Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007924.1 Hibiscus syriacus cultivar Beakdansim tig00110330_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: 1741266
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 7
Found at i:1062416 original size:27 final size:30
Alignment explanation
Indices: 1062336--1062416 Score: 69
Period size: 32 Copynumber: 2.6 Consensus size: 30
1062326 GTTAATACCG
*
1062336 GATCGATTGATTTTTGGGTCAAGTTAATACCA
1 GATCGATTGATTTTCGGGTCAAG-TAATA-CA
1062368 GATCGATTAGATTTCAAGTCGGGTCAA-T-AT-CA
1 GATCGATT-GATTT----TCGGGTCAAGTAATACA
1062400 GATCGATTGATTTTCGG
1 GATCGATTGATTTTCGG
1062417 TTTATGTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
27 4 0.09
31 5 0.12
32 18 0.42
33 5 0.12
34 2 0.05
35 1 0.02
37 8 0.19
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (30 bp):
GATCGATTGATTTTCGGGTCAAGTAATACA
Found at i:1064570 original size:27 final size:27
Alignment explanation
Indices: 1064515--1064581 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
1064505 AGATTTAGAT
* *
1064515 GGAGATGGAGCCGTTGCGGACTTTACC
1 GGAGCTGGAGCCGTTGCGGACTTCACC
*
1064542 GGAGCTGGAGCCGTTGCGGACTTCGCC
1 GGAGCTGGAGCCGTTGCGGACTTCACC
*
1064569 GGAGCTGCAGCCG
1 GGAGCTGGAGCCG
1064582 GTGGTGACGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.15, C:0.27, G:0.40, T:0.18
Consensus pattern (27 bp):
GGAGCTGGAGCCGTTGCGGACTTCACC
Found at i:1068465 original size:17 final size:16
Alignment explanation
Indices: 1068422--1068461 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1068412 GATATGAATG
1068422 AATAAAT-ATATTTTT
1 AATAAATAATATTTTT
1068437 -ATACAA-AATATTTTT
1 AATA-AATAATATTTTT
1068452 AATAAATAAT
1 AATAAATAAT
1068462 TATTGATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAATAATATTTTT
Found at i:1069773 original size:10 final size:10
Alignment explanation
Indices: 1069749--1069782 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
1069739 TAAATATTAG
1069749 TTATAAAACTT
1 TTATAAAA-TT
1069760 TTATAAAATT
1 TTATAAAATT
1069770 TTATAAATATT
1 TTATAAA-ATT
1069781 TT
1 TT
1069783 TCAAAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TTATAAAATT
Found at i:1071119 original size:73 final size:73
Alignment explanation
Indices: 1070995--1071130 Score: 209
Period size: 73 Copynumber: 1.9 Consensus size: 73
1070985 TCATCTAATC
* * * * *
1070995 AAATCATAAATGTATAGTCATGAAATCTCGAAATGGATAAGTATAGGTTAATGTTTATAAATCAT
1 AAATCATAAACGAATAGTCATAAAATCTCAAAATGGATAAGTATAGCTTAATGTTTATAAATCAT
1071060 GGAACTCT
66 GGAACTCT
* *
1071068 AAATCATAAACGAATAGTTATAAAATCTCAAAATGGGTAAGTATAGCTTAATGTTTATAAATC
1 AAATCATAAACGAATAGTCATAAAATCTCAAAATGGATAAGTATAGCTTAATGTTTATAAATC
1071131 TCGTAGCTGC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (73 bp):
AAATCATAAACGAATAGTCATAAAATCTCAAAATGGATAAGTATAGCTTAATGTTTATAAATCAT
GGAACTCT
Found at i:1071616 original size:2 final size:2
Alignment explanation
Indices: 1071609--1071634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1071599 CACATATAAA
1071609 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
1071635 CATTATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1082006 original size:21 final size:21
Alignment explanation
Indices: 1081980--1082140 Score: 209
Period size: 21 Copynumber: 7.7 Consensus size: 21
1081970 AATTGTACCA
*
1081980 AAGACGAGAAGAGCATTCATC
1 AAGACGAGAAGACCATTCATC
***
1082001 AAGACGAGAATTTCATTCATC
1 AAGACGAGAAGACCATTCATC
1082022 AAGACGAGAATG-CCATTCATC
1 AAGACGAGAA-GACCATTCATC
*
1082043 AAGACGAGAAGGCCATTCATC
1 AAGACGAGAAGACCATTCATC
1082064 AAGACGAGAAGACCATTCATC
1 AAGACGAGAAGACCATTCATC
* * *
1082085 AAGACAAGAAGACCCTTCATA
1 AAGACGAGAAGACCATTCATC
* *
1082106 AAGACGAGAAGACC-TTCGTA
1 AAGACGAGAAGACCATTCATC
1082126 AAGACGAGAAGACCA
1 AAGACGAGAAGACCA
1082141 CATCGCATGG
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
20 20 0.16
21 106 0.84
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (21 bp):
AAGACGAGAAGACCATTCATC
Found at i:1084743 original size:30 final size:30
Alignment explanation
Indices: 1084692--1084748 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1084682 TTATGAAGAG
* * *
1084692 AAAGAAGAGAAATATAGAAAGAGAAAAGGA
1 AAAGAAAAGAAAAATAGAAAGAAAAAAGGA
1084722 AAAGAAAAGAAGAAATA-AAAGAAAAAA
1 AAAGAAAAGAA-AAATAGAAAGAAAAAA
1084749 TTGAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (30 bp):
AAAGAAAAGAAAAATAGAAAGAAAAAAGGA
Found at i:1087438 original size:42 final size:42
Alignment explanation
Indices: 1087377--1087473 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
1087367 AATTTATAAG
* * *
1087377 TCCTCCGGGCCATCAGTAAGTCTTCATAGCATGATGATTAAA
1 TCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATGATTAAA
* * *
1087419 TCCTCCGGGTCAT-ATGTAAGCCTTTAGAGCAAGATGA-TAAG
1 TCCTCCGGGCCATCA-GTAAGCCTTCAGAGCAAGATGATTAAA
* *
1087460 TCATTCGGGCCATC
1 TCCTCCGGGCCATC
1087474 CATAAGACCT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
41 14 0.32
42 30 0.68
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (42 bp):
TCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATGATTAAA
Found at i:1087629 original size:42 final size:42
Alignment explanation
Indices: 1087582--1087661 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
1087572 AATTTATAAG
* *
1087582 TCCTCCGAGACATCAGTAAGTCTTTCA-AGCATGATGATTAAA
1 TCCTCCGAGACATCAGTAAGCCTTT-AGAGCAAGATGATTAAA
* * *
1087624 TCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATGAT
1 TCCTCCGAGACATCAGTAAGCCTTTAGAGCAAGATGAT
1087662 AAGTCCTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.03
42 31 0.97
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (42 bp):
TCCTCCGAGACATCAGTAAGCCTTTAGAGCAAGATGATTAAA
Found at i:1087858 original size:42 final size:41
Alignment explanation
Indices: 1087792--1087893 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
1087782 TTCCCAATTT
* * *
1087792 ATAAGTCCTCCGGGTCATCAGTAAGCCTTCCGAGCATGATG
1 ATAAATCCTCCGGGTCATCAGTAAGCCTTCAGAGCAAGATG
* *
1087833 ATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTCCGGGTCATCAGTAAGCCTTCAGAGCAAGATG
* * *
1087875 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTCCGGGTCATC
1087894 CATAAGACCT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.31
42 36 0.69
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (41 bp):
ATAAATCCTCCGGGTCATCAGTAAGCCTTCAGAGCAAGATG
Found at i:1088285 original size:42 final size:41
Alignment explanation
Indices: 1088219--1088334 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 41
1088209 TTCTCAATTT
* * * *
1088219 ATAAGTCCTCCGGTTCATCAGTAAGCCTTCCGAGCATGATG
1 ATAAATCCTCCGGGTCATCAGTAAGCCTTCAGAGCAAGATG
* *
1088260 ATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTCCGGGTCATCAGTAAGCCTTCAGAGCAAGATG
* * *
1088302 ATAAGTCCTTCGGGCCATCCA-TAAGACCTTCAG
1 ATAAATCCTCCGGGTCAT-CAGTAAG-CCTTCAG
1088335 GTAGGATGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
41 19 0.31
42 42 0.69
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (41 bp):
ATAAATCCTCCGGGTCATCAGTAAGCCTTCAGAGCAAGATG
Found at i:1088364 original size:214 final size:214
Alignment explanation
Indices: 1086964--1088560 Score: 2599
Period size: 205 Copynumber: 7.5 Consensus size: 214
1086954 TGAAGTAAAT
* * * *
1086964 CCATTAGTAAGCCTTCTGAGCATGATGATTAAATCCTCTGGGTCATATGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
*
1087029 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAAATTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
1087094 TGAAAAATGATGTTTTAAGAAGATGGATTTTTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTT
131 AGAAAAATGATGTTTTAAGAAGATGGA---TTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTT
**
1087159 CCCAATTTATAAGTCCTTTGGG
193 CCCAATTTATAAGTCCTCCGGG
1087181 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
1087246 GATGATAAGTCATTCGGGCCATCCATAAGACTTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
1087311 TGAAAAAATGATG--TT--G--GA--G--TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
131 AG-AAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
1087366 CAATTTATAAGTCCTCCGGG
195 CAATTTATAAGTCCTCCGGG
* ** *
1087386 CCATCAGTAAGTCTTCATAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
1087451 GATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
1087516 TGAAAAAATGATG--TT--G--GA--G--TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
131 AG-AAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
*
1087571 CAATTTATAAGTCCTCCGAG
195 CAATTTATAAGTCCTCCGGG
* * * *
1087591 ACATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
*
1087656 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTTAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
* *
1087721 AGAAAAATGGTGTTTTAAGAAGATGGATTTTTTTGAAAACGAAGAATGCGGGTTTCAAAATTTCC
131 AGAAAAATGATGTTTTAAGAAGATGGA-TTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
1087786 CAATTTATAAGTCCTCCGGG
195 CAATTTATAAGTCCTCCGGG
*
1087806 TCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1087871 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
1087936 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
*
1088001 AATTTATAA-TACTCCGGG
196 AATTTATAAGTCCTCCGGG
* * * *
1088019 CCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
*
1088084 GATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
1088149 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCTC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
*
1088214 AATTTATAAGTCCTCCGGT
196 AATTTATAAGTCCTCCGGG
*
1088233 TCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
*
1088298 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
1088363 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
1088428 AATTTATAAGTCCTCCGGG
196 AATTTATAAGTCCTCCGGG
* *
1088447 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGAAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
1088512 GATGATAAATCCTTCAGGTCC-TCCATAAGACCTTCGGGCAGGATGTTTT
66 GATGATAAGTCCTTC-GGGCCATCCATAAGACCTTCGGGTAGGATGTTTT
1088561 TCACCAGGAT
Statistics
Matches: 1305, Mismatches: 61, Indels: 31
0.93 0.04 0.02
Matches are distributed among these distances:
204 9 0.01
205 375 0.29
206 2 0.00
208 1 0.00
210 3 0.00
212 3 0.00
213 205 0.16
214 361 0.28
215 209 0.16
216 2 0.00
217 125 0.10
218 10 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (214 bp):
CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
AATTTATAAGTCCTCCGGG
Found at i:1088446 original size:428 final size:428
Alignment explanation
Indices: 1086969--1088560 Score: 2591
Period size: 428 Copynumber: 3.8 Consensus size: 428
1086959 TAAATCCATT
* *
1086969 AGTAAGCCTTCTGAGCATGATGATTAAATCCTCTGGGTCATATGTAAGCCTTTAGAGCAAGATGA
1 AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAAGATGA
* *
1087034 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAAATTGAAAATGAAA
66 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAAGAAA
1087099 AATGATGTTTTAAGAAGATGGATTTTTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAA
131 AATGATGTTTTAAGAAGATGGA---TTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAA
** *
1087164 TTTATAAGTCCTTTGGGCCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCT
193 TTTATAAGTCCTCCGGGCCATCAGTAAGCCTTCCAAGCATGATGATTAAATCCTCCGGGTCATCT
* * *
1087229 GTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACTTTCGGGTAGGATGTTT
258 GTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTT
*
1087294 TCAAATGAATTTGAAAATGAAAAAATGATG--TT--G--GA--G--TTTTTGAAAACGAAGAATG
323 TCAAATGAATTTGAAAAAG-AAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATG
*
1087349 CGAGTTTCAAAATTTCCCAATTTATAAGTCCTCCGGGCCATC
387 CGAGTTTCAAAATTTCCCAATTTATAAGTCCTCCGGGTCATC
* **
1087391 AGTAAGTCTTCATAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAAGATGA
1 AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAAGATGA
* * *
1087456 TAAGTCATTCGGGCCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAATGAAA
66 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAAG-AA
1087521 AAATGATG--TT--G--GA--G--TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATT
130 AAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATT
* * * *
1087576 TATAAGTCCTCCGAGACATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTCCGGGTCATCTGT
195 TATAAGTCCTCCGGGCCATCAGTAAGCCTTCCAAGCATGATGATTAAATCCTCCGGGTCATCTGT
* *
1087641 AAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTT
260 AAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTC
*
1087706 AAATGAATTTGAAAAAGAAAAATGGTGTTTTAAGAAGATGGATTTTTTTGAAAACGAAGAATGCG
325 AAATGAATTTGAAAAAGAAAAATGATGTTTTAAGAAGATGGA-TTTTTTGAAAACGAAGAATGCG
*
1087771 GGTTTCAAAATTTCCCAATTTATAAGTCCTCCGGGTCATC
389 AGTTTCAAAATTTCCCAATTTATAAGTCCTCCGGGTCATC
*
1087811 AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
1 AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAAGATGA
1087876 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAAGAAA
66 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAAGAAA
1087941 AATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATTT
131 AATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATTT
* * * *
1088006 ATAA-TACTCCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTCCGGGTCATCTGTA
196 ATAAGTCCTCCGGGCCATCAGTAAGCCTTCCAAGCATGATGATTAAATCCTCCGGGTCATCTGTA
1088070 AGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCA
261 AGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCA
1088135 AATGAATTTGAAAAAGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAG
326 AATGAATTTGAAAAAGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAG
* *
1088200 TTTCAAAATTTCTCAATTTATAAGTCCTCCGGTTCATC
391 TTTCAAAATTTCCCAATTTATAAGTCCTCCGGGTCATC
*
1088238 AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
1 AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAAGATGA
*
1088303 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGGTAGGATGTTTTCAAATGAATTTGAAAAAGAAA
66 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAAGAAA
1088368 AATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATTT
131 AATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATTT
* *
1088433 ATAAGTCCTCCGGGCCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTTCGGGTCATCTGTA
196 ATAAGTCCTCCGGGCCATCAGTAAGCCTTCCAAGCATGATGATTAAATCCTCCGGGTCATCTGTA
* * *
1088498 AGCCTTTAGAGAAAGATGATAAATCCTTC-AGGTCC-TCCATAAGACCTTCGGGCAGGATGTTTT
261 AGCCTTTAGAGCAAGATGATAAGTCCTTCGA-G-CCATCCATAAGACCTTCGGGTAGGATGTTTT
1088561 TCACCAGGAT
Statistics
Matches: 1097, Mismatches: 48, Indels: 44
0.92 0.04 0.04
Matches are distributed among these distances:
409 9 0.01
410 177 0.16
411 2 0.00
413 1 0.00
415 3 0.00
417 3 0.00
419 11 0.01
420 179 0.16
421 4 0.00
422 120 0.11
423 11 0.01
425 2 0.00
427 259 0.24
428 268 0.24
429 48 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (428 bp):
AGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATATGTAAGCCTTTAGAGCAAGATGA
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAAGAAA
AATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCCAATTT
ATAAGTCCTCCGGGCCATCAGTAAGCCTTCCAAGCATGATGATTAAATCCTCCGGGTCATCTGTA
AGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCA
AATGAATTTGAAAAAGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAG
TTTCAAAATTTCCCAATTTATAAGTCCTCCGGGTCATC
Found at i:1088516 original size:42 final size:41
Alignment explanation
Indices: 1088433--1088531 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 41
1088423 TTCCCAATTT
* * * * * *
1088433 ATAAGTCCTCCGGGCCATCAGTAAGCCTTCCGAGCATGATG
1 ATAAATCCTTCGGGTCATCAGTAAGCCTTCAGAGAAAGATG
* *
1088474 ATTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGAAAGATG
1 A-TAAATCCTTCGGGTCATCAGTAAGCCTTCAGAGAAAGATG
*
1088516 ATAAATCCTTCAGGTC
1 ATAAATCCTTCGGGTC
1088532 CTCCATAAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGCCTTCAGAGAAAGATG
Found at i:1097236 original size:13 final size:13
Alignment explanation
Indices: 1097218--1097253 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1097208 CAAGATAGGG
1097218 AGGGGCTTATAAT
1 AGGGGCTTATAAT
1097231 AGGGGCTTATAAT
1 AGGGGCTTATAAT
1097244 -GGGAGCTTAT
1 AGGG-GCTTAT
1097254 CGCAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.28, C:0.08, G:0.33, T:0.31
Consensus pattern (13 bp):
AGGGGCTTATAAT
Found at i:1098776 original size:23 final size:23
Alignment explanation
Indices: 1098749--1098797 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1098739 CTAAAATTAT
1098749 AAAATTAT-TATATATT-TTTTAAA
1 AAAATTATGTAT-T-TTCTTTTAAA
1098772 AAAATTATGTATTTTCTTTTAAA
1 AAAATTATGTATTTTCTTTTAAA
1098795 AAA
1 AAA
1098798 TCTATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 2 0.08
23 19 0.79
24 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATTATGTATTTTCTTTTAAA
Found at i:1100026 original size:16 final size:16
Alignment explanation
Indices: 1100001--1100040 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1099991 CCATCAATAC
*
1100001 AAGAAAAAGAAGAAAA
1 AAGAAGAAGAAGAAAA
*
1100017 AAGAAGAAGAAGAAGA
1 AAGAAGAAGAAGAAAA
1100033 AAGAAGAA
1 AAGAAGAA
1100041 ATAGTGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAGAAGAAGAAGAAAA
Found at i:1100029 original size:19 final size:19
Alignment explanation
Indices: 1100001--1100040 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1099991 CCATCAATAC
1100001 AAGAAAAAGAAGAAAAAAG
1 AAGAAAAAGAAGAAAAAAG
* *
1100020 AAGAAGAAGAAGAAAGAAG
1 AAGAAAAAGAAGAAAAAAG
1100039 AA
1 AA
1100041 ATAGTGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
AAGAAAAAGAAGAAAAAAG
Found at i:1102499 original size:16 final size:16
Alignment explanation
Indices: 1102464--1102505 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1102454 TCCTTACCTT
1102464 AAAATAAAAT-GTTAA
1 AAAATAAAATAGTTAA
* *
1102479 AAAATAAAATATTTCA
1 AAAATAAAATAGTTAA
1102495 AAAATAAAATA
1 AAAATAAAATA
1102506 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATAAAATAGTTAA
Found at i:1102662 original size:30 final size:29
Alignment explanation
Indices: 1102622--1102697 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
1102612 TGAAAAACAA
*
1102622 TTTA-GTAAAATGGATTACCTGAAAACTAT
1 TTTACGTAAAATGAATTACCT-AAAACTAT
* *
1102651 TTTACGTAAAATGAATTACCTAAAATTGT
1 TTTACGTAAAATGAATTACCTAAAACTAT
*
1102680 TTTACGTAAAATAAATTA
1 TTTACGTAAAATGAATTA
1102698 TATTCTGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTACGTAAAATGAATTACCTAAAACTAT
Found at i:1102689 original size:15 final size:15
Alignment explanation
Indices: 1102650--1102691 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1102640 CTGAAAACTA
1102650 TTTTACGTAAAA-TG
1 TTTTACGTAAAATTG
** *
1102664 AATTACCTAAAATTG
1 TTTTACGTAAAATTG
1102679 TTTTACGTAAAAT
1 TTTTACGTAAAAT
1102692 AAATTATATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (15 bp):
TTTTACGTAAAATTG
Found at i:1103924 original size:15 final size:16
Alignment explanation
Indices: 1103904--1103933 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1103894 ACAAAAAAGG
1103904 AAAAAAAAT-AAATAA
1 AAAAAAAATCAAATAA
1103919 AAAAAAAATCAAATA
1 AAAAAAAATCAAATA
1103934 GCTTCACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAAATCAAATAA
Found at i:1113063 original size:3 final size:3
Alignment explanation
Indices: 1113055--1113184 Score: 260
Period size: 3 Copynumber: 43.3 Consensus size: 3
1113045 CAATAATGGG
1113055 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1113103 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1113151 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1113185 AAGACCTGTG
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 127 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1113410 original size:3 final size:3
Alignment explanation
Indices: 1113404--1113468 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1113394 GAGGAGGAGA
1113404 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1113452 AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
1113469 AACCAGTGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1113999 original size:60 final size:61
Alignment explanation
Indices: 1113876--1114038 Score: 156
Period size: 60 Copynumber: 2.7 Consensus size: 61
1113866 TGATCCTTAA
* * * * * *
1113876 TCTAAATTGGTCTCTAAACTT-TTAAACA-TTCTATTTTCATCCTTAAACTATGACTATCGT
1 TCTAATTTAGTCTCCAAACTTATTGAACATTTC-AATTTCATCCTTAAACTATGACTATCAT
* * *
1113936 TCTAGA-TTAGTC-CTCAAAC-TATTGAACATTTCAGTTTCATCCTTAAACTATGATTTTCAT
1 TCTA-ATTTAGTCTC-CAAACTTATTGAACATTTCAATTTCATCCTTAAACTATGACTATCAT
* * *
1113996 TCTAATTTGGTCTCCAAACTTTTTGAACATTTCAATTTTATCC
1 TCTAATTTAGTCTCCAAACTTATTGAACATTTCAATTTCATCC
1114039 CAAATTATAT
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
59 3 0.04
60 57 0.67
61 25 0.29
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (61 bp):
TCTAATTTAGTCTCCAAACTTATTGAACATTTCAATTTCATCCTTAAACTATGACTATCAT
Found at i:1127900 original size:34 final size:34
Alignment explanation
Indices: 1127855--1127923 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1127845 ATTAATGTTA
* * *
1127855 TTTATAATAAATTATGTCACTTAGTGAACATACT
1 TTTATAATAAATGATATCACTTAATGAACATACT
* *
1127889 TTTATAGTAAATGATATCACTTAATGAATATACT
1 TTTATAATAAATGATATCACTTAATGAACATACT
1127923 T
1 T
1127924 ATTTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (34 bp):
TTTATAATAAATGATATCACTTAATGAACATACT
Found at i:1128033 original size:13 final size:13
Alignment explanation
Indices: 1128015--1128040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1128005 ATTCATCAAA
1128015 AAGGTCTTAACCT
1 AAGGTCTTAACCT
1128028 AAGGTCTTAACCT
1 AAGGTCTTAACCT
1128041 TTTGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
AAGGTCTTAACCT
Found at i:1128869 original size:20 final size:20
Alignment explanation
Indices: 1128844--1128895 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1128834 ATCGCGATTT
*
1128844 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
1128864 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
1128884 AGAAAATCGCAA
1 AGAAAATCGCAA
1128896 TGCGACTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:1128911 original size:20 final size:20
Alignment explanation
Indices: 1128888--1128998 Score: 132
Period size: 20 Copynumber: 5.4 Consensus size: 20
1128878 GTCAAAAGAA
*
1128888 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
1128908 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
1128928 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
1128951 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
1128971 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
1128991 AATCGCAA
1 AATCGCAA
1128999 CGTTGAAAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
20 58 0.75
21 3 0.04
22 2 0.03
23 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:1129091 original size:6 final size:6
Alignment explanation
Indices: 1129082--1129156 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
1129072 CATTACCATT
1129082 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1129130 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
1129157 CGAGACGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1129845 original size:6 final size:6
Alignment explanation
Indices: 1129836--1129860 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1129826 CGCCGCCGTC
1129836 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
1129861 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1130016 original size:21 final size:21
Alignment explanation
Indices: 1129946--1130016 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
1129936 ATTTTTTTTA
* *
1129946 ACTATCACAACGACACTGTAC
1 ACTATCGCAACGACACTGTAG
* * *
1129967 ACTCTCGCAACG-CGAAT-TGG
1 ACTATCGCAACGAC-ACTGTAG
**
1129987 AAAATCGCAACGACACTGTAG
1 ACTATCGCAACGACACTGTAG
1130008 ACTATCGCA
1 ACTATCGCA
1130017 TTGCGATTCT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGACACTGTAG
Found at i:1130058 original size:20 final size:22
Alignment explanation
Indices: 1130011--1130066 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1130001 ACTGTAGACT
*
1130011 ATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
1130033 ATCGCGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTCTTGGAAG
1130053 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1130067 TTCTTTTCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 14 0.42
21 1 0.03
22 18 0.55
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.34
Consensus pattern (22 bp):
ATCGCGTTGCGATTCTTGGAAG
Found at i:1130070 original size:22 final size:22
Alignment explanation
Indices: 1130011--1130113 Score: 71
Period size: 20 Copynumber: 5.0 Consensus size: 22
1130001 ACTGTAGACT
*
1130011 ATCGCATTGCGA--TTCTTGGAA
1 ATCGCGTTGCGATTTTCTTGG-A
1130032 GATCGCGTTGCGA--TTCTTGGA
1 -ATCGCGTTGCGATTTTCTTGGA
1130053 ATCGCGTTGCGATTTTCTT---
1 ATCGCGTTGCGATTTTCTTGGA
* *
1130072 TTCAGCGTTGCGATTTTC-T-AA
1 ATC-GCGTTGCGATTTTCTTGGA
* *
1130093 ATCGAGTTGCGATTTTGTTGG
1 ATCGCGTTGCGATTTTCTTGG
1130114 TCATTTTGGC
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.04
20 38 0.56
21 4 0.06
22 23 0.34
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (22 bp):
ATCGCGTTGCGATTTTCTTGGA
Found at i:1137876 original size:941 final size:941
Alignment explanation
Indices: 1136054--1137936 Score: 3766
Period size: 941 Copynumber: 2.0 Consensus size: 941
1136044 CCTTACATCG
1136054 CTATCCCGACTATCAATGACACAAAAGCACACACCCCAAGGATCATAAGGGTCATGTCCTGAAGA
1 CTATCCCGACTATCAATGACACAAAAGCACACACCCCAAGGATCATAAGGGTCATGTCCTGAAGA
1136119 GCTTCCCAAACAAATATCAAGAACCCTTTAGCTTCAGCCTCAGCAAACTTATTGATTCCATAGAC
66 GCTTCCCAAACAAATATCAAGAACCCTTTAGCTTCAGCCTCAGCAAACTTATTGATTCCATAGAC
1136184 CTGTTGTCTTTTATTCAACAGATCGGTGTCAGAAGTTAGCCCATTGGTGGTTGATGTGGAGAGTT
131 CTGTTGTCTTTTATTCAACAGATCGGTGTCAGAAGTTAGCCCATTGGTGGTTGATGTGGAGAGTT
1136249 TTTCAGCGATACTATCCACTCCACCATGAATCTTTAGTTTCTTCAAATCATGGCCTTCCACAATG
196 TTTCAGCGATACTATCCACTCCACCATGAATCTTTAGTTTCTTCAAATCATGGCCTTCCACAATG
1136314 GATCCTAACTCATCCGCACAAAGTTGAAAACCAGCAGCTTTGACTTCTTCAGGCACAACATAATC
261 GATCCTAACTCATCCGCACAAAGTTGAAAACCAGCAGCTTTGACTTCTTCAGGCACAACATAATC
1136379 ACTTTCACTTGTTTCGACACCTGAAAAAATAAAATTCAGTTAAGTTGAAAGCCAGCTTTCCTTCA
326 ACTTTCACTTGTTTCGACACCTGAAAAAATAAAATTCAGTTAAGTTGAAAGCCAGCTTTCCTTCA
1136444 AAATAAAATGCAGTTTTGCTCCAAAAATCTCACCCGAGATAAACTGGAAGGCAGTTTTCGAAACC
391 AAATAAAATGCAGTTTTGCTCCAAAAATCTCACCCGAGATAAACTGGAAGGCAGTTTTCGAAACC
1136509 AGTACAGAGATTCTCAGTTTTTCCTGCAATTTTTCAGATCAAAAATAAATAAGCTATACAATGCT
456 AGTACAGAGATTCTCAGTTTTTCCTGCAATTTTTCAGATCAAAAATAAATAAGCTATACAATGCT
1136574 AAATTTCACACTCACGATCCTATTCATAAAAGGAGCTTAGCATATAGGGGGCAATTTTTGTTCAA
521 AAATTTCACACTCACGATCCTATTCATAAAAGGAGCTTAGCATATAGGGGGCAATTTTTGTTCAA
1136639 TTTTCAACCGCAGAAAAAGAAACATAATCTCGTAAGTATAGAAAATAAAAATAAAATCAAACCAT
586 TTTTCAACCGCAGAAAAAGAAACATAATCTCGTAAGTATAGAAAATAAAAATAAAATCAAACCAT
1136704 GATATATTTAGCAGTTTAATCTTAGATCAGAAAGTAGAATTAAAAATCCAACGCACCTTATAGGA
651 GATATATTTAGCAGTTTAATCTTAGATCAGAAAGTAGAATTAAAAATCCAACGCACCTTATAGGA
1136769 TCGGCGCATAGCAGCAGCTTCGTAGCGTTTGGAGAGGTTGGCAGTGAATCGAAACCGGCGTTTCG
716 TCGGCGCATAGCAGCAGCTTCGTAGCGTTTGGAGAGGTTGGCAGTGAATCGAAACCGGCGTTTCG
1136834 GATTCTTGACGAAACCACAAACTTTCCTCCATCTTTCCAAAGCTTCCTCCGACGAGTGCTTGGGC
781 GATTCTTGACGAAACCACAAACTTTCCTCCATCTTTCCAAAGCTTCCTCCGACGAGTGCTTGGGC
1136899 TTCAAATCGAAGCTCTCGTTCAAAAAATTCACCATTCCCTTTTTTCTTTTCAATGCATTTCAAAT
846 TTCAAATCGAAGCTCTCGTTCAAAAAATTCACCATTCCCTTTTTTCTTTTCAATGCATTTCAAAT
1136964 CGCTTTCGTTCCTAAAGTTGACCGTCTGCTT
911 CGCTTTCGTTCCTAAAGTTGACCGTCTGCTT
1136995 CTATCCCGACTATCAATGACACAAAAGCACACACCCCAAGGATCATAAGGGTCATGTCCTGAAGA
1 CTATCCCGACTATCAATGACACAAAAGCACACACCCCAAGGATCATAAGGGTCATGTCCTGAAGA
1137060 GCTTCCCAAACAAATATCAAGAACCCTTTAGCTTCAGCCTCAGCAAACTTATTGATTCCATAGAC
66 GCTTCCCAAACAAATATCAAGAACCCTTTAGCTTCAGCCTCAGCAAACTTATTGATTCCATAGAC
1137125 CTGTTGTCTTTTATTCAACAGATCGGTGTCAGAAGTTAGCCCATTGGTGGTTGATGTGGAGAGTT
131 CTGTTGTCTTTTATTCAACAGATCGGTGTCAGAAGTTAGCCCATTGGTGGTTGATGTGGAGAGTT
1137190 TTTCAGCGATACTATCCACTCCACCATGAATCTTTAGTTTCTTCAAATCATGGCCTTCCACAATG
196 TTTCAGCGATACTATCCACTCCACCATGAATCTTTAGTTTCTTCAAATCATGGCCTTCCACAATG
1137255 GATCCTAACTCATCCGCACAAAGTTGAAAACCAGCAGCTTTGACTTCTTCAGGCACAACATAATC
261 GATCCTAACTCATCCGCACAAAGTTGAAAACCAGCAGCTTTGACTTCTTCAGGCACAACATAATC
1137320 ACTTTCACTTGTTTCGACACCTGAAAAAATAAAATTCAGTTAAGTTGAAAGCCAGCTTTCCTTCA
326 ACTTTCACTTGTTTCGACACCTGAAAAAATAAAATTCAGTTAAGTTGAAAGCCAGCTTTCCTTCA
1137385 AAATAAAATGCAGTTTTGCTCCAAAAATCTCACCCGAGATAAACTGGAAGGCAGTTTTCGAAACC
391 AAATAAAATGCAGTTTTGCTCCAAAAATCTCACCCGAGATAAACTGGAAGGCAGTTTTCGAAACC
1137450 AGTACAGAGATTCTCAGTTTTTCCTGCAATTTTTCAGATCAAAAATAAATAAGCTATACAATGCT
456 AGTACAGAGATTCTCAGTTTTTCCTGCAATTTTTCAGATCAAAAATAAATAAGCTATACAATGCT
1137515 AAATTTCACACTCACGATCCTATTCATAAAAGGAGCTTAGCATATAGGGGGCAATTTTTGTTCAA
521 AAATTTCACACTCACGATCCTATTCATAAAAGGAGCTTAGCATATAGGGGGCAATTTTTGTTCAA
1137580 TTTTCAACCGCAGAAAAAGAAACATAATCTCGTAAGTATAGAAAATAAAAATAAAATCAAACCAT
586 TTTTCAACCGCAGAAAAAGAAACATAATCTCGTAAGTATAGAAAATAAAAATAAAATCAAACCAT
1137645 GATATATTTAGCAGTTTAATCTTAGATCAGAAAGTAGAATTAAAAATCCAACGCACCTTATAGGA
651 GATATATTTAGCAGTTTAATCTTAGATCAGAAAGTAGAATTAAAAATCCAACGCACCTTATAGGA
1137710 TCGGCGCATAGCAGCAGCTTCGTAGCGTTTGGAGAGGTTGGCAGTGAATCGAAACCGGCGTTTCG
716 TCGGCGCATAGCAGCAGCTTCGTAGCGTTTGGAGAGGTTGGCAGTGAATCGAAACCGGCGTTTCG
1137775 GATTCTTGACGAAACCACAAACTTTCCTCCATCTTTCCAAAGCTTCCTCCGACGAGTGCTTGGGC
781 GATTCTTGACGAAACCACAAACTTTCCTCCATCTTTCCAAAGCTTCCTCCGACGAGTGCTTGGGC
1137840 TTCAAATCGAAGCTCTCGTTCAAAAAATTCACCATTCCCTTTTTTCTTTTCAATGCATTTCAAAT
846 TTCAAATCGAAGCTCTCGTTCAAAAAATTCACCATTCCCTTTTTTCTTTTCAATGCATTTCAAAT
1137905 CGCTTTCGTTCCTAAAGTTGACCGTCTGCTT
911 CGCTTTCGTTCCTAAAGTTGACCGTCTGCTT
1137936 C
1 C
1137937 ATTCAAATAT
Statistics
Matches: 942, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
941 942 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (941 bp):
CTATCCCGACTATCAATGACACAAAAGCACACACCCCAAGGATCATAAGGGTCATGTCCTGAAGA
GCTTCCCAAACAAATATCAAGAACCCTTTAGCTTCAGCCTCAGCAAACTTATTGATTCCATAGAC
CTGTTGTCTTTTATTCAACAGATCGGTGTCAGAAGTTAGCCCATTGGTGGTTGATGTGGAGAGTT
TTTCAGCGATACTATCCACTCCACCATGAATCTTTAGTTTCTTCAAATCATGGCCTTCCACAATG
GATCCTAACTCATCCGCACAAAGTTGAAAACCAGCAGCTTTGACTTCTTCAGGCACAACATAATC
ACTTTCACTTGTTTCGACACCTGAAAAAATAAAATTCAGTTAAGTTGAAAGCCAGCTTTCCTTCA
AAATAAAATGCAGTTTTGCTCCAAAAATCTCACCCGAGATAAACTGGAAGGCAGTTTTCGAAACC
AGTACAGAGATTCTCAGTTTTTCCTGCAATTTTTCAGATCAAAAATAAATAAGCTATACAATGCT
AAATTTCACACTCACGATCCTATTCATAAAAGGAGCTTAGCATATAGGGGGCAATTTTTGTTCAA
TTTTCAACCGCAGAAAAAGAAACATAATCTCGTAAGTATAGAAAATAAAAATAAAATCAAACCAT
GATATATTTAGCAGTTTAATCTTAGATCAGAAAGTAGAATTAAAAATCCAACGCACCTTATAGGA
TCGGCGCATAGCAGCAGCTTCGTAGCGTTTGGAGAGGTTGGCAGTGAATCGAAACCGGCGTTTCG
GATTCTTGACGAAACCACAAACTTTCCTCCATCTTTCCAAAGCTTCCTCCGACGAGTGCTTGGGC
TTCAAATCGAAGCTCTCGTTCAAAAAATTCACCATTCCCTTTTTTCTTTTCAATGCATTTCAAAT
CGCTTTCGTTCCTAAAGTTGACCGTCTGCTT
Found at i:1138247 original size:55 final size:55
Alignment explanation
Indices: 1138195--1138327 Score: 141
Period size: 54 Copynumber: 2.5 Consensus size: 55
1138185 GGTTTTTTGG
1138195 TGACCAAAATGTTAGCA-TCTAAAAGTCGACTGACTAAATT-AAAAAACATTTTTA
1 TGACCAAAATGTTAG-ATTCTAAAAGTCGACTGACTAAATTGAAAAAACATTTTTA
** * * * * *
1138249 TGATGAAAATGTTAGATTCTAAAAGTTGAGTGATTAAATTGAAAATATATTTTTA
1 TGACCAAAATGTTAGATTCTAAAAGTCGACTGACTAAATTGAAAAAACATTTTTA
1138304 --ACCAAAATGTTCA-ATTTCTAAAAG
1 TGACCAAAATGTT-AGA-TTCTAAAAG
1138328 GTTAGTGATC
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
53 11 0.17
54 43 0.65
55 12 0.18
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (55 bp):
TGACCAAAATGTTAGATTCTAAAAGTCGACTGACTAAATTGAAAAAACATTTTTA
Found at i:1141982 original size:17 final size:19
Alignment explanation
Indices: 1141954--1141988 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1141944 TTTAACATTA
1141954 TAAAATATAAAT-ATATGT
1 TAAAATATAAATAATATGT
1141972 TAAAA-ATAAATAATATG
1 TAAAATATAAATAATATG
1141989 ATATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (19 bp):
TAAAATATAAATAATATGT
Found at i:1149048 original size:41 final size:40
Alignment explanation
Indices: 1148938--1149068 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 40
1148928 GGCCTTTTAT
*
1148938 TTTTTAATCTCACTTTTTTACATTTATAATTAATGACCCTAAGC
1 TTTTTAATCTCAC-TTTTTACATTTATAATTAAT--CCCTAA-A
* * *
1148982 TTTTCAATCTCACTTTGTACCTTTATAATTAATCTCCTAAA
1 TTTTTAATCTCACTTTTTACATTTATAATTAATC-CCTAAA
* * *
1149023 TTTTTAATCTAACTTTTTACTTTTATAATTGAAGCCCTAAA
1 TTTTTAATCTCACTTTTTACATTTATAATT-AATCCCTAAA
1149064 TTTTT
1 TTTTT
1149069 TGAGTCGCAC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
41 38 0.50
42 8 0.11
43 18 0.24
44 12 0.16
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.50
Consensus pattern (40 bp):
TTTTTAATCTCACTTTTTACATTTATAATTAATCCCTAAA
Found at i:1150373 original size:6 final size:6
Alignment explanation
Indices: 1150362--1150395 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
1150352 TTTTTATAAA
1150362 AAAATG AAAATG AAAATG AAAATG AAAATAG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAAT-G AAA
1150396 GAATACCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:1153332 original size:34 final size:34
Alignment explanation
Indices: 1153289--1153361 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
1153279 TGGTTAGTTT
1153289 TTTTGAGGGGGACCTAAGAGTCATAGGACGGTCA
1 TTTTGAGGGGGACCTAAGAGTCATAGGACGGTCA
1153323 TTTTGAGGGGGACCTAAGAGTCATAGGACGGTCA
1 TTTTGAGGGGGACCTAAGAGTCATAGGACGGTCA
1153357 TTTTG
1 TTTTG
1153362 GATTCCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (34 bp):
TTTTGAGGGGGACCTAAGAGTCATAGGACGGTCA
Found at i:1157815 original size:23 final size:23
Alignment explanation
Indices: 1157789--1157833 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1157779 TATTATATTG
1157789 TTTATAATATTTTAGATCACGTT
1 TTTATAATATTTTAGATCACGTT
1157812 TTTATAATATTTTAGATCACGT
1 TTTATAATATTTTAGATCACGT
1157834 CTTTCCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (23 bp):
TTTATAATATTTTAGATCACGTT
Found at i:1170592 original size:25 final size:26
Alignment explanation
Indices: 1170563--1170625 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1170553 AAGTAAAATA
*
1170563 AAATAAAATATTTAACGTAT-AAAAC
1 AAATAAAATATGTAACGTATAAAAAC
* *
1170588 AAATAATATATGTATCGTATAAAAAC
1 AAATAAAATATGTAACGTATAAAAAC
1170614 ATTAATAAAATA
1 A--AATAAAATA
1170626 AAATATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 17 0.55
26 6 0.19
28 8 0.26
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (26 bp):
AAATAAAATATGTAACGTATAAAAAC
Found at i:1179894 original size:3 final size:3
Alignment explanation
Indices: 1179888--1179931 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1179878 ACATAAACGC
1179888 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1179932 TTGAACTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1181477 original size:25 final size:24
Alignment explanation
Indices: 1181449--1181499 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1181439 ATATTTTTAA
1181449 TATTTAATT-AAATAATTATTATTTT
1 TATTT-ATTAAAAT-ATTATTATTTT
* *
1181474 TATTTTTTAAAATATTTTTATTTT
1 TATTTATTAAAATATTATTATTTT
1181498 TA
1 TA
1181500 ATATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTATTAAAATATTATTATTTT
Found at i:1181506 original size:25 final size:26
Alignment explanation
Indices: 1181440--1181507 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 26
1181430 ATATTAAAAA
*
1181440 TATTTTTAATATTTAATTAAATAATTAT
1 TATTTTTAATATTT--TAAAATAATTAT
* *
1181468 TATTTTT-ATTTTTTAAAAT-ATTTT
1 TATTTTTAATATTTTAAAATAATTAT
1181492 TATTTTTAATATTTTA
1 TATTTTTAATATTTTA
1181508 TATCGGGGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 11 0.31
25 12 0.34
27 5 0.14
28 7 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTTTAATATTTTAAAATAATTAT
Found at i:1202699 original size:16 final size:16
Alignment explanation
Indices: 1202674--1202706 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1202664 ATAATATAGA
*
1202674 AAATATTTTTTTTAAT
1 AAATACTTTTTTTAAT
1202690 AAATACTTTTTTTAAT
1 AAATACTTTTTTTAAT
1202706 A
1 A
1202707 GTTTTAAAAA
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATACTTTTTTTAAT
Found at i:1202728 original size:23 final size:25
Alignment explanation
Indices: 1202683--1202733 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
1202673 AAAATATTTT
* *
1202683 TTTTAATAAATACTTTTTTTAATAG
1 TTTTAATAAAAACTTTTTCTAATAG
1202708 TTTTAA-AAAAAC-TTTTCTAATAG
1 TTTTAATAAAAACTTTTTCTAATAG
1202731 TTT
1 TTT
1202734 AGATGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.54
24 5 0.21
25 6 0.25
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTAATAAAAACTTTTTCTAATAG
Found at i:1203047 original size:73 final size:73
Alignment explanation
Indices: 1202927--1203069 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
1202917 AAAATGGGGC
* * * *
1202927 CCCACTAAATTACTATATCTTTGAGTTTTTTAAACAAAAAATGATGTTTAAAAATATTTTTTAAT
1 CCCACTAAATTACCATATCTTTAAGTATTTAAAACAAAAAATGATGTTTAAAAATATTTTTTAAT
1202992 TATTAGGA
66 TATTAGGA
* *
1203000 CCCACTAAGTTACCATAT-TTTCAAGTATTTAAAATAAAAAA-GTATGTTTAAAAATATTTTTTA
1 CCCACTAAATTACCATATCTTT-AAGTATTTAAAACAAAAAATG-ATGTTTAAAAATATTTTTTA
1203063 ATTATTA
64 ATTATTA
1203070 AACTTAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
72 4 0.06
73 58 0.94
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (73 bp):
CCCACTAAATTACCATATCTTTAAGTATTTAAAACAAAAAATGATGTTTAAAAATATTTTTTAAT
TATTAGGA
Found at i:1213472 original size:104 final size:104
Alignment explanation
Indices: 1213292--1213491 Score: 373
Period size: 104 Copynumber: 1.9 Consensus size: 104
1213282 ACATTGCAAG
* *
1213292 TGTTTGAATACTTGAATCATACTGGTTTTACTGAAGTTAATCAGTTGCAAACTACATCAGTTTAT
1 TGTTTGAATACTTGAATCATACCGGTTTTACCGAAGTTAATCAGTTGCAAACTACATCAGTTTAT
1213357 GTTGTTAACTGAATTCTACATAACAGCATTACTAAGTGA
66 GTTGTTAACTGAATTCTACATAACAGCATTACTAAGTGA
*
1213396 TGTTTGAATACTTGAATCATACCGGTTTTACCGAAGTTAATCAGTTGCAAACTTCATCAGTTTAT
1 TGTTTGAATACTTGAATCATACCGGTTTTACCGAAGTTAATCAGTTGCAAACTACATCAGTTTAT
1213461 GTTGTTAACTGAATTCTACATAACAGCATTA
66 GTTGTTAACTGAATTCTACATAACAGCATTA
1213492 AGTGTTATAA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 93 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (104 bp):
TGTTTGAATACTTGAATCATACCGGTTTTACCGAAGTTAATCAGTTGCAAACTACATCAGTTTAT
GTTGTTAACTGAATTCTACATAACAGCATTACTAAGTGA
Found at i:1217497 original size:24 final size:24
Alignment explanation
Indices: 1217430--1217486 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
1217420 GATAGGTTAA
1217430 AAATAGTTTAAGCACATATTCGTG
1 AAATAGTTTAAGCACATATTCGTG
1217454 AAATAGTTTAAGCACATATTCGTG
1 AAATAGTTTAAGCACATATTCGTG
1217478 AAATAGTTT
1 AAATAGTTT
1217487 GGGCATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (24 bp):
AAATAGTTTAAGCACATATTCGTG
Found at i:1219647 original size:187 final size:185
Alignment explanation
Indices: 1219322--1219700 Score: 569
Period size: 187 Copynumber: 2.0 Consensus size: 185
1219312 ATATATAATT
*
1219322 TTATTTTTTTAATTTTAAATAAAAAAATTAGAATCACTAGATTGTGACATGTGTCACTTAACGGG
1 TTATTTTTTTAATTTTAAATAAAAAAATTAGAATCACTAGATTGTGACACGTGTCACTTAACGGG
* *
1219387 AAATTTAACGTAGTTGACGGTCCGGGCACCTAAATAGACAACGTCTGTAACGTTAGGCACATGGA
66 AAAGTTAACGTAGTTGACGGTCCGGGCACCTAAATAGACAACGTCTATAACGTTAGGCACATGGA
* * * *
1219452 TTGGTCAAAAAATAGTTTAGTCACATATTCGAGAATTTAGGTATAGTTTGGGCAC
131 TGGGTCAAAAAATAGTTTAGGCACATATTCGAGAATTTAGGTATACTTTGGACAC
*
1219507 TTAATTTTTTTAAATTTTAAATAAAAAATTTAGAATCACTAGATTGTGACACGTGTCACTTAACG
1 TT-ATTTTTTT-AATTTTAAATAAAAAAATTAGAATCACTAGATTGTGACACGTGTCACTTAACG
* * * ** * * * *
1219572 GGAAAGTTAACGTCGTTGACGGTCTGGGCACCTATATAGGTAATGTTTATAATGTTAGGCACCTG
64 GGAAAGTTAACGTAGTTGACGGTCCGGGCACCTAAATAGACAACGTCTATAACGTTAGGCACATG
* *
1219637 GATGGGTCAAAAAATAGTTTAGGCACCTATTCGAGAATTTATGTATACTTTGGACAC
129 GATGGGTCAAAAAATAGTTTAGGCACATATTCGAGAATTTAGGTATACTTTGGACAC
1219694 TTATTTT
1 TTATTTT
1219701 GGTATTAAAT
Statistics
Matches: 173, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
185 2 0.01
186 13 0.08
187 158 0.91
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (185 bp):
TTATTTTTTTAATTTTAAATAAAAAAATTAGAATCACTAGATTGTGACACGTGTCACTTAACGGG
AAAGTTAACGTAGTTGACGGTCCGGGCACCTAAATAGACAACGTCTATAACGTTAGGCACATGGA
TGGGTCAAAAAATAGTTTAGGCACATATTCGAGAATTTAGGTATACTTTGGACAC
Found at i:1221163 original size:30 final size:30
Alignment explanation
Indices: 1221127--1221220 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 30
1221117 ATAAATATAT
1221127 GAACATGATCAAGATATTAAAAAATTAAAC
1 GAACATGATCAAGATATTAAAAAATTAAAC
* ** * * *
1221157 GAACATG---AACACCTTCAAAAATAAATAT
1 GAACATGATCAAGATATTAAAAAATTAA-AC
* * *
1221185 GAGCATGATCATGATATTAAAAATTTAAAC
1 GAACATGATCAAGATATTAAAAAATTAAAC
1221215 GAACAT
1 GAACAT
1221221 AAACTGAACA
Statistics
Matches: 44, Mismatches: 16, Indels: 8
0.65 0.24 0.12
Matches are distributed among these distances:
27 13 0.30
28 7 0.16
30 13 0.30
31 11 0.25
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (30 bp):
GAACATGATCAAGATATTAAAAAATTAAAC
Found at i:1221202 original size:58 final size:61
Alignment explanation
Indices: 1221097--1221220 Score: 200
Period size: 58 Copynumber: 2.1 Consensus size: 61
1221087 ACGCGAACTA
1221097 AACATGAACACCTTCAAAAAATAAATATATGAACATGATCAAGATATTAAAAAATTAAACG
1 AACATGAACACCTTCAAAAAATAAATATATGAACATGATCAAGATATTAAAAAATTAAACG
* * *
1221158 AACATGAACACCTTC-AAAAAT-AA-ATATGAGCATGATCATGATATTAAAAATTTAAACG
1 AACATGAACACCTTCAAAAAATAAATATATGAACATGATCAAGATATTAAAAAATTAAACG
1221216 AACAT
1 AACAT
1221221 AAACTGAACA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
58 37 0.62
59 2 0.03
60 6 0.10
61 15 0.25
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (61 bp):
AACATGAACACCTTCAAAAAATAAATATATGAACATGATCAAGATATTAAAAAATTAAACG
Found at i:1222305 original size:33 final size:33
Alignment explanation
Indices: 1222268--1222337 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
1222258 GTCATCTGAA
*
1222268 CGAGCTATGCGAGGGCATCCGAGGGCAA-CCGAG
1 CGAGCTATGCGAGGGAATCCGAGGG-AAGCCGAG
*
1222301 CGAGCTATGCGAGGGAATTCGAGGGAAGCCGAG
1 CGAGCTATGCGAGGGAATCCGAGGGAAGCCGAG
1222334 CGAG
1 CGAG
1222338 GGTAGGTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.26, C:0.23, G:0.41, T:0.10
Consensus pattern (33 bp):
CGAGCTATGCGAGGGAATCCGAGGGAAGCCGAG
Found at i:1222376 original size:29 final size:29
Alignment explanation
Indices: 1222341--1222425 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
1222331 GAGCGAGGGT
* *
1222341 AGGTCGCTCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
* *
1222370 ATGTCGCCCGGAGGGCATGACGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
1222399 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
1222426 TGTGTTGGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:1223553 original size:113 final size:112
Alignment explanation
Indices: 1223357--1223576 Score: 309
Period size: 113 Copynumber: 2.0 Consensus size: 112
1223347 GCAGAGGGCC
* * * *
1223357 CCCAAAAAATAGCCCAAAAAAGTATATATATAGTTGCGTTTTTTCAATAAACGTCACTATAGATG
1 CCCAAAAAATAGCCCAAAAAAATATATATATAGTGGCGTTTTCTCAATAAACATCACTATAGATG
*
1223422 GATCTATTGCAACGTTTTTTTAATAAAACG-CTACTATTATTGCGCAGG
66 GACCTATTGCAACGTTTTTTTAA-AAAACGTC-ACTATTATTGCGCAGG
* * *
1223470 CCCAAAAAA-ATCCCAAAATAAATATATATATAGTGGTGTTTTCTCAATAAACATCACTATAGGT
1 CCCAAAAAATAGCCCAAAA-AAATATATATATAGTGGCGTTTTCTCAATAAACATCACTATAGAT
* *
1223534 GGACCTATTGCGACGTTTTTTTAAAAAATGTCACTATTATTGC
65 GGACCTATTGCAACGTTTTTTTAAAAAACGTCACTATTATTGC
1223577 CCCGAAATCG
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
112 24 0.25
113 71 0.75
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (112 bp):
CCCAAAAAATAGCCCAAAAAAATATATATATAGTGGCGTTTTCTCAATAAACATCACTATAGATG
GACCTATTGCAACGTTTTTTTAAAAAACGTCACTATTATTGCGCAGG
Found at i:1227619 original size:35 final size:35
Alignment explanation
Indices: 1227579--1227649 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1227569 CTTAAAAACC
*
1227579 ATATTAATATACTAAATTAAAAGAAGGGCCCATAA
1 ATATTAATAAACTAAATTAAAAGAAGGGCCCATAA
*
1227614 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
1 ATATTAATAAACTAAATTAAAAGAAGGGCCCATAA
1227649 A
1 A
1227650 CTTATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGAAGGGCCCATAA
Found at i:1230454 original size:21 final size:21
Alignment explanation
Indices: 1230414--1230468 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1230404 GATTCTTGAC
1230414 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
1230434 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
1230456 AATCGCAACGCGA
1 AATCGCAATGCGA
1230469 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:1230498 original size:20 final size:20
Alignment explanation
Indices: 1230456--1230684 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
1230446 GATTTTACAG
* ** *
1230456 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1230476 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
1230496 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1230516 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1230536 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1230556 AATCGCAATGCGTATCCATA
1 AATCGCAACGCGTATCCGTA
*
1230576 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1230596 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1230616 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1230636 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1230656 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1230676 AATCACAAC
1 AATCGCAAC
1230685 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1231615 original size:12 final size:12
Alignment explanation
Indices: 1231598--1231622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1231588 ATATAATCCT
1231598 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1231610 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1231622 G
1 G
1231623 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1234014 original size:72 final size:71
Alignment explanation
Indices: 1233921--1234154 Score: 275
Period size: 72 Copynumber: 3.3 Consensus size: 71
1233911 GCAACGAGAG
1233921 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAA-AAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1233986 AAATGAA
65 AAATGAA
* * *
1233993 AATCGCAATGCGAAATGAAAATCGCAATGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAA-AAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1234058 AAATGAA
65 AAATGAA
* * * * * * *
1234065 AATCACAACGAGAGAATCG-CAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA--C
1 AATCGCAATGCGA-AAT-GAAAATCCCAAAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
*
1234126 G--A-GAG
64 GAAATGAA
1234131 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
1234155 GCAATGCGAA
Statistics
Matches: 138, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
65 1 0.01
66 16 0.12
67 3 0.02
69 2 0.01
71 16 0.12
72 91 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAAAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:1234042 original size:53 final size:52
Alignment explanation
Indices: 1233907--1234176 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
1233897 CGGAAATTAC
*
1233907 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1233954 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1234012 AATCGCAATGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
1234065 AATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1234117 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1234170 AATCGCA
1 AATCGCA
1234177 TTGCGATTCT
Statistics
Matches: 203, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 65 0.32
53 113 0.56
55 2 0.01
57 2 0.01
58 11 0.05
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1234182 original size:72 final size:69
Alignment explanation
Indices: 1233888--1234181 Score: 273
Period size: 72 Copynumber: 4.2 Consensus size: 69
1233878 GCATTTGACT
** * * *
1233888 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-AA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATCGAA
1233951 GAAA
66 GAAA
*
1233955 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
1234020 T-G-AGAGA
61 TCGAAGAAA
* * * *
1234027 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-C-ACAACGAGAGAATCGCAAT
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGA-AATGA-A-AATCGCAAT
1234088 GCGAAATGAAA
62 -CG-AA-GAAA
1234099 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAAT-CG
1234163 AAATGAAA
64 -AA-GAAA
*
1234171 ATCGCATTGCG
1 ATCGCAATGCG
1234182 ATTCTCTCGT
Statistics
Matches: 188, Mismatches: 17, Indels: 38
0.77 0.07 0.16
Matches are distributed among these distances:
64 1 0.01
65 6 0.03
66 7 0.04
67 34 0.18
69 3 0.02
70 1 0.01
71 21 0.11
72 107 0.57
73 3 0.02
74 4 0.02
75 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (69 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATCGAA
GAAA
Found at i:1234196 original size:105 final size:105
Alignment explanation
Indices: 1233907--1234173 Score: 402
Period size: 105 Copynumber: 2.5 Consensus size: 105
1233897 CGGAAATTAC
* *
1233907 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCACAA--C-
*
1233966 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1234012 AATCGCAATGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAG
1234077 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1234117 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATC
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATC
1234174 GCATTGCGAT
Statistics
Matches: 151, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
105 120 0.79
106 16 0.11
108 2 0.01
109 1 0.01
110 2 0.01
111 10 0.07
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1234216 original size:53 final size:52
Alignment explanation
Indices: 1234153--1234268 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
1234143 GAAATGAAAA
*
1234153 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
1234205 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1234258 TCGCATTGCGA
1 TCGCATTGCGA
1234269 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1234231 original size:19 final size:19
Alignment explanation
Indices: 1234191--1234278 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
1234181 GATTCTCTCG
1234191 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1234211 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1234230 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1234244 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1234263 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1234279 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1234388 original size:14 final size:14
Alignment explanation
Indices: 1234369--1234405 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1234359 CATCAATTAC
1234369 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1234383 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1234397 ACAAATCAA
1 ACAAATCAA
1234406 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1236373 original size:19 final size:19
Alignment explanation
Indices: 1236333--1236470 Score: 151
Period size: 19 Copynumber: 7.5 Consensus size: 19
1236323 GTTTACTTTT
* *
1236333 GCAACACGAAACTTAAAATC
1 GCAACGCGAAA-TGAAAATC
*
1236353 GCAACGCGAAATGAGAATC
1 GCAACGCGAAATGAAAATC
* **
1236372 GCAACGAGAAACCAAAATC
1 GCAACGCGAAATGAAAATC
1236391 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
1236410 GCAA--CGACA-G--AATC
1 GCAACGCGAAATGAAAATC
*
1236424 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
1236443 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
1236462 GCAATGCGA
1 GCAACGCGA
1236471 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 71 0.72
20 10 0.10
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:1236433 original size:33 final size:35
Alignment explanation
Indices: 1236347--1236448 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 35
1236337 CACGAAACTT
*
1236347 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G-AACC
1236385 AAAATCGCAACGCGAAATGAAAATCGCAACG-A-C
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAACC
* *
1236418 AGAATCGCAATGCGAAATGAAAATCGCAACG
1 AAAATCGCAACGCGAAATGAAAATCGCAACG
1236449 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
33 30 0.49
34 1 0.02
36 1 0.02
38 29 0.48
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (35 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAACC
Found at i:1236441 original size:52 final size:52
Alignment explanation
Indices: 1236366--1236465 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
1236356 ACGCGAAATG
1236366 AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
* * **
1236418 AGAATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA
1236466 TGCGATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (52 bp):
AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:1236501 original size:14 final size:14
Alignment explanation
Indices: 1236482--1236540 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1236472 TTTGGTTTCG
1236482 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1236496 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
1236513 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
1236529 CGTTGCGATTTT
1 CGTTGCGATTTT
1236541 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1236508 original size:33 final size:33
Alignment explanation
Indices: 1236466--1236589 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1236456 AAAATCGCAA
*
1236466 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1236499 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1236532 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1236565 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1236590 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1236520 original size:19 final size:18
Alignment explanation
Indices: 1236466--1236557 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
1236456 AAAATCGCAA
1236466 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1236485 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1236499 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1236518 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1236532 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1236551 TGCGATT
1 TGCGATT
1236558 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1236567 original size:14 final size:14
Alignment explanation
Indices: 1236515--1236571 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1236505 TTTGGTTTCG
*
1236515 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1236529 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1236548 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1236562 CGTTGCGATT
1 CGTTGCGATT
1236572 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1236753 original size:83 final size:87
Alignment explanation
Indices: 1236637--1236909 Score: 324
Period size: 93 Copynumber: 3.1 Consensus size: 87
1236627 ATGGATTGCA
* **
1236637 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAGCA
1236696 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
1236719 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
1236784 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
1236812 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAATAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----A-GATACACAGTT
*
1236877 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
1236905 TTACT
1 TTACT
1236910 AAGCAATCTA
Statistics
Matches: 172, Mismatches: 6, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 127 0.74
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:1236846 original size:93 final size:93
Alignment explanation
Indices: 1236687--1236909 Score: 428
Period size: 93 Copynumber: 2.4 Consensus size: 93
1236677 TCAGGGTATT
1236687 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236752 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236780 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1236845 TACTATTTCACAGTGTTAAATAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
1236873 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1236910 AAGCAATCTA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 128 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:1238627 original size:20 final size:20
Alignment explanation
Indices: 1238596--1238659 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1238586 TTTTGGTTGA
1238596 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1238616 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1238636 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1238657 AAT
1 AAT
1238660 CGTAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1238648 original size:21 final size:21
Alignment explanation
Indices: 1238594--1238658 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1238584 TCTTTTGGTT
1238594 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1238615 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1238635 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1238656 GAA
1 GAA
1238659 TCGTAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1239081 original size:20 final size:20
Alignment explanation
Indices: 1239056--1239247 Score: 253
Period size: 20 Copynumber: 9.6 Consensus size: 20
1239046 CTTTAAAAAT
1239056 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1239076 CGCGTTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
*
1239097 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1239116 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1239136 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1239156 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1239176 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1239196 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1239216 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1239236 CGCGTTGCGATT
1 CGCGTTGCGATT
1239248 CTTGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1241146 original size:42 final size:40
Alignment explanation
Indices: 1241085--1241170 Score: 127
Period size: 42 Copynumber: 2.1 Consensus size: 40
1241075 GTTCACCTTA
*
1241085 AAATCTGATTTTTTTTATTTAACTGTTAGTGTCCATATTG
1 AAATCTGATTTTTTTTATTTAACTGTTAGTGTCCACATTG
* *
1241125 AAATCTGAATTTTCTTTTATTTAATTGTTAGTGTCCACCTTG
1 AAATCTG-ATTTT-TTTTATTTAACTGTTAGTGTCCACATTG
1241167 AAAT
1 AAAT
1241171 TTTTTGTGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 7 0.17
41 5 0.12
42 29 0.71
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (40 bp):
AAATCTGATTTTTTTTATTTAACTGTTAGTGTCCACATTG
Found at i:1243249 original size:40 final size:40
Alignment explanation
Indices: 1243205--1243320 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 40
1243195 AATAGTAATT
* *
1243205 TACTGTATAAATAGTAACGATACTGTTTGAACAGTACCGA
1 TACTGTTTAAACAGTAACGATACTGTTTGAACAGTACCGA
* *
1243245 TACTGTTTGAACAGTACCGATACTGTTTGAACAGTACCGA
1 TACTGTTTAAACAGTAACGATACTGTTTGAACAGTACCGA
* * *
1243285 TACTGTTTAAACAATATCGATACTATTTGAACAGTA
1 TACTGTTTAAACAGTAACGATACTGTTTGAACAGTA
1243321 TCCAATGCTC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (40 bp):
TACTGTTTAAACAGTAACGATACTGTTTGAACAGTACCGA
Found at i:1243322 original size:20 final size:20
Alignment explanation
Indices: 1243217--1243320 Score: 163
Period size: 20 Copynumber: 5.2 Consensus size: 20
1243207 CTGTATAAAT
*
1243217 AGTAACGATACTGTTTGAAC
1 AGTACCGATACTGTTTGAAC
1243237 AGTACCGATACTGTTTGAAC
1 AGTACCGATACTGTTTGAAC
1243257 AGTACCGATACTGTTTGAAC
1 AGTACCGATACTGTTTGAAC
*
1243277 AGTACCGATACTGTTTAAAC
1 AGTACCGATACTGTTTGAAC
* * *
1243297 AATATCGATACTATTTGAAC
1 AGTACCGATACTGTTTGAAC
1243317 AGTA
1 AGTA
1243321 TCCAATGCTC
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTACCGATACTGTTTGAAC
Found at i:1243376 original size:21 final size:21
Alignment explanation
Indices: 1243346--1243445 Score: 137
Period size: 21 Copynumber: 4.8 Consensus size: 21
1243336 TCCATAATGA
* * *
1243346 TACAGAGGTATTGATACCTTC
1 TACAGGGGTATCGATACCTGC
*
1243367 TACAGGGGTATTGATACCTGC
1 TACAGGGGTATCGATACCTGC
*
1243388 TACAGGGGTATCGTTACCTGC
1 TACAGGGGTATCGATACCTGC
*
1243409 TACAGAGGTATCGATACCTGC
1 TACAGGGGTATCGATACCTGC
*
1243430 TACAGGGGTACCGATA
1 TACAGGGGTATCGATA
1243446 TCGTTACTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (21 bp):
TACAGGGGTATCGATACCTGC
Found at i:1243851 original size:34 final size:34
Alignment explanation
Indices: 1243812--1243893 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
1243802 CTTTGTAAAG
* * *
1243812 GGGAAAGGTTCTAGCTAAGTGCGTGTAAAAGTTA
1 GGGAAATGTTCTAGCTAAGTCCGTGTAAAAGCTA
1243846 GGGAAATGTTCTAGCTAAGTCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTAAGTCCGTGTAAAAGCTA
1243880 GGGAAATGTTCTAG
1 GGGAAATGTTCTAG
1243894 TTTAACCCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (34 bp):
GGGAAATGTTCTAGCTAAGTCCGTGTAAAAGCTA
Found at i:1243904 original size:34 final size:34
Alignment explanation
Indices: 1243812--1243916 Score: 124
Period size: 34 Copynumber: 3.1 Consensus size: 34
1243802 CTTTGTAAAG
* ** *
1243812 GGGAAAGGTTCTAGCTAAGTGCGTGTAAAAGTTA
1 GGGAAATGTTCTAGCTAAGCCCGTGTAAAAGCTA
*
1243846 GGGAAATGTTCTAGCTAAGTCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTAAGCCCGTGTAAAAGCTA
* *
1243880 GGGAAATGTTCTAGTTTAA-CCCGTG-AAAAACTA
1 GGGAAATGTTCTAG-CTAAGCCCGTGTAAAAGCTA
1243913 GGGA
1 GGGA
1243917 GTTGTAAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
33 11 0.17
34 50 0.78
35 3 0.05
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (34 bp):
GGGAAATGTTCTAGCTAAGCCCGTGTAAAAGCTA
Found at i:1255088 original size:46 final size:48
Alignment explanation
Indices: 1255003--1255094 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 48
1254993 TGAGAACAAA
1255003 AATTAACATTTATACATAGAGAATAATTAACATTTCTGATATTATAAT
1 AATTAACATTTATACATAGAGAATAATTAACATTTCTGATATTATAAT
* * *
1255051 AATTAACATTTCTA-ATATATAATAATT-ACATTTCTGATATTATA
1 AATTAACATTTATACATAGAGAATAATTAACATTTCTGATATTATA
1255095 TGTTTAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 17 0.41
47 11 0.27
48 13 0.32
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (48 bp):
AATTAACATTTATACATAGAGAATAATTAACATTTCTGATATTATAAT
Found at i:1255094 original size:23 final size:24
Alignment explanation
Indices: 1255024--1255094 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
1255014 ATACATAGAG
1255024 AATAATTAACATTTCTGATATTAT
1 AATAATTAACATTTCTGATATTAT
*
1255048 AATAATTAACATTTCTAATA-TAT
1 AATAATTAACATTTCTGATATTAT
1255071 AATAATT-ACATTTCTGATATTAT
1 AATAATTAACATTTCTGATATTAT
1255094 A
1 A
1255095 TGTTTAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 11 0.25
23 14 0.32
24 19 0.43
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (24 bp):
AATAATTAACATTTCTGATATTAT
Found at i:1256954 original size:19 final size:20
Alignment explanation
Indices: 1256916--1256957 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1256906 TAAGTAGAAG
*
1256916 TTTACCGTGTACGGTGATTA
1 TTTACCGTGTACGCTGATTA
*
1256936 TTTACCGTGT-TGCTGATTA
1 TTTACCGTGTACGCTGATTA
1256955 TTT
1 TTT
1256958 GACTGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (20 bp):
TTTACCGTGTACGCTGATTA
Found at i:1262203 original size:9 final size:9
Alignment explanation
Indices: 1262183--1262217 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1262173 TTGAATTTAA
1262183 AAAAAATCAT
1 AAAAAAT-AT
1262193 AAAAAATAT
1 AAAAAATAT
*
1262202 AAAAAATAC
1 AAAAAATAT
1262211 AAAAAAT
1 AAAAAAT
1262218 CGAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAATAT
Found at i:1262214 original size:18 final size:18
Alignment explanation
Indices: 1262183--1262232 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1262173 TTGAATTTAA
* *
1262183 AAAAAATCATAAAAAATAT
1 AAAAAAT-ACAAAAAATAG
*
1262202 AAAAAATACAAAAAATCG
1 AAAAAATACAAAAAATAG
*
1262220 AAAAATTACAAAA
1 AAAAAATACAAAA
1262233 CAATTAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAAAATACAAAAAATAG
Found at i:1264696 original size:23 final size:23
Alignment explanation
Indices: 1264670--1264715 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1264660 CACCACAGCT
*
1264670 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
1264693 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1264716 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1265448 original size:63 final size:64
Alignment explanation
Indices: 1265334--1265491 Score: 169
Period size: 63 Copynumber: 2.5 Consensus size: 64
1265324 ATCCCTTGAT
* * **
1265334 GGGTGCATCGATGCACTA-TCTATGCATCGATACATAAATCCTATTCGATGTTTGTA-TTTAAGG
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACATAAATCCTATTCAATGTTTGTATTTTAAAA
** * *
1265397 GGGTGCATCGATGCACTACTTGTGCATCGATACATTGATGGC-ATTCAATGTTTTTATTTTAAAA
1 GGGTGCATCGATGCACTACTTGTGCATCGATACATAAAT-CCTATTCAATGTTTGTATTTTAAAA
** * *
1265461 TAGTGCATCGATGCACTTCATGTGCATCGAT
1 GGGTGCATCGATGCACTACTTGTGCATCGAT
1265492 CCACCTTGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
63 46 0.57
64 34 0.43
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACATAAATCCTATTCAATGTTTGTATTTTAAAA
Found at i:1273083 original size:331 final size:331
Alignment explanation
Indices: 1272482--1273472 Score: 1896
Period size: 331 Copynumber: 3.0 Consensus size: 331
1272472 GATGCATTGG
* *
1272482 TACACATTGAATGTGCATCGATGCACATAGCCCATAAATATTATTTTAGCACAAAAATCTCTTCA
1 TACACATTGAATGTGCATCGATGCACATAGCCCAGAAATATTATTTTAGCACGAAAATCTCTTCA
1272547 AAATCTTCTC-AACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
66 AAATCTTCTCTAACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
1272611 ACTAATTATTATCCATTTCATACCTCTAAAACTTAGAAATTCAATTCTCCATATAGAATTTAAGA
131 ACTAATTATTATCCATTTCATACCTCTAAAACTTAGAAATTCAATTCTCCATATAGAATTTAAGA
1272676 ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACACTTCCTATTCCTTAATTAGCTTGA
196 ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACACTTCCTATTCCTTAATTAGCTTGA
* *
1272741 TGATAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATATAAGATTTTACTTTTCTACT
261 TGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATCTAAGATTTTACTTTTCTACT
1272806 TCATTT
326 TCATTT
1272812 TACACATTGAATGTGCATCGATGCACATAGCCCAGAAATATTATTTTAGCACGAAAATCTCTTCA
1 TACACATTGAATGTGCATCGATGCACATAGCCCAGAAATATTATTTTAGCACGAAAATCTCTTCA
1272877 AAATCTTCTCTAACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
66 AAATCTTCTCTAACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
1272942 ACTAATTATTATCCATTTCATACCTCTAAAACTTAGAAATTCAATTCTCCATATAGAATTTAAGA
131 ACTAATTATTATCCATTTCATACCTCTAAAACTTAGAAATTCAATTCTCCATATAGAATTTAAGA
* *
1273007 ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACGCTTCCTATTCCTTAATTAGCGTGA
196 ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACACTTCCTATTCCTTAATTAGCTTGA
1273072 TGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATCTAAGATTTTACTTTTCTACT
261 TGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATCTAAGATTTTACTTTTCTACT
1273137 TCATTT
326 TCATTT
1273143 TACACATTGAATGTGCATCGATGCACATAGCCCAGAAATATTATTTTAGCACGAAAATCTCTTCA
1 TACACATTGAATGTGCATCGATGCACATAGCCCAGAAATATTATTTTAGCACGAAAATCTCTTCA
1273208 AAATCTTCTCTAACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
66 AAATCTTCTCTAACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
*
1273273 ACTAATTATTATCCATTTCATACCTCTAAAA-ATAGAAATTCAATTCTCCATATAGAATTTAAGA
131 ACTAATTATTATCCATTTCATACCTCTAAAACTTAGAAATTCAATTCTCCATATAGAATTTAAGA
1273337 ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACACTTCCTATTCCTTAATTAGCTTGA
196 ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACACTTCCTATTCCTTAATTAGCTTGA
1273402 TGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATCTAAGATTTTACTTTTCTACT
261 TGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATCTAAGATTTTACTTTTCTACT
*
1273467 TTATTT
326 TCATTT
1273473 CTTTAATTCT
Statistics
Matches: 650, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
330 238 0.37
331 412 0.63
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (331 bp):
TACACATTGAATGTGCATCGATGCACATAGCCCAGAAATATTATTTTAGCACGAAAATCTCTTCA
AAATCTTCTCTAACACTTTATATTTCCCCTCTTTTTATATCCCTAACTTGCATACTCTTACTTAA
ACTAATTATTATCCATTTCATACCTCTAAAACTTAGAAATTCAATTCTCCATATAGAATTTAAGA
ATCTACTCAACTTCCAACATGTTCTTAATCTAATTCTAACACTTCCTATTCCTTAATTAGCTTGA
TGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTAATCTAAGATTTTACTTTTCTACT
TCATTT
Found at i:1278513 original size:32 final size:32
Alignment explanation
Indices: 1278477--1278549 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1278467 ATTATCAAAG
1278477 ATTGTTTATAATTTTAAAAAATTATATATATA
1 ATTGTTTATAATTTTAAAAAATTATATATATA
*
1278509 ATTGTTTATAATTTTCAAAAATTATATATATA
1 ATTGTTTATAATTTTAAAAAATTATATATATA
1278541 ATTGTTTAT
1 ATTGTTTAT
1278550 TATTATAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (32 bp):
ATTGTTTATAATTTTAAAAAATTATATATATA
Found at i:1280778 original size:132 final size:135
Alignment explanation
Indices: 1280568--1280814 Score: 365
Period size: 132 Copynumber: 1.8 Consensus size: 135
1280558 AGTGCAGCTT
* *
1280568 CAGATGTTACTCAAAAGGACAACAATTTGAATGAAAATGAACATGCTGCTCATAGCAACACCGAA
1 CAGATGTCACTCAAAAGGACAACAATTTGAATG-AAA-GAACA-GCTGCTCAGAGCAACACCGAA
* *
1280633 AACAATGAAAATGCAAGTCAGAATGAGAACAATGCCACTCAGAGCAACACAGACAATAATGAAAA
63 AACAATGAAAATGCAAGTCAGAATGAGAACAAGGCCACTCAAAGCAACACAGACAATAATGAAAA
1280698 TGCAACTG
128 TGCAACTG
* *
1280706 CAGATGTCACTCAAAATGACAACAATTTGAATG-AA-AACA-CTGCTCAGAGCAACACCGAAAGC
1 CAGATGTCACTCAAAAGGACAACAATTTGAATGAAAGAACAGCTGCTCAGAGCAACACCGAAAAC
* * *
1280768 AATGACAATGCAGGTCAGGATGAGAACAAGGCCACTCAAAGCAACAC
66 AATGAAAATGCAAGTCAGAATGAGAACAAGGCCACTCAAAGCAACAC
1280815 CGAAAGCAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
132 63 0.63
134 4 0.04
136 2 0.02
138 31 0.31
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.15
Consensus pattern (135 bp):
CAGATGTCACTCAAAAGGACAACAATTTGAATGAAAGAACAGCTGCTCAGAGCAACACCGAAAAC
AATGAAAATGCAAGTCAGAATGAGAACAAGGCCACTCAAAGCAACACAGACAATAATGAAAATGC
AACTG
Found at i:1280835 original size:54 final size:54
Alignment explanation
Indices: 1280748--1281012 Score: 311
Period size: 54 Copynumber: 4.9 Consensus size: 54
1280738 GAAAACACTG
* * *
1280748 CTCAGAGCAACACCGAAAGCAATGACAATGCAGGTCAGGATGAGAACAAGGCCA
1 CTCAAAGCAACACCGAAAGCAATGAAAATGCAGGTCAGGACGAGAACAAGGCCA
* *
1280802 CTCAAAGCAACACCGAAAGCAATGAAATTGCAGGTCAGGACGAGAACAAGGCCG
1 CTCAAAGCAACACCGAAAGCAATGAAAATGCAGGTCAGGACGAGAACAAGGCCA
* * * * * *
1280856 CTCAGAGCAACAGCGACAGCAAT-AACAATCCAGGTCAGAACGAGAACAAGGTCA
1 CTCAAAGCAACACCGAAAGCAATGAA-AATGCAGGTCAGGACGAGAACAAGGCCA
* * * * *
1280910 CTCAAAGCAACAGCGACAGCAAT-AATAATCCAGGTCAGAACGAGAACAAGGTCA
1 CTCAAAGCAACACCGAAAGCAATGAA-AATGCAGGTCAGGACGAGAACAAGGCCA
* * *
1280964 CTCAAAGCAACACTGACAA-CAATGAAAATGCAGGTCGGGTCGAGAACAA
1 CTCAAAGCAACACCGA-AAGCAATGAAAATGCAGGTCAGGACGAGAACAA
1281013 TGCTGCTCAG
Statistics
Matches: 186, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.01
54 181 0.97
55 3 0.02
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.10
Consensus pattern (54 bp):
CTCAAAGCAACACCGAAAGCAATGAAAATGCAGGTCAGGACGAGAACAAGGCCA
Found at i:1284300 original size:21 final size:20
Alignment explanation
Indices: 1284270--1284310 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1284260 TTACTTATTG
* *
1284270 TACTTTTAAATTTTTTAATT
1 TACTTTTAAACTTTTGAATT
1284290 TACTTATTAAACTTTTGAATT
1 TACTT-TTAAACTTTTGAATT
1284311 GCTCATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (20 bp):
TACTTTTAAACTTTTGAATT
Found at i:1284926 original size:15 final size:15
Alignment explanation
Indices: 1284906--1284942 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1284896 TGAGACATTA
*
1284906 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
1284921 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
1284936 CCCGCCC
1 CCCGCCC
1284943 GCCCAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:1290984 original size:21 final size:21
Alignment explanation
Indices: 1290960--1291027 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1290950 GATTCGCAAC
1290960 GCGATAGTCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGCATT
* * *
1290981 GCGATTTATTCCAAATTCG--TT
1 GCGA--TAGTCGAAGTTCGCATT
*
1291002 GCGATAGGCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGCATT
1291023 GCGAT
1 GCGAT
1291028 TCATTCCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.25
21 17 0.47
23 10 0.28
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (21 bp):
GCGATAGTCGAAGTTCGCATT
Found at i:1291054 original size:41 final size:42
Alignment explanation
Indices: 1290960--1291132 Score: 278
Period size: 41 Copynumber: 4.2 Consensus size: 42
1290950 GATTCGCAAC
* *
1290960 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1291002 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAA-TCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
* *
1291043 GCGATAGGCGAAGTTCGCGTTGCAATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
* *
1291084 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCATT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1291126 GCGATAG
1 GCGATAG
1291133 TCCAAATATT
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 2 0.02
41 73 0.59
42 48 0.39
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (42 bp):
GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
Found at i:1291065 original size:21 final size:21
Alignment explanation
Indices: 1291039--1291109 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
1291029 CATTCCAAAT
1291039 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTTCG
* ** *
1291060 CGTTGCAATTCATTCCAA-TT--
1 CGTTGCGA-T-AGGCGAAGTTCG
1291080 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTTCG
1291101 CGTTGCGAT
1 CGTTGCGAT
1291110 TCATTCCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 7 0.19
21 16 0.43
22 3 0.08
23 4 0.11
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
CGTTGCGATAGGCGAAGTTCG
Found at i:1292086 original size:41 final size:42
Alignment explanation
Indices: 1291996--1292186 Score: 298
Period size: 41 Copynumber: 4.6 Consensus size: 42
1291986 TATTTGGACT
*
1291996 ATCGCAACGCGAACTTCGCCTACCGCAACGAATTTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
1292038 ATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
*
1292079 ATCGCAACGCGAACTTCGCCTATCGCAACG-ATTTGGAAAGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
* **
1292120 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTAAAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
**
1292162 ATCGC-ACGCGAACTTCAACTATCGC
1 ATCGCAACGCGAACTTCGCCTATCGC
1292187 GTTGCGAATC
Statistics
Matches: 140, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 95 0.68
42 44 0.31
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
Found at i:1292146 original size:21 final size:21
Alignment explanation
Indices: 1291992--1292149 Score: 89
Period size: 21 Copynumber: 7.6 Consensus size: 21
1291982 CCAATATTTG
1291992 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
* * * *
1292013 GCCTACCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTC
*
1292032 GAATGAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
* *
1292055 GCCTATCGCAA--CGAA-TTG
1 GACTATCGCAACGCGAACTTC
*
1292073 GAATGAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
* * *
1292096 GCCTATCGCAA--CG-ATTTG
1 GACTATCGCAACGCGAACTTC
**
1292114 GAAAGAATCGCAACGCGAACTTC
1 G--ACTATCGCAACGCGAACTTC
1292137 GACTATCGCAACG
1 GACTATCGCAACG
1292150 AATTTAAAAT
Statistics
Matches: 97, Mismatches: 26, Indels: 28
0.64 0.17 0.19
Matches are distributed among these distances:
18 8 0.08
19 14 0.14
20 14 0.14
21 39 0.40
22 6 0.06
23 16 0.16
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:1292348 original size:3 final size:3
Alignment explanation
Indices: 1292340--1292369 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1292330 TTATTTTCTC
1292340 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1292370 GAAGTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1293483 original size:60 final size:60
Alignment explanation
Indices: 1293323--1293507 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 60
1293313 CATATAATTC
* * * *
1293323 AGGATAAAATTGAAATATTTAAAAAGTTTA-AAGACCAATTTAGAATGAAGATCACA-TATTA
1 AGGATAAAATTGAAATGTTT-AAAAGTTTAGGA-ACCAGTTTAGAATGAAG-TCATAGTATTA
* * * * * *
1293384 GGGATGAAAAATGAGATGTTCAAAAGTTGAGG-ACTAGTTTAGAATGACAGTCATAGT-TTA
1 AGGAT-AAAATTGAAATGTTTAAAAGTTTAGGAACCAGTTTAGAATGA-AGTCATAGTATTA
* *
1293444 AGGATAAAATTAAAATGTTTAAAAGTTTAGGAACCAGTTT-GAAATGAAAGTCATAG-ATCA
1 AGGATAAAATTGAAATGTTTAAAAGTTTAGGAACCAGTTTAG-AATG-AAGTCATAGTATTA
1293504 AGGA
1 AGGA
1293508 CGTATGATGC
Statistics
Matches: 98, Mismatches: 18, Indels: 17
0.74 0.14 0.13
Matches are distributed among these distances:
59 22 0.22
60 49 0.50
61 16 0.16
62 11 0.11
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (60 bp):
AGGATAAAATTGAAATGTTTAAAAGTTTAGGAACCAGTTTAGAATGAAGTCATAGTATTA
Found at i:1298442 original size:16 final size:17
Alignment explanation
Indices: 1298405--1298442 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1298395 TTAATCCAAA
*
1298405 GATTCAAAAATTGGCTT
1 GATTCAAAAATTGGATT
*
1298422 AATTCAAAAATT-GATT
1 GATTCAAAAATTGGATT
1298438 GATTC
1 GATTC
1298443 GATGTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (17 bp):
GATTCAAAAATTGGATT
Found at i:1300414 original size:16 final size:16
Alignment explanation
Indices: 1300395--1300437 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1300385 TTTTTTAATT
*
1300395 TATAAAATATTTAAAA
1 TATAAAATATATAAAA
*
1300411 TATAAAAAATATAAAA
1 TATAAAATATATAAAA
* *
1300427 AATTAAATATA
1 TATAAAATATA
1300438 AACTAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAATATATAAAA
Found at i:1300972 original size:34 final size:34
Alignment explanation
Indices: 1300930--1301002 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
1300920 AATTTAATTT
*
1300930 TTTTATAAGATTTTATAATATTTCTTTAATTAAA
1 TTTTATAAGATTTTATAATATTTCTTTAACTAAA
1300964 TTTTATAAGATTTTATAATATTTCTTTAACTAAA
1 TTTTATAAGATTTTATAATATTTCTTTAACTAAA
1300998 TTTTA
1 TTTTA
1301003 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (34 bp):
TTTTATAAGATTTTATAATATTTCTTTAACTAAA
Found at i:1305407 original size:29 final size:31
Alignment explanation
Indices: 1305342--1305398 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1305332 CATCTTTATT
*
1305342 TTATATTA-TTTTTTAATAATTATGTATTTA
1 TTATAATATTTTTTTAATAATTATGTATTTA
1305372 TTATAATATTTTTTTAAT-ATT-TGTATT
1 TTATAATATTTTTTTAATAATTATGTATT
1305399 GTATGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 10 0.40
31 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (31 bp):
TTATAATATTTTTTTAATAATTATGTATTTA
Found at i:1305637 original size:2 final size:2
Alignment explanation
Indices: 1305630--1305658 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1305620 ATTCCTCAGC
1305630 TA 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 TA T
1305659 TTGTCAGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1312251 original size:5 final size:5
Alignment explanation
Indices: 1312238--1312268 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1312228 TTTTTCTCAT
*
1312238 TTTTT TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
1312269 CTCCCTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:1314063 original size:31 final size:30
Alignment explanation
Indices: 1314028--1314113 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 30
1314018 CGTCCCCAAC
*
1314028 AGGTCGCCATGCATTCCCCAAC-ACCCCTACA
1 AGGTCGCCATGCACTCCCCAACGA--CCTACA
* *
1314059 AGGTCGCCAAGCACT-CCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCCAACGACCTACA
*
1314088 AGGTCGCCATGCACT-CCCAGCGACCT
1 AGGTCGCCATGCACTCCCCAACGACCT
1314114 TGTAGGTCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 31 0.62
30 5 0.10
31 14 0.28
ACGTcount: A:0.24, C:0.43, G:0.19, T:0.14
Consensus pattern (30 bp):
AGGTCGCCATGCACTCCCCAACGACCTACA
Found at i:1314141 original size:29 final size:29
Alignment explanation
Indices: 1314053--1314134 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1314043 CCCCAACACC
1314053 CCTACAAGGTCGCCAAGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
*
1314082 CCTACAAGGTCGCCATGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
*** *
1314111 CCTTGTAGGTCGCCAAGCAATCCC
1 CCTACAAGGTCGCCAAGCACTCCC
1314135 GACGACCAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.24, C:0.40, G:0.21, T:0.15
Consensus pattern (29 bp):
CCTACAAGGTCGCCAAGCACTCCCAGCGA
Found at i:1314616 original size:22 final size:21
Alignment explanation
Indices: 1314591--1314631 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1314581 GTTAATTAGT
*
1314591 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
1314613 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
1314632 TATATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Found at i:1314947 original size:8 final size:8
Alignment explanation
Indices: 1314934--1314968 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1314924 TTTAAAAAGT
*
1314934 TTAGTTTG
1 TTAGTTTA
1314942 TTAGTTTA
1 TTAGTTTA
*
1314950 TTAATTTA
1 TTAGTTTA
1314958 TTAGTTTA
1 TTAGTTTA
1314966 TTA
1 TTA
1314969 TATTAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (8 bp):
TTAGTTTA
Found at i:1316640 original size:28 final size:30
Alignment explanation
Indices: 1316599--1316660 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
1316589 ATTTTTTATA
1316599 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1316629 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1316657 TAAT
1 TAAT
1316661 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1317114 original size:23 final size:22
Alignment explanation
Indices: 1317084--1317126 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
1317074 GCTTGGCTAC
1317084 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTAT-GATGCAGG
1317107 AATCTCCCAGCTATGATGCA
1 AATCTCCCAGCTATGATGCA
1317127 ACCCATGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
AATCTCCCAGCTATGATGCAGG
Found at i:1317148 original size:31 final size:32
Alignment explanation
Indices: 1317113--1317175 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1317103 CAGGAATCTC
*
1317113 CCAGCTAT-GATGCAACCCATGCATGAGGGAG
1 CCAGCTATGGATGCAACCCATGCACGAGGGAG
1317144 CCAGCTATGGATGCAACCCATGCACGAGGGAG
1 CCAGCTATGGATGCAACCCATGCACGAGGGAG
1317176 GGGCTAAGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.29, C:0.27, G:0.30, T:0.14
Consensus pattern (32 bp):
CCAGCTATGGATGCAACCCATGCACGAGGGAG
Found at i:1317276 original size:29 final size:29
Alignment explanation
Indices: 1317193--1317281 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
1317183 GTCGAGGCTT
* * ***
1317193 GGTCGCCGGGATTACTTGGCGACCTACAA
1 GGTCGCTGGGAGTACTTGGCGACCTTGTA
* *
1317222 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTACTTGGCGACCTTGTA
1317251 GGTCGCTGGGAGTACTTGGCGACCTTGTA
1 GGTCGCTGGGAGTACTTGGCGACCTTGTA
1317280 GG
1 GG
1317282 GGTGTTGGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.16, C:0.22, G:0.38, T:0.24
Consensus pattern (29 bp):
GGTCGCTGGGAGTACTTGGCGACCTTGTA
Done.