Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 159 of 168
Found at i:47568206 original size:21 final size:21
Alignment explanation
Indices: 47568171--47568225 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
47568161 TAAAAATTAC
* **
47568171 TAAAAATTAT-TAAATTTTAA
1 TAAAAATTATAAAAATCGTAA
47568191 TAAAAATTATAAAAATCGTAA
1 TAAAAATTATAAAAATCGTAA
*
47568212 AAAAAATTATAAAA
1 TAAAAATTATAAAA
47568226 CATAATATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAAATTATAAAAATCGTAA
Found at i:47568244 original size:24 final size:21
Alignment explanation
Indices: 47568192--47568248 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
47568182 AAATTTTAAT
**
47568192 AAAAATTATAAAAATCGTAAA
1 AAAAATTATAAAAATAATAAA
47568213 AAAAATTATAAAACATAATATAGA
1 AAAAATTATAAAA-ATAATA-A-A
47568237 AAAAATTATAAA
1 AAAAATTATAAA
47568249 CTTTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 13 0.42
22 4 0.13
23 1 0.03
24 13 0.42
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAAATTATAAAAATAATAAA
Found at i:47571185 original size:18 final size:17
Alignment explanation
Indices: 47571159--47571192 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
47571149 TTTTTTTCTC
47571159 TCTTTTCCTTGTCCTTG
1 TCTTTTCCTTGTCCTTG
47571176 TCTTTGTCCTTGTCCTT
1 TCTTT-TCCTTGTCCTT
47571193 CTTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.29, G:0.12, T:0.59
Consensus pattern (17 bp):
TCTTTTCCTTGTCCTTG
Found at i:47573369 original size:95 final size:94
Alignment explanation
Indices: 47573184--47573510 Score: 444
Period size: 95 Copynumber: 3.4 Consensus size: 94
47573174 CGGGCAACCT
* * *
47573184 CTTGGGAAACCTACTG-TTTCCTTATGCCAAGCTACTTCAACAATGCCCCAAATAGAAAGATAAT
1 CTTGGGAAACCTACTGCTTT-CTTATGCCAAG---C-T-AACAATTCCCCGAATAGGAAGAT-A-
47573248 TTCAAGAAATGCTCTTTTGATCAATAATTCTAGCTCAGAAA
58 ---AAGAAA-GCTCTTTTGATCAATAATTCTAGCTCAGAAA
47573289 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAACG
1 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAA-G
47573354 CTCTTTTGATCAATAATTCTAGCTCAGAAA
65 CTCTTTTGATCAATAATTCTAGCTCAGAAA
*
47573384 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAACG-AAGC
1 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAGC
*
47573448 TCTTTTGATCAATAATTCTCGCTCAGAAA
66 TCTTTTGATCAATAATTCTAGCTCAGAAA
* *
47573477 CTTAGGG-AACCTACTGTTTTCTTATTCCAAGCTA
1 CTT-GGGAAACCTACTGCTTTCTTATGCCAAGCTA
47573511 CTTCAACAAT
Statistics
Matches: 212, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
93 58 0.27
94 5 0.02
95 96 0.45
99 1 0.00
100 20 0.09
101 1 0.00
102 1 0.00
105 27 0.13
106 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (94 bp):
CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAGC
TCTTTTGATCAATAATTCTAGCTCAGAAA
Found at i:47575488 original size:19 final size:19
Alignment explanation
Indices: 47575466--47575517 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
47575456 AAATGATATT
*
47575466 AAATTTATAAAAATTTAGA
1 AAATTTATAAAAATCTAGA
* *
47575485 AAATATAT-ATAATCTAGA
1 AAATTTATAAAAATCTAGA
47575503 AATATATTATAAAAA
1 AA-AT-TTATAAAAA
47575518 ATAAAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 10 0.40
19 9 0.36
20 3 0.12
21 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATTTATAAAAATCTAGA
Found at i:47586447 original size:39 final size:39
Alignment explanation
Indices: 47586393--47586469 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
47586383 CAAAGACATC
47586393 CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGTT
1 CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGTT
* * * *
47586432 CACCTCATGCGTTTCGTAATGATTGTTAGATGATAAGT
1 CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGT
47586470 CTAACACGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (39 bp):
CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGTT
Found at i:47594574 original size:2 final size:2
Alignment explanation
Indices: 47594567--47594606 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47594557 TTCTTTCCAC
47594567 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
47594607 TAAAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47599480 original size:87 final size:87
Alignment explanation
Indices: 47599378--47599553 Score: 192
Period size: 87 Copynumber: 2.0 Consensus size: 87
47599368 CTTTTTTTTT
* * * *
47599378 TTTTTGCACTCAATTGAACAATTTAACTTTCAAAATGAATCAAAAAAACCCTCAAACTTCTTCAA
1 TTTTTCCACTCAATTGAACAATTGAACTTTCAAAACGAATCAAAAAAACCCTCAAAATTCTTCAA
47599443 AACAAGCAATTAAGCCCCTG-TC
66 AA-AAGCAATTAAGCCCCTGCTC
* *** * * * * * * *
47599465 TTTTTCCACTTAATTGGGTACTTGAACTTTTAAAACGCATTAATAAGACCCTCAAAATTTTTCAA
1 TTTTTCCACTCAATTGAACAATTGAACTTTCAAAACGAATCAAAAAAACCCTCAAAATTCTTCAA
*
47599530 AAAAGCAATTAAGCCTCTGCTC
66 AAAAGCAATTAAGCCCCTGCTC
47599552 TT
1 TT
47599554 ATTAAAAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
86 16 0.22
87 56 0.78
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (87 bp):
TTTTTCCACTCAATTGAACAATTGAACTTTCAAAACGAATCAAAAAAACCCTCAAAATTCTTCAA
AAAAGCAATTAAGCCCCTGCTC
Found at i:47599598 original size:19 final size:19
Alignment explanation
Indices: 47599552--47599601 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
47599542 GCCTCTGCTC
** *
47599552 TTATTAAAAATTAGAAATA
1 TTATTAAATTTTAGAAAAA
*
47599571 -TAATAAATTTTAGAAAAA
1 TTATTAAATTTTAGAAAAA
47599589 TTATTAAATTTTA
1 TTATTAAATTTTA
47599602 ATAAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TTATTAAATTTTAGAAAAA
Found at i:47599617 original size:20 final size:20
Alignment explanation
Indices: 47599566--47599618 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
47599556 TAAAAATTAG
47599566 AAATATAATAAATTTTAGAA
1 AAATATAATAAATTTTAGAA
*
47599586 AAAT-TATTAAATTTTA-ATA
1 AAATATAATAAATTTTAGA-A
*
47599605 AAATATAAAAAATT
1 AAATATAATAAATT
47599619 AAAATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.04
19 16 0.57
20 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATATAATAAATTTTAGAA
Found at i:47599632 original size:17 final size:17
Alignment explanation
Indices: 47599610--47599652 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
47599600 TAATAAAATA
47599610 TAAAAAATTAAAATTTAT
1 TAAAAAA-TAAAATTTAT
* *
47599628 TAAAAAATAGAATTTTT
1 TAAAAAATAAAATTTAT
47599645 TAATAAAA
1 TAA-AAAA
47599653 ATTGTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAAAATAAAATTTAT
Found at i:47599793 original size:10 final size:10
Alignment explanation
Indices: 47599778--47599803 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47599768 AAATGATAAT
47599778 AAAAATAAAA
1 AAAAATAAAA
47599788 AAAAATAAAA
1 AAAAATAAAA
47599798 AAAAAT
1 AAAAAT
47599804 CAAAGTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:47599978 original size:19 final size:19
Alignment explanation
Indices: 47599910--47599990 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
47599900 TTCTTACGAC
*
47599910 TTTATAAAATTTTATAATT
1 TTTATAAAATTTTACAATT
* *
47599929 TTT-T-ATATTTCTA-TATAT
1 TTTATAAAATTT-TACAAT-T
** *
47599947 TTTATAATTTTTTACGATT
1 TTTATAAAATTTTACAATT
47599966 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTACAATT
*
47599985 TATATA
1 TTTATA
47599991 TATTACAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 7 0.14
18 7 0.14
19 28 0.57
20 7 0.14
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTATAAAATTTTACAATT
Found at i:47599998 original size:16 final size:16
Alignment explanation
Indices: 47599977--47600009 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47599967 TTATAAAATT
47599977 TTACAATTTATATATA
1 TTACAATTTATATATA
47599993 TTACAATTTATATATA
1 TTACAATTTATATATA
47600009 T
1 T
47600010 ATATTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACAATTTATATATA
Found at i:47600575 original size:23 final size:24
Alignment explanation
Indices: 47600530--47600575 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
47600520 TTTATTAAAA
*
47600530 TTTGATATGAAAGTTAAACATTGC
1 TTTGATATGAAAGGTAAACATTGC
47600554 TTTGAT-TGAAATGGTAAA-ATTG
1 TTTGATATGAAA-GGTAAACATTG
47600576 AGAGATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATGAAAGGTAAACATTGC
Found at i:47601902 original size:2 final size:2
Alignment explanation
Indices: 47601895--47601933 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
47601885 ATCAATTAGC
47601895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47601934 ACACATTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47603202 original size:19 final size:19
Alignment explanation
Indices: 47603164--47603202 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
47603154 TATGTTTTTT
*
47603164 ATTTTATTTTAAAATTAAA
1 ATTTTATTTTAAAATAAAA
47603183 ATTTTATATTT-AAATAAAA
1 ATTTTAT-TTTAAAATAAAA
47603202 A
1 A
47603203 ATGCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTATTTTAAAATAAAA
Found at i:47603258 original size:2 final size:2
Alignment explanation
Indices: 47603253--47603277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47603243 TAAAAGAGGA
47603253 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 A
47603278 AACAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47605583 original size:18 final size:19
Alignment explanation
Indices: 47605550--47605586 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
47605540 GTTCTTTTTT
*
47605550 GTGTTTGGGTGATGGGAAA
1 GTGTCTGGGTGATGGGAAA
47605569 GTGTCTGGG-GATGGGAAA
1 GTGTCTGGGTGATGGGAAA
47605587 ATGATGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.27
Consensus pattern (19 bp):
GTGTCTGGGTGATGGGAAA
Found at i:47607217 original size:3 final size:3
Alignment explanation
Indices: 47607173--47607200 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47607163 ATTTAAAAAT
47607173 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47607201 CAAATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47611140 original size:17 final size:17
Alignment explanation
Indices: 47611113--47611159 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
47611103 ATATTATCTC
47611113 AATTTTT-AATTTTTAT
1 AATTTTTCAATTTTTAT
*
47611129 AATTTTTCAATTTTTGT
1 AATTTTTCAATTTTTAT
*
47611146 GATTTTTCGAATTT
1 AATTTTTC-AATTT
47611160 CTCTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 15 0.56
18 5 0.19
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (17 bp):
AATTTTTCAATTTTTAT
Found at i:47616379 original size:18 final size:17
Alignment explanation
Indices: 47616356--47616392 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
47616346 TTAAATTTGT
47616356 TTTAAAATTAATTTAAAA
1 TTTAAAATTAA-TTAAAA
*
47616374 TTTAAAATTTATTAAAA
1 TTTAAAATTAATTAAAA
47616391 TT
1 TT
47616393 GATTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAAATTAATTAAAA
Found at i:47619352 original size:31 final size:31
Alignment explanation
Indices: 47619215--47619352 Score: 92
Period size: 31 Copynumber: 4.6 Consensus size: 31
47619205 ACGGTAAATT
* *
47619215 TTTTAAAAAATTTTATT-AGCCTTTCAAAAA
1 TTTTAAAAAATTTTATTAAGCCTTCCAAAAG
* ** **
47619245 TTTTAGAATTTTTTATTAAGCC--CCTCAA-
1 TTTTAAAAAATTTTATTAAGCCTTCCAAAAG
* * *
47619273 -TTTAAAAAATTTAATTAAATCCCT-CAAAAG
1 TTTTAAAAAATTTTATT-AAGCCTTCCAAAAG
* *
47619303 TTTT-GATAATTCTTATTAAGCCTTCCAAAAG
1 TTTTAAAAAATT-TTATTAAGCCTTCCAAAAG
*
47619334 TTTTAAAAAATTTAATTAA
1 TTTTAAAAAATTTTATTAA
47619353 ACCCTAAAAA
Statistics
Matches: 78, Mismatches: 21, Indels: 17
0.67 0.18 0.15
Matches are distributed among these distances:
27 12 0.15
28 4 0.05
29 6 0.08
30 24 0.31
31 27 0.35
32 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (31 bp):
TTTTAAAAAATTTTATTAAGCCTTCCAAAAG
Found at i:47620854 original size:17 final size:17
Alignment explanation
Indices: 47620820--47620854 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47620810 TATTTTTTAG
*
47620820 ATTAATTTTTATTTAAA
1 ATTAATTTTTATTAAAA
47620837 ATTAATTTTTATTAAAA
1 ATTAATTTTTATTAAAA
47620854 A
1 A
47620855 AATATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAATTTTTATTAAAA
Found at i:47620992 original size:38 final size:39
Alignment explanation
Indices: 47620932--47621018 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 39
47620922 TTAAAAATAT
* * *
47620932 TTATATTAAAAAACTACCATAAATATTATAAATTTTTTA
1 TTATATTAAAAAACTACAATAAATATAATAAATATTTTA
47620971 TTATATT-AAAAA-TACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACTAC-AATAAATATAATAAATATTTTA
*
47621009 TTTTATTAAA
1 TTATATTAAA
47621019 TGAACTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 3 0.07
38 30 0.71
39 9 0.21
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (39 bp):
TTATATTAAAAAACTACAATAAATATAATAAATATTTTA
Found at i:47621585 original size:14 final size:14
Alignment explanation
Indices: 47621566--47621594 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47621556 TTAACAATAA
47621566 AACAACAAAATAGT
1 AACAACAAAATAGT
47621580 AACAACAAAATAGT
1 AACAACAAAATAGT
47621594 A
1 A
47621595 GTAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AACAACAAAATAGT
Found at i:47621637 original size:11 final size:11
Alignment explanation
Indices: 47621621--47621669 Score: 80
Period size: 11 Copynumber: 4.5 Consensus size: 11
47621611 ATGGTAGCAA
47621621 AACAACAACAT
1 AACAACAACAT
47621632 AACAACAACAT
1 AACAACAACAT
* *
47621643 AACAATAACAA
1 AACAACAACAT
47621654 AACAACAACAT
1 AACAACAACAT
47621665 AACAA
1 AACAA
47621670 TAGTAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.67, C:0.24, G:0.00, T:0.08
Consensus pattern (11 bp):
AACAACAACAT
Found at i:47628399 original size:25 final size:24
Alignment explanation
Indices: 47628363--47628411 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
47628353 TTAAAAATAA
47628363 AAATGAACATGT-GAATTAAGTGTT
1 AAATGAACATGTAG-ATTAAGTGTT
*
47628387 AAATGATATATGTAGATTAAGTGTT
1 AAATGA-ACATGTAGATTAAGTGTT
47628412 TATGTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 15 0.68
26 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (24 bp):
AAATGAACATGTAGATTAAGTGTT
Found at i:47631111 original size:15 final size:15
Alignment explanation
Indices: 47631083--47631124 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
47631073 ATATATGCAT
* *
47631083 ACATACACATATATA
1 ACATACATACATATA
*
47631098 ATATACATACATATA
1 ACATACATACATATA
47631113 ACATACATACAT
1 ACATACATACAT
47631125 TTTTTATGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (15 bp):
ACATACATACATATA
Found at i:47636548 original size:6 final size:6
Alignment explanation
Indices: 47636539--47636571 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47636529 AGGAGGAGGT
*
47636539 GGTGAC GGTGAC GGTGAC GGTGAC GGTGGC GGT
1 GGTGAC GGTGAC GGTGAC GGTGAC GGTGAC GGT
47636572 TCGGTATTTC
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:0.12, C:0.15, G:0.55, T:0.18
Consensus pattern (6 bp):
GGTGAC
Found at i:47638076 original size:6 final size:7
Alignment explanation
Indices: 47638059--47638083 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47638049 GATACTTCCA
47638059 AAAAAAT
1 AAAAAAT
47638066 AAAAAAT
1 AAAAAAT
47638073 AAAAAAT
1 AAAAAAT
47638080 AAAA
1 AAAA
47638084 TTTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:47638752 original size:34 final size:35
Alignment explanation
Indices: 47638686--47638752 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
47638676 TTTACAATAA
* *
47638686 TTTTTATTTTATTTTAATTCTTGTTTTTTTTTTTG
1 TTTTTATTTCATTTTAATTCTTGTTTTATTTTTTG
47638721 TTTTT-TTTCATTTTAATT-TTGTTTCTATTTTT
1 TTTTTATTTCATTTTAATTCTTGTTT-TATTTTT
47638753 AATATTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 18 0.62
35 5 0.17
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.79
Consensus pattern (35 bp):
TTTTTATTTCATTTTAATTCTTGTTTTATTTTTTG
Found at i:47639500 original size:32 final size:32
Alignment explanation
Indices: 47639464--47639527 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
47639454 GAGAAAGTTA
*
47639464 ATTGGATACATATAAAATTACTTGCTAAATTT
1 ATTGGATACATATAAAATTACTTCCTAAATTT
* *
47639496 ATTGGTTACGTATAAAATTACTTCCTAAATTT
1 ATTGGATACATATAAAATTACTTCCTAAATTT
47639528 TACTGAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (32 bp):
ATTGGATACATATAAAATTACTTCCTAAATTT
Found at i:47640196 original size:20 final size:20
Alignment explanation
Indices: 47640173--47640210 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47640163 GGTCTTTAGT
* *
47640173 GGCCTTTGTCTATACTTGAG
1 GGCCTTTGCCTAGACTTGAG
47640193 GGCCTTTGCCTAGACTTG
1 GGCCTTTGCCTAGACTTG
47640211 GGTGGTCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (20 bp):
GGCCTTTGCCTAGACTTGAG
Found at i:47648611 original size:22 final size:22
Alignment explanation
Indices: 47648557--47648599 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
47648547 TTTATTGTTC
47648557 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
47648579 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
47648600 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:47654760 original size:20 final size:20
Alignment explanation
Indices: 47654733--47654788 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
47654723 CAAAATCTTG
47654733 AACC-TGAACCCTAAACCCA
1 AACCTTGAACCCTAAACCCA
* * * *
47654752 AACCTTGAACTCGAACCCCG
1 AACCTTGAACCCTAAACCCA
*
47654772 AACCTTAAACCCTAAAC
1 AACCTTGAACCCTAAAC
47654789 TTGAATTCGA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.14
Consensus pattern (20 bp):
AACCTTGAACCCTAAACCCA
Found at i:47654775 original size:26 final size:27
Alignment explanation
Indices: 47654698--47654769 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
47654688 CTGAATCCTG
*
47654698 AACCTTGAACTCCAAACCCAAAACCCAA
1 AACCTTGAACT-CGAACCCAAAACCCAA
* *
47654726 AATCTTGAAC-CTGAACCCTAAACCC-A
1 AACCTTGAACTC-GAACCCAAAACCCAA
47654752 AACCTTGAACTCGAACCC
1 AACCTTGAACTCGAACCC
47654770 CGAACCTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 17 0.45
27 12 0.32
28 9 0.24
ACGTcount: A:0.40, C:0.38, G:0.07, T:0.15
Consensus pattern (27 bp):
AACCTTGAACTCGAACCCAAAACCCAA
Found at i:47659086 original size:3 final size:3
Alignment explanation
Indices: 47659078--47659116 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
47659068 AGATGACCGA
47659078 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47659117 TGGGTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47659094 original size:29 final size:29
Alignment explanation
Indices: 47659034--47659095 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
47659024 AAAATTCAAT
*
47659034 TAATTGAGTGACCAAAATAAGAAAAATGA
1 TAATTGAGTGACCAAAATAAGAAAAATAA
* * *
47659063 TAATT-AGATGACCGAAATAATAATAATAA
1 TAATTGAG-TGACCAAAATAAGAAAAATAA
47659092 TAAT
1 TAAT
47659096 AATAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (29 bp):
TAATTGAGTGACCAAAATAAGAAAAATAA
Found at i:47669827 original size:16 final size:16
Alignment explanation
Indices: 47669806--47669859 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
47669796 TTTGGTTCAG
*
47669806 TGTAATAGAATATAGC
1 TGTAATAGAATAAAGC
* *
47669822 TGTAATTGAATAGAGC
1 TGTAATAGAATAAAGC
* *
47669838 TGTAATGGAATAAAAC
1 TGTAATAGAATAAAGC
47669854 TGTAAT
1 TGTAAT
47669860 TAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (16 bp):
TGTAATAGAATAAAGC
Found at i:47670115 original size:58 final size:58
Alignment explanation
Indices: 47670036--47670159 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
47670026 TTTTAATAAG
* *
47670036 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
47670094 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
47670152 ATTATTAT
1 ATTATTAT
47670160 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 37 0.63
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:47672288 original size:36 final size:36
Alignment explanation
Indices: 47672219--47672350 Score: 156
Period size: 36 Copynumber: 3.6 Consensus size: 36
47672209 CTACCTTCAT
** *
47672219 CCGATTTGCTTCCTTGTTTCTTTGCTTTTCTTTTCTG
1 CCGATTTGC-TCCCAGTTTCTTTTCTTTTCTTTTCTG
*
47672256 CCGATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTG
1 CCGATTTGCTCCCAGTTTCTTTTCTTTTCTTTTCTG
* *
47672292 CCGATTTGCTCCCCCCGTTTCTTTTCTTTTCTTTTTCGG
1 CCGATTTGCT--CCCAGTTTCTTTTCTTTTC-TTTTCTG
* *
47672331 CTGATTTGCTCACAGTTTCT
1 CCGATTTGCTCCCAGTTTCT
47672351 GCCGATTTGC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
36 33 0.40
37 17 0.21
38 17 0.21
39 15 0.18
ACGTcount: A:0.06, C:0.27, G:0.13, T:0.54
Consensus pattern (36 bp):
CCGATTTGCTCCCAGTTTCTTTTCTTTTCTTTTCTG
Found at i:47673450 original size:71 final size:69
Alignment explanation
Indices: 47673364--47673505 Score: 189
Period size: 69 Copynumber: 2.0 Consensus size: 69
47673354 TTTGTTGGTT
* * *
47673364 TGTTCTGGACATTGTTTTGATAGTCTGCTGGAAAATGTTAT-TTTAGTTTGTTAGTGAGTAGAAG
1 TGTTCTGGACATTGTTTTGATAGTCTGCTGG-AAAT-TGATCTTGA-TTTGTTAGTCAGTAGAAG
47673428 ATGAAAC
63 ATGAAAC
* *
47673435 TGTTCTGG-CAGTTGTTTTGATTGTCTGCTGGAAATTGATCTTGATTTGTTAGTCAGTAGAATAT
1 TGTTCTGGACA-TTGTTTTGATAGTCTGCTGGAAATTGATCTTGATTTGTTAGTCAGTAGAAGAT
47673499 GAAAC
65 GAAAC
47673504 TG
1 TG
47673506 GAACTTTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
69 28 0.44
70 9 0.14
71 27 0.42
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (69 bp):
TGTTCTGGACATTGTTTTGATAGTCTGCTGGAAATTGATCTTGATTTGTTAGTCAGTAGAAGATG
AAAC
Found at i:47674668 original size:37 final size:36
Alignment explanation
Indices: 47674625--47674708 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
47674615 ATCATAAATA
47674625 AATAAACTAATCAATGTTCA-AACTTTGAACATGCTTT
1 AATAAACTAATCAATG-TCAGAA-TTTGAACATGCTTT
* *
47674662 ATTAAACTAATCAATGTGAGGAATTTGAACATGCTTT
1 AATAAACTAATCAATGTCA-GAATTTGAACATGCTTT
*
47674699 AATGAACTAA
1 AATAAACTAA
47674709 CTGTTAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 2 0.05
37 37 0.90
38 2 0.05
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (36 bp):
AATAAACTAATCAATGTCAGAATTTGAACATGCTTT
Found at i:47674833 original size:22 final size:18
Alignment explanation
Indices: 47674789--47674830 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
47674779 AATTTTAGGT
47674789 CAATTATACATACACCAA
1 CAATTATACATACACCAA
47674807 CAATTATACATACACCAA
1 CAATTATACATACACCAA
47674825 CAATTA
1 CAATTA
47674831 ATTTTAGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (18 bp):
CAATTATACATACACCAA
Found at i:47674844 original size:33 final size:33
Alignment explanation
Indices: 47674807--47674883 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
47674797 CATACACCAA
47674807 CAATTATACATACACCAACAATTAATTTTAGGT
1 CAATTATACATACACCAACAATTAATTTTAGGT
47674840 CAATTATACATACACCAACAATTAATTTTAGGT
1 CAATTATACATACACCAACAATTAATTTTAGGT
47674873 CAATTATACAT
1 CAATTATACAT
47674884 GCTTTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (33 bp):
CAATTATACATACACCAACAATTAATTTTAGGT
Found at i:47674845 original size:51 final size:51
Alignment explanation
Indices: 47674760--47674863 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
47674750 AAACTTGAAG
* *
47674760 TATATATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAAT
1 TATACATACACCAACAATTAATTTTAGGTCAATTATACATACACCAACAAT
47674811 TATACATACACCAACAATTAATTTTAGGTCAATTATACATACACCAACAAT
1 TATACATACACCAACAATTAATTTTAGGTCAATTATACATACACCAACAAT
47674862 TA
1 TA
47674864 ATTTTAGGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (51 bp):
TATACATACACCAACAATTAATTTTAGGTCAATTATACATACACCAACAAT
Found at i:47678117 original size:92 final size:91
Alignment explanation
Indices: 47677953--47678162 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 91
47677943 TTGATTTTAG
* * *
47677953 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
47678018 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
47678045 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTG
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
47678109 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
47678137 CAAATTCATAAAATATAATTTATTAT
1 TAAATTCATATAAGAAAATTTATTAT
47678163 TTTAAATTAT
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:47678292 original size:66 final size:63
Alignment explanation
Indices: 47678215--47678545 Score: 238
Period size: 66 Copynumber: 5.4 Consensus size: 63
47678205 AAATATATTT
47678215 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
47678280 G
63 G
* * * * **
47678281 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
47678335 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
47678399 AG
62 AG
* * * * **
47678401 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
47678455 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
47678519 AG
62 AG
* *
47678521 AATATTAATTAGTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
47678546 AAATTATATA
Statistics
Matches: 202, Mismatches: 30, Indels: 67
0.68 0.10 0.22
Matches are distributed among these distances:
53 10 0.05
54 26 0.13
55 10 0.05
56 8 0.04
57 6 0.03
58 2 0.01
59 20 0.10
60 16 0.08
61 20 0.10
62 2 0.01
63 6 0.03
64 8 0.04
65 14 0.07
66 44 0.22
67 10 0.05
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:47678315 original size:120 final size:120
Alignment explanation
Indices: 47678177--47678589 Score: 733
Period size: 120 Copynumber: 3.4 Consensus size: 120
47678167 AATTATTTTA
* * *
47678177 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
47678239 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
47678297 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
47678362 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
47678417 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
47678482 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAGTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
47678537 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
47678590 TAAATATGAT
Statistics
Matches: 285, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 6 0.02
120 277 0.97
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:47678337 original size:15 final size:15
Alignment explanation
Indices: 47678302--47678353 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
47678292 TTAAGAATTT
*
47678302 TATTAAATTAT-ATA
1 TATTTAATTATAATA
47678316 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
47678330 TATTTAATAATAAT-
1 TATTTAATTATAATA
47678344 TATGTTAATT
1 TAT-TTAATT
47678354 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:47678457 original size:15 final size:15
Alignment explanation
Indices: 47678422--47678473 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
47678412 TTAAGAATTT
*
47678422 TATTAAATTAT-ATA
1 TATTTAATTATAATA
47678436 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
47678450 TATTTAATAATAAT-
1 TATTTAATTATAATA
47678464 TATGTTAATT
1 TAT-TTAATT
47678474 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:47678572 original size:16 final size:16
Alignment explanation
Indices: 47678551--47678592 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
47678541 TTATTAAATT
*
47678551 ATATATTTTAATTATA
1 ATATATTTTAATAATA
47678567 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
47678582 AT-TATGTTTAA
1 ATATAT-TTTAA
47678593 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:47678577 original size:15 final size:15
Alignment explanation
Indices: 47678542--47678583 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47678532 GTAAGAATTT
*
47678542 TATTAAATTAT-ATA
1 TATTTAATTATAATA
47678556 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
47678570 TATTTAATAATAAT
1 TATTTAATTATAAT
47678584 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:47678723 original size:18 final size:17
Alignment explanation
Indices: 47678695--47678729 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
47678685 ATTATTAATA
*
47678695 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
47678712 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
47678730 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:47678812 original size:157 final size:157
Alignment explanation
Indices: 47678526--47678842 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
47678516 ATAAGAATAT
*
47678526 TAATTAGTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTAGTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
47678591 AAATATGATTAAATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
47678656 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
* *
47678683 TAATTATTAATAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTAGTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
47678748 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
47678813 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
47678840 TAA
1 TAA
47678843 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTAGTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:47678988 original size:16 final size:16
Alignment explanation
Indices: 47678967--47679001 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
47678957 ATTTGCTATA
47678967 ACACCTCTAATCCAAT
1 ACACCTCTAATCCAAT
47678983 ACACCTCTAATCCAAT
1 ACACCTCTAATCCAAT
47678999 ACA
1 ACA
47679002 GCGAACCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (16 bp):
ACACCTCTAATCCAAT
Found at i:47680208 original size:24 final size:25
Alignment explanation
Indices: 47680163--47680210 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
47680153 GAAGAAAAGA
*
47680163 GTTAACAGAAAAAATGGCAATAAAT
1 GTTAACAGAAAAAATGGAAATAAAT
47680188 GTTAA-AGAAAAAA-GGAAAATAAA
1 GTTAACAGAAAAAATGG-AAATAAA
47680211 GACACAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.67
25 5 0.24
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (25 bp):
GTTAACAGAAAAAATGGAAATAAAT
Found at i:47680358 original size:23 final size:25
Alignment explanation
Indices: 47680309--47680369 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 25
47680299 AAATGTTGAG
47680309 GAAGAAATCTGCTGAAGTGAAAAAGTT
1 GAAGAAATCTGCT--AGTGAAAAAGTT
*
47680336 GAAGAAATCTGCT-G-GAAAGAGTT
1 GAAGAAATCTGCTAGTGAAAAAGTT
47680359 GAAGAAATCTG
1 GAAGAAATCTG
47680370 AGGGAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 19 0.58
24 1 0.03
27 13 0.39
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.21
Consensus pattern (25 bp):
GAAGAAATCTGCTAGTGAAAAAGTT
Found at i:47680375 original size:23 final size:23
Alignment explanation
Indices: 47680327--47680375 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
47680317 CTGCTGAAGT
**
47680327 GAAAAAGTTGAAGAAATCTGCTG
1 GAAAAAGTTGAAGAAATCTGAGG
*
47680350 GAAAGAGTTGAAGAAATCTGAGG
1 GAAAAAGTTGAAGAAATCTGAGG
47680373 GAA
1 GAA
47680376 TAAACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.31, T:0.18
Consensus pattern (23 bp):
GAAAAAGTTGAAGAAATCTGAGG
Found at i:47684117 original size:2 final size:2
Alignment explanation
Indices: 47684110--47684173 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
47684100 GATGATTGAA
47684110 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
47684152 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
47684174 TGGATTGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47693772 original size:2 final size:2
Alignment explanation
Indices: 47693761--47693804 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
47693751 TACATAGATC
47693761 AT AT -T 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
47693802 AT A
1 AT A
47693805 ATAATAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47704068 original size:21 final size:21
Alignment explanation
Indices: 47704044--47704084 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47704034 TATATATGTT
*
47704044 TAATTAAGC-TTTAGTTAATCG
1 TAATTAA-CTTTTAATTAATCG
47704065 TAATTAACTTTTAATTAATC
1 TAATTAACTTTTAATTAATC
47704085 TTTTCTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATTAACTTTTAATTAATCG
Found at i:47707116 original size:14 final size:14
Alignment explanation
Indices: 47707093--47707123 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47707083 TGCCGCATTC
*
47707093 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
47707107 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
47707121 TTA
1 TTA
47707124 AAACAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:47711590 original size:2 final size:2
Alignment explanation
Indices: 47711583--47711618 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47711573 TTAATAAAAG
47711583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47711619 AACTATGACA
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):
TA
Found at i:47712680 original size:26 final size:26
Alignment explanation
Indices: 47712638--47712693 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
47712628 GACTATATAA
* **
47712638 AAAATTTCTATAAATAAAAATTGTAT
1 AAAATTACTATAAATAAAAATAATAT
47712664 AAAATTACTA-AATATAAAAATAATAT
1 AAAATTACTATAA-ATAAAAATAATAT
47712690 AAAA
1 AAAA
47712694 AAAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATTACTATAAATAAAAATAATAT
Found at i:47717689 original size:31 final size:31
Alignment explanation
Indices: 47717645--47717725 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
47717635 GGGGGATGAG
* *
47717645 TAAATTTACAATTT-AGTCATTTAATTATTAA
1 TAAATTTATAATTTGA-TCACTTAATTATTAA
*
47717676 TAATTTTATAATTTGATCACTTAATTATTAA
1 TAAATTTATAATTTGATCACTTAATTATTAA
*
47717707 TAAATTTGTAATTTGATCA
1 TAAATTTATAATTTGATCA
47717726 TGCTTAGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (31 bp):
TAAATTTATAATTTGATCACTTAATTATTAA
Found at i:47722917 original size:23 final size:23
Alignment explanation
Indices: 47722890--47722944 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
47722880 AGCTTTGCCG
47722890 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* *
47722913 ATCAGACACTTTATGTGTTGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* *
47722936 TTTAGGCAC
1 ATCAGGCAC
47722945 CTCGTGTGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:47724054 original size:18 final size:17
Alignment explanation
Indices: 47724021--47724059 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
47724011 TTGTATAAAT
47724021 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
47724039 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
47724056 TGTG
1 TGTG
47724060 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:47725874 original size:21 final size:21
Alignment explanation
Indices: 47725839--47725886 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
47725829 CTTCAATCCC
*
47725839 CAATTTCAAATTTTATATTTT
1 CAATTTCAAATTTTAAATTTT
47725860 CAATCTTCAAA-TTTAAATTTT
1 CAAT-TTCAAATTTTAAATTTT
47725881 CAATTT
1 CAATTT
47725887 TTAATTTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.52
Consensus pattern (21 bp):
CAATTTCAAATTTTAAATTTT
Found at i:47726008 original size:38 final size:38
Alignment explanation
Indices: 47725960--47726041 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
47725950 CTCTTTGATT
47725960 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
1 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
47725998 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
1 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
47726036 TTATTC
1 TTATTC
47726042 GTTTGGATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.46
Consensus pattern (38 bp):
TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
Found at i:47729089 original size:22 final size:22
Alignment explanation
Indices: 47729048--47729089 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
47729038 TTAGAATTAT
*
47729048 AATTTTAATTATGTTTAATTGA
1 AATTTTAATTATGTTCAATTGA
47729070 AATTTTAATTAT-TTACAATT
1 AATTTTAATTATGTT-CAATT
47729090 CAATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTTAATTATGTTCAATTGA
Found at i:47732401 original size:2 final size:2
Alignment explanation
Indices: 47732390--47732437 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
47732380 TCACAACCAT
47732390 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
47732431 CA CA CA C
1 CA CA CA C
47732438 TCATTCCCCG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:47734676 original size:42 final size:42
Alignment explanation
Indices: 47734624--47734723 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
47734614 GCTCTCGGTA
**
47734624 TCGCACACTTAGTGCCTGTTATACAACATCACCATTTTAATT
1 TCGCACACTTAGTGCCCATTATACAACATCACCATTTTAATT
* **
47734666 TCGCACACTTAGTGCCCATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATACAACATCACCATTTTAATT
47734708 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
47734724 GTTCATATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATACAACATCACCATTTTAATT
Found at i:47735631 original size:16 final size:17
Alignment explanation
Indices: 47735598--47735631 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47735588 TATAAAGTTA
*
47735598 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
47735615 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
47735631 A
1 A
47735632 ATAATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:47738846 original size:43 final size:44
Alignment explanation
Indices: 47738785--47738893 Score: 193
Period size: 44 Copynumber: 2.5 Consensus size: 44
47738775 TTTGAGTACT
47738785 TCTGATCAGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
47738828 TCTGATCGGTTACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
47738872 TCTGATCAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
47738894 ATGTGATCCG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 27 0.44
44 34 0.56
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:47744897 original size:45 final size:45
Alignment explanation
Indices: 47744847--47744936 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
47744837 CTTTTGAGAT
47744847 TTTGATCATTCTCTTTTTAAGCTCTTTAACCCTCATTATTACGTA
1 TTTGATCATTCTCTTTTTAAGCTCTTTAACCCTCATTATTACGTA
47744892 TTTGATCATTCTCTTTTTAAGCTCTTTAACCCTCATTATTACGTA
1 TTTGATCATTCTCTTTTTAAGCTCTTTAACCCTCATTATTACGTA
47744937 AAATTTCTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (45 bp):
TTTGATCATTCTCTTTTTAAGCTCTTTAACCCTCATTATTACGTA
Found at i:47754475 original size:19 final size:19
Alignment explanation
Indices: 47754439--47754495 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
47754429 TTAAAAAAAA
*
47754439 ATAAAAATTTTGGAATTTTT
1 ATAAATATTTT-GAATTTTT
47754459 ATAAATATTTTGAA-TTTT
1 ATAAATATTTTGAATTTTT
*
47754477 AAAAATTATTTTGAATTTT
1 ATAAA-TATTTTGAATTTT
47754496 CTAAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 12 0.36
20 13 0.39
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTT
Found at i:47754501 original size:19 final size:18
Alignment explanation
Indices: 47754445--47754511 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
47754435 AAAAATAAAA
*
47754445 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAATTTTTA-AATT
*
47754465 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTT-TAAATT
47754484 ATTTTGAATTTTCTAAATTT
1 ATTTTGAATTTT-TAAA-TT
47754504 ATTTTGAA
1 ATTTTGAA
47754512 ATTATTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (18 bp):
ATTTTGAATTTTTAAATT
Found at i:47754507 original size:20 final size:19
Alignment explanation
Indices: 47754445--47754511 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
47754435 AAAAATAAAA
*
47754445 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTAAAAATT
47754465 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* *
47754484 ATTTTGAATTTTCTAAATTT
1 ATTTTGAATTTT-AAAAATT
47754504 ATTTTGAA
1 ATTTTGAA
47754512 ATTATTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 8 0.19
19 16 0.38
20 18 0.43
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:47756298 original size:13 final size:13
Alignment explanation
Indices: 47756280--47756304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47756270 TACAAGAGAA
47756280 TTTTTTGAGAACC
1 TTTTTTGAGAACC
47756293 TTTTTTGAGAAC
1 TTTTTTGAGAAC
47756305 TTTAACATTA
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:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTTTGAGAACC
Found at i:47759803 original size:57 final size:58
Alignment explanation
Indices: 47759697--47759830 Score: 155
Period size: 57 Copynumber: 2.3 Consensus size: 58
47759687 TTTTTAAGGA
* * *
47759697 CTAACTTGGACAAAAAAAAGGTTAAAGTCCCAATGTAAGAACAATTGCCAAGTTTAGGG
1 CTAACTTAGA-AAAAAAAAGGTTAAAGTCCCAATGTAAGAACAATTGCCAAATTCAGGG
* * * * * *
47759756 CCTAACTTA-AATAAAAAAGGTTCAGGTCCGAATGT-GGGACAATTGCCAAATTCAGGG
1 -CTAACTTAGAAAAAAAAAGGTTAAAGTCCCAATGTAAGAACAATTGCCAAATTCAGGG
47759813 CTAACTTAGAAAAAAAAA
1 CTAACTTAGAAAAAAAAA
47759831 TTAACTCCCA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
56 8 0.13
57 26 0.41
58 21 0.33
59 1 0.02
60 7 0.11
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (58 bp):
CTAACTTAGAAAAAAAAAGGTTAAAGTCCCAATGTAAGAACAATTGCCAAATTCAGGG
Found at i:47760919 original size:7 final size:7
Alignment explanation
Indices: 47760904--47760939 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
47760894 AGAGGAGAGC
47760904 AAAAA-A
1 AAAAAGA
47760910 AAAAAGA
1 AAAAAGA
47760917 AAAAAGA
1 AAAAAGA
47760924 AAAAAG-
1 AAAAAGA
47760930 AAAAAGA
1 AAAAAGA
47760937 AAA
1 AAA
47760940 GGGTATGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:47766147 original size:9 final size:9
Alignment explanation
Indices: 47766135--47766193 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
47766125 AAAATAAAAA
47766135 AATTCGGGT
1 AATTCGGGT
47766144 AATTCGGGT
1 AATTCGGGT
*
47766153 ATTTTTC-GGT
1 A--ATTCGGGT
*
47766163 AATTCGGTT
1 AATTCGGGT
*
47766172 AATTCGGTT
1 AATTCGGGT
47766181 AATTCGGGT
1 AATTCGGGT
47766190 AATT
1 AATT
47766194 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:47766165 original size:19 final size:19
Alignment explanation
Indices: 47766141--47766196 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
47766131 AAAAAATTCG
47766141 GGTAATTCGGGTATTTTTC
1 GGTAATTCGGGTATTTTTC
**
47766160 GGTAATTC-GGT-TAATTC
1 GGTAATTCGGGTATTTTTC
47766177 GGTTAATTCGGGTAATTTTT
1 GG-TAATTCGGGT-ATTTTT
47766197 AACCAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 11 0.38
21 3 0.10
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.46
Consensus pattern (19 bp):
GGTAATTCGGGTATTTTTC
Found at i:47767619 original size:2 final size:2
Alignment explanation
Indices: 47767612--47767661 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
47767602 TAATTAAAGA
47767612 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
47767654 AT AT AT AT
1 AT AT AT AT
47767662 GAAAACCTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47779354 original size:16 final size:15
Alignment explanation
Indices: 47779328--47779361 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
47779318 TATAATTAGT
*
47779328 GCAATAAAAAATATA
1 GCAATAAAAAATAAA
47779343 GCAATGAAAAAATAAA
1 GCAAT-AAAAAATAAA
47779359 GCA
1 GCA
47779362 GAGATGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.65, C:0.09, G:0.12, T:0.15
Consensus pattern (15 bp):
GCAATAAAAAATAAA
Found at i:47781572 original size:15 final size:16
Alignment explanation
Indices: 47781554--47781593 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
47781544 ATAATTAATT
47781554 AAAATTAAAATTTT-A
1 AAAATTAAAATTTTCA
47781569 AAAA-TAAAATTTTCA
1 AAAATTAAAATTTTCA
*
47781584 TAAATTAAAA
1 AAAATTAAAA
47781594 AAATAGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 9 0.41
15 8 0.36
16 5 0.23
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAAAATTTTCA
Found at i:47782152 original size:18 final size:19
Alignment explanation
Indices: 47782129--47782167 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
47782119 CAAAACACAC
47782129 TTTTT-ATACAATGGTTTT
1 TTTTTAATACAATGGTTTT
* *
47782147 TTTTTAATGCATTGGTTTT
1 TTTTTAATACAATGGTTTT
47782166 TT
1 TT
47782168 GGTTAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.64
Consensus pattern (19 bp):
TTTTTAATACAATGGTTTT
Found at i:47782330 original size:16 final size:17
Alignment explanation
Indices: 47782309--47782343 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47782299 GTTTTTAATT
47782309 ATTTTTTAATTA-ATAA
1 ATTTTTTAATTATATAA
*
47782325 ATTTTTTATTTATATAA
1 ATTTTTTAATTATATAA
47782342 AT
1 AT
47782344 AAAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTTAATTATATAA
Found at i:47782529 original size:16 final size:16
Alignment explanation
Indices: 47782508--47782538 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
47782498 TTTATATAAA
47782508 TAAAATATGAATTAAT
1 TAAAATATGAATTAAT
47782524 TAAAATATGAATTAA
1 TAAAATATGAATTAA
47782539 AAACTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAATATGAATTAAT
Found at i:47782592 original size:23 final size:23
Alignment explanation
Indices: 47782559--47782603 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47782549 ATAATATATT
* *
47782559 TATTAATTAAAAATTAAAAATAA
1 TATTAAATAAAAAATAAAAATAA
*
47782582 TATTAAATAAAAAATACAAATA
1 TATTAAATAAAAAATAAAAATA
47782604 CTGAGTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TATTAAATAAAAAATAAAAATAA
Found at i:47794853 original size:22 final size:23
Alignment explanation
Indices: 47794800--47794855 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
47794790 TTAAATTAAA
* * *
47794800 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
47794823 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
47794845 ATTAAAATTAA
1 ATTAAAATTAA
47794856 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:47794868 original size:16 final size:16
Alignment explanation
Indices: 47794831--47794870 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
47794821 TTAATAAAAT
* *
47794831 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
47794847 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
47794863 TAAAATTA
1 TAAAATTA
47794871 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:47794949 original size:59 final size:61
Alignment explanation
Indices: 47794880--47795059 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
47794870 ATCAAATTAT
*
47794880 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
47794945 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
47795008 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
47795060 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:47794976 original size:9 final size:9
Alignment explanation
Indices: 47794943--47794970 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
47794933 TTTATCAAAT
47794943 TATTAATTG
1 TATTAATTG
47794952 TATTAATTG
1 TATTAATTG
47794961 TATTAATTG
1 TATTAATTG
47794970 T
1 T
47794971 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:47794980 original size:68 final size:68
Alignment explanation
Indices: 47794859--47795029 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
47794849 AAATTAATTG
*
47794859 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
47794922 TGA
66 TGA
47794925 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
47794990 TGA
66 TGA
47794993 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
47795030 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:47797671 original size:11 final size:10
Alignment explanation
Indices: 47797652--47797683 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
47797642 TTTGAATAAA
47797652 ATATTTTTTT
1 ATATTTTTTT
47797662 ATATTTTTTT
1 ATATTTTTTT
47797672 ATAATTTTTTT
1 AT-ATTTTTTT
47797683 A
1 A
47797684 AAAAGCTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
ATATTTTTTT
Found at i:47798202 original size:19 final size:19
Alignment explanation
Indices: 47798175--47798212 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
47798165 NNNNNNNNTT
*
47798175 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
47798194 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
47798213 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:47798342 original size:27 final size:27
Alignment explanation
Indices: 47798311--47798382 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
47798301 TACCGACATT
* *
47798311 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
47798338 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
47798365 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
47798383 GCAATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:47798455 original size:22 final size:24
Alignment explanation
Indices: 47798422--47798591 Score: 144
Period size: 27 Copynumber: 7.0 Consensus size: 24
47798412 ATAAATTATC
*
47798422 TATATTTAGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
47798446 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
*
47798470 TATAATTTTGTATGAATATTGCAAT
1 TAT-ATTTTGTATGAATATTGTAAT
47798495 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
47798519 TATAATTTTGTATGAATATTGTAATGT
1 TAT-ATTTTGTATGAATATTGTAA--T
*
47798546 CGGTATATATTG--T-AATATTGTAA-
1 ---TATATTTTGTATGAATATTGTAAT
47798569 T-T-TTTTGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
47798591 T
1 T
47798592 TTTTTATAAT
Statistics
Matches: 122, Mismatches: 5, Indels: 40
0.73 0.03 0.24
Matches are distributed among these distances:
18 4 0.03
19 1 0.01
20 2 0.02
21 10 0.08
22 33 0.27
23 3 0.02
24 8 0.07
25 6 0.05
26 12 0.10
27 35 0.29
29 5 0.04
30 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (24 bp):
TATATTTTGTATGAATATTGTAAT
Found at i:47798484 original size:49 final size:49
Alignment explanation
Indices: 47798425--47798596 Score: 244
Period size: 49 Copynumber: 3.6 Consensus size: 49
47798415 AATTATCTAT
*
47798425 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
47798474 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
* ** *
47798523 ATTTTGTATGAATATTGTAA--TGTCGGTAT--ATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
47798568 ATTTTTTGTATGAATATTGTAATTTTTTT
1 A--TTTTGTATGAATATTGTAATTTTTTT
47798597 ATAATTAATT
Statistics
Matches: 109, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
45 16 0.15
47 25 0.23
49 68 0.62
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (49 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:47798609 original size:22 final size:23
Alignment explanation
Indices: 47798558--47798609 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
47798548 GTATATATTG
47798558 TAATATTGTAATTTTTTGTATGAA
1 TAAT-TTGTAATTTTTTGTATGAA
47798582 T-A-TTGTAATTTTTT-TAT-AA
1 TAATTTGTAATTTTTTGTATGAA
47798601 TTAATTTGT
1 -TAATTTGT
47798610 TAGTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.08
20 4 0.16
21 13 0.52
22 4 0.16
23 1 0.04
24 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (23 bp):
TAATTTGTAATTTTTTGTATGAA
Found at i:47798649 original size:11 final size:11
Alignment explanation
Indices: 47798633--47798676 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
47798623 TTATGTTATA
47798633 AATTTATTAGT
1 AATTTATTAGT
47798644 AATTTATTAGT
1 AATTTATTAGT
47798655 AA--T-TTAGT
1 AATTTATTAGT
*
47798663 AATTTATTACT
1 AATTTATTAGT
47798674 AAT
1 AAT
47798677 AAATTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 7 0.24
9 1 0.03
10 1 0.03
11 20 0.69
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (11 bp):
AATTTATTAGT
Found at i:47798661 original size:19 final size:19
Alignment explanation
Indices: 47798639--47798676 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47798629 TATAAATTTA
*
47798639 TTAGTAATTTATTAGTAAT
1 TTAGTAATTTATTACTAAT
47798658 TTAGTAATTTATTACTAAT
1 TTAGTAATTTATTACTAAT
47798677 AAATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
TTAGTAATTTATTACTAAT
Found at i:47798934 original size:27 final size:28
Alignment explanation
Indices: 47798896--47798972 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
47798886 CCGACCCGGC
*
47798896 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
47798923 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
47798950 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
47798973 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:47802228 original size:41 final size:41
Alignment explanation
Indices: 47802183--47802267 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
47802173 CATTGTTTTG
*
47802183 AGATAAGAATATCACACTTGGAAAAAGAATTTTGATGATAA
1 AGATAAGAATATCACACTTAGAAAAAGAATTTTGATGATAA
47802224 AGATAAGAATATCACACTTAGAAAAAGAATTTTGATGATAA
1 AGATAAGAATATCACACTTAGAAAAAGAATTTTGATGATAA
47802265 AGA
1 AGA
47802268 AATAAAGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (41 bp):
AGATAAGAATATCACACTTAGAAAAAGAATTTTGATGATAA
Found at i:47806624 original size:22 final size:21
Alignment explanation
Indices: 47806577--47806625 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
47806567 TTTAAACACT
47806577 ATACAATTTTATCTTTTACAA
1 ATACAATTTTATCTTTTACAA
*
47806598 TTACAATATTTATCTTATTA-AA
1 ATACAAT-TTTATCTT-TTACAA
47806620 ATACAA
1 ATACAA
47806626 ATTATTGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 15 0.62
23 3 0.12
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
ATACAATTTTATCTTTTACAA
Found at i:47807083 original size:14 final size:14
Alignment explanation
Indices: 47807064--47807094 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47807054 AGTCTCTTCA
47807064 TTATACTTTAATCT
1 TTATACTTTAATCT
*
47807078 TTATACTTTAATTT
1 TTATACTTTAATCT
47807092 TTA
1 TTA
47807095 ATATACTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATACTTTAATCT
Found at i:47809137 original size:16 final size:16
Alignment explanation
Indices: 47809118--47809153 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
47809108 TTTATTTGCA
* *
47809118 AATACTTTTTTTTAAG
1 AATAATTTTTTATAAG
47809134 AATAATTTTTTATAAG
1 AATAATTTTTTATAAG
47809150 AATA
1 AATA
47809154 TACAATAAGG
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:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
AATAATTTTTTATAAG
Found at i:47817950 original size:23 final size:23
Alignment explanation
Indices: 47817906--47817955 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
47817896 TTTTCTATCA
47817906 AAATTATGCAAATATACAAAACAC
1 AAATTATGCAAATATACAAAAC-C
* * *
47817930 AAATTA-GTAAATATTCCAAACC
1 AAATTATGCAAATATACAAAACC
47817952 AAAT
1 AAAT
47817956 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 12 0.52
24 6 0.26
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (23 bp):
AAATTATGCAAATATACAAAACC
Found at i:47822242 original size:3 final size:3
Alignment explanation
Indices: 47822234--47822304 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
47822224 ATGAAAACAG
47822234 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47822282 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
47822305 GGATATTTGC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:47822680 original size:3 final size:3
Alignment explanation
Indices: 47822672--47822697 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47822662 ATAAGGGGAA
47822672 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
47822698 TAGCAGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:47824905 original size:49 final size:49
Alignment explanation
Indices: 47824833--47824931 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
47824823 TAGTTCTAGA
47824833 CAACATGTTACAGTCACAGAACAATCATCCCTCGAAAGCCTCATCATTT
1 CAACATGTTACAGTCACAGAACAATCATCCCTCGAAAGCCTCATCATTT
*
47824882 CAACATGTTCCAGTCACAGAACAATCATCCCTCGAAAGCCTCATCATTT
1 CAACATGTTACAGTCACAGAACAATCATCCCTCGAAAGCCTCATCATTT
47824931 C
1 C
47824932 GGGTTAAGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.32, G:0.10, T:0.24
Consensus pattern (49 bp):
CAACATGTTACAGTCACAGAACAATCATCCCTCGAAAGCCTCATCATTT
Found at i:47828114 original size:128 final size:128
Alignment explanation
Indices: 47827886--47828144 Score: 491
Period size: 128 Copynumber: 2.0 Consensus size: 128
47827876 AACATTAGCA
*
47827886 TTTATATATGCTACACACACTGGAAACACATTCAAATAGAAATAATTCTCTCTTAATACATTTCC
1 TTTATATATGCTACACACACTGGAAACACATTCAAATAGAAATAATTCTCTCTGAATACATTTCC
47827951 TCCATGTAACTTAAACTCGACTGTGAGTGTTGGATACAACTCCGTTAAATTTTTTTCAAAGTT
66 TCCATGTAACTTAAACTCGACTGTGAGTGTTGGATACAACTCCGTTAAATTTTTTTCAAAGTT
*
47828014 TTTATATATGCTACACACACTGGAAACACATTTAAATAGAAATAATTCTCTCTGAATACATTTCC
1 TTTATATATGCTACACACACTGGAAACACATTCAAATAGAAATAATTCTCTCTGAATACATTTCC
*
47828079 TCCATGTAACTTAAACTCGACTGTGAGTGTTGGATACAACTCCGTTAATTTTTTTTCAAAGTT
66 TCCATGTAACTTAAACTCGACTGTGAGTGTTGGATACAACTCCGTTAAATTTTTTTCAAAGTT
47828142 TTT
1 TTT
47828145 CCATATATTT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (128 bp):
TTTATATATGCTACACACACTGGAAACACATTCAAATAGAAATAATTCTCTCTGAATACATTTCC
TCCATGTAACTTAAACTCGACTGTGAGTGTTGGATACAACTCCGTTAAATTTTTTTCAAAGTT
Found at i:47836153 original size:24 final size:24
Alignment explanation
Indices: 47836126--47836172 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
47836116 AATTATCAAT
47836126 TTGAATTCTAAATATTAACGGGTA
1 TTGAATTCTAAATATTAACGGGTA
* * *
47836150 TTGAATTTTAAATTTTAATGGGT
1 TTGAATTCTAAATATTAACGGGT
47836173 TTGGACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (24 bp):
TTGAATTCTAAATATTAACGGGTA
Found at i:47836317 original size:31 final size:30
Alignment explanation
Indices: 47836282--47836348 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 30
47836272 GTTATGATTG
47836282 AATCGATTTAAAATATGAAAATTGAAAATC
1 AATCGATTTAAAATATGAAAATTGAAAATC
47836312 AAATCGATTTAAAATATGAAAATTGAAAATC
1 -AATCGATTTAAAATATGAAAATTGAAAATC
47836343 AATCGA
1 AATCGA
47836349 ATAAACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.28
Consensus pattern (30 bp):
AATCGATTTAAAATATGAAAATTGAAAATC
Found at i:47837670 original size:16 final size:16
Alignment explanation
Indices: 47837646--47837677 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47837636 ATTACTTCTC
47837646 AATCCGATTCATCGAT
1 AATCCGATTCATCGAT
*
47837662 AATCTGATTCATCGAT
1 AATCCGATTCATCGAT
47837678 CTAATCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (16 bp):
AATCCGATTCATCGAT
Found at i:47838498 original size:2 final size:2
Alignment explanation
Indices: 47838491--47838545 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
47838481 TGTAGTTTAA
47838491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
47838533 -T AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT A
47838546 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 45 0.92
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:47839346 original size:30 final size:30
Alignment explanation
Indices: 47839278--47839346 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
47839268 CAATATTTTA
*
47839278 ATTTAATAAAAAATAAAATTATAATTTGATC
1 ATTTAA-AAAAAATAAAATTATAATTTAATC
* * * * *
47839309 CTCTAAAAATAATAACATTCTAATTTAATC
1 ATTTAAAAAAAATAAAATTATAATTTAATC
47839339 ATTTAAAA
1 ATTTAAAA
47839347 TCTGTATAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (30 bp):
ATTTAAAAAAAATAAAATTATAATTTAATC
Done.