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 17 of 37
Found at i:3037209 original size:19 final size:20
Alignment explanation
Indices: 3037165--3037237 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
3037155 CTGCCAGTTT
* *
3037165 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATA
*
3037185 CATGTATAGATACAATGA-A
1 CATGTATCGATACAATGATA
*
3037204 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-ATA
*
3037225 -ATGTATTGATACA
1 CATGTATCGATACA
3037238 TCTAGGTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.33
20 29 0.64
21 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:3037812 original size:19 final size:21
Alignment explanation
Indices: 3037790--3037831 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
3037780 AGGTTCTCAA
*
3037790 AAAAAATTT-TC-CCTTTGAT
1 AAAAAATTTCTCTCCCTTGAT
3037809 AAAAAATTTCTCTCCCTTGAT
1 AAAAAATTTCTCTCCCTTGAT
3037830 AA
1 AA
3037832 TCGGTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAAATTTCTCTCCCTTGAT
Found at i:3037857 original size:31 final size:31
Alignment explanation
Indices: 3037808--3037893 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
3037798 TTCCCTTTGA
* *
3037808 TAAAAA-A-TTTCTCTCCCTTGATAATCGGT
1 TAAAAAGATTTTCTCCCCCTTGATAATCGAT
3037837 TAAAAAGATTTTCTCCCCCTTGATAATCGAT
1 TAAAAAGATTTTCTCCCCCTTGATAATCGAT
* *
3037868 TAAAAAGATTTCCTACCCCTTGATAA
1 TAAAAAGATTTTCTCCCCCTTGATAA
3037894 AAAATTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 6 0.12
30 1 0.02
31 44 0.86
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (31 bp):
TAAAAAGATTTTCTCCCCCTTGATAATCGAT
Found at i:3039617 original size:22 final size:21
Alignment explanation
Indices: 3039582--3039631 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3039572 TTGTTAACTG
*
3039582 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
3039602 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
3039623 AATTTGAAG
1 ATTTTGAAG
3039632 AAGCTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:3039628 original size:21 final size:22
Alignment explanation
Indices: 3039589--3039631 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3039579 CTGATTTTGA
* *
3039589 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
3039611 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
3039632 AAGCTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:3039830 original size:20 final size:20
Alignment explanation
Indices: 3039807--3039852 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3039797 AGATGTTTCG
3039807 ATACATCCTTCAATGTATCA
1 ATACATCCTTCAATGTATCA
* *
3039827 ATACATCGTTCAATGTATCG
1 ATACATCCTTCAATGTATCA
3039847 ATACAT
1 ATACAT
3039853 TCTGGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (20 bp):
ATACATCCTTCAATGTATCA
Found at i:3040531 original size:51 final size:51
Alignment explanation
Indices: 3040465--3040580 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
3040455 TTTTACCCAG
* ***
3040465 ATGTATCGATACATTTTGTCTTTTTACCCAGATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTGTCTTTTTACCCAGATGTATCAATACATTAAACA
* *
3040516 ATGTATCGATACATTTTGTTTTTTTACCCAGATGTATCAATACATTAAAGA
1 ATGTATCGATACATTTTGTCTTTTTACCCAGATGTATCAATACATTAAACA
3040567 ATGTATCGATACAT
1 ATGTATCGATACAT
3040581 ATAATGTATC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (51 bp):
ATGTATCGATACATTTTGTCTTTTTACCCAGATGTATCAATACATTAAACA
Found at i:3040607 original size:20 final size:19
Alignment explanation
Indices: 3040547--3040618 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
3040537 TTTTACCCAG
* * *
3040547 ATGTATCAATACATTAAAGA
1 ATGTATCGATACATT-TATA
3040567 ATGTATCGATACA--TATA
1 ATGTATCGATACATTTATA
*
3040584 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATT-TATA
*
3040604 ATGTATTGATACATT
1 ATGTATCGATACATT
3040619 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 15 0.34
20 29 0.66
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:3045457 original size:19 final size:19
Alignment explanation
Indices: 3045414--3045486 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
3045404 CTCACCCAGA
*
3045414 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
3045434 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
3045453 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
3045473 TGTATCGATACATG
1 TGTATCGATACATG
3045487 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:3045559 original size:20 final size:20
Alignment explanation
Indices: 3045515--3045568 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
3045505 CTACCACTGT
*
3045515 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGATACA
*
3045535 ATGTATCGATACATGATGA-A
1 TTGTATCGATACATGAT-ACA
*
3045555 TTGTATTGATACAT
1 TTGTATCGATACAT
3045569 TGCTTGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:3047825 original size:21 final size:20
Alignment explanation
Indices: 3047791--3047833 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3047781 TATTAAAAAG
*
3047791 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
3047812 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
3047832 TT
1 TT
3047834 TGCATGCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:3047832 original size:20 final size:21
Alignment explanation
Indices: 3047791--3047833 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3047781 TATTAAAAAG
*
3047791 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
3047812 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
3047832 TT
1 TT
3047834 TGCATGCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:3053611 original size:22 final size:22
Alignment explanation
Indices: 3053586--3053627 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3053576 TTTTTAAAGA
3053586 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
3053608 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
3053628 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:3054207 original size:66 final size:66
Alignment explanation
Indices: 3054125--3054256 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
3054115 CGATACATAG
*
3054125 GTATTTGTATCGATACATTATGGTTGACTTAATCTACAAAGGTCAAAACCCTTGAATGTATCGAT
1 GTATTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCCTTGAATGTATCGAT
3054190 A
66 A
*
3054191 GTATTTGTATCGATACATTATGGTTGACTTAGGCTACAAAGGTCAAAACCCTTGAATGTATCGAT
1 GTATTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCCTTGAATGTATCGAT
3054256 A
66 A
3054257 CTCACCCAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (66 bp):
GTATTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCCTTGAATGTATCGAT
A
Found at i:3054304 original size:13 final size:13
Alignment explanation
Indices: 3054286--3054312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3054276 ACATTATGCT
3054286 TTGTATCGATACA
1 TTGTATCGATACA
3054299 TTGTATCGATACA
1 TTGTATCGATACA
3054312 T
1 T
3054313 GTTTATTGTA
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:3054322 original size:19 final size:19
Alignment explanation
Indices: 3054298--3054353 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3054288 GTATCGATAC
***
3054298 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATGACA
3054317 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
3054337 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
3054354 AACTGACAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:3054342 original size:20 final size:20
Alignment explanation
Indices: 3054298--3054352 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3054288 GTATCGATAC
***
3054298 ATTGTATCGATACAT-GTTT
1 ATTGTATCGATACATGGACA
3054317 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
3054337 ATTGTATCGATACATG
1 ATTGTATCGATACATG
3054353 AAACTGACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:3054410 original size:20 final size:20
Alignment explanation
Indices: 3054385--3054447 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
3054375 CACTGTTTGA
3054385 ATCGATACATGGTACAATGT
1 ATCGATACATGGTACAATGT
3054405 ATCGATACA---T----TGT
1 ATCGATACATGGTACAATGT
*
3054418 ATCGACACATGGTACAATGT
1 ATCGATACATGGTACAATGT
3054438 ATCGATACAT
1 ATCGATACAT
3054448 TGTATCGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
13 11 0.32
16 1 0.03
17 1 0.03
20 21 0.62
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
ATCGATACATGGTACAATGT
Found at i:3054418 original size:13 final size:13
Alignment explanation
Indices: 3054397--3054482 Score: 61
Period size: 13 Copynumber: 7.5 Consensus size: 13
3054387 CGATACATGG
*
3054397 TACAATGTATCGA
1 TACATTGTATCGA
3054410 TACATTGTATCGA
1 TACATTGTATCGA
*
3054423 CACA-TG----G-
1 TACATTGTATCGA
*
3054430 TACAATGTATCGA
1 TACATTGTATCGA
3054443 TACATTGTATCGA
1 TACATTGTATCGA
3054456 TACA-TG-AT-G-
1 TACATTGTATCGA
3054465 -A-ATTGTATCGA
1 TACATTGTATCGA
3054476 TACATTG
1 TACATTG
3054483 CTTGTAATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 24
0.67 0.05 0.28
Matches are distributed among these distances:
7 4 0.07
8 6 0.11
9 2 0.04
10 2 0.04
11 2 0.04
12 6 0.11
13 35 0.61
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3054428 original size:33 final size:33
Alignment explanation
Indices: 3054385--3054482 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
3054375 CACTGTTTGA
3054385 ATCGATACATGGTACAATGTATCGATACATTGT
1 ATCGATACATGGTACAATGTATCGATACATTGT
*
3054418 ATCGACACATGGTACAATGTATCGATACATTGT
1 ATCGATACATGGTACAATGTATCGATACATTGT
* *
3054451 ATCGATACATGATGA-ATTGTATCGATACATTG
1 ATCGATACATGGT-ACAATGTATCGATACATTG
3054483 CTTGTAATGG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 59 0.98
34 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (33 bp):
ATCGATACATGGTACAATGTATCGATACATTGT
Found at i:3059812 original size:13 final size:13
Alignment explanation
Indices: 3059796--3059820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3059786 CAATTCATCA
3059796 TGTATCGATACAT
1 TGTATCGATACAT
3059809 TGTATCGATACA
1 TGTATCGATACA
3059821 ATGTGCCATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3059820 original size:33 final size:33
Alignment explanation
Indices: 3059776--3059840 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3059766 TTTGAAGCAA
3059776 TGTATCAATACAAT-T-CATCATGTATCGATACAT
1 TGTATCAATACAATGTGC--CATGTATCGATACAT
*
3059809 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCAATACAATGTGCCATGTATCGATACA
3059841 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
TGTATCAATACAATGTGCCATGTATCGATACAT
Found at i:3059914 original size:19 final size:19
Alignment explanation
Indices: 3059870--3059925 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3059860 CTGCCAGTTT
**
3059870 CATGTATCAATACAATTGTC
1 CATGTATCAATACAA-TGAA
*
3059890 CATGTATCGATACAATGAA
1 CATGTATCAATACAATGAA
3059909 CATGTATCAATACAATG
1 CATGTATCAATACAATG
3059926 TATCGATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (19 bp):
CATGTATCAATACAATGAA
Found at i:3062741 original size:33 final size:33
Alignment explanation
Indices: 3062677--3062741 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
3062667 TTTGAAGCAA
* * *
3062677 TGCATCGATACAATTCATCATGTATCGATACAC
1 TGCATCGATACAATTCACCATGCATCCATACAC
3062710 TGCATCGATACAATGT-ACCATGCATCCATACA
1 TGCATCGATACAAT-TCACCATGCATCCATACA
3062742 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (33 bp):
TGCATCGATACAATTCACCATGCATCCATACAC
Found at i:3063488 original size:19 final size:20
Alignment explanation
Indices: 3063449--3063554 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
3063439 TGATAATCGG
3063449 TTAAAAAGATTTTCTTCCCC
1 TTAAAAAGATTTTCTTCCCC
3063469 TTAAAAAGATTTTCTTCCCTTTGATAATC
1 TTAAAAAGATTTTCTTCCC---------C
3063498 GGTTAAAAAGATTTTCTTCCCC
1 --TTAAAAAGATTTTCTTCCCC
3063520 TTAAAAAGATTTTC-TCCTCC
1 TTAAAAAGATTTTCTTCC-CC
*
3063540 TTAAAAGGATTTTCT
1 TTAAAAAGATTTTCT
3063555 CCACCATAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 25
0.73 0.01 0.26
Matches are distributed among these distances:
19 3 0.04
20 48 0.67
22 1 0.01
29 1 0.01
31 19 0.26
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (20 bp):
TTAAAAAGATTTTCTTCCCC
Found at i:3063493 original size:51 final size:51
Alignment explanation
Indices: 3063428--3063541 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
3063418 CCTTAAAAAC
3063428 TTTCTCCCCCTTGATAATCGGTTAAAAAGATTTTCTTCCCCTTAAAAAGAT
1 TTTCTCCCCCTTGATAATCGGTTAAAAAGATTTTCTTCCCCTTAAAAAGAT
* *
3063479 TTTCTTCCCTTTGATAATCGGTTAAAAAGATTTTCTTCCCCTTAAAAAGAT
1 TTTCTCCCCCTTGATAATCGGTTAAAAAGATTTTCTTCCCCTTAAAAAGAT
*
3063530 TTTCTCCTCCTT
1 TTTCTCCCCCTT
3063542 AAAAGGATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (51 bp):
TTTCTCCCCCTTGATAATCGGTTAAAAAGATTTTCTTCCCCTTAAAAAGAT
Found at i:3065496 original size:20 final size:20
Alignment explanation
Indices: 3065471--3065508 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3065461 GAGTTTTCCA
*
3065471 AATGTATCGATACATTCTTC
1 AATGTACCGATACATTCTTC
3065491 AATGTACCGATACATTCT
1 AATGTACCGATACATTCT
3065509 GGAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
AATGTACCGATACATTCTTC
Found at i:3072728 original size:13 final size:13
Alignment explanation
Indices: 3072707--3072743 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3072697 AAGGATCTTA
* *
3072707 GTATTGATACATT
1 GTATCGATACACT
3072720 GTATCGATACACT
1 GTATCGATACACT
3072733 GTATCGATACA
1 GTATCGATACA
3072744 AAGGCACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
GTATCGATACACT
Found at i:3074383 original size:16 final size:16
Alignment explanation
Indices: 3074362--3074397 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3074352 ACTTTTATTT
**
3074362 CTTTGCTTGTTTTTAA
1 CTTTGCTTGTACTTAA
3074378 CTTTGCTTGTACTTAA
1 CTTTGCTTGTACTTAA
3074394 CTTT
1 CTTT
3074398 TCTTAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.58
Consensus pattern (16 bp):
CTTTGCTTGTACTTAA
Found at i:3074633 original size:22 final size:22
Alignment explanation
Indices: 3074590--3074633 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3074580 TGAAAAAGGG
*
3074590 GGAGAAATTATTTTATATAAAA
1 GGAGAAATTATTTTATAGAAAA
3074612 GGAGAAATTATTTT-TAAGAAAA
1 GGAGAAATTATTTTAT-AGAAAA
3074634 TGGGGAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (22 bp):
GGAGAAATTATTTTATAGAAAA
Found at i:3075362 original size:32 final size:33
Alignment explanation
Indices: 3075302--3075364 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
3075292 AACCCAAAAG
*
3075302 TATCGATACATATTGCTTTGTATCGATACACTA
1 TATCGATACATATTGCTTGGTATCGATACACTA
3075335 TATCGATACATGA-T-CTTGGTATCGATACAC
1 TATCGATACAT-ATTGCTTGGTATCGATACAC
3075365 AGTGAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (33 bp):
TATCGATACATATTGCTTGGTATCGATACACTA
Found at i:3075448 original size:13 final size:13
Alignment explanation
Indices: 3075430--3075457 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3075420 TGATACATGG
3075430 TACATTGTATCGA
1 TACATTGTATCGA
3075443 TACATTGTATCGA
1 TACATTGTATCGA
3075456 TA
1 TA
3075458 TATAGTAAAA
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:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3076366 original size:6 final size:6
Alignment explanation
Indices: 3076357--3076404 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
3076347 AGGAAAAGTA
* *
3076357 AAAAAG AAAAAG AAAAAA AAAAAG AGAACAAG AAAAA- AAAGAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG A-AA-AAG AAAAAG AAAAAG AAAAA
3076405 TAAGAGTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 23 0.66
7 4 0.11
8 4 0.11
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3076379 original size:18 final size:20
Alignment explanation
Indices: 3076356--3076396 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3076346 TAGGAAAAGT
3076356 AAAAAAGA-AA-AAGAAAAA
1 AAAAAAGAGAACAAGAAAAA
3076374 AAAAAAGAGAACAAGAAAAA
1 AAAAAAGAGAACAAGAAAAA
3076394 AAA
1 AAA
3076397 GAGAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 2 0.10
20 11 0.52
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAGAGAACAAGAAAAA
Found at i:3076409 original size:20 final size:19
Alignment explanation
Indices: 3076356--3076409 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
3076346 TAGGAAAAGT
*
3076356 AAAAAAGAAAAAGAA-AAA
1 AAAAAAGAAAAACAAGAAA
*
3076374 AAAAAAG-AGAACAAGAAA
1 AAAAAAGAAAAACAAGAAA
*
3076392 AAAAAGAGAAAAATAAGA
1 AAAAA-AGAAAAACAAGA
3076410 GTTTCTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 2 0.07
20 7 0.24
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAAACAAGAAA
Found at i:3077123 original size:29 final size:29
Alignment explanation
Indices: 3077091--3077181 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
3077081 TCATTTCGTT
*
3077091 ATTTCATATATTTTAGAATTATTTTAGTA
1 ATTTCATATATTTTAGAATCATTTTAGTA
* *
3077120 ATTT-ACCATATTTTAG-ATCCA-TTTATGCA
1 ATTTCA-TATATTTTAGAAT-CATTTTA-GTA
** *
3077149 ATTTCATGCATTTTAGAGTCATTTTAGTA
1 ATTTCATATATTTTAGAATCATTTTAGTA
3077178 ATTT
1 ATTT
3077182 TCCATGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
28 7 0.15
29 35 0.73
30 6 0.12
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.51
Consensus pattern (29 bp):
ATTTCATATATTTTAGAATCATTTTAGTA
Found at i:3077191 original size:29 final size:28
Alignment explanation
Indices: 3077101--3077209 Score: 73
Period size: 29 Copynumber: 3.8 Consensus size: 28
3077091 ATTTCATATA
* * *
3077101 TTTTAGAATTATTTTAGTAATTTACCATA
1 TTTTAG-ATCATTTTAGTAATTTTCCATG
*
3077130 TTTTAGATCCA-TTTATGCAA-TTT-CATG
1 TTTTAGAT-CATTTTA-GTAATTTTCCATG
3077157 CATTTTAGAGTCATTTTAGTAATTTTCCATG
1 --TTTTAGA-TCATTTTAGTAATTTTCCATG
*
3077188 TTTTAAGACCA-TTTAGGTAATT
1 TTTT-AGATCATTTTA-GTAATT
3077210 CATGCATTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
27 3 0.05
28 12 0.19
29 34 0.53
30 11 0.17
31 4 0.06
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTTAGATCATTTTAGTAATTTTCCATG
Found at i:3077243 original size:56 final size:58
Alignment explanation
Indices: 3077111--3077294 Score: 173
Period size: 58 Copynumber: 3.2 Consensus size: 58
3077101 TTTTAGAATT
* * *
3077111 ATTTTAGTAATTTACCATATTTT-AGATCCATTTATGCAATTTCATGCATTTTAGAGTC
1 ATTTTAGTAATTTACCATGTTTTAAGA-CCATTTAGGCAATTTCATGCATTATAGAGTC
* *
3077169 ATTTTAGTAATTTTCCATGTTTTAAGACCATTTAGGTAA-TTCATGCATTAT-GCA-TC
1 ATTTTAGTAATTTACCATGTTTTAAGACCATTTAGGCAATTTCATGCATTATAG-AGTC
* * * * ** *
3077225 ATTTTAGTCATTTGCCATGATTTAAGACCCTTTATACAATATCATGCACTT-TAG-GCTC
1 ATTTTAGTAATTTACCATGTTTTAAGACCATTTAGGCAATTTCATGCA-TTATAGAG-TC
*
3077283 ATTTTATTAATT
1 ATTTTAGTAATT
3077295 AGCTGTATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
56 35 0.34
57 20 0.19
58 46 0.44
59 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (58 bp):
ATTTTAGTAATTTACCATGTTTTAAGACCATTTAGGCAATTTCATGCATTATAGAGTC
Found at i:3077418 original size:58 final size:59
Alignment explanation
Indices: 3077309--3077672 Score: 224
Period size: 58 Copynumber: 6.3 Consensus size: 59
3077299 GTATTTTAGG
* * * * * *
3077309 GACTTTTATTTCATTTTACACATGTTGATGACATTTAGGTTATTTTTCATGATCTAAGA
1 GACTTTTATGTAATTTTACACATTTTGATGCCATTTAGGTCATTTTCCATGATCTAAGA
* * * *
3077368 GA-TTTTATGAAATTTTACACATTTTGATGCCATTTAGGTCATTTACCATGATTTAGGA
1 GACTTTTATGTAATTTTACACATTTTGATGCCATTTAGGTCATTTTCCATGATCTAAGA
** * ** *
3077426 -ACTTGGATGCAATTTTGTGA-ATTTTGATGCCATTTAGGTCATTTTCCATGATCTAGGA
1 GACTTTTATGTAATTTT-ACACATTTTGATGCCATTTAGGTCATTTTCCATGATCTAAGA
* * ** * ** * * * * * *
3077484 -ACTTTTATGTCATTTCATGCATTTTAATGTTATTTTAAGTTATTTACCATTAGCT-AGG
1 GACTTTTATGTAATTTTACACATTTTGATGCCA-TTTAGGTCATTTTCCATGATCTAAGA
* * * * *
3077542 GA-TTTGGATGTAATTTTATAAATTTTGATGCCATTTAGGTCATTTTTCATTATCTAA-A
1 GACTTT-TATGTAATTTTACACATTTTGATGCCATTTAGGTCATTTTCCATGATCTAAGA
* * *** * * ** *
3077600 GACTTTTATGTTATTTCATGTATTTTGAGGTCATTTAAATCATTTTTCATGATCTAA-A
1 GACTTTTATGTAATTTTACACATTTTGATGCCATTTAGGTCATTTTCCATGATCTAAGA
* *
3077658 -ACTTCTATGCAATTT
1 GACTTTTATGTAATTT
3077673 CATGTAGTAC
Statistics
Matches: 235, Mismatches: 62, Indels: 18
0.75 0.20 0.06
Matches are distributed among these distances:
57 13 0.06
58 178 0.76
59 44 0.19
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (59 bp):
GACTTTTATGTAATTTTACACATTTTGATGCCATTTAGGTCATTTTCCATGATCTAAGA
Found at i:3080299 original size:20 final size:20
Alignment explanation
Indices: 3080253--3080308 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3080243 ATAACGAGAA
3080253 ATGTATCGATACATTTTAAGC
1 ATGTATCGATACA-TTTAAGC
***
3080274 AT-TATCGATACATTTACTT
1 ATGTATCGATACATTTAAGC
*
3080293 ATGTATCAATACATTT
1 ATGTATCGATACATTT
3080309 CCTTTCCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 6 0.20
20 22 0.73
21 2 0.07
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTAAGC
Found at i:3083795 original size:13 final size:13
Alignment explanation
Indices: 3083777--3083801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3083767 TACAAAGATC
3083777 AATGTATCGATAT
1 AATGTATCGATAT
3083790 AATGTATCGATA
1 AATGTATCGATA
3083802 CATTTCCTTG
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:3083872 original size:20 final size:21
Alignment explanation
Indices: 3083835--3083888 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3083825 AGCGATACAT
3083835 TGTATCGATACAACTACT-TA
1 TGTATCGATACAACTACTATA
** *
3083855 TGTATCGATACATTTACTATT
1 TGTATCGATACAACTACTATA
*
3083876 TGTATCAATACAA
1 TGTATCGATACAA
3083889 ATTGTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
TGTATCGATACAACTACTATA
Found at i:3084802 original size:49 final size:49
Alignment explanation
Indices: 3084642--3084977 Score: 298
Period size: 52 Copynumber: 6.7 Consensus size: 49
3084632 CGAAGAATGA
* * * * **
3084642 CAATGTTCTGATTCATGGCCAGCGACATTAGACTTGAAGA-GGA-ATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGC
** * * *
3084689 CAATGTGCTGAGACAAGGCCAACGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GATAAAGATGC
* * * * * *
3084741 CAATATGTTGATTCAAGGCCAACGATATTAGACTTAAAGATAAAGATAC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGC
* * * *
3084790 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGATGACGCAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-A--AAGATGC
* * * * *
3084842 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGC
* **
3084891 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---AAAGATGC
* *
3084943 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
3084978 GTGCCAATAT
Statistics
Matches: 232, Mismatches: 46, Indels: 17
0.79 0.16 0.06
Matches are distributed among these distances:
47 28 0.12
49 88 0.38
50 4 0.02
51 1 0.00
52 111 0.48
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGC
Found at i:3084816 original size:101 final size:101
Alignment explanation
Indices: 3084688--3084977 Score: 393
Period size: 101 Copynumber: 2.9 Consensus size: 101
3084678 AAGAGGAATG
** * * ** * *
3084688 CCAATGTGCTGAGACAAGGCCAACGACATTGGGCTTAG-GAATGTTAAAGATGCCAATATGTTGA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAG-ATGACAAAGGTGCCAATATGCTGA
*
3084752 TTCAAGGCCAACGATATTAGACTTAAAGATAAAGATA
65 TTCAAGGCCAACGATATTGGACTTAAAGATAAAGATA
* **
3084789 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGATGACGCAGGTGCCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAGATGACAAAGGTGCCAATATGCTGAT
* * *
3084854 TCAAGGCCAACGATATTGGACTTAAAGATGAAGGTG
66 TCAAGGCCAACGATATTGGACTTAAAGATAAAGATA
* * *
3084890 CCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCGCCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAGATGACAAAGGTGCCAATATGCTGAT
*
3084955 TCAAGGCCAGCGATATTGGACTT
66 TCAAGGCCAACGATATTGGACTT
3084978 GTGCCAATAT
Statistics
Matches: 167, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
101 166 0.99
102 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (101 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAGATGACAAAGGTGCCAATATGCTGAT
TCAAGGCCAACGATATTGGACTTAAAGATAAAGATA
Found at i:3085959 original size:32 final size:32
Alignment explanation
Indices: 3085904--3085967 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3085894 ACAATTGTGC
* * *
3085904 ATGTATCGATACAATGAAGATGTATCGATACA
1 ATGTATCGACACAAAGAACATGTATCGATACA
* *
3085936 ATGTATCGACACAAAGCACATGTATTGATACA
1 ATGTATCGACACAAAGAACATGTATCGATACA
3085968 TTTGGACATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (32 bp):
ATGTATCGACACAAAGAACATGTATCGATACA
Found at i:3088421 original size:13 final size:13
Alignment explanation
Indices: 3088402--3088441 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3088392 ATAGTAATCC
3088402 ATGTATCGATACA
1 ATGTATCGATACA
* *
3088415 TTGTATCGATATA
1 ATGTATCGATACA
*
3088428 ATATATCGATACA
1 ATGTATCGATACA
3088441 A
1 A
3088442 AGAACATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3093001 original size:15 final size:15
Alignment explanation
Indices: 3092983--3093017 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3092973 CGAGTCAACT
*
3092983 TCATTATTATCATCA
1 TCATCATTATCATCA
*
3092998 TCATCATTATCTTCA
1 TCATCATTATCATCA
3093013 TCATC
1 TCATC
3093018 TTTGATGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.46
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:3094721 original size:19 final size:20
Alignment explanation
Indices: 3094674--3094726 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3094664 TACCAGTTTT
* **
3094674 ATGTATCGATATAATTGTGC
1 ATGTATCGATACAATTGAAC
3094694 ATGGTATCGATACAA-TGAAC
1 AT-GTATCGATACAATTGAAC
3094714 ATGTATCGATACA
1 ATGTATCGATACA
3094727 TCTAGATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.38
20 7 0.24
21 11 0.38
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:3098244 original size:13 final size:13
Alignment explanation
Indices: 3098226--3098250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3098216 CATTTTGGGA
3098226 TGTATCGATACAG
1 TGTATCGATACAG
3098239 TGTATCGATACA
1 TGTATCGATACA
3098251 TATTGTGTGT
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:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3098248 original size:33 final size:32
Alignment explanation
Indices: 3098206--3098269 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
3098196 TACAAGCCAA
*
3098206 TGTATCGATACATTTTGGGATGTATCGATACAG
1 TGTATCGATACATATTGGG-TGTATCGATACAG
*
3098239 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
3098270 AATTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAG
Found at i:3098949 original size:18 final size:19
Alignment explanation
Indices: 3098922--3098957 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3098912 TTTTCTTTTC
3098922 TCTCCCCCTTAA-AAAATT
1 TCTCCCCCTTAATAAAATT
*
3098940 TCTCCTCCTTAATAAAAT
1 TCTCCCCCTTAATAAAAT
3098958 AATTTAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (19 bp):
TCTCCCCCTTAATAAAATT
Found at i:3100875 original size:13 final size:13
Alignment explanation
Indices: 3100857--3100891 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3100847 AAACCCCTTG
*
3100857 TATCGATACACTA
1 TATCGATACAATA
*
3100870 TATCGATACAATG
1 TATCGATACAATA
3100883 TATCGATAC
1 TATCGATAC
3100892 TTCTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:3107045 original size:13 final size:13
Alignment explanation
Indices: 3107027--3107051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3107017 CATTTTGGGA
3107027 TGTATCGATACAG
1 TGTATCGATACAG
3107040 TGTATCGATACA
1 TGTATCGATACA
3107052 TATTGTGTGT
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:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3107049 original size:33 final size:32
Alignment explanation
Indices: 3107007--3107070 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
3106997 TACAAGCCAA
*
3107007 TGTATCGATACATTTTGGGATGTATCGATACAG
1 TGTATCGATACATATTGGG-TGTATCGATACAG
*
3107040 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
3107071 AATTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAG
Found at i:3107150 original size:20 final size:21
Alignment explanation
Indices: 3107103--3107157 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
3107093 GCCAATGACC
**
3107103 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
3107124 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
3107144 TGTATCGATACATT
1 TGTATCGATACATT
3107158 GTATCGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:3112478 original size:31 final size:32
Alignment explanation
Indices: 3112443--3112525 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
3112433 CAGGTTTGGG
* *
3112443 TTTGGGTTC-GGATTCGTTTGGGTTCAA-CTCA
1 TTTGGGTTCAGG-CTCGTTCGGGTTCAAGCTCA
* *
3112474 TTTGGATTCAGGCTCGTTCGGGTTCAAGCTTA
1 TTTGGGTTCAGGCTCGTTCGGGTTCAAGCTCA
* *
3112506 TTTGAGTTCAAGCTCGTTCG
1 TTTGGGTTCAGGCTCGTTCG
3112526 AGTTTGAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 21 0.49
32 22 0.51
ACGTcount: A:0.14, C:0.18, G:0.28, T:0.40
Consensus pattern (32 bp):
TTTGGGTTCAGGCTCGTTCGGGTTCAAGCTCA
Found at i:3112528 original size:16 final size:16
Alignment explanation
Indices: 3112480--3112529 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3112470 CTCATTTGGA
* *
3112480 TTCAGGCTCGTTCGGG
1 TTCAAGCTCGTTCGAG
** *
3112496 TTCAAGCTTATTTGAG
1 TTCAAGCTCGTTCGAG
3112512 TTCAAGCTCGTTCGAG
1 TTCAAGCTCGTTCGAG
3112528 TT
1 TT
3112530 TGAACTCTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (16 bp):
TTCAAGCTCGTTCGAG
Found at i:3112798 original size:18 final size:18
Alignment explanation
Indices: 3112759--3112798 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3112749 ATATTTATAT
*
3112759 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
3112777 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
3112795 ATAA
1 ATAA
3112799 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:3114198 original size:6 final size:6
Alignment explanation
Indices: 3114183--3114215 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3114173 TTGCCTTTTT
*
3114183 TTTCTA TTTCTC TTTCTC TTTCTC TTTCTC TTT
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTT
3114216 ATTGCGTACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTC
Found at i:3114258 original size:6 final size:6
Alignment explanation
Indices: 3114247--3114273 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3114237 CTTGCCTTTT
3114247 TTTCTC TTTCTC TTTCTC TTTCTC TTT
1 TTTCTC TTTCTC TTTCTC TTTCTC TTT
3114274 ATTGCGTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTC
Found at i:3114810 original size:14 final size:15
Alignment explanation
Indices: 3114784--3114817 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3114774 ATTTTATAGG
3114784 TTAATATAAATTTTA
1 TTAATATAAATTTTA
3114799 TTAATA-AAATTTTA
1 TTAATATAAATTTTA
*
3114813 ATAAT
1 TTAAT
3114818 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATATAAATTTTA
Found at i:3120791 original size:148 final size:148
Alignment explanation
Indices: 3120519--3120816 Score: 463
Period size: 148 Copynumber: 2.0 Consensus size: 148
3120509 TCATTACAAG
* * * *
3120519 ACAAGCTTTCTCCGTGAAGAAATCTTTGGTAGACTTGTGGCGACTTGCGTTTTCATACCAGGTAA
1 ACAAGCTTTCTCCGTGAAGAAATATTTGGTAGACTAGTGGCGACTTGCATCTTCATACCAGGTAA
* * *
3120584 ATCCGCTTGCTGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTTTCTGCTTCGC
66 ATCCGCTTACCGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
3120649 TGATCTGGCCAAA-TAGCT
131 TGATCTGG-CAAAGTAGCT
* * * *
3120667 ACAAGCTTTGTCCGTGAAGAAGTATTTGGTAGACTAGTGGCGACTTGCATCTTCTTACCTGGTAA
1 ACAAGCTTTCTCCGTGAAGAAATATTTGGTAGACTAGTGGCGACTTGCATCTTCATACCAGGTAA
* *
3120732 ATCTGCTTACCGCTATTCAACCCTTGCCTGTTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
66 ATCCGCTTACCGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
3120797 TGATCTGGCAAAGTAGCT
131 TGATCTGGCAAAGTAGCT
3120815 AC
1 AC
3120817 TAGTTCACTT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
147 4 0.03
148 132 0.97
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (148 bp):
ACAAGCTTTCTCCGTGAAGAAATATTTGGTAGACTAGTGGCGACTTGCATCTTCATACCAGGTAA
ATCCGCTTACCGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
TGATCTGGCAAAGTAGCT
Found at i:3121921 original size:16 final size:16
Alignment explanation
Indices: 3121902--3121949 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3121892 AACTTGAATT
*
3121902 TGATTTAAATTTAAGA
1 TGATTTAAATTTAAAA
* *
3121918 TGATTTGAATTAAAAAA
1 TGATTTAAATT-TAAAA
*
3121935 TAATTTAAATTTAAA
1 TGATTTAAATTTAAA
3121950 CGGATCTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (16 bp):
TGATTTAAATTTAAAA
Found at i:3122228 original size:67 final size:67
Alignment explanation
Indices: 3122149--3122283 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
3122139 ATTTTCATCT
3122149 AAATGTGAATAGCATAGGACGTGATTACTGGATGGAGAAAATCAGGATACTCTTCCATCCAAACT
1 AAATGTGAATAGCATAGGACGTGATTACTGGATGGAGAAAATCAGGATACTCTTCCATCCAAACT
3122214 AA
66 AA
3122216 AAATGTGAATAGCATAGGACGTGATTACTGGATGGAGAAAATCAGGATACTCTTCCATCCAAACT
1 AAATGTGAATAGCATAGGACGTGATTACTGGATGGAGAAAATCAGGATACTCTTCCATCCAAACT
3122281 AA
66 AA
3122283 A
1 A
3122284 GTTTCTATAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (67 bp):
AAATGTGAATAGCATAGGACGTGATTACTGGATGGAGAAAATCAGGATACTCTTCCATCCAAACT
AA
Found at i:3123255 original size:89 final size:89
Alignment explanation
Indices: 3123104--3123268 Score: 258
Period size: 89 Copynumber: 1.9 Consensus size: 89
3123094 TTTCAAACTA
* ***
3123104 GTCCACACTGTTGCATACTGGTTCTTGTATCACGTATTGAAGAAAATTGCACAACTCTAGGACTT
1 GTCCACACTGTTGCATACTGGTTCTTCTATCAAACATTGAAGAAAATTGCACAACTCTAGGACTT
3123169 CCCTTGGAACCGCACATTCTCTTT
66 CCCTTGGAACCGCACATTCTCTTT
* * *
3123193 GTCCACACTGTTGTATACTGGTTCTTCTGTCAAACATTGAAGAAAATTGCACGACTCTAGGACTT
1 GTCCACACTGTTGCATACTGGTTCTTCTATCAAACATTGAAGAAAATTGCACAACTCTAGGACTT
*
3123258 TCCTTGGAACC
66 CCCTTGGAACC
3123269 TTGCACTCTC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (89 bp):
GTCCACACTGTTGCATACTGGTTCTTCTATCAAACATTGAAGAAAATTGCACAACTCTAGGACTT
CCCTTGGAACCGCACATTCTCTTT
Found at i:3129678 original size:166 final size:162
Alignment explanation
Indices: 3129194--3129712 Score: 588
Period size: 166 Copynumber: 3.2 Consensus size: 162
3129184 GTAGGGACTA
*
3129194 AAATGAAATTTTCAAAAGTTTAGGGATTAAATAGCAAAATTTAGTTTTTAGAGGTAAAATCATCA
1 AAATGAAATTTTCAAAAGTTTAGGGATTAAAT-G-AAAATTTAATTTTTAGAGGTAAAATCATCA
* * *
3129259 TTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCGTAGGGGTATAGAAATTTTTAA
64 TTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCGTAGGAGTATAAAAATTTTCAA
* * * *
3129324 AACTTGTCGTATCCTTTTAATTTTTCATC-ATGTATG
129 GACTTTTCATATCC-TTTAGTTTTTCATCGA-GTA-G
* * * **
3129360 AAATAAAATTTTTAAAAGTTTAGAGATTAAAT-AGCA---AA-TTTTAGAGGTAAAATCATCATT
1 AAATGAAATTTTCAAAAGTTTAGGGATTAAATGAAAATTTAATTTTTAGAGGTAAAATCATCATT
** *
3129420 TTAG-CA-TTTTAAAGATTAATATTATTCCTATGGCCTTCCGTA-GATGTATAAAAACTTTCAAG
66 TTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCGTAGGA-GTATAAAAATTTTCAAG
** * * * *
3129482 ACTTTTTTTATCCTTTCGATGTTCCATCGAGTAC
130 ACTTTTCATATCCTTTAG-TTTTTCATCGAGTAG
** *
3129516 AAAGTGAAATTTTTTAAAGTTTAGGGATTAAATGATAAATTTTAATTTTTAGAGATAAAATCATC
1 AAA-TGAAATTTTCAAAAGTTTAGGGATTAAATGA-AAA-TTTAATTTTTAGAGGTAAAATCATC
* * * *
3129581 ATTTTAGTCATTTTTAAATATTTCTATTATTCCTACGGCCTTTCGTAGGAGTATACAAATTTTCA
63 ATTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCGTAGGAGTATAAAAATTTTCA
*
3129646 AGACTTTTCATATCCTCTTAGTTTTTCATCGAGTTG
128 AGACTTTTCATATCCT-TTAGTTTTTCATCGAGTAG
*
3129682 AAATGAAATTTTCAAAAGTTTAAGGGCTTAA
1 AAATGAAATTTTCAAAAGTTT-AGGGATTAA
3129713 TAGATTTTTT
Statistics
Matches: 293, Mismatches: 44, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
156 7 0.02
157 93 0.32
158 4 0.01
159 27 0.09
160 1 0.00
163 4 0.01
164 25 0.09
165 18 0.06
166 109 0.37
167 5 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (162 bp):
AAATGAAATTTTCAAAAGTTTAGGGATTAAATGAAAATTTAATTTTTAGAGGTAAAATCATCATT
TTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCGTAGGAGTATAAAAATTTTCAAGA
CTTTTCATATCCTTTAGTTTTTCATCGAGTAG
Found at i:3130235 original size:154 final size:154
Alignment explanation
Indices: 3129816--3130480 Score: 542
Period size: 155 Copynumber: 4.3 Consensus size: 154
3129806 AGTGTTATTA
* * * * * * *
3129816 AGATACTTTTATGTCAAAGGTATACCCAAGGGACATTTTCATAATTTCCTAAAATCGAGTCTTAA
1 AGATACTTTCATGTCAAAAGTATACCTAAGAGACATTTTCATAATTTTCTAAAATCGAGTCCTAG
* * * *** * *
3129881 GTAGTCTTTGGGTCACTTTTATGCCAAAGGTGCATATTTTGGATAGGTTTATCCTATTTATGATC
66 GTAGTCATTGGATCGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCT-TTTATGATC
** *
3129946 ATTTTTAAGTTTTTTAGGGTTACCG
130 ATTTTTAAGTCCTTTAAGGTTACCG
** * ** * *
3129971 AGATACATTT-ATGTTGAAAGTAAACC-AAGAGGTATTTTCATAATTTT-TTAAATCAAGTCCTA
1 AGATAC-TTTCATGTCAAAAGTATACCTAAGAGACATTTTCATAATTTTCTAAAATCGAGTCCTA
* * * * *
3130033 CGTAGTCACCTGG-TCGCTTTTATGCCAAAGGTCTGCATATAGGATAGGTTCATCCTTTATATGG
65 GGTAGTCA-TTGGATCGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTTT-TATGA
* ** *
3130097 TCCTTTTGCA-TCTTTTAAGGTTACCG
128 TCATTTTTAAGTCCTTTAAGGTTACCG
* * *
3130123 AGATACTTTCATGTCAAAAGTATACCTAA-AGATATTTTCGTAATTTCTCTAGAATCGAGTCCTA
1 AGATACTTTCATGTCAAAAGTATACCTAAGAGACATTTTCATAATTT-TCTAAAATCGAGTCCTA
* * *
3130187 GGTTGTCATTGAGAT-GCTTTTATGTCAAAGGTGTGCATTTAGGATAGGTTCATCACATTTATGA
65 GGTAGTCATTG-GATCGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATC-CTTTTATGA
* * * **
3130251 TCATTTTTTACTCCTTTAAGGATATTG
128 TCATTTTTAAGTCCTTTAAGGTTACCG
* * * * ** * *
3130278 -GATATTTTCAAGTC-AAAGATATACCCT-AGGGGCATTTTTGTAATTTTTTAAAAACTGAGTCC
1 AGATACTTTCATGTCAAAAG-TATA-CCTAAGAGACATTTTCATAATTTTCTAAAATC-GAGTCC
* * * * *
3130340 TAGGTTGTCATTGAAAT-GCTTTTATGCCAAAGGTATGCATTTAGGATAGGTTCATCCCATCTAT
63 TAGGTAGTCATTG-GATCGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCAT-CCTTTTAT
* *
3130404 GGTCATTTTTAAGTCCTTTAAGGTTATCG
126 GATCATTTTTAAGTCCTTTAAGGTTACCG
* * * * * * *
3130433 GGATATTTTCATGTTAAAAGTATACCTCAGGGATATTTTAATAATTTT
1 AGATACTTTCATGTCAAAAGTATACCTAAGAGACATTTTCATAATTTT
3130481 ATATTAGAAC
Statistics
Matches: 416, Mismatches: 75, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
151 3 0.01
152 50 0.12
153 73 0.18
154 109 0.26
155 141 0.34
156 36 0.09
157 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (154 bp):
AGATACTTTCATGTCAAAAGTATACCTAAGAGACATTTTCATAATTTTCTAAAATCGAGTCCTAG
GTAGTCATTGGATCGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTTTTATGATCA
TTTTTAAGTCCTTTAAGGTTACCG
Found at i:3133293 original size:13 final size:13
Alignment explanation
Indices: 3133275--3133300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3133265 TACAGCAAGT
3133275 ATGTATCGATACA
1 ATGTATCGATACA
3133288 ATGTATCGATACA
1 ATGTATCGATACA
3133301 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3135551 original size:21 final size:21
Alignment explanation
Indices: 3135518--3135562 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3135508 TTGCAAGTTG
*
3135518 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3135540 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3135560 AAA
1 AAA
3135563 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3137386 original size:15 final size:15
Alignment explanation
Indices: 3137366--3137396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3137356 TAAAAACGTC
*
3137366 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3137381 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3137396 C
1 C
3137397 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3139489 original size:20 final size:20
Alignment explanation
Indices: 3139410--3139489 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
3139400 AATGTCCAAA
*
3139410 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
3139430 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
3139455 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
3139475 TTGTATCGATACATT
1 ATGTATCGATACATT
3139490 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:3139493 original size:13 final size:13
Alignment explanation
Indices: 3139475--3139513 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3139465 ACATTTTTCT
3139475 TTGTATCGATACA
1 TTGTATCGATACA
3139488 TTGTATCGATACA
1 TTGTATCGATACA
*
3139501 CTGTATCGATACA
1 TTGTATCGATACA
3139514 GGGTGATTAT
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3139658 original size:21 final size:21
Alignment explanation
Indices: 3139634--3139680 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3139624 AAATCTTTTG
3139634 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
3139655 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
3139675 CAAAAT
1 CAAAAT
3139681 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:3139677 original size:20 final size:19
Alignment explanation
Indices: 3139636--3139678 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
3139626 ATCTTTTGCA
3139636 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
3139656 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
3139676 AAA
1 AAA
3139679 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:3142071 original size:13 final size:13
Alignment explanation
Indices: 3142053--3142078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3142043 TACAGCAAGT
3142053 ATGTATCGATACA
1 ATGTATCGATACA
3142066 ATGTATCGATACA
1 ATGTATCGATACA
3142079 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3143660 original size:15 final size:15
Alignment explanation
Indices: 3143640--3143668 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3143630 GATAGGTTGA
3143640 TTCTTTAGGAAAGGC
1 TTCTTTAGGAAAGGC
3143655 TTCTTTAGGAAAGG
1 TTCTTTAGGAAAGG
3143669 TTGTGGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (15 bp):
TTCTTTAGGAAAGGC
Found at i:3144206 original size:112 final size:113
Alignment explanation
Indices: 3144008--3144226 Score: 314
Period size: 112 Copynumber: 1.9 Consensus size: 113
3143998 AACTTGGAAG
* * * * * *
3144008 AACATTAAATTTGTCTGATTTTTTAATAAATTCATATTTTATACATTTCGATCCATTCATGCTTA
1 AACATCAAATTTGTCTGATTTTTCAAAAAATTCATATTTTATACATCTCAATCCATTCATGCCTA
* * * *
3144073 GGAAAAGAGGGCATATGTCCTATGAGTTTTGAAATTTTTGAGCCCAAC
66 AGAAAACAGGGCATATATCCTATCAGTTTTGAAATTTTTGAGCCCAAC
**
3144121 AACATCAAATTTGTCTGA-TTTTCAAAAAATTCATATTTTATACATCTCAATCCATTTGTGCCTA
1 AACATCAAATTTGTCTGATTTTTCAAAAAATTCATATTTTATACATCTCAATCCATTCATGCCTA
*
3144185 AGAAAACAGGGCATGTATCCTATCAGTTTTGAAATTTTTGAG
66 AGAAAACAGGGCATATATCCTATCAGTTTTGAAATTTTTGAG
3144227 TCAACCAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
112 76 0.82
113 17 0.18
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (113 bp):
AACATCAAATTTGTCTGATTTTTCAAAAAATTCATATTTTATACATCTCAATCCATTCATGCCTA
AGAAAACAGGGCATATATCCTATCAGTTTTGAAATTTTTGAGCCCAAC
Found at i:3144781 original size:82 final size:82
Alignment explanation
Indices: 3144629--3144781 Score: 182
Period size: 82 Copynumber: 1.9 Consensus size: 82
3144619 TGCACATCAA
* * ** * ** *
3144629 CACTTCAGATGACATTGGCATTTGCATTGTTTCATATGCATTTGCCACTTTATTAATGGTCGCAT
1 CACTTCAGATAACATGGGCATTTGCATCATTTCATATGCACTAACCACTTTAGTAATGGTCGCAT
3144694 CGTTACATGCGCATTTG
66 CGTTACATGCGCATTTG
* * *
3144711 CACTTTAGATAACATGGGCATTTGCATCATTTCATATGCACTAACCATTTTAGTGATGTGT-GCA
1 CACTTCAGATAACATGGGCATTTGCATCATTTCATATGCACTAACCACTTTAGTAATG-GTCGCA
*
3144775 TTGTTAC
65 TCGTTAC
3144782 TTGCCTTATT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
82 56 0.97
83 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (82 bp):
CACTTCAGATAACATGGGCATTTGCATCATTTCATATGCACTAACCACTTTAGTAATGGTCGCAT
CGTTACATGCGCATTTG
Found at i:3145556 original size:87 final size:87
Alignment explanation
Indices: 3145406--3145574 Score: 194
Period size: 87 Copynumber: 1.9 Consensus size: 87
3145396 CATTTGTCTC
** *** * * * * *
3145406 TTTATTGATGATTGCATTTGCATCATTTCACTTACATTTGCATTTTGGATAACGTTAGTATTTGT
1 TTTATTGATGATTGCATTTGCATCATTTCACGCACATCAACACTTTAGATAACATTAGCATTTGG
3145471 ATCATTCCATATGCATTCACCT
66 ATCATTCCATATGCATTCACCT
* * * *
3145493 TTTATTGATGCTTGCATTTGCATTATTTCACGCACATCAACACTTTAGATGACATTGGCATTTGG
1 TTTATTGATGATTGCATTTGCATCATTTCACGCACATCAACACTTTAGATAACATTAGCATTTGG
* *
3145558 ATCGTTTCATATGCATT
66 ATCATTCCATATGCATT
3145575 TGCCACTTTA
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (87 bp):
TTTATTGATGATTGCATTTGCATCATTTCACGCACATCAACACTTTAGATAACATTAGCATTTGG
ATCATTCCATATGCATTCACCT
Found at i:3146360 original size:80 final size:80
Alignment explanation
Indices: 3146226--3146377 Score: 232
Period size: 80 Copynumber: 1.9 Consensus size: 80
3146216 ATTCCCTAAT
* * *
3146226 CATATCTCTTTCATCTAACCACTAGATGGTATTGATGCATCACAAAACCTGATTTCCTTAGGGCA
1 CATATCTCTTTCATCCAACCACTAGATAGTATTGATGCATCACAAAACCAGATTTCCTTAGGGCA
3146291 AGGATATTCAGACCA
66 AGGATATTCAGACCA
* * * * *
3146306 CATATCTTTTTCATCCAACCACTAGATAGTATTGATGTATCACAAAGCCAGATTTCCTTGGGGTA
1 CATATCTCTTTCATCCAACCACTAGATAGTATTGATGCATCACAAAACCAGATTTCCTTAGGGCA
3146371 AGGATAT
66 AGGATAT
3146378 CCCAACCATT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (80 bp):
CATATCTCTTTCATCCAACCACTAGATAGTATTGATGCATCACAAAACCAGATTTCCTTAGGGCA
AGGATATTCAGACCA
Found at i:3146739 original size:44 final size:44
Alignment explanation
Indices: 3146656--3147234 Score: 331
Period size: 44 Copynumber: 13.1 Consensus size: 44
3146646 TAACTATATT
* * * * ** *
3146656 TGGTCAAACTCTTTTCATCCTTATTCAACGTATGATTACCACCC
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
* * **
3146700 TAGTCAGATTCTTTTCATTCTCATTTGACATATGGTTACCACTT
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
* * *
3146744 TGGTCA-AATCTACCTTC-TTC-CTGTTTGACGTATGGTTACCACCC
1 TGGTCAGATTCT--TTTCATTCTC-ATTTGACGTATGGTTACCACCC
* * * *
3146788 TGGTCAAACTCTTCTCATT-TTAGTTTGACGTATGGTTACCACCC
1 TGGTCAGATTCTTTTCATTCTCA-TTTGACGTATGGTTACCACCC
* * ** * **
3146832 TGGTCAAACTCTTTAAATTTTGGTTTGACGTATGGTTACCACCC
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
* * * *
3146876 TAGTCAGATTCTTTTCATTCTGATTTGATGTATGGCTACCACCC
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
* * * * *
3146920 TGGTCA-AATCTACCTTC-TTCTTATTTGACATATGGTTACCACCT
1 TGGTCAGATTCT--TTTCATTCTCATTTGACGTATGGTTACCACCC
* * * * * *
3146964 TGGTCAAACTCTTCTT-ATTTTGGC-CTT-ACATATGGTTACCACCT
1 TGGTCAGATTCTT-TTCATTCT--CATTTGACGTATGGTTACCACCC
* * * *
3147008 TGGTCAGATTCTTTTCATTCTAACTTGATGTATGGTTTACCTA-TC
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGG-TTACC-ACCC
* * *** * * *
3147053 TCGTCA-AATCAGCCTCATT-TCTTTTTGACTTATGGTTACCACCT
1 TGGTCAGATTC-TTTTCATTCTC-ATTTGACGTATGGTTACCACCC
* * *
3147097 TGGTCAAACTT-TTTTCATT-TCAATCTAACGTATGGTTACCACCC
1 TGGTCAGA-TTCTTTTCATTCTC-ATTTGACGTATGGTTACCACCC
** * **
3147141 TAATCAGATTCTTTTCATTCTAATTTGACACATGGTTACCACCC
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
* * * **
3147185 TAGTCGGATTCTTTTCATTCTAATTTGACACATGGTTACCACCC
1 TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
*
3147229 TAGTCA
1 TGGTCA
3147235 AATCTACCTA
Statistics
Matches: 416, Mismatches: 92, Indels: 54
0.74 0.16 0.10
Matches are distributed among these distances:
43 19 0.05
44 352 0.85
45 43 0.10
46 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (44 bp):
TGGTCAGATTCTTTTCATTCTCATTTGACGTATGGTTACCACCC
Found at i:3146903 original size:132 final size:129
Alignment explanation
Indices: 3146767--3147236 Score: 444
Period size: 132 Copynumber: 3.6 Consensus size: 129
3146757 CTTCTTCCTG
*
3146767 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGTTTGACGTATGGTTACCACCC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTTA-TTTGACATATGGTTACCACCC
3146832 TGGTCAAACTCTTTAAATTTTGGTTTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT
65 TGGTCAAACTCTTT-AATTTTGGTTT-ACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT
*
3146897 GA
128 AA
* * *
3146899 TTTGATGTATGGCTACCACCCTGGTCAAATCTACCTTCT--TCTTATTTGACATATGGTTACCAC
1 TTTGACGTATGGTTACCACCCTGGTCAAA-CT--CTTCTCATTTTATTTGACATATGGTTACCAC
* * * * * *
3146962 CTTGGTCAAACTCTTCTTATTTTGGCCTTACATATGGTTACCACCTTGGTCAGATTCTTTTCATT
63 CCTGGTCAAACTCTT-TAATTTTGG-TTTACGTATGGTTACCACCCTAGTCAGATTCTTTTCATT
3147027 CTAA
126 CTAA
* * * * ** * *
3147031 CTTGATGTATGGTTTACCTA-TCTCGTCAAA-TCAGCCTCATTTCTTTTTGACTTATGGTTACCA
1 TTTGACGTATGG-TTACC-ACCCTGGTCAAACTC-TTCTCATTT-TATTTGACATATGGTTACCA
* * * *** * *
3147094 CCTTGGTCAAACTTTTTTCATTTCAATCTAACGTATGGTTACCACCCTAATCAGATTCTTTTCAT
62 CCCTGGTCAAAC-TCTTTAATTTTGGT-TTACGTATGGTTACCACCCTAGTCAGATTCTTTTCAT
3147159 TCTAA
125 TCTAA
** * ** * * * *
3147164 TTTGACACATGGTTACCACCCTAGTCGGATTCTTTTCATTCTAATTTGACACATGGTTACCACCC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATT-TTATTTGACATATGGTTACCACCC
*
3147229 TAGTCAAA
65 TGGTCAAA
3147237 TCTACCTATT
Statistics
Matches: 274, Mismatches: 48, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
129 1 0.00
130 2 0.01
131 2 0.01
132 156 0.57
133 104 0.38
134 4 0.01
135 5 0.02
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (129 bp):
TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTTATTTGACATATGGTTACCACCCT
GGTCAAACTCTTTAATTTTGGTTTACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTAA
Found at i:3146956 original size:176 final size:176
Alignment explanation
Indices: 3146683--3147013 Score: 502
Period size: 176 Copynumber: 1.9 Consensus size: 176
3146673 TCCTTATTCA
* **
3146683 ACGTATGATTACCACCCTAGTCAGATTCTTTTCATTCTCATTTGACATATGGTTACCACTTTGGT
1 ACGTATGATTACCACCCTAGTCAGATTCTTTTCATTCTCATTTGACATATGGCTACCACCCTGGT
* * *
3146748 CAAATCTACCTTCTTCCTGTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAG-T
66 CAAATCTACCTTCTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGCC
*
3146812 TTGACGTATGGTTACCACCCTGGTCAAACTCTTTAAATTTTGGTTTG
131 TT-ACATATGGTTACCACCCTGGTCAAACTCTTTAAATTTTGGTTTG
* * **
3146859 ACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGATGTATGGCTACCACCCTGGT
1 ACGTATGATTACCACCCTAGTCAGATTCTTTTCATTCTCATTTGACATATGGCTACCACCCTGGT
* * * *
3146924 CAAATCTACCTTCTTCTTATTTGACATATGGTTACCACCTTGGTCAAACTCTTCTTATTTTGGCC
66 CAAATCTACCTTCTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGCC
*
3146989 TTACATATGGTTACCACCTTGGTCA
131 TTACATATGGTTACCACCCTGGTCA
3147014 GATTCTTTTC
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
176 136 0.99
177 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (176 bp):
ACGTATGATTACCACCCTAGTCAGATTCTTTTCATTCTCATTTGACATATGGCTACCACCCTGGT
CAAATCTACCTTCTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGCC
TTACATATGGTTACCACCCTGGTCAAACTCTTTAAATTTTGGTTTG
Found at i:3147558 original size:42 final size:41
Alignment explanation
Indices: 3147510--3147640 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 41
3147500 GGCTCAGTCT
3147510 CTGGTAAACACCTTTACCCTTTGCTGACTTATCGATTTAGCC
1 CTGGTAAAC-CCTTTACCCTTTGCTGACTTATCGATTTAGCC
* * * * * *
3147552 TTGGTAAACCTTTTATCCC-TTGCTTACTTGT-TAGCTTAGTCC
1 CTGGTAAACCCTTTA-CCCTTTGCTGACTTATCGA-TTTAG-CC
* * * *
3147594 CTGGTGAACTCCTTTATCCTTTGTTGACTTATCGGTTTAGCC
1 CTGGTAAAC-CCTTTACCCTTTGCTGACTTATCGATTTAGCC
3147636 CTGGT
1 CTGGT
3147641 CAATTTTTCA
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
40 1 0.01
41 19 0.28
42 29 0.43
43 18 0.27
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (41 bp):
CTGGTAAACCCTTTACCCTTTGCTGACTTATCGATTTAGCC
Found at i:3147616 original size:84 final size:83
Alignment explanation
Indices: 3147494--3147798 Score: 312
Period size: 84 Copynumber: 3.7 Consensus size: 83
3147484 TCCCCATTTG
* * * * * * *
3147494 CTTGTTGGCTCAGTCTCTGGTAAACACCTTTACCCTTTGCTGACTTATCGATTTAGCCTTGGTAA
1 CTTGTTAGCTCAGTCCCTGGTAAACTCCTTTATCCTTTGTTGACTTATCGATTTAGCCCTGGTCA
3147559 ACCTTTTATCCCTTGCTTA
66 ACCTTTTATCCCTTG-TTA
* * *
3147578 CTTGTTAGCTTAGTCCCTGGTGAACTCCTTTATCCTTTGTTGACTTATCGGTTTAGCCCTGGTCA
1 CTTGTTAGCTCAGTCCCTGGTAAACTCCTTTATCCTTTGTTGACTTATCGATTTAGCCCTGGTCA
* *
3147643 A-TTTTTCATCTCTAT-TTA
66 ACCTTTT-ATCCCT-TGTTA
* * * * *
3147661 CTTGTCAGCTCAGTCCCTGGTAAACTCCTTTA-CCTTTTGTTGACTTATAGGTTCAACCCTGGTC
1 CTTGTTAGCTCAGTCCCTGGTAAACTCCTTTATCC-TTTGTTGACTTATCGATTTAGCCCTGGTC
*
3147725 AACCTTTCATCCCTTGTTTA
65 AACCTTTTATCCCTTG-TTA
* * * * **
3147745 CCTGTTAGCTTAGTCTCGGGTAAA-TTTTTGTATCCTTTGTTGACTTATCGATTT
1 CTTGTTAGCTCAGTCCCTGGTAAACTCCTT-TATCCTTTGTTGACTTATCGATTT
3147799 TATCCCAATA
Statistics
Matches: 182, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
82 3 0.02
83 72 0.40
84 104 0.57
85 3 0.02
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (83 bp):
CTTGTTAGCTCAGTCCCTGGTAAACTCCTTTATCCTTTGTTGACTTATCGATTTAGCCCTGGTCA
ACCTTTTATCCCTTGTTA
Found at i:3148731 original size:263 final size:265
Alignment explanation
Indices: 3148259--3148766 Score: 878
Period size: 263 Copynumber: 1.9 Consensus size: 265
3148249 TGTCACGGTC
*
3148259 AATTTTTCTATTTTTAAAAATTTTCGAAGATTTTTCTCGAAAAGCTTGGGAAATTGATTGTCGTA
1 AATTTTTCTATTTTTAAAAATTTTCAAAGATTTTTCTCGAAAAGCTTGGGAAATTGATTGTCGTA
*
3148324 TGTTTTACCGACACTAATAAGGTTTTCATGCCGATACTTGCCCCGAAAAGTCATAAATTTTCAAG
66 TGTTTTACCGACACTAATAAGGTTTTCATGCC---ACTTGCCCCAAAAAGTCATAAATTTTCAAG
*
3148389 AAAGAGATATGTATTGGCGTTTCATACCATATAGTGTCAAGATGGAATTTTGTAAATTATTTTTA
128 AAAGAGATATGTATTGGCATTTCATACCATATAGTGTCAAGATGGAATTTTGTAAATTATTTTTA
* * *
3148454 AAATTTTTTCATAATATAGTAAATATCGAATTTCACAATTTTACTTCTTTCGAAATTTTCATAAT
193 AAAATTTTTCATAATATAGTAAATACCAAATTTCACAATTTTACTTCTTTCGAAATTTTCATAAT
3148519 ATAGTAAA
258 ATAGTAAA
*
3148527 AATTTTTCTATTTTTAGAAATTTTCAAAGATTTTTCTCGAAAAGCTTGGGAAATTGATTGTCGTA
1 AATTTTTCTATTTTTAAAAATTTTCAAAGATTTTTCTCGAAAAGCTTGGGAAATTGATTGTCGTA
*
3148592 TGTTTTACCGACACTAATAAGGTTTTTAT-CC-CTTGCCCCAAAAAGAT-ATAAATTTTCAAGAA
66 TGTTTTACCGACACTAATAAGGTTTTCATGCCACTTGCCCCAAAAAG-TCATAAATTTTCAAGAA
3148654 AGAGATATGTATTGGCATTTCATACCATATAGTGTCAAGATGGAATTTTGTAAATTATTTTTAAA
130 AGAGATATGTATTGGCATTTCATACCATATAGTGTCAAGATGGAATTTTGTAAATTATTTTTAAA
*
3148719 AATTTTTCATAATATAGTAAATACCAAATTTTACAATTTTACTTCTTT
195 AATTTTTCATAATATAGTAAATACCAAATTTCACAATTTTACTTCTTT
3148767 TAAATTTATT
Statistics
Matches: 230, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
263 136 0.59
264 1 0.00
267 2 0.01
268 91 0.40
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (265 bp):
AATTTTTCTATTTTTAAAAATTTTCAAAGATTTTTCTCGAAAAGCTTGGGAAATTGATTGTCGTA
TGTTTTACCGACACTAATAAGGTTTTCATGCCACTTGCCCCAAAAAGTCATAAATTTTCAAGAAA
GAGATATGTATTGGCATTTCATACCATATAGTGTCAAGATGGAATTTTGTAAATTATTTTTAAAA
ATTTTTCATAATATAGTAAATACCAAATTTCACAATTTTACTTCTTTCGAAATTTTCATAATATA
GTAAA
Found at i:3150618 original size:28 final size:29
Alignment explanation
Indices: 3150566--3150621 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3150556 AGGACTAAAT
*
3150566 TAAAAATCAATTCTAATCATTTTTTTATA
1 TAAAAATCAATTCTAATCAATTTTTTATA
3150595 TAAAAATCAATTCTAAT-AATTTTTTAT
1 TAAAAATCAATTCTAATCAATTTTTTAT
3150622 CTTTTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAAAATCAATTCTAATCAATTTTTTATA
Found at i:3152014 original size:156 final size:155
Alignment explanation
Indices: 3151727--3152037 Score: 355
Period size: 156 Copynumber: 2.0 Consensus size: 155
3151717 TAGTTATTGT
* * * *
3151727 CGAGTCCGCTTTTATGCCAAATGTGGATATTTAGGATAAGTTCATCCCTTTTAAAATCCTTTTAA
1 CGAGTCCACTTTTATGCCAAAAGTGGATATTTAAGATAAGTTCATCCCTTCTAAAATCCTTTTAA
* * * * **
3151792 AGTCCTTTAGGAGTATCATGTACTTTTACGTCGAAGATATCTCCTAGGGCCATTTTTGTAATTTT
66 AGTCCTTTAGGAGTACCAGGTACTTTTACGTCGAAGATAGCTCATAGGGCCATTTTCATAATTTT
3151857 TTAGAACCAAATCCTAGGTCGTCAC
131 TTAGAACCAAATCCTAGGTCGTCAC
* *
3151882 CGAGTCCACTTTTATGCCGAAAAGTGGATATTTAAGATAGGTTCATCCCTTCTATAAT-CTTCTT
1 CGAGTCCACTTTTATGCC-AAAAGTGGATATTTAAGATAAGTTCATCCCTTCTAAAATCCTT-TT
* **
3151946 -AAGTCCTTTAAGG-TTACCAGGATACTTTTGTGTCGAAGGTATAGCT-ATAGAGG-CATTTTCA
64 AAAGTCCTTT-AGGAGTACCAGG-TACTTTTACGTCGAA-G-ATAGCTCATAG-GGCCATTTTCA
* * *
3152007 TAA-TTTTTAGAATCGAGTCCTAGGTCGTCAC
124 TAATTTTTTAGAACCAAATCCTAGGTCGTCAC
3152038 TCTTACACTA
Statistics
Matches: 131, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
155 34 0.26
156 77 0.59
157 13 0.10
158 7 0.05
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (155 bp):
CGAGTCCACTTTTATGCCAAAAGTGGATATTTAAGATAAGTTCATCCCTTCTAAAATCCTTTTAA
AGTCCTTTAGGAGTACCAGGTACTTTTACGTCGAAGATAGCTCATAGGGCCATTTTCATAATTTT
TTAGAACCAAATCCTAGGTCGTCAC
Found at i:3153343 original size:20 final size:20
Alignment explanation
Indices: 3153295--3153349 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
3153285 GTCAAAACCC
*
3153295 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
3153315 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
3153335 TGCATTGTATCGATA
1 TGAAATGTATCGATA
3153350 TATGAAAAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:3153442 original size:13 final size:13
Alignment explanation
Indices: 3153424--3153448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3153414 ACACACAGTA
3153424 TGTATCGATACAT
1 TGTATCGATACAT
3153437 TGTATCGATACA
1 TGTATCGATACA
3153449 CCATAAAATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3153445 original size:32 final size:33
Alignment explanation
Indices: 3153404--3153471 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
3153394 GTAGCTAAAC
**
3153404 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
3153436 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
3153469 TTG
1 TTG
3153472 ACTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:3161178 original size:21 final size:21
Alignment explanation
Indices: 3161154--3161200 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3161144 TTTGATGCTG
3161154 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
3161174 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
3161195 ATTTTG
1 ATTTTG
3161201 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:3161339 original size:13 final size:13
Alignment explanation
Indices: 3161321--3161346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3161311 ATAATCACCC
3161321 TGTATCGATACAA
1 TGTATCGATACAA
3161334 TGTATCGATACAA
1 TGTATCGATACAA
3161347 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3163451 original size:15 final size:15
Alignment explanation
Indices: 3163431--3163461 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3163421 ATTTCGTTTG
*
3163431 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3163446 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3163461 G
1 G
3163462 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3165294 original size:21 final size:21
Alignment explanation
Indices: 3165265--3165309 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3165255 AAGTTTTCAT
*
3165265 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3165285 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3165307 TTT
1 TTT
3165310 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3169567 original size:13 final size:13
Alignment explanation
Indices: 3169548--3169586 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3169538 ACAGCATTCT
3169548 CTGTATCGATACA
1 CTGTATCGATACA
*
3169561 TTGTATCGATACA
1 CTGTATCGATACA
3169574 CTGTATCGATACA
1 CTGTATCGATACA
3169587 AGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:3169762 original size:23 final size:22
Alignment explanation
Indices: 3169718--3169759 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3169708 CAAAATTCCT
*
3169718 GTTTTTCACTTCAAAATACATC
1 GTTTTTCACATCAAAATACATC
3169740 GTTTTTC-CATCAAAAT-CATC
1 GTTTTTCACATCAAAATACATC
3169760 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (22 bp):
GTTTTTCACATCAAAATACATC
Found at i:3170065 original size:21 final size:20
Alignment explanation
Indices: 3170021--3170072 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3170011 CCCCTAGGCA
*
3170021 GCACCCACCAGGTCGCGACCG
1 GCACCC-CCAGGTCGCAACCG
*
3170042 GCACCCCCAGGTCGCAATCGG
1 GCACCCCCAGGTCGCAA-CCG
3170063 GCAGCCCCCA
1 GCA-CCCCCA
3170073 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.19, C:0.48, G:0.27, T:0.06
Consensus pattern (20 bp):
GCACCCCCAGGTCGCAACCG
Found at i:3172023 original size:20 final size:20
Alignment explanation
Indices: 3171992--3172069 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
3171982 GTCAAAACCC
*
3171992 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
3172012 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* * * *
3172032 TGCATTGTATCGATACATGAA
1 TGAAATGTATCGATACA-CAT
*
3172053 AGAAATGTATCGATACA
1 TGAAATGTATCGATACA
3172070 AGTCATTGGC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:3172063 original size:21 final size:20
Alignment explanation
Indices: 3172014--3172069 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
3172004 ATACACATTT
**
3172014 AAATGTATCGATACAGATTG
1 AAATGTATCGATACAGAAAG
* *
3172034 CATTGTATCGATACATGAAAG
1 AAATGTATCGATACA-GAAAG
3172055 AAATGTATCGATACA
1 AAATGTATCGATACA
3172070 AGTCATTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (20 bp):
AAATGTATCGATACAGAAAG
Found at i:3172139 original size:13 final size:13
Alignment explanation
Indices: 3172121--3172145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3172111 ACACCCAGTA
3172121 TGTATCGATACAT
1 TGTATCGATACAT
3172134 TGTATCGATACA
1 TGTATCGATACA
3172146 CCATAAAATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3172142 original size:32 final size:33
Alignment explanation
Indices: 3172101--3172168 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
3172091 GTAGCTAAAC
**
3172101 TTGTATCGATACACC-CAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
3172133 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
3172166 TTG
1 TTG
3172169 ACTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:3173716 original size:10 final size:10
Alignment explanation
Indices: 3173697--3173741 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
3173687 TTTGACTTAG
3173697 TTTT-TCTTT
1 TTTTCTCTTT
3173706 TTTTCTCTTT
1 TTTTCTCTTT
*
3173716 TGTTCTTTCTTT
1 T-TT-TCTCTTT
3173728 TTTTCTCTTT
1 TTTTCTCTTT
3173738 TTTT
1 TTTT
3173742 TCTCCAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 4 0.13
10 16 0.52
11 4 0.13
12 7 0.23
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:3173898 original size:20 final size:19
Alignment explanation
Indices: 3173857--3173900 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3173847 AATTTTCATT
* * *
3173857 TTTTTTATTTTTCATGCCA
1 TTTTTTATTTTGCAAGCAA
3173876 TTTTTTATTTTGGCAAGCAA
1 TTTTTTATTTT-GCAAGCAA
3173896 TTTTT
1 TTTTT
3173901 GATAAGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.61
Consensus pattern (19 bp):
TTTTTTATTTTGCAAGCAA
Found at i:3174534 original size:166 final size:165
Alignment explanation
Indices: 3174299--3174836 Score: 558
Period size: 165 Copynumber: 3.3 Consensus size: 165
3174289 AGATGAATTC
* * *
3174299 TAAAAATTTTAAACCG-AGAAAATTCTCCCAAAAATATTTAT-AGAATAGAAAACTCA-ATTTTT
1 TAAAAATTTTGAACTGAAAAAAATTCTCCCAAAAATATTTATGA-AATAGAAAACT-AGATTTTT
* *
3174361 CGAAAATAAAAAAAGTTCAAGGAAAAAATGAAAAACTCATGAAAATAAATAAATTTTTCAAAACT
64 CGAAAATAAAAAAATTTCAAGGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAA-T
*
3174426 GATTTACTATGATTTAAGTGATGATATTTGAATAATAT
128 GATTTACTATGATTTAAGTGATGATATTTGAAGAATAT
* *
3174464 TAAAAATTTTGAACTGAAAAAAATTCTCCCAAAAATATTTATGAAATAAAAAACTAGATTTTTTG
1 TAAAAATTTTGAACTGAAAAAAATTCTCCCAAAAATATTTATGAAATAGAAAACTAGATTTTTCG
* * *
3174529 AAAATAAAAGAATTTCAAGG--GAAATGAAAAAACTCATGAAAATAAATGAATTTTTTAAAATTG
66 AAAATAAAAAAATTTCAAGGAAAAAATG-AAAAACTCATGAAAATAAATGAATTTTTCAAAA-TG
* *
3174592 ATTTGCTATGATTTAAGTGATGATATTTAAAGAATAT
129 ATTTACTATGATTTAAGTGATGATATTTGAAGAATAT
* * * * * * * *
3174629 TAAAATTTTTGAA-TCGAGAAAAA-CCTTCCC-AAAACATTTATGGAATAGAAAACTTGGTGTTT
1 TAAAAATTTTGAACT-GAAAAAAATTC-TCCCAAAAATATTTATGAAATAGAAAACTAGATTTTT
* * * * * *
3174691 CAAAAACAGAATAATTTCAAGAAAAAAATGAAAAACTCATG-GAATATAATGAATTTTTCAACAA
64 CGAAAATAAAAAAATTTCAAGGAAAAAATGAAAAACTCATGAAAATA-AATGAATTTTTCAA-AA
* * **
3174755 TGATTTAACT-TGATTTAAATGATAATATTTGGTGAATAT
127 TGATTT-ACTATGATTTAAGTGATGATATTTGAAGAATAT
* * ** * * *
3174794 AAAAAATTCT-AGACTGAGGAAAATCCTCCCGAAAAGATTTATG
1 TAAAAATTTTGA-ACTGAAAAAAATTCTCCCAAAAATATTTATG
3174837 GAGAAGAAAA
Statistics
Matches: 315, Mismatches: 43, Indels: 29
0.81 0.11 0.07
Matches are distributed among these distances:
164 54 0.17
165 178 0.57
166 82 0.26
167 1 0.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (165 bp):
TAAAAATTTTGAACTGAAAAAAATTCTCCCAAAAATATTTATGAAATAGAAAACTAGATTTTTCG
AAAATAAAAAAATTTCAAGGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAATGAT
TTACTATGATTTAAGTGATGATATTTGAAGAATAT
Found at i:3174861 original size:166 final size:166
Alignment explanation
Indices: 3174383--3174928 Score: 415
Period size: 165 Copynumber: 3.3 Consensus size: 166
3174373 AAGTTCAAGG
* * * *
3174383 AAAAAATGAAAAACTCAT-GAAAATAAATAAATTTTTCAAAACTGATTT-ACTATGATTTAAGTG
1 AAAAAATGAAAAACTCATGGAATAT-AATGAATTTTTCAAAATTGATTTAACTATGATTTAAATG
* * * * ** * *
3174446 ATGATATTTGAATAATATTAAAAATT-TTGAA-CTGA-AAAAAATTCTCCCAAAAATATTTATGA
65 ATAATATTTAAAGAATA-TAAAAATTCTAGAATC-GAGAAAAACCT-TCCC-AAAACATTTATGG
* * * ** ** * * *
3174508 AATAAAAAACTAGATTTTTTGAAAATAAAAG-AATTTC-AA
126 AATAGAAAACTTGGTAATTCAAAAACAGAAGAAATTCCAAA
*** * * * *
3174547 GGGAAATGAAAAAACTCAT-GAAAATAAATGAATTTTTTAAAATTGATTT-GCTATGATTTAAGT
1 AAAAAATG-AAAAACTCATGGAATAT-AATGAATTTTTCAAAATTGATTTAACTATGATTTAAAT
* * * *
3174610 GATGATATTTAAAGAATATTAAAATTTTTGAATCGAGAAAAACCTTCCCAAAACATTTATGGAAT
64 GATAATATTTAAAGAATATAAAAATTCTAGAATCGAGAAAAACCTTCCCAAAACATTTATGGAAT
** * *
3174675 AGAAAACTTGGTGTTTCAAAAACAGAA-TAATTTCAAGA
129 AGAAAACTTGGTAATTCAAAAACAGAAGAAATTCCAA-A
3174713 AAAAAATGAAAAACTCATGGAATATAATGAATTTTTCAACAA-TGATTTAACT-TGATTTAAATG
1 AAAAAATGAAAAACTCATGGAATATAATGAATTTTTCAA-AATTGATTTAACTATGATTTAAATG
*** * * *
3174776 ATAATATTTGGTGAATATAAAAAATTCTAGACT-GAGGAAAATCC-TCCCGAAAAGATTTATGGA
65 ATAATATTTAAAGAATAT-AAAAATTCTAGAATCGA-GAAAAACCTTCCC-AAAACATTTATGGA
3174839 GA-AGAAAACTCT-GTAATTCAAAAACAGAAGAAATTCCAAA
127 -ATAGAAAACT-TGGTAATTCAAAAACAGAAGAAATTCCAAA
* * * *
3174879 AGAAAATCAAAAACTCATGGAATA-AAGGGAATTTCTCAAAATTGATTTAA
1 AAAAAATGAAAAACTCATGGAATATAA-TGAATTTTTCAAAATTGATTTAA
3174929 TGGCAATTAA
Statistics
Matches: 317, Mismatches: 47, Indels: 34
0.80 0.12 0.09
Matches are distributed among these distances:
164 51 0.16
165 141 0.44
166 116 0.37
167 9 0.03
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (166 bp):
AAAAAATGAAAAACTCATGGAATATAATGAATTTTTCAAAATTGATTTAACTATGATTTAAATGA
TAATATTTAAAGAATATAAAAATTCTAGAATCGAGAAAAACCTTCCCAAAACATTTATGGAATAG
AAAACTTGGTAATTCAAAAACAGAAGAAATTCCAAA
Found at i:3175002 original size:166 final size:159
Alignment explanation
Indices: 3174647--3175103 Score: 382
Period size: 166 Copynumber: 2.8 Consensus size: 159
3174637 TTGAATCGAG
* * * *
3174647 AAAAACCTTCCCAAAACATTTATGGA-ATAGAAAACTTGGTGTTTCAAAAACAGAATAATTTCAA
1 AAAAATCTTCCCAAAAAATTTATGGAGA-AGAAAACTT-GTATTTCAAAAACAGAA-AAATTCAA
* * * *
3174711 GAAAAAAATGAAAAACTCATGGAATATAATGAATTTTTCAACAA-TGATTTAACTTG-ATTTAAA
63 -AAGAAAAT-AAAAACTCATGGAATA-AAGGAA-TTTTCAA-AATTGATTTAA-TGGCAATTAAA
* * * ** * * ** *
3174774 TGATAATATTTGGTGAATATAAAAAATTCTAGACTGAG
122 TAACAACATTTAATGAATATAAAAAATTATAAACCAAC
* * * *
3174812 GAAAATCCTCCCGAAAAGATTTATGGAGAAGAAAACTCTGTAATTCAAAAACAGAAGAAATTCCA
1 AAAAATCTTCCC-AAAAAATTTATGGAGAAGAAAACT-TGTATTTCAAAAACAGAA-AAATT-CA
3174877 AAAGAAAATCAAAAACTCATGGAATAAAGGGAATTTCTCAAAATTGATTTAATGGCAATTAAATA
62 AAAGAAAAT-AAAAACTCATGGAATAAA-GGAATTT-TCAAAATTGATTTAATGGCAATTAAATA
* *
3174942 ACAACATTTAATGAATTTTAAAAATTATAAACCAAC
124 ACAACATTTAATGAATATAAAAAATTATAAACCAAC
* * * * * * *
3174978 AAAAATCTTCCCATAAAAATTTATGTAGCAGAAAATTTATATTTTAGAAACGAAAAAAATTCACA
1 AAAAATCTTCCCA-AAAAATTTATGGAGAAGAAAACTTGTATTTCAAAAAC-AGAAAAATTCA-A
* * * **
3175043 AAGAAAATTAAAACTCAAAGTAA-AAAGGAATTTGAAAAATTGATTTAATGGCAATTAAATA
63 AAGAAAATAAAAACTC-ATGGAATAAAGGAATTTTCAAAATTGATTTAATGGCAATTAAATA
3175104 GTAATATTTA
Statistics
Matches: 239, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
162 26 0.11
163 7 0.03
164 12 0.05
165 47 0.20
166 142 0.59
167 5 0.02
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.28
Consensus pattern (159 bp):
AAAAATCTTCCCAAAAAATTTATGGAGAAGAAAACTTGTATTTCAAAAACAGAAAAATTCAAAAG
AAAATAAAAACTCATGGAATAAAGGAATTTTCAAAATTGATTTAATGGCAATTAAATAACAACAT
TTAATGAATATAAAAAATTATAAACCAAC
Found at i:3176521 original size:20 final size:20
Alignment explanation
Indices: 3176479--3176521 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3176469 ATCCTCTTTT
* * *
3176479 TATTTATGAAAACAAACATA
1 TATTAATGAAAACAAAAACA
*
3176499 TATTAATGAAAAGAAAAACA
1 TATTAATGAAAACAAAAACA
3176519 TAT
1 TAT
3176522 ATCTCAAGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (20 bp):
TATTAATGAAAACAAAAACA
Found at i:3177822 original size:168 final size:166
Alignment explanation
Indices: 3177474--3177970 Score: 534
Period size: 168 Copynumber: 3.0 Consensus size: 166
3177464 TTTGAACATC
* *
3177474 AAAATTC-TCTAAATATTATCATTTAATT-ATCATTAAATTAGTTTTGAAAAATTCCATTTATTT
1 AAAATTCATC-AAATATTATCATTTAATTCAT-ATTAAATTATTTTTAAAAAATT-CATTTATTT
* * * *
3177537 T-ATGAGTTATTGATTTTCTT--TTGGAATTC-CTCTTATTTGCAAAATACT-AACTTTTCTACT
63 TCATGAGTTTTTCATTTT-TTCCTTGAAATTCTC-CTT-TTT-CAAAAAACTGAA-TTTTCTA-T
* * * **
3177597 T-CGTCAATG-TTTT-TAGGGGGATTTTCTCTGTTTTTAATTTTT
122 TCCATAAATGTTTTTGTAGGGGGATTTTCTCAGTTTGAAATTTTT
* * * *
3177639 AAAATTAATCAAATATTATTATTTAATTCATATTAAATTATTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATCATTTAATTCATATTAAATTATTTTTAAAAAATTCATTTATTTTCA
*
3177704 TGAGTTTTTCATTTTTTCCCTTGAAATTCTCCTGTTTTCAAAAAACTGAGTTTTCTATTCCATAA
66 TGAGTTTTTCATTTTTT-CCTTGAAATTCTCCT-TTTTCAAAAAACTGAATTTTCTATTCCATAA
* * *
3177769 AGGTTTTTGTAGGGGGTTTTTCTCAGTTAGAAATTTTT
129 ATGTTTTTGTAGGGGGATTTTCTCAGTTTGAAATTTTT
* *
3177807 AAAATTCATCAAATATTATCATTCAATTCATATTAAATCATTTTTAAAAAATTCATTTATTTTCA
1 AAAATTCATCAAATATTATCATTTAATTCATATTAAATTATTTTTAAAAAATTCATTTATTTTCA
* * * * * *
3177872 TTAGTTTTTTATTTTTTCCTTGAAATGC-CCTTATTTCCGAAAAACCGAATTTTCTATCCCATAA
66 TGAGTTTTTCATTTTTTCCTTGAAATTCTCCTT-TTT-CAAAAAACTGAATTTTCTATTCCATAA
3177936 ATGTTTTTG--GGGGGATTTTCTTCAGTTTGAAATTT
129 ATGTTTTTGTAGGGGGATTTTC-TCAGTTTGAAATTT
3177971 CTATAATGCA
Statistics
Matches: 283, Mismatches: 34, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
164 11 0.04
165 70 0.25
166 43 0.15
167 59 0.21
168 100 0.35
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (166 bp):
AAAATTCATCAAATATTATCATTTAATTCATATTAAATTATTTTTAAAAAATTCATTTATTTTCA
TGAGTTTTTCATTTTTTCCTTGAAATTCTCCTTTTTCAAAAAACTGAATTTTCTATTCCATAAAT
GTTTTTGTAGGGGGATTTTCTCAGTTTGAAATTTTT
Found at i:3178034 original size:167 final size:167
Alignment explanation
Indices: 3177605--3178054 Score: 437
Period size: 168 Copynumber: 2.7 Consensus size: 167
3177595 CTTCGTCAAT
* *** * ** * * *
3177605 GTTTTT-AGGGGGATTTTCTCTGTTTTTAATTTTTAAAATTAATCAAATATTATTATTTAATTCA
1 GTTTTTGAGGGGGATTTTCTCAGTTAGAAATTTCTAAAATGCATCAAATATTATCATTCAACTCA
* * * * * * * *
3177669 TATTAAATTATTTTTCAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTTCCCTTGAAATTCT
66 CATTAAATCAGTTTTAAAAAATTCATTTATTTTCATAAGTTTTTAATTTTTTCCCTTGAAATGCT
* * *
3177734 CCTGTTTTCAAAAAACTGAGTTTTCTATTCCATAAAG
131 CCTGTTTTCAAAAAACCGAATTTTCTATCCCATAAAG
* * * *
3177771 GTTTTTGTAGGGGGTTTTTCTCAGTTAGAAATTTTTAAAATTCATCAAATATTATCATTCAATTC
1 GTTTTTG-AGGGGGATTTTCTCAGTTAGAAATTTCTAAAATGCATCAAATATTATCATTCAACTC
* * * *
3177836 ATATTAAATCATTTTTAAAAAATTCATTTATTTTCATTAGTTTTTTATTTTTT-CCTTGAAATGC
65 ACATTAAATCAGTTTTAAAAAATTCATTTATTTTCATAAGTTTTTAATTTTTTCCCTTGAAATGC
* *
3177900 -CCT-TATTTCCGAAAAACCGAATTTTCTATCCCATAAAT
130 TCCTGT-TTT-CAAAAAACCGAATTTTCTATCCCATAAAG
* * * * *
3177938 GTTTTTG-GGGGGATTTTCTTCAGTTTGAAATTTCTATAATGCAT-ATGATATTGTCATTGAACT
1 GTTTTTGAGGGGGATTTTC-TCAGTTAGAAATTTCTAAAATGCATCA-AATATTATCATTCAACT
* * * *
3178001 CCCATTAAATCAGTTTTGAGAAATTCAATTTATTTT-ATAAGTTTTGAATTTTTT
64 CACATTAAATCAGTTTTAAAAAATTC-ATTTATTTTCATAAGTTTTTAATTTTTT
3178055 AATATATATT
Statistics
Matches: 241, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
165 12 0.05
166 82 0.34
167 50 0.21
168 97 0.40
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (167 bp):
GTTTTTGAGGGGGATTTTCTCAGTTAGAAATTTCTAAAATGCATCAAATATTATCATTCAACTCA
CATTAAATCAGTTTTAAAAAATTCATTTATTTTCATAAGTTTTTAATTTTTTCCCTTGAAATGCT
CCTGTTTTCAAAAAACCGAATTTTCTATCCCATAAAG
Found at i:3179425 original size:18 final size:17
Alignment explanation
Indices: 3179402--3179438 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3179392 TTTTTAAAAT
3179402 ATAAAAGAATAAAATAAA
1 ATAAAAGAAT-AAATAAA
*
3179420 ATAAAATAATAAATAAA
1 ATAAAAGAATAAATAAA
3179437 AT
1 AT
3179439 TATTTTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
ATAAAAGAATAAATAAA
Found at i:3187475 original size:16 final size:15
Alignment explanation
Indices: 3187432--3187538 Score: 52
Period size: 16 Copynumber: 6.8 Consensus size: 15
3187422 GGGTTCGGAT
*
3187432 TCGTTTGGGTTCAAC
1 TCGTTCGGGTTCAAC
* * *
3187447 TCATTCGGATTCAGGC
1 TCGTTCGGGTTCA-AC
3187463 TCGTTCGGGTTCAAGC
1 TCGTTCGGGTTCAA-C
** * *
3187479 TTATTTGAGTTCAAGC
1 TCGTTCGGGTTCAA-C
* *
3187495 TCGTTCGAGTTTGAAC
1 TCGTTCG-GGTTCAAC
*
3187511 TCTTTCGGGTTCGAAC
1 TCGTTCGGGTTC-AAC
**
3187527 TTATTCGGGTTC
1 TCGTTCGGGTTC
3187539 GAGTTCAGGT
Statistics
Matches: 66, Mismatches: 22, Indels: 7
0.69 0.23 0.07
Matches are distributed among these distances:
15 13 0.20
16 49 0.74
17 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (15 bp):
TCGTTCGGGTTCAAC
Found at i:3187773 original size:18 final size:18
Alignment explanation
Indices: 3187734--3187773 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3187724 ATATTTATAT
*
3187734 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
3187752 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
3187770 ATAA
1 ATAA
3187774 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:3188971 original size:16 final size:16
Alignment explanation
Indices: 3188950--3188980 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3188940 TCTTGGGTTC
3188950 GAGTTCTCTCGAGTTT
1 GAGTTCTCTCGAGTTT
*
3188966 GAGTTCTTTCGAGTT
1 GAGTTCTCTCGAGTT
3188981 CAGGTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (16 bp):
GAGTTCTCTCGAGTTT
Found at i:3189201 original size:59 final size:59
Alignment explanation
Indices: 3189138--3189261 Score: 239
Period size: 59 Copynumber: 2.1 Consensus size: 59
3189128 CCAATAAGTA
3189138 TACGAAGCTCCTTGCCTTTTTTTTCTATTTCTCTTTCTCTTTCTCTTTATTGCGTACGC
1 TACGAAGCTCCTTGCCTTTTTTTTCTATTTCTCTTTCTCTTTCTCTTTATTGCGTACGC
*
3189197 TACGAAGCTCCTTGCCTTTTTTTTCTATTTCTCTTTCTTTTTCTCTTTATTGCGTACGC
1 TACGAAGCTCCTTGCCTTTTTTTTCTATTTCTCTTTCTCTTTCTCTTTATTGCGTACGC
3189256 TACGAA
1 TACGAA
3189262 TCCAATCCAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.12, C:0.26, G:0.10, T:0.52
Consensus pattern (59 bp):
TACGAAGCTCCTTGCCTTTTTTTTCTATTTCTCTTTCTCTTTCTCTTTATTGCGTACGC
Found at i:3189525 original size:2 final size:2
Alignment explanation
Indices: 3189518--3189544 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3189508 TTTATTTGTA
3189518 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3189545 ATTATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3189791 original size:14 final size:15
Alignment explanation
Indices: 3189765--3189798 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3189755 ATTTTATAGG
3189765 TTAATATAAATTTTA
1 TTAATATAAATTTTA
3189780 TTAATA-AAATTTTA
1 TTAATATAAATTTTA
*
3189794 ATAAT
1 TTAAT
3189799 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATATAAATTTTA
Found at i:3195750 original size:148 final size:148
Alignment explanation
Indices: 3195478--3195775 Score: 463
Period size: 148 Copynumber: 2.0 Consensus size: 148
3195468 TCATTACAAG
* * * *
3195478 ACAAGCTTTCTCCGTGAAGAAATCTTTGGTAGACTTGTGGCGACTTGCGTTTTCATACCAGGTAA
1 ACAAGCTTTCTCCGTGAAGAAATATTTGGTAGACTAGTGGCGACTTGCATCTTCATACCAGGTAA
* * *
3195543 ATCCGCTTGCTGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTTTCTGCTTCGC
66 ATCCGCTTACCGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
3195608 TGATCTGGCCAAA-TAGCT
131 TGATCTGG-CAAAGTAGCT
* * * *
3195626 ACAAGCTTTGTCCGTGAAGAAGTATTTGGTAGACTAGTGGCGACTTGCATCTTCTTACCTGGTAA
1 ACAAGCTTTCTCCGTGAAGAAATATTTGGTAGACTAGTGGCGACTTGCATCTTCATACCAGGTAA
* *
3195691 ATCTGCTTACCGCTATTCAACCCTTGCCTGTTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
66 ATCCGCTTACCGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
3195756 TGATCTGGCAAAGTAGCT
131 TGATCTGGCAAAGTAGCT
3195774 AC
1 AC
3195776 TAGTTCACTT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
147 4 0.03
148 132 0.97
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (148 bp):
ACAAGCTTTCTCCGTGAAGAAATATTTGGTAGACTAGTGGCGACTTGCATCTTCATACCAGGTAA
ATCCGCTTACCGCTATTCAACCCTTGCCTGCTGCTCGGTGATGAAGCTTTAATTCTCTGCTTCGC
TGATCTGGCAAAGTAGCT
Found at i:3196679 original size:18 final size:19
Alignment explanation
Indices: 3196656--3196698 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3196646 CCAAACATTA
3196656 TAAAATAAATTTA-AAATT
1 TAAAATAAATTTATAAATT
**
3196674 TAAAATTTATTTATAAATT
1 TAAAATAAATTTATAAATT
*
3196693 TTAAAT
1 TAAAAT
3196699 TTAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATAAATTTATAAATT
Found at i:3196693 original size:19 final size:18
Alignment explanation
Indices: 3196664--3196701 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3196654 TATAAAATAA
3196664 ATTTAAAATTTAAAATTT
1 ATTTAAAATTTAAAATTT
*
3196682 ATTTATAAATTTTAAATTT
1 ATTTA-AAATTTAAAATTT
3196701 A
1 A
3196702 AATATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAATTTAAAATTT
Done.