Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 19
Found at i:141030 original size:198 final size:201
Alignment explanation
Indices: 140691--141091 Score: 781
Period size: 198 Copynumber: 2.0 Consensus size: 201
140681 ACATCCACAA
140691 CTTAGATCAGCAAAAATGCCACAAAATGTACAAATATGAGAGCAAAAGTGGTGCCTTTATAGCCG
1 CTTAGATCAGCAAAAATGCCACAAAATGTACAAATATGAGAGCAAAAGTGGTGCCTTTATAGCCG
140756 GTGAAATGAACTCATATTTGACAAAATTTGATGCATAAAACAAAGATAGAGAACCAGGAAAAGAG
66 GTGAAATGAACTCATATTTGACAAAATTTGATGCATAAAACAAAGATAGAGAACCAGGAAAAGAG
140821 ATGTGAAGCTGGAAAAATCAGATGCCTATGACTTTTACTTGAAT-ATGATGA-TCATTAATAAAA
131 ATGTGAAGCTGGAAAAATCAGATGCCTATGACTTTTACTTGAATAATGATGAGTCATTAATAAAA
140884 AAGATT
196 AAGATT
140890 CTTAGATCAGCAAAAATGCCACAAAATGTACAAATATGAGAGCAAAAGT-GTGCCTTTATAGCCG
1 CTTAGATCAGCAAAAATGCCACAAAATGTACAAATATGAGAGCAAAAGTGGTGCCTTTATAGCCG
140954 GTGAAATGAACTCATATTTGACAAAATTTGATGCATAAAACAAAGATAGAGAACCAGGAAAAGAG
66 GTGAAATGAACTCATATTTGACAAAATTTGATGCATAAAACAAAGATAGAGAACCAGGAAAAGAG
141019 ATGTGAAGCTGGAAAAATCAGATGCCTATGACTTTTACTTGAATAATGATGAGTCATTAATAAAA
131 ATGTGAAGCTGGAAAAATCAGATGCCTATGACTTTTACTTGAATAATGATGAGTCATTAATAAAA
141084 AAGATT
196 AAGATT
141090 CT
1 CT
141092 GCTGCCAGAT
Statistics
Matches: 200, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
198 124 0.62
199 56 0.28
200 20 0.10
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (201 bp):
CTTAGATCAGCAAAAATGCCACAAAATGTACAAATATGAGAGCAAAAGTGGTGCCTTTATAGCCG
GTGAAATGAACTCATATTTGACAAAATTTGATGCATAAAACAAAGATAGAGAACCAGGAAAAGAG
ATGTGAAGCTGGAAAAATCAGATGCCTATGACTTTTACTTGAATAATGATGAGTCATTAATAAAA
AAGATT
Found at i:147532 original size:16 final size:17
Alignment explanation
Indices: 147513--147545 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
147503 TTTTAATCCA
147513 AAATGTTAT-TAATAAT
1 AAATGTTATCTAATAAT
*
147529 AAATTTTATCTAATAAT
1 AAATGTTATCTAATAAT
147546 GATATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
AAATGTTATCTAATAAT
Found at i:154394 original size:44 final size:44
Alignment explanation
Indices: 154331--154431 Score: 168
Period size: 44 Copynumber: 2.3 Consensus size: 44
154321 CATACCCATT
* *
154331 GTGCATCAGTGTAAAATTCAAA-ATATTTGACCGTTGGACCCTTA
1 GTGCATCGGTGCAAAATTCAAATAT-TTTGACCGTTGGACCCTTA
154375 GTGCATCGGTGCAAAATTCAAATATTTTGACCGTTGGACCCTTA
1 GTGCATCGGTGCAAAATTCAAATATTTTGACCGTTGGACCCTTA
154419 GTGCATCGGTGCA
1 GTGCATCGGTGCA
154432 CTAAGAGTGC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 52 0.96
45 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
GTGCATCGGTGCAAAATTCAAATATTTTGACCGTTGGACCCTTA
Found at i:157082 original size:44 final size:44
Alignment explanation
Indices: 156999--157101 Score: 129
Period size: 43 Copynumber: 2.3 Consensus size: 44
156989 AAAACCCGAT
* * *
156999 GGATGCATCGATGCATGACCATGTGCATCGATACACATTC-AAG
1 GGATGCATCGATGCATCAACATGTGAATCGATACACATTCAAAG
*
157042 GCG-TGCATCGATGCATCAACATGATGAATCGATGCACATTCAAAG
1 G-GATGCATCGATGCATCAACATG-TGAATCGATACACATTCAAAG
*
157087 GGATACATCGATGCA
1 GGATGCATCGATGCA
157102 CTATTAAGTG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 19 0.37
44 17 0.33
45 15 0.29
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (44 bp):
GGATGCATCGATGCATCAACATGTGAATCGATACACATTCAAAG
Found at i:162937 original size:21 final size:21
Alignment explanation
Indices: 162911--162966 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
162901 TTCATGAAAT
*
162911 GTGCATCGGTGCATAGTCA-TG
1 GTGCATCGGTGCAT-GGCATTG
*
162932 GTGCATCGATGCATGGCATTG
1 GTGCATCGGTGCATGGCATTG
*
162953 ATGCATCGGTGCAT
1 GTGCATCGGTGCAT
162967 CACTCTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (21 bp):
GTGCATCGGTGCATGGCATTG
Found at i:171033 original size:15 final size:15
Alignment explanation
Indices: 171013--171042 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
171003 AATGAAATGG
171013 TAAAATTTTATTTTA
1 TAAAATTTTATTTTA
171028 TAAAATTTTATTTTA
1 TAAAATTTTATTTTA
171043 ACTCCTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAAAATTTTATTTTA
Found at i:184022 original size:16 final size:16
Alignment explanation
Indices: 183997--184035 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
183987 GGTATTACCC
*
183997 GACCTATTTTCAACCT
1 GACCTGTTTTCAACCT
*
184013 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
184029 GACCTGT
1 GACCTGT
184036 AAATGATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:184279 original size:25 final size:24
Alignment explanation
Indices: 184235--184281 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
184225 TTATTTAATA
*
184235 AAATTAATAAAATTATTTAAATGT
1 AAATTAATAAAAATATTTAAATGT
184259 AAATTAGATAAAACATA-TTAAAT
1 AAATTA-ATAAAA-ATATTTAAAT
184282 AATGCAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATTAATAAAAATATTTAAATGT
Found at i:184328 original size:23 final size:24
Alignment explanation
Indices: 184293--184338 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
184283 ATGCAAAGGA
184293 AAATTAATATAGTTTAATTTATAC
1 AAATTAATATAGTTTAATTTATAC
184317 AAATT-ATATAGTTTAATTTATA
1 AAATTAATATAGTTTAATTTATA
184339 AAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAC
Found at i:184413 original size:25 final size:22
Alignment explanation
Indices: 184353--184415 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 22
184343 GAAAAAATAA
184353 TATTAATAATAAA-AATATTTAT
1 TATTAAT-ATAAATAATATTTAT
184375 TATGTAATATAAATTAATGATTTAAT
1 TAT-TAATATAAA-TAAT-ATTT-AT
184401 TATTAATATAAATAA
1 TATTAATATAAATAA
184416 GTTTGGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
22 8 0.22
23 4 0.11
24 6 0.17
25 13 0.36
26 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTAATATAAATAATATTTAT
Found at i:184460 original size:22 final size:23
Alignment explanation
Indices: 184404--184467 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
184394 ATTTAATTAT
* *
184404 TAAT-ATAAATAAGTTTGGTAATA
1 TAATGATAATTAA-TTTGATAATA
184427 TAATGATAATTAATTTGATAATA
1 TAATGATAATTAATTTGATAATA
184450 -AATGA-ATATTAATATTGA
1 TAATGATA-ATTAAT-TTGA
184468 ACGTGATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 17 0.47
24 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (23 bp):
TAATGATAATTAATTTGATAATA
Found at i:187749 original size:102 final size:102
Alignment explanation
Indices: 187332--187739 Score: 610
Period size: 102 Copynumber: 4.0 Consensus size: 102
187322 AACAACCAAT
* * *
187332 AGTAGCTACAAATTAAATAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAAAAGC
1 AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAATCTAACAACCTTATAAAAGC
* *
187397 AATCCAAATGAACAA-C--CAGCACAAACAAATCAAC
66 AATCCGAATGAACAACCAACAACACAAACAAATCAAC
* * *
187431 AGTAGCTACCAATTAAACAATTTATTTAAACTGTAAATAAA-GACATCTAACAGCCTTATAAAAG
1 AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGA-ATCTAACAACCTTATAAAAG
* * *
187495 CAATCCGAATGAACAACTAACAACACAAATAAATCAAT
65 CAATCCGAATGAACAACCAACAACACAAACAAATCAAC
* *
187533 AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGT-TAACAGCCTTATAAAAG
1 AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGG-AATCTAACAACCTTATAAAAG
* *
187597 GAATTCGAATGAACAACCAACAACACAAACAAATCAAC
65 CAATCCGAATGAACAACCAACAACACAAACAAATCAAC
*
187635 AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAATCTAACAACCTTATAAAAAC
1 AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAATCTAACAACCTTATAAAAGC
*
187700 AATCCGAATGAACAACCAACAATACAAACAAATCAAC
66 AATCCGAATGAACAACCAACAACACAAACAAATCAAC
187737 AGT
1 AGT
187740 CGAAACAAAT
Statistics
Matches: 277, Mismatches: 25, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
98 1 0.00
99 71 0.26
101 2 0.01
102 200 0.72
103 2 0.01
104 1 0.00
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (102 bp):
AGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAATCTAACAACCTTATAAAAGC
AATCCGAATGAACAACCAACAACACAAACAAATCAAC
Found at i:188040 original size:5 final size:6
Alignment explanation
Indices: 188011--188048 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
188001 TTTGTGTTTT
*
188011 GGGTTT GGGTTC GGGTTC GGGTTC -GGTTC GGGTT- GGGT
1 GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGT
188049 GACAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.00, C:0.11, G:0.53, T:0.37
Consensus pattern (6 bp):
GGGTTC
Found at i:188040 original size:11 final size:12
Alignment explanation
Indices: 188011--188048 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
188001 TTTGTGTTTT
*
188011 GGGTTTGGGTTC
1 GGGTTCGGGTTC
188023 GGGTTCGGGTTC
1 GGGTTCGGGTTC
188035 -GGTTCGGGTT-
1 GGGTTCGGGTTC
188045 GGGT
1 GGGT
188049 GACAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.11, G:0.53, T:0.37
Consensus pattern (12 bp):
GGGTTCGGGTTC
Found at i:188745 original size:13 final size:13
Alignment explanation
Indices: 188719--188787 Score: 75
Period size: 15 Copynumber: 4.8 Consensus size: 13
188709 TAATTTTAAT
188719 TAATTAACTATTTA
1 TAATTAA-TATTTA
188733 TAATTAATATTTA
1 TAATTAATATTTA
*
188746 TAATAATTATATATTA
1 TAAT--TAATAT-TTA
188762 TAATTAATATTAATA
1 TAATTAATATT--TA
188777 TAATTAATATT
1 TAATTAATATT
188788 AATATTAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
13 11 0.23
14 12 0.25
15 18 0.38
16 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATTAATATTTA
Found at i:188762 original size:29 final size:27
Alignment explanation
Indices: 188709--188788 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 27
188699 CATCCCTATA
*
188709 TAATTTTAAT-TAATTAACTATTTATAAT
1 TAATATTAATATAATTAA-TA-TTATAAT
*
188737 TAATATTTATAATAATTATATATTATAAT
1 TAATATTAAT-ATAATTA-ATATTATAAT
188766 TAATATTAATATAATTAATATTA
1 TAATATTAATATAATTAATATTA
188789 ATATTAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 6 0.13
28 15 0.33
29 16 0.35
30 8 0.17
31 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTAATATAATTAATATTATAAT
Found at i:188880 original size:24 final size:25
Alignment explanation
Indices: 188835--188881 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
188825 TATAATTAAT
**
188835 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
188860 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
188882 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:188908 original size:14 final size:14
Alignment explanation
Indices: 188891--188952 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
188881 ATGTTATAAA
*
188891 TTATATAGTATAGT
1 TTATATAATATAGT
188905 TTATA-AACTATAGT
1 TTATATAA-TATAGT
*
188919 TAATATAATTAATA-T
1 TTATATAA-T-ATAGT
*
188934 TAATATAATATAGT
1 TTATATAATATAGT
188948 TTATA
1 TTATA
188953 AACTATATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.10
14 21 0.52
15 12 0.30
16 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATATAATATAGT
Found at i:188938 original size:15 final size:15
Alignment explanation
Indices: 188918--189006 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 15
188908 TAAACTATAG
188918 TTAATATAATTAATA
1 TTAATATAATTAATA
*
188933 TTAATATAATATAGTTTA
1 TTAATATAAT-TA--ATA
* *
188951 TAAACTATATACT-ATA
1 TTAA-TATA-ATTAATA
188967 TTAATATAAATT-ATA
1 TTAATAT-AATTAATA
* *
188982 GTTAAGATAATTAACA
1 -TTAATATAATTAATA
188998 TTAATATAA
1 TTAATATAA
189007 ACTATATAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
15 30 0.53
16 16 0.28
18 5 0.09
19 5 0.09
20 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:188992 original size:65 final size:65
Alignment explanation
Indices: 188731--189006 Score: 240
Period size: 65 Copynumber: 4.3 Consensus size: 65
188721 ATTAACTATT
* *
188731 TATAATTAATATT--TATAATA-A--TTATATATTATA-ATTAATATTAATAT-AATTAATA-TT
1 TATAATTAATATTAATATAATATAGTTTATAAATTATATACT-ATATTAATATAAATT-ATAGTT
188788 AA
64 AA
* ** * *
188790 TATTAACTT-AGATTAATATAATATAGTTTATAGTTTATA-ATTAATATTAATATAAAATATAGT
1 TA-TAA-TTAATATTAATATAATATAGTTTATAAATTATATACT-ATATTAATATAAATTATAGT
188853 CT-A
63 -TAA
* *
188856 TA-ACATTAATATTAATATAAACTATA-TGTTATAAATTATATAGTATAGTT--TATAAACTATA
1 TATA-ATTAATATTAATAT-AA-TATAGT-TTATAAATTATATACTATA-TTAATATAAATTATA
188917 GTTAA
61 GTTAA
*
188922 TATAATTAATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAA
1 TATAATTAATATTAATATAATATAGTTTATAAATTATATACTATATTAATATAAATTATAGTTAA
* *
188987 GATAATTAACATTAATATAA
1 TATAATTAATATTAATATAA
189007 ACTATATAGT
Statistics
Matches: 181, Mismatches: 14, Indels: 38
0.78 0.06 0.16
Matches are distributed among these distances:
59 2 0.01
60 7 0.04
61 2 0.01
62 7 0.04
63 3 0.02
64 24 0.13
65 74 0.41
66 39 0.22
67 19 0.10
68 4 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (65 bp):
TATAATTAATATTAATATAATATAGTTTATAAATTATATACTATATTAATATAAATTATAGTTAA
Found at i:189004 original size:31 final size:31
Alignment explanation
Indices: 188826--189012 Score: 143
Period size: 31 Copynumber: 5.8 Consensus size: 31
188816 TTTATAGTTT
* *
188826 ATAATTAATATTAATATAAAATATAGTCTATA
1 ATAATTAATATTAATATAAACTATAGT-TAAA
*
188858 A-CATTAATATTAATATAAACTATATGTTATAA
1 ATAATTAATATTAATATAAACTATA-GTTA-AA
* *
188890 ATTATATAGTATAGTT--TATAAACTATAGTTAAT
1 ATAAT-TA--ATA-TTAATATAAACTATAGTTAAA
188923 ATAATTAATATTAATAT-AA-TATAGTTTATAA
1 ATAATTAATATTAATATAAACTATAG-TTA-AA
* *
188954 ACT-ATATACTATATTAATATAAATTATAGTTAAG
1 A-TAAT-TA--ATATTAATATAAACTATAGTTAAA
*
188988 ATAATTAACATTAATATAAACTATA
1 ATAATTAATATTAATATAAACTATA
189013 TAGTACATTA
Statistics
Matches: 127, Mismatches: 10, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
29 7 0.06
30 8 0.06
31 46 0.36
32 10 0.08
33 10 0.08
34 20 0.16
35 16 0.13
36 8 0.06
37 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (31 bp):
ATAATTAATATTAATATAAACTATAGTTAAA
Found at i:189020 original size:22 final size:22
Alignment explanation
Indices: 188995--189097 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
188985 AAGATAATTA
188995 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
*
189017 ACATTAATATAAAC--TATGGT
1 ACATTAATATAAACTATATAGT
** * *
189037 TTATAAATTATATACTATAT-GT
1 ACATTAA-TATAAACTATATAGT
* *
189059 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
189081 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
189098 TGATTATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
20 9 0.14
21 23 0.35
22 28 0.42
23 6 0.09
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:189061 original size:21 final size:21
Alignment explanation
Indices: 189002--189077 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
188992 TTAACATTAA
* *
189002 TATAAACTATATAGTACATTAA-
1 TATAAACTATAT-GT-TATAAAG
* *
189024 TATAAACTAT-GGTTTATAAAT
1 TATAAACTATATG-TTATAAAG
*
189045 TATATACTATATGTTATAAAG
1 TATAAACTATATGTTATAAAG
189066 TATAAACTATAT
1 TATAAACTATAT
189078 AGTACACTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.11
21 28 0.64
22 11 0.25
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (21 bp):
TATAAACTATATGTTATAAAG
Found at i:189146 original size:20 final size:20
Alignment explanation
Indices: 189123--189213 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
189113 GGTTACATAT
*
189123 ATAGTTTATATAAAATATAA
1 ATAGTTTATATAAAATATAC
189143 ATAGATTGTATATATACAA-ATAC
1 ATAG-TT-TATATA-A-AATATAC
*
189166 TATAGGTTATAT---ATATAC
1 -ATAGTTTATATAAAATATAC
* *
189184 ATAGTTTATATATACTATAC
1 ATAGTTTATATAAAATATAC
189204 ATAGTTTATA
1 ATAGTTTATA
189214 CATATATGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
17 11 0.19
18 4 0.07
20 19 0.33
21 2 0.03
22 11 0.19
23 5 0.09
24 6 0.10
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (20 bp):
ATAGTTTATATAAAATATAC
Found at i:189213 original size:37 final size:41
Alignment explanation
Indices: 189122--189219 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 41
189112 AGGTTACATA
189122 TATAGTTTATATAAAATATAAATAGATTGTATATATACAAATAC
1 TATAGTTTATAT---ATATAAATAGATTGTATATATACAAATAC
* * *
189166 TATAGGTTATATATATACATAG-TT-TATATATAC-TATAC
1 TATAGTTTATATATATAAATAGATTGTATATATACAAATAC
*
189204 -ATAGTTTATACATATA
1 TATAGTTTATATATATA
189220 TGTACTATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
37 14 0.29
38 4 0.08
39 9 0.18
40 2 0.04
41 9 0.18
44 11 0.22
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (41 bp):
TATAGTTTATATATATAAATAGATTGTATATATACAAATAC
Found at i:189273 original size:24 final size:21
Alignment explanation
Indices: 189238--189284 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
189228 AAGTTACATA
189238 TATAGTTGACATGTATACATATAT
1 TATAGTTGACA--T-TACATATAT
189262 TATAGGTT-ACATTACATATAT
1 TATA-GTTGACATTACATATAT
189283 TA
1 TA
189285 ACTGTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
24 7 0.32
25 3 0.14
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (21 bp):
TATAGTTGACATTACATATAT
Found at i:189316 original size:7 final size:7
Alignment explanation
Indices: 189304--189373 Score: 59
Period size: 7 Copynumber: 10.0 Consensus size: 7
189294 TATGTATAGA
189304 GTTTAGG
1 GTTTAGG
189311 GTTTAGG
1 GTTTAGG
**
189318 GTTTATA
1 GTTTAGG
* *
189325 GTTTTGA
1 GTTTAGG
*
189332 GTTTAAG
1 GTTTAGG
189339 GTTTAGG
1 GTTTAGG
**
189346 GTTTAAA
1 GTTTAGG
**
189353 GTTTAAA
1 GTTTAGG
189360 GTTTAGG
1 GTTTAGG
189367 GTTTAGG
1 GTTTAGG
189374 TTTTTTATAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:189335 original size:28 final size:28
Alignment explanation
Indices: 189300--189373 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
189290 TGTTTATGTA
*
189300 TAGAGTTTAGGGTTTAGGGTTTATAGTT
1 TAGAGTTTAGGGTTTAGGGTTTAAAGTT
* *
189328 TTGAGTTTAAGGTTTAGGGTTTAAAGTT
1 TAGAGTTTAGGGTTTAGGGTTTAAAGTT
*
189356 TAAAGTTTAGGGTTTAGG
1 TAGAGTTTAGGGTTTAGG
189374 TTTTTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (28 bp):
TAGAGTTTAGGGTTTAGGGTTTAAAGTT
Found at i:189365 original size:21 final size:21
Alignment explanation
Indices: 189331--189371 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
189321 TATAGTTTTG
*
189331 AGTTTAAGGTTTAGGGTTTAA
1 AGTTTAAAGTTTAGGGTTTAA
189352 AGTTTAAAGTTTAGGGTTTA
1 AGTTTAAAGTTTAGGGTTTA
189372 GGTTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (21 bp):
AGTTTAAAGTTTAGGGTTTAA
Found at i:189522 original size:35 final size:36
Alignment explanation
Indices: 189483--189556 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
189473 CATACTATAC
*
189483 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
189518 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
189555 AT
1 AT
189557 TAACTATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:189697 original size:2 final size:2
Alignment explanation
Indices: 189690--189838 Score: 84
Period size: 2 Copynumber: 76.5 Consensus size: 2
189680 TATTTCTTTA
*
189690 AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT AT AT AT -T ACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
189730 AT AT -T AGT -T AT AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
189770 AT -T AT A- AT AT AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT
* *
189811 AT AT AGT TT AT AT AC AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A
189839 CACTATATTA
Statistics
Matches: 113, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
1 10 0.09
2 96 0.85
3 7 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:189738 original size:68 final size:68
Alignment explanation
Indices: 189654--189838 Score: 179
Period size: 68 Copynumber: 2.7 Consensus size: 68
189644 CTATATAATT
* * **
189654 TATTACTT-TATATAGTTTATGCATA-ATATTTCTTTAATATATATATATATATATATATATATT
1 TATTACTTATAT-TAGTTTATACATACATATTTCTATAATATATATATATATATA-ATATATAAA
189717 CTATA
64 CTATA
* *
189722 TATTACTTATATTAG-TTATACATACATATATATACTATATTA-ATATAAAT-TATAATATATAA
1 TATTACTTATATTAGTTTATACATACATAT-T-T-CTATAATATATATATATATATAATATATAA
189784 ACTATA
63 ACTATA
* *
189790 TATT--TTATA-TAGTTTATACATATATAGTTTATATACATATATATATATA
1 TATTACTTATATTAGTTTATACATACATA-TTTCTATA-ATATATATATATA
189839 CACTATATTA
Statistics
Matches: 97, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
64 4 0.04
65 6 0.06
66 25 0.26
67 9 0.09
68 31 0.32
69 8 0.08
70 8 0.08
71 6 0.06
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (68 bp):
TATTACTTATATTAGTTTATACATACATATTTCTATAATATATATATATATATAATATATAAACT
ATA
Found at i:189815 original size:15 final size:15
Alignment explanation
Indices: 189795--189846 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
189785 CTATATATTT
189795 TATATAGTTTATACA
1 TATATAGTTTATACA
189810 TATATAGTTTATATACA
1 TATATAG-TT-TATACA
*
189827 TATATA-TATATACA
1 TATATAGTTTATACA
189841 CTATAT
1 -TATAT
189847 TAATATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.18
15 13 0.39
16 2 0.06
17 12 0.36
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:189845 original size:85 final size:85
Alignment explanation
Indices: 189738--190012 Score: 285
Period size: 85 Copynumber: 3.2 Consensus size: 85
189728 TTATATTAGT
*
189738 TATACATA-CATATATAT-ACTATATTAATATAAATTATAATATATAAACTATATATTTTATATA
1 TATACATAGTATATATATAACTATATTAATATAAATTATAATATATAAACTATATATTTTATATA
189801 GTTTATACATATATAGTTTA
66 GTTTATACATATATAGTTTA
* * *
189821 TATACATA-TATATATATACACTATATTAATATAAATAATATTTTATAAACTATATACTTTT-TA
1 TATACATAGTATATATATA-ACTATATTAATATAAATTATAATATATAAACTATATA-TTTTATA
*
189884 TAGTTTATACATATGTAGTTTA
64 TAGTTTATACATATATAGTTTA
* ** * * * * * *
189906 TATACATAGTTTATATATAGTTTACATAAACATAATTTAT-ATATAT-AGCT-TATAATAATTAT
1 TATACATAGTATATATATA-ACTATATTAATATAAATTATAATATATAAACTATAT-AT-TTTAT
*
189968 ATAGTTTATAATATAAATATAGTTTA
63 ATAGTTTAT-ACAT--ATATAGTTTA
*
189994 TATACATAGTTTATATATA
1 TATACATAGTATATATATA
190013 TAGTTCACAT
Statistics
Matches: 162, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
83 20 0.12
84 6 0.04
85 79 0.49
86 29 0.18
88 28 0.17
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (85 bp):
TATACATAGTATATATATAACTATATTAATATAAATTATAATATATAAACTATATATTTTATATA
GTTTATACATATATAGTTTA
Found at i:189917 original size:13 final size:13
Alignment explanation
Indices: 189899--190049 Score: 72
Period size: 13 Copynumber: 10.7 Consensus size: 13
189889 TATACATATG
189899 TAGTTTATATACA
1 TAGTTTATATACA
189912 TAGTTTATAT--A
1 TAGTTTATATACA
*
189923 TAGTTTACATAAACA
1 TAGTTT--ATATACA
* *
189938 TAATTTATATATA
1 TAGTTTATATACA
*
189951 TAGCTTATAATAATTATA
1 TAG-TT-T-AT-A-TACA
*
189969 TAGTTTATAATATAAATA
1 TAG-TT-T-ATAT--ACA
189987 TAGTTTATATACA
1 TAGTTTATATACA
*
190000 TAGTTTATATATA
1 TAGTTTATATACA
* *
190013 TAGTTCACATAAACA
1 TAGTT--TATATACA
*
190028 TAATTTATATACA
1 TAGTTTATATACA
*
190041 TAGCTTATA
1 TAGTTTATA
190050 ATAATTATAT
Statistics
Matches: 109, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
11 7 0.06
13 52 0.48
14 2 0.02
15 20 0.18
16 4 0.04
17 4 0.04
18 20 0.18
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (13 bp):
TAGTTTATATACA
Found at i:189987 original size:18 final size:18
Alignment explanation
Indices: 189943--189995 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
189933 AAACATAATT
*
189943 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
189961 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
189979 TATAAATATAGTTTATA
1 TATATATATAGTTTATA
189996 TACATAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:189998 original size:88 final size:90
Alignment explanation
Indices: 189899--190087 Score: 346
Period size: 90 Copynumber: 2.1 Consensus size: 90
189889 TATACATATG
* *
189899 TAGTTTATATACATAG-TT-TATATATAGTTTACATAAACATAATTTATATATATAGCTTATAAT
1 TAGTTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATACATAGCTTATAAT
189962 AATTATATAGTTTATAATATAAATA
66 AATTATATAGTTTATAATATAAATA
189987 TAGTTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATACATAGCTTATAAT
1 TAGTTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATACATAGCTTATAAT
190052 AATTATATAGTTTATAATATAAATA
66 AATTATATAGTTTATAATATAAATA
190077 TAGTTTATATA
1 TAGTTTATATA
190088 TAAACTTATA
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
88 16 0.16
89 2 0.02
90 79 0.81
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (90 bp):
TAGTTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATACATAGCTTATAAT
AATTATATAGTTTATAATATAAATA
Found at i:190066 original size:18 final size:19
Alignment explanation
Indices: 190040--190090 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
190030 ATTTATATAC
* *
190040 ATAGCTTATAATAAT-TAT
1 ATAGTTTATAATAATAAAT
190058 ATAGTTTATAAT-ATAAAT
1 ATAGTTTATAATAATAAAT
190076 ATAGTTTATATATAA
1 ATAGTTTATA-ATAA
190091 ACTTATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 23 0.82
19 2 0.07
20 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
ATAGTTTATAATAATAAAT
Found at i:190090 original size:17 final size:17
Alignment explanation
Indices: 190056--190114 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
190046 TATAATAATT
190056 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
190074 ATATAGTTTATATATAA
1 ATATAGTTTATATATAA
*
190091 ACTTATA-TTATATATATAT
1 A--TATAGTT-TATATATAA
190110 ATATA
1 ATATA
190115 TTATATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 11 0.30
18 13 0.35
19 13 0.35
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:190115 original size:17 final size:17
Alignment explanation
Indices: 190063--190120 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
190053 ATTATATAGT
190063 TTATA-ATATAAATATA
1 TTATATATATAAATATA
190079 GTT-TATATATAAACTTATA
1 -TTATATATATAAA--TATA
*
190098 TTATATATATATATATA
1 TTATATATATAAATATA
190115 TTATAT
1 TTATAT
190121 TTTTTCAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 2 0.06
17 19 0.53
18 2 0.06
19 13 0.36
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTATATATATAAATATA
Found at i:194281 original size:29 final size:29
Alignment explanation
Indices: 194246--194327 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
194236 AAACTAAATT
* *
194246 GATGTCATTATTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAAGTAAA
* *
194275 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTACTTACATCATTTAAGTAAA
194304 GATGTCATTACTTACATCAATTTA
1 GATGTCATTACTTACATC-ATTTA
194328 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAAGTAAA
Found at i:194745 original size:18 final size:20
Alignment explanation
Indices: 194722--194759 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
194712 AAATCGAGTT
194722 GAGTCA-CCGAGTT-GAGCC
1 GAGTCAGCCGAGTTGGAGCC
194740 GAGTCAGCCGAGTTGGAGCC
1 GAGTCAGCCGAGTTGGAGCC
194760 CTTGACCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (20 bp):
GAGTCAGCCGAGTTGGAGCC
Found at i:199024 original size:29 final size:29
Alignment explanation
Indices: 198989--199070 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
198979 AAACTAAATT
* *
198989 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
199018 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
199047 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
199071 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:210351 original size:23 final size:24
Alignment explanation
Indices: 210305--210353 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
210295 CGAATCGATA
**
210305 CCCCTCTTGAAGGGGAACTGATTC
1 CCCCTCTTGAAGGGGAACCAATTC
*
210329 CCCCT-TTGAATGGGAACCAATTC
1 CCCCTCTTGAAGGGGAACCAATTC
210352 CC
1 CC
210354 TTATTTAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (24 bp):
CCCCTCTTGAAGGGGAACCAATTC
Found at i:221836 original size:33 final size:34
Alignment explanation
Indices: 221794--221859 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
221784 AAAATAATTT
*
221794 GATGTCATTGCTTACATC-AATTTGTTAGGTGAA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
*
221827 GATGTCATTGCTTATATCAAATTAGTTAGGTGA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
221860 GAATTAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (34 bp):
GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
Found at i:226605 original size:20 final size:20
Alignment explanation
Indices: 226580--226637 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
226570 GTCAGGAGAT
226580 GCGCAAGATACTTTACATGA
1 GCGCAAGATACTTTACATGA
226600 GCGCAAGATACTTTACATGA
1 GCGCAAGATACTTTACATGA
*
226620 GCGCAAGAGACTTTACAT
1 GCGCAAGATACTTTACAT
226638 CAGCACAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
GCGCAAGATACTTTACATGA
Found at i:231689 original size:75 final size:74
Alignment explanation
Indices: 231552--231700 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 74
231542 GGCAAATACA
* * * *
231552 AATAAAATTTTTGGGTGGACACTTCAGTAAAATGAACAACTAATATAAACAAATTCGAATTCTAT
1 AATAAAATTTTAGGGTGAACACTTCAGTAAAATGAACAACTAATATAAAAAAATTAGAATTCTA-
231617 GA-TGGGCAC
65 GAGTGGGCAC
*
231626 AATAAAATTTTAGGGTGAACACATTTAGTAAAATGAACAACTAGA-ATAAAAAAATTTAG-ATTC
1 AATAAAATTTTAGGGTGAACAC-TTCAGTAAAATGAACAACTA-ATATAAAAAAA-TTAGAATTC
231689 TAGAGTGGGCAC
63 TAGAGTGGGCAC
231701 GTGCCCACCC
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
74 22 0.33
75 40 0.61
76 4 0.06
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (74 bp):
AATAAAATTTTAGGGTGAACACTTCAGTAAAATGAACAACTAATATAAAAAAATTAGAATTCTAG
AGTGGGCAC
Found at i:236813 original size:20 final size:22
Alignment explanation
Indices: 236780--236827 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
236770 AAAGATAACT
236780 ATTAAATAACAATAGAA-ACTAA
1 ATTAAATAACAATA-AAGACTAA
236802 ATTAAAT-A-AATAAAGACTAA
1 ATTAAATAACAATAAAGACTAA
*
236822 AATAAA
1 ATTAAA
236828 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 14 0.58
21 1 0.04
22 7 0.29
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (22 bp):
ATTAAATAACAATAAAGACTAA
Found at i:239983 original size:22 final size:22
Alignment explanation
Indices: 239958--240001 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
239948 AAAATACGGT
* *
239958 ATGAACAGTACCATGAATAATA
1 ATGAACAATACCATGAACAATA
*
239980 ATGAACAATATCATGAACAATA
1 ATGAACAATACCATGAACAATA
240002 CCGAATGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (22 bp):
ATGAACAATACCATGAACAATA
Found at i:249702 original size:21 final size:21
Alignment explanation
Indices: 249656--249737 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
249646 TTGGTGCAAA
* *
249656 GGGAATCGATACCCCCTTGAAT
1 GGGAATCGATACCCCC-TGTAG
*
249678 GGGAATCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGTAG
*
249699 GGGAATCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGTAG
*
249720 GGGAATAGATACCCCCTG
1 GGGAATCGATACCCCCTG
249738 GAGGTTCTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 40 0.73
22 15 0.27
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.22
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGTAG
Found at i:259216 original size:2 final size:2
Alignment explanation
Indices: 259209--259236 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
259199 AGATCCTCCC
259209 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
259237 CCTCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262714 original size:11 final size:11
Alignment explanation
Indices: 262695--262800 Score: 58
Period size: 11 Copynumber: 9.0 Consensus size: 11
262685 CTTAAAGAAT
262695 AAATGAAAAAA
1 AAATGAAAAAA
*
262706 AAAT---TAAA
1 AAATGAAAAAA
*
262714 AAATGAAAATA
1 AAATGAAAAAA
262725 AAATGAAAATAAA
1 AAATG-AAA-AAA
262738 AAATGAAAAATGAAA
1 AAATG--AAA--AAA
262753 AAATGAAAAAA
1 AAATGAAAAAA
*
262764 GAA-GAAAGAGAA
1 AAATGAAA-A-AA
262776 AAATGAAAAATGAA
1 AAATG-AAAA--AA
262790 AAATGAAAAAA
1 AAATGAAAAAA
262801 TAGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
8 7 0.09
10 4 0.05
11 19 0.25
12 7 0.09
13 16 0.21
14 15 0.20
15 8 0.11
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (11 bp):
AAATGAAAAAA
Found at i:262716 original size:8 final size:8
Alignment explanation
Indices: 262703--262816 Score: 93
Period size: 7 Copynumber: 14.6 Consensus size: 8
262693 ATAAATGAAA
*
262703 AAAAAATT
1 AAAAAATG
262711 AAAAAATG
1 AAAAAATG
262719 AAAATAA--
1 AAAA-AATG
262726 AATGAAAAT-
1 AA--AAAATG
262735 AAAAAATG
1 AAAAAATG
262743 -AAAAATG
1 AAAAAATG
262750 AAAAAATG
1 AAAAAATG
262758 AAAAAA-G
1 AAAAAATG
*
262765 AAGAAA-G
1 AAAAAATG
262772 AGAAAAATG
1 A-AAAAATG
262781 -AAAAATG
1 AAAAAATG
262788 -AAAAATG
1 AAAAAATG
262795 AAAAAATAG
1 AAAAAAT-G
262804 AGAAAAAT-
1 A-AAAAATG
262812 AAAAA
1 AAAAA
262817 GGGGGTTCAA
Statistics
Matches: 92, Mismatches: 3, Indels: 23
0.78 0.03 0.19
Matches are distributed among these distances:
7 40 0.43
8 37 0.40
9 9 0.10
10 6 0.07
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:262784 original size:6 final size:7
Alignment explanation
Indices: 262695--262799 Score: 96
Period size: 7 Copynumber: 15.4 Consensus size: 7
262685 CTTAAAGAAT
262695 AAATGAA
1 AAATGAA
262702 AAA--AA
1 AAATGAA
* *
262707 AATTAAA
1 AAATGAA
262714 AAATG-A
1 AAATGAA
262720 AAAT--A
1 AAATGAA
262725 AAATG-A
1 AAATGAA
*
262731 AAATAAA
1 AAATGAA
262738 AAATGAA
1 AAATGAA
262745 AAATGAAA
1 AAATG-AA
262753 AAATGAA
1 AAATGAA
*
262760 AAAAGAA
1 AAATGAA
*
262767 GAAAGAGAA
1 -AAA-TGAA
262776 AAATGAA
1 AAATGAA
262783 AAATGAA
1 AAATGAA
262790 AAATGAA
1 AAATGAA
262797 AAA
1 AAA
262800 ATAGAGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
5 9 0.11
6 10 0.12
7 48 0.57
8 13 0.15
9 4 0.05
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:262787 original size:30 final size:32
Alignment explanation
Indices: 262742--262816 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
262732 AATAAAAAAT
*
262742 GAAAAATGAAAAAATGAAAAAAG-AAGAA-AGA
1 GAAAAATG-AAAAATGAAAAAAGAAAAAATAGA
*
262773 GAAAAATGAAAAATGAAAAATGAAAAAATAGA
1 GAAAAATGAAAAATGAAAAAAGAAAAAATAGA
262805 GAAAAAT-AAAAA
1 GAAAAATGAAAAA
262817 GGGGGTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 13 0.32
31 17 0.43
32 10 0.25
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (32 bp):
GAAAAATGAAAAATGAAAAAAGAAAAAATAGA
Found at i:262808 original size:38 final size:38
Alignment explanation
Indices: 262704--262800 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 38
262694 TAAATGAAAA
* *
262704 AAAAATTAAAAAATGAAAATAA-AATGAAA-ATAAAAAATG
1 AAAAATGAAAAAATGAAAA-AAGAA-GAAAGA-GAAAAATG
262743 AAAAATGAAAAAATGAAAAAAGAAGAAAGAGAAAAATG
1 AAAAATGAAAAAATGAAAAAAGAAGAAAGAGAAAAATG
262781 AAAAATG-AAAAATGAAAAAA
1 AAAAATGAAAAAATGAAAAAA
262801 TAGAGAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
37 13 0.24
38 20 0.37
39 21 0.39
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (38 bp):
AAAAATGAAAAAATGAAAAAAGAAGAAAGAGAAAAATG
Found at i:262815 original size:23 final size:22
Alignment explanation
Indices: 262744--262815 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
262734 TAAAAAATGA
*
262744 AAAATGAAAAAATGA-AAAAAG
1 AAAATGAAAAAATGAGAAAAAT
*
262765 AAGAAAGAGAAAAAT--GAAAAAT
1 AA-AATGA-AAAAATGAGAAAAAT
262787 GAAAAATGAAAAAATAGAGAAAAAT
1 --AAAATGAAAAAAT-GAGAAAAAT
262812 AAAA
1 AAAA
262816 AGGGGGTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
21 2 0.05
22 15 0.38
23 14 0.35
24 2 0.05
25 7 0.17
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (22 bp):
AAAATGAAAAAATGAGAAAAAT
Found at i:262816 original size:38 final size:38
Alignment explanation
Indices: 262704--262816 Score: 133
Period size: 38 Copynumber: 2.9 Consensus size: 38
262694 TAAATGAAAA
*
262704 AAAAATTAAAAAATGAAAATAA-AATG-AAAATAAAAAATG
1 AAAAATGAAAAAATGAAAA-AAGAA-GAAAAAT-AAAAATG
* *
262743 AAAAATGAAAAAATGAAAAAAGAAGAAAGAGAAAAATG
1 AAAAATGAAAAAATGAAAAAAGAAGAAAAATAAAAATG
*
262781 AAAAATG-AAAAATGAAAAAATAGAGAAAAATAAAAA
1 AAAAATGAAAAAATGAAAAAAGA-AGAAAAATAAAAA
262817 GGGGGTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
37 14 0.22
38 28 0.43
39 23 0.35
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (38 bp):
AAAAATGAAAAAATGAAAAAAGAAGAAAAATAAAAATG
Found at i:264212 original size:37 final size:37
Alignment explanation
Indices: 264096--264237 Score: 142
Period size: 37 Copynumber: 3.8 Consensus size: 37
264086 CAAGTTAATC
* * ** * * *
264096 TTAAACCTTCACGAAAGAGCGGTGAAGTAATTCAAAC
1 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAAAG
* *
264133 TTAAGCCTTCACGGAAGAGTAGTGAAGCGATTCAAAG
1 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAAAG
**
264170 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC-ATT
1 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAAAG
** *
264206 TATAAGCCTTCACAAAAGAGTAGTAAAGCAAA
1 T-TAAGCCTTCACGGAAGAGTAGTGAAGCAAA
264238 CTCGTTTGTT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 2 0.02
37 88 0.98
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (37 bp):
TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAAAG
Found at i:264788 original size:55 final size:55
Alignment explanation
Indices: 264297--264776 Score: 590
Period size: 55 Copynumber: 8.9 Consensus size: 55
264287 GACATGTTGT
*
264297 GATTGTTCGAGTTCT-TACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAA
1 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
**
264351 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTTGTTTTATGAA
1 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
* *
264406 GATTGTTCGAGTTATATACTCTCTAAAGGAATAGAGAGCGGACCCGTTTTATGAA
1 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
* *
264461 GATTGTTCGAGTTCTATACTCTCTGGAGGAATAGAGAGCGGACCCATTTTATGAA
1 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
*
264516 GATTGTTCGAGTTCTATA--CTCTGAAGGAATAGAGAGC--ACCCATTTGT-TGAA
1 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAA
*
264567 GA-TGTTCAAGTT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
1 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
* * *
264620 GATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGATCCG-TTTATTGAA
1 GATTGTTCGAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTTA-TGAA
* * * ** ** ***
264675 GATTGTTCGAG-TCTTATACTCCCTGAATGAATAGGGAGAAGACATGTTTGCCGAA
1 GATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
* * *
264730 GATTGTTCGAG-TCTTATACTCCCTGGAA-GAATAGGGAGCAGACCCGT
1 GATTGTTCGAGTTC-TATACTCTCT-GAAGGAATAGAGAGCGGACCCGT
264777 CATTTGAAGA
Statistics
Matches: 381, Mismatches: 30, Indels: 29
0.87 0.07 0.07
Matches are distributed among these distances:
49 4 0.01
50 9 0.02
51 33 0.09
52 2 0.01
53 31 0.08
54 31 0.08
55 264 0.69
56 7 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (55 bp):
GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAA
Found at i:270268 original size:31 final size:30
Alignment explanation
Indices: 270185--270305 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 30
270175 CGGCAAAATA
* *
270185 TCCATAGGTCCCGAAGAACCTAGGTAAATTG
1 TCCATATGTCCCGAAGAACATAGGT-AATTG
* * **
270216 TCCCTATGTTCCTTAGAACATAGGTATATTG
1 TCCATATGTCCCGAAGAACATAGGTA-ATTG
270247 TCCATATGTCCCGAA-AGACATAGGTAATTCTG
1 TCCATATGTCCCGAAGA-ACATAGGTAA-T-TG
* * * *
270279 TCCATATATTCTGTAGAACATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
270306 ACCCTTTACT
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
30 3 0.04
31 44 0.62
32 23 0.32
33 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (30 bp):
TCCATATGTCCCGAAGAACATAGGTAATTG
Found at i:270271 original size:62 final size:63
Alignment explanation
Indices: 270185--270304 Score: 156
Period size: 62 Copynumber: 1.9 Consensus size: 63
270175 CGGCAAAATA
* * *
270185 TCCATAGGTCCCGAAGAACCTAGGTAAAT-TGTCCCTATGTTCCT-TAGAACATAGGTATATTG
1 TCCATAGGTCCCGAAGAACATAGGTAAATCTGTCCATATATT-CTGTAGAACATAGGTATATTG
* *
270247 TCCATATGTCCCGAA-AGACATAGGTAATTCTGTCCATATATTCTGTAGAACATAGGTA
1 TCCATAGGTCCCGAAGA-ACATAGGTAAATCTGTCCATATATTCTGTAGAACATAGGTA
270305 AACCCTTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
61 1 0.02
62 26 0.52
63 23 0.46
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (63 bp):
TCCATAGGTCCCGAAGAACATAGGTAAATCTGTCCATATATTCTGTAGAACATAGGTATATTG
Found at i:275996 original size:2 final size:2
Alignment explanation
Indices: 275989--276057 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
275979 TTACTTTTTA
*
275989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
276031 AT AT AT AT AT AT -T AT A- AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276058 TCCGCCAACC
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 59 0.95
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:276276 original size:29 final size:29
Alignment explanation
Indices: 276234--276291 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
276224 ATCAACCTAC
276234 ATCACCCCTGCCATGCGGTAAACTTGGAT
1 ATCACCCCTGCCATGCGGTAAACTTGGAT
276263 ATCACCCCTGCCATGCGGTAAACTTGGAT
1 ATCACCCCTGCCATGCGGTAAACTTGGAT
276292 CATTTGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (29 bp):
ATCACCCCTGCCATGCGGTAAACTTGGAT
Found at i:276727 original size:31 final size:31
Alignment explanation
Indices: 276691--276758 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
276681 TCAAAATACA
*
276691 TAAGATATGATCA-TCTTCGTTTTTATTTAAT
1 TAAGATATGATCACT-TTCATTTTTATTTAAT
* *
276722 TAAGATATGATCACTTTTATTTTTATTTATT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
276753 TAAGAT
1 TAAGAT
276759 GTGGTTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (31 bp):
TAAGATATGATCACTTTCATTTTTATTTAAT
Found at i:277264 original size:41 final size:40
Alignment explanation
Indices: 277208--277568 Score: 361
Period size: 41 Copynumber: 8.7 Consensus size: 40
277198 CAAAATACTA
* * *
277208 TACTTTAGTGACGTTTGTATAAAAACGCCGCTAAAGAATCG
1 TACTTTAGTGGCGTTT-TATACAAACGCCGCTATAGAATCG
* * *
277249 TAATGTAGTGGCGTTTTTATACAAACGCCGCTATA-AACTAG
1 TACTTTAGTGGCG-TTTTATACAAACGCCGCTATAGAA-TCG
* * *
277290 TATTTTAGTGGCGTTTTTATTCAAACGCCGCTATAGACA-CA
1 TACTTTAGTGGCG-TTTTATACAAACGCCGCTATAGA-ATCG
* *
277331 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCCGCTATAGAATCG
* *
277373 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACAT-G
1 TACTTTAGTGGC-GTTTTATACAAACGCCGCTATAGA-ATCG
* *
277414 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCG
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCCGCTATAGAATCG
* *
277456 TACTTTAGTGGCATTTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGC--GTTTTATACAAACGCCGCTATAGA-ATCG
* * *
277498 TACTTTTGTGGCGTTTTAAACCAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTATA-CAAACGCCGCTATAGAATCG
277539 TACTTTAGTGGCGTTTTAATACCAAACGCC
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCC
277569 ACAATTGTCA
Statistics
Matches: 268, Mismatches: 34, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
40 16 0.06
41 138 0.51
42 103 0.38
43 7 0.03
44 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (40 bp):
TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGAATCG
Found at i:277390 original size:83 final size:83
Alignment explanation
Indices: 277230--277568 Score: 479
Period size: 83 Copynumber: 4.1 Consensus size: 83
277220 GTTTGTATAA
* * * * * * * *
277230 AAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-CAAACGCCGCTATAAACTAGTAT
1 AAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTAC
* **
277293 TTTAGTGGCGTTTTTATTC
65 TTTAGTGGCATTTTTACAC
*
277312 AAACGCCGCTATAGACACATACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACT
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACT
277377 TTAGTGGCATTTTTACAC
66 TTAGTGGCATTTTTACAC
* *
277395 AAACGCCGCTATAGACATGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACT
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACT
277460 TTAGTGGCATTTTTTACAC
66 TTAGTGGCA-TTTTTACAC
277479 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAA-ACCAAACGCCGCTATAGACTCGTACT
1 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACT
*
277543 TTAGTGGCGTTTTAATAC-C
66 TTAGTGGCATTTT--TACAC
277562 AAACGCC
1 AAACGCC
277569 ACAATTGTCA
Statistics
Matches: 234, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
82 36 0.15
83 149 0.64
84 49 0.21
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (83 bp):
AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACT
TTAGTGGCATTTTTACAC
Found at i:277493 original size:125 final size:124
Alignment explanation
Indices: 277230--277568 Score: 416
Period size: 125 Copynumber: 2.7 Consensus size: 124
277220 GTTTGTATAA
* * * * * *
277230 AAACGCCGCTAAAGAATCGTAATGTAGTGGCGTTTTTATACAAACGCCGCTATAAACTAGTA-TT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGC-TTTTTAAACAAACGCCGCTATAGACTAGTACTT
* * * *
277294 TTAGTGGCGTTTTTAT-TCAAACGCCGCTATAGACACATACTTTTGTGGCGTTTTAATACC
65 TT-GTGGCGTTTTAATACCAAACGCCGCTATAGACACATACTTTAGTGGCATTTTAATACC
*
277354 AAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCGCTATAGAC-ATGTACT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGC-TTTTTAAACAAACGCCGCTATAGACTA-GTACT
** * *
277418 TTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCATTTT-TTACAC
64 TTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACATACTTTAGTGGCATTTTAATAC-C
* * * *
277479 AAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAAACCAAACGCCGCTATAGACTCGTACTT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCTTTTTAAA-CAAACGCCGCTATAGACTAGTACTT
*
277544 TAGTGGCGTTTTAATACCAAACGCC
65 TTGTGGCGTTTTAATACCAAACGCC
277569 ACAATTGTCA
Statistics
Matches: 188, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
123 1 0.01
124 74 0.39
125 113 0.60
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (124 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCTTTTTAAACAAACGCCGCTATAGACTAGTACTTT
TGTGGCGTTTTAATACCAAACGCCGCTATAGACACATACTTTAGTGGCATTTTAATACC
Found at i:281003 original size:43 final size:42
Alignment explanation
Indices: 280955--281275 Score: 403
Period size: 43 Copynumber: 7.5 Consensus size: 42
280945 AAGGTAATTA
*
280955 GCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGCG
1 GCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCG
** * *
280998 GCGTTTGTGTTTAAAAACGCCGTTATAGGTCTGACCTTTTGCA
1 GCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCG
281041 GCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCG
1 GCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCG
*
281084 GCGTTTGTTCTAAAAACGCCAG-TATAGGTCTG-CTCTTTTGCG
1 GCGTTTGTTCCAAAAACGCC-GCTATAGGTCTGAC-CTTTTGCG
*
281126 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
1 GCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCG
* * * ** * *
281169 GCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGCG
1 GCGTTTGTTCCAAAAACGCCGCTATAGGTC-TGACCTTTTGCG
* *
281212 GCGTTTGTTCCAAAAACGCCGCTATAGATATCGACCTTTTGCG
1 GCGTTTGTTCCAAAAACGCCGCTATAGGTCT-GACCTTTTGCG
*
281255 GCGTTTGTTCAAAAAACGCCG
1 GCGTTTGTTCCAAAAACGCCG
281276 TAATATATAT
Statistics
Matches: 244, Mismatches: 27, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.00
42 58 0.24
43 184 0.75
44 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (42 bp):
GCGTTTGTTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCG
Found at i:281129 original size:128 final size:128
Alignment explanation
Indices: 280955--281276 Score: 411
Period size: 128 Copynumber: 2.5 Consensus size: 128
280945 AAGGTAATTA
**
280955 GCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACT-TTTTGCGGCGTTTGTGTTTAAAAACGCC
1 GCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACTCTTTTGCGGCGTTTGT-TCAAAAAACGCC
* * *
281019 GTTATAGGTCTGACCTTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGGTC-TGACCTTTTGC
64 GTTATAGATCTGACCTTTTGCAGCGTTT-TGTCCAAAAACGCCGCTATAGATCATAACCTTTTGC
281083 G
128 G
* *
281084 GCGTTTGTTCTAAAAACGCCAG-TATAGGTCTG-CTCTTTTGCGGCGTTTGTATCCAAAAACGCC
1 GCGTTTGTTCCAAAAACGCC-GCTATAGGTCTGACTCTTTTGCGGCGTTTGT-TCAAAAAACGCC
* * * * * * *
281147 GCTATAGATCTGACCTTTTGCGGCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGCG
64 GTTATAGATCTGACCTTTTGCAGCGTTTTGTCCAAAAACGCCGCTATAGATCATAACCTTTTGCG
* *
281212 GCGTTTGTTCCAAAAACGCCGCTATAGATATCGAC-CTTTTGCGGCGTTTGTTCAAAAAACGCCG
1 GCGTTTGTTCCAAAAACGCCGCTATAGGTCT-GACTCTTTTGCGGCGTTTGTTCAAAAAACGCCG
281276 T
65 T
281277 AATATATATT
Statistics
Matches: 168, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
127 22 0.13
128 119 0.71
129 26 0.15
130 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (128 bp):
GCGTTTGTTCCAAAAACGCCGCTATAGGTCTGACTCTTTTGCGGCGTTTGTTCAAAAAACGCCGT
TATAGATCTGACCTTTTGCAGCGTTTTGTCCAAAAACGCCGCTATAGATCATAACCTTTTGCG
Found at i:281140 original size:85 final size:85
Alignment explanation
Indices: 280955--281275 Score: 434
Period size: 85 Copynumber: 3.8 Consensus size: 85
280945 AAGGTAATTA
* * *
280955 GCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTTAAAAACGCCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCTAAAAACGCCG
* *
281020 TTATAGGTCTGAC-CTTTTGCA
65 CTATAGGTCTG-CTCTTTTGCG
* *
281041 GCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCAG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCC-G
281106 -TATAGGTCTGCTCTTTTGCG
65 CTATAGGTCTGCTCTTTTGCG
* *
281126 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTTTCTAGAAACGCCGC
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGC
** *
281191 TATATATCATAACT-TTTTGCG
66 TATAGGTC-T-GCTCTTTTGCG
* *
281212 GCGTTTGT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAAAAACGCCG
281276 TAATATATAT
Statistics
Matches: 214, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
84 2 0.01
85 115 0.54
86 95 0.44
87 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (85 bp):
GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGC
TATAGGTCTGCTCTTTTGCG
Found at i:287825 original size:18 final size:19
Alignment explanation
Indices: 287794--287832 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
287784 TTACTCATAA
*
287794 TTTTTATTATCATTTTATT
1 TTTTTATCATCATTTTATT
287813 TTTTTATCA-CATTTTATT
1 TTTTTATCATCATTTTATT
287831 TT
1 TT
287833 CTCTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATCATCATTTTATT
Found at i:293679 original size:16 final size:16
Alignment explanation
Indices: 293658--293709 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
293648 TTTTTAATTT
293658 AATTACT-TAACTTTCA
1 AATTACTCTAACTTT-A
293674 AATTACTCATAA-TTT-
1 AATTACTC-TAACTTTA
293689 AATTACTCTAACTTTTA
1 AATTACTCTAAC-TTTA
293706 AATT
1 AATT
293710 TAATTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.26
16 10 0.32
17 7 0.23
18 3 0.10
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTACTCTAACTTTA
Found at i:293694 original size:15 final size:14
Alignment explanation
Indices: 293652--293699 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
293642 GTTTATTTTT
293652 TAATTTAATTACT-
1 TAATTTAATTACTC
293665 TAACTTTCAAATTACTC
1 TAA-TTT--AATTACTC
293682 ATAATTTAATTACTC
1 -TAATTTAATTACTC
293697 TAA
1 TAA
293700 CTTTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTTAATTACTC
Found at i:294542 original size:18 final size:18
Alignment explanation
Indices: 294516--294582 Score: 91
Period size: 18 Copynumber: 3.7 Consensus size: 18
294506 AAACAAGACA
*
294516 CAAATTTTGAAATAAATC
1 CAAACTTTGAAATAAATC
294534 CAAACTTTGAAATAAA-C
1 CAAACTTTGAAATAAATC
*
294551 ACAAATTTTGAAATAAATC
1 -CAAACTTTGAAATAAATC
*
294570 CAAACTTTAAAAT
1 CAAACTTTGAAAT
294583 CCTTCATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.02
18 41 0.95
19 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (18 bp):
CAAACTTTGAAATAAATC
Found at i:294560 original size:36 final size:36
Alignment explanation
Indices: 294513--294582 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
294503 TAAAAACAAG
*
294513 ACACAAATTTTGAAATAAATCCAAACTTTGAAATAA
1 ACACAAATTTTGAAATAAATCCAAACTTTAAAATAA
294549 ACACAAATTTTGAAATAAATCCAAACTTTAAAAT
1 ACACAAATTTTGAAATAAATCCAAACTTTAAAAT
294583 CCTTCATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29
Consensus pattern (36 bp):
ACACAAATTTTGAAATAAATCCAAACTTTAAAATAA
Found at i:305680 original size:67 final size:69
Alignment explanation
Indices: 305601--305734 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 69
305591 TCTTGTAGGT
*
305601 GTGTGAGAGCAATGGTGATAAAGCTGATG-AGTCAAGATGCTCTAGCCACACAT-AAAAGGGAAT
1 GTGTGAGAGCAATGGTGATAAAGATGATGAAGTCAAGATGCTCTAGCCACACATAAAAAGGGAAT
305664 GGGC
66 GGGC
*
305668 GTGTGAGAGCAATGGTGATAAAGATGATGATATTCAAGATGCTCTAGCCACACATAAAAAGGGAA
1 GTGTGAGAGCAATGGTGATAAAGATGATGA-AGTCAAGATGCTCTAGCCACACATAAAAAGGGAA
305733 TG
65 TG
305735 AGTAACCTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
67 28 0.45
69 23 0.37
70 11 0.18
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (69 bp):
GTGTGAGAGCAATGGTGATAAAGATGATGAAGTCAAGATGCTCTAGCCACACATAAAAAGGGAAT
GGGC
Found at i:309191 original size:45 final size:46
Alignment explanation
Indices: 309127--309217 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
309117 GACAAATTTG
309127 ATTGTTTAAACATAGTTAATTTT-GAAATATGAGTTGCCAATACCA
1 ATTGTTTAAACATAGTTAATTTTCGAAATATGAGTTGCCAATACCA
* *
309172 ATTGTTTGAACATAGTTAATTTTCGAAATATGAGTTGTCAATACCA
1 ATTGTTTAAACATAGTTAATTTTCGAAATATGAGTTGCCAATACCA
309218 CTAGGATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (46 bp):
ATTGTTTAAACATAGTTAATTTTCGAAATATGAGTTGCCAATACCA
Found at i:309352 original size:21 final size:22
Alignment explanation
Indices: 309297--309352 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
309287 GATACCCCAT
309297 AAGGGAACCGATTCCTCCTTTG
1 AAGGGAACCGATTCCTCCTTTG
309319 AATGGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATT-CCTCCTTTG
*
309342 -AGGGAATCGAT
1 AAGGGAACCGAT
309353 ACCCCCACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 14 0.45
24 5 0.16
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
AAGGGAACCGATTCCTCCTTTG
Found at i:314017 original size:18 final size:18
Alignment explanation
Indices: 313989--314037 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
313979 CTCCTCTTTC
* * *
313989 TTTGTTATTTTTTTTTTT
1 TTTGTTCTTTTTTATGTT
314007 TTTGGTT-TTTTTTATGTT
1 TTT-GTTCTTTTTTATGTT
314025 TTTGTTCTTTTTT
1 TTTGTTCTTTTTT
314038 CGAACTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.84
Consensus pattern (18 bp):
TTTGTTCTTTTTTATGTT
Found at i:314664 original size:3 final size:3
Alignment explanation
Indices: 314656--314709 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
314646 TCATTAAAAG
314656 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
314703 ATA ATA A
1 ATA ATA A
314710 AAAAGTAGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:315214 original size:140 final size:139
Alignment explanation
Indices: 314950--315239 Score: 390
Period size: 140 Copynumber: 2.1 Consensus size: 139
314940 TCTGGCAGTT
* * *
314950 TTTAGGTA-AATTTGGAGACAACACGGTTCCGACGTGATGAGTAAATCTGGTTATCTAAGGGTGA
1 TTTAGGGATAATTTGGAGACAACACGGTTCCGACGTGATGAGGAAATCAGGTTATCTAAGGGTGA
* * * * *
315014 CATGCTCTTACGTGATGGGGAGATCTAGTCGGTGGATGACATTGTTCCTACCTTATGAGGATGTC
66 CATGCTCCTACGTGATGAGGAGATCTAGTCGGTGGATGACATTATTCCTACCTGATGAGGACGTC
315079 TAGCCAT-A
131 TAGCCATCA
* * * *
315087 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTCAGGTTATCTAATGTTG
1 TTTAGGGATAATTT-GGAGACAACACGGTTCCGACGTGATGAGGAAATCAGGTTATCTAAGGGTG
* *
315152 ATGC-TGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTATTCCTACGTGATGAGGAC
65 A--CATGCTCCTACGTGATGAGGAGATCTAGTCGGTGGATGACATTATTCCTACCTGATGAGGAC
*
315216 GTCTGGCCATCA
128 GTCTAGCCATCA
315228 -TTAGGGATAATT
1 TTTAGGGATAATT
315240 GTTTCACGAG
Statistics
Matches: 133, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
137 7 0.05
138 5 0.04
139 45 0.34
140 74 0.56
141 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (139 bp):
TTTAGGGATAATTTGGAGACAACACGGTTCCGACGTGATGAGGAAATCAGGTTATCTAAGGGTGA
CATGCTCCTACGTGATGAGGAGATCTAGTCGGTGGATGACATTATTCCTACCTGATGAGGACGTC
TAGCCATCA
Found at i:315383 original size:36 final size:36
Alignment explanation
Indices: 315298--315384 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
315288 TCATTGTTTA
*
315298 TGTTTCAAGAGAAA-ACTGTCTCAAGAGATAAAACT
1 TGTTTCAAGAGAAACACTGTCTCAAGAGACAAAACT
* *
315333 TGTTTAAAGAGAAACA-T-TCTCAAGCGAGACAAAATT
1 TGTTTCAAGAGAAACACTGTCTCAA--GAGACAAAACT
*
315369 TGTTTCAAGGGAAACA
1 TGTTTCAAGAGAAACA
315385 AACTCAATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 6 0.14
35 14 0.32
36 24 0.55
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGAGAAACACTGTCTCAAGAGACAAAACT
Found at i:315440 original size:65 final size:66
Alignment explanation
Indices: 315333--315524 Score: 208
Period size: 66 Copynumber: 2.9 Consensus size: 66
315323 AGATAAAACT
* * * * * *
315333 TGTTTAAAGAGAAACAT-TCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACAAACTCAATG-TT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGAAAAAAATTATTTCAAGGGAAACAATCTCAATGATT
315396 TG
65 TG
* * * * * *
315398 TGTTTGAAGGGGAACTGTCTCAAGAGAGAAAAAAATTATTTCAAGAGAAACAATCACAAGGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTATTTCAAGGGAAACAATCTCAATGATTT
315463 G
66 G
* * * * *
315464 TGTTTCAAGAGAAATTGTTTCAAGAGAGATAAAACTTATTTCGAGGGAAACAATCTCAATG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTATTTCAAGGGAAACAATCTCAATG
315525 GTTATCAATT
Statistics
Matches: 103, Mismatches: 22, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
64 1 0.01
65 48 0.47
66 54 0.52
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTATTTCAAGGGAAACAATCTCAATGATTT
G
Found at i:317929 original size:11 final size:11
Alignment explanation
Indices: 317913--317950 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
317903 ATTTTTTCTT
317913 TTTTTCCTTTG
1 TTTTTCCTTTG
317924 TTTTTCCTTTG
1 TTTTTCCTTTG
*
317935 TTTTTTCTTTG
1 TTTTTCCTTTG
317946 TTTTT
1 TTTTT
317951 TTGCTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTCCTTTG
Found at i:317951 original size:11 final size:11
Alignment explanation
Indices: 317904--317951 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
317894 GCTTATTGTA
317904 TTTTTTC-TT-
1 TTTTTTCTTTG
*
317913 TTTTTCCTTTG
1 TTTTTTCTTTG
*
317924 TTTTTCCTTTG
1 TTTTTTCTTTG
317935 TTTTTTCTTTG
1 TTTTTTCTTTG
317946 TTTTTT
1 TTTTTT
317952 TGCTTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 27 0.77
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:320034 original size:164 final size:162
Alignment explanation
Indices: 319783--320108 Score: 618
Period size: 164 Copynumber: 2.0 Consensus size: 162
319773 GGGCGGGAGA
319783 ACCAAGTCGGAACTAAAACTAATTCTCTTGCATCCATTTTATATGAGAGCTTTGTCTCCCATTCC
1 ACCAAGTCGGAACTAAAACTAATTCTCTTGCATCCATTTTATATGAGAGCTTTGTCTCCCATTCC
319848 TTTGAATGTCTCTCTACACTACTTTTTTAAGTTCTCAGGGATCTCATTCTTGGCTCTTTTCATCT
66 TTTGAATGTCTCTCTACACTACTTTTTTAAGTTCTCAGGGATCTCATTCTTGGCTCTTTTCATCT
319913 TATCAGGATTTG-AATGTTGCGATCAATAGGC
131 TATCAGGATTTGAAATGTTGCGATCAATAGGC
319944 ACCAAGTCGGGAACTAAAACTAATTCTCTTGCATCCATTTTAATATGAGAGCTTTGTCCTCCCAT
1 ACCAAGTC-GGAACTAAAACTAATTCTCTTGCATCCATTTT-ATATGAGAGCTTTGT-CTCCCAT
320009 TCCTTTGAATGTCTCTCTACACTACTTTTTTAAGTTCTCAGGGATCTCATTCTTGGCTCTTTTCA
63 TCCTTTGAATGTCTCTCTACACTACTTTTTTAAGTTCTCAGGGATCTCATTCTTGGCTCTTTTCA
320074 TCTTATCAGGATTTGAAATGTTGCGATCAATAGGC
128 TCTTATCAGGATTTGAAATGTTGCGATCAATAGGC
320109 TTATCACGAT
Statistics
Matches: 161, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
161 8 0.05
162 32 0.20
163 15 0.09
164 87 0.54
165 19 0.12
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (162 bp):
ACCAAGTCGGAACTAAAACTAATTCTCTTGCATCCATTTTATATGAGAGCTTTGTCTCCCATTCC
TTTGAATGTCTCTCTACACTACTTTTTTAAGTTCTCAGGGATCTCATTCTTGGCTCTTTTCATCT
TATCAGGATTTGAAATGTTGCGATCAATAGGC
Found at i:326288 original size:13 final size:13
Alignment explanation
Indices: 326270--326294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326260 TTCCTGTAAT
326270 TTCTCCATTGTTG
1 TTCTCCATTGTTG
326283 TTCTCCATTGTT
1 TTCTCCATTGTT
326295 CTTCAACTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.12, T:0.56
Consensus pattern (13 bp):
TTCTCCATTGTTG
Found at i:342411 original size:24 final size:23
Alignment explanation
Indices: 342363--342418 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
342353 ACGGAGACAT
* *
342363 GATTAAATTATGAAGGGAGATAG
1 GATTAAATTATGAAGGGAAAAAG
342386 GATTAAATTATGAAGGGGAAAAAG
1 GATTAAATTATGAA-GGGAAAAAG
342410 GATTTAAAT
1 GA-TTAAAT
342419 AGTGGTCCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 14 0.48
24 9 0.31
25 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (23 bp):
GATTAAATTATGAAGGGAAAAAG
Found at i:346750 original size:18 final size:20
Alignment explanation
Indices: 346727--346763 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
346717 AACTTTCCAA
346727 ATTCATAA-TTTA-TTTCAG
1 ATTCATAACTTTACTTTCAG
346745 ATTCATAACTTTACTTTCA
1 ATTCATAACTTTACTTTCA
346764 AATCGTAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTCATAACTTTACTTTCAG
Found at i:347955 original size:16 final size:16
Alignment explanation
Indices: 347930--347963 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
347920 ATAATGAACA
*
347930 AAATATTTTATATTTT
1 AAATAATTTATATTTT
*
347946 AAATAATTTATTTTTT
1 AAATAATTTATATTTT
347962 AA
1 AA
347964 TTAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATAATTTATATTTT
Found at i:352935 original size:14 final size:14
Alignment explanation
Indices: 352913--353290 Score: 94
Period size: 13 Copynumber: 27.2 Consensus size: 14
352903 CATGTTTAAT
352913 TATATACTTATATA
1 TATATACTTATATA
* *
352927 TATACAC-T-TATG
1 TATATACTTATATA
*
352939 TATATACTTATGTA
1 TATATACTTATATA
* * * *
352953 CATACA-TCACATA
1 TATATACTTATATA
352966 TATATACTTATATA
1 TATATACTTATATA
*
352980 TACATACTTATGTATA
1 TATATACTTA--TATA
352996 TATTTTATACTTTTATATA
1 TA---TATAC--TTATATA
*
353015 TATACACTT-TATA
1 TATATACTTATATA
*
353028 GAGTATA--TA-AT-
1 TA-TATACTTATATA
353039 T-TATACTTTATATA
1 TATATAC-TTATATA
353053 TATATACACTT-TATA
1 TATAT--ACTTATATA
353068 TATATA--TATATA
1 TATATACTTATATA
353080 TATATA--TATAT-
1 TATATACTTATATA
* *
353091 TATATCCGTATAT-
1 TATATACTTATATA
*
353104 TATA-A-GTATAT-
1 TATATACTTATATA
*
353115 TGTATACTTATAT-
1 TATATACTTATATA
*
353128 TATATACTTTTATAA
1 TATATACTTATAT-A
*
353143 GTATATGCTTATAT-
1 -TATATACTTATATA
* * *
353157 TGTAT-GTATAAATA
1 TATATACT-TATATA
*
353171 TAATGTACATTATAATA
1 T-ATATAC-TTAT-ATA
*
353188 TATATACATATATTACA
1 TATATAC-T-TA-TATA
*
353205 TTATCATAACATTCAT-CA
1 -TAT-AT-AC-TT-ATATA
*
353223 TACATA-TTATATA
1 TATATACTTATATA
353236 TATATA--TATATA
1 TATATACTTATATA
353248 TATATA-TATATATA
1 TATATACT-TATATA
* *
353262 TGTATACATATATA
1 TATATACTTATATA
353276 TATATA--TATATA
1 TATATACTTATATA
353288 TAT
1 TAT
353291 TATAATTGTT
Statistics
Matches: 277, Mismatches: 43, Indels: 90
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.01
11 15 0.05
12 54 0.19
13 59 0.21
14 55 0.20
15 15 0.05
16 34 0.12
17 13 0.05
18 6 0.02
19 14 0.05
20 5 0.02
21 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (14 bp):
TATATACTTATATA
Found at i:353052 original size:2 final size:2
Alignment explanation
Indices: 353047--353294 Score: 111
Period size: 2 Copynumber: 129.0 Consensus size: 2
353037 ATTTATACTT
* *
353047 TA TA TA TA TA TA CA CTT 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
* ** *
353090 T- TA TA TC CG TA TA T- TA TA -A GTA TA T- TG TA TA CT- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* * * *
353128 TA TA TA CT- TT TA TA -A GTA TA TGC T- TA TA T- TG TA TG TA TA
1 TA TA TA -TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA
* * * * *
353167 AA TA TA -A TG TA CA T- TA TA -A TA TA TA TA CA TA TA T- TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
353205 T- TA TCA TA -A CA T- TCA TCA TA CA TA T- TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA
* *
353244 TA TA TA TA TA TA TA TA TA TG TA TA CA 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
353286 TA TA T- TA TA
1 TA TA TA TA TA
353295 ATTGTTTCAA
Statistics
Matches: 187, Mismatches: 32, Indels: 54
0.68 0.12 0.20
Matches are distributed among these distances:
1 19 0.10
2 157 0.84
3 11 0.06
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:353064 original size:40 final size:39
Alignment explanation
Indices: 352991--353075 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
352981 ACATACTTAT
*
352991 GTATATATTTTATACTTTTATATATATACACTTTATAGA
1 GTATATAATTTATACTTTTATATATATACACTTTATAGA
*
353030 GTATATAATTTATACTTTATATATATATACACTTTATATA
1 GTATATAATTTATACTTT-TATATATATACACTTTATAGA
353070 -TATATA
1 GTATATA
353076 TATATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 23 0.53
40 20 0.47
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (39 bp):
GTATATAATTTATACTTTTATATATATACACTTTATAGA
Found at i:354005 original size:13 final size:13
Alignment explanation
Indices: 353987--354013 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
353977 CATCGTTGAA
353987 CAATCTTCATATG
1 CAATCTTCATATG
354000 CAATCTTCATATG
1 CAATCTTCATATG
354013 C
1 C
354014 GCGTATGTAA
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:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (13 bp):
CAATCTTCATATG
Found at i:356981 original size:20 final size:21
Alignment explanation
Indices: 356954--357015 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
356944 ATTTATCGAC
*
356954 AAAAAATTACAATAAATAAA-
1 AAAAAATTAAAATAAATAAAT
* ** *
356974 ATAAAATTTTAATATTATAAAT
1 AAAAAATTAAAATA-AATAAAT
356996 AAAAAATTAAAATAAATAAA
1 AAAAAATTAAAATAAATAAA
357016 CATAGATTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 11 0.34
21 10 0.31
22 11 0.34
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAATTAAAATAAATAAAT
Found at i:357463 original size:4 final size:4
Alignment explanation
Indices: 357454--357496 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
357444 CATACCCCTT
* *
357454 TAAA TAAA TAAA TAAA TAAA TAATT TAAAA TAAA TAAA CAAA T
1 TAAA TAAA TAAA TAAA TAAA TAA-A T-AAA TAAA TAAA TAAA T
357497 CACTAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 29 0.88
5 2 0.06
6 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:357487 original size:26 final size:26
Alignment explanation
Indices: 357455--357550 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 26
357445 ATACCCCTTT
357455 AAATAAATAAATAAATAAATAATTTA
1 AAATAAATAAATAAATAAATAATTTA
* * *
357481 AAATAAATAAACAAATCACTAATTTA
1 AAATAAATAAATAAATAAATAATTTA
* * **
357507 TTCGAACTAAATAAATAAATAAATTATTCG
1 ----AAATAAATAAATAAATAAATAATTTA
357537 AAATAAATAAATAA
1 AAATAAATAAATAA
357551 CAATTACCTC
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
26 36 0.65
30 19 0.35
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAAATAAATAAATAAATAATTTA
Found at i:385297 original size:21 final size:21
Alignment explanation
Indices: 385271--385364 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
385261 GAGCCTCCGA
*
385271 TATCGATACTCAAACCCTCAG
1 TATCGATACTCAATCCCTCAG
****
385292 TATCGATAC-CAAGGGGTCAG
1 TATCGATACTCAATCCCTCAG
* *
385312 TATCGATATTTC-TTCCCTCAG
1 TATCGATA-CTCAATCCCTCAG
**
385333 TATCGATACTCCTTCCCTCAG
1 TATCGATACTCAATCCCTCAG
385354 TATCGATACTC
1 TATCGATACTC
385365 TGCATGAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 17 0.29
21 41 0.69
22 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.31
Consensus pattern (21 bp):
TATCGATACTCAATCCCTCAG
Found at i:387996 original size:9 final size:9
Alignment explanation
Indices: 387979--388008 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
387969 TTTTTAACCG
*
387979 TTAATTGAA
1 TTAACTGAA
387988 TTAACTGAA
1 TTAACTGAA
387997 TTAACTGAA
1 TTAACTGAA
388006 TTA
1 TTA
388009 TTGATAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (9 bp):
TTAACTGAA
Found at i:393278 original size:14 final size:14
Alignment explanation
Indices: 393259--393287 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
393249 GCCATACATC
393259 ACAGGTAAAAGAAG
1 ACAGGTAAAAGAAG
393273 ACAGGTAAAAGAAG
1 ACAGGTAAAAGAAG
393287 A
1 A
393288 TACTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.28, T:0.07
Consensus pattern (14 bp):
ACAGGTAAAAGAAG
Found at i:398938 original size:20 final size:20
Alignment explanation
Indices: 398882--398940 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
398872 AAATGACCAA
*
398882 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
*
398901 CAAATTTCGCAAC-TGAATTT
1 CAAA-TTCGCAACGCGAATTT
398921 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
398941 AATTTCGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:398947 original size:19 final size:19
Alignment explanation
Indices: 398903--398947 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
398893 CGCGATCTCA
*
398903 AATTTCGCAACTGAATTTC
1 AATTTCGCAACCGAATTTC
*
398922 AAATTCGCAACGCGAATTT-
1 AATTTCGCAAC-CGAATTTC
398941 AATTTCG
1 AATTTCG
398948 TAACAGGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (19 bp):
AATTTCGCAACCGAATTTC
Found at i:399717 original size:12 final size:12
Alignment explanation
Indices: 399696--399729 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
399686 ACCACATTTC
*
399696 CAATACCAAACA
1 CAATATCAAACA
399708 CAATATCAAACA
1 CAATATCAAACA
*
399720 CAATCTCAAA
1 CAATATCAAA
399730 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:399882 original size:24 final size:24
Alignment explanation
Indices: 399855--399908 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
399845 GTATTCGAAA
399855 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
399879 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
399903 TTTGAT
1 TTTGAT
399909 GATGTGATGG
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:402679 original size:25 final size:25
Alignment explanation
Indices: 402641--402692 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
402631 AAATCAATTA
*
402641 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
402666 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
402691 AA
1 AA
402693 AAAATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:403098 original size:18 final size:18
Alignment explanation
Indices: 403077--403113 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
403067 GTAATTGGAG
403077 TTTGAATTTCAATTTCAA
1 TTTGAATTTCAATTTCAA
* *
403095 TTTGAGTTTGAATTTCAA
1 TTTGAATTTCAATTTCAA
403113 T
1 T
403114 ATAAATTTTG
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:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTCAATTTCAA
Found at i:403120 original size:24 final size:24
Alignment explanation
Indices: 403069--403121 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
403059 TTTCATATGT
* * *
403069 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
403093 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
403117 AATTT
1 AATTT
403122 TGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:403468 original size:39 final size:39
Alignment explanation
Indices: 403425--403511 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
403415 TCTGATGCTC
*
403425 ATCAAAATCCAAAGCTCATATGGTGCCAAGGAAAAGAAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
* * *
403464 ATCAAAATCCAAATCTTATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
403503 ATCAAAATC
1 ATCAAAATC
403512 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
Found at i:403892 original size:66 final size:60
Alignment explanation
Indices: 403812--403951 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
403802 TTTTAGAAAC
*
403812 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACAAATC-AATT
403877 A
60 A
* * **
403878 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
403938 AACAAATCAACTTT
1 AACAAATCAACTTT
403952 CAATGTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 19 0.28
61 21 0.30
62 3 0.04
66 26 0.38
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:405365 original size:21 final size:21
Alignment explanation
Indices: 405326--405420 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
405316 GACAGGACTA
** *
405326 CTTGAACGATGACATGGGCCT
1 CTTGAACGATGGGAGGGGCCT
* *
405347 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGGGAGGGGCCT
* * *
405368 CTTTG-ATGATGAGAGTGGCCT
1 C-TTGAACGATGGGAGGGGCCT
* *
405389 CTTGAACGATAGGAGGTGCCT
1 CTTGAACGATGGGAGGGGCCT
*
405410 CTTGAATGATG
1 CTTGAACGATG
405421 ATAGGTGCAT
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
20 3 0.05
21 49 0.89
22 3 0.05
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.27
Consensus pattern (21 bp):
CTTGAACGATGGGAGGGGCCT
Found at i:405404 original size:42 final size:42
Alignment explanation
Indices: 405342--405421 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
405332 CGATGACATG
* * *
405342 GGCCTCTTGAACGGTGGGAGGGGCTTCTTTG-ATGATGAGAGT
1 GGCCTCTTGAACGATAGGAGGGGCCTC-TTGAATGATGAGAGT
*
405384 GGCCTCTTGAACGATAGGAGGTGCCTCTTGAATGATGA
1 GGCCTCTTGAACGATAGGAGGGGCCTCTTGAATGATGA
405422 TAGGTGCATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.09
42 30 0.91
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.28
Consensus pattern (42 bp):
GGCCTCTTGAACGATAGGAGGGGCCTCTTGAATGATGAGAGT
Found at i:405426 original size:21 final size:21
Alignment explanation
Indices: 405371--405428 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
405361 GGGGCTTCTT
405371 TGATGATGAGAGTGGCCTCTTGAA
1 TGATGAT-AG-GT-GCCTCTTGAA
* *
405395 CGAT-AGGAGGTGCCTCTTGAA
1 TGATGA-TAGGTGCCTCTTGAA
405416 TGATGATAGGTGC
1 TGATGATAGGTGC
405429 ATCGAGCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 19 0.68
22 3 0.11
23 3 0.11
24 3 0.11
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (21 bp):
TGATGATAGGTGCCTCTTGAA
Found at i:405597 original size:4 final size:4
Alignment explanation
Indices: 405565--405622 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
405555 GGGCCGCTGA
* * * *
405565 AAAT AAAT TAAT ATAT AAAT CATT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
405613 AAAT AAAT AA
1 AAAT AAAT AA
405623 TGCTGAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:406456 original size:16 final size:17
Alignment explanation
Indices: 406431--406474 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
406421 TAAATATCCA
406431 AATA-TACAAACAATAT
1 AATACTACAAACAATAT
406447 AAT-CTACAAACAATAT
1 AATACTACAAACAATAT
406463 AATAC-ACAAACA
1 AATACTACAAACA
406475 TTAGTAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.20
Consensus pattern (17 bp):
AATACTACAAACAATAT
Found at i:407665 original size:19 final size:20
Alignment explanation
Indices: 407643--407683 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
407633 ATCGCAACGC
407643 GATTTT-AGTTTCGCGTTGT
1 GATTTTCAGTTTCGCGTTGT
* *
407662 GATTTTCATTTTCGTGTTGT
1 GATTTTCAGTTTCGCGTTGT
407682 GA
1 GA
407684 ATTTGGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.12, C:0.10, G:0.24, T:0.54
Consensus pattern (20 bp):
GATTTTCAGTTTCGCGTTGT
Found at i:407974 original size:22 final size:22
Alignment explanation
Indices: 407949--407991 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
407939 AGATAGACAG
*
407949 ATTTCGTTGGAAATGGGGATGT
1 ATTTCGTCGGAAATGGGGATGT
* *
407971 ATTTTGTCGGAGATGGGGATG
1 ATTTCGTCGGAAATGGGGATG
407992 GATGTCACTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.40, T:0.35
Consensus pattern (22 bp):
ATTTCGTCGGAAATGGGGATGT
Found at i:408147 original size:20 final size:20
Alignment explanation
Indices: 408122--408226 Score: 108
Period size: 20 Copynumber: 5.2 Consensus size: 20
408112 GCGTAAAAAC
408122 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
408142 ATTTGACTATCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
408162 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* * *
408181 ATTT-ACAAATTCACGTTACGA
1 ATTTGAC--TTTCGCGTTGCGA
408202 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
408222 ATTTG
1 ATTTG
408227 GAAAATCGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.03
19 6 0.09
20 53 0.76
21 7 0.10
22 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:408261 original size:20 final size:20
Alignment explanation
Indices: 408175--408262 Score: 54
Period size: 20 Copynumber: 4.3 Consensus size: 20
408165 TGACTTCTGT
*
408175 GTTGCGATTTACAAATTCAC
1 GTTGCGATTTACAAATTCGC
* *
408195 GTTACGAATTTGAC--TTTCGC
1 GTTGCG-ATTT-ACAAATTCGC
** *
408215 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** *
408236 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
408256 GTTGCGA
1 GTTGCGA
408263 AATTAGAAAC
Statistics
Matches: 48, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
20 34 0.71
21 12 0.25
22 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:408299 original size:20 final size:20
Alignment explanation
Indices: 408250--408303 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
408240 CGATTTACAT
408250 ATTCGCGTTGCGAAATTAGA
1 ATTCGCGTTGCGAAATTAGA
* *
408270 A-ACTGGGTTGCGAAATTAGA
1 ATTC-GCGTTGCGAAATTAGA
408290 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
408304 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTAGA
Done.