Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 60 of 328
Found at i:16625048 original size:22 final size:23
Alignment explanation
Indices: 16625009--16625056 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
16624999 ATAATCATTT
*
16625009 AATCATTACTATTCAGTATCAGTC
1 AATCATTA-TATTCAGTAACAGTC
*
16625033 AATCATT-TATTTAGTAACAGTC
1 AATCATTATATTCAGTAACAGTC
16625055 AA
1 AA
16625057 GTACTCAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
24 7 0.32
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
AATCATTATATTCAGTAACAGTC
Found at i:16625492 original size:23 final size:25
Alignment explanation
Indices: 16625456--16625501 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
16625446 ACTTTCAAAT
**
16625456 TTTCAATTTTATTT-GTA-ATTTAA
1 TTTCAATTCAATTTAGTACATTTAA
16625479 TTTCAATTCAATTTAGTACATTT
1 TTTCAATTCAATTTAGTACATTT
16625502 TTCCATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 3 0.16
25 4 0.21
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTCAATTCAATTTAGTACATTTAA
Found at i:16625532 original size:28 final size:27
Alignment explanation
Indices: 16625501--16625581 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
16625491 TTAGTACATT
*
16625501 TTTCCATATCAATCCACATGCAATTCA
1 TTTCCATATCAATCCACATTCAATTCA
* **
16625528 CTTTCAATA-CAATATACATTTCAATTCA
1 -TTTCCATATCAATCCACA-TTCAATTCA
16625556 TTTCCA-AT-AATCACACATTCAATTCA
1 TTTCCATATCAATC-CACATTCAATTCA
16625582 ACATTATGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
26 13 0.30
27 15 0.35
28 15 0.35
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (27 bp):
TTTCCATATCAATCCACATTCAATTCA
Found at i:16626309 original size:18 final size:17
Alignment explanation
Indices: 16626270--16626321 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
16626260 TCGTTTCAAG
16626270 TTCTGTTCTTTCTATTCTTT
1 TTCT-TTCTTT-TATT-TTT
16626290 TTCTTTCTTTTATTTGTT
1 TTCTTTCTTTTATTT-TT
*
16626308 TTGTTTC-TTTATTT
1 TTCTTTCTTTTATTT
16626322 AACTATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.27
18 12 0.40
19 6 0.20
20 4 0.13
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.75
Consensus pattern (17 bp):
TTCTTTCTTTTATTTTT
Found at i:16632561 original size:5 final size:5
Alignment explanation
Indices: 16632535--16632595 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
16632525 CCCATTTTCC
* * *
16632535 TATTT TA-TT TATTT AATAT TATTT TATTT TATTT TA-TT TATTGT CTATTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATT-T -TATTT
*
16632585 TATAT TATTT T
1 TATTT TATTT T
16632596 CTTTGTTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
4 8 0.18
5 31 0.70
6 1 0.02
7 4 0.09
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:16632607 original size:31 final size:29
Alignment explanation
Indices: 16632535--16632595 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
16632525 CCCATTTTCC
*
16632535 TATTTTATTTATT-TAATATTATTTTATTT
1 TATTTTATTTATTGT-CTATTATTTTATTT
16632564 TATTTTATTTATTGTCTATTATATATTATTT
1 TATTTTATTTATTGTCTATTAT-T-TTATTT
16632595 T
1 T
16632596 CTTTGTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 19 0.68
30 2 0.07
31 7 0.25
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (29 bp):
TATTTTATTTATTGTCTATTATTTTATTT
Found at i:16635106 original size:14 final size:14
Alignment explanation
Indices: 16635087--16635113 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16635077 ATATTTGACT
16635087 TGTTCTTAATTATG
1 TGTTCTTAATTATG
16635101 TGTTCTTAATTAT
1 TGTTCTTAATTAT
16635114 TTTTTTAATA
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:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
TGTTCTTAATTATG
Found at i:16636249 original size:54 final size:54
Alignment explanation
Indices: 16636165--16636273 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
16636155 CTACTGTAGC
16636165 TGCAAATACTTTTGAACTGAAACCTAACACAATTCAAATGATACAACAATTTGT
1 TGCAAATACTTTTGAACTGAAACCTAACACAATTCAAATGATACAACAATTTGT
* * *
16636219 TGCAAATTCTTTTGAATTGAAACCTCACACAATTCAAATGATACAACAATTTGT
1 TGCAAATACTTTTGAACTGAAACCTAACACAATTCAAATGATACAACAATTTGT
16636273 T
1 T
16636274 CAGTTTGATA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
TGCAAATACTTTTGAACTGAAACCTAACACAATTCAAATGATACAACAATTTGT
Found at i:16638704 original size:21 final size:20
Alignment explanation
Indices: 16638647--16638732 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 20
16638637 TTAGGTTTTA
16638647 TATATTAAATTATATATATAT
1 TATATTAAATTAT-TATATAT
* * *
16638668 TATAATGATTATTATTATAGTTT
1 TAT-ATTA-AATTATTATA-TAT
*
16638691 TATATTAAATTATTAT-GAT
1 TATATTAAATTATTATATAT
*
16638710 TAT-TT-AATTAATAATATAT
1 TATATTAAATT-ATTATATAT
16638729 TATA
1 TATA
16638733 AATAAATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
17 4 0.08
18 6 0.12
19 9 0.18
21 11 0.22
22 10 0.20
23 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATATTAAATTATTATATAT
Found at i:16643957 original size:68 final size:66
Alignment explanation
Indices: 16643885--16644056 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
16643875 CATCATGTGT
* * * *
16643885 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
16643948 TGTAG
62 TGTAG
** * *
16643953 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
16644018 AG
65 AG
* * * *
16644020 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
16644057 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:16643990 original size:64 final size:64
Alignment explanation
Indices: 16643909--16644092 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
16643899 AGACATTATG
* * *
16643909 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
16643973 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
16644038 AA
63 AA
* * *
16644040 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
16644093 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:16645952 original size:103 final size:104
Alignment explanation
Indices: 16645770--16645970 Score: 323
Period size: 103 Copynumber: 1.9 Consensus size: 104
16645760 AAAATATAAT
* * *
16645770 GAAATTTTATGGCCCGTATTTTAGTTTAATGTTTGTATGTTTGTTCGGTAATGCCTCGTACCTTA
1 GAAATTTTATGGCCCGTATTTTAGTTTAATGTTTGTATGCTTGTTCGATAACGCCTCGTACCTTA
* * * **
16645835 TCTCGGCCTTGGGTA-GGGTAAGGGGTGTTACATTTAGC
66 TCCCAGCCTCGGGTACAAGTAAGGGGTGTTACATTTAGC
16645873 GAAATTTTATGGCCCGTATTTTAGTTTAATGTTTGTATGCTTGTTCGATAACGCCTCGTACCTTA
1 GAAATTTTATGGCCCGTATTTTAGTTTAATGTTTGTATGCTTGTTCGATAACGCCTCGTACCTTA
16645938 TCCCAGCCTCGGGTACAAGTAAGGGGTGTTACA
66 TCCCAGCCTCGGGTACAAGTAAGGGGTGTTACA
16645971 CACCTTCATT
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 74 0.83
104 15 0.17
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.38
Consensus pattern (104 bp):
GAAATTTTATGGCCCGTATTTTAGTTTAATGTTTGTATGCTTGTTCGATAACGCCTCGTACCTTA
TCCCAGCCTCGGGTACAAGTAAGGGGTGTTACATTTAGC
Found at i:16649376 original size:19 final size:23
Alignment explanation
Indices: 16649324--16649378 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
16649314 AACAAATCTC
*
16649324 CACACGCCCGTGTGGGTATAGAG
1 CACACGCCCGTGTGGCTATAGAG
*
16649347 CACACGACCGTGT-GCTAT-G-G
1 CACACGCCCGTGTGGCTATAGAG
16649367 -ACACGCCCGTGT
1 CACACGCCCGTGT
16649379 CCCGAACCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 1 0.03
22 4 0.14
23 12 0.41
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.18
Consensus pattern (23 bp):
CACACGCCCGTGTGGCTATAGAG
Found at i:16650451 original size:47 final size:46
Alignment explanation
Indices: 16650344--16650656 Score: 243
Period size: 47 Copynumber: 6.7 Consensus size: 46
16650334 GGATATATTA
* * *
16650344 CCGATGCCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T-A-G
1 CCGATG-CATGTCCCAGACATGTCTTACACTGGC-TATCTCTGTGAGG
* *
16650389 CCGATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTGTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGT-GAGG
* * *
16650436 CTGATGCATGTCCCAGACATGCCTTACACTTGCACTCATCTCTGT---G
1 CCGATGCATGTCCCAGACATGTCTTACAC-TG-GCT-ATCTCTGTGAGG
*
16650482 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTATCT-TAGT-ATGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTCT-GTGA-GG
* * * ** * *
16650530 CTGATGTATGTCCCAGACATGTCTTACACTAGCCCTCGTTTG-GATG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTATC-TCTGTGAGG
* *
16650576 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAATGTGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTC-T-GTGAGG
*
16650624 CCGAAGCATGTCCCAGACATGTCTTACACTGGC
1 CCGATGCATGTCCCAGACATGTCTTACACTGGC
16650657 ACACAAATCA
Statistics
Matches: 218, Mismatches: 29, Indels: 41
0.76 0.10 0.14
Matches are distributed among these distances:
43 5 0.02
44 26 0.12
45 13 0.06
46 45 0.21
47 83 0.38
48 36 0.17
49 2 0.01
50 8 0.04
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (46 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGTGAGG
Found at i:16650544 original size:94 final size:94
Alignment explanation
Indices: 16650346--16650658 Score: 356
Period size: 94 Copynumber: 3.4 Consensus size: 94
16650336 ATATATTACC
* *
16650346 GATGCCATGTCCCAGACATGTCTTACACTAGCA--CAACTCT-TAGCCGATG-CGTGTCCCAGAC
1 GATG-CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTGT-GCCGATGCCATGTCCCAGAC
*
16650407 A-CGTCTTACACTGGCTATCTCT-GTCGA-GGCT
64 ATGGTCTTACACTGGCTATCT-TAGT--ATGGCT
* * *
16650438 GATGCATGTCCCAGACATGCCTTACACTTGCACTCATCTCTGTGCCGATGCCATGTTCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTGTGCCGATGCCATGTCCCAGACAT
16650503 GGTCTTACACTGGCTATCTTAGTATGGCT
66 GGTCTTACACTGGCTATCTTAGTATGGCT
* * *
16650532 GATGTATGTCCCAGACATGTCTTACACTAGCCCTCGT-T-TGGATGCCGATGCCATGTCCCAGAC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCT-G-TGCCGATGCCATGTCCCAGAC
* * * * *
16650595 ATGGTCTTACACTGGCTCTCATAATGTGGCC
64 ATGGTCTTACACTGGCTATCTTAGTATGGCT
* *
16650626 GAAGCATGTCCCAGACATGTCTTACACTGGCAC
1 GATGCATGTCCCAGACATGTCTTACACTAGCAC
16650659 ACAAATCACC
Statistics
Matches: 191, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
91 26 0.14
92 5 0.03
93 16 0.08
94 124 0.65
95 20 0.10
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (94 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTGTGCCGATGCCATGTCCCAGACAT
GGTCTTACACTGGCTATCTTAGTATGGCT
Found at i:16652349 original size:3 final size:3
Alignment explanation
Indices: 16652336--16652369 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
16652326 AAGAGTAGGT
16652336 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16652370 AATTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:16656854 original size:9 final size:9
Alignment explanation
Indices: 16656842--16656898 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16656832 TTTGATAAAC
16656842 ATGATATGT
1 ATGATATGT
*
16656851 ATGATATGCAC
1 ATGATATG--T
*
16656862 ATGACATGT
1 ATGATATGT
*
16656871 ATGATATGCAC
1 ATGATATG--T
16656882 ATGATATGT
1 ATGATATGT
16656891 ATGATATG
1 ATGATATG
16656899 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:16656865 original size:20 final size:20
Alignment explanation
Indices: 16656840--16656910 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
16656830 ATTTTGATAA
16656840 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16656860 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
16656880 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16656900 ACATGAGATGT
1 ACATGATATGT
16656911 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:16656887 original size:11 final size:11
Alignment explanation
Indices: 16656851--16656905 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
16656841 CATGATATGT
16656851 ATGATATGCAC
1 ATGATATGCAC
* *
16656862 ATGACATG--T
1 ATGATATGCAC
16656871 ATGATATGCAC
1 ATGATATGCAC
*
16656882 ATGATATG--T
1 ATGATATGCAC
16656891 ATGATATGCAC
1 ATGATATGCAC
16656902 ATGA
1 ATGA
16656906 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:16656987 original size:23 final size:23
Alignment explanation
Indices: 16656957--16657168 Score: 354
Period size: 23 Copynumber: 9.1 Consensus size: 23
16656947 AGGAAGTGCA
16656957 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16656980 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16657003 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16657026 AAAGGGCTTATG-CCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
16657049 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
16657073 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16657096 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16657119 AAAGGGCTCATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16657142 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
16657166 AAA
1 AAA
16657169 AGAGGCTAGG
Statistics
Matches: 181, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
22 9 0.05
23 118 0.65
24 54 0.30
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:16657109 original size:70 final size:69
Alignment explanation
Indices: 16656957--16657168 Score: 354
Period size: 70 Copynumber: 3.0 Consensus size: 69
16656947 AGGAAGTGCA
*
16656957 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGT
16657022 TATT
66 TATT
*
16657026 AAAGGGCTTATG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCA
16657090 GTTATT
64 GTTATT
* *
16657096 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTCATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAG
16657161 TTATT
65 TTATT
16657166 AAA
1 AAA
16657169 AGAGGCTAGG
Statistics
Matches: 134, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
68 9 0.07
69 34 0.25
70 81 0.60
71 10 0.07
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (69 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGT
TATT
Found at i:16665012 original size:9 final size:9
Alignment explanation
Indices: 16665000--16665056 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16664990 TTTGATAAAC
16665000 ATGATATGT
1 ATGATATGT
*
16665009 ATGATATGCAC
1 ATGATATG--T
*
16665020 ATGACATGT
1 ATGATATGT
*
16665029 ATGATATGCAC
1 ATGATATG--T
16665040 ATGATATGT
1 ATGATATGT
16665049 ATGATATG
1 ATGATATG
16665057 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:16665023 original size:20 final size:20
Alignment explanation
Indices: 16664998--16665068 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
16664988 ATTTTGATAA
16664998 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16665018 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
16665038 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16665058 ACATGAGATGT
1 ACATGATATGT
16665069 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:16665045 original size:11 final size:11
Alignment explanation
Indices: 16665009--16665063 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
16664999 CATGATATGT
16665009 ATGATATGCAC
1 ATGATATGCAC
* *
16665020 ATGACATG--T
1 ATGATATGCAC
16665029 ATGATATGCAC
1 ATGATATGCAC
*
16665040 ATGATATG--T
1 ATGATATGCAC
16665049 ATGATATGCAC
1 ATGATATGCAC
16665060 ATGA
1 ATGA
16665064 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:16665138 original size:23 final size:23
Alignment explanation
Indices: 16665111--16665274 Score: 269
Period size: 23 Copynumber: 7.1 Consensus size: 23
16665101 GAGGAAGTGA
16665111 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16665134 AAAGGGCTTATGCCCCAGTTATC
1 AAAGGGCTTATGCCCCAGTTATT
*
16665157 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
16665181 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16665203 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16665225 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16665248 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
16665272 AAA
1 AAA
16665275 AGAGGCTAGG
Statistics
Matches: 134, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
22 34 0.25
23 66 0.49
24 34 0.25
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:16665164 original size:46 final size:46
Alignment explanation
Indices: 16665110--16665296 Score: 263
Period size: 46 Copynumber: 4.0 Consensus size: 46
16665100 GGAGGAAGTG
16665110 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
16665156 CAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
*
16665202 TAAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTA-T
* *
16665248 AAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTAT
16665296 A
1 A
16665297 TGATAAAGCA
Statistics
Matches: 127, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
44 12 0.09
45 17 0.13
46 55 0.43
47 22 0.17
48 11 0.09
49 10 0.08
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:16665208 original size:69 final size:69
Alignment explanation
Indices: 16665110--16665274 Score: 287
Period size: 68 Copynumber: 2.4 Consensus size: 69
16665100 GGAGGAAGTG
16665110 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAG
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATG-CCCAGTTATCAAAGGGCTTATGCCCCAG
16665175 TTATC
65 TTATC
*
16665180 AAAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCAGTTATCAAAGGGCTTATGCCCCAGT
*
16665244 TATT
66 TATC
*
16665248 AAAAGGGCTTTTGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
16665275 AGAGGCTAGG
Statistics
Matches: 91, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
68 43 0.47
69 35 0.38
70 13 0.14
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (69 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCAGTTATCAAAGGGCTTATGCCCCAGT
TATC
Found at i:16668021 original size:9 final size:9
Alignment explanation
Indices: 16668009--16668065 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16667999 TTTGATAAAC
16668009 ATGATATGT
1 ATGATATGT
*
16668018 ATGATATGCAC
1 ATGATATG--T
*
16668029 ATGACATGT
1 ATGATATGT
*
16668038 ATGATATGCAC
1 ATGATATG--T
16668049 ATGATATGT
1 ATGATATGT
16668058 ATGATATG
1 ATGATATG
16668066 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:16668032 original size:20 final size:20
Alignment explanation
Indices: 16668007--16668077 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
16667997 ATTTTGATAA
16668007 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16668027 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
16668047 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16668067 ACATGAGATGT
1 ACATGATATGT
16668078 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:16668054 original size:11 final size:11
Alignment explanation
Indices: 16668018--16668072 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
16668008 CATGATATGT
16668018 ATGATATGCAC
1 ATGATATGCAC
* *
16668029 ATGACATG--T
1 ATGATATGCAC
16668038 ATGATATGCAC
1 ATGATATGCAC
*
16668049 ATGATATG--T
1 ATGATATGCAC
16668058 ATGATATGCAC
1 ATGATATGCAC
16668069 ATGA
1 ATGA
16668073 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:16668142 original size:13 final size:13
Alignment explanation
Indices: 16668124--16668149 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16668114 AGGAAGTGCA
16668124 AAAGGGCTTATGC
1 AAAGGGCTTATGC
16668137 AAAGGGCTTATGC
1 AAAGGGCTTATGC
16668150 CCCAGTTATT
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:0.31, T:0.23
Consensus pattern (13 bp):
AAAGGGCTTATGC
Found at i:16668163 original size:23 final size:23
Alignment explanation
Indices: 16668137--16668325 Score: 326
Period size: 23 Copynumber: 8.1 Consensus size: 23
16668127 GGGCTTATGC
16668137 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16668160 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16668183 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
16668207 AAAGGGCTTATGCCCCAGTTATTT
1 AAAGGGCTTATGCCCCAGTTA-TT
16668231 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16668253 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16668276 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16668299 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
16668323 AAA
1 AAA
16668326 AGAGGCTAGG
Statistics
Matches: 159, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
22 14 0.09
23 89 0.56
24 55 0.35
25 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:16668250 original size:70 final size:70
Alignment explanation
Indices: 16668137--16668347 Score: 329
Period size: 70 Copynumber: 3.0 Consensus size: 70
16668127 GGGCTTATGC
16668137 AAAGGGCTTATGCCCCAGTTA-TTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
1 AAAGGGCTTATGCCCCAGTTATTTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
16668201 TTATCA
66 TTAT-A
16668207 AAAGGGCTTATGCCCCAGTTATTTAAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCCAG
1 AAAGGGCTTATGCCCCAGTTATTTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
*
16668271 TTATT
66 TTATA
* * *
16668276 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTC
1 AAAGGGCTTATGCCCCAGTTATTTAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-C
16668340 CAGTTATA
63 CAGTTATA
16668348 TGATAAAGCA
Statistics
Matches: 131, Mismatches: 5, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
69 34 0.26
70 63 0.48
71 23 0.18
72 11 0.08
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (70 bp):
AAAGGGCTTATGCCCCAGTTATTTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
TTATA
Found at i:16668297 original size:93 final size:94
Alignment explanation
Indices: 16668137--16668346 Score: 352
Period size: 93 Copynumber: 2.2 Consensus size: 94
16668127 GGGCTTATGC
16668137 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGT
*
16668202 TATCAAAAGGGCTTATGCCCCAGTTATTT
66 TATCAAAAGGGCTTATGCCCCAGTTATTA
16668231 AAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGT
* *
16668295 TATTAAAAGGGCTTTTGCCCCAGTTATTA
66 TATCAAAAGGGCTTATGCCCCAGTTATTA
*
16668324 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
16668347 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
93 85 0.78
94 16 0.15
95 8 0.07
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (94 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGT
TATCAAAAGGGCTTATGCCCCAGTTATTA
Found at i:16676183 original size:9 final size:9
Alignment explanation
Indices: 16676171--16676227 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16676161 TTTGATAAAC
16676171 ATGATATGT
1 ATGATATGT
*
16676180 ATGATATGCAC
1 ATGATATG--T
*
16676191 ATGACATGT
1 ATGATATGT
*
16676200 ATGATATGCAC
1 ATGATATG--T
16676211 ATGATATGT
1 ATGATATGT
16676220 ATGATATG
1 ATGATATG
16676228 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:16676194 original size:20 final size:20
Alignment explanation
Indices: 16676169--16676239 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
16676159 ATTTTGATAA
16676169 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16676189 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
16676209 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16676229 ACATGAGATGT
1 ACATGATATGT
16676240 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:16676216 original size:11 final size:11
Alignment explanation
Indices: 16676180--16676234 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
16676170 CATGATATGT
16676180 ATGATATGCAC
1 ATGATATGCAC
* *
16676191 ATGACATG--T
1 ATGATATGCAC
16676200 ATGATATGCAC
1 ATGATATGCAC
*
16676211 ATGATATG--T
1 ATGATATGCAC
16676220 ATGATATGCAC
1 ATGATATGCAC
16676231 ATGA
1 ATGA
16676235 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:16676316 original size:23 final size:23
Alignment explanation
Indices: 16676286--16676452 Score: 271
Period size: 23 Copynumber: 7.1 Consensus size: 23
16676276 AGGAAGTGCA
16676286 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16676309 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16676332 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
16676356 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
16676380 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16676403 AAAGGGCTCATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16676426 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
16676450 AAA
1 AAA
16676453 AGAGGCTAGG
Statistics
Matches: 137, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
23 70 0.51
24 67 0.49
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:16676364 original size:24 final size:23
Alignment explanation
Indices: 16676285--16676474 Score: 265
Period size: 24 Copynumber: 8.0 Consensus size: 23
16676275 GAGGAAGTGC
16676285 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
16676308 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
16676331 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
16676354 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
16676378 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
* *
16676402 TAAAGGGCTCATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
16676426 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
16676450 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
16676474 A
1 A
16676475 TGATAAAGCA
Statistics
Matches: 154, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
23 65 0.42
24 79 0.51
25 10 0.06
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:16676403 original size:71 final size:70
Alignment explanation
Indices: 16676284--16676473 Score: 292
Period size: 71 Copynumber: 2.7 Consensus size: 70
16676274 GGAGGAAGTG
* *
16676284 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 CAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTCATGCCCCA
16676349 GTTAT
66 GTTAT
16676354 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTCATGCCCC
1 CAAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTCATGCCCC
16676419 AGTTAT
65 AGTTAT
* * *
16676425 TAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
16676474 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
70 24 0.22
71 75 0.68
72 12 0.11
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (70 bp):
CAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTCATGCCCCA
GTTAT
Found at i:16684378 original size:41 final size:41
Alignment explanation
Indices: 16684233--16684380 Score: 142
Period size: 40 Copynumber: 3.7 Consensus size: 41
16684223 GCGACTCGCT
* * *
16684233 CAAAAGCCTTCGGGACATAGCCCGG-TTATAATAACTCA-CA
1 CAAAAGCCTTCGGGACTTAGCCCGGATT-TAGTAACTTAGCA
* * * * * *
16684273 CAAATGCCTTCGGGACTTAACCCGGTTTTGGTGAC-TCGCA
1 CAAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTTAGCA
* * *
16684313 CAAATGCCTTCGGGAATT-GACCCGGATTTAGTCACTTAGCA
1 CAAAAGCCTTCGGGACTTAG-CCCGGATTTAGTAACTTAGCA
16684354 CAAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAAAGCCTTCGGGACTTAGCCCGGAT
16684381 ACCATTCGAA
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
40 57 0.66
41 29 0.33
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (41 bp):
CAAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTTAGCA
Found at i:16692337 original size:40 final size:40
Alignment explanation
Indices: 16692255--16692406 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 40
16692245 GGATATAGCG
* * * * *
16692255 ACTCGCTCAAAAGCCTTCGGGACAT-AGCCGGTTATAATA
1 ACTCGCACAAAAGCCTTCGGGACTTAACCCGGTTTTAGTA
* *
16692294 ACTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTA
1 ACTCGCACAAAAGCCTTCGGGACTTAACCCGGTTTTAGTA
* * * * *
16692334 ACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTC
1 ACTCGCACAAAAGCCTTCGGGACTTAACCCGGTTTTAGTA
* *
16692374 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 AC-TCGCACAAAAGCCTTCGGGACTTAACCCGG
16692407 ATACCATTCG
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 22 0.23
40 47 0.50
41 25 0.27
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAAAGCCTTCGGGACTTAACCCGGTTTTAGTA
Found at i:16701083 original size:2 final size:2
Alignment explanation
Indices: 16701076--16701117 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
16701066 GAAAAGGTTA
16701076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16701118 TTTACCTCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16702255 original size:23 final size:23
Alignment explanation
Indices: 16702224--16702299 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
16702214 AAAAATAAAA
*
16702224 AATGTACAGTGAAGATTTTCTGC
1 AATGAACAGTGAAGATTTTCTGC
*
16702247 AATGAACAGTGAAG-TTTCCTTGC
1 AATGAACAGTGAAGATTTTC-TGC
* *
16702270 AATGAACAGTAAAGATTCTCTGC
1 AATGAACAGTGAAGATTTTCTGC
16702293 AATGAAC
1 AATGAAC
16702300 TTTAAATGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 4 0.09
23 39 0.85
24 3 0.07
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (23 bp):
AATGAACAGTGAAGATTTTCTGC
Found at i:16702392 original size:26 final size:26
Alignment explanation
Indices: 16702343--16702394 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
16702333 TTAATATAAG
* *
16702343 TTAAAATATAATAATTTATGAAAAAT
1 TTAAAATATAAAAATTAATGAAAAAT
*
16702369 TTAAAATATATAAAATTAATAAAAAA
1 TTAAAATATA-AAAATTAATGAAAAA
16702395 AATATATGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
TTAAAATATAAAAATTAATGAAAAAT
Found at i:16705170 original size:50 final size:50
Alignment explanation
Indices: 16705094--16705232 Score: 242
Period size: 50 Copynumber: 2.8 Consensus size: 50
16705084 CCATGGCAAC
16705094 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
16705144 AAGTGATAAGTAATAGCTTCGTCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
16705194 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTCATCA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCA
16705233 CGGCTACCTG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:16705271 original size:31 final size:31
Alignment explanation
Indices: 16705233--16705425 Score: 323
Period size: 31 Copynumber: 6.2 Consensus size: 31
16705223 TATCTCATCA
16705233 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
1 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
16705264 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
1 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
16705295 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
1 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
* * *
16705326 CTGCTACCTGATTAGTGAAAAGTGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
* *
16705357 CGGCTACCTGATCAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
* *
16705388 CTGCTACCTGATCAGTGAATAGTGGTAGCTT
1 CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
16705419 CGGCTAC
1 CGGCTAC
16705426 AAGTGACAAG
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 151 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAGTGGTAGCTT
Found at i:16705497 original size:46 final size:49
Alignment explanation
Indices: 16705447--16705651 Score: 196
Period size: 42 Copynumber: 4.5 Consensus size: 49
16705437 GATTTCCGTA
* * *
16705447 TAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTACGTG
*
16705493 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTACGTG
16705542 TAAGACCATAGCTGGGCTATGGCATCGATAT-ATGA-A--T-A-T--GTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGA-GATATGTGATTACGTG
* *
16705584 TAAGACCCTAGTTGGGCTATGGCATCGATAT-ATGA-A--T-A-T--GTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGA-GATATGTGATTACGTG
*
16705626 TAAGACTATAGCTGGGCTATGGCATC
1 TAAGACCATAGCTGGGCTATGGCATC
16705652 ATTATGTGAA
Statistics
Matches: 145, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
42 66 0.46
44 1 0.01
45 1 0.01
46 25 0.17
47 1 0.01
48 14 0.10
49 37 0.26
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (49 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTACGTG
Found at i:16705585 original size:42 final size:42
Alignment explanation
Indices: 16705539--16705695 Score: 226
Period size: 42 Copynumber: 3.7 Consensus size: 42
16705529 ATGTGATTAC
16705539 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAT
* *
16705581 GTGTAAGACCCTAGTTGGGCTATGGCATCGATATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAT
* * *
16705623 GTGTAAGACTATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
* **
16705665 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
16705696 GAAAACGAAG
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 100 0.98
43 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAT
Found at i:16711178 original size:29 final size:29
Alignment explanation
Indices: 16711127--16711184 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
16711117 GAATCATTGT
* *
16711127 CAGTAAAGGGTCGTGCACGTAGGAAGGGG
1 CAGTAAAGGGTCATGCACATAGGAAGGGG
*
16711156 CAGTAAAGGGTCATGTACATAGGAAGGGG
1 CAGTAAAGGGTCATGCACATAGGAAGGGG
16711185 GTACCTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.41, T:0.16
Consensus pattern (29 bp):
CAGTAAAGGGTCATGCACATAGGAAGGGG
Found at i:16712340 original size:164 final size:163
Alignment explanation
Indices: 16712069--16712391 Score: 592
Period size: 164 Copynumber: 2.0 Consensus size: 163
16712059 TAGGAGTGAA
* *
16712069 GGAAATCAATGTGTTGTTGACTTAGTTATTGGCACGATGTATAATTAGTAGTATAGAATTGAATG
1 GGAAATCAATGTGTTGTTGACTTAGTGATTGGCACGATGCATAATTAGTAGTATAGAATTGAATG
16712134 AATATAGAATGTATGCATGTTACCAATGGTATGAAAGGTTCAAATGTGATTGTTTGATTAGTAGT
66 AATATAGAATGTATGCATGTTACCAATGGTATGAAAGGTTCAAATGTGATTGTTTGATTAGTAGT
16712199 CTTGAGGTATACTACTAAATTGAATACATGTCAT
131 C-TGAGGTATACTACTAAATTGAATACATGTCAT
* *
16712233 GGAAATCAATGTGTTGTTGACTTAGTGATTGGCATGATGCATATTTAGTAGTATAGAATTGAATG
1 GGAAATCAATGTGTTGTTGACTTAGTGATTGGCACGATGCATAATTAGTAGTATAGAATTGAATG
16712298 AATATAGAATGTATGCATGTTACCAATGGTATGAAAGGTTCAAATGTGATTGTTTGATTAGTAGT
66 AATATAGAATGTATGCATGTTACCAATGGTATGAAAGGTTCAAATGTGATTGTTTGATTAGTAGT
*
16712363 CTGAGGTATATTACTAAATTGAATACATG
131 CTGAGGTATACTACTAAATTGAATACATG
16712392 GTTGGAATAT
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
163 27 0.18
164 127 0.82
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (163 bp):
GGAAATCAATGTGTTGTTGACTTAGTGATTGGCACGATGCATAATTAGTAGTATAGAATTGAATG
AATATAGAATGTATGCATGTTACCAATGGTATGAAAGGTTCAAATGTGATTGTTTGATTAGTAGT
CTGAGGTATACTACTAAATTGAATACATGTCAT
Found at i:16713074 original size:9 final size:8
Alignment explanation
Indices: 16713046--16713070 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16713036 TGGGTTCTTT
16713046 GTTTTCGG
1 GTTTTCGG
16713054 GTTTTCGG
1 GTTTTCGG
16713062 GTTTTCGG
1 GTTTTCGG
16713070 G
1 G
16713071 GTTTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTTCGG
Found at i:16720135 original size:27 final size:27
Alignment explanation
Indices: 16720097--16720148 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
16720087 TGTGCAAGGT
*
16720097 GTTGTGCCTACCTGTCAGGCACGACTA
1 GTTGTGCCTACCTGACAGGCACGACTA
*
16720124 GTTGTGCCTACCTGACAGGCTCGAC
1 GTTGTGCCTACCTGACAGGCACGAC
16720149 CCATTTCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (27 bp):
GTTGTGCCTACCTGACAGGCACGACTA
Found at i:16722142 original size:40 final size:40
Alignment explanation
Indices: 16722098--16722236 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 40
16722088 AACACACCAG
* *
16722098 TTTGACTCCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * ** * *
16722138 TTTGATACCCAGTGTCTAATTAGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* *
16722176 -TTGGCACCCAGTGCCTCATCGAATATATCCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATA-ATCCGAAGTAATAA
* *
16722216 ATTGACACCCAGTGTCTCATC
1 TTTGACACCCAGTGCCTCATC
16722237 AACTAGAAGT
Statistics
Matches: 75, Mismatches: 20, Indels: 7
0.74 0.20 0.07
Matches are distributed among these distances:
37 17 0.23
38 10 0.13
39 2 0.03
40 28 0.37
41 18 0.24
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
Found at i:16729246 original size:40 final size:40
Alignment explanation
Indices: 16729169--16729310 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 40
16729159 CAAACACACC
* *
16729169 AATTTGTCACCCAATG-CATCATCGGATAATTCGAAGTAAT
1 AATTTGACACCCAATGTC-TCATCGGATAATCCGAAGTAAT
* * *
16729209 AATTTGACACCCAATGTCTCATCGGCTAAACCAAAGT-A-
1 AATTTGACACCCAATGTCTCATCGGATAATCCGAAGTAAT
* ** *
16729247 AA-TTGACATCCAATACCTCATCGAATATATCCGAAGTAAT
1 AATTTGACACCCAATGTCTCATCGGATA-ATCCGAAGTAAT
* *
16729287 AAATTGACACCCAGTGTCTCATCG
1 AATTTGACACCCAATGTCTCATCG
16729311 ACTTGATGTC
Statistics
Matches: 81, Mismatches: 16, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
37 20 0.25
38 9 0.11
39 2 0.02
40 32 0.40
41 18 0.22
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (40 bp):
AATTTGACACCCAATGTCTCATCGGATAATCCGAAGTAAT
Found at i:16729308 original size:41 final size:40
Alignment explanation
Indices: 16729176--16729311 Score: 127
Period size: 37 Copynumber: 3.5 Consensus size: 40
16729166 ACCAATTTGT
* * *
16729176 CACCCAATG-CATCATCGGATAATTCGAAGTAATAATTTGA
1 CACCCAATGTC-TCATCGAATAATCCGAAGTAATAAATTGA
** * *
16729216 CACCCAATGTCTCATCGGCTAAACC-AA--AGTAAATTGA
1 CACCCAATGTCTCATCGAATAATCCGAAGTAATAAATTGA
* **
16729253 CATCCAATACCTCATCGAATATATCCGAAGTAATAAATTGA
1 CACCCAATGTCTCATCGAATA-ATCCGAAGTAATAAATTGA
*
16729294 CACCCAGTGTCTCATCGA
1 CACCCAATGTCTCATCGA
16729312 CTTGATGTCG
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 24 0.32
38 3 0.04
39 4 0.05
40 20 0.27
41 24 0.32
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (40 bp):
CACCCAATGTCTCATCGAATAATCCGAAGTAATAAATTGA
Found at i:16730198 original size:25 final size:26
Alignment explanation
Indices: 16730161--16730217 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
16730151 GAAACCCTAA
*
16730161 CTTTTCCTCCTTTATTTCTCT-TTTT
1 CTTTTCCTCCTTTACTTCTCTATTTT
* * *
16730186 CTTTTCTTTCTTTCCTTCTCTATTTT
1 CTTTTCCTCCTTTACTTCTCTATTTT
*
16730212 CGTTTC
1 CTTTTC
16730218 AATTTGTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (26 bp):
CTTTTCCTCCTTTACTTCTCTATTTT
Found at i:16733454 original size:3 final size:3
Alignment explanation
Indices: 16733448--16733477 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16733438 AACGAAAAAA
16733448 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
16733478 TCATTTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16738455 original size:16 final size:17
Alignment explanation
Indices: 16738427--16738470 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
16738417 ATTAGGAATT
16738427 AAATAACTAAAATAAAC
1 AAATAACTAAAATAAAC
16738444 AAATAA-TAAAATAAAC
1 AAATAACTAAAATAAAC
*
16738460 AAATGACTAAA
1 AAATAACTAAA
16738471 CCAATTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.18
Consensus pattern (17 bp):
AAATAACTAAAATAAAC
Found at i:16740381 original size:20 final size:19
Alignment explanation
Indices: 16740356--16740401 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
16740346 TTCATTAAGC
* *
16740356 TAATTATTTTTGTTTCATCT
1 TAATTAATTTTATTTCA-CT
16740376 TAATTAAATTTTATTTCACT
1 TAATT-AATTTTATTTCACT
16740396 TAATTA
1 TAATTA
16740402 GTCCACATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTAATTTTATTTCACT
Found at i:16740392 original size:21 final size:20
Alignment explanation
Indices: 16740363--16740401 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
16740353 AGCTAATTAT
*
16740363 TTTTGTTTCATCTTAATTAAA
1 TTTTATTTCA-CTTAATTAAA
16740384 TTTTATTTCACTTAATTA
1 TTTTATTTCACTTAATTA
16740402 GTCCACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTATTTCACTTAATTAAA
Found at i:16741396 original size:40 final size:38
Alignment explanation
Indices: 16741325--16741408 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 38
16741315 TTATAAAAAA
*
16741325 TTATATTTTTTTGAGTTTTAAATATACTTTTTAAAATT
1 TTATATTTTTTTGAATTTTAAATATACTTTTTAAAATT
* *
16741363 TTATATTTTTTT-AATTCTTAAAATAATATTTTTTTAAATT
1 TTATATTTTTTTGAATT-TT-AAAT-ATACTTTTTAAAATT
16741403 TTATAT
1 TTATAT
16741409 AATAATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 3 0.08
38 14 0.35
39 4 0.10
40 19 0.47
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (38 bp):
TTATATTTTTTTGAATTTTAAATATACTTTTTAAAATT
Found at i:16741802 original size:23 final size:24
Alignment explanation
Indices: 16741775--16741819 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
16741765 AGAGATAATG
*
16741775 TAACAATTTTAT-AATTAATATAA
1 TAACAAATTTATGAATTAATATAA
*
16741798 TAACAAATTTATGACTTAATAT
1 TAACAAATTTATGAATTAATAT
16741820 TTATACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (24 bp):
TAACAAATTTATGAATTAATATAA
Found at i:16741877 original size:39 final size:43
Alignment explanation
Indices: 16741815--16741904 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 43
16741805 TTTATGACTT
* *
16741815 AATATTTATACATTATATTAATTT-TGTCTTGA-T-T-TAAAAA
1 AATATTTATAAATTATATTAATTTAT-TCTTAATTCTATAAAAA
16741855 AATATTT-TAAATTAT-TTCAATTTATTCTTAATTCTATAAAAA
1 AATATTTATAAATTATATT-AATTTATTCTTAATTCTATAAAAA
16741897 AATATTTA
1 AATATTTA
16741905 AAAACCCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
38 2 0.05
39 17 0.40
40 9 0.21
41 1 0.02
42 13 0.31
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (43 bp):
AATATTTATAAATTATATTAATTTATTCTTAATTCTATAAAAA
Found at i:16742595 original size:24 final size:24
Alignment explanation
Indices: 16742563--16742612 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
16742553 GCTAAAAGTA
16742563 AAATATTAACTTGAAATATGAGAT
1 AAATATTAACTTGAAATATGAGAT
*
16742587 AAATCTTAACTTGAAATATGAGAT
1 AAATATTAACTTGAAATATGAGAT
16742611 AA
1 AA
16742613 GAAATAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (24 bp):
AAATATTAACTTGAAATATGAGAT
Found at i:16744252 original size:18 final size:18
Alignment explanation
Indices: 16744229--16744280 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
16744219 TTTATCTAAA
16744229 TGGGCCCACACGCCTATG
1 TGGGCCCACACGCCTATG
*
16744247 TGGGCCCACACGCCCATG
1 TGGGCCCACACGCCTATG
*
16744265 TGGGCCCACACACCTA
1 TGGGCCCACACGCCTA
16744281 GATTAGCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.42, G:0.25, T:0.13
Consensus pattern (18 bp):
TGGGCCCACACGCCTATG
Found at i:16749912 original size:46 final size:47
Alignment explanation
Indices: 16749804--16749913 Score: 145
Period size: 46 Copynumber: 2.4 Consensus size: 47
16749794 CCGGGATAAG
*
16749804 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
16749851 CACAAAGTACTTCATCGGAACAAATCC-GAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
16749897 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
16749914 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 1 0.02
46 27 0.49
47 27 0.49
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:16750685 original size:4 final size:4
Alignment explanation
Indices: 16750676--16750704 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
16750666 CCCTTTTCTA
16750676 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
16750705 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:16750793 original size:14 final size:13
Alignment explanation
Indices: 16750767--16750800 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
16750757 TCATAAATCT
16750767 ATATTCAATATATA
1 ATATT-AATATATA
16750781 ATATTAATAATATA
1 ATATTAAT-ATATA
16750795 ATATTA
1 ATATTA
16750801 TTCTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTAATATATA
Found at i:16757164 original size:47 final size:47
Alignment explanation
Indices: 16757055--16757165 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
16757045 CCGGGATAAG
*
16757055 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
16757102 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
16757149 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
16757166 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:16757930 original size:4 final size:4
Alignment explanation
Indices: 16757921--16758000 Score: 70
Period size: 4 Copynumber: 18.8 Consensus size: 4
16757911 AAATTTCCCT
** * *
16757921 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTTG TAACTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C T-TTC T--TTC
*
16757974 TTTC TATC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
16758001 TTTTTAACTT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
4 53 0.87
5 3 0.05
6 5 0.08
ACGTcount: A:0.05, C:0.25, G:0.04, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:16766145 original size:96 final size:96
Alignment explanation
Indices: 16765974--16766164 Score: 276
Period size: 96 Copynumber: 2.0 Consensus size: 96
16765964 GTGTCCGAAG
* * * *
16765974 AAGTCTGTCATCCATGGGAAAGATGGAGCAGATACGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCAATGGGAAAGATGGAGCAGACAAGAAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
16766039 AAAAATCGAAGCCAAGAGGGCAAAGAGGAGC
66 AAAAACCGAAGCCAAGAGGGCAAAGAGGAGC
* *
16766070 AAGTCTGTCATCGAAT-GGAACGATGGAGTAGACAAGAAGCCCAAGAAGCTTGGTTCGAGCAAGG
1 AAGTCTGTCATC-AATGGGAAAGATGGAGCAGACAAGAAGCCCAAGAAGCTTGGTTCGAGCAAGG
* * *
16766134 GTAAAGCCGAAGCCAAGAGGGCTAAGAGGAG
65 GAAAAACCGAAGCCAAGAGGGCAAAGAGGAG
16766165 TAAAAAAAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 82 0.98
97 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.34, T:0.13
Consensus pattern (96 bp):
AAGTCTGTCATCAATGGGAAAGATGGAGCAGACAAGAAGCCCAAGAAGCTTGGTTCGAGCAAGGG
AAAAACCGAAGCCAAGAGGGCAAAGAGGAGC
Found at i:16770373 original size:5 final size:6
Alignment explanation
Indices: 16770355--16770387 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
16770345 TTATCAAAGA
16770355 TTCTTT TTCTTT TTCTTT TTCTTT TTCTCTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCT-TT TT
16770388 TGGATACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:16770420 original size:38 final size:37
Alignment explanation
Indices: 16770369--16770440 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
16770359 TTTTCTTTTT
16770369 CTTTTTCTTTTTCTCTTTTT-GGATACTATCTCTATGAA
1 CTTTTTCTTTTTCTCTTTTTGGGATA-T-TCTCTATGAA
*
16770407 CTTTTTCTTTTTCTTTTTTTGGGATATTCTCTAT
1 CTTTTTCTTTTTCTCTTTTTGGGATATTCTCTAT
16770441 CAAAGATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 7 0.22
38 20 0.62
39 5 0.16
ACGTcount: A:0.12, C:0.17, G:0.08, T:0.62
Consensus pattern (37 bp):
CTTTTTCTTTTTCTCTTTTTGGGATATTCTCTATGAA
Found at i:16770438 original size:37 final size:38
Alignment explanation
Indices: 16770369--16770460 Score: 116
Period size: 37 Copynumber: 2.4 Consensus size: 38
16770359 TTTTCTTTTT
* *
16770369 CTTTTTCTTTTTCTCTTTTTGGATACTATCTCTATGAA
1 CTTTTTCTTTTTCTTTTTTTGGATACTATCTCTATCAA
16770407 CTTTTTCTTTTTCTTTTTTTGGGATA-T-TCTCTATCAA
1 CTTTTTCTTTTTCTTTTTTT-GGATACTATCTCTATCAA
***
16770444 AGATTTCTTTTTCTTTT
1 CTTTTTCTTTTTCTTTT
16770461 GATTAATCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 23 0.48
38 20 0.42
39 5 0.10
ACGTcount: A:0.14, C:0.16, G:0.08, T:0.62
Consensus pattern (38 bp):
CTTTTTCTTTTTCTTTTTTTGGATACTATCTCTATCAA
Found at i:16773255 original size:18 final size:19
Alignment explanation
Indices: 16773226--16773278 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
16773216 TGGTGTCAGC
*
16773226 TCATTTTCATCTCT-ACCG
1 TCATCTTCATCTCTCACCG
* *
16773244 TCATCTTTATCT-TCACCT
1 TCATCTTCATCTCTCACCG
16773262 TCATCTTCATCTC-CACC
1 TCATCTTCATCTCTCACC
16773279 CTCGATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.17, C:0.38, G:0.02, T:0.43
Consensus pattern (19 bp):
TCATCTTCATCTCTCACCG
Found at i:16774667 original size:30 final size:31
Alignment explanation
Indices: 16774609--16774671 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
16774599 CTTAACAAGA
16774609 AAATGCTTCTAAAATAATAATAAAAATTAAC
1 AAATGCTTCTAAAATAATAATAAAAATTAAC
* *
16774640 AAATGCCTT-TAAAATGATAA-GAAAATTAAC
1 AAATG-CTTCTAAAATAATAATAAAAATTAAC
16774670 AA
1 AA
16774672 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.38
31 15 0.52
32 3 0.10
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (31 bp):
AAATGCTTCTAAAATAATAATAAAAATTAAC
Found at i:16779210 original size:21 final size:21
Alignment explanation
Indices: 16779186--16779247 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
16779176 TTACTCCATG
*
16779186 TTGTGGATAAACCACTCATCA
1 TTGTGGATGAACCACTCATCA
* * **
16779207 TTGTGGATGAACTACTTATTG
1 TTGTGGATGAACCACTCATCA
*
16779228 TTGTAGATGAACCACTCATC
1 TTGTGGATGAACCACTCATC
16779248 GATGTAGATA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (21 bp):
TTGTGGATGAACCACTCATCA
Found at i:16779253 original size:21 final size:21
Alignment explanation
Indices: 16779195--16779256 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
16779185 GTTGTGGATA
*
16779195 AACCACTCATC-ATTGTGGATG
1 AACCACTCATCGA-TGTAGATG
* * * *
16779216 AACTACTTATTGTTGTAGATG
1 AACCACTCATCGATGTAGATG
16779237 AACCACTCATCGATGTAGAT
1 AACCACTCATCGATGTAGAT
16779257 AAATTGCCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (21 bp):
AACCACTCATCGATGTAGATG
Found at i:16779315 original size:42 final size:41
Alignment explanation
Indices: 16779250--16779396 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 41
16779240 CACTCATCGA
* *
16779250 TGTAGAT-AAATTGCCATTGGGTTGTAGATGCACAACATATT
1 TGTAGATAAAATTGCCACTAGGTTGT-GATGCACAACATATT
* *
16779291 TGTAGATAAAATTACCACTAGGTTGTGGGTGCACAACATATT
1 TGTAGATAAAATTGCCACTAGGTTGT-GATGCACAACATATT
* * * * * *
16779333 TGTAGATAAAACTGTCAGTAAGTTGTGTATGCATAATATATT
1 TGTAGATAAAATTGCCACTAGGTTGTG-ATGCACAACATATT
*
16779375 TGTAGAT-AAATTGTCACT-GGTT
1 TGTAGATAAAATTGCCACTAGGTT
16779397 TGTGGACAAG
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
40 3 0.03
41 17 0.19
42 68 0.77
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (41 bp):
TGTAGATAAAATTGCCACTAGGTTGTGATGCACAACATATT
Found at i:16779564 original size:21 final size:21
Alignment explanation
Indices: 16779520--16779566 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16779510 ACAGTATGGG
* *
16779520 TAAACCACTCATCGATGTAGA
1 TAAACCACTCATCGATGCAAA
16779541 TAAACCACTCATCTG-TGCAAA
1 TAAACCACTCATC-GATGCAAA
16779562 TAAAC
1 TAAAC
16779567 TGCTCTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (21 bp):
TAAACCACTCATCGATGCAAA
Found at i:16780554 original size:18 final size:18
Alignment explanation
Indices: 16780512--16780545 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16780502 AGAATGAGAG
16780512 AAAAGAG-AAGAAAAGAT
1 AAAAGAGAAAGAAAAGAT
16780529 AAAAGAGAAAGAAAAGA
1 AAAAGAGAAAGAAAAGA
16780546 AATAGGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (18 bp):
AAAAGAGAAAGAAAAGAT
Found at i:16780791 original size:14 final size:15
Alignment explanation
Indices: 16780772--16780800 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16780762 GTCTAATCTT
16780772 TATATTTTAC-TGTA
1 TATATTTTACGTGTA
16780786 TATATTTTACGTGTA
1 TATATTTTACGTGTA
16780801 GTTTTTACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (15 bp):
TATATTTTACGTGTA
Found at i:16787153 original size:10 final size:10
Alignment explanation
Indices: 16787138--16787169 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
16787128 TAAATACATT
16787138 TAATTAAAGA
1 TAATTAAAGA
16787148 TAATTAAAGA
1 TAATTAAAGA
16787158 TAATTAAA-A
1 TAATTAAAGA
16787167 TAA
1 TAA
16787170 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:16787181 original size:19 final size:18
Alignment explanation
Indices: 16787157--16787200 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
16787147 ATAATTAAAG
16787157 ATAATTAAAATAAAATCCTA
1 ATAATTAAAAT--AATCCTA
*
16787177 A-AATTTAAATAATCCTA
1 ATAATTAAAATAATCCTA
16787194 ATAATTA
1 ATAATTA
16787201 TCTTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 8 0.38
20 1 0.05
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTAAAATAATCCTA
Found at i:16797791 original size:15 final size:14
Alignment explanation
Indices: 16797771--16797865 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 14
16797761 TAATTAAAAC
16797771 AAATAAATAAATAA
1 AAATAAATAAATAA
16797785 TAAATAAATTAAAATAA
1 -AAATAAA-T-AAATAA
16797802 AACA-AAATAAACT-A
1 AA-ATAAATAAA-TAA
16797816 AAATAAAATGAAATAGGA
1 AAAT-AAAT-AAATA--A
* *
16797834 AAAGAGATAGAA-AA
1 AAATAAATA-AATAA
16797848 AAATAAATAAATAA
1 AAATAAATAAATAA
16797862 AAAT
1 AAAT
16797866 TGAGTTGCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 25
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.05
14 20 0.31
15 14 0.22
16 11 0.17
17 12 0.19
18 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:16797801 original size:10 final size:10
Alignment explanation
Indices: 16797762--16797822 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
16797752 AATTTTTATT
*
16797762 AATTAAAACA
1 AATTAAAATA
16797772 AA-T-AAATA
1 AATTAAAATA
*
16797780 AATAATAAATA
1 AATTA-AAATA
16797791 AATTAAAATA
1 AATTAAAATA
**
16797801 AAACAAAATA
1 AATTAAAATA
*
16797811 AACTAAAATA
1 AATTAAAATA
16797821 AA
1 AA
16797823 ATGAAATAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 6 0.15
9 1 0.02
10 25 0.61
11 9 0.22
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (10 bp):
AATTAAAATA
Found at i:16797802 original size:5 final size:5
Alignment explanation
Indices: 16797786--16797830 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
16797776 AATAAATAAT
* * * *
16797786 AAATA AATTA AAATA AAACA AAATA AACTA AAATA AAATG AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
16797831 GGAAAAGAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:16797830 original size:20 final size:20
Alignment explanation
Indices: 16797786--16797823 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16797776 AATAAATAAT
*
16797786 AAATAAATTAAAATAAAACA
1 AAATAAACTAAAATAAAACA
16797806 AAATAAACTAAAATAAAA
1 AAATAAACTAAAATAAAA
16797824 TGAAATAGGA
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:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAACTAAAATAAAACA
Found at i:16804225 original size:10 final size:10
Alignment explanation
Indices: 16804210--16804241 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
16804200 TAAATACATT
16804210 TAATTAAAGA
1 TAATTAAAGA
16804220 TAATTAAAGA
1 TAATTAAAGA
16804230 TAATTAAA-A
1 TAATTAAAGA
16804239 TAA
1 TAA
16804242 AATCTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:16807882 original size:2 final size:2
Alignment explanation
Indices: 16807875--16807910 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16807865 TAACTTTGAC
16807875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16807911 TTGTAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16814612 original size:59 final size:59
Alignment explanation
Indices: 16814536--16814669 Score: 223
Period size: 59 Copynumber: 2.2 Consensus size: 59
16814526 CAAATTTTTA
*
16814536 AGCGAGATTTCCTCATCATTATCCCTTAAAATTATTTCCCCTTTTTTAGACGATATCTGT
1 AGCGA-ATTCCCTCATCATTATCCCTTAAAATTATTTCCCCTTTTTTAGACGATATCTGT
* *
16814596 AGCGAATTCCCTCATCATTATCCCTTAAAATTATTTCCCTTTTTTTAGATGATATCTGT
1 AGCGAATTCCCTCATCATTATCCCTTAAAATTATTTCCCCTTTTTTAGACGATATCTGT
16814655 AGCGAATTCCACTCA
1 AGCGAATTCC-CTCA
16814670 ACTATATCTC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 61 0.87
60 9 0.13
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (59 bp):
AGCGAATTCCCTCATCATTATCCCTTAAAATTATTTCCCCTTTTTTAGACGATATCTGT
Found at i:16816922 original size:5 final size:5
Alignment explanation
Indices: 16816912--16816944 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
16816902 CAATCTCAAA
16816912 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
16816945 TGATTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:16820679 original size:16 final size:17
Alignment explanation
Indices: 16820660--16820692 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16820650 TTTTATCATC
16820660 TCTTC-GTTTTCTTTTT
1 TCTTCTGTTTTCTTTTT
16820676 TCTTCTGTTTTCTTTTT
1 TCTTCTGTTTTCTTTTT
16820693 CTTTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
TCTTCTGTTTTCTTTTT
Found at i:16820934 original size:59 final size:59
Alignment explanation
Indices: 16820829--16820940 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
16820819 ATTGTTTATA
* * * *
16820829 AATTTTAAAATATTATTTATTTAAATTAGGTCTTATACTAACTATCATATTTTAAAAAC
1 AATTTTAAAATATTATTAATTTAAAATAAGTCTCATACTAACTATCATATTTTAAAAAC
* *
16820888 AATTTTAAAATATTGTTAATTTAAAATAAGTCTCATAAC-AATTATCATATTTT
1 AATTTTAAAATATTATTAATTTAAAATAAGTCTCAT-ACTAACTATCATATTTT
16820941 TAAATTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 44 0.96
60 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (59 bp):
AATTTTAAAATATTATTAATTTAAAATAAGTCTCATACTAACTATCATATTTTAAAAAC
Found at i:16830024 original size:5 final size:5
Alignment explanation
Indices: 16830014--16830045 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
16830004 TTGTGTGTTC
16830014 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16830046 TCACAGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:16830028 original size:9 final size:9
Alignment explanation
Indices: 16830014--16830044 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
16830004 TTGTGTGTTC
16830014 TTTATTTTA
1 TTTATTTTA
16830023 TTTATTTTA
1 TTTATTTTA
16830032 TTTTATTTTA
1 -TTTATTTTA
16830042 TTT
1 TTT
16830045 TTCACAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:16834648 original size:10 final size:10
Alignment explanation
Indices: 16834633--16834657 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16834623 CCATAATTAT
16834633 TTTTTAAAAA
1 TTTTTAAAAA
16834643 TTTTTAAAAA
1 TTTTTAAAAA
16834653 TTTTT
1 TTTTT
16834658 CCAAGTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:16835167 original size:49 final size:49
Alignment explanation
Indices: 16835114--16835295 Score: 265
Period size: 49 Copynumber: 3.7 Consensus size: 49
16835104 CTAGTACGCA
*
16835114 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* * * *
16835163 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACACG
* *
16835214 TAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* *
16835263 TAGTAGCCTGCACTTAGTACTACATACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
16835296 TCACAATATA
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 71 0.61
50 6 0.05
51 39 0.34
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
Found at i:16835241 original size:100 final size:100
Alignment explanation
Indices: 16835107--16835286 Score: 333
Period size: 100 Copynumber: 1.8 Consensus size: 100
16835097 AAGCTATCTA
* *
16835107 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCAGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCT
16835172 GCACTTAGTACTACACATGTGATCGAAGTTATCGG
66 GCACTTAGTACTACACATGTGATCGAAGTTATCGG
*
16835207 GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCT
16835272 GCACTTAGTACTACA
66 GCACTTAGTACTACA
16835287 TACGTGACCT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (100 bp):
GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCT
GCACTTAGTACTACACATGTGATCGAAGTTATCGG
Found at i:16839106 original size:25 final size:25
Alignment explanation
Indices: 16839078--16839125 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16839068 TTATACCATG
* * *
16839078 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
16839103 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
16839126 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:16839194 original size:20 final size:20
Alignment explanation
Indices: 16839169--16839207 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16839159 TAAATATGGT
16839169 ATGTATGAGATGCACATGAC
1 ATGTATGAGATGCACATGAC
*
16839189 ATGTATGATATGCACATGA
1 ATGTATGAGATGCACATGA
16839208 TATGCACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (20 bp):
ATGTATGAGATGCACATGAC
Found at i:16839209 original size:11 final size:11
Alignment explanation
Indices: 16839193--16839219 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16839183 CATGACATGT
16839193 ATGATATGCAC
1 ATGATATGCAC
16839204 ATGATATGCAC
1 ATGATATGCAC
16839215 ATGAT
1 ATGAT
16839220 GTAATCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:16839384 original size:25 final size:24
Alignment explanation
Indices: 16839269--16839388 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
16839259 GAGGAAGTGA
16839269 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
16839293 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
16839317 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
16839341 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
16839365 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
16839389 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
24 77 0.88
25 11 0.12
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:16845012 original size:182 final size:182
Alignment explanation
Indices: 16844700--16845068 Score: 666
Period size: 182 Copynumber: 2.0 Consensus size: 182
16844690 AAATGATAAA
* *
16844700 ATATAGTACTAAACCATACAATCAACTCAAACAACATGTACTTAGCTTAATCATGCATTTAGCCT
1 ATATAGTACTAAACCATACAATCAACTCAAACAACATGTACTTAGCTTAACCATGCATCTAGCCT
* *
16844765 TTTCATGCCTTTCTTATTCCATGCATTTCTATTTACCAAATACTATCCATACAACTAGCCATCAA
66 TTTCATGCCTTTCTTATTCCATGCATTTCCATTCACCAAATACTATCCATACAACTAGCCATCAA
*
16844830 TCAAGCAATTTACCAACTTGTAACTATGACAAAATCAAATTCATTTATTCAT
131 TCAAGCAATTTACCAACTTGTAACTATAACAAAATCAAATTCATTTATTCAT
* *
16844882 ATATGGTACTAAACCATACAATCAACTCAAACAACATGTACTTAGCTTAACCGTGCATCTAGCCT
1 ATATAGTACTAAACCATACAATCAACTCAAACAACATGTACTTAGCTTAACCATGCATCTAGCCT
16844947 TTTCATGCCTTTCTTATTCCATGCATTTCCATTCACCAAATACTATCCATACAACTAGCCATCAA
66 TTTCATGCCTTTCTTATTCCATGCATTTCCATTCACCAAATACTATCCATACAACTAGCCATCAA
*
16845012 TCAAGCAATTTGCCAACTTGTAACTATAACAAAATCAAATTCATTTATTCAT
131 TCAAGCAATTTACCAACTTGTAACTATAACAAAATCAAATTCATTTATTCAT
16845064 ATATA
1 ATATA
16845069 CCATATTAAT
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 178 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (182 bp):
ATATAGTACTAAACCATACAATCAACTCAAACAACATGTACTTAGCTTAACCATGCATCTAGCCT
TTTCATGCCTTTCTTATTCCATGCATTTCCATTCACCAAATACTATCCATACAACTAGCCATCAA
TCAAGCAATTTACCAACTTGTAACTATAACAAAATCAAATTCATTTATTCAT
Found at i:16845669 original size:22 final size:22
Alignment explanation
Indices: 16845630--16845683 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
16845620 AGAGCACCGT
*
16845630 AGTGCTAAACAAATGGAAAT-AA
1 AGTGCTAAACAAA-GGGAATCAA
* *
16845652 AGTGCTAAACAGAGGGAATCGA
1 AGTGCTAAACAAAGGGAATCAA
16845674 AGTGCTAAAC
1 AGTGCTAAAC
16845684 CTATACAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (22 bp):
AGTGCTAAACAAAGGGAATCAA
Found at i:16852869 original size:16 final size:16
Alignment explanation
Indices: 16852845--16852884 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
16852835 GGGACCCTTT
*
16852845 CTCCCTCTAAATATTA
1 CTCCATCTAAATATTA
16852861 CTCCATCTAAATATTA
1 CTCCATCTAAATATTA
16852877 CTCCATCT
1 CTCCATCT
16852885 TGGCCCACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.38
Consensus pattern (16 bp):
CTCCATCTAAATATTA
Found at i:16857941 original size:33 final size:35
Alignment explanation
Indices: 16857903--16857999 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 35
16857893 ATAGTTATAT
16857903 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
16857936 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
16857971 --AAATATTTAAAATTTATATTTTATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
16858000 AAAATATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
32 7 0.13
33 25 0.48
34 5 0.10
35 12 0.23
36 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (35 bp):
TTAAATATTTAAAATATATTTTATATATTGCTTAA
Found at i:16858197 original size:13 final size:13
Alignment explanation
Indices: 16858181--16858218 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
16858171 TAAACCAAAA
16858181 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
16858194 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
16858207 TTTTCAAAAGCA
1 TTTTCAAAAGCA
16858219 TTGCCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.19
13 13 0.62
14 4 0.19
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:16860940 original size:48 final size:48
Alignment explanation
Indices: 16860888--16860983 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
16860878 TTAATAATCT
*
16860888 ATCTCATCTAATAGTCAATTTAAGGATCTTAATGGGGATAAACATCAA
1 ATCTCATCTAATAGTCAATTTAAGGATCTTAATGGAGATAAACATCAA
*
16860936 ATCTCATCTAATAGTCAATTTAAGGATCTTAATGGATATAAACATCAA
1 ATCTCATCTAATAGTCAATTTAAGGATCTTAATGGAGATAAACATCAA
16860984 GGTATAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (48 bp):
ATCTCATCTAATAGTCAATTTAAGGATCTTAATGGAGATAAACATCAA
Found at i:16865445 original size:3 final size:3
Alignment explanation
Indices: 16865437--16865482 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16865427 GCAATTGTTC
16865437 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
16865483 TGTTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:16865491 original size:3 final size:3
Alignment explanation
Indices: 16865485--16865534 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16865475 ATCATCATTG
16865485 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16865533 TT
1 TT
16865535 TACAAACTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16870384 original size:79 final size:79
Alignment explanation
Indices: 16870288--16870476 Score: 254
Period size: 79 Copynumber: 2.4 Consensus size: 79
16870278 TTAACATATG
* * * * *
16870288 CAAATATCGTATGTTCTTCATCAATAGAGTAACGTAAAGGGTTATAAATCAAAA-CTGGTAATAA
1 CAAATATCGTATATTCTTCATCAATAGAATAACATAAAGGGTTATAAATCAAAATC-AGTAACAA
16870352 TCAATCCAACATTTT
65 TCAATCCAACATTTT
* * * * *
16870367 CAGATATCGTATATTCTTCATCAATAGAATAATATAAAGGTTTATAAATTAGAATCAGTAACAAT
1 CAAATATCGTATATTCTTCATCAATAGAATAACATAAAGGGTTATAAATCAAAATCAGTAACAAT
16870432 CAATCCAACATTTT
66 CAATCCAACATTTT
* *
16870446 CAAATATCGCATATTCTTCATCAACAGAATA
1 CAAATATCGTATATTCTTCATCAATAGAATA
16870477 GCGCAGAGGT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 95 0.99
80 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (79 bp):
CAAATATCGTATATTCTTCATCAATAGAATAACATAAAGGGTTATAAATCAAAATCAGTAACAAT
CAATCCAACATTTT
Found at i:16873553 original size:11 final size:11
Alignment explanation
Indices: 16873539--16873614 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
16873529 GATAATCATT
16873539 TTAATATTAAA
1 TTAATATTAAA
*
16873550 TTAATAAAATAATA
1 TTAAT--ATTAA-A
*
16873564 TTAATATAAAA
1 TTAATATTAAA
16873575 TTAA-ATTAAA
1 TTAATATTAAA
16873585 TTTAATATTAAA
1 -TTAATATTAAA
*
16873597 -T-CTATTAAA
1 TTAATATTAAA
*
16873606 ATAATATTA
1 TTAATATTA
16873615 TTTTTGAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
9 7 0.13
10 7 0.13
11 19 0.37
12 9 0.17
13 4 0.08
14 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:16873554 original size:20 final size:20
Alignment explanation
Indices: 16873503--16873554 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
16873493 GTCAACTATA
*
16873503 ATTAAACTTAATTACTTTAAT
1 ATTAAA-TTAATCACTTTAAT
* *
16873524 ATTATGA-TAATCATTTTAAT
1 ATTA-AATTAATCACTTTAAT
16873544 ATTAAATTAAT
1 ATTAAATTAAT
16873555 AAAATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 4 0.16
22 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAAATTAATCACTTTAAT
Found at i:16878399 original size:25 final size:25
Alignment explanation
Indices: 16878365--16878415 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16878355 GATGATGGTG
16878365 TAAGTTTTGTATTGAATATTCAAGA
1 TAAGTTTTGTATTGAATATTCAAGA
16878390 TAAGTTTTGTATTGAATATTCAAGA
1 TAAGTTTTGTATTGAATATTCAAGA
16878415 T
1 T
16878416 GAATTATGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (25 bp):
TAAGTTTTGTATTGAATATTCAAGA
Found at i:16885824 original size:23 final size:24
Alignment explanation
Indices: 16885798--16885842 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16885788 TAAGTCGTTT
*
16885798 AATAT-TATTTGAAAATTTTATAA
1 AATATATATTCGAAAATTTTATAA
*
16885821 AATATATATTCGAAATTTTTAT
1 AATATATATTCGAAAATTTTAT
16885843 TTCTCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
AATATATATTCGAAAATTTTATAA
Found at i:16886921 original size:100 final size:105
Alignment explanation
Indices: 16886800--16887039 Score: 287
Period size: 108 Copynumber: 2.3 Consensus size: 105
16886790 CTAAAAAAAA
*
16886800 CTAAAACCGAAAACCCATCTTTACTCCATGGATATC-A-GTTTC-AT-TTAATT-TATTTTTTTT
1 CTAAAACTGAAAACCCATCTTTACTCCATGGATATCAATGTTTCTATGTTAATTCTATTTTTTTT
***
16886860 AATTTCTCGAGCTTTTATGGTTCAAAAATGGC-AGACAAAG
66 AATTTCTCGAGCTTTTACAATTCAAAAATGGCGA-ACAAAG
* * * * ** *
16886900 CTAAAACTGAAAACCTATCTTTACTCCATGGGTATCAATTTCTTTTCTTTGTTTTTTCTTTTTTT
1 CTAAAACTGAAAACCCATCTTTACTCCATGGATATCAA--T-GTTTCTATGTTAATTCTATTTTT
16886965 TTTAATTTCTCGAGCTTTTACAATTCAAAAATGGCGAACAAAG
63 TTTAATTTCTCGAGCTTTTACAATTCAAAAATGGCGAACAAAG
16887008 CTAAAA-TCGAAAACCCATCTTTACTCCATGGA
1 CTAAAACT-GAAAACCCATCTTTACTCCATGGA
16887040 AAATACAAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
100 33 0.28
101 1 0.01
105 4 0.03
106 1 0.01
107 5 0.04
108 72 0.62
109 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (105 bp):
CTAAAACTGAAAACCCATCTTTACTCCATGGATATCAATGTTTCTATGTTAATTCTATTTTTTTT
AATTTCTCGAGCTTTTACAATTCAAAAATGGCGAACAAAG
Found at i:16886973 original size:16 final size:18
Alignment explanation
Indices: 16886936--16886974 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
16886926 CATGGGTATC
16886936 AATTTCTTTTCTTTGTTT
1 AATTTCTTTTCTTTGTTT
16886954 --TTTCTTTT-TTT-TTT
1 AATTTCTTTTCTTTGTTT
16886968 AATTTCT
1 AATTTCT
16886975 CGAGCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.16
15 3 0.16
16 13 0.68
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (18 bp):
AATTTCTTTTCTTTGTTT
Found at i:16887729 original size:20 final size:20
Alignment explanation
Indices: 16887704--16887781 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
16887694 AGAAAAAAAG
16887704 GGAAGAGAAAGAGGAGTTGA
1 GGAAGAGAAAGAGGAGTTGA
*
16887724 GGAAGAGAGGAAGGGAGGAAGTTATA
1 GGAAGAGA--AA--GAGG-AGTT-GA
*
16887750 GGGAAGATAAAGAGGAGTTGA
1 -GGAAGAGAAAGAGGAGTTGA
*
16887771 GGAAGGGAAAG
1 GGAAGAGAAAG
16887782 GAAGAAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
20 17 0.37
21 1 0.02
22 6 0.13
23 4 0.09
24 4 0.09
25 6 0.13
26 1 0.02
27 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (20 bp):
GGAAGAGAAAGAGGAGTTGA
Done.