Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_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: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1008201 original size:14 final size:13
Alignment explanation
Indices: 1008181--1008219 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
1008171 TTTTACCGGA
1008181 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1008194 TGAAAAAACC-G-T
1 T-AAAAAACCGGTT
1008206 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1008219 T
1 T
1008220 TTATCCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.35
12 3 0.13
13 4 0.17
14 8 0.35
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1009519 original size:22 final size:22
Alignment explanation
Indices: 1009491--1009535 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1009481 GCTTTTCGAG
1009491 AGGGGTCATGTCCCAGACATTT
1 AGGGGTCATGTCCCAGACATTT
1009513 AGGGGTCATGTCCCAGACATTT
1 AGGGGTCATGTCCCAGACATTT
1009535 A
1 A
1009536 TCCGGATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
AGGGGTCATGTCCCAGACATTT
Found at i:1010532 original size:21 final size:21
Alignment explanation
Indices: 1010508--1010547 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1010498 TTTATTTTAT
1010508 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1010529 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1010548 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1010615 original size:33 final size:33
Alignment explanation
Indices: 1010542--1010638 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
1010532 TTTGTTTCAA
1010542 TTATCGAACTT-GAAGTTTTT-AGTATTTG-AT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1010572 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1010605 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1010638 T
1 T
1010639 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
30 11 0.18
31 9 0.15
32 8 0.13
33 33 0.54
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1010667 original size:13 final size:13
Alignment explanation
Indices: 1010624--1010678 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1010614 TTGGAAGTAT
1010624 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1010637 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1010651 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1010664 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1010677 TT
1 TT
1010679 TATTGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1011121 original size:15 final size:15
Alignment explanation
Indices: 1011069--1011124 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1011059 ATCTGGAATA
*
1011069 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1011084 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
* *
1011099 TAAAAAAACTGGTTTTT
1 T--TAAAACCGGTTTTT
1011116 TTAAAACCG
1 TTAAAACCG
1011125 AAACTGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1011241 original size:15 final size:17
Alignment explanation
Indices: 1011215--1011246 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1011205 TTCTATGGGA
1011215 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1011231 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1011247 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1015541 original size:3 final size:3
Alignment explanation
Indices: 1015535--1015561 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1015525 AAAAAAATGG
1015535 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1015562 CTTCTAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1015556 original size:44 final size:44
Alignment explanation
Indices: 1015466--1015557 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
1015456 TATTTTTATT
* *
1015466 TAATTAATTAATGTAACAAAAATTAATAATTAATATAATTCAAA
1 TAATTAATTAATGTAACAAAAATGAATAATTAATATAATTAAAA
* *
1015510 TAATTACATTAATTTAA-AAAAATGGATAA-TAATAATAA-TAATAA
1 TAATTA-ATTAATGTAACAAAAATGAATAATTAAT-ATAATTAA-AA
1015554 TAAT
1 TAAT
1015558 AATACTTCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
43 6 0.15
44 26 0.63
45 9 0.22
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (44 bp):
TAATTAATTAATGTAACAAAAATGAATAATTAATATAATTAAAA
Found at i:1015928 original size:14 final size:14
Alignment explanation
Indices: 1015902--1015937 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1015892 TGAGATAATA
1015902 AGAAGAGAAGAAATG
1 AGAAGA-AAGAAATG
1015917 AGAAGAAAGAAATG
1 AGAAGAAAGAAATG
1015931 AG-AGAAA
1 AGAAGAAA
1015938 AATGAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 10 0.48
15 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.06
Consensus pattern (14 bp):
AGAAGAAAGAAATG
Found at i:1018254 original size:15 final size:15
Alignment explanation
Indices: 1018234--1018262 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1018224 ACTTCATTTC
1018234 ATCATATCATATAAA
1 ATCATATCATATAAA
1018249 ATCATATCATATAA
1 ATCATATCATATAA
1018263 CATAGCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCATATCATATAAA
Found at i:1019612 original size:21 final size:21
Alignment explanation
Indices: 1019579--1019629 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1019569 CGATGTTCCC
1019579 TGGTATCGATACC-CTCCACATA
1 TGGTATC-ATACCTCTCC-CATA
*
1019601 -GGTATCATTACCTCTTCCATA
1 TGGTATCA-TACCTCTCCCATA
1019622 TGGTATCA
1 TGGTATCA
1019630 ACATTGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 10 0.40
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (21 bp):
TGGTATCATACCTCTCCCATA
Found at i:1022909 original size:15 final size:15
Alignment explanation
Indices: 1022889--1022917 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1022879 ACTTCATTTC
1022889 ATCATATCATATAAA
1 ATCATATCATATAAA
1022904 ATCATATCATATAA
1 ATCATATCATATAA
1022918 CATAGCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCATATCATATAAA
Found at i:1024265 original size:21 final size:21
Alignment explanation
Indices: 1024232--1024282 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1024222 CGATGTTCCC
1024232 TGGTATCGATACC-CTCCACATA
1 TGGTATC-ATACCTCTCC-CATA
*
1024254 -GGTATCATTACCTCTTCCATA
1 TGGTATCA-TACCTCTCCCATA
1024275 TGGTATCA
1 TGGTATCA
1024283 ACATTGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 10 0.40
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (21 bp):
TGGTATCATACCTCTCCCATA
Found at i:1027793 original size:17 final size:17
Alignment explanation
Indices: 1027755--1027786 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1027745 CCATGTACAC
1027755 ATGTGAGAACTATAGAT
1 ATGTGAGAACTATAGAT
1027772 ATGTGAGAAC-ATAGA
1 ATGTGAGAACTATAGA
1027787 GGTTGTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (17 bp):
ATGTGAGAACTATAGAT
Found at i:1028304 original size:2 final size:2
Alignment explanation
Indices: 1028297--1028323 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1028287 TTATGCAATC
1028297 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 A
1028324 ACATTCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1034693 original size:20 final size:20
Alignment explanation
Indices: 1034653--1034691 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1034643 CATTGCATGA
*
1034653 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
1034673 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
1034692 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1048036 original size:6 final size:5
Alignment explanation
Indices: 1048023--1048109 Score: 78
Period size: 5 Copynumber: 17.8 Consensus size: 5
1048013 ATAAAAAATA
* *
1048023 AAAAG AAAAGG AAAAG AAAA- CAAAG -AAAG -AAAG AAATA- AAATG AAAAG
1 AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG
1048071 AAAAG AAAAG AAAAG AAAA- ATGAAAG AAAAG -AAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG A--AAAG AAAAG AAAAG AAAA
1048110 ATGAAAAAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
4 16 0.23
5 44 0.63
6 9 0.13
7 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:1049592 original size:134 final size:134
Alignment explanation
Indices: 1049363--1049804 Score: 645
Period size: 134 Copynumber: 3.3 Consensus size: 134
1049353 ACAAATCAAA
* *
1049363 CTTGATTCAATCTTCCCTAAAGAACAGTGGAATAAATCAAAGTCCCCAGATATGATTTTCCCTCA
1 CTTGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
** * *
1049428 AGAAGAAGTTGAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGT
66 AGAAGAAGCGGAACATATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
*
1049493 TTAC
131 CTAC
* * *
1049497 CTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACA-TCCCCAGATCTGATTTTCCCTC
1 CTTGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAA-AGTCCCCAGATCTGATTTTCCCTC
* * *
1049561 AAGAAAAAGCGGAACATATCCCTTTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
65 AAGAAGAAGCGGAACATATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
1049626 TCTAC
130 TCTAC
* *
1049631 CTTGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAAAGTCCCCATATCTGATTTTCCCTCA
1 CTTGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * * * *
1049696 AGAAGAAGCGAAACAAAT-CATTCTCTTCCAAGATTTGATATTCCCTAAGTGACAGTGGAACAAG
66 AGAAGAAGCGGAACATATCCATT-TCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
1049760 TCTAC
130 TCTAC
* * *
1049765 CTTGATTCAATCTTCCCTGAAGAACAGTGGATTGAGTCAA
1 CTTGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAA
1049805 TGTTTCTTGA
Statistics
Matches: 275, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
133 4 0.01
134 270 0.98
135 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (134 bp):
CTTGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGGAACATATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTAC
Found at i:1049981 original size:3 final size:3
Alignment explanation
Indices: 1049973--1050025 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
1049963 TTTCATCCTA
* *
1049973 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT -TT ATT A-A ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1050019 ATT ATT A
1 ATT ATT A
1050026 CATTTCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 3 0.07
3 41 0.93
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1051766 original size:2 final size:2
Alignment explanation
Indices: 1051759--1051785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1051749 TATTCGAGTT
1051759 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1051786 TTATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1060167 original size:15 final size:15
Alignment explanation
Indices: 1060147--1060180 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1060137 TCAAATCACA
*
1060147 AGATTGATCGACTTT
1 AGATTGATCAACTTT
1060162 AGATTGATCAACTTT
1 AGATTGATCAACTTT
1060177 AGAT
1 AGAT
1060181 GGTTTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (15 bp):
AGATTGATCAACTTT
Found at i:1061942 original size:23 final size:23
Alignment explanation
Indices: 1061906--1062024 Score: 134
Period size: 23 Copynumber: 5.3 Consensus size: 23
1061896 CACCACAACT
*
1061906 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
1061927 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*** *
1061950 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*
1061973 CATATAGAATTGCACCGTAGTGT
1 CATATAGAATTGCACCGTAGTGC
*** *
1061996 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
1062019 CATATA
1 CATATA
1062025 ATAATGTCCA
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
21 6 0.08
22 2 0.03
23 70 0.90
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Found at i:1061981 original size:46 final size:46
Alignment explanation
Indices: 1061914--1062024 Score: 204
Period size: 46 Copynumber: 2.4 Consensus size: 46
1061904 CTCATATAAA
*
1061914 TGCACCGAAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
1 TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
*
1061960 TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGTCGCGTAGAGT
1 TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
1062006 TGCACCGTAGTGCCATATA
1 TGCACCGTAGTGCCATATA
1062025 ATAATGTCCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (46 bp):
TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
Found at i:1062207 original size:103 final size:103
Alignment explanation
Indices: 1062036--1062253 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
1062026 TAATGTCCAT
1062036 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1062101 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1062139 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1062204 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1062242 AAGGACCACATA
1 AAGGACCACATA
1062254 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1063717 original size:21 final size:21
Alignment explanation
Indices: 1063691--1063734 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1063681 ATTTTATTCG
* *
1063691 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1063712 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1063733 CT
1 CT
1063735 AGCCCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1067504 original size:23 final size:23
Alignment explanation
Indices: 1067468--1067586 Score: 143
Period size: 23 Copynumber: 5.3 Consensus size: 23
1067458 CACCACAGCT
*
1067468 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
1067489 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*** *
1067512 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
1067535 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*** *
1067558 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
1067581 CATATA
1 CATATA
1067587 ATAATGTCCA
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
21 6 0.08
22 2 0.03
23 72 0.90
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Found at i:1067543 original size:46 final size:46
Alignment explanation
Indices: 1067476--1067586 Score: 213
Period size: 46 Copynumber: 2.4 Consensus size: 46
1067466 CTCATATAAA
*
1067476 TGCACCGAAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
1 TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
1067522 TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
1 TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
1067568 TGCACCGTAGTGCCATATA
1 TGCACCGTAGTGCCATATA
1067587 ATAATGTCCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (46 bp):
TGCACCGTAGTGCCATATAGAATTGCACCGTAGTGCCGCGTAGAGT
Found at i:1067769 original size:103 final size:103
Alignment explanation
Indices: 1067598--1067815 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
1067588 TAATGTCCAT
1067598 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1067663 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1067701 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1067766 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1067804 AAGGACCACATA
1 AAGGACCACATA
1067816 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1069281 original size:21 final size:21
Alignment explanation
Indices: 1069255--1069298 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1069245 ATTTTATTCG
* *
1069255 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1069276 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1069297 CT
1 CT
1069299 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1071927 original size:41 final size:42
Alignment explanation
Indices: 1071835--1071929 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
1071825 CTTTCAACTA
* * *
1071835 TTCCTTTTTGTTTATTTTGTTAGGTCCACTTCTTTTATCTTT
1 TTCCTTTTTCTTTATTTTCTTAGGTCAACTTCTTTTATCTTT
*
1071877 TTCCCTTTTCTTTATTTTCTT-GGCTCAACTTC-TTTAT-TTCT
1 TTCCTTTTTCTTTATTTTCTTAGG-TCAACTTCTTTTATCTT-T
*
1071918 TTCTTTTTTCTT
1 TTCCTTTTTCTT
1071930 ATAGTAGCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
40 2 0.04
41 18 0.40
42 25 0.56
ACGTcount: A:0.08, C:0.20, G:0.06, T:0.65
Consensus pattern (42 bp):
TTCCTTTTTCTTTATTTTCTTAGGTCAACTTCTTTTATCTTT
Found at i:1079360 original size:35 final size:34
Alignment explanation
Indices: 1079275--1079361 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
1079265 AATATAATTT
* *
1079275 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGA
* *
1079309 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGA
1079347 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1079362 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGA
Found at i:1079985 original size:18 final size:18
Alignment explanation
Indices: 1079962--1080000 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1079952 TGGAAAGGCA
* *
1079962 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGAT
1079980 GCGGCATCATAAATGGAT
1 GCGGCATCATAAATGGAT
1079998 GCG
1 GCG
1080001 ATGGATGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (18 bp):
GCGGCATCATAAATGGAT
Found at i:1081685 original size:17 final size:18
Alignment explanation
Indices: 1081665--1081705 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1081655 AAATTATATT
1081665 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
1081682 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
1081700 ATTAAA
1 AGTAAA
1081706 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:1082070 original size:29 final size:29
Alignment explanation
Indices: 1082026--1082104 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
1082016 TACTGCTACG
**
1082026 GGTGTTAGATTAGGAAATATAATCTGACC
1 GGTGTTAGATCGGGAAATATAATCTGACC
*
1082055 GGTGTTAGATCGGGAAATATAATCTGATC
1 GGTGTTAGATCGGGAAATATAATCTGACC
*
1082084 GGTGTTAGATCGGTAAATATA
1 GGTGTTAGATCGGGAAATATA
1082105 TCGGTCACCG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.32
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAATCTGACC
Found at i:1083118 original size:15 final size:16
Alignment explanation
Indices: 1083100--1083133 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1083090 TATTGAAAAA
1083100 TTCA-ATGGGAGAAAT
1 TTCACATGGGAGAAAT
*
1083115 TTCACATTGGAGAAAT
1 TTCACATGGGAGAAAT
1083131 TTC
1 TTC
1083134 TCATTGTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (16 bp):
TTCACATGGGAGAAAT
Found at i:1083147 original size:16 final size:16
Alignment explanation
Indices: 1083107--1083139 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1083097 AAATTCAATG
1083107 GGAGAAATTTCACATT
1 GGAGAAATTTCACATT
*
1083123 GGAGAAATTTCTCATT
1 GGAGAAATTTCACATT
1083139 G
1 G
1083140 TGGAAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (16 bp):
GGAGAAATTTCACATT
Found at i:1087344 original size:34 final size:34
Alignment explanation
Indices: 1087285--1087351 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1087275 TTCTTGAGAG
*
1087285 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTCA
1087319 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
1087352 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTCA
Found at i:1087547 original size:22 final size:20
Alignment explanation
Indices: 1087519--1087559 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1087509 ACACACACAC
*
1087519 ACACACATATATATATATATAT
1 ACACACAAATA-ATA-ATATAT
1087541 ACACACAAATAATAATATA
1 ACACACAAATAATAATATA
1087560 AAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (20 bp):
ACACACAAATAATAATATAT
Found at i:1088023 original size:22 final size:24
Alignment explanation
Indices: 1087978--1088023 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1087968 AGAATTTATT
1087978 AATAATTATTATCAAATATATTTAA
1 AATAATTATTA-CAAATATATTTAA
1088003 AATAATTATTA-AAATAT-TTTA
1 AATAATTATTACAAATATATTTA
1088024 TTTCTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 6 0.29
25 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AATAATTATTACAAATATATTTAA
Found at i:1089419 original size:28 final size:28
Alignment explanation
Indices: 1089353--1089413 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
1089343 TCACCGGTCT
1089353 GGTTTCACTTCTTACCTTTCAAGTGAAA
1 GGTTTCACTTCTTACCTTTCAAGTGAAA
1089381 GGTTTCACTTCTTACCTTTCAAGTGAAA
1 GGTTTCACTTCTTACCTTTCAAGTGAAA
1089409 GGTTT
1 GGTTT
1089414 AGCTTCATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (28 bp):
GGTTTCACTTCTTACCTTTCAAGTGAAA
Found at i:1089962 original size:30 final size:31
Alignment explanation
Indices: 1089928--1089997 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
1089918 TTGGGACAGG
*
1089928 CTCATGATCATGACCTAGG-TTTAGGGCAC-A
1 CTCATGATCATGAACT-GGATTTAGGGCACAA
*
1089958 CTCATGACCATGAACTGGATTTAGGGCACAA
1 CTCATGATCATGAACTGGATTTAGGGCACAA
1089989 C-CATGATCA
1 CTCATGATCA
1089998 AGAAGGGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 31 0.89
31 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (31 bp):
CTCATGATCATGAACTGGATTTAGGGCACAA
Found at i:1092808 original size:50 final size:49
Alignment explanation
Indices: 1092703--1092810 Score: 114
Period size: 49 Copynumber: 2.2 Consensus size: 49
1092693 AAGTTTCAAT
* * *
1092703 AAAATATATTTTTATTAAAACTTGTCAGTTTGATGTGACAAAATTTAATA
1 AAAATATA-TTTTATTAAAACTCGTCACTTTGACGTGACAAAATTTAATA
* * *
1092753 GAAATATATTTTATTGAAACTCGTCACTTCT-ACGTGA-AGAATTTTAATA
1 AAAATATATTTTATTAAAACTCGTCACTT-TGACGTGACA-AAATTTAATA
1092802 AAAA-ATATT
1 AAAATATATT
1092811 ATTTAGACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
48 6 0.12
49 35 0.71
50 8 0.16
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (49 bp):
AAAATATATTTTATTAAAACTCGTCACTTTGACGTGACAAAATTTAATA
Found at i:1105745 original size:2 final size:2
Alignment explanation
Indices: 1105678--1105731 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1105668 AATTTATAAA
1105678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1105720 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1105732 TATTAATAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1107629 original size:122 final size:122
Alignment explanation
Indices: 1107402--1107642 Score: 321
Period size: 122 Copynumber: 2.0 Consensus size: 122
1107392 AGTTCTACTC
* * *
1107402 CTTCTTCTTCAGATGAGTTCTTCTCATTATGAACATTTCTGAAAATGTTGATGCTGGTATATGCC
1 CTTCCTCTTCAGATAAGTTCTTCTCATTATGAACATTTCTGAAAATGTTGATGCTGATATATGCC
*
1107467 CTTCTGTGATAGAGTCATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
66 CTTCTGCGATAGAGTCATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
* *
1107524 CTTCCTCTTCAGATAAGTTCTTCTCATTATGAA-ATTTCTCTGGAAAA-GTTGATGTTGATCTAT
1 CTTCCTCTTCAGATAAGTTCTTCTCATTATGAACA-TT-TCT-GAAAATGTTGATGCTGATATAT
* * *
1107587 -CTCCTTCTGCGATAGAGTCGA-GC-AAATGTTGAACAAGTTCTTCTCATTATGAACTT
63 GC-CCTTCTGCGATAGAGTC-ATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT
1107643 TCTCTGGAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
121 1 0.01
122 65 0.62
123 33 0.31
124 6 0.06
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (122 bp):
CTTCCTCTTCAGATAAGTTCTTCTCATTATGAACATTTCTGAAAATGTTGATGCTGATATATGCC
CTTCTGCGATAGAGTCATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
Found at i:1107635 original size:83 final size:84
Alignment explanation
Indices: 1107538--1107723 Score: 277
Period size: 83 Copynumber: 2.2 Consensus size: 84
1107528 CTCTTCAGAT
*
1107538 AAGTTCTTCTCATTATGAAATTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGA
1 AAGTTCTTCTCATTATGAAATTTCTCTGGAAAAGTTGATGTTGATCTACCTCCTTCTGCGATAGA
*
1107603 GTCGA-GC-AAATGTTGAAC
66 GTC-ATGCAAAAGGTTGAAC
* * * * *
1107621 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATTTTGATCTACCTCTTTCTGTGATAGA
1 AAGTTCTTCTCATTATGAAATTTCTCTGGAAAAGTTGATGTTGATCTACCTCCTTCTGCGATAGA
1107686 GTCATGCAAAAGGTTGAAC
66 GTCATGCAAAAGGTTGAAC
*
1107705 AAGCTCTTCTCATTATGAA
1 AAGTTCTTCTCATTATGAA
1107724 CTTCTTCTTC
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
82 1 0.01
83 64 0.69
84 28 0.30
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (84 bp):
AAGTTCTTCTCATTATGAAATTTCTCTGGAAAAGTTGATGTTGATCTACCTCCTTCTGCGATAGA
GTCATGCAAAAGGTTGAAC
Found at i:1107761 original size:123 final size:123
Alignment explanation
Indices: 1107621--1108028 Score: 676
Period size: 123 Copynumber: 3.3 Consensus size: 123
1107611 AATGTTGAAC
* * * *
1107621 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATTTTGATCTACCTCTTTCTGTGATAGA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGA
1107686 GTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
66 GTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
* *
1107744 AAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGA
* *
1107809 GTCGA-GC-AAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGAT
66 GTC-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGAT
* * *
1107867 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGTTGGTCTATCTCCTTCTGTGATAGA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGA
*
1107932 GTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTTAGAT
66 GTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
1107990 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
1108029 CCATTGAGTG
Statistics
Matches: 263, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
122 40 0.15
123 183 0.70
124 40 0.15
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (123 bp):
AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGA
GTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
Found at i:1107826 original size:206 final size:205
Alignment explanation
Indices: 1107417--1107845 Score: 718
Period size: 206 Copynumber: 2.1 Consensus size: 205
1107407 TCTTCAGATG
* *
1107417 AGTTCTTCTCATTATGAACATTTCTGAAAATGTTGATGCTGGTATATGCCCTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACATTTCTGAAAAGGTTGATGCTGGTATATACCCTTCTGTGATAGAGT
1107482 CATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
66 CATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
*
1107547 TCATTATGAAATTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
131 TCATTATGAAATTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
*
1107612 ATGTTGAACA
196 AGGTTGAACA
* * * * *
1107622 AGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGAT-TTTG-ATCTACCTCTTTCTGTGATAG
1 AGTTCTTCTCATTATGAACATT-TCTGAAAAGGTTGATGCTGGTATATACC-C-TTCTGTGATAG
*
1107685 AGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTC
63 AGTCATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTC
*
1107750 TTCTCATTATGAACTTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAG
128 TTCTCATTATGAAATTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAG
1107815 CAAAGGTTGAACA
193 CAAAGGTTGAACA
1107828 AGTTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
1107846 ATTCTTCTTC
Statistics
Matches: 210, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
204 5 0.02
205 24 0.11
206 181 0.86
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (205 bp):
AGTTCTTCTCATTATGAACATTTCTGAAAAGGTTGATGCTGGTATATACCCTTCTGTGATAGAGT
CATACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
TCATTATGAAATTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
AGGTTGAACA
Found at i:1111546 original size:30 final size:30
Alignment explanation
Indices: 1111512--1111583 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1111502 CGATGGTTCA
1111512 AGCTCCACCGCCACCAGTAGTAGCTATAAC
1 AGCTCCACCGCCACCAGTAGTAGCTATAAC
* * *
1111542 AGCTCCACCGCCACCGGTGGTAGCTATACC
1 AGCTCCACCGCCACCAGTAGTAGCTATAAC
1111572 AGCTCCACCGCC
1 AGCTCCACCGCC
1111584 GTCACCATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.42, G:0.19, T:0.15
Consensus pattern (30 bp):
AGCTCCACCGCCACCAGTAGTAGCTATAAC
Found at i:1111990 original size:28 final size:30
Alignment explanation
Indices: 1111947--1112006 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1111937 ATCTTTTTGT
* *
1111947 AATTATTGTTA-ATTTTT-AACAATTATAA
1 AATTATTATTATATTTTTCAACAATTAAAA
*
1111975 AATTATTATTATTTTTTTCAACAATTAAAA
1 AATTATTATTATATTTTTCAACAATTAAAA
1112005 AA
1 AA
1112007 ATGTCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 5 0.19
30 12 0.44
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
AATTATTATTATATTTTTCAACAATTAAAA
Found at i:1112337 original size:24 final size:24
Alignment explanation
Indices: 1112306--1112358 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1112296 GACACGTTTT
1112306 TCTCTACCTTTATGATATACTTTC
1 TCTCTACCTTTATGATATACTTTC
**
1112330 TCTCTACCTTTATGATATGTTTTC
1 TCTCTACCTTTATGATATACTTTC
1112354 TCTCT
1 TCTCT
1112359 CTTTTGGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.53
Consensus pattern (24 bp):
TCTCTACCTTTATGATATACTTTC
Found at i:1112362 original size:22 final size:23
Alignment explanation
Indices: 1112290--1112362 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 23
1112280 ATAATTTTAT
* *
1112290 CTTTATGACACGTTTT-TCTCTA
1 CTTTATGATATGTTTTCTCTCTA
**
1112312 CCTTTATGATATACTTTCTCTCTA
1 -CTTTATGATATGTTTTCTCTCTA
1112336 CCTTTATGATATGTTTTCTCTCT-
1 -CTTTATGATATGTTTTCTCTCTA
1112359 CTTT
1 CTTT
1112363 TGGTATATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 4 0.09
23 12 0.28
24 27 0.63
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTTATGATATGTTTTCTCTCTA
Found at i:1112914 original size:23 final size:22
Alignment explanation
Indices: 1112873--1112922 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1112863 ATTTAAAAAA
*
1112873 TAAAAAATATGAAATTTATATTT
1 TAAAAAATATGAAATTTAT-TTG
*
1112896 TAAAAAATTATTAAA-TTATTTG
1 TAAAAAA-TATGAAATTTATTTG
1112918 TAAAA
1 TAAAA
1112923 TTATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 11 0.46
24 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAAAATATGAAATTTATTTG
Found at i:1114636 original size:40 final size:39
Alignment explanation
Indices: 1114558--1114636 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
1114548 TACCGGAAAC
* *
1114558 ATTATTATTTCTACCATTTTGTTATTGTTGGGCGCTTTA
1 ATTATTATTTCTACCATTTTGTTATTATTGGGCACTTTA
* *
1114597 ATTATTTTTTCTACTGC-TTTTGTTATTATTGGTCACTTTA
1 ATTATTATTTCTAC--CATTTTGTTATTATTGGGCACTTTA
1114637 CCGGAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 13 0.38
40 20 0.59
41 1 0.03
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.57
Consensus pattern (39 bp):
ATTATTATTTCTACCATTTTGTTATTATTGGGCACTTTA
Found at i:1115164 original size:20 final size:21
Alignment explanation
Indices: 1115139--1115190 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1115129 TTTTCCCAAT
*
1115139 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
**
1115159 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
1115180 TCGCAATGCGA
1 TCGCAATGCGA
1115191 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:1115208 original size:103 final size:102
Alignment explanation
Indices: 1115093--1115338 Score: 259
Period size: 103 Copynumber: 2.4 Consensus size: 102
1115083 CGCAATTATA
* *
1115093 ACTATCGCAATGCGATTTTCC-AATTTCGCGTTGCGATTTTCCCAATTCGCAATGCGA-ATAAGT
1 ACTATCGCAATGCGATTTTCCTAA-TTCGCATTGCGA-TTTACCAATTCGCAATGCGATATAA-T
*
1115156 AAATCGCAATGCGAATTTGAAAAATCGCAATGCG-ATACTG
63 AAATCGCAATGCGAATTAGAAAAATCGCAATGCGAAT-CTG
* ** ** * *
1115196 ACTATCGCAATGCAATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAA
1 ACTATCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACCAATTCGCAATGCGA-TATAATAA
* * *
1115261 TTCGCAATGCGAATTAGGAAAATCGCAATGCGAATCTT
65 ATCGCAATGCGAATTAGAAAAATCGCAATGCGAATCTG
* * *
1115299 ACTATCGCAATGCGAATCTTACT-A-TCGCAATGCGATTTAC
1 ACTATCGCAATGCG-ATTTTCCTAATTCGCATTGCGATTTAC
1115339 ATAGCGCCAT
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
102 30 0.25
103 79 0.65
104 12 0.10
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (102 bp):
ACTATCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACCAATTCGCAATGCGATATAATAAA
TCGCAATGCGAATTAGAAAAATCGCAATGCGAATCTG
Found at i:1115225 original size:41 final size:40
Alignment explanation
Indices: 1115128--1115336 Score: 104
Period size: 41 Copynumber: 5.1 Consensus size: 40
1115118 TCGCGTTGCG
* * *
1115128 ATTTTCCCAATTCGCAATGCGAATAAGTA-AATCGCAATGCGA
1 ATTTTCCTAATTCGCAATGCG-ATATG-ACTATCGCAATGC-A
*** *
1115170 A-TTTGAAAAATCGCAATGCGATACTGACTATCGCAATGCA
1 ATTTTCCTAATTCGCAATGCGATA-TGACTATCGCAATGCA
* * ** *
1115210 ATTTTCCTAATTCGCATTGCGAT-TTACGTATTCGCGTTGCG
1 ATTTTCCTAATTCGCAATGCGATATGAC-TA-TCGCAATGCA
* * **
1115251 ATTTTCATAATTCGCAATGCGAATTAGGAAAATCGCAATGCGA
1 ATTTTCCTAATTCGCAATGCG-A-TATGACTATCGCAATGC-A
* * * * *
1115294 ATCTTACT-A-TCGCAATGCGAATCTTACTATCGCAATGCG
1 ATTTTCCTAATTCGCAATGCG-ATATGACTATCGCAATGCA
1115333 ATTT
1 ATTT
1115337 ACATAGCGCC
Statistics
Matches: 124, Mismatches: 34, Indels: 21
0.69 0.19 0.12
Matches are distributed among these distances:
39 6 0.05
40 20 0.16
41 80 0.65
42 10 0.08
43 7 0.06
44 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (40 bp):
ATTTTCCTAATTCGCAATGCGATATGACTATCGCAATGCA
Found at i:1115234 original size:21 final size:21
Alignment explanation
Indices: 1115097--1115272 Score: 85
Period size: 21 Copynumber: 8.5 Consensus size: 21
1115087 ATTATAACTA
*
1115097 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** **
1115118 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1115139 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
* * * *
1115159 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGATTTTCATAAT
** *
1115180 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
1115200 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1115221 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
1115241 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
1115262 TCGCAATGCGA
1 TCGCAATGCGA
1115273 ATTAGGAAAA
Statistics
Matches: 115, Mismatches: 32, Indels: 16
0.71 0.20 0.10
Matches are distributed among these distances:
19 2 0.02
20 44 0.38
21 67 0.58
22 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:1115307 original size:20 final size:20
Alignment explanation
Indices: 1115282--1115333 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1115272 AATTAGGAAA
1115282 ATCGCAATGCGAATCTTACT
1 ATCGCAATGCGAATCTTACT
1115302 ATCGCAATGCGAATCTTACT
1 ATCGCAATGCGAATCTTACT
1115322 ATCGCAATGCGA
1 ATCGCAATGCGA
1115334 TTTACATAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATCTTACT
Found at i:1115916 original size:19 final size:19
Alignment explanation
Indices: 1115855--1115921 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1115845 TTCGAGAATG
*
1115855 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAACA
** * *
1115875 ACTATAGCAACGCGAAATA
1 AAAATCGCAACGCGAAACA
*
1115894 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACA
1115913 AAAATCGCA
1 AAAATCGCA
1115922 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:1115939 original size:19 final size:19
Alignment explanation
Indices: 1115917--1115989 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
1115907 GAAACCAAAA
*
1115917 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1115936 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1115950 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1115969 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1115988 TC
1 TC
1115990 AACCAAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1118158 original size:21 final size:21
Alignment explanation
Indices: 1118134--1118200 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1118124 TCATTCCTCG
1118134 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1118155 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1118176 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1118197 AGAG
1 AGAG
1118201 CCGATTCACA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1118158 original size:42 final size:42
Alignment explanation
Indices: 1118082--1118200 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1118072 GACTCGCCTT
* * * * * * *
1118082 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1118124 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1118166 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1118201 CCGATTCACA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1119565 original size:13 final size:14
Alignment explanation
Indices: 1119549--1119583 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1119539 ATTGTTTAAT
1119549 TGATTTGT-AAAGG
1 TGATTTGTAAAAGG
*
1119562 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1119576 TGATTTGT
1 TGATTTGT
1119584 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1119748 original size:19 final size:19
Alignment explanation
Indices: 1119690--1119748 Score: 55
Period size: 25 Copynumber: 2.8 Consensus size: 19
1119680 AAAAAGTACT
*
1119690 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1119709 ATCGCAACGAATCGCAAAAATGAAA
1 ATCGCAACG---CG---AAATGAAA
1119734 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1119749 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
19 12 0.36
22 4 0.12
25 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1119801 original size:33 final size:32
Alignment explanation
Indices: 1119757--1119883 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
1119747 ATTAAATTCG
*
1119757 CGTTGCGATTTTCATTTTGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
1119790 CGTTGCTATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1119823 CGTTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1119856 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1119884 AGTAATTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1119846 original size:66 final size:66
Alignment explanation
Indices: 1119750--1119882 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1119740 ACGCGAAATT
*
1119750 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCTATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1119815 G
66 G
*
1119816 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1119881 G
66 G
1119882 A
1 A
1119883 TAGTAATTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1119849 original size:19 final size:19
Alignment explanation
Indices: 1119825--1119883 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
1119815 GAAATTCGCG
1119825 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTTGCA
* *
1119844 TTGCGA--TTC--TCT-CG
1 TTGCGATTTTCATTTTGCA
*
1119858 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTTGCA
1119877 TTGCGAT
1 TTGCGAT
1119884 AGTAATTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 7 0.23
15 2 0.07
16 3 0.10
17 3 0.10
18 1 0.03
19 14 0.47
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTTGCA
Found at i:1122291 original size:24 final size:24
Alignment explanation
Indices: 1122257--1122310 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1122247 CTGAAACATC
*
1122257 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1122281 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1122305 ATCAAA
1 ATCAAA
1122311 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1123107 original size:20 final size:21
Alignment explanation
Indices: 1123082--1123131 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1123072 TTCCTAATTT
*
1123082 GCAATGCGAA-TAAGTAAATC
1 GCAATGCGAATTAAGAAAATC
**
1123102 GCAATGCGAATTTGGAAAATC
1 GCAATGCGAATTAAGAAAATC
1123123 GCAATGCGA
1 GCAATGCGA
1123132 TACTGACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
GCAATGCGAATTAAGAAAATC
Found at i:1123153 original size:20 final size:20
Alignment explanation
Indices: 1123120--1123196 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1123110 AATTTGGAAA
* *
1123120 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
1123140 ATCGCAACGAGATAAT-ACAA
1 ATCGCAACGAGATACTGAC-T
*
1123160 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
1123180 TTCGCAAC-AGATTCTGA
1 ATCGCAACGAGATACTGA
1123197 AAATCGCAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
19 11 0.23
20 34 0.72
21 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1123203 original size:19 final size:20
Alignment explanation
Indices: 1123116--1123205 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
1123106 TGCGAATTTG
* * *
1123116 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
** **
1123136 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATTCT
1123156 -ACAAATCGCAACGAGATTCT
1 GA-AAATCGCAACGAGATTCT
***
1123176 GACTTTCGCAAC-AGATTCT
1 GAAAATCGCAACGAGATTCT
1123195 GAAAATCGCAA
1 GAAAATCGCAA
1123206 TCATCTTCAA
Statistics
Matches: 53, Mismatches: 15, Indels: 5
0.73 0.21 0.07
Matches are distributed among these distances:
19 16 0.30
20 36 0.68
21 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:1123543 original size:19 final size:19
Alignment explanation
Indices: 1123502--1123569 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1123492 GAAATGAAAA
1123502 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
1123518 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
1123535 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1123554 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1123570 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1125627 original size:20 final size:20
Alignment explanation
Indices: 1125604--1125657 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1125594 GAAACTTAAA
1125604 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* * *
1125624 ATCGCAACGCGGAAATGGCT
1 ATCGCAATGCGAAAATGACT
1125644 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1125658 TGCAAATCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1125721 original size:19 final size:19
Alignment explanation
Indices: 1125697--1125793 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
1125687 GAAACACAAA
*
1125697 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1125716 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1125732 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1125749 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1125765 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1125782 TCGCATTGCGAT
1 TCGCATTGCGAT
1125794 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1125740 original size:14 final size:14
Alignment explanation
Indices: 1125721--1125777 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1125711 TCATTTCGCA
1125721 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
1125735 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
1125752 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
1125768 TTGCGATTTT
1 TTGCGATTTT
1125778 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:1125749 original size:33 final size:33
Alignment explanation
Indices: 1125702--1125793 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1125692 ACAAATCGCA
*
1125702 TTGCAATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1125735 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1125768 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1125794 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1125812 original size:20 final size:19
Alignment explanation
Indices: 1125778--1125832 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1125768 TTGCGATTTT
*
1125778 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1125797 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1125817 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1125833 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1126340 original size:18 final size:18
Alignment explanation
Indices: 1126314--1126358 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1126304 GTCGATCAGA
*
1126314 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1126332 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1126350 TGATGGCTC
1 TGATGGCTC
1126359 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1127697 original size:20 final size:20
Alignment explanation
Indices: 1127672--1127725 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1127662 AATAGTTTCT
1127672 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
1127692 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
1127712 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1127726 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1127986 original size:22 final size:22
Alignment explanation
Indices: 1127959--1128002 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1127949 GATGGAGATA
1127959 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
**
1127981 GACGGATTTCTTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1128003 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1128276 original size:20 final size:20
Alignment explanation
Indices: 1128170--1128304 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1128160 CGCTTTGAAA
*
1128170 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1128191 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1128211 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1128231 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1128252 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1128272 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1128292 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1128305 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1128276 original size:61 final size:61
Alignment explanation
Indices: 1128170--1128307 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
1128160 CGCTTTGAAA
* * * *
1128170 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1128231 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1128292 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1128308 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1128323 original size:61 final size:61
Alignment explanation
Indices: 1128170--1128325 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
1128160 CGCTTTGAAA
* ** * * * *
1128170 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
1128231 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1128292 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
1128326 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1128415 original size:21 final size:21
Alignment explanation
Indices: 1128375--1128415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1128365 ACTGTAGACC
** *
1128375 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGAAATGCAATT
1128396 ATCGCAACGCGAAATGCAAT
1 ATCGCAACGCGAAATGCAAT
1128416 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAATT
Found at i:1128763 original size:12 final size:12
Alignment explanation
Indices: 1128746--1128790 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1128736 ATGACCTAAA
1128746 AATAATTTATAG
1 AATAATTTATAG
* *
1128758 AATAATTGTTTAAA
1 AATAATT-TAT-AG
1128772 AATAATTTATAG
1 AATAATTTATAG
1128784 AATAATT
1 AATAATT
1128791 GTTTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 15 0.56
13 4 0.15
14 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (12 bp):
AATAATTTATAG
Found at i:1128807 original size:26 final size:26
Alignment explanation
Indices: 1128742--1128796 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1128732 AAATATGACC
1128742 TAAAAATAATTTATAGAATAATTGTT
1 TAAAAATAATTTATAGAATAATTGTT
1128768 TAAAAATAATTTATAGAATAATTGTT
1 TAAAAATAATTTATAGAATAATTGTT
1128794 TAA
1 TAA
1128797 TTTTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (26 bp):
TAAAAATAATTTATAGAATAATTGTT
Found at i:1134131 original size:14 final size:14
Alignment explanation
Indices: 1134112--1134141 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1134102 ATGCTTTGTG
1134112 GATGTAATCTGCTC
1 GATGTAATCTGCTC
1134126 GATGTAATCTGCTC
1 GATGTAATCTGCTC
1134140 GA
1 GA
1134142 ATTTGAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (14 bp):
GATGTAATCTGCTC
Found at i:1139897 original size:40 final size:39
Alignment explanation
Indices: 1139867--1139962 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
1139857 AGTACCACGT
* * *
1139867 GAACAATATCGGTATTGTTCATGCAGTATCAATACTGTAA
1 GAACAATATCAGTACTGTTCATGCAGTATCAATACCGT-A
* *
1139907 GAACAATATCAGTACTGTTCATGCAGTATCGATACTGTAA
1 GAACAATATCAGTACTGTTCATGCAGTATCAATACCGT-A
*
1139947 GAACAATATCGGTACT
1 GAACAATATCAGTACT
1139963 TCTCACCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (39 bp):
GAACAATATCAGTACTGTTCATGCAGTATCAATACCGTA
Found at i:1139922 original size:20 final size:20
Alignment explanation
Indices: 1139893--1139962 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1139883 GTTCATGCAG
*
1139893 TATCAATACTGTAAGAACAA
1 TATCAGTACTGTAAGAACAA
* *
1139913 TATCAGTACTGTTCATG--CAG
1 TATCAGTACTG-T-AAGAACAA
1139933 TATC-GATACTGTAAGAACAA
1 TATCAG-TACTGTAAGAACAA
*
1139953 TATCGGTACT
1 TATCAGTACT
1139963 TCTCACCCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 31 0.79
21 2 0.05
22 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCAGTACTGTAAGAACAA
Found at i:1142977 original size:18 final size:18
Alignment explanation
Indices: 1142954--1142988 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1142944 ATAGATTATC
1142954 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1142972 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1142989 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1146601 original size:29 final size:29
Alignment explanation
Indices: 1146567--1146625 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1146557 CCTAAATTAA
1146567 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1146596 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1146625 T
1 T
1146626 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1151285 original size:29 final size:29
Alignment explanation
Indices: 1151251--1151309 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1151241 CCTAAATTAA
1151251 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1151280 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1151309 T
1 T
1151310 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1152560 original size:2 final size:2
Alignment explanation
Indices: 1152553--1152592 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1152543 AACTACACTG
* *
1152553 AT AT AT AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1152593 CCCTTGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1157901 original size:20 final size:20
Alignment explanation
Indices: 1157876--1157914 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1157866 CCTAGTTCCT
1157876 GATTTTTAGGTA-TTATTTCA
1 GATTTTTAGG-AGTTATTTCA
1157896 GATTTTTAGGAGTTATTTC
1 GATTTTTAGGAGTTATTTC
1157915 CCATTTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (20 bp):
GATTTTTAGGAGTTATTTCA
Found at i:1157920 original size:20 final size:20
Alignment explanation
Indices: 1157877--1157920 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1157867 CTAGTTCCTG
*
1157877 ATTTTTAGGTATTATTTCAG
1 ATTTTTAGGTATTATTTCAC
*
1157897 ATTTTTAGG-AGTTATTTCCC
1 ATTTTTAGGTA-TTATTTCAC
1157917 ATTT
1 ATTT
1157921 GTTGTGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (20 bp):
ATTTTTAGGTATTATTTCAC
Found at i:1161423 original size:57 final size:57
Alignment explanation
Indices: 1161335--1161506 Score: 290
Period size: 57 Copynumber: 3.0 Consensus size: 57
1161325 TTGTAGATGA
*
1161335 AGCCTGATCTTCCGGATCTTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACC
1 AGCCTGATCTTCCGGATCTTGCAAGCGTAACCGTTTAGGCAATCTGCTAGACTCACC
* *
1161392 AGCCTGATCTTCCAGATCTTGCAAGCGTAACCGTTTAGTCAATCTGCTAGACTCACC
1 AGCCTGATCTTCCGGATCTTGCAAGCGTAACCGTTTAGGCAATCTGCTAGACTCACC
* * *
1161449 AGCCTGATCTTCCGGCTCTTGCAAGAGTAACTGTTTAGGCAATCTGCTAGACTCACC
1 AGCCTGATCTTCCGGATCTTGCAAGCGTAACCGTTTAGGCAATCTGCTAGACTCACC
1161506 A
1 A
1161507 TGCTCCACAA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 107 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (57 bp):
AGCCTGATCTTCCGGATCTTGCAAGCGTAACCGTTTAGGCAATCTGCTAGACTCACC
Found at i:1165973 original size:23 final size:23
Alignment explanation
Indices: 1165943--1165994 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1165933 TTCTAATAAT
*
1165943 ATAATATAAT-ATTTATTATTATA
1 ATAATATAATCAATTA-TATTATA
*
1165966 ATAATATACTCAATTATATTATA
1 ATAATATAATCAATTATATTATA
1165989 ATAATA
1 ATAATA
1165995 AAAGGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAATATAATCAATTATATTATA
Found at i:1167629 original size:34 final size:34
Alignment explanation
Indices: 1167591--1167665 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
1167581 AATTTTACCT
1167591 TATATATTTAGGAATAATTACAATAATACCCCTA
1 TATATATTTAGGAATAATTACAATAATACCCCTA
1167625 TATATATTTAGGAATAATTACAATAATACCCCTA
1 TATATATTTAGGAATAATTACAATAATACCCCTA
1167659 TATATAT
1 TATATAT
1167666 ATATATATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.37
Consensus pattern (34 bp):
TATATATTTAGGAATAATTACAATAATACCCCTA
Found at i:1172979 original size:16 final size:17
Alignment explanation
Indices: 1172952--1172984 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1172942 TATCGCCGAC
1172952 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
1172969 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
1172985 TGTGAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:1177911 original size:204 final size:203
Alignment explanation
Indices: 1177533--1177951 Score: 811
Period size: 204 Copynumber: 2.1 Consensus size: 203
1177523 GTCTCCATCA
* *
1177533 TCTTTTTCCATTTAAGGAAAAATCCTAGCACCTCATCCTTTGTCTTCATTGGATACACCCAAACT
1 TCTTCTTCCCTTTAAGGAAAAATCCTAGCACCTCATCCTTTGTCTTCATTGGATACACCCAAACT
1177598 CTCCGGGAAAAATCATCAACAAAGGTGACATAATAGTGTTCCTCCCAATGAAGTTGTCTTGGAAG
66 CTCCGGGAAAAATCATCAACAAAGGTGACATAATAGTGTTCCTCCCAATGAAGTTGTCTTGGAAG
1177663 GCCCCCATACATCTGAATGAACATAATCCAAATACCTTAGTATCATGGATTGCTGTTCCAAATTT
131 GCCCCCATACATCTGAATGAACATAATCCAAATACCTTAGTATCATGGATTGCTGTTCCAAATTT
1177728 CACCCTCG
196 CACCCTCG
1177736 TCTTCTTCCCTTTAAGGAAAAATCCTAGCACCTCATCCTTTGTCTTCATTGGATACACCCAAACT
1 TCTTCTTCCCTTTAAGGAAAAATCCTAGCACCTCATCCTTTGTCTTCATTGGATACACCCAAACT
1177801 CTCCGGGAAAAATCATCAACAAAGGTGAACATAATAGTGTTCCTCCCAATGAAGTTGTCTTGGAA
66 CTCCGGGAAAAATCATCAACAAAGGTG-ACATAATAGTGTTCCTCCCAATGAAGTTGTCTTGGAA
1177866 GGCCCCCATACATCTGAATGAACATAATCCAAATACCTTAGTATCATGGATTGCTGTTCCAAATT
130 GGCCCCCATACATCTGAATGAACATAATCCAAATACCTTAGTATCATGGATTGCTGTTCCAAATT
1177931 TCACCCTCG
195 TCACCCTCG
1177940 TCTTCTTCCCTT
1 TCTTCTTCCCTT
1177952 GCGCATATGC
Statistics
Matches: 213, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
203 90 0.42
204 123 0.58
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (203 bp):
TCTTCTTCCCTTTAAGGAAAAATCCTAGCACCTCATCCTTTGTCTTCATTGGATACACCCAAACT
CTCCGGGAAAAATCATCAACAAAGGTGACATAATAGTGTTCCTCCCAATGAAGTTGTCTTGGAAG
GCCCCCATACATCTGAATGAACATAATCCAAATACCTTAGTATCATGGATTGCTGTTCCAAATTT
CACCCTCG
Found at i:1184727 original size:67 final size:67
Alignment explanation
Indices: 1184530--1184712 Score: 253
Period size: 67 Copynumber: 2.7 Consensus size: 67
1184520 AAAGAAGAAA
* * *
1184530 TAAAATCACTTCTTTTTCATTGCTGTTTAT-GGAAGCTTGTTA-GCTATATAATCAATGTTCTGT
1 TAAAATCACTTCTTTTTCATTTCTATTTATGGGAA-CTTG-TAGGCTATATAATCAATGCTCTGT
1184593 TAGC
64 TAGC
* * ** *
1184597 TAAAATCACTTATTTTTTATTTCTATTTCCGGGAACTTATAGGCTATATAATCAATGCTCTGTTA
1 TAAAATCACTTCTTTTTCATTTCTATTTATGGGAACTTGTAGGCTATATAATCAATGCTCTGTTA
1184662 GC
66 GC
*
1184664 TAAAATCACTTCTTTTTCATTTCCATTTATGGGAACTTGTAGGCTATAT
1 TAAAATCACTTCTTTTTCATTTCTATTTATGGGAACTTGTAGGCTATAT
1184713 GATTGATGCC
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
66 2 0.02
67 94 0.94
68 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (67 bp):
TAAAATCACTTCTTTTTCATTTCTATTTATGGGAACTTGTAGGCTATATAATCAATGCTCTGTTA
GC
Found at i:1191646 original size:65 final size:64
Alignment explanation
Indices: 1191566--1191708 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 64
1191556 TTATGGGCAA
* * *
1191566 GGTGTATCGATGCATATTGAATGTGCATCGATGCA-CTCTTTAAAGAAG-AAACATCGAATGCAA
1 GGTGTATCGATGCATA-AGAA-GTGCATCGATGCATCCCTTTAAA-AAGAAAACATCGAAGGCAA
1191629 TT
63 TT
* * * *
1191631 GGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCTTTAAAATGAAAACATCGAAGGTAATT
1 GGTGTATCGATGCATAAGAAGTGCATCGATGCATCCCTTTAAAAAGAAAACATCGAAGGCAATT
*
1191695 TGTGTATCGATGCA
1 GGTGTATCGATGCA
1191709 CATGTTAAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
63 15 0.22
64 37 0.55
65 15 0.22
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (64 bp):
GGTGTATCGATGCATAAGAAGTGCATCGATGCATCCCTTTAAAAAGAAAACATCGAAGGCAATT
Found at i:1191742 original size:20 final size:20
Alignment explanation
Indices: 1191717--1191754 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1191707 CACATGTTAA
1191717 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
1191737 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
1191755 TCAAGGGGAA
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:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:1192957 original size:439 final size:439
Alignment explanation
Indices: 1192139--1193026 Score: 1760
Period size: 439 Copynumber: 2.0 Consensus size: 439
1192129 TTAATTGTCC
*
1192139 ATGATATATGCACCCATGATAATATGATGTAAGTTAAATTATGTAATATGATACATAACTGTGAA
1 ATGATATATGCACCCATGATAATATGATATAAGTTAAATTATGTAATATGATACATAACTGTGAA
1192204 ATACGTGAAGGAATGTATATATGATAAAGATTATATAAGAGAATATATAAGATTATCAAATAAGT
66 ATACGTGAAGGAATGTATATATGATAAAGATTATATAAGAGAATATATAAGATTATCAAATAAGT
1192269 TATGAGATAAGTTATATGACATTGATATATAGGCTAGATGAAAGTATACACATGAATATATGTAC
131 TATGAGATAAGTTATATGACATTGATATATAGGCTAGATGAAAGTATACACATGAATATATGTAC
1192334 AAGTTTATATGTTACTTTATATGCTATGGGATATACCCATGAACATATGTGATGTGATATATGCT
196 AAGTTTATATGTTACTTTATATGCTATGGGATATACCCATGAACATATGTGATGTGATATATGCT
1192399 ATGAGAAATGACCCATGTGACTAAGTGTGAAATGATATAAGTTACATGAGGTGAATGATATAATA
261 ATGAGAAATGACCCATGTGACTAAGTGTGAAATGATATAAGTTACATGAGGTGAATGATATAATA
1192464 AGAAGCTATGGGATAAGAAGATATGAGTTTATGTGATATGATATGAGATATATGGTTACACATAC
326 AGAAGCTATGGGATAAGAAGATATGAGTTTATGTGATATGATATGAGATATATGGTTACACATAC
1192529 ATGTGGTATGTGACAGAAGAGAAAGAATACGTGATATGAAAAGTTATAA
391 ATGTGGTATGTGACAGAAGAGAAAGAATACGTGATATGAAAAGTTATAA
1192578 ATGATATATGCACCCATGATAATATGATATAAGTTAAATTATGTAATATGATACATAACTGTGAA
1 ATGATATATGCACCCATGATAATATGATATAAGTTAAATTATGTAATATGATACATAACTGTGAA
1192643 ATACGTGAAGGAATGTATATATGATAAAGATTATATAAGAGAATATATAAGATTATCAAATAAGT
66 ATACGTGAAGGAATGTATATATGATAAAGATTATATAAGAGAATATATAAGATTATCAAATAAGT
1192708 TATGAGATAAGTTATATGACATTGATATATAGGCTAGATGAAAGTATACACATGAATATATGTAC
131 TATGAGATAAGTTATATGACATTGATATATAGGCTAGATGAAAGTATACACATGAATATATGTAC
1192773 AAGTTTATATGTTACTTTATATGCTATGGGATATACCCATGAACATATGTGATGTGATATATGCT
196 AAGTTTATATGTTACTTTATATGCTATGGGATATACCCATGAACATATGTGATGTGATATATGCT
1192838 ATGAGAAATGACCCATGTGACTAAGTGTGAAATGATATAAGTTACATGAGGTGAATGATATAATA
261 ATGAGAAATGACCCATGTGACTAAGTGTGAAATGATATAAGTTACATGAGGTGAATGATATAATA
1192903 AGAAGCTATGGGATAAGAAGATATGAGTTTATGTGATATGATATGAGATATATGGTTACACATAC
326 AGAAGCTATGGGATAAGAAGATATGAGTTTATGTGATATGATATGAGATATATGGTTACACATAC
1192968 ATGTGGTATGTGACAGAAGAGAAAGAATACGTGATATGAAAAGTTATAA
391 ATGTGGTATGTGACAGAAGAGAAAGAATACGTGATATGAAAAGTTATAA
1193017 ATGATA-ATGC
1 ATGATATATGC
1193027 CCATGTTATG
Statistics
Matches: 448, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
438 4 0.01
439 444 0.99
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (439 bp):
ATGATATATGCACCCATGATAATATGATATAAGTTAAATTATGTAATATGATACATAACTGTGAA
ATACGTGAAGGAATGTATATATGATAAAGATTATATAAGAGAATATATAAGATTATCAAATAAGT
TATGAGATAAGTTATATGACATTGATATATAGGCTAGATGAAAGTATACACATGAATATATGTAC
AAGTTTATATGTTACTTTATATGCTATGGGATATACCCATGAACATATGTGATGTGATATATGCT
ATGAGAAATGACCCATGTGACTAAGTGTGAAATGATATAAGTTACATGAGGTGAATGATATAATA
AGAAGCTATGGGATAAGAAGATATGAGTTTATGTGATATGATATGAGATATATGGTTACACATAC
ATGTGGTATGTGACAGAAGAGAAAGAATACGTGATATGAAAAGTTATAA
Found at i:1193119 original size:31 final size:31
Alignment explanation
Indices: 1193081--1193145 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1193071 AGAGTCGAGG
1193081 GTTTACCTAGGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
1193112 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
1193143 GTT
1 GTT
1193146 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:1194230 original size:31 final size:31
Alignment explanation
Indices: 1194195--1194285 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
1194185 AAGAGTCGAG
* *
1194195 GGTTACCTATGTTCTTCGAGACATATGGATA
1 GGTTACCTATGTTCTTCGGGACATATGGACA
* *
1194226 GGTTACCTTTGTTCTTCGGGACATATAGACA
1 GGTTACCTATGTTCTTCGGGACATATGGACA
* *
1194257 -GTTACCTAGGTTCTTCGGGACCTATGGAC
1 GGTTACCTATGTTCTTCGGGACATATGGAC
1194286 CGGTCCTTCG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 25 0.48
31 27 0.52
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCGGGACATATGGACA
Found at i:1195506 original size:21 final size:21
Alignment explanation
Indices: 1195448--1195500 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1195438 CTAAATATAA
1195448 AACCCTAATTTCCAAATCAAG
1 AACCCTAATTTCCAAATCAAG
* * *
1195469 TATCATAATTTCCAAATC-AG
1 AACCCTAATTTCCAAATCAAG
1195489 AACCCTAATTTC
1 AACCCTAATTTC
1195501 TAAAATTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (21 bp):
AACCCTAATTTCCAAATCAAG
Found at i:1195956 original size:2 final size:2
Alignment explanation
Indices: 1195951--1195982 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1195941 TTTTATTTAT
1195951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1195983 GGAAAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1201966 original size:130 final size:130
Alignment explanation
Indices: 1201825--1202072 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1201815 TATTTATATA
*
1201825 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
1201890 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1201955 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
1202020 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1202073 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1202103 original size:130 final size:129
Alignment explanation
Indices: 1201839--1202103 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
1201829 ATTTGGTCCT
* *
1201839 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
1201904 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1201969 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
1202034 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1202098 -A
128 CA
1202099 AAATT
1 AAATT
1202104 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1202427 original size:28 final size:27
Alignment explanation
Indices: 1202396--1202458 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1202386 AGTTGATACA
*
1202396 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1202424 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1202452 ATATTTT
1 ATATTTT
1202459 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1202559 original size:16 final size:18
Alignment explanation
Indices: 1202538--1202571 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1202528 ATTTCTTATT
1202538 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1202554 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1202572 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1202718 original size:21 final size:21
Alignment explanation
Indices: 1202694--1202736 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202684 TATTACCTTA
1202694 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1202715 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1202736 A
1 A
1202737 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1202754 original size:35 final size:35
Alignment explanation
Indices: 1202705--1202790 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
1202695 ATTGAAGTAT
** * *
1202705 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
1202740 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
1202775 TTTAGAATAAAATTGA
1 TTTAGAATAAAATTGA
1202791 TGACTGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:1202956 original size:16 final size:17
Alignment explanation
Indices: 1202920--1202958 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1202910 GCAAATAGAA
*
1202920 TAAATGTTGGGGGACTG
1 TAAATGTTGGGGGACTC
1202937 TAAATGTTGGGGGAC-C
1 TAAATGTTGGGGGACTC
1202953 TAAATG
1 TAAATG
1202959 CAAGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (17 bp):
TAAATGTTGGGGGACTC
Found at i:1213114 original size:19 final size:20
Alignment explanation
Indices: 1213092--1213147 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 20
1213082 TGTTTCGCCA
1213092 CCTGAAATTTTAGTTCAC-C
1 CCTGAAATTTTAGTTCACAC
*
1213111 CCTGAAATTTTAGTTCGCAC
1 CCTGAAATTTTAGTTCACAC
1213131 CCTGAAATTTTAGTTCA
1 CCTGAAATTTTAGTTCA
1213148 TTCCCCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (20 bp):
CCTGAAATTTTAGTTCACAC
Found at i:1220376 original size:22 final size:22
Alignment explanation
Indices: 1220351--1220397 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1220341 TCGGTCGAAT
1220351 CGGTCCGACCGGTCGGAAGAAC
1 CGGTCCGACCGGTCGGAAGAAC
1220373 CGGTCCGACCGGTCGGAAGAAC
1 CGGTCCGACCGGTCGGAAGAAC
1220395 CGG
1 CGG
1220398 ACGACGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.38, T:0.09
Consensus pattern (22 bp):
CGGTCCGACCGGTCGGAAGAAC
Found at i:1220493 original size:19 final size:20
Alignment explanation
Indices: 1220453--1220494 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1220443 ATTTAATAAA
1220453 AAATAATTTTTTATATCACAT
1 AAATAATTTTTTATAT-ACAT
1220474 AAATAATTTTTTATAT-CAT
1 AAATAATTTTTTATATACAT
1220493 AA
1 AA
1220495 GTCATATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
21 16 0.76
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATAATTTTTTATATACAT
Found at i:1221920 original size:14 final size:14
Alignment explanation
Indices: 1221901--1221941 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1221891 TTAGATTTTT
1221901 TTAAAATTACATTA
1 TTAAAATTACATTA
*
1221915 TTAAAATTATATTA
1 TTAAAATTACATTA
1221929 --AAAATT-CATTA
1 TTAAAATTACATTA
1221940 TT
1 TT
1221942 GATAATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
14 13 0.57
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAATTACATTA
Done.