Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold437
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: 279167
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.29
Warning! 42356 characters in sequence are not A, C, G, or T
Found at i:8040 original size:12 final size:12
Alignment explanation
Indices: 8023--8061 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
8013 GCAGAGGTTA
8023 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
8035 CAGCGAGAGAAA
1 CAGCGAGAGAAG
8047 CAGCG-GTAGAAG
1 CAGCGAG-AGAAG
8059 CAG
1 CAG
8062 AGGTTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 1 0.04
12 23 0.96
ACGTcount: A:0.41, C:0.18, G:0.38, T:0.03
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:8565 original size:42 final size:42
Alignment explanation
Indices: 8494--8745 Score: 328
Period size: 42 Copynumber: 6.0 Consensus size: 42
8484 GTTTGTGAAA
* * **
8494 TAAGCGCTGCTAAAGAGCACT-A-CTGTTAGCGGCGTTTTTGAC
1 TAAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTCC
* * * * *
8536 AAAGCGCCACTATAGAACATTATTTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTCC
8579 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* * *
8621 CAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTCG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
*
8663 TAAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCC
*
8706 TTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
8746 TTCTGTAAGC
Statistics
Matches: 184, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.01
42 108 0.59
43 75 0.41
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:8591 original size:85 final size:84
Alignment explanation
Indices: 8494--8745 Score: 337
Period size: 85 Copynumber: 3.0 Consensus size: 84
8484 GTTTGTGAAA
* * ** * *
8494 TAAGCGCTGCTAAAGAGCACT-A-CTGTTAGCGGCGTTTTTGACAAAGCGCCACTATAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTCCAAAGCGCCACTAAAGAACATG
*
8557 ATTTTTAGCGGCGTTTTCTTCC
64 ATCTTTAGCGGCGTTTT-TTCC
*
8579 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCCACTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCACTAAAGAACATGAT
*
8644 CTTTAGCGGCGTTTTTTCG
66 CTTTAGCGGCGTTTTTTCC
* ** *
8663 TAAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTTCCTTAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCCAAAGCGCCACTAAAGAACATGA
8728 TCTTTAGCGGCGTTTTTT
65 TCTTTAGCGGCGTTTTTT
8746 TTCTGTAAGC
Statistics
Matches: 151, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
84 37 0.25
85 112 0.74
86 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCACTAAAGAACATGAT
CTTTAGCGGCGTTTTTTCC
Found at i:10243 original size:20 final size:19
Alignment explanation
Indices: 10218--10263 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
10208 AACAAACATT
*
10218 TTTTTTACAAAATTTAATCA
1 TTTTTTACAAAAGTTAA-CA
* *
10238 TTTTTTCCATAAGTTAACA
1 TTTTTTACAAAAGTTAACA
10257 TTTTTTA
1 TTTTTTA
10264 TTTTTGTGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTTTTACAAAAGTTAACA
Found at i:11218 original size:15 final size:17
Alignment explanation
Indices: 11191--11224 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11181 TAATGGATGG
11191 AAATAATTATTTT-ATA
1 AAATAATTATTTTAATA
11207 AAATAA-TATTTTAATA
1 AAATAATTATTTTAATA
11223 AA
1 AA
11225 TTTGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATTATTTTAATA
Found at i:13995 original size:73 final size:73
Alignment explanation
Indices: 13866--14004 Score: 176
Period size: 73 Copynumber: 1.9 Consensus size: 73
13856 TTGCTTACAT
* * *
13866 CATCATTGGTTTGATGATAACTTCCACGTTGCAAGACTTGTTTGTCTGCATATGGATTGT-CTTC
1 CATCATGGGTTTGATGATAACATCCACGTTGCAAGACTTGTTTGTCGGCATATGGATT-TCCTTC
13930 TTTTGTCTC
65 TTTTGTCTC
* * *
13939 CATCATGGGTTTGATGATGACATCCACGTTGCCAA-ACTT-TGTTGTCGGTATGTGGATTTCCTT
1 CATCATGGGTTTGATGATAACATCCACGTTG-CAAGACTTGT-TTGTCGGCATATGGATTTCCTT
14002 CTT
64 CTT
14005 ATCAAGTTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
72 2 0.04
73 52 0.91
74 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (73 bp):
CATCATGGGTTTGATGATAACATCCACGTTGCAAGACTTGTTTGTCGGCATATGGATTTCCTTCT
TTTGTCTC
Found at i:21123 original size:19 final size:19
Alignment explanation
Indices: 21099--21136 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21089 AATTAGTCCT
21099 CTGTTAAAAATTTTATCCA
1 CTGTTAAAAATTTTATCCA
21118 CTGTTAAAAATTTTATCCA
1 CTGTTAAAAATTTTATCCA
21137 TTTCTATTGT
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:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (19 bp):
CTGTTAAAAATTTTATCCA
Found at i:27495 original size:46 final size:46
Alignment explanation
Indices: 27442--27532 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
27432 AAGAAAAGGA
27442 GATGTTAAATGATTGAGGGTATAAATTTAGCCAAAAAAGTCTCTGT
1 GATGTTAAATGATTGAGGGTATAAATTTAGCCAAAAAAGTCTCTGT
* *
27488 GATGTTAAATGATTGAGGGTATAATTTTAGGCAAAAAAGTCTCTG
1 GATGTTAAATGATTGAGGGTATAAATTTAGCCAAAAAAGTCTCTG
27533 CATGTAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (46 bp):
GATGTTAAATGATTGAGGGTATAAATTTAGCCAAAAAAGTCTCTGT
Found at i:34212 original size:27 final size:28
Alignment explanation
Indices: 34150--34216 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
34140 AAATAAAAAA
*
34150 TAACCAAAATATTATAACTTTTTTTTAT
1 TAACCAAAATATTATAACATTTTTTTAT
* *
34178 TTATCAAAATATTATAA-ATTTTTTTAT
1 TAACCAAAATATTATAACATTTTTTTAT
34205 TAACCAAAATAT
1 TAACCAAAATAT
34217 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.56
28 15 0.44
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
TAACCAAAATATTATAACATTTTTTTAT
Found at i:35402 original size:28 final size:29
Alignment explanation
Indices: 35371--35435 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
35361 TTTTTTTGGT
* *
35371 ATATTTTGGTAAAT-TAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAAGTTATA
35399 ATATTTTGGTAAATAAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAAGTTATA
35428 ATATTTTG
1 ATATTTTG
35436 TTTATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 14 0.41
29 20 0.59
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTATA
Found at i:44704 original size:38 final size:39
Alignment explanation
Indices: 44662--44771 Score: 125
Period size: 38 Copynumber: 2.8 Consensus size: 39
44652 TTGGATAGTT
* *
44662 CGAAGCAAAGTTGACACCCAGTGTCCCATC-AACCTAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* * * *
44700 CGAAGTAAAG-TGATACCCAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
44738 CGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAAAGT--TGACACCCAGTGTCTCATCGA
44772 CTTGAGGTCG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 16 0.27
38 24 0.41
41 19 0.32
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:45666 original size:26 final size:25
Alignment explanation
Indices: 45602--45667 Score: 61
Period size: 26 Copynumber: 2.8 Consensus size: 25
45592 ACCCTATTTC
45602 TCGTTTCTTTC---TTT-TCCTTTT
1 TCGTTTCTTTCTTGTTTCTCCTTTT
* *
45623 TCTTTTCTTTCTTTTTTCTCCTTGTT
1 TCGTTTCTTTCTTGTTTCTCCTT-TT
45649 TCGTTTCTATT-TTGTTTCT
1 TCGTTTCT-TTCTTGTTTCT
45668 TTTTATGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 10 0.28
24 3 0.08
25 5 0.14
26 16 0.44
27 2 0.06
ACGTcount: A:0.02, C:0.21, G:0.06, T:0.71
Consensus pattern (25 bp):
TCGTTTCTTTCTTGTTTCTCCTTTT
Found at i:45994 original size:29 final size:29
Alignment explanation
Indices: 45952--46008 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
45942 GTCTTTTCTT
*
45952 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAATAAAATAATC
45981 AATTTAATTT-ATAATATAATAAAATAAT
1 AATTT-ATTTCATAATATAATAAAATAAT
46009 AACAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTTATTTCATAATATAATAAAATAATC
Found at i:46029 original size:37 final size:37
Alignment explanation
Indices: 45962--46032 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
45952 AATTTATTTC
* * *
45962 ATAATATAATAATATAATCAATTTAATTTATAATATA
1 ATAAAATAATAAAATAATCAATATAATTTATAATATA
*
45999 ATAAAATAATAACAATAAT-AATATATTTTATAAT
1 ATAAAATAATAA-AATAATCAATATAATTTATAAT
46033 TAAACAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (37 bp):
ATAAAATAATAAAATAATCAATATAATTTATAATATA
Found at i:51966 original size:23 final size:22
Alignment explanation
Indices: 51916--51968 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
51906 GGGAGCCGAA
*
51916 ATTAAATTGTAATTTTTACGAT
1 ATTAAATTGTAATTTTTACAAT
*
51938 AATAAATATGTAATTTTTA-AAT
1 ATTAAAT-TGTAATTTTTACAAT
51960 GATTAAATT
1 -ATTAAATT
51969 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTAAATTGTAATTTTTACAAT
Found at i:52120 original size:31 final size:31
Alignment explanation
Indices: 52082--52148 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
52072 GATTCGCACC
52082 TGAAAATATATCTTATTTCAATTTTAGATAT
1 TGAAAATATATCTTATTTCAATTTTAGATAT
*
52113 TGAAAATATGTCTTATTTCAATTTTAGATAT
1 TGAAAATATATCTTATTTCAATTTTAGATAT
52144 TGAAA
1 TGAAA
52149 CAAACACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (31 bp):
TGAAAATATATCTTATTTCAATTTTAGATAT
Found at i:53829 original size:32 final size:31
Alignment explanation
Indices: 53771--53836 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
53761 TCAATGTTAT
* * *
53771 TTTGCTACTGTTTGCTACTATTTTGTTGCTA
1 TTTGCTACTGTTTACTACTATATTGTTACTA
* *
53802 TTTGCTGCTAGTTTACTATTATATTGTTACTA
1 TTTGCTACT-GTTTACTACTATATTGTTACTA
53834 TTT
1 TTT
53837 TGTTGTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (31 bp):
TTTGCTACTGTTTACTACTATATTGTTACTA
Found at i:57079 original size:8 final size:8
Alignment explanation
Indices: 57066--57107 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
57056 ATTAATTAAG
57066 TTCTTTTT
1 TTCTTTTT
57074 TTCTTTTT
1 TTCTTTTT
*
57082 CTT-TTTCT
1 -TTCTTTTT
*
57090 TTCTTTCT
1 TTCTTTTT
57098 TTCTTTTT
1 TTCTTTTT
57106 TT
1 TT
57108 TTGGGGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 2 0.07
8 26 0.87
9 2 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTCTTTTT
Found at i:57088 original size:12 final size:11
Alignment explanation
Indices: 57069--57109 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
57059 AATTAAGTTC
57069 TTTTTTTCTTT
1 TTTTTTTCTTT
57080 TTCTTTTTCTTT
1 TT-TTTTTCTTT
*
57092 CTTTCTTTCTTT
1 -TTTTTTTCTTT
57104 TTTTTT
1 TTTTTT
57110 GGGGTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.27
12 17 0.65
13 2 0.08
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:57704 original size:2 final size:2
Alignment explanation
Indices: 57697--57726 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57687 AATTGCCCAA
57697 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
57727 GAAAACAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59743 original size:13 final size:12
Alignment explanation
Indices: 59725--59761 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
59715 TATCATCGTC
59725 ATTATTTGTTTTT
1 ATTATTT-TTTTT
59738 ATTATTTATTTTT
1 ATTATTT-TTTTT
59751 ATTATTTTTTT
1 ATTATTTTTTT
59762 CTTTGATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (12 bp):
ATTATTTTTTTT
Found at i:65535 original size:143 final size:143
Alignment explanation
Indices: 65277--66065 Score: 1098
Period size: 143 Copynumber: 5.5 Consensus size: 143
65267 GATTAAAGTC
* * * *
65277 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAAATTGAAGCAATCAACCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
65342 CTGAAGTTGCAGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCGTTGCAGTGTAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTAGCGTTGCAGTGGAACAG
65407 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * *
65420 ATTATGGCGGATATTATCTTCCTAAAGTTGCAGT-GAAGCAGATTGAAGCCACCAGCCTTATCCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAA-CAGATTGAAGCCACCAGCCTTATCTC
* * * * *
65484 CCTGAAGTTACAACGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
65 CCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTAGCGTTGCAGTGGAACA
*
65549 AATTAAAGCTACAA
130 GATTAAAGCTACAA
*
65563 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACC-GACCTTATCTC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAG-CCTTATCTC
* * * * *
65627 CCTGAAGTTACAGCAGAGCAGACTAAAGACAGGGAATCTTATTTCTCTAGCGTTGCAGTGGAACA
65 CCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTAGCGTTGCAGTGGAACA
*
65692 GATTAAAGCTATAA
130 GATTAAAGCTACAA
* * * * *
65706 ATTATAGCGGACCTTATCTTCCTAAAGTTGCAGTGGAACATATTGAAGCCACTAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* *
65771 CTAAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCTCTAGCGTTGCAGTAGAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTAGCGTTGCAGTGGAACAG
65836 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* ** * *
65849 ATTATGGTGGATCTTATCTTTTTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
65914 CTAAAGTTGCAACGGAGCAAACTGAAGACAGCGGATCTTATTTCTCTAGCGTTGTAGTGAAATAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTAGCGTTGCAGTGGAACAG
65979 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * *
65992 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTAGAGC-GTATTGAAGCCACTAGCCTTATCTC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAG-ATTGAAGCCACCAGCCTTATCTC
66056 CCTAAAGTTG
65 CCTAAAGTTG
66066 TAGTGAAGCA
Statistics
Matches: 581, Mismatches: 60, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
142 5 0.01
143 572 0.98
144 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (143 bp):
ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTAGCGTTGCAGTGGAACAG
ATTAAAGCTACAA
Found at i:67616 original size:12 final size:12
Alignment explanation
Indices: 67599--67624 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
67589 TTCTTGTACC
67599 ATATTTATTATT
1 ATATTTATTATT
67611 ATATTTATTATT
1 ATATTTATTATT
67623 AT
1 AT
67625 TACTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTATTATT
Found at i:69090 original size:20 final size:21
Alignment explanation
Indices: 69065--69105 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
69055 CTCACCCTCT
*
69065 TTCTTTGTT-TTCTTTTTTTG
1 TTCTTTCTTCTTCTTTTTTTG
*
69085 TTCTTTCTTCTTTTTTTTTTG
1 TTCTTTCTTCTTCTTTTTTTG
69106 AAAATGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (21 bp):
TTCTTTCTTCTTCTTTTTTTG
Found at i:80199 original size:10 final size:11
Alignment explanation
Indices: 80175--80199 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80165 TTTGTACCTC
80175 AAAATGTTTGA
1 AAAATGTTTGA
80186 AAAATGTTTGA
1 AAAATGTTTGA
80197 AAA
1 AAA
80200 GATAGTCAAT
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (11 bp):
AAAATGTTTGA
Found at i:95738 original size:7 final size:7
Alignment explanation
Indices: 95728--95798 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 7
95718 GAAAAAAAAG
95728 AAAAATC
1 AAAAATC
95735 -AAAATC
1 AAAAATC
*
95741 -AAAGTC
1 AAAAATC
95747 -AAAAT-
1 AAAAATC
* *
95752 GAAAATG
1 AAAAATC
95759 AAAAAAATC
1 A-AAA-ATC
95768 AAAAATC
1 AAAAATC
95775 AAAAATC
1 AAAAATC
95782 AAAAAT-
1 AAAAATC
95788 AAAAAT-
1 AAAAATC
95794 AAAAA
1 AAAAA
95799 AAAGAAAGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
6 31 0.55
7 16 0.29
8 6 0.11
9 3 0.05
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.14
Consensus pattern (7 bp):
AAAAATC
Found at i:95799 original size:7 final size:7
Alignment explanation
Indices: 95761--95798 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
95751 TGAAAATGAA
95761 AAAAATC
1 AAAAATC
95768 AAAAATC
1 AAAAATC
95775 AAAAATC
1 AAAAATC
95782 AAAAAT-
1 AAAAATC
95788 AAAAAT-
1 AAAAATC
95794 AAAAA
1 AAAAA
95799 AAAGAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATC
Found at i:95848 original size:47 final size:50
Alignment explanation
Indices: 95762--95858 Score: 128
Period size: 47 Copynumber: 2.0 Consensus size: 50
95752 GAAAATGAAA
95762 AAAATCAAAAATCAAAAATCAAAAATAAAAATAAAAAAAAGAAAGAAGAA
1 AAAATCAAAAATCAAAAATCAAAAATAAAAATAAAAAAAAGAAAGAAGAA
* * * * *
95812 AAAATC-AAAATC-AAGATC-AAAATGAAAATGAGAAAAAGACAGAAGAA
1 AAAATCAAAAATCAAAAATCAAAAATAAAAATAAAAAAAAGAAAGAAGAA
95859 TGAAAAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 25 0.60
48 5 0.12
49 6 0.14
50 6 0.14
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (50 bp):
AAAATCAAAAATCAAAAATCAAAAATAAAAATAAAAAAAAGAAAGAAGAA
Found at i:98234 original size:98 final size:98
Alignment explanation
Indices: 98065--98892 Score: 1437
Period size: 98 Copynumber: 8.4 Consensus size: 98
98055 TACAGCGGAG
* * * * * * * *
98065 CAGATTGAAG-CTAGTAATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAAT-AAAGGATC
1 CAGATTGAAGCCGA-TAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACA-GATC
* * *
98128 TTATCTCTCTAAAGTTACAGTATAGTAGATCACAT
64 TTATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
* * * * *
98163 CAGATTGTAGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98228 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
98261 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98326 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
98359 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98424 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
98457 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98522 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
98555 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98620 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
98653 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98718 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
98751 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
98816 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
* * *
98849 CAGATTGTAGCCGATAATCCTATCTCCCT-GAGATTACAGTGGAG
1 CAGATTGAAGCCGATAATTCTATCTCCCTGGAG-TTGCAGTGGAG
98893 CAGACCGAAG
Statistics
Matches: 711, Mismatches: 16, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
97 3 0.00
98 704 0.99
99 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (98 bp):
CAGATTGAAGCCGATAATTCTATCTCCCTGGAGTTGCAGTGGAGTGGGTTAAAATCACAGATCTT
ATCTCTCTGAAGTTACAGGAGAGTAGATCACAT
Found at i:98988 original size:44 final size:44
Alignment explanation
Indices: 98849--98993 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 44
98839 TAGATCACAT
* * **
98849 CAGATTGTAGCCGATA-ATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCC-ATAGATCTTATCTCCCTGAGATTACAACGGAG
** * * **
98893 CAGACCGAAG-AATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAG
1 CAGATTGAAGCCA--T-AGATCTTATCTCCCTGAGATTACAACGGAG
* *
98939 CAGATTGAAGCCATAGATCTTATCTCCTTGAGATTATAACGGAG
1 CAGATTGAAGCCATAGATCTTATCTCCCTGAGATTACAACGGAG
*
98983 TAGATTGAAGC
1 CAGATTGAAGC
98994 TAGTAATCCT
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
42 1 0.01
44 43 0.53
45 2 0.02
46 34 0.42
47 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
CAGATTGAAGCCATAGATCTTATCTCCCTGAGATTACAACGGAG
Found at i:105727 original size:19 final size:18
Alignment explanation
Indices: 105678--105741 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 18
105668 AGAATATTTC
* *
105678 AAAAAAAAAAAGAAGAAAT
1 AAAAAAAGAAA-AAGAAAG
* *
105697 AATAAGAAGAAAAGATAAAG
1 AA-AAAAAGAAAA-AGAAAG
*
105717 AAAAAAAGAAAAAGAAGG
1 AAAAAAAGAAAAAGAAAG
105735 AAAAAAA
1 AAAAAAA
105742 ATAAAAGGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 11 0.31
19 12 0.33
20 13 0.36
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (18 bp):
AAAAAAAGAAAAAGAAAG
Found at i:105741 original size:13 final size:12
Alignment explanation
Indices: 105681--105742 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 12
105671 ATATTTCAAA
105681 AAAAAAAAGAAG
1 AAAAAAAAGAAG
*
105693 AAATAATAAGAAG
1 AAA-AAAAAGAAG
*
105706 AAAAGATAAAGAAAA
1 AAAA-A-AAAG-AAG
105721 AAAGAAAAAGAAGG
1 AAA-AAAAAGAA-G
105735 AAAAAAAA
1 AAAAAAAA
105743 TAAAAGGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 4 0.10
13 19 0.47
14 10 0.25
15 6 0.15
16 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:105742 original size:14 final size:13
Alignment explanation
Indices: 105680--105742 Score: 63
Period size: 14 Copynumber: 4.7 Consensus size: 13
105670 AATATTTCAA
105680 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
* *
105693 AAATAATAAGAAG
1 AAAAAAAAAGAAG
* *
105706 AAAAGATAAAGAAA
1 AAAA-AAAAAGAAG
105720 AAAAGAAAAAGAAG
1 AAAA-AAAAAGAAG
*
105734 GAAAAAAAA
1 AAAAAAAAA
105743 TAAAAGGAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 19 0.47
14 21 0.52
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:107309 original size:89 final size:89
Alignment explanation
Indices: 107094--107309 Score: 308
Period size: 89 Copynumber: 2.4 Consensus size: 89
107084 GTTGAAGATT
* *
107094 GCAGATCTTGTCTTCCTGTACCGGCAGTGAAGCAGATAGAAGACACAAGCCTTGCCTCCCTGAGT
1 GCAGATCTTGTCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACAAAAGCCTTGCCTCCCTGAGT
**
107159 TTGCAGCAGAGTAGACTAAAAGCA
66 TTGCAGCAGAACAGACTAAAAGCA
* * *
107183 GTAGATCTTGTCTTCCTGTACCGGTAGCGAAGCAGATCGAAGACAAAAG-CTTGACCTCCCTGAG
1 GCAGATCTTGTCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACAAAAGCCTTG-CCTCCCTGAG
* * *
107247 TTTGTAGCGGAACAGACTAAAAGTA
65 TTTGCAGCAGAACAGACTAAAAGCA
* *
107272 GCAGATCTTGTCTTCTTGTACTGGCAGTGAAGCAGATC
1 GCAGATCTTGTCTTCCTGTACCGGCAGTGAAGCAGATC
107310 AAAAACTAAC
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
88 4 0.04
89 107 0.96
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (89 bp):
GCAGATCTTGTCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACAAAAGCCTTGCCTCCCTGAGT
TTGCAGCAGAACAGACTAAAAGCA
Found at i:107411 original size:87 final size:87
Alignment explanation
Indices: 107319--107479 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 87
107309 CAAAAACTAA
* *
107319 CCTTATCTCCCTGAGCAGCAGC-GTAGTAGGTTAAAGATTGCAGATCTTATCCCCCTAAGTAGTA
1 CCTTATCTCCCTGAGCAGCAGCAG-AGTAGGTCAAAGATTGCAGATCTTATCCCCCTAAGCAGTA
*
107383 GTGGAGCAGATCGAAAGCACCAG
65 GAGGAGCAGATCGAAAGCACCAG
* * * *
107406 CCTTATCTCCCTGAGTAGCAGCAGAGTAGGTCGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTATCTCCCTGAGCAGCAGCAGAGTAGGTCAAAGATTGCAGATCTTATCCCCCTAAGCAGTAG
107471 AGGAGCAGA
66 AGGAGCAGA
107480 CAGAAGAAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 65 0.98
88 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (87 bp):
CCTTATCTCCCTGAGCAGCAGCAGAGTAGGTCAAAGATTGCAGATCTTATCCCCCTAAGCAGTAG
AGGAGCAGATCGAAAGCACCAG
Found at i:107821 original size:44 final size:44
Alignment explanation
Indices: 107731--107910 Score: 129
Period size: 44 Copynumber: 4.0 Consensus size: 44
107721 CCTTATCTCA
* * * * *
107731 CTGAAGTTGCAGTGTAGTGGATT-GAA-GCT-AATCTTAT-CTCC
1 CTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCTTATAC-CT
*
107772 CTGAAGTTGCAGTGGAGCTGATTAAAACGATGAATCTTATACCT
1 CTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCTTATACCT
* * * *
107816 CTGAAGTTGCAGTAGG-TCGGATTAAATCTTATCATATCAAATCTTAT-CTCC
1 CTGAAGTTGCAGT-GGAGCGGATTAAA----A-C-GAT-GAATCTTATAC-CT
*
107867 CTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCT
1 CTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCTTATACCT
107911 TTTAAGCTAC
Statistics
Matches: 108, Mismatches: 16, Indels: 27
0.72 0.11 0.18
Matches are distributed among these distances:
41 20 0.19
42 2 0.02
43 2 0.02
44 38 0.35
45 6 0.06
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 5 0.05
51 31 0.29
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCTTATACCT
Found at i:107933 original size:95 final size:95
Alignment explanation
Indices: 107760--107965 Score: 324
Period size: 95 Copynumber: 2.2 Consensus size: 95
107750 GATTGAAGCT
* * * *
107760 AATCTTATCTCCCTGAAGTTGCAGTGGAGCTGATTAAAACGATGAATCTTATACCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGCTA
107825 CAGTAGGTCGGATTAAATCTTATCATATCA
66 CAGTAGGTCGGATTAAATCTTATCATATCA
* *
107855 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTTTTAAGCTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGCTA
* *
107920 CAG-AGGGTTGGATTAAATCTTATCATATTA
66 CAGTA-GGTCGGATTAAATCTTATCATATCA
107950 AATCTTATCTCCCTGA
1 AATCTTATCTCCCTGA
107966 GGTCGCAATA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 1 0.01
95 101 0.99
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (95 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGCTA
CAGTAGGTCGGATTAAATCTTATCATATCA
Found at i:108756 original size:13 final size:13
Alignment explanation
Indices: 108740--108772 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
108730 ATTTTCATTA
108740 TTTATCTTTATTT
1 TTTATCTTTATTT
*
108753 TTTATTTTTATTT
1 TTTATCTTTATTT
108766 TTT-TCTT
1 TTTATCTT
108773 ACAAACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 3 0.17
13 15 0.83
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATCTTTATTT
Found at i:109934 original size:42 final size:41
Alignment explanation
Indices: 109849--109955 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
109839 TAACTACGCA
* * *
109849 TATATATACATATATTTTT-TATTTTCATAACTTAAAATTT
1 TATACATACATATATTTTTATATTTCCATAACTTAAAATAT
* * **
109889 TATACATACATATATTTTTCATATTTCCATAATTTTATGTAT
1 TATACATACATATATTTTT-ATATTTCCATAACTTAAAATAT
*
109931 TATACATATA-ATATCTTTTATATTT
1 TATACATACATATAT-TTTTATATTT
109956 TTATAGTTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 18 0.32
41 10 0.18
42 28 0.50
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (41 bp):
TATACATACATATATTTTTATATTTCCATAACTTAAAATAT
Found at i:118251 original size:16 final size:16
Alignment explanation
Indices: 118230--118265 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
118220 TGGTTCGCTC
118230 TAATGGAATAGAGGCA
1 TAATGGAATAGAGGCA
* *
118246 TAATGGATTAGAGGCG
1 TAATGGAATAGAGGCA
118262 TAAT
1 TAAT
118266 AGCAATTCAA
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:0.39, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGCA
Found at i:118310 original size:45 final size:44
Alignment explanation
Indices: 118246--118341 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
118236 AATAGAGGCA
* *
118246 TAATGGATTAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAATG
1 TAATGGAATAGAGACGTAATAG-AATTC-ATGTGTTTGGTTGAATG
* *
118291 TAATGGAATAGAGACGTAATAGTATTCTTGTGTTTGGTTGAATG
1 TAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAATG
*
118335 GAATGGA
1 TAATGGA
118342 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.53
45 20 0.44
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.35
Consensus pattern (44 bp):
TAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAATG
Found at i:118424 original size:6 final size:6
Alignment explanation
Indices: 118413--119101 Score: 1337
Period size: 6 Copynumber: 114.8 Consensus size: 6
118403 AGGTAAATGA
*
118413 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTAAA TT-TT- TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATT--G TTATTG TTATTG
118461 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118509 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118557 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118605 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118653 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118701 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118749 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118797 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118845 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118893 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118941 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
118989 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
119037 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG
119085 TTATTG TTATTG TTATT
1 TTATTG TTATTG TTATT
119102 AAGCTTGTTG
Statistics
Matches: 678, Mismatches: 1, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
4 2 0.00
5 2 0.00
6 670 0.99
7 2 0.00
8 2 0.00
ACGTcount: A:0.17, C:0.00, G:0.16, T:0.67
Consensus pattern (6 bp):
TTATTG
Found at i:138366 original size:24 final size:23
Alignment explanation
Indices: 138329--138485 Score: 96
Period size: 24 Copynumber: 6.8 Consensus size: 23
138319 TAATCATATG
**
138329 TGATAAATCCAAAATAATAGTACA
1 TGATAAATTTAAAATAATA-TACA
* *
138353 TAATAACTTTAAAAT-AT-TA-A
1 TGATAAATTTAAAATAATATACA
138373 TGATAAATTTTAAAATAAATATACA
1 TGATAAA-TTTAAAAT-AATATACA
*
138398 TGATAAATTTAAAATAATGTTACCA
1 TGATAAATTTAAAATAAT-ATA-CA
*
138423 TG---AATTTAAAATAATGATA-T
1 TGATAAATTTAAAATAAT-ATACA
* *
138443 TGATAAA-TTACAAATAATAAAACG
1 TGATAAATTTA-AAATAAT-ATACA
* *
138467 TGATAAATCTAAACTAATA
1 TGATAAATTTAAAATAATA
138486 ATATACAATA
Statistics
Matches: 106, Mismatches: 14, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
20 8 0.08
21 10 0.09
22 19 0.18
23 19 0.18
24 36 0.34
25 14 0.13
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (23 bp):
TGATAAATTTAAAATAATATACA
Found at i:139367 original size:19 final size:19
Alignment explanation
Indices: 139339--139375 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
139329 ATCTTTATCT
*
139339 TCTAAGATTGCATATCATA
1 TCTAAAATTGCATATCATA
139358 TCTAAAATTGCATATCAT
1 TCTAAAATTGCATATCAT
139376 TGAAGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAAATTGCATATCATA
Found at i:155217 original size:31 final size:31
Alignment explanation
Indices: 155182--155244 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
155172 TTAACATCCT
155182 AATGACTTAAATAAAAACTTTCAAATAGTTC
1 AATGACTTAAATAAAAACTTTCAAATAGTTC
* * *
155213 AATGACTTAAATGAAAGCTTTTAAATAGTTC
1 AATGACTTAAATAAAAACTTTCAAATAGTTC
155244 A
1 A
155245 GTGAGCATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCAAATAGTTC
Found at i:167410 original size:3 final size:3
Alignment explanation
Indices: 167404--167437 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
167394 CTTCCTGGTG
*
167404 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
167438 AGCGCCGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:168428 original size:21 final size:21
Alignment explanation
Indices: 168398--168438 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
168388 CAAATTTTCG
168398 AAATTAAAAG-TAAAAAAATT
1 AAATTAAAAGTTAAAAAAATT
*
168418 AAATTCAAAAGTTCAAAAAAT
1 AAATT-AAAAGTTAAAAAAAT
168439 ACAAGAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATTAAAAGTTAAAAAAATT
Found at i:172530 original size:19 final size:19
Alignment explanation
Indices: 172505--172558 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
172495 AATCTTAAAG
172505 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
172524 TATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
172543 GATATGCAATCGTAGA
1 GATATGCAATCTTAGA
172559 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:175404 original size:49 final size:47
Alignment explanation
Indices: 175351--175510 Score: 149
Period size: 49 Copynumber: 3.3 Consensus size: 47
175341 ATGCATGGTT
* *
175351 TAATTGAAATGCAAATTAAATGAACAAATGAGTTACATAATGCATGACA
1 TAATT-AAATGCAAATT-AATGAACATATGAGTTACTTAATGCATGACA
* * * *
175400 TAATTTAAGATGCAACTTAATTAACATAGGAGTTACTTAATACATGACA
1 TAA-TTAA-ATGCAAATTAATGAACATATGAGTTACTTAATGCATGACA
** * * * *
175449 TAATTAAAACACAAACTTTATGAACATATGAGATGCTTTAATGCATGACT
1 TAATT-AAATGCAAA-TTAATGAACATATGAGTTAC-TTAATGCATGACA
175499 TAATTAAATGCA
1 TAATTAAATGCA
175511 GAACACATAA
Statistics
Matches: 88, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
48 6 0.07
49 56 0.64
50 26 0.30
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (47 bp):
TAATTAAATGCAAATTAATGAACATATGAGTTACTTAATGCATGACA
Found at i:179822 original size:18 final size:17
Alignment explanation
Indices: 179790--179823 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
179780 ATAAAAATAA
179790 TTAATTTACTTTTTAAT
1 TTAATTTACTTTTTAAT
*
179807 TTAATGTTATTTTTTAA
1 TTAAT-TTACTTTTTAA
179824 CGAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TTAATTTACTTTTTAAT
Found at i:181039 original size:24 final size:25
Alignment explanation
Indices: 181007--181053 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
180997 ACCCTACTAG
181007 AATAATAAAA-TTATAAATTAATAC
1 AATAATAAAATTTATAAATTAATAC
*
181031 AATAATAAAATTTATAACTTAAT
1 AATAATAAAATTTATAAATTAAT
181054 TTTCACACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAATAAAATTTATAAATTAATAC
Found at i:187103 original size:16 final size:16
Alignment explanation
Indices: 187084--187117 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
187074 ATCATTATAT
187084 TTTATTCAATA-ATTAA
1 TTTATT-AATATATTAA
187100 TTTATTAATATATTAA
1 TTTATTAATATATTAA
187116 TT
1 TT
187118 ATGATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTAATATATTAA
Found at i:188409 original size:14 final size:14
Alignment explanation
Indices: 188392--188426 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
188382 ATAAAAGTAC
*
188392 ATATGTAAGTATGT
1 ATATATAAGTATGT
188406 ATATATAAGTATGT
1 ATATATAAGTATGT
*
188420 ACATATA
1 ATATATA
188427 TATATAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (14 bp):
ATATATAAGTATGT
Found at i:188475 original size:3 final size:3
Alignment explanation
Indices: 188467--188546 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
188457 GGTAAATGAC
188467 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
188515 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
188547 AACTAATTAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:189265 original size:6 final size:6
Alignment explanation
Indices: 189254--189305 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
189244 TATAATATAC
189254 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
189302 AAAA
1 AAAA
189306 AAGAAATGCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:190277 original size:41 final size:42
Alignment explanation
Indices: 190220--190330 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 42
190210 AGCTTTCGTA
*
190220 TGCTCCACTGCAACTTCAG-GAGGATAAG-ACTGGATGCGATC
1 TGCTCTACTGCAACTTCAGAGA-GATAAGAACTGGATGCGATC
*
190261 TGCTCTACTGCAACTTCAGAGAGATAAGAACTGGATGTGATC
1 TGCTCTACTGCAACTTCAGAGAGATAAGAACTGGATGCGATC
* * *
190303 GGCTCTACTGCAACTTCGGGGAGATAAG
1 TGCTCTACTGCAACTTCAGAGAGATAAG
190331 GTTTGTAGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 24 0.38
42 39 0.62
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (42 bp):
TGCTCTACTGCAACTTCAGAGAGATAAGAACTGGATGCGATC
Found at i:190339 original size:127 final size:130
Alignment explanation
Indices: 190177--190414 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 130
190167 GTCTTAATCC
* *
190177 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTTC-GTATGCTCCACTGCAACTTCAGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGC-TTCAATATGCCCCACTGCAACTTCAGGA
* *
190241 GGATAAGACT-G-GA-TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAACTGGATGTGATC
65 GGATAAGACTAGTGACTGCAACCTGCTCTACTGCAACTTCAGAGAGATAAGAACTGGATGTGATC
190303 G
130 G
* * * * *
190304 GCTCTACTGCAACTTCGGGGAGATAAGG-TTTGTAGCTTCAATTTGCCCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAGCTTCAATATGCCCCACTGCAACTTCAGGA
** *
190368 GGATAAGGTTAGTGACTTCAACCTGCTCTACTGCAACTTCAGAGAGA
65 GGATAAGACTAGTGACTGCAACCTGCTCTACTGCAACTTCAGAGAGA
190415 CATGGTTTGT
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
126 3 0.03
127 57 0.61
128 4 0.04
129 2 0.02
130 28 0.30
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (130 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATATGCCCCACTGCAACTTCAGGAG
GATAAGACTAGTGACTGCAACCTGCTCTACTGCAACTTCAGAGAGATAAGAACTGGATGTGATCG
Found at i:190432 original size:44 final size:44
Alignment explanation
Indices: 190304--190452 Score: 165
Period size: 44 Copynumber: 3.4 Consensus size: 44
190294 GATGTGATCG
* **
190304 GCTCTACTGCAACTTCGGGGAGATAAGGTTTG-TAGCTTCAATTT
1 GCTCTACTGCAACTTCAGGGAGATAAGGTTTGTTA-CTTCAACCT
* * * * *
190348 GCCCCACTGCAACTTCAGGGGGATAAGGTTAGTGACTTCAACCT
1 GCTCTACTGCAACTTCAGGGAGATAAGGTTTGTTACTTCAACCT
* * * *
190392 GCTCTACTGCAACTTCAGAGAGACATGGTTTGTTATTTCAACCT
1 GCTCTACTGCAACTTCAGGGAGATAAGGTTTGTTACTTCAACCT
*
190436 ACTCTACTGCAACTTCA
1 GCTCTACTGCAACTTCA
190453 AAGATGTAAG
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 85 0.99
45 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAGGGAGATAAGGTTTGTTACTTCAACCT
Found at i:190466 original size:44 final size:44
Alignment explanation
Indices: 190384--190473 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
190374 GGTTAGTGAC
* * *
190384 TTCAACCTGCTCTACTGCAACTTCAGAGAGACATGGTTTGTTAT
1 TTCAACCTACTCTACTGCAACTTCAAAGAGACATGGTTTGTAAT
190428 TTCAACCTACTCTACTGCAACTTCAAAGATGTA-A-GGTTTGTAAT
1 TTCAACCTACTCTACTGCAACTTCAAAGA-G-ACATGGTTTGTAAT
190472 TT
1 TT
190474 ATAGCTTCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 38 0.93
45 2 0.05
46 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (44 bp):
TTCAACCTACTCTACTGCAACTTCAAAGAGACATGGTTTGTAAT
Found at i:190607 original size:44 final size:44
Alignment explanation
Indices: 190483--190660 Score: 150
Period size: 44 Copynumber: 4.0 Consensus size: 44
190473 TATAGCTTCC
* * *
190483 ATAAGACTTGCTATTTTCGACTTGCCCCACTGCAACTTCAGGGAG
1 ATAAGACTTG-TATCTTCAACTTGCCTCACTGCAACTTCAGGGAG
* * *
190528 ATAGGACTAGTAACTTCAA-TCTG-CTCCACTGCAACTTCAGGGAG
1 ATAAGACTTGTATCTTCAACT-TGCCT-CACTGCAACTTCAGGGAG
* *
190572 ATAAGACTTGTATCTTCAACTTGCCTCATTACAACTTCATGGG-G
1 ATAAGACTTGTATCTTCAACTTGCCTCACTGCAACTTCA-GGGAG
** * * *
190616 ATAAGTTTTGCTAT-TTTAACCTG-CTCTACTGCAACTTCAGAGAG
1 ATAAGACTTG-TATCTTCAACTTGCCTC-ACTGCAACTTCAGGGAG
190660 A
1 A
190661 CAAAATTTGA
Statistics
Matches: 107, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
43 7 0.07
44 83 0.78
45 17 0.16
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
ATAAGACTTGTATCTTCAACTTGCCTCACTGCAACTTCAGGGAG
Found at i:190899 original size:46 final size:46
Alignment explanation
Indices: 190756--191530 Score: 757
Period size: 46 Copynumber: 17.0 Consensus size: 46
190746 CAGGCTTGTG
** * **
190756 TCTTCGATCTGCTTCGCTGCCGGATACAGGAAGACAAGAATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAG-ATCTGCTA
* *
190803 TCTTCAATCTC-CTCCGCTGCCAAATACA-GAAAACAAGATCTGCTA
1 TCTTCGATC-CACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
190848 TCTTCGATCCACTCCGCTGCTAAATATAGGAAGACAAAATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
190894 TCTTCGATCCACTCTGCTGCCAAATATAGGAAGACAAGATATGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
190940 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
190986 TCTTCGATCCACTCCACTGCCAAATACAGGAAGATAAGATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * *
191032 TCTTCGATCCACTCCGCTGCCAAATACAAGAAGATAAAATCTGTTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * *
191078 TCTTCGATCTC-TTTCGCTGCCAAATATAGGAAAACAAGATCTGCTA
1 TCTTCGATC-CACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
191124 TCTTCGATCTC-CTTCGCTGCCAAATACAGGAAGACAAGATTTACTA
1 TCTTCGATC-CACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
191170 TCTTCGATCTC-CTCCGCTGCCAAATACAAGAAGATAAGATCTGCTA
1 TCTTCGATC-CACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
191216 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* ***********
191262 TCTTCGATCTC-CTCCGCTACCAAATAC----AGA-NNNNNNNNNNN
1 TCTTCGATC-CACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*********************** *
191303 NNNNNNNNNNNNNNNNNNNNNNNATAC-GGAAAACAAGATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
191348 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
191394 TCTTCGATCTC-TTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATC-CACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
191440 TATTCGATCCACTCCACTGCTAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
191486 TCTTCGATCCACTCCACTGCCAAATATAGGAAGACAAGATTTGCT
1 TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
191531 GCTTTTAGTC
Statistics
Matches: 591, Mismatches: 123, Indels: 29
0.80 0.17 0.04
Matches are distributed among these distances:
41 4 0.01
42 3 0.01
44 3 0.01
45 37 0.06
46 519 0.88
47 25 0.04
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.24
Consensus pattern (46 bp):
TCTTCGATCCACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
Found at i:191903 original size:26 final size:26
Alignment explanation
Indices: 191874--191926 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
191864 GCTGGTAACA
191874 CTTATCTCTTACTTAGCCGGATTGCC
1 CTTATCTCTTACTTAGCCGGATTGCC
191900 CTTATCTCTTACTTAGCCGGATTGCC
1 CTTATCTCTTACTTAGCCGGATTGCC
191926 C
1 C
191927 CCACTGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.38
Consensus pattern (26 bp):
CTTATCTCTTACTTAGCCGGATTGCC
Found at i:192636 original size:100 final size:101
Alignment explanation
Indices: 192428--192722 Score: 423
Period size: 100 Copynumber: 2.9 Consensus size: 101
192418 AAAATGCTTG
192428 AAAAAGATTATCAAAATGGACAATATGGAATTTTATTGAGAAAAAAGCTCGAAATGAATAAATCA
1 AAAAAGATTATCAAAATGGACAATATGGAATTTTATTGAGAAAAAAGCTCG-AA-GAATAAATCA
**
192493 AGATAGCAAATTTTGCTAAGATATGAACTGAATAAGAT
64 AGATAGCAAATTTTGCTAAGATACAAACTGAATAAGAT
* * * * * * *
192531 GAAAAGTATTATGAAAATGGATAAGATAGAATTTTATTGAGAACAAGGCTCG-A-AATAAATCAA
1 AAAAAG-ATTATCAAAATGGACAATATGGAATTTTATTGAGAAAAAAGCTCGAAGAATAAATCAA
*
192594 GATAGCAAATTTTGCTAAGATACAAATTGAATAAGAT
65 GATAGCAAATTTTGCTAAGATACAAACTGAATAAGAT
*
192631 AAAAAGATTATCACAATGGACAATATGGAATTTTATTGAGAAAAAAGCTCGAAATGAATAAATCA
1 AAAAAGATTATCAAAATGGACAATATGGAATTTTATTGAGAAAAAAGCTCG-AA-GAATAAATCA
*
192696 AGATAGCAAAATTTGCTAAGATACAAA
64 AGATAGCAAATTTTGCTAAGATACAAA
192723 ATGAGAATAA
Statistics
Matches: 168, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
99 38 0.23
100 49 0.29
101 1 0.01
102 1 0.01
103 40 0.24
104 39 0.23
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (101 bp):
AAAAAGATTATCAAAATGGACAATATGGAATTTTATTGAGAAAAAAGCTCGAAGAATAAATCAAG
ATAGCAAATTTTGCTAAGATACAAACTGAATAAGAT
Found at i:195172 original size:21 final size:20
Alignment explanation
Indices: 195148--195190 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
195138 TGCATTTGCA
195148 TTCGCTCTAATTTTTCCAACC
1 TTCGCTC-AATTTTTCCAACC
* * *
195169 TTCGTTCCATTTTTCTAACC
1 TTCGCTCAATTTTTCCAACC
195189 TT
1 TT
195191 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.16, C:0.30, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCGCTCAATTTTTCCAACC
Found at i:198146 original size:6 final size:6
Alignment explanation
Indices: 198135--198170 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
198125 TATAATATAC
198135 AAAATA AAAATA AAAATA AAAATA AAAATA AGAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA A-AAAT
198171 GCAAATCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:206575 original size:42 final size:42
Alignment explanation
Indices: 206451--206604 Score: 209
Period size: 42 Copynumber: 3.6 Consensus size: 42
206441 ATGTCGCTAA
* * **
206451 CTTTTGCGGCGCTTACAGAAAAAAACGCTACTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
*
206495 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
* *
206538 ATTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
206580 CTTTAGCGGTGCTTAGGAAAAAACG
1 CTTTAGCGGCGCTTAGGAAAAAACG
206605 TTCTTTAGCG
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
42 49 0.50
43 37 0.38
44 12 0.12
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:206615 original size:27 final size:27
Alignment explanation
Indices: 206577--206630 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
206567 TAAAGATCAT
* *
206577 GTTCTTTAGCGGTGCTTAGGAAAAAAC
1 GTTCTTTAGCGGCGCTTAGAAAAAAAC
*
206604 GTTCTTTAGCGGCGCTTTGAAAAAAAC
1 GTTCTTTAGCGGCGCTTAGAAAAAAAC
206631 ACCGCTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (27 bp):
GTTCTTTAGCGGCGCTTAGAAAAAAAC
Found at i:206671 original size:42 final size:42
Alignment explanation
Indices: 206607--206704 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
206597 AAAAAACGTT
*
206607 CTTTAGCGGCGCTTTGAAAAAAACACCGCTAA-AGATCGTGTA
1 CTTTAGCGGCGCTTTGAAAAAAACACCGCTAATAG-TAGTGTA
** ** * *
206649 CTTTAGCGGCGC-TTGTTCAAAAATGCCGTTAATAGTAGTGTT
1 CTTTAGCGGCGCTTTG-AAAAAAACACCGCTAATAGTAGTGTA
206691 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
206705 ATTTCACAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.07
42 40 0.87
43 3 0.07
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTGAAAAAAACACCGCTAATAGTAGTGTA
Found at i:206691 original size:111 final size:112
Alignment explanation
Indices: 206492--206705 Score: 274
Period size: 111 Copynumber: 1.9 Consensus size: 112
206482 TAAAGATCAT
* *
206492 GTTCTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTTATGAA
1 GTTCTTTAGCGGCGCTAAGGAAAAAAACACCGCTAAAGATCATGTTATTTAGCGGCGCTTATGAA
*
206557 AAAACGCCGCTAAAGATCATGTTCTTTAGCGGTGCTTAGGAAAAAAC
66 AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAC
** * * **
206604 GTTCTTTAGCGGCGCT-TTGAAAAAAACACCGCTAAAGATCGTG-TACTTTAGCGGCGCTTGTTC
1 GTTCTTTAGCGGCGCTAAGGAAAAAAACACCGCTAAAGATCATGTTA-TTTAGCGGCGCTTATGA
* *
206667 AAAAATGCCGTTAATAG-T-AGTGTTCTTTAGCGGCGCTTA
65 AAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTA
206706 TTTCACAAAC
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
110 3 0.03
111 67 0.76
112 18 0.20
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (112 bp):
GTTCTTTAGCGGCGCTAAGGAAAAAAACACCGCTAAAGATCATGTTATTTAGCGGCGCTTATGAA
AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAC
Found at i:207191 original size:21 final size:21
Alignment explanation
Indices: 207167--207229 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
207157 TCTATCGCTG
207167 CTTCTCTCGCTGCGGCCTCTA
1 CTTCTCTCGCTGCGGCCTCTA
** * *
207188 CTTCTCTCGCTGTAGCATCTG
1 CTTCTCTCGCTGCGGCCTCTA
*
207209 CTTCCCTCGCTGCGGCCTCTA
1 CTTCTCTCGCTGCGGCCTCTA
207230 ATTTAATTTG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.06, C:0.41, G:0.19, T:0.33
Consensus pattern (21 bp):
CTTCTCTCGCTGCGGCCTCTA
Found at i:217432 original size:146 final size:146
Alignment explanation
Indices: 217082--217492 Score: 393
Period size: 146 Copynumber: 2.8 Consensus size: 146
217072 TTAACCATTT
* *
217082 GCGGCGTTTATAAAT-AAGCGCCACTAACTATAAG-TCGAAACGCAGTCGTTTCATCAACAAATA
1 GCGGCGTTT-TAAATAAAGCGCCACTAACTATAAGATCAAAACGCAGTCGTTTCATCAACAATTA
* * * * * * **
217145 GCGCACACCTGTGGCGTTTTTGAATAAACGCCACTAAT-A-ATACAACAAAACGGCCTCGTATCG
65 ACTCAAACCTGTGGCG-TTTT-AAAAAACGCCACTAATAACATTCAA-AAAACGACAGCGTATCG
* * *
217208 ATAAATGTTAAAACATTTTT
127 ATAAATGTTAAAACAATGTG
* * * * *
217228 GCGGCGTTTTAATTAAAGCGCCACTAACTATAA-ATCAAAATGCAGTCGCTTCATCAACACTTAC
1 GCGGCGTTTTAAATAAAGCGCCACTAACTATAAGATCAAAACGCAGTCGTTTCATCAACAATTAA
* * * *
217292 CTCAAACCCGTGGCGTTTTAAAAAATCGCCACTAATAACATTTAAAAAACGACAGCGTTTCTATA
66 CTCAAACCTGTGGCGTTTTAAAAAA-CGCCACTAATAACATTCAAAAAACGACAGCGTATCGATA
*
217357 AATGTTAGAACAATGTG
130 AATGTTAAAACAATGTG
* * * ** *
217374 GCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATC-AAACGAAGTCGTTTCCCCAACATTTAA
1 GCGGCGTTTTAAATAAAGCGCCACTAACTATAAGATCAAAACGCAGTCGTTTCATCAACAATTAA
* * * * * * *
217438 CTCAAGCTTGTGGCGTTTCCAAAAACACGCCATTAATACCATTGACAAAACGACA
66 CTCAAACCTGTGGCGTTT-TAAAAA-ACGCCACTAATAACATTCAAAAAACGACA
217493 ACATTTCGAT
Statistics
Matches: 218, Mismatches: 39, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
144 5 0.02
145 18 0.08
146 158 0.72
147 36 0.17
148 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (146 bp):
GCGGCGTTTTAAATAAAGCGCCACTAACTATAAGATCAAAACGCAGTCGTTTCATCAACAATTAA
CTCAAACCTGTGGCGTTTTAAAAAACGCCACTAATAACATTCAAAAAACGACAGCGTATCGATAA
ATGTTAAAACAATGTG
Found at i:217531 original size:147 final size:146
Alignment explanation
Indices: 217205--217543 Score: 351
Period size: 146 Copynumber: 2.3 Consensus size: 146
217195 CGGCCTCGTA
** * * * *
217205 TCGATAAATGTTAAAACATTTTTGCGGCGTTTTAATTAAAGCGCCACTAACTATAAATCAAAATG
1 TCGATAAATCATAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAATCAAAACG
* * * * *
217270 CAGTCGCTTCATCAACACTTACCTCAAACCCGTGGCGTTTTAAAAAATCGCCACTAATAACATTT
66 AAGTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCAAAAAATCGCCACTAATAACATTG
* *
217335 AAAAAACGACAGCGTT
131 AAAAAACGACAACATT
* ** * * *
217351 TCTATAAATGTTAGAACAATGTGGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATC-AAAC
1 TCGATAAATCATAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAA-ATCAAAAC
* * * * ** * *
217415 GAAGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCGTTTCCAAAAACA-CGCCATTAATACCA
65 GAAGTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTT-CAAAAA-ATCGCCACTAATAACA
*
217479 TTGACAAAACGACAACATT
128 TTGAAAAAACGACAACATT
* *
217498 TCGATAAA-CATAAATACAATTTTGTGGCGTTTTATGTAAAGCGCCA
1 TCGATAAATCATAAA-ACAATTTTGCGGCGTTTTAAGTAAAGCGCCA
217544 GTAATAGCAA
Statistics
Matches: 157, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
146 87 0.55
147 69 0.44
148 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (146 bp):
TCGATAAATCATAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAATCAAAACG
AAGTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCAAAAAATCGCCACTAATAACATTG
AAAAAACGACAACATT
Found at i:218899 original size:40 final size:40
Alignment explanation
Indices: 218837--218913 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
218827 GTCTTAGGTT
* *
218837 TCTTTGCGGCGATTTATGAAAAACGCCGCTAAATCCTTGA
1 TCTTTGCGGCGATTAATAAAAAACGCCGCTAAATCCTTGA
*
218877 TCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAATCC
1 TCTTT-GCGGCGATTAATAAAAAACGCCGCTAAATCC
218914 CCGCATGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (40 bp):
TCTTTGCGGCGATTAATAAAAAACGCCGCTAAATCCTTGA
Found at i:218929 original size:114 final size:111
Alignment explanation
Indices: 218668--218980 Score: 299
Period size: 114 Copynumber: 2.8 Consensus size: 111
218658 GGCGCTTACC
* * *
218668 AAAAACGCCGCTAAATCCCCGAATACTCAGAGAACGGTGTCGTTCGGCTTATGTTTATTTGCGGC
1 AAAAACGCCGCTAAATCCCCGAATGCTCAGAAAACGGTGTCGTT-GGCTTAGGTTT-TTTGCGGC
* * * * *
218733 GCTTCCATACAAATGCCGCTAAAGTACTGAACATTAGCGGCGCTACCTC
64 GCTT-TATAAAAACGCCGCTAAAGTACTGAACATTAGCGGCGCTACATA
** **
218782 AAAAACGCCGCTAGGTTACCGAATGCTCAGAAAACGGTGTCGTTGGTCTTAGGTTTCTTTGCGGC
1 AAAAACGCCGCTAAATCCCCGAATGCTCAGAAAACGGTGTCGTTGG-CTTAGGTTT-TTTGCGGC
* * * *
218847 GATTTATGAAAAACGCCGCTAAA-TCCTTGATCTTTAGCGGCGCTTA-ATA
64 GCTTTAT-AAAAACGCCGCTAAAGTAC-TGAACATTAGCGGCGC-TACATA
* * * ** **
218896 AAAAACGCCGCTAAATCCCCGCATGCCCGGAAAACGACGTCGTTGGGCCGAGG-TTTTTGCGGCG
1 AAAAACGCCGCTAAATCCCCGAATGCTCAGAAAACGGTGTCGTT-GGCTTAGGTTTTTTGCGGCG
*
218960 CTTTATAGAAATCGCCGCTAA
65 CTTTATA-AAAACGCCGCTAA
218981 TGCTTTTTCT
Statistics
Matches: 163, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
111 1 0.01
112 26 0.16
113 8 0.05
114 124 0.76
115 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (111 bp):
AAAAACGCCGCTAAATCCCCGAATGCTCAGAAAACGGTGTCGTTGGCTTAGGTTTTTTGCGGCGC
TTTATAAAAACGCCGCTAAAGTACTGAACATTAGCGGCGCTACATA
Found at i:220790 original size:20 final size:19
Alignment explanation
Indices: 220762--220800 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
220752 AATTAAAATG
220762 TTTTTTTATAATTAATTAA
1 TTTTTTTATAATTAATTAA
**
220781 TTTTTATTATTTTTAATTAA
1 TTTTT-TTATAATTAATTAA
220801 AATTATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTTATAATTAATTAA
Found at i:223556 original size:68 final size:68
Alignment explanation
Indices: 223478--223634 Score: 226
Period size: 68 Copynumber: 2.3 Consensus size: 68
223468 GATGTGGCAT
* * * * *
223478 ACCTT-CTCGTCACGATGTCGTAGCCTTGCTTGGTTGCTAAGGATGTCATGTCATCTCGACGTGC
1 ACCTTGCTCGTCTCGACGTCGTAGCCTTGCTTGGTTGCCAAGGATGTCACGTCATCTCGACGCGC
223542 TAC
66 TAC
* ** *
223545 ACCTTGCTCGTCTCGACATCGTAGCCTTGCTTGGTTGCCAAGGATGTTGCGTCATCTTGACGCGC
1 ACCTTGCTCGTCTCGACGTCGTAGCCTTGCTTGGTTGCCAAGGATGTCACGTCATCTCGACGCGC
223610 TAC
66 TAC
223613 ACCTTGCTCGTCTCGACGTCGT
1 ACCTTGCTCGTCTCGACGTCGT
223635 CTATCATCTC
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 5 0.06
68 74 0.94
ACGTcount: A:0.15, C:0.29, G:0.24, T:0.32
Consensus pattern (68 bp):
ACCTTGCTCGTCTCGACGTCGTAGCCTTGCTTGGTTGCCAAGGATGTCACGTCATCTCGACGCGC
TAC
Found at i:225852 original size:22 final size:22
Alignment explanation
Indices: 225827--225868 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
225817 GAAAATTTTG
225827 AAAACACGAAAATTTTTAAAAA
1 AAAACACGAAAATTTTTAAAAA
* *
225849 AAAACATGAAATTTTTTAAA
1 AAAACACGAAAATTTTTAAA
225869 CACGAGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAACACGAAAATTTTTAAAAA
Found at i:225889 original size:38 final size:39
Alignment explanation
Indices: 225810--225961 Score: 102
Period size: 39 Copynumber: 4.0 Consensus size: 39
225800 GAAATTTTTT
225810 AAAACACGAAAATTTTGAAAACACGAAAATTTTTAAAAA
1 AAAACACGAAAATTTTGAAAACACGAAAATTTTTAAAAA
* ** * **
225849 AAAACATG-AAATTTTTTAAACACGAGAATTTTTTTTAAA
1 AAAACACGAAAATTTTGAAAACACGA-AAATTTTTAAAAA
* ** * *
225888 AACACAAAAAAAATTTTG-AAACACGGAAATTTGT-----
1 AAAAC-ACGAAAATTTTGAAAACACGAAAATTTTTAAAAA
* * *
225922 GAAACACGAGAATTATTGAAAACACGAAAATTTTTTAAAA
1 AAAACACGAAAATT-TTGAAAACACGAAAATTTTTAAAAA
225962 CACGACAATT
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
33 6 0.07
34 6 0.07
35 14 0.17
38 15 0.18
39 27 0.33
40 8 0.10
41 7 0.08
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (39 bp):
AAAACACGAAAATTTTGAAAACACGAAAATTTTTAAAAA
Found at i:226027 original size:17 final size:17
Alignment explanation
Indices: 225753--226031 Score: 139
Period size: 17 Copynumber: 15.5 Consensus size: 17
225743 ACAATAACTT
*
225753 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* * *
225771 TTTTTGATACATGAGAA
1 TTTTTGAAACACGAAAA
* * *
225788 TTTTGGTAACACGAAAT
1 TTTTTGAAACACGAAAA
*
225805 TTTTTAAAACACGAAAA
1 TTTTTGAAACACGAAAA
225822 -TTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
225839 TTTTTAAAAAAAAAC-ATGAAA
1 TTTTT---GAAACACGA--AAA
* *
225860 TTTTTTAAACACGAGAATTT
1 TTTTTGAAACACGA-AA--A
* *
225880 TTTTTAAAAACACAAAAAAA
1 TTTTT-GAAACAC--GAAAA
* *
225900 ATTTTGAAACACGGAAA
1 TTTTTGAAACACGAAAA
* *
225917 TTTGTGAAACACGAGAA
1 TTTTTGAAACACGAAAA
*
225934 TTATTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
225952 TTTTTTAAAACACGACAA
1 -TTTTTGAAACACGAAAA
* *
225970 TTTTTGAAATACGAGAAT
1 TTTTTGAAACACGA-AAA
** **
225988 TTTTTTTAATGCGAAAA
1 TTTTTGAAACACGAAAA
226005 TTTTTTGAAACACGAAAA
1 -TTTTTGAAACACGAAAA
*
226023 CTTTTGAAA
1 TTTTTGAAA
226032 ATGCGAAAAG
Statistics
Matches: 194, Mismatches: 50, Indels: 35
0.70 0.18 0.13
Matches are distributed among these distances:
16 4 0.02
17 84 0.43
18 63 0.32
19 12 0.06
20 14 0.07
21 14 0.07
22 2 0.01
23 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:226035 original size:36 final size:35
Alignment explanation
Indices: 225786--226040 Score: 115
Period size: 35 Copynumber: 7.1 Consensus size: 35
225776 GATACATGAG
* * **
225786 AATTTTGGTAACACG-AAATTTTTTAAAACACGAA
1 AATTTTTGAAACACGAAAATTTTTTAAAATGCGAA
* **
225820 AA-TTTTGAAAACACGAAAATTTTTAAAAAAAAAC-ATGA
1 AATTTTTG-AAACACGAAAATTTTT--TAAAATGCGA--A
* * ** *
225858 AATTTTTTAAACACGAGAATTTTTTTTAAAAACACAAAAA
1 AATTTTTGAAACACGA-AA-ATTTTTT-AAAATGC--GAA
* * * * *
225898 AAATTTTGAAACACGGAAATTTGTGAAACA--CGAG
1 AATTTTTGAAACACGAAAATTTTTTAAA-ATGCGAA
* ** *
225932 AATTATTGAAAACACGAAAATTTTTTAAAACACGAC
1 AATTTTTG-AAACACGAAAATTTTTTAAAATGCGAA
* * **
225968 AATTTTTGAAATACGAGAATTTTTTTTAATGCGAA
1 AATTTTTGAAACACGAAAATTTTTTAAAATGCGAA
* *
226003 AATTTTTTGAAACACGAAAACTTTTGAAAATGCGAA
1 AA-TTTTTGAAACACGAAAATTTTTTAAAATGCGAA
226039 AA
1 AA
226041 GTCAAAATTT
Statistics
Matches: 167, Mismatches: 36, Indels: 34
0.70 0.15 0.14
Matches are distributed among these distances:
33 4 0.02
34 16 0.10
35 47 0.28
36 41 0.25
37 9 0.05
38 16 0.10
39 14 0.08
40 19 0.11
42 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.31
Consensus pattern (35 bp):
AATTTTTGAAACACGAAAATTTTTTAAAATGCGAA
Found at i:226038 original size:18 final size:19
Alignment explanation
Indices: 225995--226040 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
225985 AATTTTTTTT
*
225995 AATGCGAAAATTTTTTGAA
1 AATGCGAAAATCTTTTGAA
226014 ACA--CGAAAA-CTTTTGAA
1 A-ATGCGAAAATCTTTTGAA
226031 AATGCGAAAA
1 AATGCGAAAA
226041 GTCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
16 1 0.04
17 8 0.35
18 12 0.52
19 1 0.04
20 1 0.04
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (19 bp):
AATGCGAAAATCTTTTGAA
Found at i:226088 original size:18 final size:18
Alignment explanation
Indices: 226051--226089 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
226041 GTCAAAATTT
*
226051 TTTTTGAAATACGAGTAA
1 TTTTTGAAATACGAGAAA
226069 TTTTTGAAAATACGA-AAA
1 TTTTTG-AAATACGAGAAA
226087 TTT
1 TTT
226090 AAAACACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (18 bp):
TTTTTGAAATACGAGAAA
Found at i:226930 original size:12 final size:13
Alignment explanation
Indices: 226911--226964 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
226901 TTTTTTTATT
*
226911 TTTCCTTTTCTTC
1 TTTCTTTTTCTTC
*
226924 TCTCTTTTTCCTTC
1 TTTCTTTTT-CTTC
226938 TTTCTTTTTCTT-
1 TTTCTTTTTCTTC
*
226950 TTTCTTCTTCTTC
1 TTTCTTTTTCTTC
226963 TT
1 TT
226965 CGGGCCGTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.31
13 12 0.34
14 12 0.34
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTTTCTTC
Found at i:226952 original size:6 final size:6
Alignment explanation
Indices: 226903--226961 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
226893 GTGATATATT
* * *
226903 TTTTTA TTTTTC CTTTTC TTCTCTC TTTTTCC TTCTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC TTTTTC TTTTTC
*
226954 TTCTTC TT
1 TTTTTC TT
226962 CTTCGGGCCG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 30 0.68
7 11 0.25
8 3 0.07
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:227727 original size:6 final size:6
Alignment explanation
Indices: 227715--227770 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
227705 GAAAACAAAC
* * *
227715 AAATAA TAATAA TAATAA GAA--A AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
227761 AAATAA AAAT
1 AAATAA AAAT
227771 GGGCTAAAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
4 3 0.07
6 42 0.93
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:229654 original size:102 final size:99
Alignment explanation
Indices: 229481--229682 Score: 350
Period size: 102 Copynumber: 2.0 Consensus size: 99
229471 AATGAGAGCT
* * *
229481 TGGCCGAATGTTAAAGCCATCAATGTCTTTCTTCTTGAATTTTCGGTGAAGATGAATAGTGGAAG
1 TGGCCGAATGTTAAAGCCAACAATGGCTTTCTTCTTGAATTTTCGGTGAAGATGAACAGTGGAAG
229546 ATGACAATACATTTTGTTTTATTTTAATTTAACA
66 ATGACAATACATTTTGTTTTATTTTAATTTAACA
229580 TGGCCGAATGTTAAAGCCAACAATGGCTTTCTTCTCCTTGAATTTTCGGTGAAGATGAACAGTGG
1 TGGCCGAATGTTAAAGCCAACAATGGCTTTC-T-T-CTTGAATTTTCGGTGAAGATGAACAGTGG
229645 AAGATGACAATACATTTTGTTTTATTTTAATTTAACA
63 AAGATGACAATACATTTTGTTTTATTTTAATTTAACA
229682 T
1 T
229683 TATTTACGAA
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
99 29 0.30
100 1 0.01
101 1 0.01
102 66 0.68
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (99 bp):
TGGCCGAATGTTAAAGCCAACAATGGCTTTCTTCTTGAATTTTCGGTGAAGATGAACAGTGGAAG
ATGACAATACATTTTGTTTTATTTTAATTTAACA
Found at i:229916 original size:13 final size:13
Alignment explanation
Indices: 229898--229922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229888 ACAAACGATA
229898 AAATTTTCACACG
1 AAATTTTCACACG
229911 AAATTTTCACAC
1 AAATTTTCACAC
229923 ATATAAATCA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:230667 original size:31 final size:29
Alignment explanation
Indices: 230625--230694 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
230615 ATCCCAAAAC
* *
230625 TATACAAGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TGTGCAATTG
* *
230656 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATGAACTATGATTTTGTGCAATTG
230685 TATACATGAA
1 TATACATGAA
230695 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTG
Found at i:230688 original size:29 final size:30
Alignment explanation
Indices: 230646--230704 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
230636 TATGGTTTAA
230646 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
230675 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
230705 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:230713 original size:30 final size:29
Alignment explanation
Indices: 230650--230713 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
230640 GTTTAATGTG
*
230650 CAATTGTATACATGAACTTTGATTTTGTG
1 CAATTGTATACATGAACTTTGATTTTGTC
* *
230679 CAATTTTATACATGAAATTTTGA-TTTGATC
1 CAATTGTATACATG-AACTTTGATTTTG-TC
230709 CAATT
1 CAATT
230714 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (29 bp):
CAATTGTATACATGAACTTTGATTTTGTC
Found at i:233357 original size:3 final size:3
Alignment explanation
Indices: 233326--233412 Score: 56
Period size: 3 Copynumber: 30.0 Consensus size: 3
233316 TAGAATGATA
* *
233326 AAT AAT AAGT AA- AAT AA- AAG AAT -AT AAT AAT AAT AA- CAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
233368 TAT AAT TAT AAT ATT AAT ATT AAT AAT CAT ATT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
233413 TAAATGAAGT
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
2 7 0.11
3 53 0.84
4 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:233655 original size:3 final size:3
Alignment explanation
Indices: 233642--233683 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
233632 TAAATAAATA
233642 AAT AGAT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AA- AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
233684 ATAGACGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:233661 original size:11 final size:11
Alignment explanation
Indices: 233647--233683 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
233637 AAATAAATAG
233647 ATAATAATAAA
1 ATAATAATAAA
233658 ATAATAATAAA
1 ATAATAATAAA
233669 ATAATAATAAA
1 ATAATAATAAA
233680 ATAA
1 ATAA
233684 ATAGACGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:234039 original size:3 final size:3
Alignment explanation
Indices: 234026--234067 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
234016 TAAATAAATA
234026 AAT AGAT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AA- AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
234068 ATAGACGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:234045 original size:11 final size:11
Alignment explanation
Indices: 234031--234067 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
234021 AAATAAATAG
234031 ATAATAATAAA
1 ATAATAATAAA
234042 ATAATAATAAA
1 ATAATAATAAA
234053 ATAATAATAAA
1 ATAATAATAAA
234064 ATAA
1 ATAA
234068 ATAGACGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:234108 original size:384 final size:386
Alignment explanation
Indices: 233383--234156 Score: 1534
Period size: 384 Copynumber: 2.0 Consensus size: 386
233373 TTATAATATT
233383 AATATTAATAATCATATTAGTAATAATAATTAAATGAAGTAATTTAAAGTAAATAAAAAATAAAA
1 AATATTAATAATCATATTAGTAATAATAATTAAATGAAGTAATTTAAAGTAAATAAAAAATAAAA
233448 GCTGCACGATTAAAAAGATAAATGGACATAACATGAAAGTGCTAAAGATAATAAGAGAAATAATA
66 GCTGCACGATTAAAAAGATAAATGGACATAACATGAAAGTGCTAAAGATAATAAGAGAAATAATA
233513 AAATAACAAGAACACACTAAAAAAATAAAAATAAAAAAATAAATGACAACAAAAATGTACCAATA
131 AAATAACAAGAACACACTAAAAAAATAAAAATAAAAAAATAAATGACAACAAAAATGTACCAATA
233578 AAAGCATGTATATATAATCTAATTCTTAAGTATGTATAGAAAATGAGTAATAAGTAAATAAATAA
196 AAAGCATGTATATATAATCTAATTCTTAAGTATGTATAGAAAATGAGTAATAAGTAAATAAATAA
233643 ATAGATAATAATAAAATAATAATAAAATAATAATAAAATAAATAGACGAATGAATGCTCGATGAA
261 ATAGATAATAATAAAATAATAATAAAATAATAATAAAATAAATAGACGAATGAATGCTCGATGAA
233708 AAGAAAATAAAAAAAGCCAATTTTAAATATAAACAAAAAGTAAAGGAATAATAAATAAGCA
326 AAGAAAATAAAAAAAGCCAATTTTAAATATAAACAAAAAGTAAAGGAATAATAAATAAGCA
233769 AATA-TAATAATCAT-TTAGTAATAATAATTAAATGAAGTAATTTAAAGTAAATAAAAAATAAAA
1 AATATTAATAATCATATTAGTAATAATAATTAAATGAAGTAATTTAAAGTAAATAAAAAATAAAA
233832 GCTGCACGATTAAAAAGATAAATGGACATAACATGAAAGTGCTAAAGATAATAAGAGAAATAATA
66 GCTGCACGATTAAAAAGATAAATGGACATAACATGAAAGTGCTAAAGATAATAAGAGAAATAATA
233897 AAATAACAAGAACACACTAAAAAAATAAAAATAAAAAAATAAATGACAACAAAAATGTACCAATA
131 AAATAACAAGAACACACTAAAAAAATAAAAATAAAAAAATAAATGACAACAAAAATGTACCAATA
233962 AAAGCATGTATATATAATCTAATTCTTAAGTATGTATAGAAAATGAGTAATAAGTAAATAAATAA
196 AAAGCATGTATATATAATCTAATTCTTAAGTATGTATAGAAAATGAGTAATAAGTAAATAAATAA
234027 ATAGATAATAATAAAATAATAATAAAATAATAATAAAATAAATAGACGAATGAATGCTCGATGAA
261 ATAGATAATAATAAAATAATAATAAAATAATAATAAAATAAATAGACGAATGAATGCTCGATGAA
234092 AAGAAAATAAAAAAAGCCAATTTTAAATATAAACAAAAAGTAAAGGAATAATAAATAAGCA
326 AAGAAAATAAAAAAAGCCAATTTTAAATATAAACAAAAAGTAAAGGAATAATAAATAAGCA
234153 AATA
1 AATA
234157 GGTAAATAAA
Statistics
Matches: 388, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
384 374 0.96
385 10 0.03
386 4 0.01
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (386 bp):
AATATTAATAATCATATTAGTAATAATAATTAAATGAAGTAATTTAAAGTAAATAAAAAATAAAA
GCTGCACGATTAAAAAGATAAATGGACATAACATGAAAGTGCTAAAGATAATAAGAGAAATAATA
AAATAACAAGAACACACTAAAAAAATAAAAATAAAAAAATAAATGACAACAAAAATGTACCAATA
AAAGCATGTATATATAATCTAATTCTTAAGTATGTATAGAAAATGAGTAATAAGTAAATAAATAA
ATAGATAATAATAAAATAATAATAAAATAATAATAAAATAAATAGACGAATGAATGCTCGATGAA
AAGAAAATAAAAAAAGCCAATTTTAAATATAAACAAAAAGTAAAGGAATAATAAATAAGCA
Found at i:235722 original size:44 final size:44
Alignment explanation
Indices: 235674--236013 Score: 252
Period size: 44 Copynumber: 7.4 Consensus size: 44
235664 TTGTCACTCT
* *
235674 AATCTGCTCCACTACAACTTTAGGGAAATAAGACTCGTAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGTAGCTTC
* ** *
235718 AATCTACTCCACTGCAA-TTTCAAGGTGATAAGATTTGTAACTCGTAGCTTT
1 AATCTGCTCCACTGCAACTTT--AGG-G---AGATAAG--ACTCGTAGCTTC
* * * *
235769 AATCTGTTCCACTGTAACTTCAGGGAGATAAGATCTGTAACATGTAGCTTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA-C--T--C--GTAGCTTC
* * * * * * *
235820 AATTTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTCG-TAGCTTC
***
235865 AATCTGCTTGGCTGCAACTTTAGGGAGATAAGACTCGTAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGTAGCTTC
* * * *
235909 AATCTACTCTACTGCAACTTCAGGGAGATAAGACTCATAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGTAGCTTC
* * **
235953 AATCTACTCCACTGCAACTTTAGGGAGATAAGATTTTTAGC-TC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGTAGCTTC
*
235996 TAATTTGCTCCACTGCAA
1 -AATCTGCTCCACTGCAA
236014 ATTCAAGAAG
Statistics
Matches: 238, Mismatches: 40, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
43 5 0.02
44 111 0.47
45 39 0.16
46 7 0.03
47 1 0.00
48 1 0.00
49 6 0.03
50 3 0.01
51 63 0.26
52 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGTAGCTTC
Found at i:235782 original size:51 final size:51
Alignment explanation
Indices: 235706--235853 Score: 181
Period size: 51 Copynumber: 2.9 Consensus size: 51
235696 GGGAAATAAG
* ** * * *
235706 ACTCGTAGCTTCAATCTACTCCACTGCAATTTCAAGGTGATAAGATTTGTA
1 ACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATCTGTA
* *
235757 ACTCGTAGCTTTAATCTGTTCCACTGTAACTTCAGGGAGATAAGATCTGTA
1 ACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATCTGTA
* * *
235808 ACAT-GTAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGAT
1 AC-TCGTAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGAT
235854 TCGCTATCTT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 84 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (51 bp):
ACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATCTGTA
Found at i:238276 original size:31 final size:30
Alignment explanation
Indices: 238210--238351 Score: 141
Period size: 31 Copynumber: 4.7 Consensus size: 30
238200 GTATATGTTT
238210 TATACATTGCTGAATTTGATTTGTATAT--A
1 TATACATTGCTGAATTTGA-TTGTATATAGA
* * *
238239 TATACATTACCGAATTTGAATTGTTTATAGA
1 TATACATTGCTGAATTTG-ATTGTATATAGA
238270 TATACATTG-TCGAATTTGATTTGTATAT-GA
1 TATACATTGCT-GAATTTGA-TTGTATATAGA
*
238300 TTATACATTGCTGAATTTGATTCGTATATGGA
1 -TATACATTGCTGAATTTGATT-GTATATAGA
* *
238332 TATATATTACTGAA-TTGATT
1 TATACATTGCTGAATTTGATT
238352 TGACCATAGG
Statistics
Matches: 96, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
29 23 0.24
30 12 0.12
31 58 0.60
32 3 0.03
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.46
Consensus pattern (30 bp):
TATACATTGCTGAATTTGATTGTATATAGA
Found at i:238347 original size:62 final size:59
Alignment explanation
Indices: 238210--238353 Score: 166
Period size: 62 Copynumber: 2.4 Consensus size: 59
238200 GTATATGTTT
*
238210 TATACATTGCTGAATTTGATTTGTATATATATACATTACCGAATTTGAATTGTTTATAGA
1 TATACATT-CTGAATTTGATTTGTATATATATACATTACCGAATTTGAATTGTATATAGA
* * * *
238270 TATACATTGTCGAATTTGATTTGTATATGATTATACATTGCTGAATTTG-ATTCGTATATGGA
1 TATACATTCT-GAATTTGATTTGTATAT-A-TATACATTACCGAATTTGAATT-GTATATAGA
*
238332 TATATATTACTGAA-TTGATTTG
1 TATACATT-CTGAATTTGATTTG
238354 ACCATAGGAT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
59 1 0.01
60 25 0.35
61 12 0.17
62 33 0.46
63 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (59 bp):
TATACATTCTGAATTTGATTTGTATATATATACATTACCGAATTTGAATTGTATATAGA
Found at i:238591 original size:43 final size:43
Alignment explanation
Indices: 238471--238582 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
238461 TTCGATGTGT
* **
238471 GATTTCATGTAAGACCATGTTTGGGCTATTGGCATCGATTTGA
1 GATTTCATGTAAGACCATGTCTGGGCTATTGGCATCGATTCAA
*
238514 GATTTCGTGTAAGACCATAG-CTGGGCTATTGGCATCG-TTACAA
1 GATTTCATGTAAGACCAT-GTCTGGGCTATTGGCATCGATT-CAA
238557 GATTTCCATGTAAGACCATGTCTGGG
1 GATTT-CATGTAAGACCATGTCTGGG
238583 ACATGGCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 2 0.03
43 40 0.67
44 18 0.30
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
GATTTCATGTAAGACCATGTCTGGGCTATTGGCATCGATTCAA
Done.