Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001284.1 Hibiscus syriacus cultivar Beakdansim tig00002518_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: 86703
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3825 original size:22 final size:22
Alignment explanation
Indices: 3797--3847 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
3787 TTATATGCCA
3797 ACATACTATACAAAATCAACAT
1 ACATACTATACAAAATCAACAT
3819 ACATACTATACAAAATCAACAT
1 ACATACTATACAAAATCAACAT
3841 ACATACT
1 ACATACT
3848 TTATTAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (22 bp):
ACATACTATACAAAATCAACAT
Found at i:4256 original size:18 final size:18
Alignment explanation
Indices: 4233--4267 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4223 ACTGAATATT
*
4233 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
4251 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
4268 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:4920 original size:19 final size:19
Alignment explanation
Indices: 4896--4946 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
4886 TAATCTTAAG
4896 GGGGTGCATCGATGCATGA
1 GGGGTGCATCGATGCATGA
4915 GGGGTGCATCGATGCATGA
1 GGGGTGCATCGATGCATGA
*
4934 GGAGTGCATCGAT
1 GGGGTGCATCGAT
4947 ACATAATTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
GGGGTGCATCGATGCATGA
Found at i:6004 original size:38 final size:40
Alignment explanation
Indices: 5935--6012 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 40
5925 TAATGTAAGA
5935 TATATTTGAGAATAAGATTACTGTATTGTAATATTACTCT
1 TATATTTGAGAATAAGATTACTGTATTGTAATATTACTCT
* * *
5975 TATA-TTGGGAATAAGA-TATTTTATTGTAATATTACTCT
1 TATATTTGAGAATAAGATTACTGTATTGTAATATTACTCT
6013 AAGAATTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 20 0.57
39 11 0.31
40 4 0.11
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (40 bp):
TATATTTGAGAATAAGATTACTGTATTGTAATATTACTCT
Found at i:6682 original size:23 final size:22
Alignment explanation
Indices: 6656--6721 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
6646 CACCACAGCT
*
6656 CGTATAATTGCACCGAAGTGCCA
1 CGTA-AATTGCACCGTAGTGCCA
*
6679 CGTAGAATTGCACCGTAGTGCCG
1 CGTA-AATTGCACCGTAGTGCCA
6702 CG--AATTGCACCGTAGTGCCA
1 CGTAAATTGCACCGTAGTGCCA
6722 TAAAATAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 17 0.44
23 22 0.56
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (22 bp):
CGTAAATTGCACCGTAGTGCCA
Found at i:6708 original size:20 final size:20
Alignment explanation
Indices: 6683--6720 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6673 GTGCCACGTA
6683 GAATTGCACCGTAGTGCCGC
1 GAATTGCACCGTAGTGCCGC
6703 GAATTGCACCGTAGTGCC
1 GAATTGCACCGTAGTGCC
6721 ATAAAATAAT
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:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (20 bp):
GAATTGCACCGTAGTGCCGC
Found at i:7479 original size:56 final size:55
Alignment explanation
Indices: 7376--7481 Score: 131
Period size: 56 Copynumber: 1.9 Consensus size: 55
7366 CATAAATCAT
** * *
7376 ATTCGATGTTTGTATTTAATGGGGTACATCGATGCACTCCTTATGCATCGATGGA
1 ATTCGATGTTTGTATTTAAAAGAGTACATCGATGCACTCCATATGCATCGATGGA
* * * *
7431 ATTCGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTTCATGTGCATCG
1 ATTCGATGTTTGTA-TTTAAAAGAGTACATCGATGCACTCCATATGCATCG
7482 GTACACCTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
55 13 0.31
56 29 0.69
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (55 bp):
ATTCGATGTTTGTATTTAAAAGAGTACATCGATGCACTCCATATGCATCGATGGA
Found at i:13485 original size:23 final size:23
Alignment explanation
Indices: 13459--13523 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
13449 CAGCTCGTAT
13459 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* **
13482 AATTACACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCATGTAG
*
13505 AATTGCACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
13524 ATAATAATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:13781 original size:30 final size:30
Alignment explanation
Indices: 13746--13834 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
13736 TATTACGTAA
* * * *
13746 ACATATTATTTTCATACCTTTGTCACATTG
1 ACATATCATTTCCATACCTTTATCACATAG
*
13776 GCATATCATTTCCATACCTTTATCACATAG
1 ACATATCATTTCCATACCTTTATCACATAG
13806 ACATATCATTTCCATACCTTTATCACATA
1 ACATATCATTTCCATACCTTTATCACATA
13835 ACTCATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.40
Consensus pattern (30 bp):
ACATATCATTTCCATACCTTTATCACATAG
Found at i:14272 original size:63 final size:64
Alignment explanation
Indices: 14197--14319 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 64
14187 GCACTACACC
* * ** *
14197 ATGCATCGATGCATAAAT-CCTATTCGATGTTTGTA-TTTAATGGGGTGCATCGATGCACTCCTT
1 ATGCATCAATGCATAAATGCC-ATTCAATGTTTGTATTTTAAAAGAGTGCATCGATGCACTCCTT
** *
14260 ATGCATCAATGCATCGATGGCATTCAATGTTTGTATTTTAAAAGAGTGCATCGATGCACT
1 ATGCATCAATGCATAAATGCCATTCAATGTTTGTATTTTAAAAGAGTGCATCGATGCACT
14320 TCATGTGCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 28 0.56
64 22 0.44
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCAATGCATAAATGCCATTCAATGTTTGTATTTTAAAAGAGTGCATCGATGCACTCCTT
Found at i:15901 original size:16 final size:16
Alignment explanation
Indices: 15864--15910 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
15854 TTTTCATATC
15864 ATAAAAT-TATAAAAT
1 ATAAAATATATAAAAT
* *
15879 AT-TAATATATTAAAT
1 ATAAAATATATAAAAT
15894 ATAAAATATATAAAAT
1 ATAAAATATATAAAAT
15910 A
1 A
15911 ATTTTAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 3 0.12
15 11 0.42
16 12 0.46
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAATATATAAAAT
Found at i:25626 original size:2 final size:2
Alignment explanation
Indices: 25619--25649 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25609 CAGCAAAAGC
25619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25650 AGATTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27804 original size:226 final size:226
Alignment explanation
Indices: 27397--27881 Score: 866
Period size: 226 Copynumber: 2.1 Consensus size: 226
27387 GTTATATTGT
* * *
27397 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTCCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTCCACTGTGAAAACATATTTATTATTA
*
27462 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAAT
66 TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAAT
27527 AATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
131 AATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AA
*
27592 AAAATTGAAACATATATTACATAACTTTAAAA
195 AAAATTGAAACATAAATTACATAACTTTAAAA
* *
27624 ATA-TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTCCACTGT-GAAAACATATTTATTATT
*
27688 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
65 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
27753 TAATTTT-TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
130 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
27817 AAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAATTGAAACATAAATTACATAACTTTAAAA
27849 AAAGTATATATCATTTTTATAAAAGTGTCCATA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATA
27882 TGTATAAAAG
Statistics
Matches: 247, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
225 35 0.14
226 123 0.50
227 89 0.36
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (226 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTCCACTGTGAAAACATATTTATTATTA
TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAAT
AATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
AAATTGAAACATAAATTACATAACTTTAAAA
Found at i:27954 original size:20 final size:19
Alignment explanation
Indices: 27917--27977 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
27907 AATAAATATT
*
27917 AAAATGAT-ATACCAGGTAA
1 AAAATGATAAAACC-GGTAA
27936 AAATATGATAAAACCGGTAA
1 AAA-ATGATAAAACCGGTAA
27956 CAAAATGATAAAACCGGTAA
1 -AAAATGATAAAACCGGTAA
27976 AA
1 AA
27978 CGTTACCAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 26 0.68
21 7 0.18
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAATGATAAAACCGGTAA
Found at i:28158 original size:17 final size:19
Alignment explanation
Indices: 28119--28161 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
28109 AGGTAAATAT
28119 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
28139 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
28156 ATGATA
1 ATGATA
28162 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:30397 original size:21 final size:21
Alignment explanation
Indices: 30373--30416 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
30363 AAGACAATCA
30373 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
30394 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
30415 AG
1 AG
30417 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:30491 original size:33 final size:33
Alignment explanation
Indices: 30449--30514 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
30439 AAATAGATGG
*
30449 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
30482 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
30515 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:32327 original size:19 final size:19
Alignment explanation
Indices: 32303--32351 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
32293 AATGTAGGGT
32303 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
32322 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
32341 TATTTTTGTAT
1 TAATTTTGTAT
32352 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:33151 original size:198 final size:197
Alignment explanation
Indices: 32470--34008 Score: 2543
Period size: 198 Copynumber: 7.9 Consensus size: 197
32460 CAATATGGCC
* * *
32470 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGC-ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
32535 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
64 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* * * * * *
32600 GAATATGTCTAAATAATGTATCAACACTAATTTAGTTTGTGTCAATATTTTTGTTCCAGAATGAA
129 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAA
32665 TGGAA
193 TGGAA
*
32670 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGC-ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* * *
32735 TAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTGTGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
32800 AATATGTCT-AATAATGTGTCGACACTAATTTAGTT-GTGTCGATATTTTTGTTCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAAT
32863 GGAA
194 GGAA
32867 AAC-GGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGC-ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
32931 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAATCGGTACAAGTTTACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
32996 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
130 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
33061 GAA
195 GAA
33064 AACAGGGTGCACCTATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACC-ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
33129 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
33194 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTAGTGTCGATATTTTTGGTCCAGAATGAATG
130 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
33259 GAA
195 GAA
33262 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
33326 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
33391 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
130 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
33456 GAA
195 GAA
* *
33459 AACAGGGTGCACCCATAAAGTGTCGATCC------CAAAA---TC-AT--C--GA--A-C---CC
1 AACAGGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
33504 AAAA-GTATAATGTAATATGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
33568 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
130 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
33633 GAA
195 GAA
*
33636 AACAGGGTGCACCTATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
1 AACAGGGTGCACC-ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
33701 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
33766 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
130 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
33831 GAA
195 GAA
33834 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
33899 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAAGTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
33964 AATATGTCTAAATAATGTGTAGACACTTTTTAGTTTGTGTCGATA
130 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATA
34009 CTAATTTAAA
Statistics
Matches: 1279, Mismatches: 31, Indels: 60
0.93 0.02 0.04
Matches are distributed among these distances:
176 2 0.00
177 152 0.12
178 5 0.00
181 1 0.00
182 1 0.00
183 4 0.00
184 1 0.00
186 3 0.00
187 2 0.00
188 2 0.00
189 3 0.00
191 1 0.00
192 4 0.00
193 1 0.00
194 1 0.00
196 138 0.11
197 282 0.22
198 537 0.42
199 79 0.06
200 60 0.05
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (197 bp):
AACAGGGTGCACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATGG
AA
Found at i:35493 original size:6 final size:6
Alignment explanation
Indices: 35469--35584 Score: 97
Period size: 6 Copynumber: 19.3 Consensus size: 6
35459 AGCGGTCGCA
* * * *
35469 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GAAGAT GACGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * * * * *
35517 GACGAT GATGAT GACGAT GAAGCT GACGAT GACGAT GATGAC GATGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* *
35565 GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA
35585 TGATCCAAAC
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:35586 original size:24 final size:24
Alignment explanation
Indices: 35472--35588 Score: 126
Period size: 24 Copynumber: 4.9 Consensus size: 24
35462 GGTCGCAGAA
* *
35472 GATGAAGCTGACGATGAAGATGAC
1 GATGAAGATGACGATGATGATGAC
*
35496 GATGAAGATGACGATGAAGATGAC
1 GATGAAGATGACGATGATGATGAC
* * *
35520 GATGATGATGACGATGAAGCTGAC
1 GATGAAGATGACGATGATGATGAC
* * * *
35544 GATGACGATGATGACGATGATGAT
1 GATGAAGATGACGATGATGATGAC
* *
35568 GATGATGATGAAGATGATGAT
1 GATGAAGATGACGATGATGAT
35589 CCAAACAAGT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 81 1.00
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.21
Consensus pattern (24 bp):
GATGAAGATGACGATGATGATGAC
Found at i:35588 original size:12 final size:12
Alignment explanation
Indices: 35472--35575 Score: 136
Period size: 12 Copynumber: 8.4 Consensus size: 12
35462 GGTCGCAGAA
*
35472 GATGAAGCTGAC
1 GATGAAGATGAC
35484 GATGAAGATGAC
1 GATGAAGATGAC
35496 GATGAAGATGAC
1 GATGAAGATGAC
35508 GATGAAGATGAC
1 GATGAAGATGAC
*
35520 GATGATGATGAC
1 GATGAAGATGAC
*
35532 GATGAAGCTGAC
1 GATGAAGATGAC
35544 GATGACGATGATGAC
1 GATGA--A-GATGAC
* *
35559 GATGATGATGAT
1 GATGAAGATGAC
35571 GATGA
1 GATGA
35576 TGAAGATGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
12 71 0.87
14 1 0.01
15 10 0.12
ACGTcount: A:0.37, C:0.10, G:0.34, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:37362 original size:183 final size:182
Alignment explanation
Indices: 37090--37579 Score: 854
Period size: 183 Copynumber: 2.7 Consensus size: 182
37080 ATGCTATCGA
* *
37090 TATAAATATACCTGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* * *
37155 TCGGTACTTTATGTCCAGATTGGAAGAAAAATATATCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACATTT
* *
37220 ACACATCGGAACCTATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
37273 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
37338 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACATTT
*
37403 ACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
* * *
37456 TATAAATATACCGGTTTTATGAGTGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
37521 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
37580 GTAATTTTAA
Statistics
Matches: 294, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
183 290 0.99
184 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (182 bp):
TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACATTTA
CACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:40075 original size:25 final size:25
Alignment explanation
Indices: 40047--40111 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
40037 TTATCATTAA
40047 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
40072 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
40097 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
40112 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:40439 original size:22 final size:21
Alignment explanation
Indices: 40393--40439 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
40383 AAATTACATA
*
40393 ACTTTTAAAAAAGTATCGATC
1 ACTTTTAAAAAAGTATCGAAC
40414 -CTTTTATATAAAAGTAT-GAAC
1 ACTTTTA-A-AAAAGTATCGAAC
40435 ACTTT
1 ACTTT
40440 CAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (21 bp):
ACTTTTAAAAAAGTATCGAAC
Found at i:40488 original size:23 final size:23
Alignment explanation
Indices: 40457--40529 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
40447 ATAGGTAAAC
*
40457 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
40480 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
40503 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
40526 ATAT
1 ATAT
40530 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:40557 original size:21 final size:21
Alignment explanation
Indices: 40533--40572 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40523 GTTATATTGT
* *
40533 AAAGTATCTATATTTTTTTTA
1 AAAGTATCCATACTTTTTTTA
*
40554 AAAGTGTCCATACTTTTTT
1 AAAGTATCCATACTTTTTT
40573 CACTGTGGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
AAAGTATCCATACTTTTTTTA
Found at i:40978 original size:18 final size:18
Alignment explanation
Indices: 40957--40993 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40947 GTAATTGGAG
40957 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
40975 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
40993 T
1 T
40994 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:41001 original size:24 final size:24
Alignment explanation
Indices: 40949--40995 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40939 TTTCATATGT
* *
40949 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
40973 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
40996 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:41296 original size:39 final size:39
Alignment explanation
Indices: 41252--41338 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
41242 TCTAATGCTC
*
41252 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* * *
41291 TTCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
41330 ATCAAAATC
1 ATCAAAATC
41339 TACAACTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:41788 original size:23 final size:23
Alignment explanation
Indices: 41757--41829 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
41747 ATAGGTAAAA
*
41757 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
41780 ATATAATGTAATATGTAACGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
41803 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
41826 ATAT
1 ATAT
41830 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:42216 original size:23 final size:23
Alignment explanation
Indices: 42185--42257 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
42175 ATAGGTAAAA
*
42185 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
42208 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
42231 ATATAATGTAATCGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
42254 ATAT
1 ATAT
42258 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:42353 original size:428 final size:431
Alignment explanation
Indices: 41554--43891 Score: 4272
Period size: 427 Copynumber: 5.5 Consensus size: 431
41544 GTTAATGTTG
*
41554 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
41618 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAATACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* * *
41683 AAATTACATAAGTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTAAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
* *
41748 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAACGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
*
41813 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
*
41878 TGGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
41943 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
41984 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAATTTTTT-TGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
42047 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* *
42111 AAATTACATAACTTTAAAAGAAGTATCGATCTTTTTTATAAAAAGTATGGTCACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
42176 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
*
42241 ATCGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
42306 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
42371 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
42412 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
42477 ATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
*
42542 AAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
42607 TAGGTAAAAATATGATGTAATATGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
*
42672 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCTTTTTTATAAAAGTGTCCATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
42737 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
42802 CGTCTAATGATTTATTTTTTACGTTACG--ATATA-TATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
42840 TTAAATT-AAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
42904 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* *
42969 AAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
43034 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATATTGTAATAGGTATCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
*
43099 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTG
261 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
43164 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
*
43229 CGCCTAATGATTTATTTTTTACGTTACG--ATATA-TATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
43267 TTAAATTAAAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
43331 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* *
43395 AAATTACATAACTTTAAAAGAAGTATTGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
43460 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATGGGTATCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
* * *
43525 ATAGGTAGTGATTATATTGTAAAGTGTTTATCATTTTTATAAAAGTGTCCATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
*
43590 TGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
43655 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
43696 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
43760 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
*
43825 AAATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
43890 TA
196 TA
43892 TAATGTAATA
Statistics
Matches: 1852, Mismatches: 47, Indels: 18
0.97 0.02 0.01
Matches are distributed among these distances:
426 292 0.16
427 502 0.27
428 379 0.20
429 178 0.10
430 203 0.11
431 298 0.16
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (431 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:42647 original size:23 final size:23
Alignment explanation
Indices: 42616--42688 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
42606 ATAGGTAAAA
* *
42616 ATATGATGTAATATGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
42639 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
42662 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
42685 ATAT
1 ATAT
42689 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:43075 original size:23 final size:23
Alignment explanation
Indices: 43043--43115 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
43033 ATAGGTAAAA
*
43043 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
43066 ATATATTGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
43089 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
43112 ATAT
1 ATAT
43116 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:43500 original size:23 final size:23
Alignment explanation
Indices: 43469--43541 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
43459 ATAGGTAAAA
* *
43469 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGATT
* * *
43492 ATATAATGTAATGGGTATCGTTT
1 ATATAATGTAATAGGTAGCGATT
*
43515 ATATAATGTAATAGGTAGTGATT
1 ATATAATGTAATAGGTAGCGATT
43538 ATAT
1 ATAT
43542 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:45091 original size:16 final size:17
Alignment explanation
Indices: 45063--45096 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
45053 TGATAAACTA
*
45063 CAAAATGTCTACTCTTT
1 CAAAATGTCTACTATTT
45080 CAAAAT-TCTACTATTT
1 CAAAATGTCTACTATTT
45096 C
1 C
45097 TTTGTGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (17 bp):
CAAAATGTCTACTATTT
Found at i:50016 original size:82 final size:84
Alignment explanation
Indices: 49893--50049 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 84
49883 ACACTCTCTC
* * *
49893 ATATTTTACTCACTAAACTTCAAAAGATTGCAATTTAATAATTAAACTTTATATATTGA-TTTTT
1 ATATTTTACTCACTAAACTTCAAAAGATTGCAATTCAATAATTAAACTTTATACATTAATTTTTT
49957 TAATCACTCTGCTGTTAAA
66 TAATCACTCTGCTGTTAAA
* * * * *
49976 ATATTTTACTCACT-AATTTTAAAAGTTTTCAATTCAATAATTAATCTTTATACATTAATTTTTT
1 ATATTTTACTCACTAAACTTCAAAAGATTGCAATTCAATAATTAAACTTTATACATTAA-TTTTT
50040 TTAATCACTC
65 TTAATCACTC
50050 CGCCCATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 36 0.56
83 14 0.22
84 14 0.22
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.46
Consensus pattern (84 bp):
ATATTTTACTCACTAAACTTCAAAAGATTGCAATTCAATAATTAAACTTTATACATTAATTTTTT
TAATCACTCTGCTGTTAAA
Found at i:51534 original size:21 final size:21
Alignment explanation
Indices: 51457--51535 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
51447 AATTCTCTTC
*
51457 ATAAAAAGATTAAATCATTTT-
1 ATAAAAAGATTAAGTC-TTTTA
*
51478 ATAAAAAGATTAAGTCCTTTCA
1 ATAAAAAGATTAAGT-CTTTTA
* * *
51500 ACAAAAGGA-GAAGTCTTTTA
1 ATAAAAAGATTAAGTCTTTTA
*
51520 ATAAAAAGGTTAAGTC
1 ATAAAAAGATTAAGTC
51536 ATTTCATCGA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 11 0.24
21 26 0.58
22 8 0.18
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (21 bp):
ATAAAAAGATTAAGTCTTTTA
Found at i:53026 original size:16 final size:18
Alignment explanation
Indices: 52991--53031 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
52981 TTCCAAAAGT
52991 AATTTGCAGGTTCAAAGC-
1 AATTTGCA-GTTCAAAGCA
*
53009 AATTTGCA-TTCAATGCA
1 AATTTGCAGTTCAAAGCA
53026 AATTTG
1 AATTTG
53032 TCTGTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.33
17 6 0.29
18 8 0.38
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (18 bp):
AATTTGCAGTTCAAAGCA
Found at i:54830 original size:21 final size:21
Alignment explanation
Indices: 54734--54822 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
54724 AACAATTCTC
* * *
54734 TTCATGAAAAGATTAAATCCT
1 TTCATCAAAAGGTTAAGTCCT
* * *
54755 TTTATGAAAAGGTTAAGCCCT
1 TTCATCAAAAGGTTAAGTCCT
** *
54776 TTCATCAAAAGGAGAAGTCTT
1 TTCATCAAAAGGTTAAGTCCT
*
54797 TTAATCAAAAGGTTAAGTCCT
1 TTCATCAAAAGGTTAAGTCCT
54818 TTCAT
1 TTCAT
54823 TGAAAGGTCT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTCATCAAAAGGTTAAGTCCT
Found at i:55553 original size:17 final size:17
Alignment explanation
Indices: 55510--55565 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 17
55500 TTTGGTTTAC
*
55510 GGAATGTAAGATTATCA
1 GGAATGTAAGATTACCA
55527 GTGAGAATGTAAGATTACCA
1 --G-GAATGTAAGATTACCA
55547 GGAATGTAAGATTACCA
1 GGAATGTAAGATTACCA
55564 GG
1 GG
55566 GAATACGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
17 18 0.51
18 1 0.03
19 1 0.03
20 15 0.43
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (17 bp):
GGAATGTAAGATTACCA
Found at i:56099 original size:23 final size:23
Alignment explanation
Indices: 56064--56110 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
56054 CCAAAAAATT
* *
56064 CACTATTAGTAATGTAAGATTAC
1 CACTATTAGTAATATAAAATTAC
56087 CACTATT-GATAATATAAAATTAC
1 CACTATTAG-TAATATAAAATTAC
56110 C
1 C
56111 GAAAATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (23 bp):
CACTATTAGTAATATAAAATTAC
Found at i:57216 original size:20 final size:20
Alignment explanation
Indices: 57184--57239 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
57174 TTTTTAATAT
57184 TTTAATAATAAAAAAATTAA
1 TTTAATAATAAAAAAATTAA
57204 TTTAA-AATAAAAAAATTAA
1 TTTAATAATAAAAAAATTAA
* *
57223 TTTATTTATAAAAAAAT
1 TTTAATAATAAAAAAAT
57240 CTCAAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAATAATAAAAAAATTAA
Found at i:57807 original size:29 final size:29
Alignment explanation
Indices: 57774--57836 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
57764 GATGAAAATG
*
57774 TTAGGAACCTA-TTTTTAGAGAAAAATTCT
1 TTAGGAACCTATTTTTTA-AGAAAAATTAT
* * *
57803 TTAGGCACTTATTTTTTACGAAAAATTAT
1 TTAGGAACCTATTTTTTAAGAAAAATTAT
57832 TTAGG
1 TTAGG
57837 CACTAAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
TTAGGAACCTATTTTTTAAGAAAAATTAT
Found at i:58496 original size:31 final size:31
Alignment explanation
Indices: 58456--58530 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
58446 ATATTTCACC
*
58456 AAAAGTTTAAAGGTAAAATTAATATTTTATCT
1 AAAA-TTTAAAGATAAAATTAATATTTTATCT
* * * * *
58488 AAATTTTAATGATCAAATTAGTATTTTATTT
1 AAAATTTAAAGATAAAATTAATATTTTATCT
58519 AAAATTTAAAGA
1 AAAATTTAAAGA
58531 ACAACTCGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (31 bp):
AAAATTTAAAGATAAAATTAATATTTTATCT
Found at i:71344 original size:33 final size:29
Alignment explanation
Indices: 71304--71384 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
71294 AGAATTGATT
*
71304 TGAAATATCATATTTATATGACAATTTATA
1 TGAAATATCATATTTATATGA-AATTAATA
* * *
71334 TGAATTAAT-ATAATTTCTAT-AAATTAATT
1 TGAAAT-ATCAT-ATTTATATGAAATTAATA
71363 TGAAATATCATATTTATATGAA
1 TGAAATATCATATTTATATGAA
71385 TTTTGGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
28 9 0.22
29 15 0.37
30 8 0.20
31 9 0.22
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (29 bp):
TGAAATATCATATTTATATGAAATTAATA
Found at i:82673 original size:25 final size:25
Alignment explanation
Indices: 82627--82674 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
82617 GTCTATTCAT
* * **
82627 AATATTATTTTACTTTTTTTTAAAA
1 AATATTAATTTAATTTAATTTAAAA
82652 AATATTAATTTAATTTAATTTAA
1 AATATTAATTTAATTTAATTTAA
82675 TGTTCAATAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
AATATTAATTTAATTTAATTTAAAA
Found at i:83113 original size:34 final size:35
Alignment explanation
Indices: 83065--83130 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
83055 TAAACGAATG
83065 TAAACGAACATAATAAATGAACAT-AATGAACGTA
1 TAAACGAACATAATAAATGAACATAAATGAACGTA
* * *
83099 TAAACTAACGTAATAAATGAATATAAATGAAC
1 TAAACGAACATAATAAATGAACATAAATGAAC
83131 ATAAAACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.23
Consensus pattern (35 bp):
TAAACGAACATAATAAATGAACATAAATGAACGTA
Found at i:83336 original size:14 final size:14
Alignment explanation
Indices: 83319--83375 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
83309 AGATTGGGGT
*
83319 AAACATAAATGAAC
1 AAACATAAACGAAC
83333 AAACATAAACGAAC
1 AAACATAAACGAAC
*
83347 GAAA-GTAAACGAAC
1 -AAACATAAACGAAC
83361 AAACATAAACGAAC
1 AAACATAAACGAAC
83375 A
1 A
83376 TAAATGAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 3 0.08
14 32 0.84
15 3 0.08
ACGTcount: A:0.63, C:0.18, G:0.11, T:0.09
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:84184 original size:84 final size:84
Alignment explanation
Indices: 84085--84254 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 84
84075 TACATGTATA
84085 TAGTTTTCTTATGATTAATTATTGTAGTATAATAAACGTTTT-TGGCTTATTTATATATATATTG
1 TAGTTTTCTTATGATTAATTATTGTAGTATAATAAACGTTTTATGGCTTA-TTATATATATATTG
84149 ATGGTATTAATTATAAATGG
65 ATGGTATTAATTATAAATGG
84169 TAGTTTTCTTATGATTAATTATTGTAGTATAATAAACGTTTTATGGCTTATTATATATATATTGA
1 TAGTTTTCTTATGATTAATTATTGTAGTATAATAAACGTTTTATGGCTTATTATATATATATTGA
84234 TGGTATTAATTATAAATGG
66 TGGTATTAATTATAAATGG
84253 TA
1 TA
84255 AATACATATA
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 78 0.92
85 7 0.08
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (84 bp):
TAGTTTTCTTATGATTAATTATTGTAGTATAATAAACGTTTTATGGCTTATTATATATATATTGA
TGGTATTAATTATAAATGG
Found at i:84396 original size:35 final size:35
Alignment explanation
Indices: 84357--84443 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
84347 ATCATCAAAT
* ** *
84357 TAAAACGTGAATTGGGCTTCA-GATTTCAGTGCACA
1 TAAAACGTGAATTGGGCTT-ATGACTAAAATGCACA
* *
84392 TAAAACGTGAATTAGGC-TATGGCTAAAATGCACA
1 TAAAACGTGAATTGGGCTTATGACTAAAATGCACA
84426 TAAAACGTGAATTGGGCT
1 TAAAACGTGAATTGGGCT
84444 AAACGTGAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.02
34 26 0.60
35 16 0.37
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (35 bp):
TAAAACGTGAATTGGGCTTATGACTAAAATGCACA
Found at i:85510 original size:16 final size:16
Alignment explanation
Indices: 85489--85525 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
85479 ATTTTCATAG
85489 TCTAATGATAGTATAT
1 TCTAATGATAGTATAT
*
85505 TCTAATGATAGTTTAT
1 TCTAATGATAGTATAT
85521 T-TAAT
1 TCTAAT
85526 TTAATTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (16 bp):
TCTAATGATAGTATAT
Done.