
GAATTTAGAGAGAAATTGAGAAATTTAGAGAATATAGAAAATTGA
Found at i:5289731 original size:18 final size:20
Alignment explanation
Indices: 5289645--5289733 Score: 56
Period size: 20 Copynumber: 4.2 Consensus size: 20
5289635 TTTATTTGGG
*
5289645 AATTTAGAGAGAAATTGAGA
1 AATTTAGAGAGAAATAGAGA
* * *
5289665 AATTTTGAGAATATAGATAAATTGA
1 AATTTAGAG-AGA-A-ATAGA--GA
*
5289690 GAATTTAGAGAGAAATTGAGA
1 -AATTTAGAGAGAAATAGAGA
*
5289711 AATTTAGAG-GGAATAGA-A
1 AATTTAGAGAGAAATAGAGA
5289729 AATTT
1 AATTT
5289734 TGGAGGGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
18 6 0.11
19 6 0.11
20 17 0.32
21 4 0.08
22 1 0.02
23 6 0.11
24 1 0.02
25 4 0.08
26 8 0.15
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.29
Consensus pattern (20 bp):
AATTTAGAGAGAAATAGAGA
Found at i:5290936 original size:80 final size:80
Alignment explanation
Indices: 5290718--5291159 Score: 717
Period size: 80 Copynumber: 5.5 Consensus size: 80
5290708 GGGAGCCACT
* * * *
5290718 CTAAGGATATACCTT-GGATCTACCCAATGACATCCTTAGATCCGTAGGGTTACCTTAAGCACAC
1 CTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACCTTATGCACAC
*
5290782 AGCTAAGGGAACCAAC
65 AGCAAAGGGAACCAAC
5290798 CTAAGGATATACCTTGGG-CCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
1 CTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
5290862 GCAAAGGGAACCAAC
66 GCAAAGGGAACCAAC
*
5290877 CTAAGGATATACCTTGGGACTTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
1 CTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
*
5290942 GCAAAAGGAACCAAC
66 GCAAAGGGAACCAAC
* *
5290957 CTAAGGATATACATTGGGACCTACCCAAGATATCCTTAGGTCTGTAGGGTTACCTTATGCACACA
1 CTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
* * *
5291022 ACAAATGGTACCAAC
66 GCAAAGGGAACCAAC
*
5291037 CTAAGGATATACCTTGGGACCTACCCAAGAAATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
1 CTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
*
5291102 GCAAATGGAACCAAC
66 GCAAAGGGAACCAAC
* *
5291117 CTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
1 CTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
5291160 ATAAGAACTT
Statistics
Matches: 339, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
79 66 0.19
80 271 0.80
81 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (80 bp):
CTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACA
GCAAAGGGAACCAAC
Found at i:5296446 original size:80 final size:80
Alignment explanation
Indices: 5296207--5296676 Score: 701
Period size: 80 Copynumber: 5.8 Consensus size: 80
5296197 CTTGCCCTCA
* *
5296207 GCACACAACAAAAAGGATAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAG
1 GCACACAAC-AAAAGGA-A-CCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAG
* *
5296271 ATCCGTAGGGTTACCTTAA
62 GTCCGTAGGGTTACCTTAT
* * * * *
5296290 GCACACAGCTAAGGGAACTAACCTAAGGATATACCTTGGG-CCTACCCAAGATATCCTTAGGCCC
1 GCACACAACAAAAGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
5296354 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
*
5296369 GCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
1 GCACACAACAAAAGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
5296434 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
* *
5296449 GCACACAACAAAAGGAACTAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCT
1 GCACACAACAAAAGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
5296514 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
* * * *
5296529 GCACACAACAAATGGTACCAACATAAGGATATACCTTGGGACCTACCCAAGAAATCCTTAGGTCC
1 GCACACAACAAAAGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
5296594 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
* * * * *
5296609 GTACACAGCAAATGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
1 GCACACAACAAAAGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
5296674 GTA
66 GTA
5296677 AGAACTTATA
Statistics
Matches: 356, Mismatches: 29, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
79 63 0.18
80 277 0.78
81 3 0.01
82 5 0.01
83 8 0.02
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (80 bp):
GCACACAACAAAAGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
GTAGGGTTACCTTAT
Found at i:5300564 original size:2 final size:2
Alignment explanation
Indices: 5300557--5300586 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5300547 ATCTATAGAT
5300557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5300587 AACACTATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5300737 original size:2 final size:2
Alignment explanation
Indices: 5300725--5300794 Score: 63
Period size: 2 Copynumber: 35.0 Consensus size: 2
5300715 ATAAACCATG
* **
5300725 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA -A CC TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
**
5300768 TA TA TA TA TA TA -A CC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5300795 AAACTATGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.04
2 51 0.91
3 3 0.05
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5300752 original size:17 final size:19
Alignment explanation
Indices: 5300725--5300794 Score: 86
Period size: 19 Copynumber: 3.4 Consensus size: 19
5300715 ATAAACCATG
*
5300725 TATAGTATATATAAACTATA
1 TATA-TATATATAACCTATA
5300745 TATATATATATAACCTATATATA
1 TATATATATATAACC----TATA
5300768 TATATATATATAACCTATA
1 TATATATATATAACCTATA
5300787 TATATATA
1 TATATATA
5300795 AAACTATGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
19 22 0.49
20 4 0.09
23 19 0.42
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (19 bp):
TATATATATATAACCTATA
Found at i:5300754 original size:19 final size:19
Alignment explanation
Indices: 5300714--5300794 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 19
5300704 TACATGTATG
* *
5300714 TATAAACCATGTATAGTATA
1 TATAAACTATATATA-TATA
5300734 TATAAACTATATATATATA
1 TATAAACTATATATATATA
*
5300753 TATAACCTATATATATATATA
1 TATAAAC--TATATATATATA
5300774 TATATAACCTATATATATATA
1 TATA-AA-CTATATATATATA
5300795 AAACTATGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.19
20 13 0.25
21 28 0.53
22 1 0.02
23 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:5300767 original size:23 final size:23
Alignment explanation
Indices: 5300741--5300794 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
5300731 ATATATAAAC
5300741 TATATATATATATATAACCTATA
1 TATATATATATATATAACCTATA
5300764 TATATATATATATATAACCTATA
1 TATATATATATATATAACCTATA
5300787 TATATATA
1 TATATATA
5300795 AAACTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATATATATATATAACCTATA
Found at i:5300892 original size:7 final size:7
Alignment explanation
Indices: 5300880--5300959 Score: 52
Period size: 7 Copynumber: 11.3 Consensus size: 7
5300870 AGTTTTATAA
5300880 AAACCCT
1 AAACCCT
5300887 AAACCCT
1 AAACCCT
***
5300894 AAACAAA
1 AAACCCT
* *
5300901 AAATCTT
1 AAACCCT
5300908 AAACCCT
1 AAACCCT
**
5300915 AAACTTT
1 AAACCCT
5300922 AAACCCT
1 AAACCCT
**
5300929 AAAATACT
1 -AAACCCT
5300937 AAACCCT
1 AAACCCT
* *
5300944 AATCCAT
1 AAACCCT
5300951 AAACCCT
1 AAACCCT
5300958 AA
1 AA
5300960 TATAAATACA
Statistics
Matches: 51, Mismatches: 21, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
7 46 0.90
8 5 0.10
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:5300931 original size:21 final size:21
Alignment explanation
Indices: 5300878--5300918 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5300868 ATAGTTTTAT
5300878 AAAAACCCTAAACCCTAAACA
1 AAAAACCCTAAACCCTAAACA
* *
5300899 AAAAATCTTAAACCCTAAAC
1 AAAAACCCTAAACCCTAAAC
5300919 TTTAAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAACCCTAAACCCTAAACA
Found at i:5300941 original size:15 final size:14
Alignment explanation
Indices: 5300900--5300945 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
5300890 CCCTAAACAA
5300900 AAAATCTTAAACCCT
1 AAAATC-TAAACCCT
* *
5300915 AAACTTTAAACCCT
1 AAAATCTAAACCCT
5300929 AAAATACTAAACCCT
1 AAAAT-CTAAACCCT
5300944 AA
1 AA
5300946 TCCATAAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATCTAAACCCT
Found at i:5301380 original size:2 final size:2
Alignment explanation
Indices: 5301306--5301371 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
5301296 ATGAACCATG
* * * *
5301306 TA TA -A TA TA TA TA AA CTA TA TA TA TA TA TA TA AA TA AA TA AA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5301348 TA AA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
5301372 AACTATATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (2 bp):
TA
Found at i:5301449 original size:576 final size:571
Alignment explanation
Indices: 5300707--5301849 Score: 1747
Period size: 567 Copynumber: 2.0 Consensus size: 571
5300697 CTTATAGTAC
* * * * *
5300707 ATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATATAACCTATATATATATA
1 ATGTATGTATAAACCATGTATAATATATATAAACTATATATATATATATAACATAAATAAATAAA
* * *
5300772 TATATATAACCTATATATATATAAAACTATGTAAAGTAAATTAATTATATAATTTATAGAAATAC
66 TAAATATAA-CTATATATATATAAAACTATATAAAGTAAAGTAATTATATAATTTATAGAAATAC
5300837 TATGCATAAACTATATAAAGTAATAAAATATATAGTTTTATAAAAACCCTAAACCCTAAACAAAA
130 TATGCATAAACTATATAAAGTAATAAAATATATAG-TTTATAAAAACCCTAAACCCTAAACAAAA
* * * *
5300902 AAT-CTTAAACCCTAAACTTTAAACCCTAAAATACTAAACCCTAATCCATAAACCCTAATATAAA
194 AATAC-TAAACCATAAACTTTAAA-CC------A-TAAACACTAAACCATAAACCATAATATAAA
* * *
5300966 TACACTTCCACTAATGCATATATATTTGTAATAAAATAGTGGGCTTATGTATTGGGCCTATGCAA
250 TACACTACCACTAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGCCTATGCAA
5301031 ACTAATGTAAATGGACTAACACTAATACAAATGGACTTATTTTTGGGTTTTATTATTACTTATTC
315 ACTAATGTAAATGGACTAACACTAATACAAATGGACTTATTTTTGGGTTTTATTATTACTTATTC
*
5301096 ATAACAATAAAATAAATGGGCTATTAATGTGAATTAACCTAACATACAACTAAAATACTAATTAT
380 ATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATACAACTAAAATACTAATTAT
* * *
5301161 GTAAATGAAATTAATATGACATGTACTACTATTTATGAATCATATAATATGCAATGTGACATACT
445 GCAAATGAAATTAATATGACATGTACAACTATTTATGAACCATATAATATGCAATGTGACATACT
*
5301226 AATTATTTAACACCTAATTAATCATGTTTTATATAATTTATATTTAAATAATTTTATATAAT
510 AATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATATAAT
*
5301288 ATGTATGTATGAACCATGTATAATATATATAAACTATATATATATATATAA-ATAAATAAATAAA
1 ATGTATGTATAAACCATGTATAATATATATAAACTATATATATATATATAACATAAATAAATAAA
* * *
5301352 TAAATAT-A-TATATATATAT-AAACTATATAAAGTAAAGTATTTATGTAGTTTATAGAAATACT
66 TAAATATAACTATATATATATAAAACTATATAAAGTAAAGTAATTATATAATTTATAGAAATACT
* * * * *
5301414 ATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACTCTAAACCCTAAATAGAAAA
131 ATGCATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAACCCTAAACAAAAAA
* * **
5301479 TACTAAACCATAAACTTTAAACCATAAACACTAAACCATAAACCATAATGTAAATAGACTAGTAC
196 TACTAAACCATAAACTTTAAACCATAAACACTAAACCATAAACCATAATATAAATACACTACCAC
* * *
5301544 TAATGCATATATATTTTTAATAAAAGAGTGAGCTTATGTATTGGGCTTATGTAAACTAATGTAAA
261 TAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGCCTATGCAAACTAATGTAAA
** * * * * *
5301609 TGGACTAGTACTATTGCAAATGGACTTATTTTTTGGTTTTATTATTATTTATTCATAATAACAAA
326 TGGACTAACACTAATACAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAA
*
5301674 ATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAAT
391 ATAAATGGGCTATTAATGTGAATTAACCTAACATACAACTAAAATACTAATTATGCAAATGAAAT
*
5301739 TAATATGGCATGTACAACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAAC
456 TAATATGACATGTACAACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAAC
5301804 ACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTAT
521 ACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTAT
5301850 TAAATAATTT
Statistics
Matches: 516, Mismatches: 45, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
567 320 0.62
568 1 0.00
574 2 0.00
575 45 0.09
576 72 0.14
577 11 0.02
579 1 0.00
580 15 0.03
581 49 0.09
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (571 bp):
ATGTATGTATAAACCATGTATAATATATATAAACTATATATATATATATAACATAAATAAATAAA
TAAATATAACTATATATATATAAAACTATATAAAGTAAAGTAATTATATAATTTATAGAAATACT
ATGCATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAACCCTAAACAAAAAA
TACTAAACCATAAACTTTAAACCATAAACACTAAACCATAAACCATAATATAAATACACTACCAC
TAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGCCTATGCAAACTAATGTAAA
TGGACTAACACTAATACAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAA
ATAAATGGGCTATTAATGTGAATTAACCTAACATACAACTAAAATACTAATTATGCAAATGAAAT
TAATATGACATGTACAACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAAC
ACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATATAAT
Found at i:5301486 original size:21 final size:20
Alignment explanation
Indices: 5301451--5301492 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5301441 TATATAGTTT
* *
5301451 ATAGAAACTCTAAACCCTAA
1 ATAGAAAATCTAAACCATAA
5301471 ATAGAAAATACTAAACCATAA
1 ATAGAAAAT-CTAAACCATAA
5301492 A
1 A
5301493 CTTTAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAGAAAATCTAAACCATAA
Found at i:5301492 original size:7 final size:7
Alignment explanation
Indices: 5301482--5301526 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
5301472 TAGAAAATAC
5301482 TAAACCA
1 TAAACCA
**
5301489 TAAACTT
1 TAAACCA
5301496 TAAACCA
1 TAAACCA
5301503 TAAA-CA
1 TAAACCA
5301509 CTAAACCA
1 -TAAACCA
5301517 TAAACCA
1 TAAACCA
5301524 TAA
1 TAA
5301527 TGTAAATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:5301499 original size:14 final size:14
Alignment explanation
Indices: 5301480--5301521 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
5301470 AATAGAAAAT
5301480 ACTAAACCATAAAC
1 ACTAAACCATAAAC
**
5301494 TTTAAACCATAAAC
1 ACTAAACCATAAAC
5301508 ACTAAACCATAAAC
1 ACTAAACCATAAAC
5301522 CATAATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (14 bp):
ACTAAACCATAAAC
Found at i:5301868 original size:13 final size:13
Alignment explanation
Indices: 5301836--5301862 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5301826 TAATTTACAT
5301836 TTAAATAATTTTA
1 TTAAATAATTTTA
5301849 TTAAATAATTTTA
1 TTAAATAATTTTA
5301862 T
1 T
5301863 ATAATATGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:5302013 original size:14 final size:14
Alignment explanation
Indices: 5301994--5302044 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
5301984 TAGTTTATAG
5301994 AAACCCTAAATCAT
1 AAACCCTAAATCAT
*
5302008 AAACCCTAAA-CTTT
1 AAACCCTAAATC-AT
*
5302022 AAACCATAAAT-ACT
1 AAACCCTAAATCA-T
5302036 AAACCCTAA
1 AAACCCTAA
5302045 TCTAAATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 29 0.97
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:5302425 original size:2 final size:2
Alignment explanation
Indices: 5302364--5302417 Score: 81
Period size: 2 Copynumber: 26.0 Consensus size: 2
5302354 ATAAACCATG
*
5302364 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5302408 TA TA TA TA TA
1 TA TA TA TA TA
5302418 ACTATATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 45 0.94
3 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5302537 original size:14 final size:14
Alignment explanation
Indices: 5302500--5302578 Score: 72
Period size: 14 Copynumber: 5.6 Consensus size: 14
5302490 TAGTTTATAG
* *
5302500 AAACCTTAAACACT
1 AAACCCTAAACATT
* *
5302514 AAATCATAAACATT
1 AAACCCTAAACATT
5302528 AAACCCTAAA-ATTT
1 AAACCCTAAACA-TT
*
5302542 AAACTCTAAACATT
1 AAACCCTAAACATT
*
5302556 AAACTCTAAATCA-T
1 AAACCCTAAA-CATT
5302570 AAACCCTAA
1 AAACCCTAA
5302579 TATAATTGGA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
13 1 0.02
14 51 0.93
15 3 0.05
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAACATT
Found at i:5302551 original size:21 final size:21
Alignment explanation
Indices: 5302506--5302578 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
5302496 ATAGAAACCT
*
5302506 TAAACACT-AAATCATAAA-CA
1 TAAACCCTAAAATC-TAAATCA
*
5302526 TTAAACCCTAAAATTTAAACTC-
1 -TAAACCCTAAAATCTAAA-TCA
** *
5302548 TAAACATTAAACTCTAAATCA
1 TAAACCCTAAAATCTAAATCA
5302569 TAAACCCTAA
1 TAAACCCTAA
5302579 TATAATTGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.05
21 33 0.82
22 4 0.10
23 1 0.03
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAAAATCTAAATCA
Found at i:5302950 original size:20 final size:20
Alignment explanation
Indices: 5302898--5302950 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
5302888 TAAATAATTT
*
5302898 TATATAATATGTATGTATAAAC
1 TATATAA-A-GTATATATAAAC
* * *
5302920 CATGTATAGTATATATAAAC
1 TATATAAAGTATATATAAAC
5302940 TATATAAAGTA
1 TATATAAAGTA
5302951 AATTAATTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 19 0.79
21 1 0.04
22 4 0.17
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (20 bp):
TATATAAAGTATATATAAAC
Found at i:5303030 original size:7 final size:7
Alignment explanation
Indices: 5303020--5303091 Score: 54
Period size: 7 Copynumber: 10.3 Consensus size: 7
5303010 TAGTTTATAA
5303020 AAACCCT
1 AAACCCT
*
5303027 AAACACT
1 AAACCCT
* **
5303034 AAATCAA
1 AAACCCT
5303041 AAACCCT
1 AAACCCT
**
5303048 AAACTTT
1 AAACCCT
5303055 AAACCCT
1 AAACCCT
**
5303062 AAACATT
1 AAACCCT
*
5303069 AAACACT
1 AAACCCT
*
5303076 AAACCAT
1 AAACCCT
5303083 AAACCCT
1 AAACCCT
5303090 AA
1 AA
5303092 TATAAATGAA
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:5303058 original size:14 final size:14
Alignment explanation
Indices: 5303041--5303091 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
5303031 ACTAAATCAA
*
5303041 AAACCCTAAACTTT
1 AAACCCTAAACATT
5303055 AAACCCTAAACATT
1 AAACCCTAAACATT
*
5303069 AAACACTAAACCA-T
1 AAACCCTAAA-CATT
5303083 AAACCCTAA
1 AAACCCTAA
5303092 TATAAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 31 0.94
15 2 0.06
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAACATT
Found at i:5303063 original size:28 final size:28
Alignment explanation
Indices: 5303020--5303091 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
5303010 TAGTTTATAA
* * *
5303020 AAACCCTAAACACTAAATCA-AAAACCCT
1 AAACCATAAACCCTAAA-CATAAAACACT
** *
5303048 AAACTTTAAACCCTAAACATTAAACACT
1 AAACCATAAACCCTAAACATAAAACACT
5303076 AAACCATAAACCCTAA
1 AAACCATAAACCCTAA
5303092 TATAAATGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (28 bp):
AAACCATAAACCCTAAACATAAAACACT
Found at i:5303065 original size:21 final size:21
Alignment explanation
Indices: 5303020--5303091 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
5303010 TAGTTTATAA
* *
5303020 AAACCCTAAACACTAAATCAA
1 AAACCCTAAACACTAAACCAT
** *
5303041 AAACCCTAAACTTTAAACCCT
1 AAACCCTAAACACTAAACCAT
**
5303062 AAACATTAAACACTAAACCAT
1 AAACCCTAAACACTAAACCAT
5303083 AAACCCTAA
1 AAACCCTAA
5303092 TATAAATGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACACTAAACCAT
Found at i:5303263 original size:14 final size:14
Alignment explanation
Indices: 5303246--5303292 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
5303236 TTTTTTTCTT
5303246 TATATAAATTAAAC
1 TATATAAATTAAAC
5303260 TATAT-AATT----
1 TATATAAATTAAAC
5303269 TATATAAATTAAAC
1 TATATAAATTAAAC
*
5303283 TATATTAATT
1 TATATAAATT
5303293 TTCCTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:5303271 original size:23 final size:24
Alignment explanation
Indices: 5303244--5303293 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
5303234 TATTTTTTTC
5303244 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
5303267 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
5303291 TTT
1 TTT
5303294 TCCTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:5303557 original size:16 final size:16
Alignment explanation
Indices: 5303536--5303578 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
5303526 CGGATTATTT
*
5303536 ACAGGTCATGTTAAAA
1 ACAGGTCAGGTTAAAA
*
5303552 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
5303568 ACAGGTCAGGT
1 ACAGGTCAGGT
5303579 AATACCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:5304514 original size:10 final size:10
Alignment explanation
Indices: 5304475--5304514 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5304465 TTCATCACAC
5304475 CAAATTCTCT
1 CAAATTCTCT
*
5304485 CAATTTCTCT
1 CAAATTCTCT
*
5304495 CAACTTCTCT
1 CAAATTCTCT
*
5304505 CAAATACTCT
1 CAAATTCTCT
5304515 TATAATCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:5304572 original size:9 final size:9
Alignment explanation
Indices: 5304560--5304593 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5304550 TAATATTTTG
5304560 TATTTAATT
1 TATTTAATT
*
5304569 TATTTAA-G
1 TATTTAATT
5304577 TATTTAATT
1 TATTTAATT
5304586 TATTTAAT
1 TATTTAAT
5304594 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:5304599 original size:17 final size:17
Alignment explanation
Indices: 5304559--5304597 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5304549 TTAATATTTT
5304559 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
5304576 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
5304593 -TATTT
1 GTATTT
5304598 TACTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:5304701 original size:8 final size:8
Alignment explanation
Indices: 5304688--5304714 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5304678 GCTGATACGG
5304688 TAACATTT
1 TAACATTT
5304696 TAACATTT
1 TAACATTT
5304704 TAACATTT
1 TAACATTT
5304712 TAA
1 TAA
5304715 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (8 bp):
TAACATTT
Found at i:5308685 original size:20 final size:20
Alignment explanation
Indices: 5308660--5308699 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5308650 CGTTAAACAA
5308660 GGGGAATCGGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
5308680 GGGGAATCGGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
5308700 ATATTCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.40, T:0.15
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTGG
Found at i:5310850 original size:30 final size:29
Alignment explanation
Indices: 5310800--5310859 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
5310790 GAGAATATGA
* *
5310800 AAAGAAGCTATGTGACTATATGTATATGTG
1 AAAGAAGCTATGAGACTATATG-ACATGTG
5310830 AAAGAAGCTATGAG-CTTATATGACATGTG
1 AAAGAAGCTATGAGAC-TATATGACATGTG
5310859 A
1 A
5310860 TGTGAAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (29 bp):
AAAGAAGCTATGAGACTATATGACATGTG
Found at i:5311196 original size:35 final size:36
Alignment explanation
Indices: 5311157--5311235 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
5311147 TATGTGATAT
*
5311157 ATATATGTGT-TTTATGATATGAAT-TATATG-ATAAG
1 ATATATGTGTGTTAATGAT-T-AATGTATATGTATAAG
*
5311192 ATATATGTGTGTTAATGATTATTGTATATGTTATAAG
1 ATATATGTGTGTTAATGATTAATGTATATG-TATAAG
5311229 ATATATG
1 ATATATG
5311236 ATATGAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 2 0.05
35 17 0.45
36 7 0.18
37 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (36 bp):
ATATATGTGTGTTAATGATTAATGTATATGTATAAG
Found at i:5312493 original size:12 final size:12
Alignment explanation
Indices: 5312476--5312500 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5312466 TGGTGATGAG
5312476 AATGTATTGGAT
1 AATGTATTGGAT
5312488 AATGTATTGGAT
1 AATGTATTGGAT
5312500 A
1 A
5312501 CAGTTGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AATGTATTGGAT
Found at i:5324145 original size:33 final size:33
Alignment explanation
Indices: 5324108--5324188 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
5324098 AGTCCTACTT
*
5324108 GGACTCAAATGC-TTCAGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTT-AGTTTTAGTGTTTCAATA
*
5324141 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTAGTTTTAGTGTTTCAATA
*
5324174 GTACTCAAATACGTT
1 GGACTCAAATACGTT
5324189 GATTTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (33 bp):
GGACTCAAATACGTTAGTTTTAGTGTTTCAATA
Found at i:5324189 original size:33 final size:33
Alignment explanation
Indices: 5324124--5324189 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5324114 AAATGCTTCA
5324124 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
*
5324157 GTTTTAGTGTTTCAATAGTACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
5324190 ATTTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (33 bp):
GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
Found at i:5324256 original size:3 final size:3
Alignment explanation
Indices: 5324243--5324287 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
5324233 GGCCTGCAAA
5324243 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
5324286 AA
1 AA
5324288 AATGTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 5 0.13
3 32 0.84
4 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5324698 original size:83 final size:83
Alignment explanation
Indices: 5324529--5324767 Score: 298
Period size: 83 Copynumber: 2.9 Consensus size: 83
5324519 AATCTTGGTC
* * * * * * * *
5324529 GATAACCCTTATTGCCTTGAGCTATGCTGCAAATGATGGTGCCTTTAAGCTGAGTGGAGTCGAAC
1 GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT-GTGCCTTGAAGCTGAGCGTAGTCGAAC
* * *
5324594 TCGGAGGTCCTTGTTGACA
65 TAGAAGGTCCTTATTGACA
* * *
5324613 GATAACCCTTCTAGCCTTGATTTATGTTGTAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACT
1 GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACT
* * *
5324678 ATAAGGTCTTTATTGGCA
66 AGAAGGTCCTTATTGACA
*
5324696 GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATTATGTGCCTTGAAGCTGAGCGTAGTCGAACT
1 GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACT
*
5324761 CGAAGGT
66 AGAAGGT
5324768 TTGATGTTTC
Statistics
Matches: 132, Mismatches: 23, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
83 101 0.77
84 31 0.23
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (83 bp):
GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACT
AGAAGGTCCTTATTGACA
Found at i:5324810 original size:30 final size:30
Alignment explanation
Indices: 5324774--5324834 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5324764 AGGTTTGATG
*
5324774 TTTCAAGAGAAACATTTTCAAAGGTTTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTT
* * *
5324804 TTTCAAGAGAAATAATTTCGAGGGTTTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTT
5324834 T
1 T
5324835 GTGTTTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.44
Consensus pattern (30 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTTTT
Found at i:5324876 original size:36 final size:36
Alignment explanation
Indices: 5324836--5325075 Score: 193
Period size: 36 Copynumber: 6.9 Consensus size: 36
5324826 GGTTTTTTTG
* *
5324836 TGTTTCAAGAGAAACTATCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
5324872 TGTTTCAAAAGAAATTGTCTC-A-AGA-A-AAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
5324904 AG-TTCTAAAAGAAGCTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
5324940 TGTTTCAAG-GAAA-AGATATTC-A-AG-G----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
5324969 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
5325005 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
5325042 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
5325076 CTTGGAAACT
Statistics
Matches: 163, Mismatches: 23, Indels: 36
0.73 0.10 0.16
Matches are distributed among these distances:
29 14 0.09
30 6 0.04
31 6 0.04
32 20 0.12
33 3 0.02
34 6 0.04
35 7 0.04
36 63 0.39
37 38 0.23
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:5325044 original size:37 final size:37
Alignment explanation
Indices: 5324964--5325073 Score: 204
Period size: 36 Copynumber: 3.0 Consensus size: 37
5324954 GATATTCAAG
5324964 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
5325001 -AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
5325037 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
5325074 AACTTGGAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
36 35 0.50
37 35 0.50
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (37 bp):
GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:5329983 original size:14 final size:14
Alignment explanation
Indices: 5329929--5329974 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
5329919 GAGAGAAGAA
5329929 TAATA-AAAAATAT
1 TAATATAAAAATAT
5329942 TAATATAAAAATAT
1 TAATATAAAAATAT
*
5329956 TAATATAATAATAT
1 TAATATAAAAATAT
5329970 TAATA
1 TAATA
5329975 AATATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 5 0.16
14 26 0.84
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATATAAAAATAT
Found at i:5330424 original size:33 final size:33
Alignment explanation
Indices: 5330343--5330424 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
5330333 AGTCCTACTT
* * *
5330343 GGACTCAAATGCTTTAGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
**
5330376 AAACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
5330409 GGACTCAAATACGTTG
1 GGACTCAAATACGTTG
5330425 ATTTATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (33 bp):
GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
Found at i:5330486 original size:3 final size:3
Alignment explanation
Indices: 5330478--5330518 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5330468 GGCCTACAAA
5330478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5330519 AAAATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5332633 original size:11 final size:11
Alignment explanation
Indices: 5332617--5332641 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5332607 CTTTCTCCTT
5332617 AGACATTAAAG
1 AGACATTAAAG
5332628 AGACATTAAAG
1 AGACATTAAAG
5332639 AGA
1 AGA
5332642 GCAACTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (11 bp):
AGACATTAAAG
Found at i:5346459 original size:4 final size:4
Alignment explanation
Indices: 5346450--5346487 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
5346440 GACATTGTAT
5346450 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
5346488 GTTGTTGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5348050 original size:2 final size:2
Alignment explanation
Indices: 5348043--5348082 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5348033 TACCATTTTC
5348043 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
5348083 CATAATAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5350862 original size:2 final size:2
Alignment explanation
Indices: 5350784--5350846 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5350774 TTTTAAACAT
5350784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5350826 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5350847 GTAGTATTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5350900 original size:32 final size:30
Alignment explanation
Indices: 5350864--5350923 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
5350854 TAAATATATT
5350864 TTCATTGGCCAT-GTGCTAGCTTTTGCCTTTAC
1 TTCA-TGGCCATGGTGCTA-CTTTT-CCTTTAC
*
5350896 TTCATGGTCATGGTGCTACTTTTCCTTT
1 TTCATGGCCATGGTGCTACTTTTCCTTT
5350924 TCAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.19
31 11 0.42
32 10 0.38
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (30 bp):
TTCATGGCCATGGTGCTACTTTTCCTTTAC
Found at i:5360795 original size:21 final size:21
Alignment explanation
Indices: 5360769--5360811 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5360759 ATTCTGGGTT
* *
5360769 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
5360790 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
5360811 A
1 A
5360812 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Done.