Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 1 of 85
Found at i:1967 original size:21 final size:22
Alignment explanation
Indices: 1931--1975 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1921 GGTTCCATTT
*
1931 TTTTCTTTTTTTTTCTGTCTTG
1 TTTTCTTTTATTTTCTGTCTTG
*
1953 TTTTC-TTTATTTTCTTTCTTG
1 TTTTCTTTTATTTTCTGTCTTG
1974 TT
1 TT
1976 CTTTAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTATTTTCTGTCTTG
Found at i:7446 original size:6 final size:6
Alignment explanation
Indices: 7435--7460 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7425 GTAATGGTAG
7435 CAGTAA CAGTAA CAGTAA CAGTAA CA
1 CAGTAA CAGTAA CAGTAA CAGTAA CA
7461 ATATTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CAGTAA
Found at i:7538 original size:45 final size:45
Alignment explanation
Indices: 7443--7547 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
7433 AGCAGTAACA
7443 GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
* * * *
7488 ATAACAGTAACGGTAACAGTATTCGACACACAAAGTG-TCGAAT-T
1 GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCT-GAATCT
7532 GGTAACAGTAACAGTA
1 -GTAACAGTAACAGTA
7548 GTCGGCATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.04
45 50 0.96
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
Found at i:13802 original size:22 final size:20
Alignment explanation
Indices: 13763--13818 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
13753 ATTTTATTCT
*
13763 ATTTTTATTTTTAGAAATTTA
1 ATTTTTATTTTT-TAAATTTA
13784 ACTTCTTTATTTTTTAAATTTA
1 A-TT-TTTATTTTTTAAATTTA
*
13806 ATTGTTATTTTTT
1 ATTTTTATTTTTT
13819 TTGTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 10 0.32
23 9 0.29
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
ATTTTTATTTTTTAAATTTA
Found at i:21716 original size:3 final size:3
Alignment explanation
Indices: 21708--21738 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21698 TTCTAACGCA
21708 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21739 CATTAATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:26709 original size:28 final size:27
Alignment explanation
Indices: 26658--26717 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
26648 TATATATACC
* *
26658 TATATAAAAAAAACCCATATGTATATTA
1 TATATAAAAAAAAACCATACGTATA-TA
* *
26686 TATATAAAAAAAAACTATGCGTATATA
1 TATATAAAAAAAAACCATACGTATATA
26713 TATAT
1 TATAT
26718 GTATAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.33
Consensus pattern (27 bp):
TATATAAAAAAAAACCATACGTATATA
Found at i:28336 original size:44 final size:45
Alignment explanation
Indices: 28260--28357 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
28250 AAGACTTGTA
* **
28260 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
* *
28305 TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
28349 TCTTCGATC
1 TCTTCGATC
28358 GATTCCACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 32 0.67
45 16 0.33
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
Found at i:28780 original size:45 final size:45
Alignment explanation
Indices: 28704--29227 Score: 540
Period size: 45 Copynumber: 11.7 Consensus size: 45
28694 TATCTTTGAT
* * * *
28704 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAAAAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* *
28749 GAAGACAAGATCTGGTATCTTTGATCCACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* * * * * * * *
28794 GAAGACAGGATATAGTATCTTTGATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* * * * *
28838 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
*
28883 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* * * * * *
28928 GAAGACAGGATCTGGTATCTTTGATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* * * *
28972 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAA
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* *
29017 GAAGACAAGATCTGGTATCTTTGATCCACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* * * * * *
29062 GAAGACAGGATCTAGTATCTTTGATCTACTTC-ACGCCAGTATAT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* * * * *
29106 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* *
29151 GAAGACAAGATCTGGTATCTTTGATCAACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* *
29196 GAAGCCAGGATCTGGTATCTTTGATCTACTTC
1 GAAGACAAGATCTGGTATCTTTGATCTACTTC
29228 ACGCCAGTAC
Statistics
Matches: 387, Mismatches: 82, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
44 99 0.26
45 288 0.74
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (45 bp):
GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
Found at i:28869 original size:89 final size:89
Alignment explanation
Indices: 28704--29249 Score: 551
Period size: 89 Copynumber: 6.1 Consensus size: 89
28694 TATCTTTGAT
* * * * * *
28704 GAAGACAAGATCT-GTTTTCTTCGATCTACTTCGCCACCAGAAAAGGAAGACAAGATCTGGTATC
1 GAAGACAAGATCTAG-TATCTTTGATCTACTTC-ACACCAGTATATGAAGACAAGATCTGGTATC
* * *
28768 TTTGATCCACTTCGCTACCAATATAG
64 TTTGATCTACTTCGCCACCAGTATAG
* * * * * *
28794 GAAGACAGGATATAGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTATATGAAGACAAGATCTGGTATCTT
* *
28859 CGATCTACTTCGCCACCAGTATGG
66 TGATCTACTTCGCCACCAGTATAG
* * * * *
28883 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCAC-ACCAGTATATGAAGACAAGATCTGGTATCT
* * * *
28948 TTGATCTACTTC-ACGCCAGTACAT
65 TTGATCTACTTCGCCACCAGTATAG
* * * * *
28972 GAAGACAAGATCT-GTTTTCTTCGATCTACTTCGCCACCAGAATAAGAAGACAAGATCTGGTATC
1 GAAGACAAGATCTAG-TATCTTTGATCTACTTC-ACACCAGTATATGAAGACAAGATCTGGTATC
* * *
29036 TTTGATCCACTTCGCTACCAATATAG
64 TTTGATCTACTTCGCCACCAGTATAG
* * * *
29062 GAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTATATGAAGACAAGATCTGGTATCTT
* *
29127 CGATCTACTTCGCCACCAGTATGG
66 TGATCTACTTCGCCACCAGTATAG
* * * * * * *
29151 GAAGACAAGATCTGGTATCTTTGATCAACTTCGCTACCAATATAGGAAGCCAGGATCTGGTATCT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCAC-ACCAGTATATGAAGACAAGATCTGGTATCT
* * * *
29216 TTGATCTACTTC-ACGCCAGTACAT
65 TTGATCTACTTCGCCACCAGTATAG
29240 GAAGACAAGA
1 GAAGACAAGA
29250 CTTGCTGAAG
Statistics
Matches: 371, Mismatches: 78, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
88 1 0.00
89 240 0.65
90 128 0.35
91 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (89 bp):
GAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTATATGAAGACAAGATCTGGTATCTT
TGATCTACTTCGCCACCAGTATAG
Found at i:28946 original size:134 final size:134
Alignment explanation
Indices: 28702--29249 Score: 979
Period size: 134 Copynumber: 4.1 Consensus size: 134
28692 ACTATCTTTG
*
28702 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAAAAGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
*
28767 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATATAGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
28832 GTAC
131 GTAC
* *
28836 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
* *
28901 CTTTGATCTACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
28966 GTAC
131 GTAC
*
28970 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAAGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
29035 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
*
29100 GTAT
131 GTAC
* *
29104 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
* * *
29169 CTTTGATCAACTTCGCTACCAATATAGGAAGCCAGGATCTGGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
29234 GTAC
131 GTAC
29238 ATGAAGACAAGA
1 ATGAAGACAAGA
29250 CTTGCTGAAG
Statistics
Matches: 395, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 395 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (134 bp):
ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
GTAC
Found at i:29567 original size:44 final size:43
Alignment explanation
Indices: 29510--29592 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
29500 AACCTCTCCA
* * *
29510 TTTTTTACTCAAAGCTCCCTTTGTAGGGTTTCACATTGGCCTT
1 TTTTTTACTCAAAGCGCCATTTGTAGGCTTTCACATTGGCCTT
*
29553 TTTTTTAACTCAAAGCGCCATTTGTAGGCTTTCACCTTGG
1 TTTTTT-ACTCAAAGCGCCATTTGTAGGCTTTCACATTGG
29593 TCCCACCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 6 0.17
44 29 0.83
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (43 bp):
TTTTTTACTCAAAGCGCCATTTGTAGGCTTTCACATTGGCCTT
Found at i:37842 original size:28 final size:27
Alignment explanation
Indices: 37791--37850 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
37781 TATATATACC
* *
37791 TATATAAAAAAAACCCATATGTATATTA
1 TATATAAAAAAAAACCATACGTATA-TA
* *
37819 TATATAAAAAAAAACTATGCGTATATA
1 TATATAAAAAAAAACCATACGTATATA
37846 TATAT
1 TATAT
37851 GTATAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.33
Consensus pattern (27 bp):
TATATAAAAAAAAACCATACGTATATA
Found at i:40727 original size:19 final size:19
Alignment explanation
Indices: 40693--40744 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
40683 AAAATATTTA
*
40693 CTTATAAATATTTTTATAAT
1 CTTATATAT-TTTTTATAAT
*
40713 TTTATATATTTTTTATAAT
1 CTTATATATTTTTTATAAT
*
40732 CTTATGTATTTTT
1 CTTATATATTTTT
40745 ATCAAGAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
CTTATATATTTTTTATAAT
Found at i:43654 original size:15 final size:16
Alignment explanation
Indices: 43627--43666 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
43617 AAATTTGTTT
*
43627 TTTTAATAAATTT-AAG
1 TTTTAA-AAATTTCAAA
43643 TTTTAAAAATTTCAAA
1 TTTTAAAAATTTCAAA
43659 TTTTAAAA
1 TTTTAAAA
43667 TCCACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTTAAAAATTTCAAA
Found at i:48096 original size:39 final size:39
Alignment explanation
Indices: 48050--48130 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
48040 ATAATTTAAA
* **
48050 TTTATATATTCCGTATATCATAATATTAATGAATTTGAG
1 TTTATATATTCCATATATCATAATATTAACAAATTTGAG
* *
48089 TTTATATATTCTATATATTATAATATTAACAAATTTGAG
1 TTTATATATTCCATATATCATAATATTAACAAATTTGAG
48128 TTT
1 TTT
48131 TTTAGTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (39 bp):
TTTATATATTCCATATATCATAATATTAACAAATTTGAG
Found at i:48177 original size:15 final size:15
Alignment explanation
Indices: 48157--48187 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48147 CATTTAGTTT
48157 TAATTTTGGAAGTGA
1 TAATTTTGGAAGTGA
48172 TAATTTTGGAAGTGA
1 TAATTTTGGAAGTGA
48187 T
1 T
48188 TTCAGTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
TAATTTTGGAAGTGA
Found at i:51816 original size:440 final size:441
Alignment explanation
Indices: 50980--51865 Score: 1765
Period size: 440 Copynumber: 2.0 Consensus size: 441
50970 GAAATGATAA
50980 ATTAAGTAAAATTCATGTCCAAAATTAATTAAAATAAATAATAAAAATATATTATCATCTATATT
1 ATTAAGTAAAATTCATGTCCAAAATTAATTAAAATAAATAATAAAAATATATTATCATCTATATT
51045 TTATAATATTAACTATCATTTAAATATATATTGTCTACTTTATAACATAAATATTTTATCTTTTA
66 TTATAATATTAACTATCATTTAAATATATATTGTCTACTTTATAACATAAATATTTTATCTTTTA
51110 AAAAATACTCTTCTTCTTCTTTTTTACAAACAAAGACTGGACATATTTATTGAAGTAATACAACA
131 AAAAATACTCTTCTTCTTCTTTTTTACAAACAAAGACTGGACATATTTATTGAAGTAATACAACA
51175 ATGAGAATAAAAAACAAAAACCAGCCAAATAAATATAAACCCTAGGACTTAAAACATTTTTCATC
196 ATGAGAATAAAAAACAAAAACCAGCCAAATAAATATAAACCCTAGGACTTAAAACATTTTTCATC
51240 TAAAAATAAGAATATTAAAATACTGAAAAACCTCCAAATTTACCGTTATCTACATCCATTACTAA
261 TAAAAATAAGAATATTAAAATACTGAAAAACCTCCAAATTTACCGTTATCTACATCCATTACTAA
51305 TCGTAGACAGTGACAAAGACACTCGACAGATGATAAGCAAAAAAAAAGTACTCTTTTAACTACAA
326 TCGTAGACAGTGACAAAGACACTCGACAGATGATAAGCAAAAAAAAAGTACTCTTTTAACTACAA
51370 TACTAAAAGCGTCCGCTAACCATTTTTCTATTAAGATATTAATCAAGACGG
391 TACTAAAAGCGTCCGCTAACCATTTTTCTATTAAGATATTAATCAAGACGG
51421 ATTAAGTAAAATTC-TGTCCAAAATTAATTAAAATAAATAATAAAAATATATTATCATCTATATT
1 ATTAAGTAAAATTCATGTCCAAAATTAATTAAAATAAATAATAAAAATATATTATCATCTATATT
51485 TTATAATATTAACTATCATTTAAATATATATTGTCTACTTTATAACATAAATATTTTATCTTTTA
66 TTATAATATTAACTATCATTTAAATATATATTGTCTACTTTATAACATAAATATTTTATCTTTTA
51550 AAAAATACTCTTCTTCTTCTTTTTTACAAACAAAGACTGGACATATTTATTGAAGTAATACAACA
131 AAAAATACTCTTCTTCTTCTTTTTTACAAACAAAGACTGGACATATTTATTGAAGTAATACAACA
51615 ATGAGAATAAAAAACAAAAACCAGCCAAATAAATATAAACCCTAGGACTTAAAACATTTTTCATC
196 ATGAGAATAAAAAACAAAAACCAGCCAAATAAATATAAACCCTAGGACTTAAAACATTTTTCATC
51680 TAAAAATAAGAATATTAAAATACTGAAAAACCTCCAAATTTACCGTTATCTACATCCATTACTAA
261 TAAAAATAAGAATATTAAAATACTGAAAAACCTCCAAATTTACCGTTATCTACATCCATTACTAA
51745 TCGTAGACAGTGACAAAGACACTCGACAGATGATAAGCAAAAAAAAAGTACTCTTTTAACTACAA
326 TCGTAGACAGTGACAAAGACACTCGACAGATGATAAGCAAAAAAAAAGTACTCTTTTAACTACAA
51810 TACTAAAAGCGTCCGCTAACCATTTTTCTATTAAGATATTAATCAAGACGG
391 TACTAAAAGCGTCCGCTAACCATTTTTCTATTAAGATATTAATCAAGACGG
51861 ATTAA
1 ATTAA
51866 CTTAGTGTTA
Statistics
Matches: 445, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
440 431 0.97
441 14 0.03
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (441 bp):
ATTAAGTAAAATTCATGTCCAAAATTAATTAAAATAAATAATAAAAATATATTATCATCTATATT
TTATAATATTAACTATCATTTAAATATATATTGTCTACTTTATAACATAAATATTTTATCTTTTA
AAAAATACTCTTCTTCTTCTTTTTTACAAACAAAGACTGGACATATTTATTGAAGTAATACAACA
ATGAGAATAAAAAACAAAAACCAGCCAAATAAATATAAACCCTAGGACTTAAAACATTTTTCATC
TAAAAATAAGAATATTAAAATACTGAAAAACCTCCAAATTTACCGTTATCTACATCCATTACTAA
TCGTAGACAGTGACAAAGACACTCGACAGATGATAAGCAAAAAAAAAGTACTCTTTTAACTACAA
TACTAAAAGCGTCCGCTAACCATTTTTCTATTAAGATATTAATCAAGACGG
Found at i:57802 original size:14 final size:12
Alignment explanation
Indices: 57783--57829 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
57773 CCCCTATCTG
57783 TTATTAGTTATTT
1 TTATTA-TTATTT
57796 ATTATTAATTATTT
1 -TTATT-ATTATTT
*
57810 TTACTATTATTT
1 TTATTATTATTT
57822 TTATTATT
1 TTATTATT
57830 GTATAATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 14 0.47
13 4 0.13
14 11 0.37
15 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:58025 original size:27 final size:25
Alignment explanation
Indices: 57986--58043 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
57976 ATATTTAAAA
57986 ACATAT-TACTTTA-ATTTTCATAAAT
1 ACATATATACTTTACATTTT-AT-AAT
*
58011 ATATATATACATTTACATTTTATAAT
1 ACATATATAC-TTTACATTTTATAAT
58037 ACATATA
1 ACATATA
58044 CATCTTCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.18
26 12 0.43
27 6 0.21
28 5 0.18
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (25 bp):
ACATATATACTTTACATTTTATAAT
Found at i:59384 original size:3 final size:3
Alignment explanation
Indices: 59376--59409 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
59366 TTCTAAAGCA
59376 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
59410 CATTAACCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:59760 original size:21 final size:24
Alignment explanation
Indices: 59718--59761 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
59708 AACTATCATT
59718 TAAATATATATTATCTACTTTAACA
1 TAAATATATATTATCTA-TTTAACA
59743 TAAATAT-T-TTATCT-TTTAA
1 TAAATATATATTATCTATTTAA
59762 AAAATACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
23 6 0.32
24 1 0.05
25 7 0.37
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATATATATTATCTATTTAACA
Found at i:66948 original size:81 final size:83
Alignment explanation
Indices: 66849--67000 Score: 238
Period size: 81 Copynumber: 1.9 Consensus size: 83
66839 TACACATATG
*
66849 TATAAAAAAATATGAAATATGCATTTATATATATACACATGTATATAAAAAAATTAAGAAATA-A
1 TATAAAAAAATATGAAATATGCATTTATATATATACACATATATATAAAAAAA-TAAGAAATATA
66913 -AAAAATGTAAAGTATGTA
65 TAAAAATGTAAAGTATGTA
* * *
66931 TATAAAAAAAT-TGAAATATGCATTTATATATATACACATATGTATAGAAAAATATGAAATATAT
1 TATAAAAAAATATGAAATATGCATTTATATATATACACATATATATAAAAAAATAAGAAATATAT
66995 AAAAAT
66 AAAAAT
67001 ATATGAATGT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 8 0.12
81 39 0.61
82 17 0.27
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (83 bp):
TATAAAAAAATATGAAATATGCATTTATATATATACACATATATATAAAAAAATAAGAAATATAT
AAAAATGTAAAGTATGTA
Found at i:67540 original size:3 final size:3
Alignment explanation
Indices: 67532--67575 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
67522 ATACATGGTT
*
67532 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
67576 GATGCAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:72041 original size:22 final size:22
Alignment explanation
Indices: 71987--72047 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
71977 TTGTACTATA
* *
71987 CTTTATGTACTTGGTTTCTTTTT
1 CTTTATGTA-ATGCTTTCTTTTT
72010 -TTTAAT-TAATGCTTTCTTTTT
1 CTTT-ATGTAATGCTTTCTTTTT
72031 CTTTATGTAATTGCTTT
1 CTTTATGTAA-TGCTTT
72048 GTATAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 13 0.41
22 11 0.34
23 8 0.25
ACGTcount: A:0.15, C:0.11, G:0.10, T:0.64
Consensus pattern (22 bp):
CTTTATGTAATGCTTTCTTTTT
Found at i:80491 original size:22 final size:20
Alignment explanation
Indices: 80457--80499 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 20
80447 AGTTCTTTTT
80457 TATTTCAAAAAATATATATACA
1 TATTTCAAAAAATA-A-ATACA
80479 TATTT-AAAGAAATAAATACA
1 TATTTCAAA-AAATAAATACA
80499 T
1 T
80500 TAAATCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.30
21 4 0.20
22 10 0.50
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
TATTTCAAAAAATAAATACA
Found at i:96218 original size:70 final size:69
Alignment explanation
Indices: 96099--96235 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 69
96089 TATGAATATT
96099 TATTTACAGATATTATTATTTTAAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAAA
1 TATTTACAGATATTATTATTTTAAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAAA
96164 TAAA
66 TAAA
* *
96168 TATTTAGAGATATTATTATTTTAAAAAAATACTATGAAGTACCTAGTGTTTTAAACTGGGTTAAA
1 TATTTACAGATATTATTATTTT-AAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAA
96233 ATA
65 ATA
96236 TTTAAATATA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 21 0.32
70 44 0.68
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (69 bp):
TATTTACAGATATTATTATTTTAAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAAA
TAAA
Found at i:98054 original size:13 final size:13
Alignment explanation
Indices: 98036--98060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
98026 TTCAAATAAA
98036 TTTTAAAATTTAT
1 TTTTAAAATTTAT
98049 TTTTAAAATTTA
1 TTTTAAAATTTA
98061 AAAATTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAAATTTAT
Found at i:98060 original size:20 final size:20
Alignment explanation
Indices: 98032--98069 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
98022 AATATTCAAA
* *
98032 TAAATTTTAAAATTTATTTT
1 TAAAATTTAAAAATTATTTT
98052 TAAAATTTAAAAATTATT
1 TAAAATTTAAAAATTATT
98070 AAAAAAATAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATTTAAAAATTATTTT
Found at i:98076 original size:20 final size:19
Alignment explanation
Indices: 98053--98098 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
98043 ATTTATTTTT
*
98053 AAAATTTAAAAATTATTAAA
1 AAAATTTAAAAAGTA-TAAA
*
98073 AAAATATAAAAAGTATAAA
1 AAAATTTAAAAAGTATAAA
*
98092 AATATTT
1 AAAATTT
98099 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTTAAAAAGTATAAA
Found at i:99933 original size:29 final size:29
Alignment explanation
Indices: 99878--99934 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
99868 CTGGACCAAA
**
99878 TTAGTCCCTATACTATTAAATTGATCAAT
1 TTAGTCCCTATACTATTAAAAAGATCAAT
*
99907 TTAGTCCC-ATATTATTAAAAAGAATCAA
1 TTAGTCCCTATACTATTAAAAAG-ATCAA
99935 ATAAGGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAGTCCCTATACTATTAAAAAGATCAAT
Found at i:106946 original size:23 final size:23
Alignment explanation
Indices: 106899--106946 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
106889 GATTAAAATT
* *
106899 AAATTGTAATTTTTATAATAGTA
1 AAATTGTAATTTTTAAAAGAGTA
* *
106922 AAATTTTAATTTTTAAAAGATTA
1 AAATTGTAATTTTTAAAAGAGTA
106945 AA
1 AA
106947 TCAAAATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
AAATTGTAATTTTTAAAAGAGTA
Found at i:112319 original size:23 final size:22
Alignment explanation
Indices: 112255--112319 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
112245 AAAGAGATAG
*
112255 AATTTTTTATTTATTTCTAATTT
1 AATTTTTTATTTACTT-TAATTT
*
112278 AA-TTTTTATTTAACGTTAATTTT
1 AATTTTTTATTT-ACTTTAA-TTT
112301 AATTCTTTTATTTA-TTTAA
1 AATT-TTTTATTTACTTTAA
112320 AAAAATCACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 12 0.34
23 13 0.37
24 2 0.06
25 8 0.23
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
AATTTTTTATTTACTTTAATTT
Found at i:114815 original size:21 final size:21
Alignment explanation
Indices: 114789--114830 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
114779 CAATGAAAAT
*
114789 TTTTGAACAA-TTTAATGATCA
1 TTTTGAA-AAGTTAAATGATCA
114810 TTTTGAAAAGTTAAATGATCA
1 TTTTGAAAAGTTAAATGATCA
114831 AAACAAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTTGAAAAGTTAAATGATCA
Found at i:127454 original size:45 final size:45
Alignment explanation
Indices: 127403--127492 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
127393 TGGAACCATG
127403 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
1 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
127448 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
1 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
127493 GCAGGCTGTT
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:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
Found at i:128104 original size:30 final size:30
Alignment explanation
Indices: 128070--128126 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
128060 TGCATTTCCA
128070 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
1 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
128100 TTCTGCTGCTGAATTTGAGGAGCCAAA
1 TTCTGCTGCTGAATTTGAGGAGCCAAA
128127 GGATATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (30 bp):
TTCTGCTGCTGAATTTGAGGAGCCAAAATG
Found at i:132739 original size:2 final size:2
Alignment explanation
Indices: 132732--132775 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
132722 AATGATTCTA
*
132732 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A- AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
132772 -G AG A
1 AG AG A
132776 AACTGGAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:134275 original size:27 final size:27
Alignment explanation
Indices: 134245--134296 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
134235 TTTTAGTCCT
134245 GTGCCGCCATTCTCATTAGCACCACTG
1 GTGCCGCCATTCTCATTAGCACCACTG
*
134272 GTGCCGCCATTCTCATTGGCACCAC
1 GTGCCGCCATTCTCATTAGCACCAC
134297 CTTCAGCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.38, G:0.19, T:0.25
Consensus pattern (27 bp):
GTGCCGCCATTCTCATTAGCACCACTG
Found at i:143253 original size:2 final size:2
Alignment explanation
Indices: 143248--143272 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
143238 GCCATATATA
143248 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
143273 ATACACTCCC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:152246 original size:28 final size:28
Alignment explanation
Indices: 152215--152271 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
152205 AAACAGAGGG
152215 AGAAACAGAAGAGAATGAAAAAAAAAGA
1 AGAAACAGAAGAGAATGAAAAAAAAAGA
* *
152243 AGAAACAGAAGAGAATGGAAAAGAAAGA
1 AGAAACAGAAGAGAATGAAAAAAAAAGA
152271 A
1 A
152272 AAGAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.68, C:0.04, G:0.25, T:0.04
Consensus pattern (28 bp):
AGAAACAGAAGAGAATGAAAAAAAAAGA
Found at i:154331 original size:11 final size:11
Alignment explanation
Indices: 154317--154341 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
154307 AAGAGAATGG
154317 AAAAAAAAAGA
1 AAAAAAAAAGA
154328 AAAAAAAAAGA
1 AAAAAAAAAGA
154339 AAA
1 AAA
154342 GTTAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:154814 original size:29 final size:31
Alignment explanation
Indices: 154743--154819 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
154733 TTAACGACTC
* *
154743 AGTGACTAAAATGTTACAATACTATAACGTA
1 AGTGACTAAAATGTAACAATACTATAACATA
**
154774 AGTGACTAAAATGTAAC-ATTTTA-AACATA
1 AGTGACTAAAATGTAACAATACTATAACATA
154803 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
154820 CTGAGGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 4 0.10
31 16 0.38
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAATACTATAACATA
Found at i:154837 original size:31 final size:29
Alignment explanation
Indices: 154773--154841 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
154763 ACTATAACGT
** *
154773 AAGTGACTAAAATGTAACATTTTAAACAT
1 AAGTGACTAAAATGTAACATGGTAAACAA
*
154802 AAGTGACTAAAATGTAACCTGAGGTAAACAA
1 AAGTGACTAAAATGTAACAT--GGTAAACAA
154833 AAGTGACTA
1 AAGTGACTA
154842 TTTTAGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGTAAACAA
Found at i:160189 original size:23 final size:23
Alignment explanation
Indices: 160151--160205 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
160141 TTCTACCATG
* **
160151 AATTTTTAAAATAAAACTTAATTT
1 AATTTTTAATATAAAAAATAA-TT
160175 AATTTTTAATA-AAAAAATAATT
1 AATTTTTAATATAAAAAATAATT
160197 -ATTTTTAAT
1 AATTTTTAAT
160206 CTAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 7 0.25
24 10 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTTAATATAAAAAATAATT
Found at i:163583 original size:25 final size:27
Alignment explanation
Indices: 163555--163616 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
163545 ATGATTTTCT
163555 TTTAAAAATTATA-ATTTTTAAT-AAA
1 TTTAAAAATTATATATTTTTAATAAAA
* * *
163580 TTTAAAATTTTTATATTTTTATTAAAA
1 TTTAAAAATTATATATTTTTAATAAAA
*
163607 TTTAATAATT
1 TTTAAAAATT
163617 TTTCTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 11 0.37
26 8 0.27
27 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTAAAAATTATATATTTTTAATAAAA
Found at i:163590 original size:18 final size:16
Alignment explanation
Indices: 163554--163592 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
163544 TATGATTTTC
*
163554 TTTTAAAAATTATAAT
1 TTTTAAAAATTAAAAT
163570 TTTTAATAAATTTAAAAT
1 TTTTAA-AAA-TTAAAAT
163588 TTTTA
1 TTTTA
163593 TATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAAAATTAAAAT
Found at i:163607 original size:27 final size:28
Alignment explanation
Indices: 163563--163619 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
163553 CTTTTAAAAA
163563 TTATAATTTTTAATAAATTTAA-AATTT
1 TTATAATTTTTAATAAATTTAATAATTT
*
163590 TTAT-ATTTTTATTAAAATTTAATAATTT
1 TTATAATTTTTAAT-AAATTTAATAATTT
163618 TT
1 TT
163620 CTAAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.30
27 12 0.44
28 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATAATTTTTAATAAATTTAATAATTT
Found at i:163617 original size:20 final size:20
Alignment explanation
Indices: 163580--163629 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
163570 TTTTAATAAA
*
163580 TTTAAAATTT-TTATATTTT
1 TTTAAAATTTAATATATTTT
163599 TATTAAAATTTAATA-ATTTT
1 T-TTAAAATTTAATATATTTT
*
163619 TCTAAAATTTA
1 TTTAAAATTTA
163630 TTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
20 15 0.56
21 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAAAATTTAATATATTTT
Found at i:176741 original size:13 final size:12
Alignment explanation
Indices: 176707--176739 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
176697 AATACACAAA
176707 TAACTAAAATTTC
1 TAAC-AAAATTTC
176720 TAACAAAATTTC
1 TAACAAAATTTC
176732 TAACAAAA
1 TAACAAAA
176740 ATGACTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
TAACAAAATTTC
Found at i:178378 original size:182 final size:182
Alignment explanation
Indices: 178071--178608 Score: 1049
Period size: 182 Copynumber: 3.0 Consensus size: 182
178061 TCTTCCCCCA
* *
178071 GATGCAATATGCTATAACATCAACAAAACCAGTTATGGTTTTCCTGATAACAGAGTAAGAATTAA
1 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
*
178136 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAATCACAAAACCAGTTCC
66 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
178201 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
131 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
178253 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
1 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
178318 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
66 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
178383 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
131 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
178435 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
1 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
178500 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
66 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
178565 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAAC
131 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAAC
178609 AGGTTTGCTG
Statistics
Matches: 353, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 353 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (182 bp):
GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
Found at i:182068 original size:32 final size:31
Alignment explanation
Indices: 181981--182071 Score: 148
Period size: 31 Copynumber: 2.9 Consensus size: 31
181971 GCCCATTTTA
*
181981 ATTTTAAAAAT-TTTAAAAAATTAAAAAAAGT
1 ATTTTAAAAATATTT-TAAAATTAAAAAAAGT
182012 ATTTTAAAAATATTTTAAAATTAAAAAAAGT
1 ATTTTAAAAATATTTTAAAATTAAAAAAAGT
*
182043 ATTTTAAAAATATTTTAAAATTTAAAAAA
1 ATTTTAAAAATATTTTAAAATTAAAAAAA
182072 TTAAAAAAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 54 0.95
32 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
ATTTTAAAAATATTTTAAAATTAAAAAAAGT
Found at i:182101 original size:11 final size:11
Alignment explanation
Indices: 181981--182062 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
181971 GCCCATTTTA
181981 ATTTT-AAAA-
1 ATTTTAAAAAT
181990 ATTTTAAAAA-
1 ATTTTAAAAAT
**
182000 ATTAAAAAAAGT
1 ATTTTAAAAA-T
182012 ATTTTAAAAAT
1 ATTTTAAAAAT
182023 ATTTT--AAA-
1 ATTTTAAAAAT
**
182031 ATTAAAAAAAGT
1 ATTTTAAAAA-T
182043 ATTTTAAAAAT
1 ATTTTAAAAAT
182054 ATTTTAAAA
1 ATTTTAAAA
182063 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
8 3 0.05
9 8 0.14
10 15 0.26
11 16 0.28
12 16 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:182109 original size:38 final size:39
Alignment explanation
Indices: 182004--182111 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
181994 TAAAAAATTA
** *
182004 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAGTATTT
1 AAAAAA-TATTTT-AAAAT-TTAAAAAATT-AAAAAAGTATGT
*
182047 TAAAAATATTTTAAAATTTAAAAAATTAAAAAAGTATGT
1 AAAAAATATTTTAAAATTTAAAAAATTAAAAAAGTATGT
*
182086 AAAAAATATTTTAAAATTAAAAAAAT
1 AAAAAATATTTTAAAATTTAAAAAAT
182112 AAATATATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
39 35 0.59
40 8 0.14
41 5 0.08
42 6 0.10
43 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (39 bp):
AAAAAATATTTTAAAATTTAAAAAATTAAAAAAGTATGT
Found at i:185045 original size:19 final size:19
Alignment explanation
Indices: 185021--185058 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
185011 CTATTACGCC
185021 TCTATTCCATTATATTCAA
1 TCTATTCCATTATATTCAA
185040 TCTATTCCATTATATTCAA
1 TCTATTCCATTATATTCAA
185059 CCAAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTATTCCATTATATTCAA
Found at i:197653 original size:16 final size:16
Alignment explanation
Indices: 197632--197663 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
197622 GTTTCAATGT
197632 TGATTGAAGGTAGAAC
1 TGATTGAAGGTAGAAC
*
197648 TGATTGAAGGTGGAAC
1 TGATTGAAGGTAGAAC
197664 ATTTTGGTTG
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:0.34, C:0.06, G:0.34, T:0.25
Consensus pattern (16 bp):
TGATTGAAGGTAGAAC
Found at i:231187 original size:33 final size:33
Alignment explanation
Indices: 231145--231211 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
231135 GGAGAAAAGA
*
231145 TTAACTAACATAAGAGAAATTTCAGGCAAATAT
1 TTAACTAACATAAGACAAATTTCAGGCAAATAT
231178 TTAACTAACATAAGACAAATTTCAGGCAAATAT
1 TTAACTAACATAAGACAAATTTCAGGCAAATAT
231211 T
1 T
231212 ATCTTTGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (33 bp):
TTAACTAACATAAGACAAATTTCAGGCAAATAT
Found at i:236297 original size:93 final size:94
Alignment explanation
Indices: 236180--236367 Score: 369
Period size: 93 Copynumber: 2.0 Consensus size: 94
236170 TAAATTCATT
236180 AAATATCATTTTCTATTACATCTTTATAATTGTATATTTTAAATAAAATAATTTAATTTTAACAA
1 AAATATCATTTTCTATTACATCTTTATAATTGTATATTTTAAATAAAATAATTTAATTTTAACAA
236245 TGTTAAAATTTTAAATTCAAAAGTAAAAA
66 TGTTAAAATTTTAAATTCAAAAGTAAAAA
236274 AAATATCA-TTTCTATTACATCTTTATAATTGTATATTTTAAATAAAATAATTTAATTTTAACAA
1 AAATATCATTTTCTATTACATCTTTATAATTGTATATTTTAAATAAAATAATTTAATTTTAACAA
236338 TGTTAAAATTTTAAATTCAAAAGTAAAAA
66 TGTTAAAATTTTAAATTCAAAAGTAAAAA
236367 A
1 A
236368 CTAAATTTCT
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 86 0.91
94 8 0.09
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (94 bp):
AAATATCATTTTCTATTACATCTTTATAATTGTATATTTTAAATAAAATAATTTAATTTTAACAA
TGTTAAAATTTTAAATTCAAAAGTAAAAA
Found at i:237686 original size:24 final size:24
Alignment explanation
Indices: 237641--237687 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
237631 TTATAAAATC
*
237641 AATTATAGAATTAAATTTATATAA
1 AATTATAGAAATAAATTTATATAA
*
237665 AATTATA-AAATAATTTTAATATA
1 AATTATAGAAATAAATTT-ATATA
237688 TTTTAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AATTATAGAAATAAATTTATATAA
Found at i:242284 original size:2 final size:2
Alignment explanation
Indices: 242277--242320 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
242267 GAAGAGCACT
242277 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
242319 GA
1 GA
242321 TCAAACTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:249134 original size:14 final size:14
Alignment explanation
Indices: 249111--249147 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
249101 TAAACCTTAT
*
249111 TAGGAAAAATTTTG
1 TAGGATAAATTTTG
249125 TAGGATAAATTTTG
1 TAGGATAAATTTTG
249139 TAGGATAAA
1 TAGGATAAA
249148 AACCTAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (14 bp):
TAGGATAAATTTTG
Found at i:251032 original size:21 final size:21
Alignment explanation
Indices: 251008--251049 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
250998 TCAAACTCAC
251008 ACATAGTGGAAAAACCAAATG
1 ACATAGTGGAAAAACCAAATG
251029 ACATAGTGGAAAAACCAAATG
1 ACATAGTGGAAAAACCAAATG
251050 CATTTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (21 bp):
ACATAGTGGAAAAACCAAATG
Found at i:256849 original size:34 final size:34
Alignment explanation
Indices: 256806--256871 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
256796 AGTAAAATAT
*
256806 TTTTCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
256839 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
256872 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:258855 original size:21 final size:21
Alignment explanation
Indices: 258831--258872 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
258821 TCAAACTCAC
258831 ACATAGTGGAAAAACCAAATG
1 ACATAGTGGAAAAACCAAATG
258852 ACATAGTGGAAAAACCAAATG
1 ACATAGTGGAAAAACCAAATG
258873 CATTTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (21 bp):
ACATAGTGGAAAAACCAAATG
Found at i:259924 original size:18 final size:17
Alignment explanation
Indices: 259898--259933 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
259888 TTTGGTTATA
259898 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
259916 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
259933 T
1 T
259934 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:260413 original size:8 final size:8
Alignment explanation
Indices: 260402--260439 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
260392 CAAAAACACA
260402 TTTTTTTC
1 TTTTTTTC
260410 TTTTCTTTC
1 TTTT-TTTC
*
260419 TTTCTTT-
1 TTTTTTTC
260426 TTTTTTTC
1 TTTTTTTC
260434 TTTTTT
1 TTTTTT
260440 GGGTGATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:264447 original size:16 final size:16
Alignment explanation
Indices: 264426--264463 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
264416 TAAATTACTG
*
264426 ATTACAACTTTATTCC
1 ATTACAACTCTATTCC
264442 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
264458 ATTACA
1 ATTACA
264464 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:264584 original size:24 final size:24
Alignment explanation
Indices: 264531--264576 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
264521 TCTTTCTAGA
* *
264531 ATATTTAGTATTTATTAGTATAAC
1 ATATTTAGAATTTATTAGCATAAC
264555 ATATTTAGAATTTATTAGCATA
1 ATATTTAGAATTTATTAGCATA
264577 GTTTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (24 bp):
ATATTTAGAATTTATTAGCATAAC
Found at i:268257 original size:9 final size:9
Alignment explanation
Indices: 268240--268276 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
268230 TGAGTTTTCG
268240 AATTCGAAT
1 AATTCGAAT
*
268249 AACTCGAAT
1 AATTCGAAT
268258 AATTCGAAT
1 AATTCGAAT
268267 AATTCGAAT
1 AATTCGAAT
268276 A
1 A
268277 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:268353 original size:21 final size:21
Alignment explanation
Indices: 268312--268354 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
268302 ACCCCAAACT
* *
268312 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
268333 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
268354 C
1 C
268355 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:281050 original size:23 final size:26
Alignment explanation
Indices: 281021--281071 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
281011 ATTTTTTTGT
281021 TACTTATTTT-T-T-AACTTTGAAAA
1 TACTTATTTTGTATGAACTTTGAAAA
*
281044 TACTTATTTTGTATGAATTTTGAAAA
1 TACTTATTTTGTATGAACTTTGAAAA
281070 TA
1 TA
281072 TCAATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 1 0.04
26 12 0.50
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (26 bp):
TACTTATTTTGTATGAACTTTGAAAA
Found at i:284425 original size:26 final size:28
Alignment explanation
Indices: 284396--284455 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
284386 TTACACTTTA
*
284396 ATCACATGATTTA-TT-TTATTTCACAT
1 ATCACATAATTTACTTATTATTTCACAT
284422 ATCACATAATTTATCTTACTTATTTCACAT
1 ATCACATAATTTA-CTTA-TTATTTCACAT
284452 ATCA
1 ATCA
284456 AATTTCTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.41
28 2 0.07
30 15 0.52
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (28 bp):
ATCACATAATTTACTTATTATTTCACAT
Found at i:298345 original size:75 final size:75
Alignment explanation
Indices: 298222--298373 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
298212 TCATACTCTT
298222 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
1 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
298287 TACATGCAAG
66 TACATGCAAG
298297 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
1 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
298362 TACATGCAAG
66 TACATGCAAG
298372 GA
1 GA
298374 ACAATAGTGC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (75 bp):
GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
TACATGCAAG
Found at i:300349 original size:46 final size:45
Alignment explanation
Indices: 300234--300446 Score: 202
Period size: 46 Copynumber: 4.7 Consensus size: 45
300224 AGGCGCAATG
* *
300234 GTGTCTTTCAACCATGGTCTTATTTATTATTGACT-T-GATGTT--ATA
1 GTGTCTTTCAACCATGGTCTTATTCATT-TT--CTGTCG-TGTTCCATT
*
300279 ATGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTGTTGCCATT
1 GTGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTGTT-CCATT
* * * * *
300325 GTATCTTTCAACTATGGTCTTATTCATTTTTTGTTGTGTTTCTATT
1 GTGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTG-TTCCATT
* * *
300371 GTGTCTTTTAACCATGGTCTTATTCATTTT-TCGTCGTGTTTCATA
1 GTGTCTTTCAACCATGGTCTTATTCATTTTCT-GTCGTGTTCCATT
* * *
300416 GTGTCTTTCAACTATGTTCATATTCATTTTC
1 GTGTCTTTCAACCATGGTCTTATTCATTTTC
300447 CACCGAGTTG
Statistics
Matches: 140, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.01
43 5 0.04
44 3 0.02
45 57 0.41
46 71 0.51
47 2 0.01
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (45 bp):
GTGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTGTTCCATT
Found at i:300485 original size:137 final size:137
Alignment explanation
Indices: 300234--300486 Score: 312
Period size: 137 Copynumber: 1.8 Consensus size: 137
300224 AGGCGCAATG
* * *
300234 GTGTCTTTCAACCATGGTCTTATTTATTATTGACTTGATGTTATAATGTCTTTCAACCATGGTCT
1 GTGTCTTTCAACCATGGTCTTATTCATTATTGACGTGATGTTATAATGTCTTTCAACCATGGTCA
*** * ** *
300299 TATTCATTTTCTGTCGTGTTGCCATTGTATCTTTCAACTATGGTCTTATTCATTTTTTGTTGTGT
66 TATTCATTTTCCACCGAGTTGCCATAATATCATTCAACTATGGTCTTATTCATTTTTTGTTGTGT
300364 TTCTATT
131 TTCTATT
* * * * * *
300371 GTGTCTTTTAACCATGGTCTTATTCATTTTTCGTCGTG-T-TTCATAGTGTCTTTCAACTATGTT
1 GTGTCTTTCAACCATGGTCTTATTCATTATT-GACGTGATGTT-ATAATGTCTTTCAACCATGGT
* *
300434 CATATTCATTTTCCACCGAGTTGCCATAATATCATTCAATTATGGTTTTATTC
64 CATATTCATTTTCCACCGAGTTGCCATAATATCATTCAACTATGGTCTTATTC
300487 GTTTGATTCG
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
136 2 0.02
137 90 0.94
138 4 0.04
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (137 bp):
GTGTCTTTCAACCATGGTCTTATTCATTATTGACGTGATGTTATAATGTCTTTCAACCATGGTCA
TATTCATTTTCCACCGAGTTGCCATAATATCATTCAACTATGGTCTTATTCATTTTTTGTTGTGT
TTCTATT
Found at i:309926 original size:20 final size:20
Alignment explanation
Indices: 309882--309920 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
309872 CACTAACTTT
309882 AAATGGAATACAATGAGATA
1 AAATGGAATACAATGAGATA
309902 AAATGGAAT-CAAATGAGAT
1 AAATGGAATAC-AATGAGAT
309921 GTAATGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (20 bp):
AAATGGAATACAATGAGATA
Found at i:311089 original size:14 final size:14
Alignment explanation
Indices: 311070--311096 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
311060 ACATATCTAA
311070 AGTGTTCCATCCAC
1 AGTGTTCCATCCAC
311084 AGTGTTCCATCCA
1 AGTGTTCCATCCA
311097 TAATAATGCT
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:0.33, G:0.15, T:0.30
Consensus pattern (14 bp):
AGTGTTCCATCCAC
Found at i:312807 original size:13 final size:13
Alignment explanation
Indices: 312789--312813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312779 TAATTTAATA
312789 TTATTTTGTGTGT
1 TTATTTTGTGTGT
312802 TTATTTTGTGTG
1 TTATTTTGTGTG
312814 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:315887 original size:4 final size:4
Alignment explanation
Indices: 315878--315903 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
315868 ACATAATAGC
315878 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
315904 ATCACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:329752 original size:8 final size:9
Alignment explanation
Indices: 329729--329755 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
329719 TTTTGCTACT
329729 TATTTTTAA
1 TATTTTTAA
329738 TATTTTTAA
1 TATTTTTAA
329747 TATTTTTAA
1 TATTTTTAA
329756 AATTAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:332956 original size:12 final size:12
Alignment explanation
Indices: 332941--332972 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
332931 ATCACCACCC
332941 CCACCACCGCCG
1 CCACCACCGCCG
*
332953 CCACCACCGCTG
1 CCACCACCGCCG
332965 CCACCACC
1 CCACCACC
332973 ACCCATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.66, G:0.12, T:0.03
Consensus pattern (12 bp):
CCACCACCGCCG
Found at i:341008 original size:6 final size:6
Alignment explanation
Indices: 340997--341022 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
340987 TCGTGAAACG
340997 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
341023 CGAAAACGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:341806 original size:40 final size:40
Alignment explanation
Indices: 341754--342360 Score: 711
Period size: 40 Copynumber: 14.8 Consensus size: 40
341744 GTTTCTTTCG
* **
341754 TCTGCTCCACTACTGCTTAGGGAGATAAGACTAGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
* * * * *
341794 TTTGCTCCACTACTGCTTAGGGAGATAATATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATATGA
** ** * *
341837 TCCACTCCACTACAACTTCAGGGAGATAGGA-TTGATTTCTTTTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGA-----TATGA
341881 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
341921 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
341961 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
342001 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
342041 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
** *
342081 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGAC---TTGATAT-GA
* *
342124 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGTTTATTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGAC---TTGATAT-GA
* *
342167 TCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
* *
342207 TCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
** *
342247 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATAT-GA
* *
342291 TCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
* *
342331 TCTGCTCCACTACTACTTAGGAAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
342361 TCTGGTTTTT
Statistics
Matches: 505, Mismatches: 40, Indels: 44
0.86 0.07 0.07
Matches are distributed among these distances:
39 5 0.01
40 325 0.64
41 4 0.01
42 1 0.00
43 104 0.21
44 62 0.12
45 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGA
Found at i:342267 original size:286 final size:289
Alignment explanation
Indices: 341754--342360 Score: 875
Period size: 286 Copynumber: 2.1 Consensus size: 289
341744 GTTTCTTTCG
* *
341754 TCTGCTCCACTACTGCTTAGGGAGATAAGACTAGATGCGATTTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTAGATACGATCTGCTCCACTACTGCTTAGGGAGA
* * * * *
341819 TAATATCTGTGGTTTTAATCCACTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTTTGTCT
66 TAAGATCTGTGGTTTTAATCCACTCCACTACAACTTCAGGGAGATAAGACTGATTTATTTCGTCT
* *
341884 GCTCCACTACTGCTTAGGGAGATAAGACTTGATATGATCTGCTCCACTACTGCTTAGGGAGATAA
131 GCTCCACTACTGCTTAGAGAGATAAGACTTGATATGATCTGCTCCACTACTGCTTAGAGAGATAA
341949 GACTTGATATGATCTGCTCCACTACTGCTTAGGGAGATAAGA-C-TTGATAT-GATCTGCTCCAC
196 GACTTGATATGATCTGCTCCACTACTGCTTAGGGAGATAAGATCGTTGATATCG-TCTGCTCCAC
*
342011 TACTGCTTAGGGAGATAAGACTTGATATGA
260 TACTGCTTAGGGAGATAAAACTTGATATGA
* *
342041 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATATGATCTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTAGATACGATCTGCTCCACTACTGCTTAGGGAGA
* ** ** ** *
342106 TAAGA-CTG-GTTTCTTTCGTCTGCTCCACTACTGCTT-AGGGAGATAAGACTGGTTTATTTCGT
66 TAAGATCTGTG-GT-TTTAATCCACTCCACTACAACTTCAGGGAGATAAGACTGATTTATTTCGT
*
342168 CTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGAGAGAT
129 CTGCTCCACTACTGCTTAGAGAGATAAGACTTGATATGATCTGCTCCACTACTGCTTAGAGAGAT
* ** *
342233 AAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTC
194 AAGACTTGATATGATCTGCTCCACTACTGCTTAGGGAGATAAGATC--GTTGATATCGTCTGCTC
*
342298 CACTACTGCTTAGGGAGATAAAACTTGATGTGA
257 CACTACTGCTTAGGGAGATAAAACTTGATATGA
* *
342331 TCTGCTCCACTACTACTTAGGAAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
342361 TCTGGTTTTT
Statistics
Matches: 285, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
285 1 0.00
286 130 0.46
287 83 0.29
290 70 0.25
291 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (289 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTAGATACGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTGTGGTTTTAATCCACTCCACTACAACTTCAGGGAGATAAGACTGATTTATTTCGTCT
GCTCCACTACTGCTTAGAGAGATAAGACTTGATATGATCTGCTCCACTACTGCTTAGAGAGATAA
GACTTGATATGATCTGCTCCACTACTGCTTAGGGAGATAAGATCGTTGATATCGTCTGCTCCACT
ACTGCTTAGGGAGATAAAACTTGATATGA
Found at i:342489 original size:45 final size:45
Alignment explanation
Indices: 342434--342552 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 45
342424 GCTGTCGATG
* * *
342434 CAGGAGGGCAAGATCTGTTATCTTT-AGTCTGC-TCTACTGTTAGTA
1 CAGGAAGGCAAGATCTGCTATCTTTGA-TCTGCTTC-ACCGTTAGTA
* *
342479 CAGGGAGGCAAGA-CTGGCT-TCTTTGATCTGCTTCGCCGTTAGTA
1 CAGGAAGGCAAGATCT-GCTATCTTTGATCTGCTTCACCGTTAGTA
*
342523 CAGGAAGGCAAGATCTGCTATCTTCGATCT
1 CAGGAAGGCAAGATCTGCTATCTTTGATCT
342553 ACTACTTCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
44 35 0.56
45 27 0.44
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGGAAGGCAAGATCTGCTATCTTTGATCTGCTTCACCGTTAGTA
Found at i:342712 original size:87 final size:87
Alignment explanation
Indices: 342557--343158 Score: 829
Period size: 87 Copynumber: 6.9 Consensus size: 87
342547 CGATCTACTA
* *
342557 CTTCGCCGTTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
1 CTTCGCTG-TTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
342622 GGCAAGGCTTGCTTTTCGATCTG
65 GGCAAGGCTTGCTTTTCGATCTG
* * *
342645 C-TCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCACTGTAACCGATGGA
1 CTTC-GCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* *
342709 GGCAAGGTTTTG-TTTTCGATCTA
65 GGCAAGG-CTTGCTTTTCGATCTG
* * *
342732 CTTCACTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAG
* *
342797 GCAAGACTTTCTTTTCGATCTG
66 GCAAGGCTTGCTTTTCGATCTG
* * *
342819 C-TCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCACTGTAACCGATGGA
1 CTTC-GCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* *
342883 GGCAAGGTTTTG-TTTTCGATCTA
65 GGCAAGG-CTTGCTTTTCGATCTG
* * *
342906 CTTCACTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAG
*
342971 GCAAGGCTTTCTTTTCGATCTG
66 GCAAGGCTTGCTTTTCGATCTG
* * * * *
342993 C-TCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCACCGTAACCGATAGA
1 CTTC-GCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
*
343057 GGCAAGGTTTTG-TTTTCGATCTG
65 GGCAAGG-CTTGCTTTTCGATCTG
* *
343080 CTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAG
*
343145 GCAAGGCTTTCTTT
66 GCAAGGCTTGCTTT
343159 GATCTGTTCT
Statistics
Matches: 447, Mismatches: 55, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
86 10 0.02
87 420 0.94
88 17 0.04
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (87 bp):
CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAG
GCAAGGCTTGCTTTTCGATCTG
Found at i:342768 original size:174 final size:174
Alignment explanation
Indices: 342566--343158 Score: 1105
Period size: 174 Copynumber: 3.4 Consensus size: 174
342556 ACTTCGCCGT
* * *
342566 TTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
1 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
*
342631 TGCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
66 TTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
342696 TGTAACCGATGGAGGCAAGGTTTTGTTTTCGATCTACTTCACTG
131 TGTAACCGATGGAGGCAAGGTTTTGTTTTCGATCTACTTCACTG
*
342740 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGACT
1 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
342805 TTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
66 TTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
342870 TGTAACCGATGGAGGCAAGGTTTTGTTTTCGATCTACTTCACTG
131 TGTAACCGATGGAGGCAAGGTTTTGTTTTCGATCTACTTCACTG
342914 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
1 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
342979 TTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
66 TTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
* * * *
343044 CGTAACCGATAGAGGCAAGGTTTTGTTTTCGATCTGCTTCGCTG
131 TGTAACCGATGGAGGCAAGGTTTTGTTTTCGATCTACTTCACTG
343088 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
1 TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
343153 TTCTTT
66 TTCTTT
343159 GATCTGTTCT
Statistics
Matches: 409, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 409 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (174 bp):
TTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCT
TTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCAC
TGTAACCGATGGAGGCAAGGTTTTGTTTTCGATCTACTTCACTG
Found at i:344125 original size:13 final size:12
Alignment explanation
Indices: 344107--344160 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
344097 TTGGCCTCTC
344107 CTTTTTCTCTTTT
1 CTTTTTCT-TTTT
344120 CTTTTTCGTTTTT
1 CTTTTTC-TTTTT
344133 C-TTTTCTTTTTT
1 CTTTTTC-TTTTT
*
344145 CTTTTTGTTTTT
1 CTTTTTCTTTTT
344157 -TTTT
1 CTTTT
344161 CTCAAGTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
11 4 0.11
12 16 0.43
13 16 0.43
14 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:344137 original size:18 final size:17
Alignment explanation
Indices: 344109--344162 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
344099 GGCCTCTCCT
344109 TTTTCTCTTTTCTTTTTC
1 TTTT-TCTTTTCTTTTTC
344127 GTTTTTCTTTTCTTTTTTC
1 -TTTTTCTTTTC-TTTTTC
*
344146 TTTTTGTTTT-TTTTTC
1 TTTTTCTTTTCTTTTTC
344162 T
1 T
344163 CAAGTGAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 7 0.21
18 16 0.48
19 10 0.30
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTC
Found at i:344138 original size:25 final size:23
Alignment explanation
Indices: 344108--344163 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 23
344098 TGGCCTCTCC
344108 TTTTTCTCTTTTCTTTTTCGTTTT
1 TTTTTCTCTTTTCTTTTT-GTTTT
*
344132 TCTTTTCTTTTTTCTTTTTGTTTT
1 T-TTTTCTCTTTTCTTTTTGTTTT
344156 TTTTTCTC
1 TTTTTCTC
344164 AAGTGAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 7 0.24
25 16 0.55
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTTCTCTTTTCTTTTTGTTTT
Found at i:346060 original size:62 final size:62
Alignment explanation
Indices: 345881--346062 Score: 337
Period size: 62 Copynumber: 2.9 Consensus size: 62
345871 CTCAAAGCAC
* *
345881 TTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTGATGCATGAACGCGTAT
1 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCGTAT
345943 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCGTAT
1 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCGTAT
*
346005 TTTTGGATTTTAGGAAATTTGTTGCATGCAATGAAATGTAATGTTGATGCATGAATGC
1 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGC
346063 AAAAAAGAGA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
62 117 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (62 bp):
TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCGTAT
Found at i:351604 original size:19 final size:20
Alignment explanation
Indices: 351580--351619 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
351570 AGTCTGAGAG
351580 AGTGAAACAG-ATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
*
351599 AGTGAATCAGAATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
351619 A
1 A
351620 ATAGAGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.15, G:0.20, T:0.12
Consensus pattern (20 bp):
AGTGAAACAGAATCCAAGAA
Found at i:351792 original size:3 final size:3
Alignment explanation
Indices: 351784--351817 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
351774 CTTTTGTTTC
351784 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
351818 GGGTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:351908 original size:29 final size:29
Alignment explanation
Indices: 351867--351924 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
351857 TTATAAGGAT
*
351867 TGGATTAAATTAGTCCATTTATTATTAAA
1 TGGATTAAATTAGTCCATATATTATTAAA
* *
351896 TGGATTAATTTAGTCCATATGTTATTAAA
1 TGGATTAAATTAGTCCATATATTATTAAA
351925 AAGAATCAAA
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:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (29 bp):
TGGATTAAATTAGTCCATATATTATTAAA
Found at i:352592 original size:22 final size:21
Alignment explanation
Indices: 352549--352593 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
352539 TAAACCCTCA
*
352549 AAATTTTTAAAAATTATTATT
1 AAATTTTTAAAAATTATAATT
*
352570 AAATTTCTTAAAAATTGTAATT
1 AAATTT-TTAAAAATTATAATT
352592 AA
1 AA
352594 GTCTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTTTTAAAAATTATAATT
Found at i:359573 original size:17 final size:19
Alignment explanation
Indices: 359540--359574 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
359530 ATTGTTTGTA
359540 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
359559 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
359575 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:365438 original size:15 final size:17
Alignment explanation
Indices: 365420--365451 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
365410 CAGAATAGAA
365420 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
365435 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
365452 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:367295 original size:29 final size:32
Alignment explanation
Indices: 367252--367335 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 32
367242 AATAGTCTAT
*
367252 ATTTTTATAATTTTTAAAAATTTAAA-T-CAA
1 ATTTTTATTATTTTTAAAAATTTAAAGTACAA
*
367282 ATTTTTATTATTTTTAAAAA-CTAAAGTAC-A
1 ATTTTTATTATTTTTAAAAATTTAAAGTACAA
*
367312 A-TTTTATTATTATTTAAAATTTTA
1 ATTTTTATTATT-TTTAAAAATTTA
367336 TCAATTATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 14 0.30
30 29 0.63
31 3 0.07
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (32 bp):
ATTTTTATTATTTTTAAAAATTTAAAGTACAA
Found at i:368736 original size:17 final size:15
Alignment explanation
Indices: 368699--368738 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
368689 TTGTTCACTT
368699 TTTTAATTTCATCCG
1 TTTTAATTTCATCCG
368714 -TTTAATTTCATCCTAG
1 TTTTAATTTCATCC--G
368730 TTTTAATTT
1 TTTTAATTT
368739 AGCCCCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTTAATTTCATCCG
Found at i:369201 original size:27 final size:28
Alignment explanation
Indices: 369163--369235 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
369153 AAAAATAAAA
369163 ATTTACCAAAATATTATAACTTTTT-TT
1 ATTTACCAAAATATTATAACTTTTTATT
*
369190 ATTTACCAAAATATTACT--TTTTTTAATT
1 ATTTACCAAAATATTA-TAACTTTTT-ATT
369218 ATTTACCAAAATA-TATAA
1 ATTTACCAAAATATTATAA
369236 AAAAACACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
26 6 0.15
27 18 0.45
28 16 0.40
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTATAACTTTTTATT
Found at i:369228 original size:28 final size:26
Alignment explanation
Indices: 369163--369231 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 26
369153 AAAAATAAAA
369163 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATATTAT-ACTTTTTTT
*
369190 ATTTACCAAAATATTACT-TTTTTTAATT
1 ATTTACCAAAATATTA-TACTTTTT--TT
369218 ATTTACCAAAATAT
1 ATTTACCAAAATAT
369232 ATAAAAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 5 0.13
27 16 0.42
28 17 0.45
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTACCAAAATATTATACTTTTTTT
Found at i:369322 original size:27 final size:27
Alignment explanation
Indices: 369283--369341 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
369273 TCTGGGTTAG
*
369283 GCCAATGGAATTGGCAGCACCAAAT-GT
1 GCCAATGCAATTGGCAGCACC-AATGGT
* *
369310 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCAATTGGCAGCACCAATGGT
369337 GCCAA
1 GCCAA
369342 AGGACTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (27 bp):
GCCAATGCAATTGGCAGCACCAATGGT
Found at i:369594 original size:19 final size:19
Alignment explanation
Indices: 369570--369631 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
369560 NNNNNNTCTC
369570 ATTTAATAACTCTATTTTA
1 ATTTAATAACTCTATTTTA
* * *
369589 ATTTAATAA-ACTATTCTC
1 ATTTAATAACTCTATTTTA
369607 ATTTAATAACTCTATTTTA
1 ATTTAATAACTCTATTTTA
369626 ATTTAA
1 ATTTAA
369632 AAAAATTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAATAACTCTATTTTA
Found at i:369669 original size:27 final size:28
Alignment explanation
Indices: 369618--369714 Score: 187
Period size: 28 Copynumber: 3.5 Consensus size: 28
369608 TTTAATAACT
369618 CTATTTTAATTTAAAAAAATTAAGTAAA
1 CTATTTTAATTTAAAAAAATTAAGTAAA
369646 CTATTTTAATTT-AAAAAATTAAGTAAA
1 CTATTTTAATTTAAAAAAATTAAGTAAA
369673 CTATTTTAATTTAAAAAAATTAAGTAAA
1 CTATTTTAATTTAAAAAAATTAAGTAAA
369701 CTATTTTAATTTAA
1 CTATTTTAATTTAA
369715 TAGTTTATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
27 27 0.40
28 41 0.60
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (28 bp):
CTATTTTAATTTAAAAAAATTAAGTAAA
Found at i:370565 original size:19 final size:19
Alignment explanation
Indices: 370543--370608 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 19
370533 GTAAATTATT
* *
370543 TTAATTTAAAATAGAGTTG
1 TTAAATTAAAATAGAGTTA
* * *
370562 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
370580 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
370599 TTAAA-TAAAA
1 TTAAATTAAAA
370609 AAGTGAGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
18 19 0.50
19 19 0.50
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:370609 original size:19 final size:19
Alignment explanation
Indices: 370550--370609 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
370540 ATTTTAATTT
* *
370550 AAAATAGAGTTGTTAAATG
1 AAAATAGAGTTATTAAATA
* * *
370569 AGAATAG-TTTATTAAATT
1 AAAATAGAGTTATTAAATA
370587 AAAATAGAGTTATTAAATA
1 AAAATAGAGTTATTAAATA
370606 AAAA
1 AAAA
370610 AGTGAGTTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 14 0.42
19 19 0.58
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (19 bp):
AAAATAGAGTTATTAAATA
Found at i:370893 original size:26 final size:26
Alignment explanation
Indices: 370841--370905 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
370831 TTTTTGATAC
* *
370841 ATTTTGGTGAATAATTAAAAATGTAAT
1 ATTTTGGTAAATAA-TAAAAATATAAT
370868 ATTTTGGTAAATAA-AAAAATTATAAT
1 ATTTTGGTAAATAATAAAAA-TATAAT
370894 ATTTTGGTAAAT
1 ATTTTGGTAAAT
370906 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 5 0.14
26 17 0.49
27 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTGGTAAATAATAAAAATATAAT
Found at i:375415 original size:25 final size:25
Alignment explanation
Indices: 375387--375444 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
375377 AAAAAAAATC
*
375387 AAAATCAAAATG-AAAAACAAAAAAG
1 AAAATCAAAAAGCAAAAAC-AAAAAG
*
375412 AAAAT-AAAAAGCAAAAGCAAAAAG
1 AAAATCAAAAAGCAAAAACAAAAAG
375436 AGAAATCAA
1 A-AAATCAA
375445 TCAAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 12 0.43
25 14 0.50
26 2 0.07
ACGTcount: A:0.74, C:0.09, G:0.10, T:0.07
Consensus pattern (25 bp):
AAAATCAAAAAGCAAAAACAAAAAG
Found at i:375857 original size:14 final size:13
Alignment explanation
Indices: 375839--375873 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
375829 AAAAGATGAT
375839 GAAAAATGAAAAA
1 GAAAAATGAAAAA
*
375852 GAAAAATGAAAGA
1 GAAAAATGAAAAA
375865 GTAAAAATG
1 G-AAAAATG
375874 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:377972 original size:22 final size:18
Alignment explanation
Indices: 377930--377965 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
377920 ACAAGCCAAT
377930 ATACAAAATAATTAATGA
1 ATACAAAATAATTAATGA
377948 ATACAAAATAATTAATGA
1 ATACAAAATAATTAATGA
377966 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
ATACAAAATAATTAATGA
Found at i:378058 original size:3 final size:3
Alignment explanation
Indices: 378050--378088 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
378040 AAAACAGTAA
378050 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
378089 GGTGATAATT
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:387845 original size:20 final size:19
Alignment explanation
Indices: 387820--387863 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
387810 ATTTATAGAA
387820 TTTTTTAAATTTTTGAAGAT
1 TTTTTTAAATTTTTGAA-AT
* *
387840 TTTTTTGAATTTTTGTAAT
1 TTTTTTAAATTTTTGAAAT
387859 TTTTT
1 TTTTT
387864 CAAGGGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (19 bp):
TTTTTTAAATTTTTGAAAT
Found at i:392034 original size:278 final size:279
Alignment explanation
Indices: 391527--392083 Score: 1107
Period size: 278 Copynumber: 2.0 Consensus size: 279
391517 AAAGGAAAAA
391527 AAATGAGAGTTTTTTTTAGGGAAAAAAATGAAATTATGTTTTTTTTCTTCTTTTGTAAGTAAAGT
1 AAATGAGAGTTTTTTTTAGGGAAAAAAATGAAATTATGTTTTTTTTCTTCTTTTGTAAGTAAAGT
391592 TTAAAGATATTTTCTTAAATTATTTTTATTTTAAATAAATATAATTATATATGTATGCAATATTT
66 TTAAAGATATTTTCTTAAATTATTTTTATTTTAAATAAATATAATTATATATGTATGCAATATTT
391657 TTACGTAATATGATGTTATATCAATAATTATGTTAGAGAATCAAATTAACATTTAATGTATAAAA
131 TTACGTAATATGATGTTATATCAATAATTATGTTAGAGAATCAAATTAACATTTAATGTATAAAA
391722 TTACACAAAATCAAAGTAACTAAATTAAAATACATGGACAAAAACCATATTAGGTATAGTACACT
196 TTACACAAAATCAAAGTAACTAAATTAAAATACATGGACAAAAACCATATTAGGTATAGTACACT
391787 TTGAAAAAATAATAATAAT
261 TTGAAAAAATAATAATAAT
391806 AAATGAGAGTTTTTTTT-GGGAAAAAAATGAAATTATGTTTTTTTTCTTCTTTTGTAAGTAAAGT
1 AAATGAGAGTTTTTTTTAGGGAAAAAAATGAAATTATGTTTTTTTTCTTCTTTTGTAAGTAAAGT
391870 TTAAAGATATTTTCTTAAATTATTTTTATTTTAAATAAATATAATTATATATGTATGCAATATTT
66 TTAAAGATATTTTCTTAAATTATTTTTATTTTAAATAAATATAATTATATATGTATGCAATATTT
391935 TTACGTAATATGATGTTATATCAATAATTATGTTAGAGAATCAAATTAACATTTAATGTATAAAA
131 TTACGTAATATGATGTTATATCAATAATTATGTTAGAGAATCAAATTAACATTTAATGTATAAAA
392000 TTACACAAAATCAAAGTAACTAAATTAAAATACATGGACAAAAACCATATTAGGTATAGTACACT
196 TTACACAAAATCAAAGTAACTAAATTAAAATACATGGACAAAAACCATATTAGGTATAGTACACT
392065 TTGAAAAAATAATAATAAT
261 TTGAAAAAATAATAATAAT
392084 GTTTTAATTT
Statistics
Matches: 278, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
278 261 0.94
279 17 0.06
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (279 bp):
AAATGAGAGTTTTTTTTAGGGAAAAAAATGAAATTATGTTTTTTTTCTTCTTTTGTAAGTAAAGT
TTAAAGATATTTTCTTAAATTATTTTTATTTTAAATAAATATAATTATATATGTATGCAATATTT
TTACGTAATATGATGTTATATCAATAATTATGTTAGAGAATCAAATTAACATTTAATGTATAAAA
TTACACAAAATCAAAGTAACTAAATTAAAATACATGGACAAAAACCATATTAGGTATAGTACACT
TTGAAAAAATAATAATAAT
Found at i:398863 original size:44 final size:44
Alignment explanation
Indices: 398795--398883 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
398785 TTAAAATTAC
*
398795 ATCATACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
1 ATCACACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
*
398839 ATCACACTTTTACGGAGTCTAAAATCGGATACCAATATGGACCT
1 ATCACACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
398883 A
1 A
398884 ATTGCAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (44 bp):
ATCACACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
Found at i:399116 original size:2 final size:2
Alignment explanation
Indices: 399109--399159 Score: 52
Period size: 2 Copynumber: 25.0 Consensus size: 2
399099 ATAAAATGAA
*
399109 AT AT AT AT AT AT AT AT AT AT AT CAA AGT GA- AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT -AT A-T -AT AT AT AT AT AT AT
399150 AT AT AT AT AT
1 AT AT AT AT AT
399160 CAAAGTGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 1 0.02
4 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:399161 original size:29 final size:30
Alignment explanation
Indices: 399108--399169 Score: 117
Period size: 29 Copynumber: 2.1 Consensus size: 30
399098 AATAAAATGA
399108 AATATATATATATATATATATATCAAAGTG
1 AATATATATATATATATATATATCAAAGTG
399138 AATATATATATA-ATATATATATCAAAGTG
1 AATATATATATATATATATATATCAAAGTG
399167 AAT
1 AAT
399170 TTAATTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
AATATATATATATATATATATATCAAAGTG
Found at i:400445 original size:20 final size:22
Alignment explanation
Indices: 400416--400461 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
400406 AAAAAAAGTG
400416 TTAAAGTTAGAT-TTT-GTTAA
1 TTAAAGTTAGATATTTAGTTAA
* *
400436 TTAAATTTAGATATTTATTTAA
1 TTAAAGTTAGATATTTAGTTAA
400458 TTAA
1 TTAA
400462 CGAAATCGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTAAAGTTAGATATTTAGTTAA
Found at i:403289 original size:4 final size:5
Alignment explanation
Indices: 403267--403301 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
403257 CTAAATCAAA
403267 TTAAT TTAAT TTAAT TTAA- TTAA- TTAAT TTAAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
403302 TATCCGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:413546 original size:2 final size:2
Alignment explanation
Indices: 413507--413535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
413497 ATTACTTTTA
413507 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 A
413536 CACCTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:422042 original size:30 final size:30
Alignment explanation
Indices: 422008--422065 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
421998 GTAGTCGTTC
*
422008 AACTATTAAAAAGTTTTTGTTTAAGTCACT
1 AACTATTAAAAAGTTTTTATTTAAGTCACT
*
422038 AACTATTAGAAAGTTTTTATTTAAGTCA
1 AACTATTAAAAAGTTTTTATTTAAGTCA
422066 TTGAATCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
AACTATTAAAAAGTTTTTATTTAAGTCACT
Found at i:423314 original size:15 final size:15
Alignment explanation
Indices: 423278--423316 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
423268 TTTTCCCTCA
*
423278 TCTTTTATTCAAACT
1 TCTTTTATTTAAACT
*
423293 T-TTTTATTTAAATT
1 TCTTTTATTTAAACT
423307 TCTTTTATTT
1 TCTTTTATTT
423317 TTTCCTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTTTTATTTAAACT
Found at i:424918 original size:36 final size:36
Alignment explanation
Indices: 424871--424943 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
424861 AGGTACTTAA
424871 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
1 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
424907 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
1 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
424943 A
1 A
424944 TACTTCATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (36 bp):
AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
Done.