Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:2282249 original size:24 final size:24
Alignment explanation
Indices: 2282217--2282305 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
2282207 GATATAAGAA
*
2282217 ATCAAAACAGAATTCAAATCAGAT
1 ATCAGAACAGAATTCAAATCAGAT
* *
2282241 ATCAGAACAGAATCCAAATCAGAA
1 ATCAGAACAGAATTCAAATCAGAT
* **
2282265 ATCAGAACATAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAATCA-GAT
*
2282289 ATCATAACAGAATTCAA
1 ATCAGAACAGAATTCAA
2282306 GTAAGAAATC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 52 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAATCAGAT
Found at i:2282279 original size:48 final size:48
Alignment explanation
Indices: 2282210--2282318 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
2282200 AAACAGAGAT
*
2282210 ATAAGAAATCAAAACAGAATTCAAATCA-GATATCAGAACAGAATCCAA
1 ATAAGAAATCAGAACAGAATTCAAATCATG-TATCAGAACAGAATCCAA
* * ** * *
2282258 ATCAGAAATCAGAACATAATTCAGGTCATGTATCATAACAGAATTCAA
1 ATAAGAAATCAGAACAGAATTCAAATCATGTATCAGAACAGAATCCAA
*
2282306 GTAAGAAATCAGA
1 ATAAGAAATCAGA
2282319 TAAAATATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 50 0.98
49 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (48 bp):
ATAAGAAATCAGAACAGAATTCAAATCATGTATCAGAACAGAATCCAA
Found at i:2282316 original size:24 final size:24
Alignment explanation
Indices: 2282210--2282318 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
2282200 AAACAGAGAT
*
2282210 ATAAGAAATCAAAACAGAATTCAA
1 ATAAGAAATCAGAACAGAATTCAA
* * *
2282234 ATCAGATATCAGAACAGAATCCAA
1 ATAAGAAATCAGAACAGAATTCAA
* * *
2282258 ATCAGAAATCAGAACATAATTCAG
1 ATAAGAAATCAGAACAGAATTCAA
* * * *
2282282 GTCATG-TATCATAACAGAATTCAA
1 AT-AAGAAATCAGAACAGAATTCAA
*
2282306 GTAAGAAATCAGA
1 ATAAGAAATCAGA
2282319 TAAAATATTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 62 0.95
25 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (24 bp):
ATAAGAAATCAGAACAGAATTCAA
Found at i:2287056 original size:17 final size:16
Alignment explanation
Indices: 2287036--2287069 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2287026 TATTGGTGTA
2287036 TTAATATTATTTATTAT
1 TTAATATTATTT-TTAT
2287053 TTAATATTATTTTTAT
1 TTAATATTATTTTTAT
2287069 T
1 T
2287070 ACCATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAATATTATTTTTAT
Found at i:2287086 original size:28 final size:26
Alignment explanation
Indices: 2287050--2287107 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
2287040 TATTATTTAT
* *
2287050 TATTTAATATTATTTTTATTACCATTA
1 TATTTAATATTATTATTATTA-CATAA
2287077 TATTGTAATATTATTATTATTACATAA
1 TATT-TAATATTATTATTATTACATAA
2287104 TATT
1 TATT
2287108 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTTAATATTATTATTATTACATAA
Found at i:2291381 original size:34 final size:34
Alignment explanation
Indices: 2291343--2291415 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
2291333 TCAAGGTGTT
2291343 ATCATCAGAAACAGAAATATGCACTCCAGGCGCA
1 ATCATCAGAAACAGAAATATGCACTCCAGGCGCA
* * *
2291377 ATCATCATATACAGAAATATGCACTCCAGGTGCA
1 ATCATCAGAAACAGAAATATGCACTCCAGGCGCA
2291411 ATCAT
1 ATCAT
2291416 TAAATGTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (34 bp):
ATCATCAGAAACAGAAATATGCACTCCAGGCGCA
Found at i:2300210 original size:21 final size:21
Alignment explanation
Indices: 2300159--2300211 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2300149 ATTATTACTA
2300159 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2300180 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2300201 TCGCAATGCGA
1 TCGCAATGCGA
2300212 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2300243 original size:20 final size:20
Alignment explanation
Indices: 2300220--2300334 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
2300210 GAATAAGTAA
*
2300220 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2300240 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
2300261 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2300281 TTCGCAACACGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2300301 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2300321 TTCGCAACGAGATA
1 ATCGCAACGCGATA
2300335 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 62 0.77
21 15 0.19
22 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2300263 original size:41 final size:41
Alignment explanation
Indices: 2300218--2300354 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
2300208 GCGAATAAGT
* *
2300218 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATACA
* *
2300259 AAATCGCAACGCGATACTGACTTTCGCAACACGATACTTAC-
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATACA
** *
2300300 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATACA
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATACA
* *
2300340 TAATCGCAATGCGAT
1 AAATCGCAACGCGAT
2300355 TTTCAAAGTG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.38
41 44 0.54
42 3 0.04
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATACA
Found at i:2300549 original size:22 final size:22
Alignment explanation
Indices: 2300521--2300564 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2300511 CACTCTCTCA
*
2300521 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
*
2300543 CCCATCTCAGGCGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
2300565 TACCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCAGACGAAATCCGTC
Found at i:2300852 original size:20 final size:20
Alignment explanation
Indices: 2300813--2300871 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2300803 TTTATTCTCT
* **
2300813 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
2300833 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
2300853 TGTTACGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
2300872 AGAAACAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2301062 original size:25 final size:24
Alignment explanation
Indices: 2301008--2301062 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2300998 TGTTTATTAT
* *
2301008 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2301032 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2301058 TGTTT
1 TGTTT
2301063 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2302211 original size:18 final size:18
Alignment explanation
Indices: 2302190--2302237 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2302180 TCCACTTCGG
2302190 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2302208 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2302226 GAGCCATCACCT
1 GAGCCATCACCT
2302238 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2302825 original size:19 final size:20
Alignment explanation
Indices: 2302782--2302826 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2302772 CGTAACACGA
2302782 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
2302802 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
2302821 AAATGA
1 AAATGA
2302827 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:2302864 original size:19 final size:19
Alignment explanation
Indices: 2302810--2302892 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
2302800 GGAAATGGCT
2302810 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2302829 ATCACAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2302843 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2302862 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2302881 ATTGCAATGCGA
1 ATCGCAATGCGA
2302893 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 37 0.71
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2302953 original size:20 final size:20
Alignment explanation
Indices: 2302930--2303005 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
2302920 TTACGGTTTT
2302930 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
2302950 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
2302970 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
*
2302990 CATTTTCGCGTTGCGA
1 CATTTCCGCGTTGCGA
2303006 AAGTAAGTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.14, C:0.28, G:0.25, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2303016 original size:20 final size:20
Alignment explanation
Indices: 2302976--2303031 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2302966 TAGCCATTTC
* * *
2302976 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
2302996 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
2303016 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
2303032 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:2303023 original size:40 final size:40
Alignment explanation
Indices: 2302931--2303025 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
2302921 TACGGTTTTC
* *
2302931 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGATAGCC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCA
* * *
2302971 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCA
*
2303011 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
2303026 AAGTAAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 45 0.94
41 3 0.06
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCA
Found at i:2303416 original size:42 final size:41
Alignment explanation
Indices: 2303369--2303451 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 41
2303359 GCCCGACTCA
*
2303369 CCTATCATCACTCAAGAGTCCCCTCCAATCGTTCAAGAGGCC
1 CCTATCATCACTCAAGAGTCCCC-CCAACCGTTCAAGAGGCC
* * *
2303411 CCTATCATCCCTCAAGAGTCCCCCCCACCTTTCAAGAGGCC
1 CCTATCATCACTCAAGAGTCCCCCCAACCGTTCAAGAGGCC
2303452 ACTGTCATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 15 0.41
42 22 0.59
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.20
Consensus pattern (41 bp):
CCTATCATCACTCAAGAGTCCCCCCAACCGTTCAAGAGGCC
Found at i:2303425 original size:21 final size:21
Alignment explanation
Indices: 2303369--2303433 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2303359 GCCCGACTCA
2303369 CCTATCATCACTCAAGAGTCC
1 CCTATCATCACTCAAGAGTCC
* ** *
2303390 CCT-CCAATCGTTCAAGAGGCC
1 CCTATC-ATCACTCAAGAGTCC
*
2303411 CCTATCATCCCTCAAGAGTCC
1 CCTATCATCACTCAAGAGTCC
2303432 CC
1 CC
2303434 CCCACCTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.22
Consensus pattern (21 bp):
CCTATCATCACTCAAGAGTCC
Found at i:2305027 original size:20 final size:20
Alignment explanation
Indices: 2305002--2305040 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2304992 ATGTTGAAGG
2305002 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
2305022 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
2305041 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:2305068 original size:19 final size:19
Alignment explanation
Indices: 2305046--2305091 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2305036 GCAACGAGAG
2305046 AATCGCAATGCAAAATAAA
1 AATCGCAATGCAAAATAAA
* *
2305065 AATCGCAATGCGAAATGAA
1 AATCGCAATGCAAAATAAA
2305084 AATCGCAA
1 AATCGCAA
2305092 CGAGAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCAAAATAAA
Found at i:2305098 original size:19 final size:19
Alignment explanation
Indices: 2305058--2305098 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2305048 TCGCAATGCA
* *
2305058 AAATAAAAATCGCAATGCG
1 AAATAAAAATCGCAACGAG
*
2305077 AAATGAAAATCGCAACGAG
1 AAATAAAAATCGCAACGAG
2305096 AAA
1 AAA
2305099 ATCGCAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (19 bp):
AAATAAAAATCGCAACGAG
Found at i:2305154 original size:20 final size:20
Alignment explanation
Indices: 2305129--2305184 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2305119 TCGTATTGCG
*
2305129 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2305149 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2305169 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
2305185 TTTCCCGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2305188 original size:14 final size:14
Alignment explanation
Indices: 2305169--2305198 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2305159 TGCGATAGCC
*
2305169 ATTTTCGCGTTGCG
1 ATTTTCCCGTTGCG
2305183 ATTTTCCCGTTGCG
1 ATTTTCCCGTTGCG
2305197 AT
1 AT
2305199 AGTCAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
ATTTTCCCGTTGCG
Found at i:2305876 original size:20 final size:20
Alignment explanation
Indices: 2305730--2305883 Score: 166
Period size: 20 Copynumber: 7.7 Consensus size: 20
2305720 GATTCTGTAT
* * *
2305730 TATCTCGTTGAGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
2305750 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2305770 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2305790 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2305810 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
2305830 TATCGCGATGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2305851 TATCGCGTTGCGACAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2305871 TATCGCATTGCGA
1 TATCGCGTTGCGA
2305884 TTTTCCAAAT
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
19 2 0.02
20 100 0.85
21 13 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2305903 original size:41 final size:41
Alignment explanation
Indices: 2305771--2305904 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2305761 GAAAGTCAGA
* * *** *
2305771 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTC-AGT
1 ATCGCGTTGCGAAAGTCAGTATCGCGATGCGATTTTCAAAT
** *
2305811 ATCGCGTTGCGAAAGTCAGTATCGCGATGCGATTTTGTATT
1 ATCGCGTTGCGAAAGTCAGTATCGCGATGCGATTTTCAAAT
*
2305852 ATCGCGTTGCGACAGTCAGTATCGC-ATTGCGATTTTCCAAAT
1 ATCGCGTTGCGAAAGTCAGTATCGCGA-TGCGATTTT-CAAAT
*
2305894 -TCGCATTGCGA
1 ATCGCGTTGCGA
2305905 TTTACTTATT
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
40 32 0.41
41 45 0.57
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (41 bp):
ATCGCGTTGCGAAAGTCAGTATCGCGATGCGATTTTCAAAT
Found at i:2305917 original size:20 final size:21
Alignment explanation
Indices: 2305873--2305924 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2305863 ACAGTCAGTA
*
2305873 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2305894 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2305914 TCGCATTGCGA
1 TCGCATTGCGA
2305925 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2305966 original size:21 final size:22
Alignment explanation
Indices: 2305914--2305966 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2305904 ATTTACTTAT
2305914 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2305935 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2305956 TCGCATTGCGA
1 TCGCATTGCGA
2305967 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2309791 original size:2 final size:2
Alignment explanation
Indices: 2309784--2309815 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2309774 CTCGACTCTG
2309784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2309816 TTCAGGGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2310657 original size:23 final size:23
Alignment explanation
Indices: 2310631--2310687 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
2310621 ATCAAGTTCA
*
2310631 ATAATATATTAGGTAACACTTAT
1 ATAATATAATAGGTAACACTTAT
* *
2310654 ATAATGTAATAGGTAGCACTTAT
1 ATAATATAATAGGTAACACTTAT
*
2310677 ATAATAAAATA
1 ATAATATAATA
2310688 AGTATTTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTAACACTTAT
Found at i:2311161 original size:198 final size:199
Alignment explanation
Indices: 2310753--2311252 Score: 656
Period size: 198 Copynumber: 2.5 Consensus size: 199
2310743 AATAGGTACC
* * * *
2310753 AAACCAGTTTATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGTTTTCGA
1 AAACCAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * * *
2310818 TGTTTTTGGGATCGATACAATTT--TAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCAT
66 TATTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTACACCTCGTTGGGCAT
* *
2310881 TCATTCTGGAAAAAAGTATCGACACATATTTAAAAAGTGTCGATACATTATGTTGACATATTCTC
130 TCATTCTGGAAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTCTC
2310946 TCATA
195 TCATA
** * *
2310951 AAACTGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATCATAATTATCGGTTTCGA
1 AAACCAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
2311016 TATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTACACCTCATTTGGGCAT
66 TATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTACACCTC-GTTGGGCAT
* * * * * *
2311081 TCATTCTGGACAATAAGTATC-A-ACAAATTCCACAAGTGTCGATACATTATGTTTACATGTTTT
130 TCATTCTGGA-AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTCT
*
2311144 GT-AGT-
194 CTCA-TA
* * * *
2311149 TAACCAGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTTGA
1 AAACCAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
2311214 TATTTTTAGGG-TCGATACTTTTAGA-AAATGTATCGACAC
66 TATTTTT-GGGATCGATACTTTTA-ATAAATGTATCGACAC
2311253 ATCTTTTCAC
Statistics
Matches: 265, Mismatches: 30, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
197 3 0.01
198 165 0.62
199 69 0.26
200 19 0.07
201 9 0.03
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (199 bp):
AAACCAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTACACCTCGTTGGGCATT
CATTCTGGAAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTCTCT
CATA
Found at i:2314006 original size:19 final size:19
Alignment explanation
Indices: 2313982--2314025 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2313972 ATTCACATAC
*
2313982 AAAATTATAAATCGTATAA
1 AAAATTATAAATCATATAA
* *
2314001 AAAATTATGAATCATATAC
1 AAAATTATAAATCATATAA
2314020 AAAATT
1 AAAATT
2314026 TTCCCTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAATTATAAATCATATAA
Found at i:2316200 original size:198 final size:198
Alignment explanation
Indices: 2315549--2317333 Score: 2363
Period size: 198 Copynumber: 9.0 Consensus size: 198
2315539 ATTGAAGGAA
*
2315549 AAAAAGTATCGACACAACTTTAAACAA-TGTCGATACATTATGTAGACCTATTTTCTAATTAACC
1 AAAAAGTATCGACACAAATTTAAA-AAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACC
* * * *
2315613 GGTATATTTCTACCGGTTACATTGGAAATTTACCTATTACATTATATTTATCAGTTTCGATATTT
65 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * * *
2315678 ATGGGATCGATACTTTTTATAAATGTATTGACATTTTATTCGTACACCCCGTTAGGCATTCTTTC
130 TTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTC
*
2315743 TGGTA
194 TGGTC
* *
2315748 AAAAAGTATCGACACAACTTTAAAAAGTGTCGACACATTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * * * *
2315813 ATATATTTCTACCGGTTACATTGGAAATTTACCTATTACATTATATTTATCGCTTTCGATGTTTA
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * *
2315878 TGGGATCGATACTTTTTATAAATGTATTGACACTTTATGCGTGCACTCCGTTAGGCATTCTTTCT
131 TGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTCT
2315943 GGTC
195 GGTC
* ** * * *
2315947 AAAACGTATCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTTTCTAATTAAACG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
2316012 GTATATTTCTACCAGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * *
2316077 TGGGATCGATACAATCT-TAAATGTATCGACACTTTATTCGTACACCCCGTTGGGCATTCTTTCT
131 TGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTCT
2316141 GGTC
195 GGTC
* *
2316145 AAAACGTATCGACACAAATTTAAAAAGTGTCGATACGTTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
2316210 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTTTCGGTTTCGATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * * * * ** ** *
2316275 TGGGATCGATATCATTT-TCAGTGTATCGACACTTTATGCATGCACTCTTTTATGCATTCATTCT
131 TGGGATCGATA-CTTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTCT
*
2316339 GGAC
195 GGTC
* * * * * *
2316343 AAAAAGTATCGACACAAATTTCACAAGTGTCGATACATGATTTAGTCCTATTTTCTAATTAACTG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * * *
2316408 GTATATTTCTATCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTCAATATTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
2316473 TGGGATCGATACAATTTTA-AAA-GTATCGACACTTTATTCGTACACCCCGTTGGGCATTCTTTC
131 TGGGATCGATAC--TTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTC
2316536 TGGTC
194 TGGTC
* **
2316541 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACTA
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
2316606 GTATATTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTTTCGGTTTCGATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * ** * *
2316671 TGGGATCGATATCATTTT-T-AGTGTATCGACACTTTATGCGTGCACTCTTTTAGGCATTCATTC
131 TGGGATCGATA-C-TTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTC
*
2316734 TGGAC
194 TGGTC
* ** * * * *
2316739 AAAAAGTTTCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTCTCTAATTAACCA
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * *
2316804 ATATATTTCTACCGGTTACATTGTAAATTTACATATTACATTATATTTATCGGTTTCGATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * *
2316869 TGGGATAGATACGTTTTATAAATGTATCGACACTTTATTCATGCACCTCGTTGGGCATTCATTCT
131 TGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTCT
*
2316934 AGTC
195 GGTC
* **
2316938 AAAACA-TATCGACAAAAATTTAAAAAGCATCGATACATTATGTAGACCTATTTTCTAATTAACC
1 AAAA-AGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACC
* *
2317002 GGTATATTTCTACCGGTTACATTGGAAA-TTACCTATTACATTATAATTATC-TTATTCGATGTT
65 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGT-TTCGATGTT
* *
2317065 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCAGTTGGTCATTCAT
129 TTTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTGCACC-CCGTTGGGCATTC-T
*
2317130 TT-TGGAC
191 TTCTGGTC
* * * * *
2317137 AAAAAGTATTGATAC-AATTTAAAAAGTGTCGATATATTATATAGACATATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * *
2317201 GTATATATCTACCGGTTACATTGTAAATTTACATATTACATTATAATTATC-TTATTCGATGTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGT-TTCGATGTTT
* *
2317265 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGGCATTCATT
130 TTGGGATCGATACTTTT-ATAAATGTATCGACACTTTATTCGTGCACC-CCGTTGGGCATTCTTT
2317330 CTGG
193 CTGG
2317334 AGATTACTGA
Statistics
Matches: 1405, Mismatches: 163, Indels: 36
0.88 0.10 0.02
Matches are distributed among these distances:
197 8 0.01
198 840 0.60
199 554 0.39
200 3 0.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTATAAATGTATCGACACTTTATTCGTGCACCCCGTTGGGCATTCTTTCTG
GTC
Found at i:2318611 original size:24 final size:24
Alignment explanation
Indices: 2318584--2318647 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
2318574 AGTGGAGCCG
2318584 AAATTTATATTGAAATTCAAACTC
1 AAATTTATATTGAAATTCAAACTC
* * *
2318608 AAATTGAAATTTAAATTCAAACTC
1 AAATTTATATTGAAATTCAAACTC
*
2318632 CAATTTCATA-TGAAAT
1 AAATTT-ATATTGAAAT
2318648 AAACTTGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATTTATATTGAAATTCAAACTC
Found at i:2318615 original size:18 final size:18
Alignment explanation
Indices: 2318592--2318628 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2318582 CGAAATTTAT
2318592 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2318610 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2318628 A
1 A
2318629 CTCCAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2321229 original size:15 final size:15
Alignment explanation
Indices: 2321188--2321237 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
2321178 GAAGAATCAA
*
2321188 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
2321204 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
*
2321221 TTGGTTGAGAAAAGC
1 TTGGTTGAGAAGAGC
2321236 TT
1 TT
2321238 TGAGAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 13 0.43
16 3 0.10
17 6 0.20
18 8 0.27
ACGTcount: A:0.26, C:0.06, G:0.38, T:0.30
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:2321880 original size:20 final size:20
Alignment explanation
Indices: 2321854--2321905 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2321844 CTTCGATTTA
*
2321854 ATCGACACTTGGGTTGTTGT
1 ATCGACACTTGGGTAGTTGT
*
2321874 GTCGACACTTGGGTAGTTGT
1 ATCGACACTTGGGTAGTTGT
2321894 ATCGACACTTGG
1 ATCGACACTTGG
2321906 ATATTTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (20 bp):
ATCGACACTTGGGTAGTTGT
Found at i:2322914 original size:181 final size:182
Alignment explanation
Indices: 2322523--2323157 Score: 893
Period size: 182 Copynumber: 3.5 Consensus size: 182
2322513 TGTCATTCCG
* * *
2322523 ATATCCGGCAGCGTTTTACCGATTTTGTTATTTCGAGACCGGTTTTGTCATATTTTTATCTGTTA
1 ATATCCGGTAGCGTTTTACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTA
** * *
2322588 TATCGTTATGGATCGATATTTTTTTATAAATTATCGACACTTTATAGGTGCTATTACTGCTTCTC
66 TATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTC
* *
2322653 TTTTAAATTCCCAAAGTGTCGATACTTATATAAAAATAGCGACACTTTCAAT
131 TTTTAAATTCCCAAAGTGTCGATACTTATATTAAAATATCGACACTTTCAAT
* *
2322705 ATATCCGGTAGCGATTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTA
1 ATATCCGGTAGCGTTTTACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTA
* *
2322770 TATCGTTATGGATCAATACATTTTTATAAAGTATCGACAATTTATAGGCG-TATTACTGCTTCTC
66 TATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTC
* *
2322834 TTTGAAATTCCCAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAAT
131 TTTTAAATTCCCAAAGTGTCGATACTTATATTAAAATATCGACACTTTCAAT
* * *
2322886 ATATCCGGTAGCGTTTTACCGATTTTGTCATTTCTATACCGGTTTTGTAATATTTTTACCTGTTA
1 ATATCCGGTAGCGTTTTACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTA
* *
2322951 TATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCCATTACTGATTCTC
66 TATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTC
** * *
2323016 TTTTAAATTCCCAAAGTGTCGATACTTAT-TTCAATCTAATCGATACTTTCAAC
131 TTTTAAATTCCCAAAGTGTCGATACTTATATT-AAAAT-ATCGACACTTTCAAT
* * * * * *
2323069 ATATCCGATAGC-CTTTACCGGTTTTGTCATAATT--AAACCGGTTTTGCCATATTTTTACTTGT
1 ATATCCGGTAGCGTTTTACCGATTTTGTCAT--TTCGAGACCGGTTTTGTCATATTTTTACCTGT
* * * *
2323131 TATATTGATATGGATCTATATATTTTT
64 TATATCGTTATGGATCGATACATTTTT
2323158 TATTTGATCG
Statistics
Matches: 408, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
181 172 0.42
182 210 0.51
183 24 0.06
184 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
ATATCCGGTAGCGTTTTACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTA
TATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTC
TTTTAAATTCCCAAAGTGTCGATACTTATATTAAAATATCGACACTTTCAAT
Found at i:2323830 original size:58 final size:59
Alignment explanation
Indices: 2323757--2323935 Score: 163
Period size: 58 Copynumber: 3.1 Consensus size: 59
2323747 TTTCAGTATT
* * * * *
2323757 TAAATTTTTAATTTTTTAAAATTATATCTAATATTTTA-TTTATATTTCGTTTTAGTACT
1 TAAATCTTTAATTTTTTAAAATCATATCTAATATTTTACTTT-TATTTCATTTTAATACC
* *
2323816 TAAA-CTTTAATTTTTCT-AAATCATATTTAATA-TTTAGCTTTTTTTTCATTTTAATACC
1 TAAATCTTTAATTTTT-TAAAATCATATCTAATATTTTA-CTTTTATTTCATTTTAATACC
* * * * *
2323874 TAAATTTTTAATTTTTTCAAAATCATATCTAACA-TTTACTATTTGTTTC-GTTTAGTACC
1 TAAATCTTTAATTTTTT-AAAATCATATCTAATATTTTACT-TTTATTTCATTTTAATACC
2323933 TAA
1 TAA
2323936 TGTGTGATTT
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
57 4 0.04
58 41 0.41
59 31 0.31
60 24 0.24
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.55
Consensus pattern (59 bp):
TAAATCTTTAATTTTTTAAAATCATATCTAATATTTTACTTTTATTTCATTTTAATACC
Found at i:2329889 original size:2 final size:2
Alignment explanation
Indices: 2329882--2329907 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2329872 AAACTCACTA
2329882 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2329908 TCTGAATAGA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2335252 original size:143 final size:143
Alignment explanation
Indices: 2334926--2335501 Score: 668
Period size: 143 Copynumber: 4.0 Consensus size: 143
2334916 TAGAAAAGTC
** * * *
2334926 AACTTTTCAGTGCTTAATTAATTATCTTAAGAAATTTTTCAGTGATATATAAACTCATTTCAGCA
1 AACTTTTCAGTGCCCAATTAATTATCTTAAGCAATTTTTCAGTGATATATCAACTCATTTTAGCA
* *
2334991 AACTTTTCAGTGGTGATATATCACTTAATATCAGAAAAAACGTGCATTTCTCATAGGCAAAATGA
66 AACTTTTCAGTGATGATATATCACTTAATATCA-AAAAAACGTGCATTTCTCATAGGCAAAATAA
2335056 TGCACCATGGTAGA
130 TGCACCATGGTAGA
* * * *
2335070 AACTTTTCTGTGCCCAATTAATTATCTTAAGCAACTTTTCAATGATATATCAACTCATTTT-GAT
1 AACTTTTCAGTGCCCAATTAATTATCTTAAGCAATTTTTCAGTGATATATCAACTCATTTTAG-C
* * * *
2335134 AAACTTTTTAGTGATGATATATCACTTCATATCATAAAAACGTACATTTCTCATAGGCAAAATAA
65 AAACTTTTCAGTGATGATATATCACTTAATATCAAAAAAACGTGCATTTCTCATAGGCAAAATAA
*
2335199 TGCACCAT-GTCTGA
130 TGCACCATGGT-AGA
* * * *
2335213 AACTTTTCAGTGCCCAATTAATTACCTTCAA-TAATTTTTCAGTAATATATCAACTTATTTTAGC
1 AACTTTTCAGTGCCCAATTAATTATCTT-AAGCAATTTTTCAGTGATATATCAACTCATTTTAGC
* * *
2335277 AAACTTTTCAGCGGTGATATATCATTTAATATCAAAAAAACGTGCATTTCTCATAGGC--AA-AA
65 AAACTTTTCAGTGATGATATATCACTTAATATCAAAAAAACGTGCATTTCTCATAGGCAAAATAA
*
2335339 TGCACCATGGTAAA
130 TGCACCATGGTAGA
*** * * * * * *
2335353 AAAAATTCAATGTCCAATTAATTATCTTCAGCAACTTTTT-GGTGATATATCAACTCATTTCAAC
1 AACTTTTCAGTGCCCAATTAATTATCTTAAGCAA-TTTTTCAGTGATATATCAACTCATTTTAGC
* * * * *
2335417 AAACTTTTTAGT-AGTAATTTATCACTTCATAT--AAAAAATGTGCATTTCTCATAGGCAAAATA
65 AAACTTTTCAGTGA-TGATATATCACTTAATATCAAAAAAACGTGCATTTCTCATAGGCAAAATA
*
2335479 ATGCACCATGGAAGA
129 ATGCACCATGGTAGA
2335494 AACCTTTT
1 AA-CTTTT
2335502 AGATCATAAA
Statistics
Matches: 361, Mismatches: 59, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
138 23 0.06
139 1 0.00
140 80 0.22
141 25 0.07
142 4 0.01
143 141 0.39
144 87 0.24
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (143 bp):
AACTTTTCAGTGCCCAATTAATTATCTTAAGCAATTTTTCAGTGATATATCAACTCATTTTAGCA
AACTTTTCAGTGATGATATATCACTTAATATCAAAAAAACGTGCATTTCTCATAGGCAAAATAAT
GCACCATGGTAGA
Found at i:2335442 original size:283 final size:284
Alignment explanation
Indices: 2334926--2335488 Score: 794
Period size: 283 Copynumber: 2.0 Consensus size: 284
2334916 TAGAAAAGTC
** * *
2334926 AACTTTTCAGTGCTTAATTAATTATCTTAAGAAATTTTTCAGTGATATATAAACTCATTTCAGCA
1 AACTTTTCAGTGCCCAATTAATTACCTTAAGAAATTTTTCAGTAATATATAAACTCATTTCAGCA
*
2334991 AACTTTTCAGTGGTGATATATCACTTAATATCAGAAAAAACGTGCATTTCTCATAGGCAAAATGA
66 AACTTTTCAGCGGTGATATATCACTTAATATCAGAAAAAACGTGCATTTCTCATAGGCAAAA-GA
* *** **
2335056 TGCACCATGGTAGAAACTTTTCTGTGCCCAATTAATTATCTTAAGCAACTTTTCAATGATATATC
130 TGCACCATGGTAAAAAAAATTCAATGCCCAATTAATTATCTTAAGCAACTTTTCAATGATATATC
** * *
2335121 AACTCATTTTGATAAACTTTTTAGTGATGATATATCACTTCATATCATAAAAACGTACATTTCTC
195 AACTCATTTCAACAAACTTTTTAGTGATAATATATCACTTCATAT-A-AAAAACGTACATTTCTC
2335186 ATAGGCAAAATAATGCACCATGTCTGA
258 ATAGGCAAAATAATGCACCATGTCTGA
* * * *
2335213 AACTTTTCAGTGCCCAATTAATTACCTTCAA-TAATTTTTCAGTAATATATCAACTTATTTTAGC
1 AACTTTTCAGTGCCCAATTAATTACCTT-AAGAAATTTTTCAGTAATATATAAACTCATTTCAGC
*
2335277 AAACTTTTCAGCGGTGATATATCATTTAATATCA-AAAAAACGTGCATTTCTCATAGGC-AAA-A
65 AAACTTTTCAGCGGTGATATATCACTTAATATCAGAAAAAACGTGCATTTCTCATAGGCAAAAGA
* * ***
2335339 TGCACCATGGTAAAAAAAATTCAATGTCCAATTAATTATCTTCAGCAACTTTTTGGTGATATATC
130 TGCACCATGGTAAAAAAAATTCAATGCCCAATTAATTATCTTAAGCAACTTTTCAATGATATATC
* * *
2335404 AACTCATTTCAACAAACTTTTTAGT-AGTAATTTATCACTTCATATAAAAAATGTGCATTTCTCA
195 AACTCATTTCAACAAACTTTTTAGTGA-TAATATATCACTTCATATAAAAAACGTACATTTCTCA
2335468 TAGGCAAAATAATGCACCATG
259 TAGGCAAAATAATGCACCATG
2335489 GAAGAAACCT
Statistics
Matches: 246, Mismatches: 28, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
281 37 0.15
282 2 0.01
283 93 0.38
285 3 0.01
286 24 0.10
287 85 0.35
288 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (284 bp):
AACTTTTCAGTGCCCAATTAATTACCTTAAGAAATTTTTCAGTAATATATAAACTCATTTCAGCA
AACTTTTCAGCGGTGATATATCACTTAATATCAGAAAAAACGTGCATTTCTCATAGGCAAAAGAT
GCACCATGGTAAAAAAAATTCAATGCCCAATTAATTATCTTAAGCAACTTTTCAATGATATATCA
ACTCATTTCAACAAACTTTTTAGTGATAATATATCACTTCATATAAAAAACGTACATTTCTCATA
GGCAAAATAATGCACCATGTCTGA
Found at i:2337898 original size:20 final size:20
Alignment explanation
Indices: 2337860--2337900 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2337850 TTTATTTAAC
***
2337860 TTATAATAGAAATTTTATTT
1 TTATAATAGAAAAAATATTT
2337880 TTATAATAGAAAAAATATTT
1 TTATAATAGAAAAAATATTT
2337900 T
1 T
2337901 ATAGTTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTATAATAGAAAAAATATTT
Found at i:2345802 original size:14 final size:14
Alignment explanation
Indices: 2345783--2345830 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2345773 TCAACCCGGA
* *
2345783 CTGAGTCATCTCTT
1 CTGAGTCAACTCGT
*
2345797 CTGAGTTAACTCGT
1 CTGAGTCAACTCGT
*
2345811 CAGAGTCAACTCGT
1 CTGAGTCAACTCGT
2345825 CTGAGT
1 CTGAGT
2345831 TAACCTGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:2345855 original size:13 final size:13
Alignment explanation
Indices: 2345837--2345862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2345827 GAGTTAACCT
2345837 GTTAACTTTGACC
1 GTTAACTTTGACC
2345850 GTTAACTTTGACC
1 GTTAACTTTGACC
2345863 CAAAAATTCA
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:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
GTTAACTTTGACC
Found at i:2347914 original size:31 final size:30
Alignment explanation
Indices: 2347876--2347979 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 30
2347866 TAAGACAACC
2347876 CTTGGGTAGGCTCTGTGGCCCTGAGATCTTT
1 CTTGGGTAGGC-CTGTGGCCCTGAGATCTTT
* *
2347907 CTTGGGTAGGCCTTGTGACCCCGAGAT-TCTT
1 CTTGGGTAGGCC-TGTGGCCCTGAGATCT-TT
* *
2347938 CTTGGGTAGGCCTCGTAGCCCTGAGAACTTT
1 CTTGGGTAGGCCT-GTGGCCCTGAGATCTTT
2347969 CTTGGGTAGGC
1 CTTGGGTAGGC
2347980 TTTCAGGCCC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.05
31 59 0.94
32 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (30 bp):
CTTGGGTAGGCCTGTGGCCCTGAGATCTTT
Found at i:2349851 original size:29 final size:30
Alignment explanation
Indices: 2349794--2349852 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
2349784 GCGAGCAGCT
*
2349794 TGATTGAATAAATTAAATAGTTAAGTGGTA
1 TGATTGAATAAATTAAATAGTCAAGTGGTA
2349824 TGATTG-ATAAAATTAAA-AGATCAA-TGGTA
1 TGATTGAAT-AAATTAAATAG-TCAAGTGGTA
2349853 GAAGTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.34
Consensus pattern (30 bp):
TGATTGAATAAATTAAATAGTCAAGTGGTA
Found at i:2356570 original size:105 final size:105
Alignment explanation
Indices: 2356257--2356911 Score: 940
Period size: 105 Copynumber: 6.2 Consensus size: 105
2356247 GTCAATCTGT
* * * ** * *
2356257 TTGTGAAGTTGGAATTGGCTATGGAA-TTGAGAAATTGTTTGCTGACAGTCGGTC-GTCCCTTAG
1 TTGTGAAGTTGAAATTGGCTCT-GAATTTGAGAAA-TGTTTGTTGACAACCAG-CGGTCCCTTCG
* * * * * * *
2356320 -CTGGGAAGTCGAGCTTGTGCTGTCTTGAGTTCAATATCCTTCG
63 TC-GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * **
2356363 CTGTGAAGTTGAAATTGGCTCTGACA-TTGAGAAGTTGTTTGTTGACAGTCAGCGGTCCCTTCGT
1 TTGTGAAGTTGAAATTGGCTCTGA-ATTTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGT
* *** * * *
2356427 GGTGAAGTTGAACTTGTACTGTCTTGAGTACAAAATCCTTCG
64 CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * *
2356469 TTGTGAAGTTGAAATTGGCTCTGAGTTGGAGAAATGTTTGGTGAAAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
2356534 TGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
2356574 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
2356639 TGAAGTTGAACTTGCGTTGTTTGGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
2356679 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
2356744 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
2356784 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
2356849 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
2356889 TTGTGAAGTTGAAATTGGCTCTG
1 TTGTGAAGTTGAAATTGGCTCTG
2356912 GGTAAAACCT
Statistics
Matches: 506, Mismatches: 38, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
105 392 0.77
106 114 0.23
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
Found at i:2357687 original size:12 final size:12
Alignment explanation
Indices: 2357672--2357696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2357662 TTTTCTCTTA
2357672 TTTTTTCCTTTT
1 TTTTTTCCTTTT
2357684 TTTTTTCCTTTT
1 TTTTTTCCTTTT
2357696 T
1 T
2357697 CAATTTAGGG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCCTTTT
Found at i:2357752 original size:1 final size:1
Alignment explanation
Indices: 2357742--2357787 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
2357732 CGTTCTTCTC
* * * *
2357742 TTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2357788 CAACTTAGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:2357755 original size:8 final size:8
Alignment explanation
Indices: 2357742--2357787 Score: 67
Period size: 8 Copynumber: 5.6 Consensus size: 8
2357732 CGTTCTTCTC
2357742 TTTTTGTT
1 TTTTTGTT
2357750 TTTTTGTTTT
1 TTTTTG--TT
2357760 TTTTTGTT
1 TTTTTGTT
2357768 TTTTTGTT
1 TTTTTGTT
2357776 TTTTT-TT
1 TTTTTGTT
2357783 TTTTT
1 TTTTT
2357788 CAACTTAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.19
8 21 0.58
10 8 0.22
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (8 bp):
TTTTTGTT
Found at i:2357765 original size:18 final size:18
Alignment explanation
Indices: 2357742--2357787 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2357732 CGTTCTTCTC
2357742 TTTTTGTTTTTTTGTTTT
1 TTTTTGTTTTTTTGTTTT
2357760 TTTTTGTTTTTTTGTTTT
1 TTTTTGTTTTTTTGTTTT
2357778 TTTTT-TTTTT
1 TTTTTGTTTTT
2357788 CAACTTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (18 bp):
TTTTTGTTTTTTTGTTTT
Found at i:2368494 original size:10 final size:10
Alignment explanation
Indices: 2368479--2368534 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
2368469 ATAAAGTAAT
2368479 AATAAAAATA
1 AATAAAAATA
*
2368489 AATAAATATA
1 AATAAAAATA
*
2368499 ATTATAATAA-A
1 A--ATAAAAATA
2368510 AATAAAAATA
1 AATAAAAATA
**
2368520 AATAGGAATA
1 AATAAAAATA
2368530 AATAA
1 AATAA
2368535 TAAAAATAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
9 6 0.17
10 23 0.64
11 2 0.06
12 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (10 bp):
AATAAAAATA
Found at i:2368509 original size:25 final size:27
Alignment explanation
Indices: 2368476--2368542 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 27
2368466 TATATAAAGT
*
2368476 AATAATAAAAATAAATAAATA-TAAT-
1 AATAATAAAAATAAATAAATAGGAATA
*
2368501 TATAATAAAAATAAAAATAAATAGGAATA
1 AATAATAAAAAT--AAATAAATAGGAATA
2368530 AATAATAAAAATA
1 AATAATAAAAATA
2368543 GCAAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 11 0.31
27 10 0.29
28 3 0.09
29 11 0.31
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (27 bp):
AATAATAAAAATAAATAAATAGGAATA
Found at i:2370868 original size:23 final size:24
Alignment explanation
Indices: 2370837--2370920 Score: 86
Period size: 23 Copynumber: 3.6 Consensus size: 24
2370827 AATTGGTGTT
* *
2370837 GGAAGTCAAAATTGGAGGTTTTGG
1 GGAAGTCAAAATTGGAGGCTTAGG
2370861 GGAA-TCAAAATTGGAGGCTTAGG
1 GGAAGTCAAAATTGGAGGCTTAGG
* *
2370884 AGAAGTCAAAATTAGG-GGCTT--T
1 GGAAGTCAAAATT-GGAGGCTTAGG
*
2370906 GGAAGTCATAATTGG
1 GGAAGTCAAAATTGG
2370921 GGGTACCGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.04
22 11 0.21
23 20 0.38
24 17 0.33
25 2 0.04
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.26
Consensus pattern (24 bp):
GGAAGTCAAAATTGGAGGCTTAGG
Found at i:2374050 original size:24 final size:24
Alignment explanation
Indices: 2373984--2374054 Score: 119
Period size: 23 Copynumber: 3.0 Consensus size: 24
2373974 GGAGATTGTT
2373984 GGAAGTCAAAATTGGAGGCTTTGG
1 GGAAGTCAAAATTGGAGGCTTTGG
2374008 GGAA-TCAAAATTGGAGGCTTTGG
1 GGAAGTCAAAATTGGAGGCTTTGG
2374031 GGAAGTCAAAATTAGG-GGCTTTGG
1 GGAAGTCAAAATT-GGAGGCTTTGG
2374055 AATTCATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
23 23 0.51
24 20 0.44
25 2 0.04
ACGTcount: A:0.30, C:0.08, G:0.37, T:0.25
Consensus pattern (24 bp):
GGAAGTCAAAATTGGAGGCTTTGG
Found at i:2377276 original size:16 final size:17
Alignment explanation
Indices: 2377257--2377300 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2377247 TATAAATTAT
2377257 AATTTTA-ATAAT-TCAA
1 AATTTTAGATAATCT-AA
2377273 AATTTTAGAT-ATCTAA
1 AATTTTAGATAATCTAA
2377289 AATTTTAGATAA
1 AATTTTAGATAA
2377301 AAATATCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
AATTTTAGATAATCTAA
Found at i:2383183 original size:16 final size:16
Alignment explanation
Indices: 2383151--2383198 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
2383141 TAAATTGAAC
2383151 TGATATTTACC-GACT
1 TGATATTTACCTGACT
2383166 TGATATTTACCTGACT
1 TGATATTTACCTGACT
2383182 TGATATTTACCTG-CT
1 TGATATTTACCTGACT
2383197 TG
1 TG
2383199 TAGTATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 15 0.47
16 17 0.53
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.44
Consensus pattern (16 bp):
TGATATTTACCTGACT
Found at i:2383257 original size:2 final size:2
Alignment explanation
Indices: 2383250--2383291 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2383240 TTTCTTCCCG
2383250 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2383290 TA
1 TA
2383292 CAAAACCCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2383432 original size:43 final size:43
Alignment explanation
Indices: 2383371--2383462 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
2383361 GAACAGATAA
*
2383371 CACAACAACTACGGTTTCACATATCATCTCAGCCGTCAGCATC
1 CACAACAACTACGGTTTCACATATCATCTCAGCCGTCAACATC
*
2383414 CACAACAACTACGGTTTCACATATCATCTCAGTCGTCAACATC
1 CACAACAACTACGGTTTCACATATCATCTCAGCCGTCAACATC
2383457 CACAAC
1 CACAAC
2383463 CATTGGATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.23
Consensus pattern (43 bp):
CACAACAACTACGGTTTCACATATCATCTCAGCCGTCAACATC
Found at i:2388168 original size:137 final size:137
Alignment explanation
Indices: 2387920--2388190 Score: 386
Period size: 137 Copynumber: 2.0 Consensus size: 137
2387910 ACCTCCCCAG
* * *
2387920 AGAAGAAAACCAAATGGAAGATGCCTTGGTAACTTTGGCAGTCGCATTTAAGATAGATGAGTATT
1 AGAAGAAAACAAAATGGAAGATGCCTTGGTAACTTTGGCAGTCACATTTAAGATAGATGAGCATT
* * * *
2387985 CGAGTATAATACCTATTGAAATGCAGACCTATGAATATCCAGCTCATTGTTTTAACATTGAAGAA
66 CGAGCATAATACCTATTGAAATGCAGACCTATGAATATCCAGCTCATTATTTCAACATTAAAGAA
2388050 GAAGCAT
131 GAAGCAT
* * *
2388057 AGAAGAAAATAAAATGGCAGATGCCTTGGTAACTTTGGCAG-CTACATTTAAGATAGCTGAGCAT
1 AGAAGAAAACAAAATGGAAGATGCCTTGGTAACTTTGGCAGTC-ACATTTAAGATAGATGAGCAT
*
2388121 TCGAGCATGATACCTATTGAAATGCA-AGCCTATGAATATCCTA-CTCATTATTTCAACATTAAA
65 TCGAGCATAATACCTATTGAAATGCAGA-CCTATGAATATCC-AGCTCATTATTTCAACATTAAA
*
2388184 TAAGAAG
128 GAAGAAG
2388191 AGGTGAAACC
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
136 2 0.02
137 116 0.97
138 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (137 bp):
AGAAGAAAACAAAATGGAAGATGCCTTGGTAACTTTGGCAGTCACATTTAAGATAGATGAGCATT
CGAGCATAATACCTATTGAAATGCAGACCTATGAATATCCAGCTCATTATTTCAACATTAAAGAA
GAAGCAT
Found at i:2391226 original size:62 final size:62
Alignment explanation
Indices: 2391129--2391292 Score: 233
Period size: 62 Copynumber: 2.6 Consensus size: 62
2391119 TTCCCCTCAC
*
2391129 AGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCCCAGTA-G
1 AGTCAATCCTTGACTTTCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCCCA-TAGG
* * *
2391191 AGTCAAAT-TTTGACTTTCTCGTGAAGAGAAGTCAACATTTATTATTTTTGACTCCCCATAGG
1 AGTC-AATCCTTGACTTTCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCCCATAGG
* * *
2391253 AGTCAATCCTTGATTTTCTCGTAAAGAGAAGTCAATCTTT
1 AGTCAATCCTTGACTTTCTCGTGAAGAGAAGTCAACCTTT
2391293 TTAATTTGAT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
61 5 0.06
62 82 0.91
63 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (62 bp):
AGTCAATCCTTGACTTTCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCCCATAGG
Found at i:2391477 original size:90 final size:90
Alignment explanation
Indices: 2391324--2391624 Score: 426
Period size: 90 Copynumber: 3.4 Consensus size: 90
2391314 AAATTAATTC
*
2391324 AGATTTGGTCTCCACGGAAGAGTAGTGGAAGCGAATCAACCTCGAGTCTGATCTTCATGGAAGAG
1 AGATTTGGTCTCCACGGAAGAGTAGTGGAAGCGAATCAACCTTGAGTCTGATCTTCATGGAAGAG
2391389 TAGTGGAACATATTCTTCTTATTTT
66 TAGTGGAACATATTCTTCTTATTTT
* * *
2391414 AGATTTGGTCTCCACAGAAGAGTAGTGGAAGTGAATCAACCTTGAGTCTGATCTTCACGGAAGAG
1 AGATTTGGTCTCCACGGAAGAGTAGTGGAAGCGAATCAACCTTGAGTCTGATCTTCATGGAAGAG
* * *
2391479 TAGTGGAACATATTCTTTTTAATTC
66 TAGTGGAACATATTCTTCTTATTTT
* * * * *
2391504 AAATTTGGTCTCCACGGAAGAGTAGTGGAAGCAAATTAA-TTTCAAGTCTGATCTTCATGGAAGA
1 AGATTTGGTCTCCACGGAAGAGTAGTGGAAGCGAATCAACCTT-GAGTCTGATCTTCATGGAAGA
*
2391568 GTAGTGGAACAGATTCTTCTTATTTT
65 GTAGTGGAACATATTCTTCTTATTTT
* * **
2391594 AGATTTAGCCTTAACGGAAGAGTAGT-GAAGC
1 AGATTTGGTCTCCACGGAAGAGTAGTGGAAGC
2391625 AAAGCAATCT
Statistics
Matches: 186, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
89 7 0.04
90 179 0.96
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (90 bp):
AGATTTGGTCTCCACGGAAGAGTAGTGGAAGCGAATCAACCTTGAGTCTGATCTTCATGGAAGAG
TAGTGGAACATATTCTTCTTATTTT
Found at i:2391486 original size:43 final size:43
Alignment explanation
Indices: 2391336--2391486 Score: 133
Period size: 43 Copynumber: 3.4 Consensus size: 43
2391326 ATTTGGTCTC
* *
2391336 CACGGAAGAGTAGTGGAAGCGAATCAACCTCGAGTCTGATCTT
1 CACGGAAGAGTAGTGGAAGTGAATCAACCTTGAGTCTGATCTT
* * * ** * * * * *
2391379 CATGGAAGAGTAGTGGAACAT-ATTCTTCTTATTTTAGATTTGGTCTC
1 CACGGAAGAGTAGTGGAA-GTGAATCAAC---CTTGAG-TCTGATCTT
*
2391426 CACAGAAGAGTAGTGGAAGTGAATCAACCTTGAGTCTGATCTT
1 CACGGAAGAGTAGTGGAAGTGAATCAACCTTGAGTCTGATCTT
2391469 CACGGAAGAGTAGTGGAA
1 CACGGAAGAGTAGTGGAA
2391487 CATATTCTTT
Statistics
Matches: 78, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
43 44 0.56
44 4 0.05
46 4 0.05
47 26 0.33
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (43 bp):
CACGGAAGAGTAGTGGAAGTGAATCAACCTTGAGTCTGATCTT
Found at i:2391654 original size:36 final size:36
Alignment explanation
Indices: 2391602--2391694 Score: 125
Period size: 36 Copynumber: 2.6 Consensus size: 36
2391592 TTAGATTTAG
*
2391602 CCTTAACGGAAGAGTAGTGAAGCAAAGCAATCT-TAA
1 CCTTCACGGAAGAGTAGTGAAGCAAAGCAAT-TATAA
* *
2391638 CCTTCACGGAAGAGTAGTAAAGTAAAGCAATTATAA
1 CCTTCACGGAAGAGTAGTGAAGCAAAGCAATTATAA
* *
2391674 ACTTCACAGAAGAGTAGTGAA
1 CCTTCACGGAAGAGTAGTGAA
2391695 CCAAGATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 1 0.02
36 49 0.98
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (36 bp):
CCTTCACGGAAGAGTAGTGAAGCAAAGCAATTATAA
Found at i:2392126 original size:137 final size:136
Alignment explanation
Indices: 2391825--2392253 Score: 538
Period size: 137 Copynumber: 3.1 Consensus size: 136
2391815 GTGAACCAGC
*
2391825 ATCATCCTTAGATAGACAAAACTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTTAAAG
1 ATCATCCTTAGATAGCCAAAACTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTTAAAG
* ** * *
2391890 ATGATCAGACGTTTTTCATCACAAAGGAATAATGTCATCCACCGATCAGAACTCCTCATCACGAA
66 ATGGTCAGACG-TCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAA
*
2391955 GGA-ACAA
130 GGAGA-TA
* * *
2391962 CATCATCCTTAAATAGCCAAAACTCCTCATCACAAAGGAACCGTGTTATCTCAAATACCATTAAA
1 -ATCATCCTTAGATAGCCAAAACTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTTAAA
*
2392027 GATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGTA
65 GATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAA
*
2392092 GGAGTTGA
130 GGAGAT-A
* * * ** * * * *
2392100 GTCATCCTTAGATAGTCAGATGTCCTCATCACGAAGGAAACATTTTATCTCAAATATCTTTAAAG
1 ATCATCCTTAGATAGCCAAAACTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTTAAAG
* * * * * * *
2392165 ATGGCCAGACATCCTCATCACGAAGGAACAATGT-ATCCATCTATCAGAAGTCCTCAACAAGAAG
66 ATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAG
*
2392229 GAGCATC
131 GAG-ATA
2392236 ATCATCCTTAGATAGCCA
1 ATCATCCTTAGATAGCCA
2392254 GATGTCCTCA
Statistics
Matches: 252, Mismatches: 36, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
136 43 0.17
137 137 0.54
138 72 0.29
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (136 bp):
ATCATCCTTAGATAGCCAAAACTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTTAAAG
ATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAG
GAGATA
Found at i:2399444 original size:216 final size:209
Alignment explanation
Indices: 2399066--2399545 Score: 834
Period size: 216 Copynumber: 2.3 Consensus size: 209
2399056 ATTTAAGAAT
*
2399066 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATTAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
2399131 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAATGTACTAAATTATAC
66 AGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
2399196 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAATAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAG-----A--AATAAGTATGGATCAATTTCAGA
2399261 TGCAAATAAAATTTGGAGGAC
189 TGCAAATAAAATTTGGAGGAC
*
2399282 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACGCATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
2399347 AGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 AGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
2399412 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTATGGGTCAATTTCATATGCAAAT
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTATGGATCAATTTCAGATGCAAAT
2399477 AAAATTTGGAGGAC
196 AAAATTTGGAGGAC
2399491 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
2399546 AAAGGGATCA
Statistics
Matches: 256, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
209 96 0.38
211 1 0.00
216 159 0.62
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (209 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
AGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTATGGATCAATTTCAGATGCAAAT
AAAATTTGGAGGAC
Found at i:2399635 original size:2 final size:2
Alignment explanation
Indices: 2399628--2399936 Score: 62
Period size: 2 Copynumber: 153.5 Consensus size: 2
2399618 AAAACAACTA
* * *
2399628 AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT AT AT AA AGT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T
* * *
2399672 AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * * * *
2399714 GT AT AA ACT AT AT AT ACC AT GT AT AA ACT AT A- AT ACT AT AT AGT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT AT A-T AT AT A-T
* * * *
2399758 TT AT AT AT GA- ACT AT -T GA- ACT AT AT AG AA ACT AT AT AGT TT
1 AT AT AT AT -AT A-T AT AT -AT A-T AT AT AT AT A-T AT AT A-T AT
* * *
2399799 AT AT AT AA AT -T AT AT AT GA- AT -T AT AT AT AA ACT AT AC A- AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
2399839 TT AT AT TT AT AT AT -T AT GT AT A- AT -T AT AA AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2399877 AT -T AT AT AA AT -T AT AT AGT TT AT -T A- AT AT AA ACT AT AT AGT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T
*
2399918 TT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2399937 GTTTATAGGG
Statistics
Matches: 217, Mismatches: 50, Indels: 80
0.63 0.14 0.23
Matches are distributed among these distances:
1 19 0.09
2 177 0.82
3 21 0.10
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2399688 original size:22 final size:22
Alignment explanation
Indices: 2399629--2399943 Score: 109
Period size: 22 Copynumber: 14.6 Consensus size: 22
2399619 AAACAACTAA
*
2399629 TATATA-TATATATAATATAAAC
1 TATATAGTTTATAT-ATATAAAC
*
2399651 TATATAG-TT-TATATATAAAG
1 TATATAGTTTATATATATAAAC
2399671 TATAT-GTATTATATATATAAAC
1 TATATAGT-TTATATATATAAAC
* **
2399693 TATATAGTTTATATATATTATG
1 TATATAGTTTATATATATAAAC
* * *
2399715 TATAAACTATATATACCATGTATAAAC
1 TATATAGT-T-TAT---ATATATAAAC
* *
2399742 TATAATACTATATAGTTTATATATGAAC
1 TAT-ATAGT-T-TA---TATATATAAAC
* *
2399770 TAT-T-G--AACTATATAGAAAC
1 TATATAGTTTA-TATATATAAAC
*
2399789 TATATAG-TT-TATATATAAAT
1 TATATAGTTTATATATATAAAC
**
2399809 TATATA-TGAATTATATATAAAC
1 TATATAGTTTA-TATATATAAAC
* * * *
2399831 TATACAATTTATATTTATATA-
1 TATATAGTTTATATATATAAAC
*
2399852 T-TAT-GTATA-AT-TATAAA-
1 TATATAGTTTATATATATAAAC
* *
2399869 TAATATA-TAT-TATAT--AAAT
1 T-ATATAGTTTATATATATAAAC
2399888 TATATAGTTTAT-TAATATAAAC
1 TATATAGTTTATAT-ATATAAAC
*
2399910 TATATAGTTTATATATATATA-
1 TATATAGTTTATATATATAAAC
2399931 TATATAGTTTATA
1 TATATAGTTTATA
2399944 GGGTTTAGGG
Statistics
Matches: 222, Mismatches: 38, Indels: 67
0.68 0.12 0.20
Matches are distributed among these distances:
17 6 0.03
18 10 0.05
19 28 0.13
20 34 0.15
21 21 0.09
22 83 0.37
23 6 0.03
24 3 0.01
26 1 0.00
27 9 0.04
28 20 0.09
31 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (22 bp):
TATATAGTTTATATATATAAAC
Found at i:2399696 original size:29 final size:29
Alignment explanation
Indices: 2399664--2399725 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2399654 ATAGTTTATA
*
2399664 TATAAAGTATATGTAT-TATATATATAAAC
1 TATAAAGTATATATATAT-TATATATAAAC
* * *
2399693 TATATAGTTTATATATATTATGTATAAAC
1 TATAAAGTATATATATATTATATATAAAC
2399722 TATA
1 TATA
2399726 TATACCATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (29 bp):
TATAAAGTATATATATATTATATATAAAC
Found at i:2399814 original size:13 final size:11
Alignment explanation
Indices: 2399797--2399915 Score: 66
Period size: 11 Copynumber: 10.6 Consensus size: 11
2399787 ACTATATAGT
2399797 TTATATATAAA
1 TTATATATAAA
*
2399808 TTATATATGAA
1 TTATATATAAA
2399819 TTATATATAAA
1 TTATATATAAA
* * *
2399830 --CTATACAAT
1 TTATATATAAA
*
2399839 TTATATTTATATA
1 TTATA--TATAAA
*
2399852 TTATGTAT-AA
1 TTATATATAAA
*
2399862 TTATAAATAATA
1 TTATATATAA-A
2399874 TATATTATATAAA
1 T-TA-TATATAAA
**
2399887 TTATATAGTTTA
1 TTATATA-TAAA
2399899 TTA-ATATAAA
1 TTATATATAAA
*
2399909 CTATATA
1 TTATATA
2399916 GTTTATATAT
Statistics
Matches: 79, Mismatches: 19, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
9 6 0.08
10 11 0.14
11 36 0.46
12 9 0.11
13 11 0.14
14 6 0.08
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TTATATATAAA
Found at i:2399860 original size:17 final size:17
Alignment explanation
Indices: 2399840--2399893 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2399830 CTATACAATT
* *
2399840 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
2399857 TATAATTATAAATAATA
1 TATATTTATAAATTATA
2399874 TATATTATATAAATTATA
1 TATATT-TATAAATTATA
2399892 TA
1 TA
2399894 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:2399892 original size:138 final size:137
Alignment explanation
Indices: 2399647--2399899 Score: 318
Period size: 138 Copynumber: 1.8 Consensus size: 137
2399637 TATATAATAT
* * *
2399647 AAACTATATAGTTTATATATAAAGTATATGTATTATATATATAAACTATATAGTTTATATATATT
1 AAACTATATAGTTTATATATAAAGTATATATAATATATATATAAACTATAAAGTTTATATATATT
* *
2399712 ATGTATAAACTATATATACCATGTATAAACTATAATACTATATAGTTTATATATGAACTATTGAA
66 ATGTATAAACTATAAATA-CATATATAAACTATAATACTATATAGTTTATATATGAACTATTGAA
2399777 CTATATAG
130 CTATATAG
* *
2399785 AAACTATATAGTTTATATATAAATTATATATGAAT-TATATATAAACTATACAATTTATATTTAT
1 AAACTATATAGTTTATATATAAAGTATATAT-AATATATATATAAACTATA-AAGTT-TA--TAT
* * *
2399849 ATATTATGTAT-AATTATAAATA-ATATATATTA-TATAA-ATTATATAGTTTAT
61 ATATTATGTATAAACTATAAATACATATATA-AACTATAATACTATATAGTTTAT
2399900 TAATATAAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
138 57 0.58
139 16 0.16
140 3 0.03
141 9 0.09
142 14 0.14
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (137 bp):
AAACTATATAGTTTATATATAAAGTATATATAATATATATATAAACTATAAAGTTTATATATATT
ATGTATAAACTATAAATACATATATAAACTATAATACTATATAGTTTATATATGAACTATTGAAC
TATATAG
Found at i:2399975 original size:6 final size:6
Alignment explanation
Indices: 2399961--2399997 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
2399951 GGGATTAGGG
* *
2399961 TTTATA TTAATA TTAATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
2399998 AAACTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:2400065 original size:22 final size:21
Alignment explanation
Indices: 2400007--2400071 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
2399997 TAAACTACAT
*
2400007 ACTATAATTTATATGTATAT-
1 ACTATAATTTATATTTATATA
* *
2400027 ACCATATTTATACTATTTATATAA
1 ACTATAATT-TA-TATTTATAT-A
*
2400051 ACTATAATTTATATTTGTATA
1 ACTATAATTTATATTTATATA
2400072 TTATATATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 7 0.20
21 3 0.09
22 16 0.46
23 2 0.06
24 7 0.20
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (21 bp):
ACTATAATTTATATTTATATA
Found at i:2400065 original size:31 final size:31
Alignment explanation
Indices: 2400030--2400092 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2400020 TGTATATACC
2400030 ATATTTATACTATT-TATATAAACTATAATTT
1 ATATTTATA-TATTATATATAAACTATAATTT
* * *
2400061 ATATTTGTATATTATATATGAACTATAGTTT
1 ATATTTATATATTATATATAAACTATAATTT
2400092 A
1 A
2400093 CATATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (31 bp):
ATATTTATATATTATATATAAACTATAATTT
Found at i:2400086 original size:44 final size:44
Alignment explanation
Indices: 2400007--2400151 Score: 123
Period size: 44 Copynumber: 3.1 Consensus size: 44
2399997 TAAACTACAT
* * ** *
2400007 ACTATAATTTATATGTATATACCATAT-TTATACTATTTATATAA
1 ACTATAATTTATATTTGTATATTATATATGA-ACTATTTATATAA
2400051 ACTATAATTTATATTTGTATATTATATATGAACTATAGTTTACATATAA
1 ACTATAATTTATATTTGTATATTATATATGAAC--TA-TTT--ATATAA
* * *
2400100 ACTATATAGTTTATAGTTG-ATATTTACATATGAACTATATATATAA
1 ACTATA-A-TTTATATTTGTATA-TTATATATGAACTATTTATATAA
2400146 ACTATA
1 ACTATA
2400152 TAGTTTACAT
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
44 25 0.30
45 2 0.02
46 14 0.17
47 3 0.04
48 2 0.02
49 14 0.17
50 4 0.05
51 20 0.24
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (44 bp):
ACTATAATTTATATTTGTATATTATATATGAACTATTTATATAA
Found at i:2400159 original size:33 final size:32
Alignment explanation
Indices: 2400038--2400184 Score: 122
Period size: 33 Copynumber: 4.6 Consensus size: 32
2400028 CCATATTTAT
* * * *
2400038 ACTATTTATATAAACTATA-ATTTATATTTGT
1 ACTATATATATAAACTATATATTTACATATGA
* * *
2400069 A-TATTATATATGAACTATA-GTTTACATATAA
1 ACTA-TATATATAAACTATATATTTACATATGA
* * *
2400100 ACTATATAGTTTATAGT-TGATATTTACATATGA
1 ACTATATA-TATAAACTAT-ATATTTACATATGA
2400133 ACTATATATATAAACTATATAGTTTACATATGA
1 ACTATATATATAAACTATATA-TTTACATATGA
* *
2400166 CCTATATATATATACTATA
1 ACTATATATATAAACTATA
2400185 GTTGATATTT
Statistics
Matches: 91, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
30 2 0.02
31 27 0.30
32 15 0.16
33 47 0.52
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (32 bp):
ACTATATATATAAACTATATATTTACATATGA
Found at i:2400175 original size:2 final size:2
Alignment explanation
Indices: 2400168--2400291 Score: 54
Period size: 2 Copynumber: 57.0 Consensus size: 2
2400158 ACATATGACC
* *
2400168 TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA GTT TA
1 TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA -TA TA
** * * *
2400212 TA TA TGA CC TA TA TA TA TA TA CTA TA GTT TG TA TT TA TA TA CTA
1 TA TA T-A TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA
*
2400256 TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA GTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA
2400292 ATTTACATAT
Statistics
Matches: 93, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
1 2 0.02
2 73 0.78
3 18 0.19
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2400192 original size:20 final size:19
Alignment explanation
Indices: 2400169--2400278 Score: 63
Period size: 20 Copynumber: 5.9 Consensus size: 19
2400159 CATATGACCT
2400169 ATATATATATACTATAGTTG
1 ATATATATATACTATA-TTG
* *
2400189 ATATTTATATACTATATAG
1 ATATATATATACTATATTG
**
2400208 -T-T-TATATA-TGA-CCT-
1 ATATATATATACT-ATATTG
2400222 ATATATATATACTATAGTTTG
1 ATATATATATACTATA--TTG
* *
2400243 -TATTTATATACTATATATT
1 ATATATATATACTATAT-TG
*
2400262 ATATATATAAACTATAT
1 ATATATATATACTATAT
2400279 ATACTATAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
15 2 0.03
16 8 0.12
17 8 0.12
18 3 0.04
19 3 0.04
20 44 0.65
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATATATATACTATATTG
Found at i:2400203 original size:66 final size:64
Alignment explanation
Indices: 2400038--2400206 Score: 161
Period size: 66 Copynumber: 2.6 Consensus size: 64
2400028 CCATATTTAT
* * * * * *
2400038 ACTATTTATATAAACTATAATTTATATTTGTATA-T-TATATATGAACTATAGTTTACATATAA
1 ACTATATATATATACTATAGTTGATATTTATATACTATATATATAAACTATAGTTTACATATAA
*
2400100 ACTATATA-GT-T--TATAGTTGATATTTACATATGAACTATATATATAAACTATATAGTTTACA
1 ACTATATATATATACTATAGTTGATATTT--ATAT--ACTATATATATAAAC--TATAGTTTACA
*
2400161 TATGA
60 TATAA
*
2400166 CCTATATATATATACTATAGTTGATATTTATATACTATATA
1 ACTATATATATATACTATAGTTGATATTTATATACTATATA
2400207 GTTTATATAT
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
58 12 0.14
60 3 0.04
61 1 0.01
62 8 0.09
63 1 0.01
64 10 0.12
66 30 0.35
67 1 0.01
68 5 0.06
70 14 0.16
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (64 bp):
ACTATATATATATACTATAGTTGATATTTATATACTATATATATAAACTATAGTTTACATATAA
Found at i:2400204 original size:33 final size:34
Alignment explanation
Indices: 2400111--2400206 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 34
2400101 CTATATAGTT
2400111 TATAGTTGATATTTACATATGAACTATATATATAAAC
1 TATAGTTGATATTT--ATATG-ACTATATATATAAAC
* * *
2400148 TATA-TAG-T-TTACATATGACCTATATATATATAC
1 TATAGTTGATATT-TATATGA-CTATATATATAAAC
2400181 TATAGTTGATATTTATAT-ACTATATA
1 TATAGTTGATATTTATATGACTATATA
2400207 GTTTATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
32 1 0.02
33 29 0.59
34 5 0.10
35 6 0.12
36 4 0.08
37 4 0.08
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (34 bp):
TATAGTTGATATTTATATGACTATATATATAAAC
Found at i:2400206 original size:22 final size:22
Alignment explanation
Indices: 2400172--2400214 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2400162 ATGACCTATA
2400172 TATATATACTATAGTTGATATT
1 TATATATACTATAGTTGATATT
*
2400194 TATATACTA-TATAGTTTATAT
1 TATATA-TACTATAGTTGATAT
2400215 ATGACCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TATATATACTATAGTTGATATT
Found at i:2400221 original size:53 final size:54
Alignment explanation
Indices: 2400136--2400291 Score: 219
Period size: 53 Copynumber: 2.9 Consensus size: 54
2400126 CATATGAACT
* * *
2400136 ATATATATAAACTATATAGTTTACATATGACCTATATATATATACTATAG-TTG
1 ATATTTATATACTATATAGTTTATATATGACCTATATATATATACTATAGTTTG
2400189 ATATTTATATACTATATAGTTTATATATGACCTATATATATATACTATAGTTTG
1 ATATTTATATACTATATAGTTTATATATGACCTATATATATATACTATAGTTTG
* * *
2400243 -TATTTATATACTATATA-TTATATATATAAACTATATATACTATAGTATA
1 ATATTTATATACTATATAGTT-TATATATGACCTATATATA-TATACTATA
2400292 ATTTACATAT
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
52 2 0.02
53 81 0.86
54 11 0.12
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (54 bp):
ATATTTATATACTATATAGTTTATATATGACCTATATATATATACTATAGTTTG
Found at i:2400430 original size:51 final size:50
Alignment explanation
Indices: 2400375--2400583 Score: 161
Period size: 51 Copynumber: 4.3 Consensus size: 50
2400365 AAACTATATA
*
2400375 ATATATAAACTATATGGTATATATAAACTATACATTATATATTTCATTAGT
1 ATATATAAACTATATGGTATATATAAACTATACATTA-ATAGTTCATTAGT
* * *
2400426 ATATATAAACTATA---TAT-TATATAGT-T-CATTAGTA-TGT-A-TA--
1 ATATATAAACTATATGGTATATATAAACTATACATTAATAGT-TCATTAGT
** * * * * *
2400466 ACCTATATAGTATATGGTATATACAAACTATATATTATATAGTTCATTACT
1 ATATATAAACTATATGGTATATATAAACTATACATTA-ATAGTTCATTAGT
* * *
2400517 ATATATAAACTATATAGTATATATAAACTATATATTGAAAAGTTCATTAGT
1 ATATATAAACTATATGGTATATATAAACTATACATT-AATAGTTCATTAGT
*
2400568 ATATTATAACCTATAT
1 ATA-TATAAACTATAT
2400584 ATTAATTTAT
Statistics
Matches: 122, Mismatches: 21, Indels: 29
0.71 0.12 0.17
Matches are distributed among these distances:
40 10 0.08
42 2 0.02
43 5 0.04
44 8 0.07
45 6 0.05
46 5 0.04
47 9 0.07
48 5 0.04
49 2 0.02
51 58 0.48
52 12 0.10
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (50 bp):
ATATATAAACTATATGGTATATATAAACTATACATTAATAGTTCATTAGT
Found at i:2400433 original size:33 final size:32
Alignment explanation
Indices: 2400355--2400540 Score: 170
Period size: 33 Copynumber: 5.9 Consensus size: 32
2400345 ATTTATACTA
* **
2400355 TAGTATATATAAACTATATAATATATAAACTAT
1 TAGTATATATAAACTATATATTATATATTC-AT
* *
2400388 ATGGTATATATAAACTATACATTATATATTTCAT
1 -TAGTATATATAAACTATATATTATATA-TTCAT
2400422 TAGTATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATATTATATA-TTCAT
* * *
2400455 TAGTATGTAT-AAC-CTATA-TA-GTA-T-A-
1 TAGTATATATAAACTATATATTATATATTCAT
* *
2400480 TGGTATATACAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATATTATATA-TTCAT
* *
2400513 TACTATATATAAACTATATAGTATATAT
1 TAGTATATATAAACTATATATTATATAT
2400541 AAACTATATA
Statistics
Matches: 123, Mismatches: 20, Indels: 20
0.75 0.12 0.12
Matches are distributed among these distances:
25 7 0.06
26 4 0.03
27 5 0.04
28 2 0.02
29 4 0.03
30 2 0.02
31 5 0.04
32 5 0.04
33 62 0.50
34 26 0.21
35 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (32 bp):
TAGTATATATAAACTATATATTATATATTCAT
Found at i:2400486 original size:58 final size:57
Alignment explanation
Indices: 2400422--2400613 Score: 202
Period size: 58 Copynumber: 3.4 Consensus size: 57
2400412 TATATTTCAT
*
2400422 TAGTATATATAAACTATATATTATATAGTTCATTAGTATGTATAACCTATATAGTATA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTAT-TATAACCTATATACTATA
* * *
2400480 TGGTATATACAAACTATATATTATATAGTTCATTACTA-TAT-A--TA-A-ACTATA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATTATAACCTATATACTATA
* * *
2400531 TAGTATATATAAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTATATATTAATT
1 TAGTATATATAAACTATATATT-ATATAGTTCATTAG--TATTATAACCTATATACT-ATA
*
2400591 TATTA-ATATAAACATATATATTA
1 TAGTATATATAAAC-TATATATTA
2400614 ATTGAAAGAA
Statistics
Matches: 112, Mismatches: 11, Indels: 21
0.78 0.08 0.15
Matches are distributed among these distances:
51 35 0.31
52 2 0.02
53 4 0.04
54 3 0.03
55 2 0.02
56 3 0.03
57 2 0.02
58 36 0.32
59 11 0.10
60 14 0.12
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (57 bp):
TAGTATATATAAACTATATATTATATAGTTCATTAGTATTATAACCTATATACTATA
Found at i:2401256 original size:112 final size:113
Alignment explanation
Indices: 2400987--2401312 Score: 536
Period size: 112 Copynumber: 2.9 Consensus size: 113
2400977 AAAATCAATT
2400987 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
1 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
* *
2401052 CCAAAATATTTTCGTGTTTTTTTTCGATCAAACACCCAAATATTCTTCT
66 CCAAAACATTTTCGTG-TTTTTTTCGATCAAACACCCAAATATTCTTCC
*
2401101 GCGTTCTTCATTTGTTCATCCAGTTCTT-CCCAAAACCCTCATTTGATCTTCAAAAA-ACCTAAA
1 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
*
2401164 CCAAAACATTTTCGTGTTTTTTTCGACCAAACACCCAAATATTCTTCC
66 CCAAAACATTTTCGTGTTTTTTTCGATCAAACACCCAAATATTCTTCC
*
2401212 GTGTTCTTCATTTATTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
1 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
*
2401277 -CATAAACCA-TTTCGTG-TTTTTTGGATCAAACACCCA
66 CCA-AAA-CATTTTCGTGTTTTTTTCGATCAAACACCCA
2401313 CAAATTCATC
Statistics
Matches: 200, Mismatches: 8, Indels: 10
0.92 0.04 0.05
Matches are distributed among these distances:
111 56 0.28
112 70 0.35
113 45 0.22
114 29 0.14
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (113 bp):
GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
CCAAAACATTTTCGTGTTTTTTTCGATCAAACACCCAAATATTCTTCC
Found at i:2401483 original size:12 final size:12
Alignment explanation
Indices: 2401468--2401603 Score: 89
Period size: 12 Copynumber: 11.3 Consensus size: 12
2401458 TCTTAACCCC
*
2401468 TAACTTAAACCT
1 TAACCTAAACCT
2401480 TAACCTAAACCT
1 TAACCTAAACCT
* *
2401492 TAACCCAAACCC
1 TAACCTAAACCT
2401504 TAACC-ATAACCT
1 TAACCTA-AACCT
* *
2401516 TAACCCAAACCC
1 TAACCTAAACCT
* *
2401528 AAACCCAAACC-
1 TAACCTAAACCT
*
2401539 CAACCTAAACCT
1 TAACCTAAACCT
* *
2401551 TAAACCCAAACCC
1 T-AACCTAAACCT
*
2401564 AAACCTAAACCT
1 TAACCTAAACCT
* * *
2401576 AAACTTGAA-CT
1 TAACCTAAACCT
*
2401587 TATACCTAAACCC
1 TA-ACCTAAACCT
2401600 TAAC
1 TAAC
2401604 TTGAACCCAA
Statistics
Matches: 98, Mismatches: 20, Indels: 12
0.75 0.15 0.09
Matches are distributed among these distances:
11 13 0.13
12 72 0.73
13 13 0.13
ACGTcount: A:0.44, C:0.38, G:0.01, T:0.18
Consensus pattern (12 bp):
TAACCTAAACCT
Found at i:2401556 original size:7 final size:6
Alignment explanation
Indices: 2401473--2401598 Score: 78
Period size: 6 Copynumber: 21.0 Consensus size: 6
2401463 ACCCCTAACT
* * * *
2401473 TAAACC TTAACC TAAACC TTAACC CAAACCC T-AACC -ATAACC TTAACC
1 TAAACC TAAACC TAAACC TAAACC TAAA-CC TAAACC TA-AACC TAAACC
* * * * * *
2401521 CAAACC CAAACC CAAACC -CAACC TAAACC TTAAACC CAAACC CAAACC
1 TAAACC TAAACC TAAACC TAAACC TAAACC -TAAACC TAAACC TAAACC
* * * *
2401569 TAAACC TAAACT TGAACT TATACC TAAACC
1 TAAACC TAAACC TAAACC TAAACC TAAACC
2401599 CTAACTTGAA
Statistics
Matches: 95, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
5 6 0.06
6 81 0.85
7 8 0.08
ACGTcount: A:0.44, C:0.38, G:0.01, T:0.17
Consensus pattern (6 bp):
TAAACC
Found at i:2401599 original size:36 final size:35
Alignment explanation
Indices: 2401473--2401579 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 35
2401463 ACCCCTAACT
* ** *
2401473 TAAACCTTAACCTAAACCTTAACCCAAACCCTAACC
1 TAAACCTTAACCCAAACCCAAACCCAAA-CCAAACC
*
2401509 -ATAACCTTAACCCAAACCCAAACCCAAACCCAACC
1 TA-AACCTTAACCCAAACCCAAACCCAAACCAAACC
*
2401544 TAAACCTTAAACCCAAACCCAAACCTAAACCTAAAC
1 TAAACCTT-AACCCAAACCCAAACCCAAACC-AAAC
2401580 TTGAACTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
35 13 0.21
36 45 0.74
37 3 0.05
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (35 bp):
TAAACCTTAACCCAAACCCAAACCCAAACCAAACC
Found at i:2401898 original size:31 final size:30
Alignment explanation
Indices: 2401852--2402355 Score: 515
Period size: 31 Copynumber: 16.0 Consensus size: 30
2401842 TATATATGTT
* *
2401852 TGATATACTCGTTTATTTATGTTGATGTAAA
1 TGATGTACTGGTTTATTT-TGTTGATGTAAA
2401883 TGATGTACTGGTTTATTGTTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* *
2401914 TGATGTGCTGATTTATTATTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
*
2401945 TGATGTACTGGTTTATTGCTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* * *
2401976 TGATGTGCTGGTTTATTGCTATTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* * * *
2402007 TGATATACTAGTTTATTGCTGTTAATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
2402038 TGATGTACTGGTTTATTGTTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* *
2402069 TGATATACTGGTTTATTGTTTTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
*
2402100 TGGTGTACTGGTTTATTGTTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
**
2402131 TGATGTGTTGGTTTATTGCTATTATTGCTATTGATGTAAA
1 TGATGTACTGG----TT--TATT-TTG---TTGATGTAAA
* * *
2402171 TGATATATTGGTTTATTGATGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
*
2402202 TGATGTACTGATTTATTGTTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* *
2402233 TGATATACTGGTTTATTGCTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* *
2402264 TGATGTACTGTTTTATTGCTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
*
2402295 TGATATACTGGTTTATTATTGTTGATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
* * *
2402326 TTATATACTGGTTTATTGTTG-TAATGTAAA
1 TGATGTACTGGTTTATT-TTGTTGATGTAAA
2402356 CTAACTATGG
Statistics
Matches: 414, Mismatches: 49, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
30 8 0.02
31 369 0.89
32 1 0.00
34 6 0.01
35 2 0.00
36 2 0.00
37 7 0.02
40 19 0.05
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.48
Consensus pattern (30 bp):
TGATGTACTGGTTTATTTTGTTGATGTAAA
Found at i:2401937 original size:62 final size:62
Alignment explanation
Indices: 2401852--2402355 Score: 625
Period size: 62 Copynumber: 8.0 Consensus size: 62
2401842 TATATATGTT
* *
2401852 TGATATACTCGTTTATT-TATGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
1 TGATGTACTGGTTTATTGT-TGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
* * * *
2401914 TGATGTGCTGATTTATTATTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTAAA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
* * * * * * *
2401976 TGATGTGCTGGTTTATTGCTATTGATGTAAATGATATACTAGTTTATTGCTGTTAATGTAAA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
* *
2402038 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGTTTTTGATGTAAA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
* **
2402100 TGGTGTACTGGTTTATTGTTGTTGATGTAAATGATGTGTTGGTTTATTGCTATTATTGCTATTGA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTG------TTG---TTGA
2402165 TGTAAA
57 TGTAAA
* * * *
2402171 TGATATATTGGTTTATTGATGTTGATGTAAATGATGTACTGATTTATTGTTGTTGATGTAAA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
* * * *
2402233 TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGTTTTATTGCTGTTGATGTAAA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
* * * * *
2402295 TGATATACTGGTTTATTATTGTTGATGTAAATTATATACTGGTTTATTGTTG-TAATGTAAA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
2402356 CTAACTATGG
Statistics
Matches: 390, Mismatches: 42, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
61 8 0.02
62 324 0.83
63 1 0.00
65 3 0.01
68 2 0.01
71 52 0.13
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.48
Consensus pattern (62 bp):
TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAA
Found at i:2401981 original size:93 final size:93
Alignment explanation
Indices: 2401852--2402343 Score: 617
Period size: 93 Copynumber: 5.2 Consensus size: 93
2401842 TATATATGTT
* ** *
2401852 TGATATACTCGTTTATTTATGTTGATGTAAATGATGTACTGGTTTATTGTTGTTGATGTAAATGA
1 TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTAAATGA
* *
2401917 TGTGCTGATTTATTATTGTTGATGTAAA
66 TGTACTGATTTATTGTTGTTGATGTAAA
* * *
2401945 TGATGTACTGGTTTATTGCTGTTGATGTAAATGATGTGCTGGTTTATTGCTATTGATGTAAATGA
1 TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTAAATGA
* * *
2402010 TATACT-AGTTTATTGCTGTTAATGTAAA
66 TGTACTGA-TTTATTGTTGTTGATGTAAA
* * * * * *
2402038 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGTTTTTGATGTAAATGG
1 TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTAAATGA
*
2402103 TGTACTGGTTTATTGTTGTTGATGTAAA
66 TGTACTGATTTATTGTTGTTGATGTAAA
* ** * * *
2402131 TGATGTGTTGGTTTATTGCTATTATTGCTATTGATGTAAATGATATATTGGTTTATTGATGTTGA
1 TGATATACTGGTTTATTGC------TG---TTGATGTAAATGATGTACTGGTTTATTGCTGTTGA
2402196 TGTAAATGATGTACTGATTTATTGTTGTTGATGTAAA
57 TGTAAATGATGTACTGATTTATTGTTGTTGATGTAAA
*
2402233 TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGTTTTATTGCTGTTGATGTAAATGA
1 TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTAAATGA
* * *
2402298 TATACTGGTTTATTATTGTTGATGTAAA
66 TGTACTGATTTATTGTTGTTGATGTAAA
*
2402326 TTATATACTGGTTTATTG
1 TGATATACTGGTTTATTG
2402344 TTGTAATGTA
Statistics
Matches: 347, Mismatches: 41, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
92 1 0.00
93 259 0.75
96 2 0.01
99 2 0.01
102 83 0.24
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.48
Consensus pattern (93 bp):
TGATATACTGGTTTATTGCTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTAAATGA
TGTACTGATTTATTGTTGTTGATGTAAA
Found at i:2402156 original size:40 final size:40
Alignment explanation
Indices: 2402112--2402188 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2402102 GTGTACTGGT
* * * *
2402112 TTATTGTTGTTGATGTAAATGATGTGTTGGTTTATTGCTA
1 TTATTGCTATTGATGTAAATGATATATTGGTTTATTGCTA
2402152 TTATTGCTATTGATGTAAATGATATATTGGTTTATTG
1 TTATTGCTATTGATGTAAATGATATATTGGTTTATTG
2402189 ATGTTGATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.22, T:0.52
Consensus pattern (40 bp):
TTATTGCTATTGATGTAAATGATATATTGGTTTATTGCTA
Found at i:2402395 original size:63 final size:64
Alignment explanation
Indices: 2402318--2402464 Score: 242
Period size: 63 Copynumber: 2.3 Consensus size: 64
2402308 TATTATTGTT
*
2402318 GATGTAAATTATATACTGGTTTATTGTTGTAATGTAAACTAACTATGG-TTTTTTTTGCAAGGG
1 GATGTAAATGATATACTGGTTTATTGTTGTAATGTAAACTAACTATGGTTTTTTTTTGCAAGGG
* *
2402381 GGTGTAAATGATATACTGGTTTATTGTTGTAGTGTAAACTAACTATGGTTTTTTTTTTTGCAAGG
1 GATGTAAATGATATACTGGTTTATTGTTGTAATGTAAACTAACTATGG--TTTTTTTTTGCAAGG
2402446 G
64 G
2402447 GATGTAAATGATATACTG
1 GATGTAAATGATATACTG
2402465 TCTGAAGCAA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
63 45 0.58
66 32 0.42
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (64 bp):
GATGTAAATGATATACTGGTTTATTGTTGTAATGTAAACTAACTATGGTTTTTTTTTGCAAGGG
Found at i:2402417 original size:93 final size:93
Alignment explanation
Indices: 2402194--2402418 Score: 260
Period size: 93 Copynumber: 2.4 Consensus size: 93
2402184 TATTGATGTT
* * *
2402194 GATGTAAATGATGTACTGATTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGCTGTTGAT
1 GATGTAAATGATATACTGGTTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGCTGTTAAT
** * **
2402259 GTAAATGATGTACTGTTTTATTGCTGTT
66 GTAAATGAACTACTGTTTTATTGCAGGG
* * *
2402287 GATGTAAATGATATACTGGTTTATTATTGTTGATGTAAATTATATACTGGTTTATTGTTG-TAAT
1 GATGTAAATGATATACTGGTTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGCTGTTAAT
*
2402351 GTAAACT-AACTA-TGGTTTTTTTTGCAAGGG
66 GTAAA-TGAACTACT-G-TTTTATTGC-AGGG
* *
2402381 GGTGTAAATGATATACTGGTTTATTGTTGTAG-TGTAAA
1 GATGTAAATGATATACTGGTTTATTGTTGTTGATGTAAA
2402419 CTAACTATGG
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
91 1 0.01
92 12 0.11
93 70 0.62
94 30 0.27
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (93 bp):
GATGTAAATGATATACTGGTTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGCTGTTAAT
GTAAATGAACTACTGTTTTATTGCAGGG
Found at i:2404611 original size:13 final size:13
Alignment explanation
Indices: 2404593--2404619 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2404583 GAAATCATTC
2404593 CGAATTGGAGATT
1 CGAATTGGAGATT
2404606 CGAATTGGAGATT
1 CGAATTGGAGATT
2404619 C
1 C
2404620 TGTCTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (13 bp):
CGAATTGGAGATT
Found at i:2404796 original size:20 final size:20
Alignment explanation
Indices: 2404773--2404836 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
2404763 TTATGCTTTA
2404773 TTCTGTTTTATATTGTTTGC
1 TTCTGTTTTATATTGTTTGC
*
2404793 TTCTATTTTATATTGTTTGC
1 TTCTGTTTTATATTGTTTGC
* *
2404813 TTCTGTTTGATATTGCTTGC
1 TTCTGTTTTATATTGTTTGC
2404833 TTCT
1 TTCT
2404837 ACTTGATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.11, C:0.12, G:0.14, T:0.62
Consensus pattern (20 bp):
TTCTGTTTTATATTGTTTGC
Found at i:2404842 original size:20 final size:20
Alignment explanation
Indices: 2404782--2404846 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2404772 ATTCTGTTTT
*
2404782 ATATTGTTTGCTTCTATTTT
1 ATATTGTTTGCTTCTATTTG
*
2404802 ATATTGTTTGCTTCTGTTTG
1 ATATTGTTTGCTTCTATTTG
* *
2404822 ATATTGCTTGCTTCTACTTG
1 ATATTGTTTGCTTCTATTTG
2404842 ATATT
1 ATATT
2404847 TGTAAGGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.15, C:0.12, G:0.14, T:0.58
Consensus pattern (20 bp):
ATATTGTTTGCTTCTATTTG
Found at i:2404965 original size:23 final size:23
Alignment explanation
Indices: 2404933--2404995 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
2404923 TGCTTTCTTA
2404933 ATACAA-GATGCTTGCTGAATTG
1 ATACAATGATGCTTGCTGAATTG
* *
2404955 ATGCAATGATGCTTGTTGAATTG
1 ATACAATGATGCTTGCTGAATTG
* *
2404978 GTACATTGATGCTTGCTG
1 ATACAATGATGCTTGCTG
2404996 GTTGATATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (23 bp):
ATACAATGATGCTTGCTGAATTG
Found at i:2405731 original size:51 final size:51
Alignment explanation
Indices: 2405658--2405754 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
2405648 ATATAAAACT
* *
2405658 AAATTTCAAAAAATAATCATATTAATTTGATTATTATAATAATTTATGATA
1 AAATTTCAAAAAATAATCATATTAATTTAATTATCATAATAATTTATGATA
* * *
2405709 AAATTTTAAAAAGTAATTATATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAATAATCATATTAATTTAATTATCATAATAATTTA
2405755 ATTATCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (51 bp):
AAATTTCAAAAAATAATCATATTAATTTAATTATCATAATAATTTATGATA
Found at i:2405753 original size:17 final size:17
Alignment explanation
Indices: 2405731--2405764 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2405721 GTAATTATAT
2405731 TAATTTAATTATCATAA
1 TAATTTAATTATCATAA
2405748 TAATTTAATTATCATAA
1 TAATTTAATTATCATAA
2405765 GTTTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTAATTATCATAA
Found at i:2405913 original size:16 final size:16
Alignment explanation
Indices: 2405879--2405914 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2405869 TGAGTCAATT
*
2405879 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
2405895 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
2405911 ACAG
1 ACAG
2405915 ATCGGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:2408237 original size:32 final size:31
Alignment explanation
Indices: 2408200--2408279 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
2408190 ACTAATTTAT
*
2408200 TTATCACTGAAAAGTTTATGAAATGAAGTGA
1 TTATCACTGAAAAGTTTATGAAATGAAGTAA
* * * *
2408231 TATATCAATGAAAAGTATATGAAGTGAGGTAA
1 T-TATCACTGAAAAGTTTATGAAATGAAGTAA
*
2408263 TTAGCCACTGAAAAGTT
1 TTA-TCACTGAAAAGTT
2408280 ATTATCCTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 3 0.08
32 36 0.92
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (31 bp):
TTATCACTGAAAAGTTTATGAAATGAAGTAA
Found at i:2408409 original size:31 final size:32
Alignment explanation
Indices: 2408354--2408418 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
2408344 CATTTTTTAG
* *
2408354 AAGTTTCTGAAATAAATTGATATATGAATGAA
1 AAGTTTCTGAAATAAAGTGATATATCAATGAA
*
2408386 AAGTTTCTG-AATGAAGTGATATATCAATGAA
1 AAGTTTCTGAAATAAAGTGATATATCAATGAA
2408417 AA
1 AA
2408419 TCCTTGCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (32 bp):
AAGTTTCTGAAATAAAGTGATATATCAATGAA
Found at i:2412193 original size:21 final size:21
Alignment explanation
Indices: 2412169--2412218 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2412159 TTTGGGATTG
**
2412169 ATCCTTTTGGTCGAGGGATCA
1 ATCCTTTTGCCCGAGGGATCA
* *
2412190 ATCCTTTTTCCCGAGGGATCG
1 ATCCTTTTGCCCGAGGGATCA
2412211 ATCCTTTT
1 ATCCTTTT
2412219 AAAAAGGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (21 bp):
ATCCTTTTGCCCGAGGGATCA
Found at i:2416941 original size:24 final size:23
Alignment explanation
Indices: 2416894--2416941 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2416884 TGAAAATAAT
2416894 AATAAAATAATTCAAAGTGATCAA
1 AATAAAATAATTCAAAGT-ATCAA
2416918 AATAAAAGTAATTCAATAGT-TCAA
1 AATAAAA-TAATTCAA-AGTATCAA
2416942 TGAGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 8 0.36
26 3 0.14
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (23 bp):
AATAAAATAATTCAAAGTATCAA
Found at i:2418353 original size:2 final size:2
Alignment explanation
Indices: 2418346--2418375 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2418336 TTTGATTTAC
2418346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2418376 CAAAAGGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2423858 original size:2 final size:2
Alignment explanation
Indices: 2423851--2423946 Score: 183
Period size: 2 Copynumber: 48.0 Consensus size: 2
2423841 ATGGATTGAG
2423851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2423893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2423935 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2423947 GTGAGATTTT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2427595 original size:2 final size:2
Alignment explanation
Indices: 2427588--2427664 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
2427578 AAGGCATTAG
*
2427588 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2427630 TA TA TA 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 TA TA TA T
2427665 TGCCCAGTAC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2434696 original size:20 final size:19
Alignment explanation
Indices: 2434662--2434706 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
2434652 AAAATGACCC
2434662 AATTTCACATCCTAACATT
1 AATTTCACATCCTAACATT
*
2434681 AATTTCAACATTCTAACATT
1 AATTTC-ACATCCTAACATT
2434701 AATTTC
1 AATTTC
2434707 CAGCATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTCACATCCTAACATT
Found at i:2435923 original size:29 final size:31
Alignment explanation
Indices: 2435869--2435930 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
2435859 ATTTGGTTTA
*
2435869 TAAACTTTTCCAAACTTTATACTTTGGTCAC
1 TAAACTTTTCCAAAATTTATACTTTGGTCAC
*
2435900 TAAAC-TTT-CAAAATTTATATTTTGGTCAC
1 TAAACTTTTCCAAAATTTATACTTTGGTCAC
2435929 TA
1 TA
2435931 CCCAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.72
30 3 0.10
31 5 0.17
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (31 bp):
TAAACTTTTCCAAAATTTATACTTTGGTCAC
Found at i:2441253 original size:18 final size:18
Alignment explanation
Indices: 2441220--2441272 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2441210 CACTGAACAC
* *
2441220 TTGTCCTGAAGAACCA-T
1 TTGTCCCGAAGGACCACT
*
2441237 TATGTCCCGAATGACCACT
1 T-TGTCCCGAAGGACCACT
2441256 TTGTCCCGAAGGACCAC
1 TTGTCCCGAAGGACCAC
2441273 ATAGAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 1 0.03
18 27 0.90
19 2 0.07
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (18 bp):
TTGTCCCGAAGGACCACT
Found at i:2442658 original size:30 final size:30
Alignment explanation
Indices: 2442624--2442691 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
2442614 ATTCAAAAAC
2442624 TTTTCTAAAATTATTA-AATTGGTCCCCA-AT
1 TTTTCTAAAATTA-TAGAA-TGGTCCCCAGAT
*
2442654 TTTTCAAAAATTATAGAATGGTCCCCAGAT
1 TTTTCTAAAATTATAGAATGGTCCCCAGAT
2442684 TTTTCTAA
1 TTTTCTAA
2442692 GGCTTGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (30 bp):
TTTTCTAAAATTATAGAATGGTCCCCAGAT
Found at i:2447925 original size:10 final size:10
Alignment explanation
Indices: 2447912--2447945 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2447902 TTTTTTGAAA
2447912 TTTTGGTTTTT
1 TTTTGG-TTTT
*
2447923 TTTTTGTTTT
1 TTTTGGTTTT
2447933 TTTTGGTTTT
1 TTTTGGTTTT
2447943 TTT
1 TTT
2447946 AAAATAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (10 bp):
TTTTGGTTTT
Found at i:2447926 original size:11 final size:11
Alignment explanation
Indices: 2447912--2447945 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2447902 TTTTTTGAAA
2447912 TTTTGGTTTTT
1 TTTTGGTTTTT
*
2447923 TTTTTG-TTTT
1 TTTTGGTTTTT
2447933 TTTTGGTTTTT
1 TTTTGGTTTTT
2447944 TT
1 TT
2447946 AAAATAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTGGTTTTT
Found at i:2447935 original size:20 final size:21
Alignment explanation
Indices: 2447898--2447945 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2447888 TCGTTTGCAA
2447898 TTTTTTTTTTG-AAATTTTGG
1 TTTTTTTTTTGTAAATTTTGG
***
2447918 TTTTTTTTTTGTTTTTTTTGG
1 TTTTTTTTTTGTAAATTTTGG
2447939 TTTTTTT
1 TTTTTTT
2447946 AAAATAGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTGTAAATTTTGG
Found at i:2449267 original size:31 final size:30
Alignment explanation
Indices: 2449208--2449267 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
2449198 TTTGGTCCCT
* * * *
2449208 AAACTTTTTAAAGTTTATACTTTGGTCACC
1 AAACTTTATAAAATTTATAATTTAGTCACC
2449238 AAACTTTATAAAATCTTATAATTTAGTCAC
1 AAACTTTATAAAAT-TTATAATTTAGTCAC
2449268 TAACTAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (30 bp):
AAACTTTATAAAATTTATAATTTAGTCACC
Done.