Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 24 of 37
Found at i:4165398 original size:33 final size:33
Alignment explanation
Indices: 4165358--4165425 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
4165348 CCGTTACAAG
* * *
4165358 CAATGTATCGATA-AAATTCATCATGTATCGATA
1 CAATGTATCAATACAAA-GCATAATGTATCGATA
4165391 CAATGTATCAATACAAAGCATAATGTATCGATA
1 CAATGTATCAATACAAAGCATAATGTATCGATA
4165424 CA
1 CA
4165426 TCTGGGTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (33 bp):
CAATGTATCAATACAAAGCATAATGTATCGATA
Found at i:4167522 original size:42 final size:43
Alignment explanation
Indices: 4167462--4167542 Score: 155
Period size: 42 Copynumber: 1.9 Consensus size: 43
4167452 TGCACCCTTT
4167462 TTTTAAAATCCAAATTAAAAGAAATAAGCTCAATTAATCCAGA
1 TTTTAAAATCCAAATTAAAAGAAATAAGCTCAATTAATCCAGA
4167505 TTTT-AAATCCAAATTAAAAGAAATAAGCTCAATTAATC
1 TTTTAAAATCCAAATTAAAAGAAATAAGCTCAATTAATC
4167543 TGGATCCTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
42 34 0.89
43 4 0.11
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.30
Consensus pattern (43 bp):
TTTTAAAATCCAAATTAAAAGAAATAAGCTCAATTAATCCAGA
Found at i:4167953 original size:45 final size:46
Alignment explanation
Indices: 4167828--4167954 Score: 139
Period size: 49 Copynumber: 2.7 Consensus size: 46
4167818 AGATGAGAGG
* *
4167828 AGTGCCAATGTGCCAATTCAAGGCCAGCGACATTGGGCTAAGGGAAA
1 AGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTAA-GGAAA
* * * *
4167875 AGTGGACCATTGTTCTGATTCAAGGCTAGCGACATTGGGCTAA-TAAA
1 AGT-G-CCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTAAGGAAA
* * *
4167922 GGTGCCAATATGCTAATTCAATGCTAGCGACAT
1 AGTGCCAATGTGCTAATTCAAGGCTAGCGACAT
4167955 CAGACAGTGG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
45 24 0.36
46 1 0.02
47 8 0.12
48 1 0.02
49 32 0.48
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (46 bp):
AGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTAAGGAAA
Found at i:4168276 original size:58 final size:58
Alignment explanation
Indices: 4168017--4168630 Score: 674
Period size: 58 Copynumber: 10.6 Consensus size: 58
4168007 TAAAAAAAGG
* * * * *
4168017 TGCCACTAACTTGTGTGTGCTTTGAAAAAAGTTGCCACTGGCTTGTGGGTTTTGAAAAGAG-
1 TGCCACTGACTTGTG-G-GCTTTG--AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * * *
4168078 TGCCACTAACTTGTGGGCTTTGAATGGGTGCCACTGACTTGTGGGTTTTG-AAAG-GG
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* *
4168134 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAG-GG
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* *
4168190 TGCCACTGACTTGTGGGCTTTGATAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGT
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * *
4168248 TGCCATTGACTCGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTCAAAAGAGT
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * *
4168306 TGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGT
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * **
4168364 TGCCACTGACTTGTGTGGGTTTTGAAAGGGTGCCACCAACTTGTGGGCTTTGAAAAGAGT
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * *
4168424 TGCCACCGACTCGTGTGGGCTTTGGAATGAGTGCCACTAACTTGTGGGCTTTGAAAAGAG-
1 TGCCACTGACT--TGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * * *
4168484 TGCAACTGACTTGT-GGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTTTG-AAAG-GA
1 TGCCACTGACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * * *
4168541 TGCCACTAACTTGTGGGCTTTGAAAAGAGTTACCACTGACTCGTGGGCTTTG-AAAG-GA
1 TGCCACTGACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAGT
*
4168599 TGCCACTAACTTGTGGGCTTTGAAAGGATGCC
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCC
4168631 TGAAAGCTTA
Statistics
Matches: 496, Mismatches: 46, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
55 1 0.00
56 110 0.22
57 55 0.11
58 202 0.41
59 9 0.02
60 76 0.15
61 43 0.09
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (58 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
Found at i:4168517 original size:265 final size:257
Alignment explanation
Indices: 4168012--4168623 Score: 870
Period size: 265 Copynumber: 2.3 Consensus size: 257
4168002 TTTTTTAAAA
* * * * *
4168012 AAAGG-TGCCACTAACTTGTGTGTGCTTTGAAAAAAGTTGCCACTGGCTTGTGGGTTTTGAAAAG
1 AAAGGATGCCACTAACTTGTG-G-GCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGG
*
4168076 AGTGCCACTAACTTGTGGGCTTTG-AATGGGTGCCACTGACTTGTGGGTTTTGAAAGGGTGCCAC
64 A-TGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGTTTTGAAAGGGTGCCAC
** * * *
4168140 TGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
128 CAACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTGTG
* * * * **
4168205 GGCTTTGATAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCATTGACTCGTGGGCTTTG
193 GGCTTTGAAAAGATGCAACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTTTG
* * * *
4168270 AAAGGATGCCATTGACTTGTGGGCTTTCAAAAGAGTTGCCACCGACTCGTGGGCTTTGAAAGGAT
1 AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGAT
*
4168335 GCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGTGGGTTTTGAAAGGGTGCCAC
66 GCCACTAACTTGTGGGCTTTGAAAAG-GGTGCCACTGAC-T-TGTGGGTTTTGAAAGGGTGCCAC
* *
4168400 CAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGGAATGAGTGCCACTAAC
128 CAACTTGTGGGCTTTG-AAAG-GGTGCCACCGACT--TGTGGGCTTT-GAAAGAGTGCCACTAAC
4168465 TTGTGGGCTTTGAAAAGAGTGCAACTGACTTGT-GGCTTTGAAAAGAGTTGCCACCGACTCGTGG
188 TTGTGGGCTTTGAAAAGA-TGCAACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGG
4168529 GCTTTG
252 GCTTTG
*
4168535 AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTTACCACTGACTCGTGGGCTTTGAAAGGAT
1 AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGAT
4168600 GCCACTAACTTGTGGGCTTTGAAA
66 GCCACTAACTTGTGGGCTTTGAAA
4168624 GGATGCCTGA
Statistics
Matches: 314, Mismatches: 29, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
256 22 0.07
257 38 0.12
258 17 0.05
259 14 0.04
260 37 0.12
261 4 0.01
262 11 0.04
264 10 0.03
265 148 0.47
266 13 0.04
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (257 bp):
AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGAT
GCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGTTTTGAAAGGGTGCCACCAA
CTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTGTGGGC
TTTGAAAAGATGCAACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTTTG
Found at i:4168624 original size:28 final size:28
Alignment explanation
Indices: 4168012--4168630 Score: 630
Period size: 28 Copynumber: 21.4 Consensus size: 28
4168002 TTTTTTAAAA
*
4168012 AAAGG-TGCCACTAACTTGTGTGTGCTTTG
1 AAAGGATGCCACTGACTTGTG-G-GCTTTG
* * * *
4168041 AAAAAAGTTGCCACTGGCTTGTGGGTTTTG
1 --AAAGGATGCCACTGACTTGTGGGCTTTG
* *
4168071 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
* * *
4168100 AATGGGTGCCACTGACTTGTGGGTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
4168128 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
4168156 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
4168184 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
4168212 ATAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
4168240 AAAAGTGTTGCCATTGACTCGTGGGCTTTG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTG
* *
4168270 AAAGGATGCCATTGACTTGTGGGCTTTCA
1 AAAGGATGCCACTGACTTGTGGGCTTT-G
* * *
4168299 AAAGAGTTGCCACCGACTCGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
*
4168328 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
4168356 AAAAGAGTTGCCACTGACTTGTGTGGGTTTTG
1 -AAAG-GATGCCACTGAC-T-TGTGGGCTTTG
* **
4168388 AAAGGGTGCCACCAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
4168416 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 -AAAG-GATGCCACTGACT--TGTGGGCTTTG
* * *
4168448 GAATGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
* *
4168477 AAAAGAGTGCAACTGACTTGT-GGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
* * *
4168505 AAAAGAGTTGCCACCGACTCGTGGGCTTTG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTG
*
4168535 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
4168563 AAAAGAGTTACCACTGACTCGTGGGCTTTG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTG
*
4168593 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
4168621 AAAGGATGCC
1 AAAGGATGCC
4168631 TGAAAGCTTA
Statistics
Matches: 500, Mismatches: 68, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
28 241 0.48
29 100 0.20
30 104 0.21
31 21 0.04
32 34 0.07
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:4169398 original size:13 final size:13
Alignment explanation
Indices: 4169380--4169405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4169370 CAATTTTTTG
4169380 TGTATCGATACAT
1 TGTATCGATACAT
4169393 TGTATCGATACAT
1 TGTATCGATACAT
4169406 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4169470 original size:21 final size:21
Alignment explanation
Indices: 4169444--4169519 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
4169434 CTGCCAAGAA
*
4169444 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
4169465 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
4169485 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
4169506 ATGTATCGATACAT
1 ATGTATCGATACAT
4169520 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:4169490 original size:20 final size:20
Alignment explanation
Indices: 4169465--4169537 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4169455 CATCTTTTTT
4169465 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
4169485 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
4169506 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
4169526 ATGTATCGATAC
1 ATGTATCGATAC
4169538 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:4169501 original size:41 final size:41
Alignment explanation
Indices: 4169444--4169537 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
4169434 CTGCCAAGAA
*
4169444 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4169485 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4169526 ATGTATCGATAC
1 ATGTATCGATAC
4169538 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:4172007 original size:13 final size:13
Alignment explanation
Indices: 4171989--4172027 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4171979 ATAATCACCC
*
4171989 TGTATCGATACAG
1 TGTATCGATACAA
4172002 TGTATCGATACAA
1 TGTATCGATACAA
4172015 TGTATCGATACAA
1 TGTATCGATACAA
4172028 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4172038 original size:20 final size:20
Alignment explanation
Indices: 4172013--4172091 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
4172003 GTATCGATAC
4172013 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
4172033 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
4172058 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
4172078 CATGTATCGATACA
1 AATGTATCGATACA
4172092 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:4174135 original size:15 final size:15
Alignment explanation
Indices: 4174099--4174136 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4174089 TACATCAATT
* *
4174099 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
4174114 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
4174129 TCATTTTG
1 TCATTTTG
4174137 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:4178217 original size:13 final size:13
Alignment explanation
Indices: 4178199--4178224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4178189 CAATTTTTTG
4178199 TGTATCGATACAT
1 TGTATCGATACAT
4178212 TGTATCGATACAT
1 TGTATCGATACAT
4178225 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4178289 original size:21 final size:21
Alignment explanation
Indices: 4178263--4178338 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
4178253 CTGCCAAGAA
*
4178263 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
4178284 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
4178304 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
4178325 ATGTATCGATACAT
1 ATGTATCGATACAT
4178339 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:4178309 original size:20 final size:20
Alignment explanation
Indices: 4178284--4178356 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4178274 CATCTTTTTT
4178284 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
4178304 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
4178325 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
4178345 ATGTATCGATAC
1 ATGTATCGATAC
4178357 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:4178320 original size:41 final size:41
Alignment explanation
Indices: 4178263--4178356 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
4178253 CTGCCAAGAA
*
4178263 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4178304 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4178345 ATGTATCGATAC
1 ATGTATCGATAC
4178357 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:4178691 original size:30 final size:29
Alignment explanation
Indices: 4178657--4178852 Score: 200
Period size: 30 Copynumber: 6.6 Consensus size: 29
4178647 AATGCCACTA
4178657 ACTTGTGGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGGGCTTTGAAAAG-GTTGCCACCG
*
4178687 ACTTGTGTGGCCTTTG-AAAGGGTGCCACCG
1 ACTTGTG-GG-CTTTGAAAAGGTTGCCACCG
*
4178717 ACTTATGGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGGGCTTTGAAAAG-GTTGCCACCG
* * **
4178747 ACTCGTGTAGGCTTTG-AAAGGATGCCACTA
1 ACT--TGTGGGCTTTGAAAAGGTTGCCACCG
*
4178777 ACTTGTGGGCTTTGAAAAGAGTTACCACCG
1 ACTTGTGGGCTTTGAAAAG-GTTGCCACCG
* **
4178807 ACTTGTGTGGGCTTTG-AAAGGGTGCCATTG
1 AC-T-TGTGGGCTTTGAAAAGGTTGCCACCG
4178837 ACTTGTGGGCTTTGAA
1 ACTTGTGGGCTTTGAA
4178853 GAGATGAATG
Statistics
Matches: 138, Mismatches: 17, Indels: 23
0.78 0.10 0.13
Matches are distributed among these distances:
28 26 0.19
29 12 0.09
30 60 0.43
31 15 0.11
32 25 0.18
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (29 bp):
ACTTGTGGGCTTTGAAAAGGTTGCCACCG
Found at i:4178742 original size:60 final size:59
Alignment explanation
Indices: 4178649--4178852 Score: 309
Period size: 60 Copynumber: 3.4 Consensus size: 59
4178639 ATCCTAACAA
*
4178649 TGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGCCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGG-CTTTGAAAGGG
* * * *
4178709 TGCCACCGACTTATGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTAGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGT-GGCTTTGAAAGGG
* *
4178769 TGCCACTAACTTGTGGGCTTTGAAAAGAGTTACCACCGACTTGTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGT-GGCTTTGAAAGGG
*
4178829 TGCCATTGACTTGTGGGCTTTGAA
1 TGCCACTGACTTGTGGGCTTTGAA
4178853 GAGATGAATG
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
60 127 0.98
61 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (59 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGCTTTGAAAGGG
Found at i:4180079 original size:9 final size:9
Alignment explanation
Indices: 4180066--4180120 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 9
4180056 TTTTTGTTAT
4180066 TTTTTCTTGG
1 TTTTT-TTGG
4180076 TTTTTTTGG
1 TTTTTTTGG
4180085 TTGTTTTTGG
1 TT-TTTTTGG
**
4180095 TTTTTTTCT
1 TTTTTTTGG
*
4180104 TATTTTTTTG
1 T-TTTTTTGG
4180114 TTTTTTT
1 TTTTTTT
4180121 TGGGTATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 18 0.46
10 21 0.54
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.80
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:4180121 original size:9 final size:9
Alignment explanation
Indices: 4180053--4180122 Score: 52
Period size: 10 Copynumber: 7.2 Consensus size: 9
4180043 GACTCCTTTC
4180053 TGTTTTTTGT
1 TGTTTTTT-T
*
4180063 TATTTTTTCT
1 TGTTTTTT-T
4180073 TGGTTTTTTT
1 T-GTTTTTTT
*
4180083 GGTTGTTTTT
1 TGTT-TTTTT
*
4180093 GGTTTTTTT
1 TGTTTTTTT
4180102 CT-TATTTTTT
1 -TGT-TTTTTT
4180112 TGTTTTTTT
1 TGTTTTTTT
4180121 TG
1 TG
4180123 GGTATGAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 18 0.36
10 26 0.52
11 6 0.12
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (9 bp):
TGTTTTTTT
Found at i:4183358 original size:13 final size:13
Alignment explanation
Indices: 4183340--4183366 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4183330 ACATGCTGCT
4183340 TTGTATCGATACA
1 TTGTATCGATACA
4183353 TTGTATCGATACA
1 TTGTATCGATACA
4183366 T
1 T
4183367 GTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4183378 original size:19 final size:21
Alignment explanation
Indices: 4183352--4183407 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
4183342 GTATCGATAC
**
4183352 ATTGTATCGATACATGTTC-A
1 ATTGTATCGATACATGGACAA
4183372 A-TGTATCGATACATGGACAA
1 ATTGTATCGATACATGGACAA
4183392 ATTGTATCGATACATG
1 ATTGTATCGATACATG
4183408 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 15 0.47
20 3 0.09
21 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (21 bp):
ATTGTATCGATACATGGACAA
Found at i:4183382 original size:32 final size:33
Alignment explanation
Indices: 4183323--4183385 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
4183313 CACCCAGATA
**
4183323 TATCGATACATGCTGCTTTGTATCGATACATTG
1 TATCGATACATGCTGCAATGTATCGATACATTG
*
4183356 TATCGATACATG-TTCAATGTATCGATACAT
1 TATCGATACATGCTGCAATGTATCGATACAT
4183386 GGACAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (33 bp):
TATCGATACATGCTGCAATGTATCGATACATTG
Found at i:4198533 original size:20 final size:20
Alignment explanation
Indices: 4198508--4198633 Score: 117
Period size: 20 Copynumber: 5.8 Consensus size: 20
4198498 TTTTAACTAG
4198508 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
4198528 ATGTATCGATACATCTGGAAAAAAAGACAGA
1 ATGTATCGATACAT-T-G------A-A-A-A
*
4198559 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
4198579 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
4198599 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
4198619 ATGTATCGATACATT
1 ATGTATCGATACATT
4198634 TGGGTAAAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
20 63 0.72
21 1 0.01
22 2 0.02
23 1 0.01
28 1 0.01
29 2 0.02
30 2 0.02
31 15 0.17
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:4201613 original size:21 final size:21
Alignment explanation
Indices: 4201584--4201623 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4201574 GATTCTTGAA
*
4201584 TGATCTTGTGTTGTTAATTGT
1 TGATCTTGTGTGGTTAATTGT
*
4201605 TGATGTTGTGTGGTTAATT
1 TGATCTTGTGTGGTTAATT
4201624 TTTCATAAAT
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:0.15, C:0.03, G:0.28, T:0.55
Consensus pattern (21 bp):
TGATCTTGTGTGGTTAATTGT
Found at i:4203146 original size:21 final size:21
Alignment explanation
Indices: 4203122--4203198 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
4203112 AATTTATCCA
4203122 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
4203143 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
4203164 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
4203185 AATGTATCGATACA
1 AATGTATCGATACA
4203199 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:4203258 original size:19 final size:19
Alignment explanation
Indices: 4203234--4203301 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
4203224 AATTCAACAA
4203234 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4203253 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4203268 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
4203285 ATGGTATCGATACATAA
1 TTTGTATCGATACATAA
4203302 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4203273 original size:13 final size:13
Alignment explanation
Indices: 4203255--4203279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4203245 ACATAAGTTT
4203255 TGTATCGATACAA
1 TGTATCGATACAA
4203268 TGTATCGATACA
1 TGTATCGATACA
4203280 TAAGTATGGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4203277 original size:32 final size:32
Alignment explanation
Indices: 4203236--4203298 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4203226 TTCAACAATT
* *
4203236 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATGGTATCGATACAA
4203268 TGTATCGATACATAAGTATGGTATCGATACA
1 TGTATCGATACATAAGTATGGTATCGATACA
4203299 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATGGTATCGATACAA
Found at i:4203359 original size:13 final size:13
Alignment explanation
Indices: 4203341--4203366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4203331 CATTTTTCTG
4203341 TGTATCGATACAT
1 TGTATCGATACAT
4203354 TGTATCGATACAT
1 TGTATCGATACAT
4203367 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4218354 original size:11 final size:11
Alignment explanation
Indices: 4218338--4218379 Score: 66
Period size: 11 Copynumber: 3.6 Consensus size: 11
4218328 CATTCTCTTC
4218338 AAAAAAAAACA
1 AAAAAAAAACA
4218349 AAAAAAAAACA
1 AAAAAAAAACA
4218360 AAAAACAAAACA
1 AAAAA-AAAACA
4218372 AAGAAAAA
1 AA-AAAAA
4218380 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.55
12 10 0.34
13 3 0.10
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:4218355 original size:12 final size:12
Alignment explanation
Indices: 4218338--4218379 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
4218328 CATTCTCTTC
4218338 AAAAAAAAAC-A
1 AAAAAAAAACAA
4218349 AAAAAAAAACAA
1 AAAAAAAAACAA
*
4218361 AAAACAAAACAA
1 AAAAAAAAACAA
*
4218373 AGAAAAA
1 AAAAAAA
4218380 GAGAGAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:4219615 original size:26 final size:26
Alignment explanation
Indices: 4219526--4219615 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
4219516 AAGTTGGTGG
*
4219526 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
4219552 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
** *
4219581 CATTTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
4219607 CACCTTTCA
1 CACCTTTCA
4219616 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 6 0.13
28 6 0.13
29 9 0.20
30 3 0.07
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:4219779 original size:27 final size:27
Alignment explanation
Indices: 4219694--4219779 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
4219684 TTGGTGGCAT
4219694 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
4219721 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
4219749 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
4219776 TTTC
1 TTTC
4219780 AAAGCCCACC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:4219933 original size:55 final size:55
Alignment explanation
Indices: 4219389--4219917 Score: 859
Period size: 55 Copynumber: 9.6 Consensus size: 55
4219379 GATGCTTTTT
* *
4219389 CCTTTCAAAGCCCACACAAGTTGATGGCATTTTCCAATCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
*
4219444 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
4219499 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
*
4219554 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
4219609 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
*
4219664 CCTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
4219719 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
*
4219774 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * **
4219829 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAATCCTCAAAGAGCAGGATG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
**
4219884 CCTTTCAAAGCCCACATGAGTTGGTGGCACTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
4219918 TACTCCTCAA
Statistics
Matches: 447, Mismatches: 20, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
54 7 0.02
55 430 0.96
56 10 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
Found at i:4220729 original size:19 final size:19
Alignment explanation
Indices: 4220705--4220759 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
4220695 AATTCAACAA
4220705 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4220724 TTTGTATCGATAAATAAGT
1 TTTGTATCGATACATAAGT
*
4220743 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4220760 TTAGCTACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4220817 original size:13 final size:13
Alignment explanation
Indices: 4220799--4220824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4220789 CATTTTTTTG
4220799 TGTATCGATACAT
1 TGTATCGATACAT
4220812 TGTATCGATACAT
1 TGTATCGATACAT
4220825 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4223266 original size:24 final size:25
Alignment explanation
Indices: 4223239--4223290 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
4223229 ATTTCTTCAC
4223239 AATCA-AGGATACTCCAACCCCGTT
1 AATCACAGGATACTCCAACCCCGTT
*
4223263 AATCATCGGGGATACTCCAACCCCGTT
1 AATCA-C-AGGATACTCCAACCCCGTT
4223290 A
1 A
4223291 TTTCCAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
27 19 0.79
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (25 bp):
AATCACAGGATACTCCAACCCCGTT
Found at i:4223310 original size:28 final size:27
Alignment explanation
Indices: 4223249--4223313 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
4223239 AATCAAGGAT
* *
4223249 ACTCCAACCCCGTTAATCATCGGGGAT
1 ACTCCAACCCCGTTAATCATAGGGGAC
*
4223276 ACTCCAACCCCGTTATTTCCA-AGGGGAC
1 ACTCCAACCCCGTTA-AT-CATAGGGGAC
4223304 ACTCCAACCC
1 ACTCCAACCC
4223314 TGGCTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.45
28 16 0.48
29 2 0.06
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.20
Consensus pattern (27 bp):
ACTCCAACCCCGTTAATCATAGGGGAC
Found at i:4227106 original size:34 final size:35
Alignment explanation
Indices: 4227039--4227106 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
4227029 CCAAGTGATT
4227039 AAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
1 AAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
4227074 AAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGG
1 AAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGG
4227107 ATTGTAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (35 bp):
AAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
Found at i:4231724 original size:19 final size:19
Alignment explanation
Indices: 4231700--4231736 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4231690 AAAGCTCCTA
*
4231700 ACATCATAAATGTATAGAT
1 ACATCACAAATGTATAGAT
4231719 ACATCACAAATGTATAGA
1 ACATCACAAATGTATAGA
4231737 ATTTCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (19 bp):
ACATCACAAATGTATAGAT
Found at i:4231905 original size:16 final size:17
Alignment explanation
Indices: 4231867--4231912 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
4231857 AAACTAACTA
*
4231867 ATCCGAACTCGAAAATG
1 ATCCGAATTCGAAAATG
**
4231884 GCCCGAATTC-AAAATG
1 ATCCGAATTCGAAAATG
4231900 ATCCGAA-TCGAAA
1 ATCCGAATTCGAAA
4231913 TAACCCGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
15 2 0.09
16 14 0.61
17 7 0.30
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (17 bp):
ATCCGAATTCGAAAATG
Found at i:4233305 original size:28 final size:28
Alignment explanation
Indices: 4233271--4233732 Score: 450
Period size: 28 Copynumber: 16.1 Consensus size: 28
4233261 CATTCATCTC
*
4233271 TTCAAAGCCCACAGGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4233299 TTCAAAGCCCACAAGTCAGTGACATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4233327 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4233355 TTCAAAGCCCACAAGTTAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4233383 TTCAAAGCCCACAAGTCAATGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4233410 CTTCAAAGCCCACAGGTCAGTGGAATCCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4233439 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4233467 TTCAAAGCCCACACAAATCAGTGGTACAT--T
1 TTCAAAG-CC-CACAAGTCAGTGG--CATCCT
* * *
4233497 TTTAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* *
4233529 TTCAAAGCCTACAAGTCAGTGGTAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* ** *
4233556 CTTCAAAAGACCACAAGTTGGTGGCACCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
**
4233586 TTCAAAGCCCACAAGTCAGTGGCCCCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4233614 TTCAAAGCCTACAAGTCAATGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
** *
4233644 TTCAAAGCCCACATAAAACAGTGTCA-CCTT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCC-T
* *
4233674 TTCAAAACCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4233702 TTCAAAGCCCACAAAAGTTAGTGGCA-CCT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCCT
4233731 TT
1 TT
4233733 TTTTTAAAAG
Statistics
Matches: 361, Mismatches: 52, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.01
28 219 0.61
29 34 0.09
30 85 0.24
31 2 0.01
32 18 0.05
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:4233960 original size:48 final size:48
Alignment explanation
Indices: 4233838--4233969 Score: 192
Period size: 48 Copynumber: 2.8 Consensus size: 48
4233828 GGCACCTTTA
* * *
4233838 TTAGCTCAATGTCATTGGCCTTGAATCAACACATTGTCCACTTTTCCT
1 TTAGCTCAATGTCATTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* *
4233886 TTAGCTCAATGTCACTGGCCTTGAATTAGCACATTGTCCATTTTTCCC
1 TTAGCTCAATGTCATTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* * *
4233934 TTAGCTCGATGTCGTTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCATTGGCCTTGAATTAGCACATTG
4233970 GCAGTCTTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (48 bp):
TTAGCTCAATGTCATTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
Found at i:4234800 original size:20 final size:20
Alignment explanation
Indices: 4234775--4234850 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
4234765 TTTTACTTAG
4234775 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
4234795 ATGTAT-TATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
4234814 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
4234834 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
4234851 ATCTTTTTTC
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
19 15 0.36
20 27 0.64
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:4234848 original size:90 final size:90
Alignment explanation
Indices: 4234724--4234890 Score: 253
Period size: 90 Copynumber: 1.9 Consensus size: 90
4234714 GATACATTAC
* ** *
4234724 ATGTATCGATACATTTTTTAATATATCGATACATTCTATCTTTTTACTTAGATGTATCGATACAT
1 ATGTATCGATACATTCTACAATATATCGATACATTCTATCTTTTTACCTAGATGTATCGATACAT
4234789 TTTTCAATGTATTATACATGTATGA
66 TTTTCAATGTATTATACATGTATGA
* * * *
4234814 ATGTATCGATATATTCTACAATGTATCGATACATTTTATCTTTTTTCCTAGATGTATCGATACAT
1 ATGTATCGATACATTCTACAATATATCGATACATTCTATCTTTTTACCTAGATGTATCGATACAT
*
4234879 TTTTCGATGTAT
66 TTTTCAATGTAT
4234891 CGATACATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 68 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (90 bp):
ATGTATCGATACATTCTACAATATATCGATACATTCTATCTTTTTACCTAGATGTATCGATACAT
TTTTCAATGTATTATACATGTATGA
Found at i:4248116 original size:13 final size:13
Alignment explanation
Indices: 4248095--4248125 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4248085 CGATAAATGG
*
4248095 TACAATGTATCGA
1 TACATTGTATCGA
4248108 TACATTGTATCGA
1 TACATTGTATCGA
4248121 TACAT
1 TACAT
4248126 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:4248121 original size:33 final size:33
Alignment explanation
Indices: 4248079--4248145 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
4248069 CTACCACTGT
*
4248079 TTGTATCGATAAATGGT-ACAATGTATCGATACA
1 TTGTATCGATAAATGATGA-AATGTATCGATACA
* *
4248112 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATAAATGATGAAATGTATCGATACA
4248145 T
1 T
4248146 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
TTGTATCGATAAATGATGAAATGTATCGATACA
Found at i:4254329 original size:13 final size:13
Alignment explanation
Indices: 4254311--4254335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4254301 CAATATTCCT
4254311 TGTATCGATACAC
1 TGTATCGATACAC
4254324 TGTATCGATACA
1 TGTATCGATACA
4254336 TAGGGTACTA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:4256883 original size:20 final size:20
Alignment explanation
Indices: 4256844--4256894 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
4256834 TTATGCTTTC
**
4256844 TATCGATACAT-GTTAATTG
1 TATCGATACATGGACAATTG
4256863 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTG
*
4256883 TATCAATACATG
1 TATCGATACATG
4256895 AGATTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTG
Found at i:4256949 original size:20 final size:20
Alignment explanation
Indices: 4256924--4256976 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
4256914 TACCACTGTT
4256924 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
4256944 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
4256964 TGTATCGATACAT
1 TGTATCGATACAT
4256977 TGTATCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:4256980 original size:13 final size:13
Alignment explanation
Indices: 4256959--4256989 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4256949 CGATACATGG
*
4256959 TACAATGTATCGA
1 TACATTGTATCGA
4256972 TACATTGTATCGA
1 TACATTGTATCGA
4256985 TACAT
1 TACAT
4256990 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:4257006 original size:33 final size:33
Alignment explanation
Indices: 4256939--4257009 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
4256929 CGATACATGG
* * *
4256939 TACAATGTATCGATACATGGTACAATGTATCGA
1 TACATTGTATCGATACATGATACAATGTACCGA
*
4256972 TACATTGTATCGATACATGATGA-ATTGTACCGA
1 TACATTGTATCGATACATGAT-ACAATGTACCGA
4257005 TACAT
1 TACAT
4257010 AGCTTGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (33 bp):
TACATTGTATCGATACATGATACAATGTACCGA
Found at i:4259978 original size:10 final size:10
Alignment explanation
Indices: 4259965--4260017 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
4259955 AAATATAAAA
4259965 AAATATTTAT
1 AAATATTTAT
4259975 AAATA-TTAT
1 AAATATTTAT
4259984 ATAA-ATTTAT
1 A-AATATTTAT
4259994 -AATATTT-T
1 AAATATTTAT
* *
4260002 AAATAATTAA
1 AAATATTTAT
4260012 AAATAT
1 AAATAT
4260018 AAATAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
8 3 0.09
9 16 0.46
10 16 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATATTTAT
Found at i:4260009 original size:19 final size:18
Alignment explanation
Indices: 4259965--4260024 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
4259955 AAATATAAAA
4259965 AAAT-ATTTATAAATATT
1 AAATAATTTATAAATATT
* *
4259982 ATATAAATTTATAATATTTT
1 AAAT-AATTTATAA-ATATT
*
4260002 AAATAA-TTAAAAATA-T
1 AAATAATTTATAAATATT
4260018 AAATAAT
1 AAATAAT
4260025 AAAAAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.21
17 5 0.15
18 5 0.15
19 10 0.29
20 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATTTATAAATATT
Found at i:4260020 original size:16 final size:16
Alignment explanation
Indices: 4260001--4260043 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
4259991 TATAATATTT
*
4260001 TAAATAATTAAAAATA
1 TAAATAATAAAAAATA
4260017 TAAATAATAAAAAATA
1 TAAATAATAAAAAATA
4260033 TAAATAA-AAAA
1 TAAATAATAAAA
4260044 TTAAATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAATAATAAAAAATA
Found at i:4260025 original size:9 final size:9
Alignment explanation
Indices: 4260001--4260039 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
4259991 TATAATATTT
4260001 TAAATAAT-
1 TAAATAATA
4260009 TAAA-AATA
1 TAAATAATA
4260017 TAAATAATA
1 TAAATAATA
4260026 -AAA-AATA
1 TAAATAATA
4260033 TAAATAA
1 TAAATAA
4260040 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.26
8 14 0.52
9 6 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
TAAATAATA
Found at i:4260048 original size:12 final size:13
Alignment explanation
Indices: 4260022--4260050 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4260012 AAATATAAAT
4260022 AATAAAAAATATA
1 AATAAAAAATATA
4260035 AATAAAAAAT-TA
1 AATAAAAAATATA
4260047 AATA
1 AATA
4260051 CATGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAAAATATA
Found at i:4260089 original size:15 final size:14
Alignment explanation
Indices: 4260069--4260106 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
4260059 TTCTTCCTCA
4260069 TGTTTTTTCTTTTT
1 TGTTTTTTCTTTTT
*
4260083 CTTTTTTTTCTTTTT
1 -TGTTTTTTCTTTTT
4260098 TGTTTTTTC
1 TGTTTTTTC
4260107 ATTTGCTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (14 bp):
TGTTTTTTCTTTTT
Found at i:4260375 original size:8 final size:8
Alignment explanation
Indices: 4260361--4260391 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4260351 CAATATCTCC
4260361 CTTTTTTT
1 CTTTTTTT
4260369 -TTTTTTT
1 CTTTTTTT
4260376 CTTTTTTT
1 CTTTTTTT
4260384 CTTTTTTT
1 CTTTTTTT
4260392 ATTAATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
CTTTTTTT
Found at i:4264326 original size:21 final size:22
Alignment explanation
Indices: 4264280--4264326 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
4264270 GTATATCAGT
* *
4264280 TTAAAGATAAAATAAAGTAATT
1 TTAAAGATAAAATAAAGCAATA
*
4264302 TTAAA-ATAAAATAAAGCGATA
1 TTAAAGATAAAATAAAGCAATA
4264323 TTAA
1 TTAA
4264327 TAGTATATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
TTAAAGATAAAATAAAGCAATA
Found at i:4264676 original size:15 final size:16
Alignment explanation
Indices: 4264639--4264679 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4264629 ATTTTATTTA
4264639 AAAATTT-TAAATATT
1 AAAATTTATAAATATT
*
4264654 AAATATTTATAATTA-T
1 AAA-ATTTATAAATATT
4264670 AAAATTTATA
1 AAAATTTATA
4264680 TCTGCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATTTATAAATATT
Found at i:4265421 original size:4 final size:4
Alignment explanation
Indices: 4265406--4265439 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
4265396 TTTATGCAAC
*
4265406 TATT TCATT TATT TATC TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT TATT T
4265440 TTTTGTTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:4266166 original size:23 final size:22
Alignment explanation
Indices: 4266140--4266185 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4266130 AAAATTTTAT
4266140 AATTAATAAAATTTAAATTAAAA
1 AATTAATAAAA-TTAAATTAAAA
** *
4266163 AATTTTTAAAATTATATTAAAA
1 AATTAATAAAATTAAATTAAAA
4266185 A
1 A
4266186 TTATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAATAAAATTAAATTAAAA
Found at i:4266184 original size:22 final size:23
Alignment explanation
Indices: 4266146--4266193 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
4266136 TTATAATTAA
4266146 TAAAATTTAAATTAAAAAATT-TT
1 TAAAATTTAAATT-AAAAATTATT
*
4266169 TAAAA-TTATATTAAAAATTATT
1 TAAAATTTAAATTAAAAATTATT
4266191 TAA
1 TAA
4266194 TTAAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 11 0.48
23 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAATTTAAATTAAAAATTATT
Found at i:4266406 original size:3 final size:3
Alignment explanation
Indices: 4266400--4266441 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4266390 GTACTTTTAC
4266400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4266442 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4266448 original size:3 final size:3
Alignment explanation
Indices: 4266442--4266467 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4266432 AATAATAATA
4266442 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
4266468 AGTTGAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4266718 original size:38 final size:38
Alignment explanation
Indices: 4266645--4266718 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
4266635 ATTTTTTTAT
* * * *
4266645 AATTTTAATTATTACTTATTTATTTAAATATTTTTAAA
1 AATTTTAATTATTACTTATATATTAAAAAAATTTTAAA
*
4266683 AATTTTAA-TATATATTTATATATTAAAAAAATTTTA
1 AATTTTAATTAT-TACTTATATATTAAAAAAATTTTA
4266719 CTTTTAGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 3 0.10
38 27 0.90
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (38 bp):
AATTTTAATTATTACTTATATATTAAAAAAATTTTAAA
Found at i:4269897 original size:36 final size:34
Alignment explanation
Indices: 4269819--4269897 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 34
4269809 GTAAAAATCA
*
4269819 AATTAATTTAAAATTTTATTTTACTATTTATTAT
1 AATTAATTTAAAATATTATTTTACTATTTATTAT
*
4269853 -ATT-A-TTAAAATATTATTTTA-TATTAATTTTTAT
1 AATTAATTTAAAATATTATTTTACTA-T--TTATTAT
4269886 AATTAATTTAAA
1 AATTAATTTAAA
4269898 TAAAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 2 0.05
31 16 0.43
32 1 0.03
33 9 0.24
34 3 0.08
35 1 0.03
36 5 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
AATTAATTTAAAATATTATTTTACTATTTATTAT
Found at i:4270038 original size:27 final size:27
Alignment explanation
Indices: 4270007--4270063 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
4269997 ATTTAACTTA
* *
4270007 AAAAGATCTATTTTAAAAGAATTTATG
1 AAAAGATATATTTTAAAAGAACTTATG
4270034 AAAAGATATATTTTAAAAGAACTTATG
1 AAAAGATATATTTTAAAAGAACTTATG
4270061 AAA
1 AAA
4270064 TTATAGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAAGATATATTTTAAAAGAACTTATG
Found at i:4270374 original size:2 final size:2
Alignment explanation
Indices: 4270369--4270396 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4270359 TTACTCTTTG
4270369 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
4270397 TAAAAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4273340 original size:15 final size:16
Alignment explanation
Indices: 4273306--4273360 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 16
4273296 TTTTTTATGT
*
4273306 TTTAAAAAATATTTTA
1 TTTAAAAAATATTATA
*
4273322 TTTATAAAAT-TTATA
1 TTTAAAAAATATTATA
** *
4273337 TTTAATTATTATT-TA
1 TTTAAAAAATATTATA
4273352 TTTAAAAAA
1 TTTAAAAAA
4273361 ATTTAATTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAAAATATTATA
Found at i:4273352 original size:30 final size:30
Alignment explanation
Indices: 4273318--4273375 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
4273308 TAAAAAATAT
*
4273318 TTTATTT-ATAAAATTTATATTTAATTATTA
1 TTTATTTAAAAAAATTTA-ATTTAATTATTA
*
4273348 TTTATTTAAAAAAATTTAATTTATTTAT
1 TTTATTTAAAAAAATTTAATTTAATTAT
4273376 AAATAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTATTTAAAAAAATTTAATTTAATTATTA
Found at i:4273388 original size:30 final size:31
Alignment explanation
Indices: 4273327--4273398 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
4273317 TTTTATTTAT
* * * *
4273327 AAAATTTATATTTAATTATTATTTATTTAAA
1 AAAATTTATATTTAATTATAAATAATCTAAA
*
4273358 AAAATTTA-ATTTATTTATAAATAATCTAAA
1 AAAATTTATATTTAATTATAAATAATCTAAA
*
4273388 ATAATTATATA
1 AAAATT-TATA
4273399 GCCCAAAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 22 0.67
31 10 0.30
32 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAATTTATATTTAATTATAAATAATCTAAA
Found at i:4276906 original size:18 final size:18
Alignment explanation
Indices: 4276885--4276971 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 18
4276875 CTAAAATGAA
4276885 GAATTCTCATAAAAAAAG
1 GAATTCTCATAAAAAAAG
* *
4276903 GAATTCTCACAAAAAAAA
1 GAATTCTCATAAAAAAAG
* *
4276921 GAGATTATCGTAAAAAATAATG
1 GA-ATTCTCAT-AAAAA-AA-G
*
4276943 G-ATTCTTACAAAAAAAAAG
1 GAATTC-T-CATAAAAAAAG
4276962 GAATTCTCAT
1 GAATTCTCAT
4276972 CGTAAATAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
18 20 0.38
19 8 0.15
20 14 0.27
21 8 0.15
22 2 0.04
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.24
Consensus pattern (18 bp):
GAATTCTCATAAAAAAAG
Found at i:4276918 original size:20 final size:20
Alignment explanation
Indices: 4276895--4276970 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
4276885 GAATTCTCAT
4276895 AAAAAAAGGAATTCTCAC-A
1 AAAAAAAGGAATTCTCACAA
* **
4276914 AAAAAAA-GAGATTATCGTAA
1 AAAAAAAGGA-ATTCTCACAA
* *
4276934 AAAATAATGG-ATTCTTACAA
1 AAAA-AAAGGAATTCTCACAA
4276954 AAAAAAAGGAATTCTCA
1 AAAAAAAGGAATTCTCA
4276971 TCGTAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
18 2 0.05
19 16 0.38
20 21 0.50
21 2 0.05
22 1 0.02
ACGTcount: A:0.57, C:0.11, G:0.12, T:0.21
Consensus pattern (20 bp):
AAAAAAAGGAATTCTCACAA
Found at i:4277021 original size:42 final size:40
Alignment explanation
Indices: 4276883--4277027 Score: 100
Period size: 40 Copynumber: 3.6 Consensus size: 40
4276873 TTCTAAAATG
* *
4276883 AAGAATTCTCAT-AAAAA-AA-GGAATTCTCACAAAAAAAA
1 AAGAATTCTAATAAAAAATAATGG-ATTATCACAAAAAAAA
* * ** * *
4276921 GAG-ATTATCGTAAAAAATAATGGATTCTTACAAAAAAAA
1 AAGAATTCTAATAAAAAATAATGGATTATCACAAAAAAAA
* * *** *
4276960 AGGAATTCTCATCGTAAATAATGGATTATCATAAGAAAAATA
1 AAGAATTCTAATAAAAAATAATGGATTATCACAA-AAAAA-A
*
4277002 AAGAATTCTAATAAAAAATAAAGGAT
1 AAGAATTCTAATAAAAAATAATGGAT
4277028 ATTCACCAGA
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
37 6 0.07
38 7 0.09
39 18 0.22
40 24 0.30
41 5 0.06
42 21 0.26
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (40 bp):
AAGAATTCTAATAAAAAATAATGGATTATCACAAAAAAAA
Found at i:4277151 original size:19 final size:19
Alignment explanation
Indices: 4277102--4277153 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4277092 AATAAGAGAT
*
4277102 TCTAAAGGATTCTCACAAA
1 TCTAAAGGATTTTCACAAA
*
4277121 TATAAAGGATTTTCACATAA
1 TCTAAAGGATTTTCACA-AA
4277141 -CTAAAGGATTTTC
1 TCTAAAGGATTTTC
4277154 CCTTTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 27 0.93
20 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (19 bp):
TCTAAAGGATTTTCACAAA
Found at i:4278729 original size:23 final size:23
Alignment explanation
Indices: 4278679--4278723 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4278669 AAATGGAAAA
**
4278679 AAGTATTAGTGATAGATTATTTT
1 AAGTATTAGTGATAGAAAATTTT
*
4278702 AAGTATTAGTGATTGAAAATTT
1 AAGTATTAGTGATAGAAAATTT
4278724 ATAGTAGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (23 bp):
AAGTATTAGTGATAGAAAATTTT
Found at i:4280188 original size:13 final size:13
Alignment explanation
Indices: 4280170--4280220 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
4280160 ACATTTCACC
4280170 ATGTATCGATACA
1 ATGTATCGATACA
4280183 ATGTATCGATACA
1 ATGTATCGATACA
* * *
4280196 TTATATCAATACA
1 ATGTATCGATACA
*
4280209 CTGTATCGATAC
1 ATGTATCGATAC
4280221 TAAGTAAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4282934 original size:13 final size:13
Alignment explanation
Indices: 4282918--4282956 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
4282908 AGTGCCCTTA
4282918 TATCGATATAATG
1 TATCGATATAATG
*
4282931 TATCGATACAATG
1 TATCGATATAATG
4282944 TATCGATACTAAT
1 TATCGATA-TAAT
4282957 ATTATTGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (13 bp):
TATCGATATAATG
Found at i:4287085 original size:21 final size:22
Alignment explanation
Indices: 4287056--4287096 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4287046 CTTTTCAAGA
4287056 ATTTCATTCTCAACAATTTTTG
1 ATTTCATTCTCAACAATTTTTG
**
4287078 ATTT-ATTCTCTTCAATTTT
1 ATTTCATTCTCAACAATTTT
4287097 AAAATTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTCATTCTCAACAATTTTTG
Found at i:4287948 original size:20 final size:20
Alignment explanation
Indices: 4287923--4287973 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
4287913 GTGGGGCATA
4287923 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGTC-TC
*
4287943 ATGTATCGATATAATGTCTC
1 ATGTATCGATACAATGTCTC
*
4287963 ATATATCGATA
1 ATGTATCGATA
4287974 TATTTCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATGTCTC
Found at i:4288938 original size:76 final size:77
Alignment explanation
Indices: 4288800--4288972 Score: 296
Period size: 76 Copynumber: 2.3 Consensus size: 77
4288790 TTAAAACGAT
4288800 TTTCTCCCCCTTTTTGTTATCAAAAGAAAAATTTTCCCCCTTTGTCAAATGCCAAATGCTAAATT
1 TTTCTCCCCCTTTTTGTTATCAAAAGAAAAATTTTCCCCCTTTGTCAAATGCCAAATGCTAAATT
*
4288865 TATTTTCAAAAA
66 TATTTCCAAAAA
*
4288877 TTTCTCCCCCTTTTTGTTATCAAAAG-AAAA-TTTCTCCCGTTTGTCAAATGCCAAATGCTAAAT
1 TTTCTCCCCCTTTTTGTTATCAAAAGAAAAATTTTC-CCCCTTTGTCAAATGCCAAATGCTAAAT
4288940 TTATTTCCAAAAA
65 TTATTTCCAAAAA
*
4288953 TTTCTCCTCCTTTTTGTTAT
1 TTTCTCCCCCTTTTTGTTAT
4288973 AGCAAAAACG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
75 4 0.04
76 62 0.67
77 26 0.28
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.42
Consensus pattern (77 bp):
TTTCTCCCCCTTTTTGTTATCAAAAGAAAAATTTTCCCCCTTTGTCAAATGCCAAATGCTAAATT
TATTTCCAAAAA
Found at i:4291697 original size:13 final size:13
Alignment explanation
Indices: 4291679--4291705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4291669 ACATTATGCT
4291679 TTGTATCGATACA
1 TTGTATCGATACA
4291692 TTGTATCGATACA
1 TTGTATCGATACA
4291705 T
1 T
4291706 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4291714 original size:19 final size:19
Alignment explanation
Indices: 4291690--4291745 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
4291680 TGTATCGATA
*
4291690 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
*
4291709 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
4291728 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
4291746 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:4293442 original size:12 final size:12
Alignment explanation
Indices: 4293410--4293444 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
4293400 AACCGTCAAA
*
4293410 GATAATGAAGAT
1 GATAATGATGAT
4293422 GATAATGATGAT
1 GATAATGATGAT
4293434 GATAATGATGA
1 GATAATGATGA
4293445 GGTTGACTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (12 bp):
GATAATGATGAT
Found at i:4296646 original size:20 final size:20
Alignment explanation
Indices: 4296604--4296656 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4296594 GTTGGGCATA
* *
4296604 ATGTATCAATACAATTCTTC
1 ATGTATCGATACAATTCTCC
4296624 ATGTATCGATACAATGTC-CC
1 ATGTATCGATACAAT-TCTCC
*
4296644 ATGGATCGATACA
1 ATGTATCGATACA
4296657 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTCTCC
Found at i:4296730 original size:19 final size:20
Alignment explanation
Indices: 4296687--4296730 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4296677 GCCAGTTTCT
**
4296687 TGTATCGATACAATTGAGTA
1 TGTATCGATACAATTGAACA
4296707 TGTATCGATACAA-TGAACA
1 TGTATCGATACAATTGAACA
4296726 TGTAT
1 TGTAT
4296731 AGCTATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAATTGAACA
Found at i:4296784 original size:13 final size:13
Alignment explanation
Indices: 4296766--4296792 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4296756 TACAATGAGC
4296766 ATGTATCGATACA
1 ATGTATCGATACA
4296779 ATGTATCGATACA
1 ATGTATCGATACA
4296792 A
1 A
4296793 AATATTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4306878 original size:73 final size:72
Alignment explanation
Indices: 4306660--4306907 Score: 263
Period size: 73 Copynumber: 3.5 Consensus size: 72
4306650 AAATAAACCA
* * *
4306660 AAATGCATG-AATAAATTATAAGAAAATTGCTAATTGGTCCCTTAGCATTCAGCCAAACA-AAAA
1 AAATGCATGAAATAAATTATAGGAAAATTGCTAATAGGTCCCTTAGCATTCAACCAAACATAAAA
*
4306723 TGGCCTT
66 TGGCCAT
* * * ** * *
4306730 AAATGCATGAAATAAATTGT-GAGAAAAATGCTAATAAGTCCCTTAGCATTTGACTAAACATAAG
1 AAATGCATGAAATAAATTATAG-GAAAATTGCTAATAGGTCCCTTAGCATTCAACCAAACATAAA
*
4306794 ACGGCTC-T
65 ATGGC-CAT
* * **
4306802 AAATGCATGAAATAAAATTAT-GGCAAAATTGCTGATAGGTCCCTTAGCATTCAACCAAGCATGG
1 AAATGCATGAAAT-AAATTATAGG-AAAATTGCTAATAGGTCCCTTAGCATTCAACCAAACATAA
* *
4306866 GATGGACAT
64 AATGGCCAT
4306875 AAATGCATGAAATAAATTATAGGAAAATTGCTA
1 AAATGCATGAAATAAATTATAGGAAAATTGCTA
4306908 GTAGATCTTT
Statistics
Matches: 146, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
70 9 0.06
71 40 0.27
72 38 0.26
73 59 0.40
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (72 bp):
AAATGCATGAAATAAATTATAGGAAAATTGCTAATAGGTCCCTTAGCATTCAACCAAACATAAAA
TGGCCAT
Found at i:4306925 original size:72 final size:73
Alignment explanation
Indices: 4306801--4306950 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 73
4306791 AAGACGGCTC
*
4306801 TAAATGCATGAAATAAAATTATGGCAAAATTGCTGATAGGTCCCTTAGCATTCAACCAAGCATGG
1 TAAATGCATGAAATAAAATTATGGCAAAATTGCTGATAGATCCCTTAGCATTCAACCAAGCATGG
*
4306866 GATGGACA
66 AATGGACA
* * *
4306874 TAAATGCATGAAAT-AAATTATAGG-AAAATTGCT-AGTAGAT-CTTTAAGCATTCAGCTAAGCA
1 TAAATGCATGAAATAAAATTAT-GGCAAAATTGCTGA-TAGATCCCTT-AGCATTCAACCAAGCA
*
4306935 TGGAATGGCCA
63 TGGAATGGACA
4306946 TAAAT
1 TAAAT
4306951 ATGTTTGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
71 4 0.06
72 48 0.71
73 16 0.24
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (73 bp):
TAAATGCATGAAATAAAATTATGGCAAAATTGCTGATAGATCCCTTAGCATTCAACCAAGCATGG
AATGGACA
Found at i:4307048 original size:42 final size:42
Alignment explanation
Indices: 4307000--4307082 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
4306990 AAAGTTTGGG
*
4307000 TAACACTAATTTTAACCTTTAATAGCTTTAAAATTTAAAGGC
1 TAACACTAATTTTAACCCTTAATAGCTTTAAAATTTAAAGGC
*
4307042 TAACACTAATTTTAACCCTTAATAGCTTTAAATTTTAAAGG
1 TAACACTAATTTTAACCCTTAATAGCTTTAAAATTTAAAGG
4307083 AAAAATTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (42 bp):
TAACACTAATTTTAACCCTTAATAGCTTTAAAATTTAAAGGC
Found at i:4307931 original size:27 final size:27
Alignment explanation
Indices: 4307901--4307960 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
4307891 CAAATTATAA
*
4307901 AAAAATAAAAATAGAAAA-AGGAAAGAG
1 AAAAATAAAAAT-GAAAACAGCAAAGAG
**
4307928 AAAAATGTAAATGAAAACAGCAAAGAG
1 AAAAATAAAAATGAAAACAGCAAAGAG
4307955 AAAAAT
1 AAAAAT
4307961 CTGTTTTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.10
Consensus pattern (27 bp):
AAAAATAAAAATGAAAACAGCAAAGAG
Found at i:4308165 original size:26 final size:26
Alignment explanation
Indices: 4308110--4308165 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
4308100 AAGAATCCTA
*
4308110 TTTTTATTGTTTTGTAACTTCGTTTG
1 TTTTTATTGTTTTGTAACTTCATTTG
* * *
4308136 TTTTTTTTTTTTTGTAAACTTTATTT-
1 TTTTTATTGTTTTGT-AACTTCATTTG
4308162 TTTT
1 TTTT
4308166 AGAGTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.73
Consensus pattern (26 bp):
TTTTTATTGTTTTGTAACTTCATTTG
Found at i:4316065 original size:19 final size:19
Alignment explanation
Indices: 4316039--4316090 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
4316029 AGATAGTAAA
4316039 AAAAAAAAGAGAAAAATGAGG
1 AAAAAAAAGA-AAAAATG-GG
4316060 AAAAAAAAGAAAAAATGGG
1 AAAAAAAAGAAAAAATGGG
*
4316079 AAAACAAAGAAA
1 AAAAAAAAGAAA
4316091 TGCGATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 7 0.23
21 10 0.33
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAAAAAATGGG
Found at i:4316065 original size:20 final size:20
Alignment explanation
Indices: 4316040--4316088 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4316030 GATAGTAAAA
4316040 AAAAAAAGAG-AAAAATGAGG
1 AAAAAAAGAGAAAAAATG-GG
4316060 AAAAAAA-AGAAAAAATGGG
1 AAAAAAAGAGAAAAAATGGG
4316079 AAAACAAAGA
1 AAAA-AAAGA
4316089 AATGCGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 8 0.31
20 17 0.65
21 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAAAAAGAGAAAAAATGGG
Found at i:4316344 original size:10 final size:10
Alignment explanation
Indices: 4316331--4316377 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
4316321 ATAAAGCAAT
4316331 AAAAAAAGAA
1 AAAAAAAGAA
*
4316341 AAAAAGAGAA
1 AAAAAAAGAA
* *
4316351 AGAAAAAGTA
1 AAAAAAAGAA
*
4316361 AAAAAATGAA
1 AAAAAAAGAA
4316371 AAAAAAA
1 AAAAAAA
4316378 TGAGGCTCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:4320407 original size:155 final size:155
Alignment explanation
Indices: 4320176--4320460 Score: 360
Period size: 155 Copynumber: 1.8 Consensus size: 155
4320166 TCCTAGGTCA
** * * * *
4320176 TCACCAAGTTGCTTTTATGCCAAAGGGGTATATTTAGGATAGGTTCATCCTTTTTATATTATTTT
1 TCACCAAGTCACTTTTATGCCAAAGGGATAAATTTACGATAGGTTCATCCTTTTTATATCATTTT
* * * * *
4320241 TCTTTCTTTTAGAATTA-TGTGGATACTTTCACGTCAAA-AGTATACCTCTAGAGCATTTTGATA
66 TATGTCCTTTAGAATTATTG-GGATACTTTCACGTCAAAGA-TAAATCT-TAGAGCATTTTGATA
4320304 ATTCTTCTTAAAACATATTCCTAGATAG
128 ATTCTTCTTAAAACATATTCCTAGATAG
* * *
4320332 TCACCAAGTCACTTTTATGTCAAAGGTATAAATTTACGATAGGTTTAT-CTTTTTATATCATTTT
1 TCACCAAGTCACTTTTATGCCAAAGGGATAAATTTACGATAGGTTCATCCTTTTTATATCATTTT
** * *
4320396 TATGTCCTTTAGGGTTATTGGGATACTTTCACGTCGAAGATAAATCTTAGAGCATTTTGGTAATT
66 TATGTCCTTTAGAATTATTGGGATACTTTCACGTCAAAGATAAATCTTAGAGCATTTTGATAATT
4320461 TTTTTTAGAA
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
154 17 0.16
155 49 0.45
156 43 0.39
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (155 bp):
TCACCAAGTCACTTTTATGCCAAAGGGATAAATTTACGATAGGTTCATCCTTTTTATATCATTTT
TATGTCCTTTAGAATTATTGGGATACTTTCACGTCAAAGATAAATCTTAGAGCATTTTGATAATT
CTTCTTAAAACATATTCCTAGATAG
Found at i:4322512 original size:16 final size:16
Alignment explanation
Indices: 4322472--4322503 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4322462 TTATGTAAGA
*
4322472 ATTCATTTTTGCTTTT
1 ATTCAATTTTGCTTTT
4322488 ATTCAATTTTGCTTTT
1 ATTCAATTTTGCTTTT
4322504 CTTTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.66
Consensus pattern (16 bp):
ATTCAATTTTGCTTTT
Found at i:4328326 original size:60 final size:60
Alignment explanation
Indices: 4328136--4328814 Score: 438
Period size: 60 Copynumber: 11.4 Consensus size: 60
4328126 GTTTAGATAT
* * * * *
4328136 AGTCATGGTTTAGGTTTCTAGTTTTATTCGAGTCATTTCTTTGAGTCTTGGTTTTGCCCA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTCAAGCCATTTCTTTGAGTCTTGGTTTTACCCA
* * * * * * * ** * *
4328196 AATCATTGTTTATG-TTCTAGGTTCATCCAGGCTATTTC-TTGAATCTTAATTGTACTCA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTCAAGCCATTTCTTTGAGTCTTGGTTTTACCCA
* * ** **
4328254 AGTCATTATTTAGGCTTCTAGTTTTGTTCAAGCCATTTCTTTGAGTCTTGGTTTCGCCCA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTCAAGCCATTTCTTTGAGTCTTGGTTTTACCCA
* * *
4328314 AGTCATTGTTTAGGGTTT-TGGTTTCATCCAGGCCATTTC-TTGAGTCTTGGTTTTACCCA
1 AGTCATTGTTTA-GGTTTCTAGTTTCATTCAAGCCATTTCTTTGAGTCTTGGTTTTACCCA
* * * * * * *
4328373 AGTTATTATTT-GGATTTCTAGTTTCATCCAAGCCATTTCCTTGAGTCTCGATTTTACCAA
1 AGTCATTGTTTAGG-TTTCTAGTTTCATTCAAGCCATTTCTTTGAGTCTTGGTTTTACCCA
* * *
4328433 AGTCATTGTTTAGGTTT-TGGTTTCATGC-AGACCATTT-TCTTGAGTCTTGGTTTTACTCA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTCAAG-CCATTTCT-TTGAGTCTTGGTTTTACCCA
* * * * * * * * *
4328492 AGTCATTGTTAAGGTTTTTGGTTTTA-TCCAGCCCATTTCTTTTAGTGTTAGTTTTGCCCA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTCAAG-CCATTTCTTTGAGTCTTGGTTTTACCCA
* * * * *
4328552 AGTTATTGTTTAGGGTTCTAGTTTTATTCATA-CCATTTCTTTGAGTCTTAGTTTTACAACA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTCA-AGCCATTTCTTTGAGTCTTGGTTTTAC-CCA
* * * * * * * * *
4328613 AGTCATTATTTAGGTTTCTAATTTCA-TCTAGGCTAGTTCCTTAAGTCATGGTTTTACCTA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTC-AAGCCATTTCTTTGAGTCTTGGTTTTACCCA
* * * * * * * * * *
4328673 AGTCATTGTTTAGATTTTTGGATTT-A-TCTAGGCCATTTTTTTTAGTTTTAGTTTCACTCA
1 AGTCATTGTTTAGGTTTCTAG-TTTCATTC-AAGCCATTTCTTTGAGTCTTGGTTTTACCCA
** * * * * *
4328733 AGTCATTACTTAGGTTTCTGGTTTTA-TCTAGGCCATTT-TGTTGAGTATTGG-TTTGCCCA
1 AGTCATTGTTTAGGTTTCTAGTTTCATTC-AAGCCATTTCT-TTGAGTCTTGGTTTTACCCA
* *
4328792 AGTCATTATTTA-GTTTCTTGTTT
1 AGTCATTGTTTAGGTTTCTAGTTT
4328815 TGTCTAGGAC
Statistics
Matches: 481, Mismatches: 118, Indels: 42
0.75 0.18 0.07
Matches are distributed among these distances:
57 2 0.00
58 40 0.08
59 149 0.31
60 234 0.49
61 55 0.11
62 1 0.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (60 bp):
AGTCATTGTTTAGGTTTCTAGTTTCATTCAAGCCATTTCTTTGAGTCTTGGTTTTACCCA
Found at i:4328396 original size:119 final size:118
Alignment explanation
Indices: 4328144--4328804 Score: 573
Period size: 119 Copynumber: 5.6 Consensus size: 118
4328134 ATAGTCATGG
* * * *
4328144 TTTAGGTTTCTAGTTTTATTCGAGTCATTTCTTTGAGTCTTGGTTTTGCCCAAATCATTGTTTAT
1 TTTAGGTTTCTAGTTTTATTCAAGCCATTTCTTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTAG
* * * * * *
4328209 GTTCTAGG-TTCATCCAGGCTATTTCTTGAATCTTAATTGTACTCAAGTCATTA
66 GTT-TTGGTTTCATCCAGACCATTTCTTGAGTCTTAGTTTTACTCAAGTCATTA
* * *
4328262 TTTAGGCTTCTAGTTTTGTTCAAGCCATTTCTTTGAGTCTTGGTTTCGCCCAAGTCATTGTTTAG
1 TTTAGGTTTCTAGTTTTATTCAAGCCATTTCTTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTA-
* * * *
4328327 GGTTTTGGTTTCATCCAGGCCATTTCTTGAGTCTTGGTTTTACCCAAGTTATTA
65 GGTTTTGGTTTCATCCAGACCATTTCTTGAGTCTTAGTTTTACTCAAGTCATTA
* * * * * * *
4328381 TTT-GGATTTCTAGTTTCATCCAAGCCATTTCCTTGAGTCTCGATTTTACCAAAGTCATTGTTTA
1 TTTAGG-TTTCTAGTTTTATTCAAGCCATTTCTTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTA
* * *
4328445 GGTTTTGGTTTCATGCAGACCATTTTCTTGAGTCTTGGTTTTACTCAAGTCATTG
65 GGTTTTGGTTTCATCCAGACCA-TTTCTTGAGTCTTAGTTTTACTCAAGTCATTA
* * * * * * * *
4328500 TTAAGGTTTTTGGTTTTA-TCCAGCCCATTTCTTTTAGTGTTAGTTTTGCCCAAGTTATTGTTTA
1 TTTAGGTTTCTAGTTTTATTCAAG-CCATTTCTTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTA
* * * * * *
4328564 GGGTTCTAGTTTTATTCATACCATTTCTTTGAGTCTTAGTTTTACAACAAGTCATTA
65 -GGTTTTGGTTTCATCCAGACCATTTC-TTGAGTCTTAGTTTTAC-TCAAGTCATTA
* * * * * * * * * *
4328621 TTTAGGTTTCTAATTTCA-TCTAGGCTAGTTCCTTAAGTCATGGTTTTACCTAAGTCATTGTTTA
1 TTTAGGTTTCTAGTTTTATTC-AAGCCATTTCTTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTA
* * * * * * *
4328685 GATTTTTGGATTT-ATCTAGGCCATTTTTTTTAGTTTTAGTTTCACTCAAGTCATTA
65 G-GTTTTGG-TTTCATCCAGACCA-TTTCTTGAGTCTTAGTTTTACTCAAGTCATTA
* * * * *
4328741 CTTAGGTTTCTGGTTTTA-TCTAGGCCATTT-TGTTGAGTATTGG-TTTGCCCAAGTCATTATTT
1 TTTAGGTTTCTAGTTTTATTC-AAGCCATTTCT-TTGAGTCTTGGTTTTGCCCAAGTCATTGTTT
4328803 AG
64 AG
4328805 TTTCTTGTTT
Statistics
Matches: 434, Mismatches: 95, Indels: 27
0.78 0.17 0.05
Matches are distributed among these distances:
118 86 0.20
119 185 0.43
120 78 0.18
121 78 0.18
122 7 0.02
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.47
Consensus pattern (118 bp):
TTTAGGTTTCTAGTTTTATTCAAGCCATTTCTTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTAG
GTTTTGGTTTCATCCAGACCATTTCTTGAGTCTTAGTTTTACTCAAGTCATTA
Found at i:4328822 original size:58 final size:59
Alignment explanation
Indices: 4328611--4328843 Score: 186
Period size: 60 Copynumber: 3.9 Consensus size: 59
4328601 AGTTTTACAA
** * * * ** ** *
4328611 CAAGTCATTATTTAGGTTTCTAATTTCATCTAGGCTAGTTCCTTAAGTCATGGTTTTAC-
1 CAAGTCATTATTTA-GTTTCTTGTTTTATCTAGGCCATTTTATTAAGTTTTGGTTTCACT
* * * * *
4328670 CTAAGTCATTGTTTAGATTT-TTGGATTTATCTAGGCCATTTTTTTTAGTTTTAGTTTCACT
1 C-AAGTCATTATTTAG-TTTCTT-GTTTTATCTAGGCCATTTTATTAAGTTTTGGTTTCACT
* * * * *
4328731 CAAGTCATTACTTAGGTTTCTGGTTTTATCTAGGCCATTTTGTTGAGTATTGGTTTGC-C-
1 CAAGTCATTATTTA-GTTTCTTGTTTTATCTAGGCCATTTTATTAAGTTTTGGTTT-CACT
* *
4328790 CAAGTCATTATTTAGTTTCTTGTTTTGTCTAGGACATTTTATTAAGTTTTGGTT
1 CAAGTCATTATTTAGTTTCTTGTTTTATCTAGGCCATTTTATTAAGTTTTGGTT
4328844 CTACCTTAAG
Statistics
Matches: 138, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
58 34 0.25
59 16 0.12
60 84 0.61
61 4 0.03
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.49
Consensus pattern (59 bp):
CAAGTCATTATTTAGTTTCTTGTTTTATCTAGGCCATTTTATTAAGTTTTGGTTTCACT
Found at i:4329174 original size:47 final size:47
Alignment explanation
Indices: 4329099--4329193 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
4329089 GAGAAATTGT
* *
4329099 AAAAACCACATATTTGCCATCACATTTTTCTT-TTTCAGCTCGTTATC
1 AAAAACCACATATTTCCCATCACATTTTTCTTATTT-AGCACGTTATC
**
4329146 AAAAACCACATA-TTCCCTATCATGTTTTTCTTATTTAGCACGTTATC
1 AAAAACCACATATTTCCC-ATCACATTTTTCTTATTTAGCACGTTATC
4329193 A
1 A
4329194 CTTTGTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 4 0.10
47 35 0.83
48 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.40
Consensus pattern (47 bp):
AAAAACCACATATTTCCCATCACATTTTTCTTATTTAGCACGTTATC
Found at i:4329841 original size:41 final size:40
Alignment explanation
Indices: 4329796--4329894 Score: 90
Period size: 41 Copynumber: 2.4 Consensus size: 40
4329786 ACTATTTATG
* *
4329796 AACTTGTCAGTTTTGTCTCGGTTAACCATTCACTATTAGTT
1 AACTTGT-AGTTTTGTCTCGATCAACCATTCACTATTAGTT
* * * * * *
4329837 AACTTATAGATTCTATCTTGATCAACCCTTCACTCTTAGTT
1 AACTTGTAG-TTTTGTCTCGATCAACCATTCACTATTAGTT
*
4329878 GACTTGTTAGTTTTGTC
1 AACTTG-TAGTTTTGTC
4329895 ATCGTTTACC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
40 2 0.05
41 39 0.89
42 3 0.07
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (40 bp):
AACTTGTAGTTTTGTCTCGATCAACCATTCACTATTAGTT
Found at i:4330099 original size:15 final size:16
Alignment explanation
Indices: 4330066--4330099 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4330056 ACTTATCAGT
*
4330066 TTTATCCTGGTCAACC
1 TTTATCCTAGTCAACC
4330082 TTTATCCTAGTC-ACC
1 TTTATCCTAGTCAACC
4330097 TTT
1 TTT
4330100 TGTTAACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (16 bp):
TTTATCCTAGTCAACC
Found at i:4334871 original size:11 final size:12
Alignment explanation
Indices: 4334854--4334887 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4334844 TTTTTTCATA
4334854 TTATATTATGTT
1 TTATATTATGTT
*
4334866 TT-TATTATTTT
1 TTATATTATGTT
4334877 TTATATTATGT
1 TTATATTATGT
4334888 ATAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATATTATGTT
Found at i:4335890 original size:30 final size:30
Alignment explanation
Indices: 4335856--4335916 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
4335846 TTCTCTAAAA
* * *
4335856 TAAATATTTATATACGACATTTGTATTTTT
1 TAAATATCTACATACGACATTTGCATTTTT
* *
4335886 TAAATATCTACATATGATATTTGCATTTTT
1 TAAATATCTACATACGACATTTGCATTTTT
4335916 T
1 T
4335917 TCTCAAAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (30 bp):
TAAATATCTACATACGACATTTGCATTTTT
Found at i:4336108 original size:2 final size:2
Alignment explanation
Indices: 4336101--4336147 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4336091 GCTGGCCATT
4336101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4336143 TA TA T
1 TA TA T
4336148 CATACCTAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4337791 original size:68 final size:69
Alignment explanation
Indices: 4337659--4337793 Score: 177
Period size: 68 Copynumber: 2.0 Consensus size: 69
4337649 TGTTATAAAT
* * **
4337659 AAATTTATTTAATCAAAATCTTTCAATAGAATTAAAATTTTTATTTAAATTATGATTAGTTTTAT
1 AAATTTATTTAACCAAAATCTTTCAATAGAATTAAAATTTTTATTTAAATTATGAATAAATTTAT
4337724 TATA
66 TATA
* *
4337728 AAATTT-TTTAACCAAAATTTTTCAATAGAATTAAAATTTTTATTGATGAA-TAT-AATAAATTT
1 AAATTTATTTAACCAAAATCTTTCAATAGAATTAAAATTTTTATT--TAAATTATGAATAAATTT
4337790 ATTA
64 ATTA
4337794 ATAATAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
68 46 0.79
69 9 0.16
70 3 0.05
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (69 bp):
AAATTTATTTAACCAAAATCTTTCAATAGAATTAAAATTTTTATTTAAATTATGAATAAATTTAT
TATA
Found at i:4338268 original size:7 final size:7
Alignment explanation
Indices: 4338256--4338280 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4338246 TATTTTTATA
4338256 TATAAAT
1 TATAAAT
4338263 TATAAAT
1 TATAAAT
4338270 TATAAAT
1 TATAAAT
4338277 TATA
1 TATA
4338281 TGCGAGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAAAT
Found at i:4338383 original size:23 final size:24
Alignment explanation
Indices: 4338339--4338383 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
4338329 ACTTTTTTTT
** *
4338339 TAAAAAAATAATATTTTTAATAAG
1 TAAAAAAATAATATAATAAATAAG
4338363 TAAAAAAAT-ATATAATAAATA
1 TAAAAAAATAATATAATAAATA
4338384 TAATAAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAAAATAATATAATAAATAAG
Found at i:4338409 original size:15 final size:15
Alignment explanation
Indices: 4338391--4338439 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4338381 ATATAATAAG
*
4338391 ATATATTTAAATATT
1 ATATATTTATATATT
*
4338406 ATATTTTTATATATT
1 ATATATTTATATATT
*
4338421 -TAATATATATATATT
1 AT-ATATTTATATATT
4338436 ATAT
1 ATAT
4338440 TGATATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATTTATATATT
Found at i:4338415 original size:8 final size:8
Alignment explanation
Indices: 4338391--4338439 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
4338381 ATATAATAAG
4338391 ATATATTT
1 ATATATTT
*
4338399 AAATA-TT
1 ATATATTT
*
4338406 ATATTTTT
1 ATATATTT
4338414 ATATATTT
1 ATATATTT
*
4338422 A-ATATAT
1 ATATATTT
4338429 ATATA-TT
1 ATATATTT
4338436 ATAT
1 ATAT
4338440 TGATATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
7 16 0.48
8 17 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
ATATATTT
Found at i:4338429 original size:13 final size:13
Alignment explanation
Indices: 4338391--4338450 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
4338381 ATATAATAAG
4338391 ATATATTTAA-AT
1 ATATATTTAATAT
4338403 ATTATATTT--T-T
1 A-TATATTTAATAT
4338414 ATATATTTAATAT
1 ATATATTTAATAT
4338427 ATATATATT-ATAT
1 ATATAT-TTAATAT
4338440 -TGATATTTAAT
1 AT-ATATTTAAT
4338451 TTTTTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
12 5 0.12
13 24 0.60
14 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:4338564 original size:14 final size:14
Alignment explanation
Indices: 4338547--4338573 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4338537 TTAATTTTAA
4338547 AAATAAAAAAATTC
1 AAATAAAAAAATTC
4338561 AAATAAAAAAATT
1 AAATAAAAAAATT
4338574 GTAGAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAAAAAATTC
Found at i:4338912 original size:4 final size:4
Alignment explanation
Indices: 4338903--4338930 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4338893 AAACCAGTAT
4338903 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
4338931 CATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:4338983 original size:22 final size:23
Alignment explanation
Indices: 4338932--4338984 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
4338922 ATTTATTTAC
4338932 ATATATTTTTATGTAATGATACAAA
1 ATATATTTTTA-GTAAT-ATACAAA
4338957 A-ATATTTTTA-TAAT-TACATAA
1 ATATATTTTTAGTAATATACA-AA
4338978 ATATATT
1 ATATATT
4338985 ATAGTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.15
21 3 0.12
22 9 0.35
24 9 0.35
25 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATATTTTTAGTAATATACAAA
Found at i:4339378 original size:221 final size:223
Alignment explanation
Indices: 4339039--4339553 Score: 571
Period size: 221 Copynumber: 2.3 Consensus size: 223
4339029 ATAAATATTT
* * * * * * * *
4339039 TAGTTACATAAATTATATTATATATTATACAAATTATTATAATTGATAATATAAATCAA-TATTA
1 TAGTTACATAAATTATATTATCTCTCATATAAGTTATTATCATAGATAATAAAAAT-AAGTATTA
* *
4339103 CATATTTTTATTACAATTACATATATATTATTTATTTACATAAATTATGATAAAAGATAATAAAA
65 C--ATCTTTATTACAATTA-ATATATATTATCTATTTACATAAATTATGATAAAAGATAATAAAA
* * * * * *
4339168 ATTGTGATACATA-AT-TTTATTGCATTTACATTAAATTTTTGTAAGTTATAAAAATATATTATC
127 ATTGT-A-AAATATATATTTATTACATTTACATAAAATTTTTATAAGTCATAAAAATATATTAGC
* * * *
4339231 AATAGGTAATATAAA-TAGTATTATATAAAACACA
190 AA-AGATAATAGAAAGTAATATTACATAAAACACA
*
4339265 TAGTTACATAAATTATATTATCTCTCATATAAGTTTATTATCATAGATAATAGAAATAAGTATTA
1 TAGTTACATAAATTATATTATCTCTCATATAAG-TTATTATCATAGATAATAAAAATAAGTATTA
* *
4339330 CATCTTT-TTACAATT-ATATATATTATCTA-TTATATAAATTATGATAAAAGATAATAAAATTT
65 CATCTTTATTACAATTAATATATATTATCTATTTACATAAATTATGATAAAAGATAATAAAAATT
* *
4339392 GTAAAATATATATTTATTATATTTACATAAAATTTTTATAAGTCATATAAATATATTAGCAAAGA
130 GTAAAATATATATTTATTACATTTACATAAAATTTTTATAAGTCATAAAAATATATTAGCAAAGA
* *
4339457 TAATAGAAAGTAATATTACATAAAATATA
195 TAATAGAAAGTAATATTACATAAAACACA
* * * * *
4339486 -AGAATTATATAAATTATATTATCTCTTGCATTTACG-TATTATCATATATAATAAAAATATGTA
1 TAG--TTACATAAATTATATTATCTC-T-CATATAAGTTATTATCATAGATAATAAAAATAAGTA
4339549 TTACA
62 TTACA
4339554 AATTTTTATT
Statistics
Matches: 248, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
219 4 0.02
220 15 0.06
221 91 0.37
222 62 0.25
223 1 0.00
224 14 0.06
225 5 0.02
226 30 0.12
227 26 0.10
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (223 bp):
TAGTTACATAAATTATATTATCTCTCATATAAGTTATTATCATAGATAATAAAAATAAGTATTAC
ATCTTTATTACAATTAATATATATTATCTATTTACATAAATTATGATAAAAGATAATAAAAATTG
TAAAATATATATTTATTACATTTACATAAAATTTTTATAAGTCATAAAAATATATTAGCAAAGAT
AATAGAAAGTAATATTACATAAAACACA
Done.