Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008668.1 Hibiscus syriacus cultivar Beakdansim tig00111671_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: 2122653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:196293 original size:44 final size:45
Alignment explanation
Indices: 196169--196296 Score: 177
Period size: 47 Copynumber: 2.8 Consensus size: 45
196159 TATAAAATCT
*
196169 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTATCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAAAATA
* * *
196214 CTTACCATTTAAATTTCATAAACTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTATCAAAATA
**
196261 CTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTTTA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
196297 CTTGGTTACC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 25 0.34
45 10 0.14
46 2 0.03
47 36 0.49
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAAAATA
Found at i:199979 original size:13 final size:13
Alignment explanation
Indices: 199961--200001 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
199951 CCGAAGTGCC
199961 CCGTAGAATTGCA
1 CCGTAGAATTGCA
199974 CCGTAG---TGC-
1 CCGTAGAATTGCA
199983 CCGTAGAATTGCA
1 CCGTAGAATTGCA
199996 CCGTAG
1 CCGTAG
200002 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:199988 original size:22 final size:22
Alignment explanation
Indices: 199947--200013 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
199937 CTCGTATAAA
*
199947 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGTAGTG-CCCGTAGAAT
199970 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
199992 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
200014 GATGTCCCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.74
23 11 0.26
ACGTcount: A:0.24, C:0.28, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:201777 original size:22 final size:21
Alignment explanation
Indices: 201731--201773 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
201721 TTCATATTCG
* *
201731 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
201752 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
201773 C
1 C
201774 CTTGCCCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:204956 original size:13 final size:13
Alignment explanation
Indices: 204938--204978 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
204928 CCGAAGTGCC
204938 CCGTAGAATTGCA
1 CCGTAGAATTGCA
204951 CCGTAG---TGC-
1 CCGTAGAATTGCA
204960 CCGTAGAATTGCA
1 CCGTAGAATTGCA
204973 CCGTAG
1 CCGTAG
204979 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:204965 original size:22 final size:22
Alignment explanation
Indices: 204924--204990 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
204914 CTCGTATAAA
*
204924 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGTAGTG-CCCGTAGAAT
204947 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
204969 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
204991 GATGTCCCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.74
23 11 0.26
ACGTcount: A:0.24, C:0.28, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:206726 original size:21 final size:21
Alignment explanation
Indices: 206700--206745 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
206690 TTCATATTCG
* *
206700 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
206721 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
206742 CTTG
1 CTTG
206746 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:210100 original size:13 final size:13
Alignment explanation
Indices: 210082--210106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210072 TATTCATCCT
210082 TTAATCGCAACCC
1 TTAATCGCAACCC
210095 TTAATCGCAACC
1 TTAATCGCAACC
210107 ATTTCTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (13 bp):
TTAATCGCAACCC
Found at i:212197 original size:44 final size:44
Alignment explanation
Indices: 212078--212206 Score: 195
Period size: 47 Copynumber: 2.9 Consensus size: 44
212068 TATAAAACCT
* *
212078 CTTACCATTATCCCATAAGCTCGTAAGCTTATTTTATCAAAATA
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
212122 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
212169 CTTGCCATTATTCCATAAGCTCGTAAGCTTATTTTACC
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACC
212207 TGGTTACCAT
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
44 36 0.46
45 2 0.03
46 2 0.03
47 38 0.49
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:216043 original size:58 final size:58
Alignment explanation
Indices: 215979--216089 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
215969 AAAAAATGAA
215979 TAGTTGAGTG-ACTATTTTGTAACTTTTAAT-AGTCGATAGACTCAACAAAATAACTTTT
1 TAGTTGA-TGAACTATTTTGTAACTTTTAATAAGTCGAT-GACTCAACAAAATAACTTTT
* * * *
216037 TAGTTGATGAATTATTTTGTAACTTTTAATAATTTGATTACTCAACAAAATAA
1 TAGTTGATGAACTATTTTGTAACTTTTAATAAGTCGATGACTCAACAAAATAA
216090 TATCTTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
57 2 0.04
58 40 0.85
59 5 0.11
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (58 bp):
TAGTTGATGAACTATTTTGTAACTTTTAATAAGTCGATGACTCAACAAAATAACTTTT
Found at i:222636 original size:13 final size:13
Alignment explanation
Indices: 222618--222642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
222608 ATTCATCCTT
222618 TTAATCGCAACCC
1 TTAATCGCAACCC
222631 TTAATCGCAACC
1 TTAATCGCAACC
222643 ATTTCTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (13 bp):
TTAATCGCAACCC
Found at i:224758 original size:44 final size:45
Alignment explanation
Indices: 224638--224767 Score: 199
Period size: 47 Copynumber: 2.9 Consensus size: 45
224628 TATAAAACCT
* *
224638 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTATCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
224683 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
224730 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTTACC
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC
224768 TGGTTACCAT
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
44 29 0.37
45 10 0.13
46 2 0.03
47 38 0.48
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:237676 original size:21 final size:21
Alignment explanation
Indices: 237650--237689 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
237640 TGGACAAATG
* *
237650 GATGTCTAGATTCATCCTAGA
1 GATGTCTACATTAATCCTAGA
237671 GATGTCTACATTAATCCTA
1 GATGTCTACATTAATCCTA
237690 AAGCTCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (21 bp):
GATGTCTACATTAATCCTAGA
Found at i:240056 original size:20 final size:20
Alignment explanation
Indices: 240014--240057 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
240004 TCTAATAAAG
* *
240014 ATCTTTAGATTATTTGTTTT
1 ATCTTTAGATTATTTGATAT
240034 ATCTTTAGATTATTTGATAT
1 ATCTTTAGATTATTTGATAT
240054 ATCT
1 ATCT
240058 AAATCTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (20 bp):
ATCTTTAGATTATTTGATAT
Found at i:241630 original size:81 final size:79
Alignment explanation
Indices: 241473--241627 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 79
241463 CTTGTTAGAA
*
241473 GTGATATTTGCTGTAAATTCAATGAAGATGAAGAGAGAGAACATGAAGAAGTGCATGATTTGCAT
1 GTGATGTTTGCTGTAAATTCAATGAAGATGAAGAGAGAGAACA--AAGAAGTGCATGATTTGCAT
241538 GAAGAAGAAGAAAAAG
64 GAAGAAGAAGAAAAAG
*
241554 GTGATGTTTGCAT-TAAATTCAATGAAGATGAAGAGATAGAAC-AAGAAGTGCATGATTTGCATG
1 GTGATGTTTGC-TGTAAATTCAATGAAGATGAAGAGAGAGAACAAAGAAGTGCATGATTTGCATG
241617 AAGAAGAAGAA
65 AAGAAGAAGAA
241628 GAAGAAGGGA
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
78 32 0.45
81 38 0.54
82 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.23
Consensus pattern (79 bp):
GTGATGTTTGCTGTAAATTCAATGAAGATGAAGAGAGAGAACAAAGAAGTGCATGATTTGCATGA
AGAAGAAGAAAAAG
Found at i:245009 original size:81 final size:79
Alignment explanation
Indices: 244836--245135 Score: 338
Period size: 81 Copynumber: 3.7 Consensus size: 79
244826 CCTCCGTTTC
* * * * *
244836 GGTGAAGGTGTATCATTTCTC-ACCCTCCGTTTCCGAGGTGGTGATAAATCAG---CATCTGCTC
1 GGTGATGGTGTATCA-TTC-CGAACCTCCGTTTCC-TGGAGGAGATAAATCAGTACCATCTGCTC
244897 TGTTTACTAAAGGTTCT
63 TGTTTACTAAAGGTTCT
* * *
244914 GGTGAAGGTGTATCATTCCGAGCTCTCCGTTTCCTAGGAGGAGATAAATCAGTACCATCGGCTCT
1 GGTGATGGTGTATCATTCCGAAC-CTCCGTTTCCT-GGAGGAGATAAATCAGTACCATCTGCTCT
*
244979 GTTTACTAAAGGTTTT
64 GTTTACTAAAGGTTCT
* * * *
244995 GGTGATTGTATATCATTCCGAACCCTCCGTCTCCGTGGAGGTGATAAATCAGTACCATCTGCTCT
1 GGTGATGGTGTATCATTCCGAA-CCTCCGTTTCC-TGGAGGAGATAAATCAGTACCATCTGCTCT
*
245060 GTTTACTAAAGGTTCA
64 GTTTACTAAAGGTTCT
* * *
245076 GGTGATGGTGTGTCATTCCGAACCATCCGTTTTCGTGGAGGAGATAAATCAGTATCATCT
1 GGTGATGGTGTATCATTCCGAACC-TCCG-TTTCCTGGAGGAGATAAATCAGTACCATCT
245136 CTAGATGCCT
Statistics
Matches: 190, Mismatches: 22, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
76 1 0.01
77 5 0.03
78 39 0.21
80 2 0.01
81 138 0.73
82 5 0.03
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (79 bp):
GGTGATGGTGTATCATTCCGAACCTCCGTTTCCTGGAGGAGATAAATCAGTACCATCTGCTCTGT
TTACTAAAGGTTCT
Found at i:249213 original size:2 final size:2
Alignment explanation
Indices: 249206--249277 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
249196 TCGAATTTTG
249206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
249247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
249278 CCGAATTTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250339 original size:16 final size:16
Alignment explanation
Indices: 250318--250367 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
250308 GCCACTAATG
250318 TTTATAGATTTCAACT
1 TTTATAGATTTCAACT
250334 TTTATAGATTTCAACT
1 TTTATAGATTTCAACT
*
250350 TTTATAGATTTTAACT
1 TTTATAGATTTCAACT
250366 TT
1 TT
250368 CAGTCTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTATAGATTTCAACT
Found at i:253525 original size:9 final size:9
Alignment explanation
Indices: 253498--253580 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 9
253488 AATCAAGAAG
*
253498 AAAAAAGAA
1 AAAAAACAA
* *
253507 AAGAAGCAA
1 AAAAAACAA
253516 AAAAAACAA
1 AAAAAACAA
253525 AGAAAAACAA
1 A-AAAAACAA
*
253535 AGAAAA-AA
1 AAAAAACAA
*
253543 AAGAAACAA
1 AAAAAACAA
**
253552 GAACAAAAGGA
1 -AA-AAAACAA
*
253563 AAAAAAGAA
1 AAAAAACAA
253572 AAAAAACAA
1 AAAAAACAA
253581 GAATCAAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
8 6 0.11
9 34 0.60
10 13 0.23
11 4 0.07
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:253530 original size:10 final size:10
Alignment explanation
Indices: 253513--253548 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
253503 AGAAAAGAAG
253513 CAAA-AAAAA
1 CAAAGAAAAA
253522 CAAAGAAAAA
1 CAAAGAAAAA
253532 CAAAGAAAAA
1 CAAAGAAAAA
253542 -AAAGAAA
1 CAAAGAAA
253549 CAAGAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 11 0.42
10 15 0.58
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
CAAAGAAAAA
Found at i:253540 original size:23 final size:22
Alignment explanation
Indices: 253495--253594 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 22
253485 TCCAATCAAG
*
253495 AAGAAAAAAGAAAAGAAGCAAAAAA
1 AAGAAAAAA-AACA-AAG-AAAAAA
*
253520 AACAAAGAAAAACAAAGAAAAAA
1 AAGAAA-AAAAACAAAGAAAAAA
* *
253543 AAGAAACAAGAACAAAAGGAAAAA
1 AAGAAA-AAAAAC-AAAGAAAAAA
*
253567 AAGAAAAAAAAC-AAGAATCAAA
1 AAGAAAAAAAACAAAGAA-AAAA
253589 AAGAAA
1 AAGAAA
253595 GAGGAACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.06
22 9 0.14
23 21 0.33
24 18 0.29
25 8 0.13
26 3 0.05
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (22 bp):
AAGAAAAAAAACAAAGAAAAAA
Found at i:253559 original size:19 final size:18
Alignment explanation
Indices: 253495--253583 Score: 60
Period size: 19 Copynumber: 4.9 Consensus size: 18
253485 TCCAATCAAG
*
253495 AAGAAAAAAGAAAAGAAGC
1 AAGAAAAAA-AAAAGAAAC
*
253514 AA-AAAAAACAAAGAAAAAC
1 AAGAAAAAA-AAA-AGAAAC
*
253533 AA-AGAAAAAAAAGAAAC
1 AAGAAAAAAAAAAGAAAC
**
253550 AAGAACAAAAGGAA-AAA-
1 AAGAA-AAAAAAAAGAAAC
253567 AAGAAAAAAAACAAGAA
1 AAGAAAAAAAA-AAGAA
253584 TCAAAAAGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
16 4 0.07
17 14 0.25
18 18 0.33
19 19 0.35
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAAGAAAC
Found at i:253570 original size:33 final size:32
Alignment explanation
Indices: 253492--253577 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 32
253482 AGATCCAATC
*
253492 AAGAAGAAAAAAG-AAAAGAAGCAAAAAAAACA
1 AAGAA-AAAAAAGAAAAAAAAGCAAAAAAAACA
*
253524 AAGAAAAACAAAGAAAAAAAAG-AAACAAGAACAA
1 AAGAAAAA-AAAGAAAAAAAAGCAAA-AAAAAC-A
*
253558 AAGGAAAAAAAGAAAAAAAA
1 AAGAAAAAAAAGAAAAAAAA
253578 CAAGAATCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 3 0.06
32 12 0.26
33 24 0.51
34 8 0.17
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (32 bp):
AAGAAAAAAAAGAAAAAAAAGCAAAAAAAACA
Found at i:253576 original size:17 final size:17
Alignment explanation
Indices: 253498--253576 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 17
253488 AATCAAGAAG
* *
253498 AAAAAAGAAAAGAAGCA
1 AAAAAAGAAAAAAAGGA
*
253515 AAAAAA-ACAAAGAA--A
1 AAAAAAGA-AAAAAAGGA
* *
253530 AACAAAGAAAAAAAAG-
1 AAAAAAGAAAAAAAGGA
* *
253546 AAACAAGAACAAAAGGA
1 AAAAAAGAAAAAAAGGA
253563 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
253577 ACAAGAATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.22
16 14 0.29
17 24 0.49
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAGGA
Found at i:253577 original size:10 final size:10
Alignment explanation
Indices: 253492--253577 Score: 52
Period size: 10 Copynumber: 8.1 Consensus size: 10
253482 AGATCCAATC
*
253492 AAGAAGAAAA
1 AAGAAAAAAA
253502 AAGAAAAGAAGCA
1 AAGAAAA-AA--A
*
253515 AA-AAAAACA
1 AAGAAAAAAA
*
253524 AAGAAAAACA
1 AAGAAAAAAA
253534 AAG-AAAAAA
1 AAGAAAAAAA
253543 AAGAAACAAGAA
1 AAGAAA-AA-AA
253555 CAA-AAGGAAAAA
1 -AAGAA--AAAAA
253567 AAGAAAAAAA
1 AAGAAAAAAA
253577 A
1 A
253578 CAAGAATCAA
Statistics
Matches: 62, Mismatches: 3, Indels: 22
0.71 0.03 0.25
Matches are distributed among these distances:
9 11 0.18
10 24 0.39
11 7 0.11
12 12 0.19
13 7 0.11
14 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:253590 original size:46 final size:49
Alignment explanation
Indices: 253488--253605 Score: 129
Period size: 46 Copynumber: 2.5 Consensus size: 49
253478 GCAAAGATCC
*
253488 AATCAAGAAGAAAAAAGAA-AAGAAGCAAAAAAAACAAAGAAAAACAAAG
1 AATCAAAAAGAAAAAAGAACAA-AAGCAAAAAAAACAAAGAAAAACAAAG
* * * *
253537 AA-AAAAAAGAAACAAGAACAAAAG-GAAAAAAAGAAA-AAAAAC-AAG
1 AATCAAAAAGAAAAAAGAACAAAAGCAAAAAAAACAAAGAAAAACAAAG
* *
253582 AATCAAAAAGAAAGAGGAACAAAA
1 AATCAAAAAGAAAAAAGAACAAAA
253606 AGCACATGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 5 0.08
46 24 0.41
47 10 0.17
48 16 0.27
49 4 0.07
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.02
Consensus pattern (49 bp):
AATCAAAAAGAAAAAAGAACAAAAGCAAAAAAAACAAAGAAAAACAAAG
Found at i:253606 original size:29 final size:29
Alignment explanation
Indices: 253499--253594 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
253489 ATCAAGAAGA
*
253499 AAAAAGAAAAGAAGCAAAAAAAACAAAGAA-
1 AAAAAGAAAAAAAG-AAAAAAAAC-AAGAAC
* * *
253529 AAACA-AAGAAAA-AAAAGAAACAAGAAC
1 AAAAAGAAAAAAAGAAAAAAAACAAGAAC
*
253556 AAAAGGAAAAAAAGAAAAAAAACAAGAATC
1 AAAAAGAAAAAAAGAAAAAAAACAAGAA-C
253586 AAAAAGAAA
1 AAAAAGAAA
253595 GAGGAACAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
26 5 0.09
27 11 0.21
28 6 0.11
29 18 0.34
30 13 0.25
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.01
Consensus pattern (29 bp):
AAAAAGAAAAAAAGAAAAAAAACAAGAAC
Found at i:254254 original size:22 final size:22
Alignment explanation
Indices: 254226--254280 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
254216 GCTATCCCAT
254226 CAAACCTTTGAGCATAAAAGGC
1 CAAACCTTTGAGCATAAAAGGC
* *
254248 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATAAAAGGC
254270 CAAACCTTTGA
1 CAAACCTTTGA
254281 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATAAAAGGC
Found at i:254631 original size:106 final size:106
Alignment explanation
Indices: 254442--254648 Score: 351
Period size: 106 Copynumber: 2.0 Consensus size: 106
254432 CAATTCAAGA
* * *
254442 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1 CTGGTAGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
254507 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCG
66 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
254548 CTGGTAGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGCTATTGG
1 CTGGTAGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
254613 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
254649 CTATTGGACT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
CTGGTAGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
Found at i:254648 original size:43 final size:43
Alignment explanation
Indices: 254587--254691 Score: 201
Period size: 43 Copynumber: 2.4 Consensus size: 43
254577 CAGAGCCAAT
*
254587 TTCAACTTCACAACGAAGGCTATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGCTATTGGACTCCAGACAACGCAAG
254630 TTCAACTTCACGACGAAGGCTATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGCTATTGGACTCCAGACAACGCAAG
254673 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
254692 GACCGCTGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGCTATTGGACTCCAGACAACGCAAG
Found at i:254760 original size:149 final size:149
Alignment explanation
Indices: 254481--254797 Score: 537
Period size: 149 Copynumber: 2.1 Consensus size: 149
254471 CAGAGCCAAT
*
254481 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGA
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
* * * *
254545 CCGCTGGTAGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGCTAT
65 CCGCTGGTAGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATAT
254610 TGGACTCCAGACAACGCAAG
130 TGGACTCCAGACAACGCAAG
*
254630 TTCAACTTCACGACGAAGGCTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
254695 CGCTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATT
66 CGCTGGTAGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATT
254760 GGACTCCAGACAACGCAAG
131 GGACTCCAGACAACGCAAG
254779 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
254798 GACCGCTGGT
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
149 157 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (149 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTAGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATT
GGACTCCAGACAACGCAAG
Found at i:254819 original size:106 final size:106
Alignment explanation
Indices: 254630--255815 Score: 1948
Period size: 106 Copynumber: 11.2 Consensus size: 106
254620 ACAACGCAAG
*
254630 TTCAACTTCAC-GACGAAGGCTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
1 TTCAACTTCACAG-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
* *
254694 CCGCTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
65 CCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
*
254736 TTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
254801 CGCTGGTCGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
* *
254842 TTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* *
254907 CGCTGGTTGTCAATAAACAATTTAC-CAATTTCATAGCCAAT
66 CGCTGGTTGTCAATAAACAACTT-CTCAATTTCAGAGCCAAT
*
254948 TTCAACTTCACAGCGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
255013 CGTTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
* *
255054 TTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
255119 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
* *
255160 TTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
255225 CGCTGGTTGTCAATAAAAAATTTCCCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
255266 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
255331 CGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
*
255372 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
255437 CGCTGGTTGTCAATAAATAATTTCCCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
* * *
255478 TTCAACTTCACAACGAAGGATATCGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
255543 CGATGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
*
255584 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* *
255649 CGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
* *
255690 TTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
255755 CGCTGGTTGTCAAAAAAACAACTTC-CTAATCTCGGAGCCAAT
66 CGCTGGTTGTC-AATAAACAACTTCTC-AATTTCAGAGCCAAT
255797 TTCAACTTCAC-GACGAAGG
1 TTCAACTTCACAG-CGAAGG
255816 GACCGCTGGT
Statistics
Matches: 1018, Mismatches: 56, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
105 1 0.00
106 975 0.96
107 42 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
Found at i:254899 original size:255 final size:255
Alignment explanation
Indices: 254442--254903 Score: 834
Period size: 255 Copynumber: 1.8 Consensus size: 255
254432 CAATTCAAGA
* *
254442 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1 CTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* *
254507 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTAGTCAATAAACAATTTCCC
66 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTAGTCAATAAACAACTTCCC
* *
254572 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGCTATTGGACTCCAGACAACGCAAGTTCAACT
131 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
254637 TCACGACGAAGGCTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
196 TCACGACGAAGGCTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
254697 CTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
1 CTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* *
254762 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTCGTCAATAAACAACTTCTC
66 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTAGTCAATAAACAACTTCCC
* *
254827 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGTAAGTTCAACT
131 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
254892 TCACGACGAAGG
196 TCACGACGAAGG
254904 GACCGCTGGT
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
255 197 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (255 bp):
CTGGTCGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTAGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGCTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
Found at i:255852 original size:276 final size:276
Alignment explanation
Indices: 255521--256044 Score: 877
Period size: 276 Copynumber: 1.9 Consensus size: 276
255511 ACAACGCAAG
* * *
255521 TTCAACTTCATGACGAAGGGACCGATGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
255586 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
*
255651 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
131 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* * * * *
255716 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCC
196 ACCCAAGACAACACAAGATCAACTTCACGACAAAGGGACCGCTGATTGTCAAAAAAACAACTTCC
255781 TAATCTCGGAGCCAAT
261 TAATCTCGGAGCCAAT
* * *
255797 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
255862 CAACTTCACAACGAAGGCTATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
66 CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
* *
255927 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATATTGG
131 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* *
255992 ACCCAAGACAACACAAGATCAACTTCACGACAAAGGGGCGGCTGATTGTCAAA
196 ACCCAAGACAACACAAGATCAACTTCACGACAAAGGGACCGCTGATTGTCAAA
256045 TTCATTCAGA
Statistics
Matches: 229, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
276 229 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (276 bp):
TTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
ACCCAAGACAACACAAGATCAACTTCACGACAAAGGGACCGCTGATTGTCAAAAAAACAACTTCC
TAATCTCGGAGCCAAT
Found at i:255869 original size:63 final size:64
Alignment explanation
Indices: 255733--255878 Score: 231
Period size: 63 Copynumber: 2.3 Consensus size: 64
255723 ACAACGCAAG
* *
255733 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCCTAATCTCGGAGCCAAT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCCCAATCTCAGAGCCAAT
* * *
255797 TTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AATAAACAATTTCCCAATTTCAGAGCCAAT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCCCAATCTCAGAGCCAAT
*
255860 TTCAACTTCACAACGAAGG
1 TTCAACTTCACGACGAAGG
255879 CTATTGGACT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 43 0.57
64 33 0.43
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (64 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCCCAATCTCAGAGCCAAT
Found at i:255909 original size:170 final size:169
Alignment explanation
Indices: 255627--255974 Score: 615
Period size: 170 Copynumber: 2.1 Consensus size: 169
255617 ACAACGCAAG
255627 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
* *
255692 CAACTTCACAGCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAACGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
* *
255757 CTGGTTGTCAAAAAAACAACTTCCTAATCTCGGAGCCAAT
131 CTGGTTGTC-AAAAAACAACTTCCCAATCTCAGAGCCAAT
255797 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
* *
255862 CAACTTCACAACGAAGGCTATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
66 CAACTTCACAACGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
* *
255927 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
131 CTGGTTGTCAAAAAACAACTTCCCAATCTCAGAGCCAAT
255966 TTCAACTTC
1 TTCAACTTC
255975 TCAGCGAAGG
Statistics
Matches: 170, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
169 35 0.21
170 135 0.79
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (169 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGAACCG
CTGGTTGTCAAAAAACAACTTCCCAATCTCAGAGCCAAT
Found at i:255983 original size:106 final size:106
Alignment explanation
Indices: 255797--256190 Score: 398
Period size: 106 Copynumber: 3.8 Consensus size: 106
255787 CGGAGCCAAT
* *
255797 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* * *
255862 CAACTTCACAACGAAGGCTATTGGACTCAAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAG
255903 TTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* *
255968 CAACTTCTCAGCGAAGGATATTGGACCCAAGACAACACAAG
66 CAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAG
* * ** * * *
256009 ATCAACTTCACGACAAAGGGGCGGCTGATTGTC-----A-AA-TT--C-A-TTCAGAGTCAATTT
1 TTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* * * * *
256063 TAACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAG
66 CAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAG
* * ** * ** * * * * *
256104 CTCAATTTCAC-AGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATT
1 TTCAACTTCACGA-CGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATT
* *
256168 TCAACTTCACAGCGGAGGATATT
65 TCAACTTCACAACGAAGGATATT
256191 AGACTCGGAA
Statistics
Matches: 244, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
94 1 0.00
95 74 0.30
96 1 0.00
97 1 0.00
99 2 0.01
100 3 0.01
101 3 0.01
102 2 0.01
104 1 0.00
106 156 0.64
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAG
Found at i:256123 original size:95 final size:95
Alignment explanation
Indices: 255954--256138 Score: 246
Period size: 95 Copynumber: 1.9 Consensus size: 95
255944 ACTTCCCAAT
* * *
255954 TTCAGAGCCAATTTCAACTTCTCAGCGAAGGATATTGGACCCAAGACAACACAAGATCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGATCAACTTCA
*
256019 CGACAAAGGGGCGGCTGATTGTCAAATTCA
66 CGACAAAGGGGCGGCTGACTGTCAAATTCA
* * * * * * *
256049 TTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAGCTCAATTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGATCAACTTCA
*
256114 C-AGCGAAGGGGCGGCTGACTGTCAA
66 CGA-CAAAGGGGCGGCTGACTGTCAA
256139 CAAACAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 1 0.01
95 76 0.99
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (95 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGATCAACTTCA
CGACAAAGGGGCGGCTGACTGTCAAATTCA
Found at i:257482 original size:16 final size:16
Alignment explanation
Indices: 257461--257510 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
257451 GCCACTAATG
257461 TTTATAGATTTCAACT
1 TTTATAGATTTCAACT
257477 TTTATAGATTTCAACT
1 TTTATAGATTTCAACT
*
257493 TTTATAGATTTTAACT
1 TTTATAGATTTCAACT
257509 TT
1 TT
257511 CAGTCTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTATAGATTTCAACT
Found at i:258851 original size:18 final size:18
Alignment explanation
Indices: 258828--258923 Score: 120
Period size: 18 Copynumber: 5.2 Consensus size: 18
258818 GACCGTCACA
*
258828 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
* *
258846 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCCGTTG
*
258864 ACCCGACCCGACCAGTTG
1 ACCCGACCCGACCCGTTG
*
258882 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
258900 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
258921 ACC
1 ACC
258924 GTTGACCGAC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
18 58 0.84
21 11 0.16
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:258927 original size:15 final size:16
Alignment explanation
Indices: 258907--258940 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
258897 TTGACCCGAC
258907 CCGTTGACC-CGTTGA
1 CCGTTGACCACGTTGA
258922 CCGTTGACCGACGTTGA
1 CCGTTGACC-ACGTTGA
258939 CC
1 CC
258941 AATGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (16 bp):
CCGTTGACCACGTTGA
Found at i:260054 original size:18 final size:18
Alignment explanation
Indices: 260028--260062 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
260018 TCGAAAGGAC
*
260028 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
260046 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
260063 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:266294 original size:68 final size:68
Alignment explanation
Indices: 266185--266320 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
266175 CTCCTCCACT
266185 CTATCATTTATGCTAACCATTTTCTTCGGAGGTCTAGCTTCGGGTCGAATTGCAGACGTTGCTGG
1 CTATCATTTATGCTAACCATTTTCTTCGGAGGTCTAGCTTCGGGTCGAATTGCAGACGTTGCTGG
266250 TGC
66 TGC
266253 CTATCATTTATGCTAACCATTTTCTTCGGAGGTCTAGCTTCGGGTCGAATTGCAGACGTTGCTGG
1 CTATCATTTATGCTAACCATTTTCTTCGGAGGTCTAGCTTCGGGTCGAATTGCAGACGTTGCTGG
266318 TGC
66 TGC
266321 TTCATCCTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (68 bp):
CTATCATTTATGCTAACCATTTTCTTCGGAGGTCTAGCTTCGGGTCGAATTGCAGACGTTGCTGG
TGC
Found at i:272302 original size:36 final size:37
Alignment explanation
Indices: 272239--272315 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
272229 AAGATGAGAC
272239 AAACCTAGACACTTTATTTCAAATTGGTATCCGAGCT
1 AAACCTAGACACTTTATTTCAAATTGGTATCCGAGCT
272276 AAACCTAGACACTTT-TTTCAAATTGGTATCCGAGCT
1 AAACCTAGACACTTTATTTCAAATTGGTATCCGAGCT
272312 AAAC
1 AAAC
272316 ATTTTCGCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 25 0.62
37 15 0.38
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (37 bp):
AAACCTAGACACTTTATTTCAAATTGGTATCCGAGCT
Found at i:272332 original size:245 final size:247
Alignment explanation
Indices: 272031--272485 Score: 896
Period size: 245 Copynumber: 1.9 Consensus size: 247
272021 TTTAGTACCC
272031 AACCTAGACACTTTATTTCAAATTGGTATCCGAGCTAAACATTTTCGCTCGAATTAGTACTAAAA
1 AACCTAGACACTTTATTTCAAATTGGTATCCGAGCTAAACATTTTCGCTCGAATTAGTACTAAAA
272096 GAATTATTTGTTCTCAAATTGATATCTGAATTTTGATTCAAGCCACCAATACAAAATTGTAAAAA
66 GAATTATTTGTTCTCAAATTGATATCTGAATTTTGATTCAAGCCACCAATACAAAATTGTAAAAA
272161 TTTAATATAAAAGGACAATAG-TTGAATTAAATTCCAAGTACTAACAACCAACAACTCGTTGTCC
131 TTTAATATAAAAGGACAATAGATTGAATTAAATTCCAAGTACTAACAACCAACAACTCGTTGTCC
272225 TAGTAAGATGAGACAAACCTAGACACTTTATTTCAAATTGGTATCCGAGCTA
196 TAGTAAGATGAGACAAACCTAGACACTTTATTTCAAATTGGTATCCGAGCTA
272277 AACCTAGACACTTT-TTTCAAATTGGTATCCGAGCTAAACATTTTCGCTCGAATTAGTACTAAAA
1 AACCTAGACACTTTATTTCAAATTGGTATCCGAGCTAAACATTTTCGCTCGAATTAGTACTAAAA
272341 GAATTATTTGTTCTCAAATTGATATCTGAATTTTGATTCAAGCCACCAATACAAAATTGTAAAAA
66 GAATTATTTGTTCTCAAATTGATATCTGAATTTTGATTCAAGCCACCAATACAAAATTGTAAAAA
272406 TTTAATATAAAAGGACAATAGATTGAATTAAATTCCAAGTACTAACAACCAACAACTCGTTGTCC
131 TTTAATATAAAAGGACAATAGATTGAATTAAATTCCAAGTACTAACAACCAACAACTCGTTGTCC
272471 TAGTAAGATGAGACA
196 TAGTAAGATGAGACA
272486 TTAAATCCCT
Statistics
Matches: 208, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
245 136 0.65
246 72 0.35
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (247 bp):
AACCTAGACACTTTATTTCAAATTGGTATCCGAGCTAAACATTTTCGCTCGAATTAGTACTAAAA
GAATTATTTGTTCTCAAATTGATATCTGAATTTTGATTCAAGCCACCAATACAAAATTGTAAAAA
TTTAATATAAAAGGACAATAGATTGAATTAAATTCCAAGTACTAACAACCAACAACTCGTTGTCC
TAGTAAGATGAGACAAACCTAGACACTTTATTTCAAATTGGTATCCGAGCTA
Found at i:275777 original size:16 final size:17
Alignment explanation
Indices: 275751--275785 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
275741 GTGGCCAACC
*
275751 AAATCCAAAACCAGACA
1 AAATCCAAAACCACACA
275768 AAATCC-AAACCACACA
1 AAATCCAAAACCACACA
275784 AA
1 AA
275786 CACTCTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.60, C:0.31, G:0.03, T:0.06
Consensus pattern (17 bp):
AAATCCAAAACCACACA
Found at i:276374 original size:18 final size:17
Alignment explanation
Indices: 276348--276381 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
276338 TAAGATCTTG
276348 ATTTCATGAATTTGCAGA
1 ATTTCATG-ATTTGCAGA
*
276366 ATTTTATGATTTGCAG
1 ATTTCATGATTTGCAG
276382 TGGGAAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (17 bp):
ATTTCATGATTTGCAGA
Found at i:279135 original size:99 final size:99
Alignment explanation
Indices: 279012--279204 Score: 296
Period size: 99 Copynumber: 1.9 Consensus size: 99
279002 AATTTCATAT
* * *
279012 TCAAGTTGACTTACAAAATAGAACTTGAATAACTCGAAATTTTTAGTGATTTGTGGATTGATTTT
1 TCAAGTTAACTTACAAAATAGAACTTGAATAACTCGAAATATTTAGTGATTTGTAGATTGATTTT
279077 CAAGCTTGAGTAGAGCTATAAAATATATACAATA
66 CAAGCTTGAGTAGAGCTATAAAATATATACAATA
* * * *
279111 TCAAGTTAAGTTATAAAATAGAACTTTAATAACTCGAAATATTTAGTGATTTGTATATTGATTTT
1 TCAAGTTAACTTACAAAATAGAACTTGAATAACTCGAAATATTTAGTGATTTGTAGATTGATTTT
* * *
279176 CAAGTTTGAGTCGAGTTATAAAATATATA
66 CAAGCTTGAGTAGAGCTATAAAATATATA
279205 TATATATATG
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 84 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (99 bp):
TCAAGTTAACTTACAAAATAGAACTTGAATAACTCGAAATATTTAGTGATTTGTAGATTGATTTT
CAAGCTTGAGTAGAGCTATAAAATATATACAATA
Found at i:289494 original size:13 final size:13
Alignment explanation
Indices: 289476--289503 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
289466 TTTTGAGTTA
289476 AATTAATTTTTTT
1 AATTAATTTTTTT
289489 AATTAATTTTTTT
1 AATTAATTTTTTT
289502 AA
1 AA
289504 GATTAATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTAATTTTTTT
Found at i:290646 original size:28 final size:28
Alignment explanation
Indices: 290605--290664 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
290595 TTTTGTCCCT
*
290605 CTAAAATTTTATAAGTTCAAATTCACCC
1 CTAAAATTTAATAAGTTCAAATTCACCC
*
290633 CTAAAATTTAATAAGTTCAAATTCACGC
1 CTAAAATTTAATAAGTTCAAATTCACCC
290661 CTAA
1 CTAA
290665 TATAAAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (28 bp):
CTAAAATTTAATAAGTTCAAATTCACCC
Found at i:296555 original size:151 final size:151
Alignment explanation
Indices: 296333--296608 Score: 552
Period size: 151 Copynumber: 1.8 Consensus size: 151
296323 ATGGCTAACG
296333 AATTTCAACGTGCTTGTCTCATGTCACACCAAAATTATGTCCTTTTGATGAGGCTGGTTTGATGC
1 AATTTCAACGTGCTTGTCTCATGTCACACCAAAATTATGTCCTTTTGATGAGGCTGGTTTGATGC
296398 CCAAAAGACCTAAAATGACGTATTGTTGGAGTAAAATTATTAAATTATTGCATTTGAATGATGGC
66 CCAAAAGACCTAAAATGACGTATTGTTGGAGTAAAATTATTAAATTATTGCATTTGAATGATGGC
296463 TATGAATTTCAACGTGCTGTC
131 TATGAATTTCAACGTGCTGTC
296484 AATTTCAACGTGCTTGTCTCATGTCACACCAAAATTATGTCCTTTTGATGAGGCTGGTTTGATGC
1 AATTTCAACGTGCTTGTCTCATGTCACACCAAAATTATGTCCTTTTGATGAGGCTGGTTTGATGC
296549 CCAAAAGACCTAAAATGACGTATTGTTGGAGTAAAATTATTAAATTATTGCATTTGAATG
66 CCAAAAGACCTAAAATGACGTATTGTTGGAGTAAAATTATTAAATTATTGCATTTGAATG
296609 GATTCAAACT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 125 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (151 bp):
AATTTCAACGTGCTTGTCTCATGTCACACCAAAATTATGTCCTTTTGATGAGGCTGGTTTGATGC
CCAAAAGACCTAAAATGACGTATTGTTGGAGTAAAATTATTAAATTATTGCATTTGAATGATGGC
TATGAATTTCAACGTGCTGTC
Found at i:298607 original size:60 final size:58
Alignment explanation
Indices: 298436--298612 Score: 185
Period size: 60 Copynumber: 3.0 Consensus size: 58
298426 TTACATGTTT
** * *
298436 GGATGAAATTGAAATATTCAAAAGTTTGGGACCAATTTAGAAATAGGGTCATAGTTTAG
1 GGATGAAATTGAAATATTCAAAAGTTTAAGACCAATTTA-AAATAAGGTTATAGTTTAG
* * * * * *
298495 GGATGAAAAT-ATAATGTTCTAAAGTTTAATGACTAATTTAGAATGAGAGTTATAGTTTAG
1 GGATGAAATTGA-AATATTCAAAAGTTTAA-GACCAATTTAAAATAAG-GTTATAGTTTAG
* *
298555 GGATGTAATTGGAATATTCAAAAGTTTAAGAACCAATTTAAAATTAAGGTTATAGTTT
1 GGATGAAATTGAAATATTCAAAAGTTTAAG-ACCAATTTAAAA-TAAGGTTATAGTTT
298613 GAGGACCAAT
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
58 1 0.01
59 27 0.29
60 63 0.67
61 3 0.03
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.34
Consensus pattern (58 bp):
GGATGAAATTGAAATATTCAAAAGTTTAAGACCAATTTAAAATAAGGTTATAGTTTAG
Found at i:299067 original size:2 final size:2
Alignment explanation
Indices: 299060--299120 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
299050 AATTAAAAAC
299060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
299101 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
299121 GTGTGTGTGT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:303128 original size:12 final size:12
Alignment explanation
Indices: 303111--303138 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
303101 CCTGGACAAA
303111 AAAAATTAAAAT
1 AAAAATTAAAAT
303123 AAAAATTAAAAT
1 AAAAATTAAAAT
303135 AAAA
1 AAAA
303139 TAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATTAAAAT
Found at i:305607 original size:60 final size:60
Alignment explanation
Indices: 305502--305634 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
305492 GAACATATGA
** * * * * *
305502 ATAGTCAGTTGACTATTTTGTAATTTTTAATAGTCGAGCGGCTCAAAAAAGCAAT-TCTCT
1 ATAGTCAGGGGACTACTATGTAACTTTTAATAGTCAAGCGACTCAAAAAAGCAATATC-CT
* * * *
305562 ATAGTCAGGGGACTACTATGTAACTTTTAATAGTCAAGTGACTCAATAAATCAGTATCCT
1 ATAGTCAGGGGACTACTATGTAACTTTTAATAGTCAAGCGACTCAAAAAAGCAATATCCT
*
305622 ATAGTCGGGGGAC
1 ATAGTCAGGGGAC
305635 CATTTGTGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 58 0.97
61 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (60 bp):
ATAGTCAGGGGACTACTATGTAACTTTTAATAGTCAAGCGACTCAAAAAAGCAATATCCT
Found at i:309208 original size:9 final size:11
Alignment explanation
Indices: 309171--309216 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
309161 ACACCAATTT
309171 TAAATATAAATA
1 TAAA-ATAAATA
309183 GTAAAATAAATA
1 -TAAAATAAATA
309195 TAAAA-AAA-A
1 TAAAATAAATA
*
309204 TAAAATATATA
1 TAAAATAAATA
309215 TA
1 TA
309217 CTCATGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 6 0.20
10 5 0.17
11 8 0.27
12 7 0.23
13 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
TAAAATAAATA
Found at i:309425 original size:2 final size:2
Alignment explanation
Indices: 309418--309464 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
309408 CCTTAGATTA
309418 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
309460 AT AT A
1 AT AT A
309465 GTCTTCCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:310088 original size:29 final size:29
Alignment explanation
Indices: 310056--310113 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
310046 ACATTCTCGG
*
310056 AAATGTTAAAAGGTTAACATATTAGGTAA
1 AAATGTTAAAAGATTAACATATTAGGTAA
310085 AAATGTTAAAAGATTAACATATTAGGTAA
1 AAATGTTAAAAGATTAACATATTAGGTAA
310114 CGAAATTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (29 bp):
AAATGTTAAAAGATTAACATATTAGGTAA
Found at i:310764 original size:2 final size:2
Alignment explanation
Indices: 310757--310795 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
310747 AGAAGGTGGA
310757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310796 AACTCTTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:316407 original size:4 final size:4
Alignment explanation
Indices: 316398--316422 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
316388 ATATTTACCC
316398 TAGA TAGA TAGA TAGA TAGA TAGA T
1 TAGA TAGA TAGA TAGA TAGA TAGA T
316423 TTTATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (4 bp):
TAGA
Found at i:317795 original size:20 final size:21
Alignment explanation
Indices: 317762--317801 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
317752 ACTTGATTAA
*
317762 AAAAATTAATGAATAAAAATT
1 AAAAATTAAAGAATAAAAATT
*
317783 AAAAA-TAAAGAATGAAAAT
1 AAAAATTAAAGAATAAAAAT
317802 GAAATGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAATTAAAGAATAAAAATT
Found at i:317812 original size:20 final size:20
Alignment explanation
Indices: 317789--317827 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
317779 AATTAAAAAT
317789 AAAGAATGAAAATG-AAATGC
1 AAAGAAT-AAAATGCAAATGC
*
317809 AAAGACTAAAATGCAAATG
1 AAAGAATAAAATGCAAATG
317828 ATGCAGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (20 bp):
AAAGAATAAAATGCAAATGC
Found at i:320943 original size:64 final size:64
Alignment explanation
Indices: 320842--320962 Score: 233
Period size: 64 Copynumber: 1.9 Consensus size: 64
320832 GCTCAGCCAT
320842 AATTAGCTAGTAGGGATTTTCATGTGATTTAAGACGTGAAAAGAAACAGCATTTAATGAGCAAC
1 AATTAGCTAGTAGGGATTTTCATGTGATTTAAGACGTGAAAAGAAACAGCATTTAATGAGCAAC
*
320906 AATTAGCTAGTAGGGTTTTTCATGTGATTTAAGACGTGAAAAGAAACAGCATTTAAT
1 AATTAGCTAGTAGGGATTTTCATGTGATTTAAGACGTGAAAAGAAACAGCATTTAAT
320963 TCTTAATTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (64 bp):
AATTAGCTAGTAGGGATTTTCATGTGATTTAAGACGTGAAAAGAAACAGCATTTAATGAGCAAC
Found at i:321323 original size:100 final size:105
Alignment explanation
Indices: 321189--321376 Score: 296
Period size: 108 Copynumber: 1.8 Consensus size: 105
321179 AATTCACAAA
*
321189 TTAAAAATTATGATTATTGGAATCCATTAAATG-A-A-T-A-AAAGAAAATTTTGTTCTTCCTAG
1 TTAAAAAATATGATTATTGGAATCCATTAAATGAACAGTGATAAAGAAAATTTTGTTCTTCCTAG
321249 AGAAAATATATCATGTTAGTTGAATGTTCAATTTAATCCG
66 AGAAAATATATCATGTTAGTTGAATGTTCAATTTAATCCG
*
321289 TTAAAAAATATGATTATTGGAATCCATTAAATGAACTCAGTGATTAAAGAAAATTTTGTTCTTCT
1 TTAAAAAATATGATTATTGGAATCCATTAAATGAA--CAGTGA-TAAAGAAAATTTTGTTCTTCC
321354 TAGAGAAAATATATCATGTTAGT
63 TAGAGAAAATATATCATGTTAGT
321377 CATGGTCGTC
Statistics
Matches: 78, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
100 32 0.41
101 1 0.01
104 1 0.01
105 1 0.01
106 1 0.01
108 42 0.54
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (105 bp):
TTAAAAAATATGATTATTGGAATCCATTAAATGAACAGTGATAAAGAAAATTTTGTTCTTCCTAG
AGAAAATATATCATGTTAGTTGAATGTTCAATTTAATCCG
Found at i:329791 original size:181 final size:182
Alignment explanation
Indices: 329487--329849 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 182
329477 TACATATTTC
329487 TTAACGTTATCGATTCATTTTATTTTAGCCTCTCAGTTATGTCATATATTCGTTATGGATTAAGA
1 TTAACGTTATCGATTCATTTTATTTTAGCCTCTCAGTTATGTCATATATTCGTTATGGATTAAGA
329552 GTGGAAGAACTTAAACTAGACGGGCCGATAATGTTAGAGACTATTTATTCTTAATTTTTAAATTG
66 GTGGAAGAACTTAAACTAGACGGGCCGATAATGTTAGAGACTATTTATTCTTAATTTTTAAATTG
329617 ATGATCGAAGTTGGACATACCCTAAAT-AAAGGGACTATTCACATAGTTTAT
131 ATGATCGAAGTTGGACATACCCTAAATAAAAGGGACTATTCACATAGTTTAT
329668 TTAACGTTATCGATTCATTTTATTTTAGCCTCTCAGTTATGTCATATATTCGTTATGGATTAAGA
1 TTAACGTTATCGATTCATTTTATTTTAGCCTCTCAGTTATGTCATATATTCGTTATGGATTAAGA
329733 GTGGAAGAACTTAAACTAGACGGGCCGATAATGTTAGAGACTATTTATTCTTAATTTTTAAATTG
66 GTGGAAGAACTTAAACTAGACGGGCCGATAATGTTAGAGACTATTTATTCTTAATTTTTAAATTG
329798 ATGATCGAAGTTGGACATACCCTAAATAAAAGGGACTATTCACATAGTTTAT
131 ATGATCGAAGTTGGACATACCCTAAATAAAAGGGACTATTCACATAGTTTAT
329850 CCGTATTTTA
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 157 0.87
182 24 0.13
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (182 bp):
TTAACGTTATCGATTCATTTTATTTTAGCCTCTCAGTTATGTCATATATTCGTTATGGATTAAGA
GTGGAAGAACTTAAACTAGACGGGCCGATAATGTTAGAGACTATTTATTCTTAATTTTTAAATTG
ATGATCGAAGTTGGACATACCCTAAATAAAAGGGACTATTCACATAGTTTAT
Found at i:329887 original size:2 final size:2
Alignment explanation
Indices: 329880--329912 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
329870 ACATATTAGA
329880 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
329913 TTACTTGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:331370 original size:22 final size:22
Alignment explanation
Indices: 331342--331400 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
331332 ATTAAATCTC
331342 TATTTTTATTAAATAAAAATAA
1 TATTTTTATTAAATAAAAATAA
331364 TATTTTTATTAAATAAAAATAA
1 TATTTTTATTAAATAAAAATAA
*
331386 TATTTTTAATAAATA
1 TATTTTTATTAAATA
331401 TATTATTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTTTTATTAAATAAAAATAA
Found at i:331398 original size:18 final size:20
Alignment explanation
Indices: 331346--331408 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 20
331336 AATCTCTATT
331346 TTTATTAAATAAAAATAATA
1 TTTATTAAATAAAAATAATA
331366 TTTTTATTAAATAAAAATAATA
1 --TTTATTAAATAAAAATAATA
* *
331388 TTT-TT-AATAAATATATTA
1 TTTATTAAATAAAAATAATA
331406 TTT
1 TTT
331409 CAACTCGAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.36
19 2 0.05
20 3 0.08
22 20 0.51
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATTAAATAAAAATAATA
Found at i:331772 original size:18 final size:17
Alignment explanation
Indices: 331746--331783 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
331736 TTATATTCTC
331746 TTTTTTCTTCTATTTTA
1 TTTTTTCTTCTATTTTA
331763 TTTTTATCTTCTATTTTA
1 TTTTT-TCTTCTATTTTA
331781 TTT
1 TTT
331784 ATTGTGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTCTATTTTA
Found at i:334158 original size:5 final size:5
Alignment explanation
Indices: 334148--334173 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
334138 CAGCTCTCTG
334148 TCATC TCATC TCATC TCATC TCATC T
1 TCATC TCATC TCATC TCATC TCATC T
334174 GATCCCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.42
Consensus pattern (5 bp):
TCATC
Found at i:335929 original size:2 final size:2
Alignment explanation
Indices: 335922--335976 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
335912 GCTTCTTTGG
*
335922 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
335964 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
335977 GTGTGTGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:336349 original size:28 final size:29
Alignment explanation
Indices: 336303--336364 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
336293 AAATTAATAA
*
336303 AAAAATGATCAAAAATATTATTAGACA-T
1 AAAAACGATCAAAAATATTATTAGACACT
* * *
336331 AAAAACGATCGAAAGTATTATTAGATACT
1 AAAAACGATCAAAAATATTATTAGACACT
336360 AAAAA
1 AAAAA
336365 ATAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (29 bp):
AAAAACGATCAAAAATATTATTAGACACT
Found at i:336377 original size:12 final size:12
Alignment explanation
Indices: 336360--336392 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
336350 ATTAGATACT
336360 AAAAAATAATTA
1 AAAAAATAATTA
336372 AAAAAAT-ATTA
1 AAAAAATAATTA
336383 AAAAAATAAT
1 AAAAAATAAT
336393 ATTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATAATTA
Found at i:336899 original size:27 final size:27
Alignment explanation
Indices: 336861--336914 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
336851 GTCGCTATCC
336861 TCTCAGACTACTTTTAGATGTTGAATT
1 TCTCAGACTACTTTTAGATGTTGAATT
336888 TCTCAGACTACTTTTAGATGTTGAATT
1 TCTCAGACTACTTTTAGATGTTGAATT
336915 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (27 bp):
TCTCAGACTACTTTTAGATGTTGAATT
Found at i:337379 original size:24 final size:24
Alignment explanation
Indices: 337345--337391 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
337335 CCAACACGCT
337345 AGCATCCGAGGCCATCCGACCGAG
1 AGCATCCGAGGCCATCCGACCGAG
* *
337369 AGCATCTGAGGCCATCCTACCGA
1 AGCATCCGAGGCCATCCGACCGA
337392 TGCCATCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.13
Consensus pattern (24 bp):
AGCATCCGAGGCCATCCGACCGAG
Found at i:337398 original size:24 final size:24
Alignment explanation
Indices: 337347--337401 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
337337 AACACGCTAG
*
337347 CATCCGAGGCCATCCGACCGAGAG
1 CATCCGAGGCCATCCGACCGAGAC
* *
337371 CATCTGAGGCCATCCTACCGATG-C
1 CATCCGAGGCCATCCGACCGA-GAC
337395 CATCCGA
1 CATCCGA
337402 ACGAGATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.15
Consensus pattern (24 bp):
CATCCGAGGCCATCCGACCGAGAC
Found at i:337434 original size:23 final size:23
Alignment explanation
Indices: 337398--337452 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
337388 CCGATGCCAT
*
337398 CCGAACGAGATATGCGAGGGCAA
1 CCGAGCGAGATATGCGAGGGCAA
* *
337421 CTGAGCGAGCTATGCGAGGGCAA
1 CCGAGCGAGATATGCGAGGGCAA
337444 CCGAGCGAG
1 CCGAGCGAG
337453 GGTAGGTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.38, T:0.09
Consensus pattern (23 bp):
CCGAGCGAGATATGCGAGGGCAA
Found at i:337569 original size:23 final size:23
Alignment explanation
Indices: 337535--337594 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
337525 CTCGGTTGCC
337535 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
*
337558 CTCGGTTGCCCTCACATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
337581 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
337595 GATGCTCTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 2 0.06
23 29 0.94
ACGTcount: A:0.12, C:0.37, G:0.25, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:337597 original size:10 final size:10
Alignment explanation
Indices: 337582--337638 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
337572 CATAGCTCGT
337582 TCGGATGGCC
1 TCGGATGGCC
337592 TCGGAT-GCTC
1 TCGGATGGC-C
337602 TCGGATGGCC
1 TCGGATGGCC
*
337612 TCGGAT-GCTT
1 TCGGATGGC-C
337622 TCGGATGGCC
1 TCGGATGGCC
337632 TCGGATG
1 TCGGATG
337639 CCCAGCGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 33 0.80
11 4 0.10
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:337607 original size:20 final size:20
Alignment explanation
Indices: 337582--337639 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
337572 CATAGCTCGT
337582 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
337602 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
337622 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
337640 CCAGCGTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:337712 original size:29 final size:29
Alignment explanation
Indices: 337679--337735 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
337669 CAATCTCTTG
337679 TAGGTCG-CCGGGAAGACATGGCGACCTAA
1 TAGGTCGTCC-GGAAGACATGGCGACCTAA
*
337708 TAGGTCGTCCGGAAGGCATGGCGACCTA
1 TAGGTCGTCCGGAAGACATGGCGACCTA
337736 CAGCCAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.16
Consensus pattern (29 bp):
TAGGTCGTCCGGAAGACATGGCGACCTAA
Found at i:339524 original size:5 final size:5
Alignment explanation
Indices: 339514--339563 Score: 86
Period size: 5 Copynumber: 10.4 Consensus size: 5
339504 TTAATGGCTC
339514 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTC-T TTC-T TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
339562 TT
1 TT
339564 AATTGAAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.18
5 36 0.82
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTCTT
Found at i:341170 original size:60 final size:60
Alignment explanation
Indices: 341059--341171 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
341049 ATAGTCTGAC
* * * **
341059 GATCATTTTATAATTTTTAATAGTTTAATGACTCAATAAAATAACGTTTTATAATTAAAG
1 GATCATTTTATAACTTTTAATAGTTTAAGGACTCAACAAAATAACACTTTATAATTAAAG
* * *
341119 GATCATTTTGTAACTTTTAATAG-TTAAGGGACTCGACAAAGTAACACTTTATA
1 GATCATTTTATAACTTTTAATAGTTTAA-GGACTCAACAAAATAACACTTTATA
341172 GTTGAGGGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 4 0.09
60 40 0.91
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTTTAAGGACTCAACAAAATAACACTTTATAATTAAAG
Found at i:345044 original size:43 final size:43
Alignment explanation
Indices: 344983--345068 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
344973 TGATAAAGTG
344983 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
1 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
345026 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
1 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
345069 GTCAAAACTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (43 bp):
CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
Found at i:347453 original size:106 final size:106
Alignment explanation
Indices: 347324--347816 Score: 914
Period size: 106 Copynumber: 4.7 Consensus size: 106
347314 TGTGCACGAT
* *
347324 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
347389 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
347430 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTACAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
347495 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
347536 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
347601 TTGGCTTTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
347642 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
347707 TTCGCTTTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
347748 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
347813 TTGG
66 TTGG
347817 GAAATGTTTA
Statistics
Matches: 378, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 378 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
Found at i:347626 original size:212 final size:211
Alignment explanation
Indices: 347324--348044 Score: 1205
Period size: 212 Copynumber: 3.5 Consensus size: 211
347314 TGTGCACGAT
*
347324 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
347389 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
66 TTGGCTCTGAAATTG-GAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
347454 GCGTTGTCTGGAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGG
130 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGG
347519 TTATTGACAACCAGCGG
195 TTATTGACAACCAGCGG
347536 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
347601 TTGGCTTTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
66 TTGGCTCTGAAATTG-GAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * *
347666 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTCGCTTTGAAATTGAGAAGTTGG
130 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGG
347731 TTATTGACAACCAGCGG
195 TTATTGACAACCAGCGG
*
347748 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
347813 TTGG----GAAA-T----G-T--TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 TTGGCTCTGAAATTGGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
347866 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTT
131 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGT
*
347931 TGTTGACAACCAGCGG
196 TATTGACAACCAGCGG
* * *
347947 TCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
**
348012 TTGGCTCTGAAATTGGAAAGTTATTTATTGACA
66 TTGGCTCTGAAATTGG-AAGTTGGTTATTGACA
348045 GACAACTTTT
Statistics
Matches: 482, Mismatches: 14, Indels: 26
0.92 0.03 0.05
Matches are distributed among these distances:
199 185 0.38
201 1 0.00
202 1 0.00
203 4 0.01
204 1 0.00
207 1 0.00
208 4 0.01
209 1 0.00
210 1 0.00
212 283 0.59
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (211 bp):
TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCTCTGAAATTGGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGT
TATTGACAACCAGCGG
Found at i:347811 original size:43 final size:43
Alignment explanation
Indices: 347750--347904 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
347740 ACCAGCGGTC
347750 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
* * * * * ** ***
347793 CCTTCGTTGTGAAGTTGAAATTGGGAAATGTT-TATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-----ACGTTGTCTGGA-GTCCA-ATAT
*
347842 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
*
347886 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
347905 ATTGGCTCTG
Statistics
Matches: 81, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
43 38 0.47
44 1 0.01
45 6 0.07
46 4 0.05
47 4 0.05
48 7 0.09
49 1 0.01
50 20 0.25
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
Found at i:347864 original size:199 final size:200
Alignment explanation
Indices: 347607--348015 Score: 721
Period size: 199 Copynumber: 2.0 Consensus size: 200
347597 GAAATTGGCT
* *
347607 TTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
1 TTGAAATTGGGAAGATGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
*
347672 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTCGCTTTGAAATTGAGAAGTTGGTTATTG
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTCGCTCTGAAATTGAGAAGTTGGTTATTG
* *
347737 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTG
131 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTG
347802 TGAAG
196 TGAAG
* *
347807 TTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 TTGAAATTGGGAAGATGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
* * *
347871 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTG
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTCGCTCTGAAATTGAGAAGTTGGTTATTG
347936 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTG
131 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTG
348001 TGAAG
196 TGAAG
348006 TTGAAATTGG
1 TTGAAATTGG
348016 CTCTGAAATT
Statistics
Matches: 199, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
199 187 0.94
200 12 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (200 bp):
TTGAAATTGGGAAGATGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTCGCTCTGAAATTGAGAAGTTGGTTATTG
ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTG
TGAAG
Found at i:347890 original size:93 final size:93
Alignment explanation
Indices: 347713--348015 Score: 417
Period size: 93 Copynumber: 3.1 Consensus size: 93
347703 GAAATTCGCT
* * *
347713 TTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
1 TTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
347778 TCTGGAGTCCAATATCCTTCGTTGTGAAG
65 TCTGGAGTCCAATATCCTTCGTTGTGAAG
*
347807 TTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
347872 CTGGAGTCCAATATCCTTCGTTGTGAAG
66 CTGGAGTCCAATATCCTTCGTTGTGAAG
*
347900 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1 TTGAAATT-G----G-----GA-AA--TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
347965 GAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
53 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
348006 TTGAAATTGG
1 TTGAAATTGG
348016 CTCTGAAATT
Statistics
Matches: 188, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
93 85 0.45
94 13 0.07
98 1 0.01
101 1 0.01
103 2 0.01
104 2 0.01
105 1 0.01
106 83 0.44
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (93 bp):
TTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAG
Found at i:348006 original size:106 final size:105
Alignment explanation
Indices: 347808--348044 Score: 386
Period size: 106 Copynumber: 2.2 Consensus size: 105
347798 GTTGTGAAGT
* * *
347808 TGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATT-GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGT
*
347872 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
347913 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGT
1 TGAAATTG-GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGT
347978 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
348019 TGAAATTGGAAAGTTATTTATTGACA
1 TGAAATTGG-AAGTTGTTTATTGACA
348045 GACAACTTTT
Statistics
Matches: 122, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
104 1 0.01
105 11 0.09
106 110 0.90
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (105 bp):
TGAAATTGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTC
TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:352198 original size:43 final size:43
Alignment explanation
Indices: 352137--352222 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
352127 TGATAAAGTG
352137 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
1 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
352180 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
1 CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
352223 GTCAAAACTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (43 bp):
CTGAGGTGGACCACGTGCTTGAAGATTCCGGTCATTGGAAAGC
Found at i:354869 original size:111 final size:111
Alignment explanation
Indices: 354678--354899 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
354668 TATAAATCAT
* * *
354678 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTTAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
354743 TATTTAGTTGATTTATTTAATGCATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
354789 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
354854 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAATAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
354900 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:358096 original size:12 final size:12
Alignment explanation
Indices: 358044--358100 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
358034 ATGATGGAAG
358044 TGATGATGAGTT
1 TGATGATGAGTT
358056 TGACT-ATGAGTT
1 TGA-TGATGAGTT
* *
358068 TGACGATGAATT
1 TGATGATGAGTT
358080 TGATGATGAGTT
1 TGATGATGAGTT
*
358092 CGATGATGA
1 TGATGATGA
358101 TGAGGATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 37 0.97
13 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.30, T:0.37
Consensus pattern (12 bp):
TGATGATGAGTT
Found at i:358885 original size:6 final size:6
Alignment explanation
Indices: 358869--358899 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
358859 TACAAGGACT
*
358869 ACCAGC TCCAGC ACCAGC ACCAGC ACCAGC A
1 ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC A
358900 GCAATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.48, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCAGC
Found at i:360966 original size:24 final size:24
Alignment explanation
Indices: 360929--360992 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
360919 GAAAATTAAG
* * * *
360929 TAAACGACCCTATAAATGATTCGA
1 TAAACGAACTTATAAATAAATCGA
**
360953 TAAATTAACTTATAAATAAATCGA
1 TAAACGAACTTATAAATAAATCGA
360977 TAAACGAACTTATAAA
1 TAAACGAACTTATAAA
360993 CAAGTCTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (24 bp):
TAAACGAACTTATAAATAAATCGA
Found at i:374609 original size:35 final size:35
Alignment explanation
Indices: 374563--374632 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
374553 AAGAAGTAAG
374563 AAAAGATGTTGGTCCTAAACACCCTTAAAAGCCTT
1 AAAAGATGTTGGTCCTAAACACCCTTAAAAGCCTT
374598 AAAAGATGTTGGTCCTAAACACCCTTAAAAGCCTT
1 AAAAGATGTTGGTCCTAAACACCCTTAAAAGCCTT
374633 TCCTCATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (35 bp):
AAAAGATGTTGGTCCTAAACACCCTTAAAAGCCTT
Found at i:376516 original size:29 final size:29
Alignment explanation
Indices: 376483--376544 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
376473 ATAACATCTT
* *
376483 ATAGTCATAGGGTTATTTTGTAACTTTTA
1 ATAGTCATAGGATTATTTTGCAACTTTTA
* *
376512 ATAGTTATAGGATTATTTTGCAATTTTTA
1 ATAGTCATAGGATTATTTTGCAACTTTTA
376541 ATAG
1 ATAG
376545 CCAGATGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (29 bp):
ATAGTCATAGGATTATTTTGCAACTTTTA
Found at i:376950 original size:35 final size:36
Alignment explanation
Indices: 376876--376953 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
376866 AACACAGTCA
* **
376876 TCAATTACATTCTAAACCCCAAAATCCAAAAATGTT
1 TCAATTACACTCTAAACCCCAAAATCCAAAAATACT
* *
376912 TCAATTACACTCTAAACCTCAAATTCC-AAAATACT
1 TCAATTACACTCTAAACCCCAAAATCCAAAAATACT
376947 TCAATTA
1 TCAATTA
376954 TATGCCCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 13 0.35
36 24 0.65
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (36 bp):
TCAATTACACTCTAAACCCCAAAATCCAAAAATACT
Found at i:377827 original size:35 final size:37
Alignment explanation
Indices: 377740--377828 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 37
377730 TGAGAATAGA
* **
377740 TTAT-GAATTTGGGG-TTGGACATGTAATTGAAGTAT
1 TTATAGAATTTGGGGTTTAGACATGTAATTGAAACAT
* *
377775 TTATGGAATTTGAGGTTTAGA-ATGTAATTGAAACAT
1 TTATAGAATTTGGGGTTTAGACATGTAATTGAAACAT
377811 TT-TAGAATTTGGGGTTTA
1 TTATAGAATTTGGGGTTTA
377829 TAACGTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 18 0.39
36 24 0.52
37 4 0.09
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (37 bp):
TTATAGAATTTGGGGTTTAGACATGTAATTGAAACAT
Found at i:388898 original size:195 final size:195
Alignment explanation
Indices: 388566--388956 Score: 782
Period size: 195 Copynumber: 2.0 Consensus size: 195
388556 GATAGAGTGA
388566 CTCCATAAGTCTATCCAAAACATCTGAAGTATCAACATCAAAGTACGGCTTATATGCAGCAACAG
1 CTCCATAAGTCTATCCAAAACATCTGAAGTATCAACATCAAAGTACGGCTTATATGCAGCAACAG
388631 TGAATTTATGAAGCCAACCACCTCCTTGTGATTCATCAGAGCCCCTAGGAGAGCCAGCAGCAGGT
66 TGAATTTATGAAGCCAACCACCTCCTTGTGATTCATCAGAGCCCCTAGGAGAGCCAGCAGCAGGT
388696 CTTGAAAATGAATCTGCCTCAAAAAATGTCATCATTTGTCACCAAACACAACAACTAATTTTGTT
131 CTTGAAAATGAATCTGCCTCAAAAAATGTCATCATTTGTCACCAAACACAACAACTAATTTTGTT
388761 CTCCATAAGTCTATCCAAAACATCTGAAGTATCAACATCAAAGTACGGCTTATATGCAGCAACAG
1 CTCCATAAGTCTATCCAAAACATCTGAAGTATCAACATCAAAGTACGGCTTATATGCAGCAACAG
388826 TGAATTTATGAAGCCAACCACCTCCTTGTGATTCATCAGAGCCCCTAGGAGAGCCAGCAGCAGGT
66 TGAATTTATGAAGCCAACCACCTCCTTGTGATTCATCAGAGCCCCTAGGAGAGCCAGCAGCAGGT
388891 CTTGAAAATGAATCTGCCTCAAAAAATGTCATCATTTGTCACCAAACACAACAACTAATTTTGTT
131 CTTGAAAATGAATCTGCCTCAAAAAATGTCATCATTTGTCACCAAACACAACAACTAATTTTGTT
388956 C
1 C
388957 ATGCAACAAA
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 196 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (195 bp):
CTCCATAAGTCTATCCAAAACATCTGAAGTATCAACATCAAAGTACGGCTTATATGCAGCAACAG
TGAATTTATGAAGCCAACCACCTCCTTGTGATTCATCAGAGCCCCTAGGAGAGCCAGCAGCAGGT
CTTGAAAATGAATCTGCCTCAAAAAATGTCATCATTTGTCACCAAACACAACAACTAATTTTGTT
Found at i:396560 original size:3 final size:3
Alignment explanation
Indices: 396546--396617 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
396536 TGTTTCTATC
*
396546 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
396594 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
396618 TTTATAATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:403791 original size:227 final size:227
Alignment explanation
Indices: 403345--403836 Score: 857
Period size: 227 Copynumber: 2.2 Consensus size: 227
403335 GTTATATTGT
*
403345 AAAGTATCTATCC-TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTAT
1 AAAGTATATA-CCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTAT
*
403409 CTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT
65 ATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT
403474 AATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
130 AATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
*
403539 AAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAATTGAAAAATAAATTACATAACTTTAAAA
403572 AAAGTATATACCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATT
1 AAAGTATATACCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATATTTATTATT
403637 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAAT-ATA-TTTATAAAATATCAAAACAATCAA
63 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
403700 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-
128 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
*
403764 AAAAATATTGAAAAATAAATTACATAACTTTAAAA
193 AAAAAAATTGAAAAATAAATTACATAACTTTAAAA
* * *
403799 AAAGTATATATCATTTTTATAAAAGTGTTCGTACTTAT
1 AAAGTATATACCATTTTTATAAAAGTGTCCATACTTAT
403837 AAAAGTAGGT
Statistics
Matches: 254, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
226 2 0.01
227 109 0.43
228 90 0.35
229 6 0.02
230 47 0.19
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (227 bp):
AAAGTATATACCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATA
TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAAATTGAAAAATAAATTACATAACTTTAAAA
Found at i:403943 original size:21 final size:21
Alignment explanation
Indices: 403887--403941 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
403877 GCTACCGGTT
403887 CGTGTCGATCCAAATTAAAAA
1 CGTGTCGATCCAAATTAAAAA
403908 CGTGTCGATCCAAATT-AAAA
1 CGTGTCGATCCAAATTAAAAA
*
403928 TGTGTCGATCCAAA
1 CGTGTCGATCCAAA
403942 ATGATATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
CGTGTCGATCCAAATTAAAAA
Found at i:403976 original size:20 final size:19
Alignment explanation
Indices: 403939--403998 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
403929 GTGTCGATCC
* * *
403939 AAAATGATATAACAGGTAA
1 AAAATGACAAAACCGGTAA
403958 AAATATGACAAAACCGGTATA
1 AAA-ATGACAAAACCGGTA-A
* *
403979 GAAATGATAAAACCGGTAA
1 AAAATGACAAAACCGGTAA
403998 A
1 A
403999 GCGCTACCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.18
Consensus pattern (19 bp):
AAAATGACAAAACCGGTAA
Found at i:404154 original size:20 final size:19
Alignment explanation
Indices: 404131--404177 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
404121 CGATATATCA
404131 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
404151 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
404171 GGTAAAA
1 GGTAAAA
404178 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:404211 original size:178 final size:181
Alignment explanation
Indices: 403924--404391 Score: 685
Period size: 178 Copynumber: 2.6 Consensus size: 181
403914 GATCCAAATT
* * * *
403924 AAAATGTGTCGATCCAAAATGATATAACAGGTAAAAATATGACAAAACCGGTATA-GAAATGATA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGATA
* * * * *
403988 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
* *
404053 GTGAATTT-AAAGAGAAGCAG-TTTAAATCCTA-AAAGTGTCGATACTTT-TA
129 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
*
404102 AAAATGTATCGATCCAAAACGATATATCAGGTAAAAATATGATAAAACCGGTAACAAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAA
* *
404167 AACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTGT
66 AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
** *
404232 GAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAA
131 GAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
* * * *
404283 AAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAA
*
404348 AACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
404392 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
177 27 0.10
178 109 0.42
179 8 0.03
180 15 0.06
181 103 0.39
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (181 bp):
AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
Found at i:404335 original size:20 final size:19
Alignment explanation
Indices: 404312--404358 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
404302 CGATATAACA
*
404312 GGTAAAAATATGATAAAACT
1 GGTAAAAA-ATGATAAAACC
*
404332 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
404352 GGTAAAA
1 GGTAAAA
404359 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:404354 original size:181 final size:178
Alignment explanation
Indices: 403932--404391 Score: 681
Period size: 181 Copynumber: 2.6 Consensus size: 178
403922 TTAAAATGTG
* *
403932 TCGATCCAAAATGATATAACAGGTAAAAATATGACAAAACCGGTAT-AGAAATGATAAAACCGGT
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGATAAAACCGGT
* * * * *
403996 AAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTT
65 AAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTT
* * *
404061 AAAGAGAAGCAGTTTAAATCCTAAAAGTGTCGATACTTTTAAAAATGTA
130 AAAGAGAAGCAGTTTAAAGCCTAAAAGTGTCGATACTTTAAAAAATATA
* *
404110 TCGATCCAAAACGATATATCAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
* *
404175 AAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTGTGAATTTA
66 AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTT-
** *
404239 AAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAATATA
130 AAAGAGAAGCAG-TTTAAAGCCTA-AAAGTGTCGATACTTT-AAAAAATATA
* *
404291 TCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
*
404356 AAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACGATACCGGATATATTGAAAGTGTCGATACTTT
404392 CGTAAGTACG
Statistics
Matches: 255, Mismatches: 22, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
177 26 0.10
178 102 0.40
179 9 0.04
180 15 0.06
181 103 0.40
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (178 bp):
TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
AAGAGAAGCAGTTTAAAGCCTAAAAGTGTCGATACTTTAAAAAATATA
Found at i:406599 original size:21 final size:21
Alignment explanation
Indices: 406573--406637 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
406563 AAGACAATCA
*
406573 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
406594 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
406615 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
406636 AG
1 AG
406638 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:406713 original size:33 final size:33
Alignment explanation
Indices: 406671--406736 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
406661 AAATAGATGG
*
406671 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
406704 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
406737 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:408548 original size:19 final size:19
Alignment explanation
Indices: 408524--408572 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
408514 AATGTAGGGT
408524 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
408543 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
408562 TAATTTTGTAT
1 TAATTTTGTAT
408573 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:409035 original size:200 final size:200
Alignment explanation
Indices: 408691--409866 Score: 2185
Period size: 200 Copynumber: 5.9 Consensus size: 200
408681 CAATATGGCC
* * *
408691 AACAGGGTACAACAATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
408756 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
408821 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
408886 TGGAA
196 TGGAA
408891 AACAGGGAT-CAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAA
1 AACAGGG-TGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAA
*
408955 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACTGGTTTTATGAG
65 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
*
409020 AGAATATGCCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
130 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
409085 ATGGAA
195 ATGGAA
* * *
409091 AACATGGTGCAACTATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
409156 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
409221 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
409286 TGGAA
196 TGGAA
* *
409291 AACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
409356 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
409421 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTTCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
409486 TGGAA
196 TGGAA
* *
409491 AACAGGGTGCAACCATAAAGTGCCGATCCATATATAAAAGGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
409556 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
409621 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
409686 TGGAA
196 TGGAA
* *
409691 AACAGGGTGCAACCATAAAGTGTCGATCTATATAT-AAAAGTATCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
409755 CCAAAACTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
409820 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
409867 CTAATTTAAA
Statistics
Matches: 951, Mismatches: 23, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
199 139 0.15
200 811 0.85
201 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
TGGAA
Found at i:411351 original size:3 final size:3
Alignment explanation
Indices: 411343--411411 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
411333 TGAAGCTGAC
* * * * * * *
411343 GAT GAT GAT GAC GAT GAA GCT GAC GAT CAA GAT GAT GAC GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
411391 GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT
411412 CCAAATAAGT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.07, G:0.32, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:411354 original size:12 final size:12
Alignment explanation
Indices: 411339--411411 Score: 83
Period size: 12 Copynumber: 5.8 Consensus size: 12
411329 AAGATGAAGC
411339 TGACGATGATGA
1 TGACGATGATGA
* *
411351 TGACGATGAAGC
1 TGACGATGATGA
411363 TGACGATCAAGATGA
1 TGACGAT---GATGA
411378 TGACGATGATGA
1 TGACGATGATGA
*
411390 TGATGATGATGA
1 TGACGATGATGA
*
411402 TGATGATGAT
1 TGACGATGAT
411412 CCAAATAAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
12 43 0.81
15 10 0.19
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:412922 original size:183 final size:183
Alignment explanation
Indices: 412614--413553 Score: 1622
Period size: 183 Copynumber: 5.1 Consensus size: 183
412604 CAAAGTTTTC
* * *
412614 ACACTTTTTAATATTGTG-CTGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * * *
412678 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
412741 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATATGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
412797 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGCCGATA-CATTG
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-
* * *
412861 TCAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
65 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
412926 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
412980 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
413045 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
413110 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
413163 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
413228 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
413293 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
413346 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCA-TT
413410 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
65 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
*
413475 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTTTTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGG-TCTACAACCTATATCG
413530 ACACGTTT-TAATATTGTGTCGGTA
1 ACAC-TTTCTAATATTGTGTCGGTA
413554 ATTTTAAGTA
Statistics
Matches: 730, Mismatches: 19, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
182 2 0.00
183 634 0.87
184 88 0.12
185 3 0.00
186 3 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:413428 original size:19 final size:20
Alignment explanation
Indices: 413390--413428 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
413380 AGATTGGAAG
*
413390 AAAAATGTGTCGATACATTTT
1 AAAAAAGTGTCGA-ACATTTT
413411 AAAAAAGTGTCG-ACATTT
1 AAAAAAGTGTCGAACATTT
413429 ACACATCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAAAAGTGTCGAACATTTT
Found at i:416043 original size:25 final size:25
Alignment explanation
Indices: 416015--416079 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
416005 TTATCATTAA
416015 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
416040 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
416065 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
416080 TCTTTTGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:416452 original size:23 final size:23
Alignment explanation
Indices: 416421--416493 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
416411 ATAGGTAAAA
*
416421 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
416444 ATATAATGTAATATGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
416467 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
416490 ATAT
1 ATAT
416494 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:416518 original size:46 final size:45
Alignment explanation
Indices: 416421--416518 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
416411 ATAGGTAAAA
* * *
416421 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTAGCCTTT
* *
416467 ATATAATGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTAGCCTTT
*
416513 TTATAA
1 ATATAA
416519 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTAGCCTTT
Found at i:416941 original size:23 final size:23
Alignment explanation
Indices: 416910--416982 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
416900 ATAGGTAAAA
*
416910 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
416933 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
416956 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
416979 ATAT
1 ATAT
416983 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Done.