Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 87 of 171
Found at i:28595170 original size:14 final size:15
Alignment explanation
Indices: 28595139--28595173 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
28595129 TTTAAAACCT
*
28595139 AACCAAACCCATTTG
1 AACCAAACCCAATTG
28595154 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
28595168 AACCAA
1 AACCAA
28595174 GTCCAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:28595217 original size:10 final size:10
Alignment explanation
Indices: 28595199--28595234 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28595189 AGTCAAACTG
*
28595199 TTGACCGGCG
1 TTGACCGGCA
*
28595209 TTGATCGGCA
1 TTGACCGGCA
28595219 TTGACCGGCA
1 TTGACCGGCA
28595229 TTGACC
1 TTGACC
28595235 ACTGACCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.25
Consensus pattern (10 bp):
TTGACCGGCA
Found at i:28595254 original size:20 final size:20
Alignment explanation
Indices: 28595229--28595270 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
28595219 TTGACCGGCA
28595229 TTGACCACTGACCGTTGACT
1 TTGACCACTGACCGTTGACT
**
28595249 TTGACCGTTGACCGTTGACT
1 TTGACCACTGACCGTTGACT
28595269 TT
1 TT
28595271 TTTTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGACCACTGACCGTTGACT
Found at i:28596310 original size:3 final size:3
Alignment explanation
Indices: 28596298--28596330 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
28596288 TAGAATATTC
28596298 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28596331 TTGGGATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:28606410 original size:29 final size:30
Alignment explanation
Indices: 28606347--28606420 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
28606337 ATTTTTGAGG
* *
28606347 AATTTGGGGATCAAAATCAAAATTTTTAGAA
1 AATTT-GGGATTAAAATCAAAACTTTTAGAA
* *
28606378 AATTTGGGATTAAAATC-GAACTTTTGGAA
1 AATTTGGGATTAAAATCAAAACTTTTAGAA
28606407 AATTTGAGG-TTAAA
1 AATTTG-GGATTAAA
28606421 TGTGACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 20 0.53
30 13 0.34
31 5 0.13
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (30 bp):
AATTTGGGATTAAAATCAAAACTTTTAGAA
Found at i:28606449 original size:28 final size:28
Alignment explanation
Indices: 28606397--28606450 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
28606387 TTAAAATCGA
*
28606397 ACTTTTGGAAAATTTGAGGTTAAATGTG
1 ACTTTTGGAAAATTTGAGGTAAAATGTG
28606425 ACTTTTGG-AAATTTGAGGGTAAAATG
1 ACTTTTGGAAAATTTGA-GGTAAAATG
28606451 GTAATTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
ACTTTTGGAAAATTTGAGGTAAAATGTG
Found at i:28606695 original size:30 final size:30
Alignment explanation
Indices: 28606533--28606694 Score: 159
Period size: 30 Copynumber: 5.4 Consensus size: 30
28606523 TTCGGGGACA
* * *
28606533 AAAATGAAATTTTGGCA-AAGTTTG-GGGTG
1 AAAATGTAATTTTAG-AGAAGTTTGAGGGTT
* * * ** *
28606562 AAAATGTGATTTTGGAAAAGTTCAAGCGTT
1 AAAATGTAATTTTAGAGAAGTTTGAGGGTT
*
28606592 AAAATGTAATTTTAGAGAAGTTTAAGGGTT
1 AAAATGTAATTTTAGAGAAGTTTGAGGGTT
*
28606622 AAAATGCAATTTTAG-GAAAGTTTGAGGGTT
1 AAAATGTAATTTTAGAG-AAGTTTGAGGGTT
* * *
28606652 AAAATGTCATTTTTGAGAAGTTTGAGGGTC
1 AAAATGTAATTTTAGAGAAGTTTGAGGGTT
28606682 AAAATGTAATTTT
1 AAAATGTAATTTT
28606695 TTAAATAAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 19 0.17
30 90 0.81
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTAGAGAAGTTTGAGGGTT
Found at i:28608405 original size:17 final size:17
Alignment explanation
Indices: 28608382--28608441 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
28608372 GGATATTATT
28608382 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
28608399 GATTTAAATAATAAAATA
1 AATTTAAAT-TTAAAATA
*
28608417 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
28608434 AATTTAAA
1 AATTTAAA
28608442 AATAGGTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:28608964 original size:39 final size:39
Alignment explanation
Indices: 28608921--28609490 Score: 255
Period size: 39 Copynumber: 14.7 Consensus size: 39
28608911 GATGGTTGCA
* *
28608921 ATCTGCCCTTGGCTCGGAGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * * ** * * **
28608960 ATCTG-CCTCAAGCTCGGGATAAAAGATCGAATGGTTGCA
1 ATCTGCCCT-AGGCTCGGGGTAAGAGATTGGTTGATGGTG
*
28608999 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * * * * * *
28609038 AACTGCCCTAAGCTCGGGGTAAAAGATCGAATGGCT-GTA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTG-GTTGATGGTG
*
28609077 ATCTG-CCTCAGGCTTGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCT-AGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * * * * **
28609116 ATCTGCCCTAAGCTCGAGGTAAAAGATCGAATGGAT-GCA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTG-GTTGATGGTG
* * * ** * ** *
28609155 ATTTGCCCCAAGCTCGAAGTAAGAGAGTGACTGATAGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * ***
28609194 ATTTACCC-CGAGCTCGGGGTAAGAGA-T--CAAATGGCTG
1 ATCTGCCCTAG-GCTCGGGGTAAGAGATTGGTTGATGG-TG
* ** **
28609231 CAATCTGCCCCAAAACTCGGGGTAAGAGATTGACTGATGGTG
1 --ATCTG-CCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* *
28609273 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * * * * ** * * *
28609312 ATTTGCCTTAGCCTTGGGGTAAAAGATCGAATGGTTGTA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * *
28609351 ATCTGCCCTAGACTCGGGGTAAGAGATT-G--GCT-GTA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * *
28609386 ATTTGCCTTAGGTTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * * * * * *
28609425 ATCTACCCTAGGCTCGGGGTAAAAGATCGGATGGTTGTA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
* * *
28609464 ATTTACCCCAGGCTCGGGGTAAGAGAT
1 ATCTGCCCTAGGCTCGGGGTAAGAGAT
28609491 AGGAATCTTC
Statistics
Matches: 393, Mismatches: 117, Indels: 42
0.71 0.21 0.08
Matches are distributed among these distances:
35 27 0.07
36 7 0.02
37 2 0.01
38 16 0.04
39 299 0.76
40 34 0.09
41 1 0.00
42 2 0.01
43 5 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (39 bp):
ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTG
Found at i:28609044 original size:78 final size:77
Alignment explanation
Indices: 28608912--28609490 Score: 475
Period size: 78 Copynumber: 7.5 Consensus size: 77
28608902 TGGATATTGG
* * *
28608912 ATGGTTGCAATCTGCCCTTGGCTCGGAGTAAGAGATTGGTTGATGGTGATCTGCCTCAAGCTCGG
1 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGCTCGG
*
28608977 GATAAAAGATCGA
65 GGTAAAAGATCGA
*
28608990 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGAACTGCCCTAAGCTCGG
1 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCGG
28609055 GGTAAAAGATCGA
65 GGTAAAAGATCGA
* * * *
28609068 ATGGCTGTAATCTG-CCTCAGGCTTGGGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCG
1 ATGGTTGCAATCTGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCG
*
28609132 AGGTAAAAGATCGA
64 GGGTAAAAGATCGA
* * * * ** * * * * * *
28609146 ATGGATGCAATTTGCCCCAAGCTCGAAGTAAGAGAGTGACTGATAGTGATTTACCCCGAGCTCGG
1 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCAAGCTCGG
* *
28609211 GGTAAGAGATCAA
65 GGTAAAAGATCGA
* * ** * *
28609224 ATGGCTGCAATCTGCCCCAAAACTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCG
1 ATGGTTGCAATCTG-CCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCG
* * *
28609289 GGGTAAGAGATTGG
64 GGGTAAAAGATCGA
* * * ** * * * * * * ** * * * *
28609303 CTGATGGTGATTTGCCTTAGCCTTGGGGTAAAAGATCGAATGGTTGTAATCTGCCCTAGACTCGG
1 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAG-CTCGG
28609368 GGT--AAGA--GA
65 GGTAAAAGATCGA
* * * * * * * *
28609377 TTGGCTGTAATTTGCCTTAGGTTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCGG
1 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCGG
*
28609442 GGTAAAAGATCGG
65 GGTAAAAGATCGA
* * * *
28609455 ATGGTTGTAATTTACCCCAGGCTCGGGGTAAGAGAT
1 ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGAT
28609491 AGGAATCTTC
Statistics
Matches: 398, Mismatches: 91, Indels: 24
0.78 0.18 0.05
Matches are distributed among these distances:
74 49 0.12
75 1 0.00
76 7 0.02
77 8 0.02
78 271 0.68
79 62 0.16
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (77 bp):
ATGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCTCGGG
GTAAAAGATCGA
Found at i:28609307 original size:118 final size:112
Alignment explanation
Indices: 28609147--28609452 Score: 315
Period size: 118 Copynumber: 2.7 Consensus size: 112
28609137 AAAGATCGAA
* * * ** * * * *
28609147 TGGATGCAATTTGCCCCAAGCTCGAAGTAAGAGAGTGACTGATAGTGATTTACCCCGAGCTCGGG
1 TGGATGTAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTA-CCCTAGCTCGGG
*
28609212 GTAAGAGATCAAATGGCTGCAATCTGCCCCAAAACTCGGGGTAAGAGAT
65 GTAAAAGATCAAATGGCTGCAATCTG-CCCAAAACTCGGGGTAAGAGAT
* * *
28609261 TGACTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCTTAGCCT
1 TG---GAT-GTAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTACCCTAG-CT
* * * * * *
28609326 TGGGGTAAAAGATCGAATGGTTGTAATCTGCCCTAGACTCGGGGTAAGAGAT
61 CGGGGTAAAAGATCAAATGGCTGCAATCTGCCCAAAACTCGGGGTAAGAGAT
* * ** * *
28609378 TGGCTGTAATTTGCCTTAGGTTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCGGG
1 TGGATGTAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTACCCTA-GCTCGGG
28609443 GTAAAAGATC
65 GTAAAAGATC
28609453 GGATGGTTGT
Statistics
Matches: 157, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
113 59 0.38
114 5 0.03
117 29 0.18
118 64 0.41
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (112 bp):
TGGATGTAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTACCCTAGCTCGGGG
TAAAAGATCAAATGGCTGCAATCTGCCCAAAACTCGGGGTAAGAGAT
Found at i:28609819 original size:49 final size:49
Alignment explanation
Indices: 28609730--28609824 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
28609720 TAAGATACTA
* * * * *
28609730 GGTTCGTCTTTGCGACCTCAACCTTTTCCTTCAACTCTTCATGGTACAG
1 GGTTCGCCATTGCGACCTCAACCTTTCCCATCAACGCTTCATGGTACAG
*
28609779 GGTTCGCCATTGCGGCCTCAACCTTTCCCATC-ACAGCTTCATGGTA
1 GGTTCGCCATTGCGACCTCAACCTTTCCCATCAAC-GCTTCATGGTA
28609825 TCGGATTCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.05
49 37 0.95
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.33
Consensus pattern (49 bp):
GGTTCGCCATTGCGACCTCAACCTTTCCCATCAACGCTTCATGGTACAG
Found at i:28610874 original size:23 final size:23
Alignment explanation
Indices: 28610847--28610976 Score: 96
Period size: 23 Copynumber: 5.6 Consensus size: 23
28610837 CACCTCGACC
28610847 TCTCTTTTTCTTTTTCCTTTTTT
1 TCTCTTTTTCTTTTTCCTTTTTT
*
28610870 TCTCTTTTTTATTTTTCTTCTTGTTTT
1 TCTC-TTTTTCTTTTTC--CTT-TTTT
28610897 T-TCCTTTTT-TATTTTCCTTTTTCT
1 TCT-CTTTTTCT-TTTTCCTTTTT-T
28610921 TCT-TTTTT-TTATTT--TTTTCTT
1 TCTCTTTTTCTT-TTTCCTTTT-TT
28610942 TCTC-TTTTCTTTTTTCCTTTTTT
1 TCTCTTTTTC-TTTTTCCTTTTTT
*
28610965 CCT-TTTTTCTTT
1 TCTCTTTTTCTTT
28610977 CTTCATTAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 33
0.72 0.02 0.27
Matches are distributed among these distances:
21 12 0.13
22 8 0.09
23 27 0.30
24 20 0.22
25 2 0.02
26 14 0.16
27 6 0.07
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.78
Consensus pattern (23 bp):
TCTCTTTTTCTTTTTCCTTTTTT
Found at i:28610918 original size:33 final size:31
Alignment explanation
Indices: 28610881--28610979 Score: 96
Period size: 34 Copynumber: 3.1 Consensus size: 31
28610871 CTCTTTTTTA
28610881 TTTTTCTTCTTGTTTTTTCCTTTTTTAT-TTTCC
1 TTTTTCTTCTT-TTTTTTCCTTTTTT-TCTTT-C
*
28610914 TTTTTCTTCTTTTTTTT-ATTTTTTTCTTTC
1 TTTTTCTTCTTTTTTTTCCTTTTTTTCTTTC
*
28610944 TCTTTTCTTTTTTCCTTTTTTCC-TTTTTTCTTTC
1 T-TTTTC-TTCTT--TTTTTTCCTTTTTTTCTTTC
28610978 TT
1 TT
28610980 CATTAAATCC
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
30 3 0.05
31 14 0.25
32 10 0.18
33 12 0.21
34 18 0.32
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (31 bp):
TTTTTCTTCTTTTTTTTCCTTTTTTTCTTTC
Found at i:28610950 original size:51 final size:50
Alignment explanation
Indices: 28610850--28610972 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 50
28610840 CTCGACCTCT
28610850 CTTTTTCTTTTTCCTTTTTTTCTCTTTTTTATTTTTCTTCTTGTTTTTTC
1 CTTTTTCTTTTTCCTTTTTTTCTCTTTTTTATTTTTCTTCTTGTTTTTTC
*
28610900 CTTTTT-TATTTTCCTTTTTCTTCTTTTTTTTATTTTT-TTCTT-TCTCTTTTC
1 CTTTTTCT-TTTTCCTTTTT-TTCTCTTTTTTATTTTTCTTCTTGT-T-TTTTC
*
28610951 TTTTTTCCTTTTTTCCTTTTTT
1 CTTTTT-C-TTTTTCCTTTTTT
28610973 CTTTCTTCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
49 2 0.03
50 23 0.36
51 26 0.41
52 1 0.02
53 11 0.17
54 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (50 bp):
CTTTTTCTTTTTCCTTTTTTTCTCTTTTTTATTTTTCTTCTTGTTTTTTC
Found at i:28610954 original size:27 final size:26
Alignment explanation
Indices: 28610857--28610979 Score: 92
Period size: 27 Copynumber: 4.7 Consensus size: 26
28610847 TCTCTTTTTC
*
28610857 TTTTTCCTTT-TTTTCTCTTTTTTATT
1 TTTTTCTTTTCTTTTCT-TTTTTTATT
*
28610883 TTTCTTCTTGTT-TTTTCCTTTTTTATT
1 TTT-TTCTT-TTCTTTTCTTTTTTTATT
** *
28610910 TTCCT-TTTTCTTCT-TTTTTTTATT
1 TTTTTCTTTTCTTTTCTTTTTTTATT
**
28610934 TTTTTCTTTCTCTTTTCTTTTTTCCTT
1 TTTTTCTTT-TCTTTTCTTTTTTTATT
* *
28610961 TTTTCCTTTTTTCTTTCTT
1 TTTTTCTTTTCT-TTTCTT
28610980 CATTAAATCC
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
24 14 0.18
25 8 0.10
26 11 0.14
27 37 0.48
28 7 0.09
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (26 bp):
TTTTTCTTTTCTTTTCTTTTTTTATT
Found at i:28616820 original size:30 final size:29
Alignment explanation
Indices: 28616785--28616880 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
28616775 ATTAAAATCG
28616785 AACTTTTAAAAATTTTGAGGTCGAAAATGT
1 AACTTTTAAAAATTTTGAGGTC-AAAATGT
* ** *
28616815 GACTTTT-GGAATTTTGAGGGCAAAATGGT
1 AACTTTTAAAAATTTTGAGGTCAAAAT-GT
* *
28616844 AATTTTGTAAAAA-TTTGGGGTCAAAATGGT
1 AACTTT-TAAAAATTTTGAGGTCAAAAT-GT
*
28616874 AATTTTT
1 AACTTTT
28616881 GGATGTTCGA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
28 5 0.09
29 18 0.34
30 28 0.53
31 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (29 bp):
AACTTTTAAAAATTTTGAGGTCAAAATGT
Found at i:28616881 original size:59 final size:58
Alignment explanation
Indices: 28616788--28616956 Score: 171
Period size: 58 Copynumber: 2.9 Consensus size: 58
28616778 AAAATCGAAC
* * * * *
28616788 TTTTAAAAATTTTGAGGTCGAAAAT-GTGACTTTTGGAAT-TTTGAGGGCAAAATGGTAAT
1 TTTTAAAAA-TTTGGGGTC-AAAATGGTAATTTTTGG-ATGTTCGAGGGCAAAACGGTAAT
*
28616847 TTTGTAAAAATTTGGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAACGGTAAT
1 TTT-TAAAAATTTGGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAACGGTAAT
** ** * * *
28616906 TTTTGGATGTTCGGGTTCAAGATGGTAATTTTTGGATGTTCGAGGGCAAAA
1 TTTTAAAAATTTGGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAA
28616957 ATGCATTTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 47 0.51
59 40 0.43
60 6 0.06
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (58 bp):
TTTTAAAAATTTGGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAACGGTAAT
Found at i:28616903 original size:29 final size:30
Alignment explanation
Indices: 28616861--28616956 Score: 144
Period size: 29 Copynumber: 3.3 Consensus size: 30
28616851 TAAAAATTTG
28616861 GGGTCAAAATGGTAATTTTTGGATGTTCGA
1 GGGTCAAAATGGTAATTTTTGGATGTTCGA
*
28616891 GGGT-AAAACGGTAATTTTTGGATGTTCG-
1 GGGTCAAAATGGTAATTTTTGGATGTTCGA
* *
28616919 GGTTCAAGATGGTAATTTTTGGATGTTCGA
1 GGGTCAAAATGGTAATTTTTGGATGTTCGA
28616949 GGG-CAAAA
1 GGGTCAAAA
28616957 ATGCATTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 3 0.05
29 49 0.84
30 6 0.10
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGGTAATTTTTGGATGTTCGA
Found at i:28616966 original size:29 final size:29
Alignment explanation
Indices: 28616866--28616967 Score: 102
Period size: 29 Copynumber: 3.5 Consensus size: 29
28616856 ATTTGGGGTC
*
28616866 AAAATGGTAATTTTTGGATGTTCGAGGGTA
1 AAAAT-GTAATTTTTGGATGTTCGAGGGCA
** *
28616896 AAACGGTAATTTTTGGATGTTCG-GGTTC-
1 AAAATGTAATTTTTGGATGTTCGAGG-GCA
*
28616924 AAGATGGTAATTTTTGGATGTTCGAGGGCA
1 AAAAT-GTAATTTTTGGATGTTCGAGGGCA
*
28616954 AAAATG-CATTTTTG
1 AAAATGTAATTTTTG
28616968 AAAAAGTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
28 11 0.19
29 38 0.66
30 9 0.16
ACGTcount: A:0.27, C:0.07, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTGGATGTTCGAGGGCA
Found at i:28617017 original size:30 final size:30
Alignment explanation
Indices: 28616954--28617145 Score: 183
Period size: 30 Copynumber: 6.4 Consensus size: 30
28616944 TTCGAGGGCA
* * * *
28616954 AAAATGCATTTTTGAAAAAGTTTG-GAGTG
1 AAAATGTAATTTTGAAAAAGTTTGAGGGTC
*
28616983 AAAATGTGATTTTGAAAAAGTTTGAGGGTC
1 AAAATGTAATTTTGAAAAAGTTTGAGGGTC
* * * *
28617013 AAAATGTAATTTTGAAGAAGCTCGAGGGTT
1 AAAATGTAATTTTGAAAAAGTTTGAGGGTC
* *
28617043 AAAATGTAATTTT-AGGAAAGTTTGAGGGTT
1 AAAATGTAATTTTGA-AAAAGTTTGAGGGTC
* * *
28617073 AAAATGTGATTTTTG-AGAAGTTTGGGGGTC
1 AAAATGT-AATTTTGAAAAAGTTTGAGGGTC
* * * *
28617103 AAAATGTAATTTTTACAAAGTTTGAAGGTA
1 AAAATGTAATTTTGAAAAAGTTTGAGGGTC
28617133 AAAATGTAATTTT
1 AAAATGTAATTTT
28617146 TAAATAAAAT
Statistics
Matches: 132, Mismatches: 26, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
29 27 0.20
30 100 0.76
31 5 0.04
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGAAAAAGTTTGAGGGTC
Found at i:28617137 original size:90 final size:89
Alignment explanation
Indices: 28616970--28617145 Score: 230
Period size: 90 Copynumber: 2.0 Consensus size: 89
28616960 CATTTTTGAA
28616970 AAAGTTTGGAGTGAAAATGTGATTTTGAAAAAGTTTGAGGGTCAAAATGTAATTTTGAAGAAGCT
1 AAAGTTTGGAGTGAAAATGTGATTTTGAAAAAGTTTGAGGGTCAAAATGTAATTTTGAAGAAGCT
* *
28617035 CGAGGGTTAAAATGTAATTTTAGG
66 CGAAGGTAAAAATGTAATTTTAGG
* * * * *
28617059 AAAGTTTGAGGGTTAAAATGTGATTTTTG-AGAAGTTTGGGGGTCAAAATGTAATTTTTACA-AA
1 AAAGTTTG-GAGTGAAAATGTGA-TTTTGAAAAAGTTTGAGGGTCAAAATGTAATTTTGA-AGAA
* *
28617122 GTTTGAAGGTAAAAATGTAATTTT
63 GCTCGAAGGTAAAAATGTAATTTT
28617146 TAAATAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
89 8 0.11
90 61 0.81
91 6 0.08
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (89 bp):
AAAGTTTGGAGTGAAAATGTGATTTTGAAAAAGTTTGAGGGTCAAAATGTAATTTTGAAGAAGCT
CGAAGGTAAAAATGTAATTTTAGG
Found at i:28617146 original size:30 final size:29
Alignment explanation
Indices: 28616827--28617149 Score: 163
Period size: 30 Copynumber: 10.9 Consensus size: 29
28616817 CTTTTGGAAT
* *
28616827 TTTGAGGG-CAAAATGGTAATTTTGTAAAAA
1 TTTGAGGGTAAAAAT-GTAATTTT-TAAAAG
* ** *
28616857 TTTG-GGGTCAAAATGGTAATTTTTGGATG
1 TTTGAGGGTAAAAAT-GTAATTTTTAAAAG
* ** ** *
28616886 TTCGAGGGTAAAACGGTAATTTTTGGATG
1 TTTGAGGGTAAAAATGTAATTTTTAAAAG
* * * * ** *
28616915 TTCG-GGTTCAAGATGGTAATTTTTGGATG
1 TTTGAGGGTAAAAAT-GTAATTTTTAAAAG
* * *
28616944 TTCGAGGGCAAAAATG-CATTTTTGAAAAAG
1 TTTGAGGGTAAAAATGTAATTTTT--AAAAG
* * * *
28616974 TTTG-GAGTGAAAATGTGATTTTGAAAAAG
1 TTTGAGGGTAAAAATGTAATTTT-TAAAAG
* *
28617003 TTTGAGGGTCAAAATGTAATTTTGAAGAAG
1 TTTGAGGGTAAAAATGTAATTTTTAA-AAG
* * *
28617033 CTCGAGGGTTAAAATGTAA-TTTTAGGAAAG
1 TTTGAGGGTAAAAATGTAATTTTTA--AAAG
* * *
28617063 TTTGAGGGTTAAAATGTGATTTTTGAGAAG
1 TTTGAGGGTAAAAATGTAATTTTT-AAAAG
* *
28617093 TTTGGGGGTCAAAATGTAATTTTTACAAAG
1 TTTGAGGGTAAAAATGTAATTTTTA-AAAG
*
28617123 TTTGAAGGTAAAAATGTAATTTTTAAA
1 TTTGAGGGTAAAAATGTAATTTTTAAA
28617150 TAAAATAGGG
Statistics
Matches: 232, Mismatches: 46, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
28 11 0.05
29 71 0.31
30 144 0.62
31 5 0.02
32 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTGAGGGTAAAAATGTAATTTTTAAAAG
Found at i:28617146 original size:60 final size:61
Alignment explanation
Indices: 28616947--28617146 Score: 203
Period size: 60 Copynumber: 3.3 Consensus size: 61
28616937 TTGGATGTTC
* * * * * * *
28616947 GAGGGCAAAAATG-CATTTTTGAAAAAGTTT-GGAGTGAAAATGTGATTTTGAAAAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAAGAAGTTTGGGGGTCAAAATGTAATTTTTAAAAAGTTT
* * * * * *
28617006 GAGGGTCAAAATGTAA-TTTTGAAGAAGCTCGAGGGTTAAAATGTAA-TTTTAGGAAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAAGAAGTTTGGGGGTCAAAATGTAATTTTTA-AAAAGTTT
* * *
28617066 GAGGGTTAAAATGTGATTTTTG-AGAAGTTTGGGGGTCAAAATGTAATTTTTACAAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAAGAAGTTTGGGGGTCAAAATGTAATTTTTAAAAAGTTT
*
28617126 GAAGGTAAAAATGTAATTTTT
1 GAGGGTAAAAATGTAATTTTT
28617147 AAATAAAATA
Statistics
Matches: 114, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
59 26 0.23
60 78 0.68
61 10 0.09
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (61 bp):
GAGGGTAAAAATGTAATTTTTGAAGAAGTTTGGGGGTCAAAATGTAATTTTTAAAAAGTTT
Found at i:28618868 original size:17 final size:17
Alignment explanation
Indices: 28618846--28618887 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
28618836 GGACATTATT
*
28618846 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
28618863 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
28618880 AATTTAAA
1 AATTTAAA
28618888 AATGGGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:28621610 original size:2 final size:2
Alignment explanation
Indices: 28621603--28621627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28621593 TTTTATTCTT
28621603 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28621628 TTACATACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28621658 original size:38 final size:38
Alignment explanation
Indices: 28621615--28621687 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
28621605 TATATATATA
*
28621615 TATATATATATATTTACATACTTAGTTTATT-TTTACTT
1 TATATATACATATTTAC-TACTTAGTTTATTCTTTACTT
* *
28621653 TATATATACATATTTACTATTTTGTTTATTCTTTA
1 TATATATACATATTTACTACTTAGTTTATTCTTTA
28621688 TATATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 11 0.35
38 20 0.65
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (38 bp):
TATATATACATATTTACTACTTAGTTTATTCTTTACTT
Found at i:28621713 original size:25 final size:25
Alignment explanation
Indices: 28621685--28621760 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
28621675 TGTTTATTCT
28621685 TTATATATATTTTTAATATGTATTA
1 TTATATATATTTTTAATATGTATTA
* * * * *
28621710 TTATATATATATAT-ATTTCTATTCT
1 TTATATATATTTTTAATATGTATT-A
*
28621735 TTATATATATTTTTAATACGTATTA
1 TTATATATATTTTTAATATGTATTA
28621760 T
1 T
28621761 ATTTTTATTC
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
24 7 0.18
25 25 0.66
26 6 0.16
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (25 bp):
TTATATATATTTTTAATATGTATTA
Found at i:28621741 original size:19 final size:19
Alignment explanation
Indices: 28621717--28621781 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
28621707 TTATTATATA
*
28621717 TATATATATTTCTATTCTT
1 TATATATATTTTTATTCTT
* *
28621736 TATATATATTTTTAATAC-G
1 TATATATATTTTT-ATTCTT
28621755 TAT-TATATTTTTATTCTT
1 TATATATATTTTTATTCTT
*
28621773 TCTATATAT
1 TATATATAT
28621782 ATATACATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.08
18 11 0.30
19 20 0.54
20 3 0.08
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATATATTTTTATTCTT
Found at i:28623280 original size:152 final size:152
Alignment explanation
Indices: 28623004--28623297 Score: 473
Period size: 152 Copynumber: 1.9 Consensus size: 152
28622994 GCTGACACCC
*
28623004 CAGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTTGAAACACATAGTGGAGGCAA
1 CAGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGAAACACATAGTGGAGGCAA
* * ** *
28623069 TTATGAGTTGGAAAAATGCCATTTGAATCTTGAACCCGTGTGTTACGTAAAAAACTTCAATCGCA
66 TCACGAGTTGGAAAAACACCATTTGAATCTTGAACCCATGTGTTACGTAAAAAACTTCAATCGCA
28623134 -ACAACAACCCTTGACATGGGTT
131 GA-AACAACCCTTGACATGGGTT
* * *
28623156 CAGGTATCCTCTCTAGCCAATATGATTAAAAATATGCAAAGATTCGTAACACATCGTGGAGGCAA
1 CAGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGAAACACATAGTGGAGGCAA
* *
28623221 TCACGAGTTGGAAGAACACCATTTGAATCTTGAACCCATGTGTTACGTGAAAAACTTCAATCGCA
66 TCACGAGTTGGAAAAACACCATTTGAATCTTGAACCCATGTGTTACGTAAAAAACTTCAATCGCA
28623286 GAAACAACCCTT
131 GAAACAACCCTT
28623298 ACTCGAACAT
Statistics
Matches: 130, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
152 129 0.99
153 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (152 bp):
CAGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGAAACACATAGTGGAGGCAA
TCACGAGTTGGAAAAACACCATTTGAATCTTGAACCCATGTGTTACGTAAAAAACTTCAATCGCA
GAAACAACCCTTGACATGGGTT
Found at i:28633560 original size:42 final size:42
Alignment explanation
Indices: 28633503--28633597 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
28633493 CTAGATTGGC
* * *
28633503 CCATGTGGCTTAAATCAATGACTCACACAGTCTACCACACTA
1 CCATGTGACTCAAATCAATGACTCACACAGTCTACCACACAA
* * * * *
28633545 CTATGTGACTCAAATCAATGTCTCACACGGTTTAGCACACAA
1 CCATGTGACTCAAATCAATGACTCACACAGTCTACCACACAA
28633587 CCATGTGACTC
1 CCATGTGACTC
28633598 TACTCAGTCT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (42 bp):
CCATGTGACTCAAATCAATGACTCACACAGTCTACCACACAA
Found at i:28638147 original size:46 final size:46
Alignment explanation
Indices: 28638095--28638203 Score: 157
Period size: 46 Copynumber: 2.4 Consensus size: 46
28638085 GCATGCCTAT
28638095 GTGAAATGTGATATGTAAGCATGATACATGCTAAAATGTGGAAATC
1 GTGAAATGTGATATGTAAGCATGATACATGCTAAAATGTGGAAATC
* * * *
28638141 GTGAAATGTGATATATGAGCATGCTACATGCTAAAATGTGTAAATC
1 GTGAAATGTGATATGTAAGCATGATACATGCTAAAATGTGGAAATC
*
28638187 GTGACATG-GATTATGTA
1 GTGAAATGTGA-TATGTA
28638204 TGGGATCTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 2 0.04
46 53 0.96
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (46 bp):
GTGAAATGTGATATGTAAGCATGATACATGCTAAAATGTGGAAATC
Found at i:28638551 original size:8 final size:8
Alignment explanation
Indices: 28638523--28638556 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
28638513 TGTCTTAAAC
28638523 ATGTGATT
1 ATGTGATT
28638531 ATTGTGA-T
1 A-TGTGATT
28638539 ATGTGATT
1 ATGTGATT
28638547 ATGTGATT
1 ATGTGATT
28638555 AT
1 AT
28638557 CAAGATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 5 0.21
8 14 0.58
9 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (8 bp):
ATGTGATT
Found at i:28639273 original size:19 final size:19
Alignment explanation
Indices: 28639249--28639307 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
28639239 ATTTTTTATC
*
28639249 ATGTGAAATTGATGCGAAT
1 ATGTGAAATTGATGTGAAT
28639268 ATGTGAAATTGATGTGAAT
1 ATGTGAAATTGATGTGAAT
*
28639287 ATGTGAAATAGATGTGAAT
1 ATGTGAAATTGATGTGAAT
28639306 AT
1 AT
28639308 CAAATGTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (19 bp):
ATGTGAAATTGATGTGAAT
Found at i:28639284 original size:11 final size:11
Alignment explanation
Indices: 28639249--28639304 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
28639239 ATTTTTTATC
28639249 ATGTGAAATTG
1 ATGTGAAATTG
*
28639260 ATGCG-AA-T-
1 ATGTGAAATTG
28639268 ATGTGAAATTG
1 ATGTGAAATTG
28639279 ATGTG-AA-T-
1 ATGTGAAATTG
*
28639287 ATGTGAAATAG
1 ATGTGAAATTG
28639298 ATGTGAA
1 ATGTGAA
28639305 TATCAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
8 9 0.25
9 6 0.17
10 5 0.14
11 16 0.44
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (11 bp):
ATGTGAAATTG
Found at i:28649111 original size:21 final size:22
Alignment explanation
Indices: 28649063--28649123 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
28649053 AAACAGTTCA
* **
28649063 AATTTCTACCGGTACCTGTACT
1 AATTTCTACCGATACAAGTACT
28649085 AA-TTCTACCGATACAAGTA-T
1 AATTTCTACCGATACAAGTACT
28649105 AATTTCTACCGATACAAGT
1 AATTTCTACCGATACAAGT
28649124 CATGCATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.09
21 30 0.86
22 2 0.06
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (22 bp):
AATTTCTACCGATACAAGTACT
Found at i:28649940 original size:51 final size:51
Alignment explanation
Indices: 28649868--28650094 Score: 339
Period size: 51 Copynumber: 4.5 Consensus size: 51
28649858 GGAATTTATA
* * * *
28649868 TACTCACGATGACACTGAGTCATCAGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* *
28649919 TACTCACGATGATACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* * * *
28649970 TACTCACGATGAGACTTAGCCATCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
*
28650021 TACTCACGATGACACTAAGTCATCAGACCTTTAATCCGT-AAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
*
28650071 TACTCACGATGACATTTAGTCATC
1 TACTCACGATGACACTTAGTCATC
28650095 GAACTCTTTC
Statistics
Matches: 160, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 33 0.21
51 127 0.79
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
Found at i:28659865 original size:28 final size:28
Alignment explanation
Indices: 28659834--28659890 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28659824 TTCTCAAAAA
28659834 AAAAAAAAAAAAAAACT-GTAATTTAACT
1 AAAAAAAAAAAAAAA-TAGTAATTTAACT
* * *
28659862 AAAAAAATAATAAAATAGTGATTTAACT
1 AAAAAAAAAAAAAAATAGTAATTTAACT
28659890 A
1 A
28659891 TTAGTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAAAAAAAAAAAAATAGTAATTTAACT
Found at i:28660017 original size:52 final size:52
Alignment explanation
Indices: 28659955--28660070 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
28659945 TAGTTTTAAT
*
28659955 TCTCAATATTTATACATTTTATCAATTTGGTCTTGATTCTAAAAAATATAAC
1 TCTCAATATTTATACATTTTATCAATTTGGACTTGATTCTAAAAAATATAAC
*
28660007 TCTCAATATTTATACATTTTGTCAATTTGGACTTGATTCTAAAAAATATAAC
1 TCTCAATATTTATACATTTTATCAATTTGGACTTGATTCTAAAAAATATAAC
*
28660059 TCTCAACATTTA
1 TCTCAATATTTA
28660071 CATACTATGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (52 bp):
TCTCAATATTTATACATTTTATCAATTTGGACTTGATTCTAAAAAATATAAC
Found at i:28660086 original size:52 final size:52
Alignment explanation
Indices: 28659976--28660086 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
28659966 ATACATTTTA
* * * * *
28659976 TCAATTTGGTCTTGATTCTAAAAAATATAACTCTCAATATTTATACATTTTG
1 TCAATTTGGACTTGATTCTAAAAAATATAACTCTCAACATTTACACACTATG
*
28660028 TCAATTTGGACTTGATTCTAAAAAATATAACTCTCAACATTTACATACTATG
1 TCAATTTGGACTTGATTCTAAAAAATATAACTCTCAACATTTACACACTATG
*
28660080 TTAATTT
1 TCAATTT
28660087 TAAAAGTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.42
Consensus pattern (52 bp):
TCAATTTGGACTTGATTCTAAAAAATATAACTCTCAACATTTACACACTATG
Found at i:28664887 original size:31 final size:30
Alignment explanation
Indices: 28664827--28664887 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28664817 GTTAGCAATC
* *
28664827 ATTTTCATTTTAATCCTTTAATTTTAATAA
1 ATTTTCATTTTAATACGTTAATTTTAATAA
28664857 ATTTTCATTTTATATTACGTTAA-TTTAATAA
1 ATTTTCATTTTA-A-TACGTTAATTTTAATAA
28664888 TATTATATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 9 0.33
32 6 0.22
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (30 bp):
ATTTTCATTTTAATACGTTAATTTTAATAA
Found at i:28664968 original size:21 final size:21
Alignment explanation
Indices: 28664949--28664989 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
28664939 TCTCTTTTTA
*
28664949 TATTTTT-AAAAA-TTAATTT
1 TATTTTTGAAAAACTAAATTT
28664968 TATTTTTGAAAAACTAAATTT
1 TATTTTTGAAAAACTAAATTT
28664989 T
1 T
28664990 TACAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTTGAAAAACTAAATTT
Found at i:28669800 original size:30 final size:30
Alignment explanation
Indices: 28669757--28669830 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
28669747 ACCATGTGCT
*
28669757 AGCCCGTATGGCTCACATGGCCGTCTGTCC
1 AGCCCGTATGGCTCACATGGCCGTCTGCCC
* * * *
28669787 AGCTCGTGTGGCTCACATGGTCGTGTGCCC
1 AGCCCGTATGGCTCACATGGCCGTCTGCCC
28669817 AGCCCGTATGGCTC
1 AGCCCGTATGGCTC
28669831 CTAAAATCTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.24
Consensus pattern (30 bp):
AGCCCGTATGGCTCACATGGCCGTCTGCCC
Found at i:28672847 original size:23 final size:23
Alignment explanation
Indices: 28672819--28672918 Score: 121
Period size: 23 Copynumber: 4.4 Consensus size: 23
28672809 ATTTAAAACA
* *
28672819 AAACATTATGGCCGAAGAGTTAC
1 AAACATAATGGCAGAAGAGTTAC
* *
28672842 AAACATAATGGCAGGAGAGCTAC
1 AAACATAATGGCAGAAGAGTTAC
*
28672865 AAACATAATGACAGAAGAGTTAC
1 AAACATAATGGCAGAAGAGTTAC
* * *
28672888 AAACATAATGGTAGGAGAGTTAT
1 AAACATAATGGCAGAAGAGTTAC
28672911 AAA-ATAAT
1 AAACATAAT
28672919 AATAACTGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 5 0.08
23 61 0.92
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (23 bp):
AAACATAATGGCAGAAGAGTTAC
Found at i:28674139 original size:29 final size:29
Alignment explanation
Indices: 28674094--28674165 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
28674084 ACATTAACAA
* * * *
28674094 GACACCTCTACATTTTCAAGTGGTTCTAG
1 GACACCCCCACATTTCCAAGTGATTCTAG
28674123 GACACCCCCCACATTTCCAAGTGATTCTAG
1 GACA-CCCCCACATTTCCAAGTGATTCTAG
28674153 GACACCCCCACAT
1 GACACCCCCACAT
28674166 GTTTTGTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 13 0.34
30 25 0.66
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (29 bp):
GACACCCCCACATTTCCAAGTGATTCTAG
Found at i:28676429 original size:41 final size:41
Alignment explanation
Indices: 28676323--28676519 Score: 261
Period size: 41 Copynumber: 4.8 Consensus size: 41
28676313 AAAAGTAGAC
* * * *
28676323 CAATAGTGGCGCTTATGGGAAAGCACCGCTAAAGGTCAGAG
1 CAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATCATAG
*** *
28676364 CAATAGCGGCGCTT-TCACATAAGCGCTGCTAAAGATCATAG
1 CAATAGCGGCGCTTATGGGA-AAGCGCCGCTAAAGATCATAG
*
28676405 CAATAGCGGCGCTTATGGGAAAGCGCCGCTAAATATCATAG
1 CAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATCATAG
* * *
28676446 CAATAGCGACACTTATGGGAAAGCGTCGCTAAAGATCATAG
1 CAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATCATAG
*
28676487 CAATAGCGGCGCTTATGGAAAAGCGCCGCTAAA
1 CAATAGCGGCGCTTATGGGAAAGCGCCGCTAAA
28676520 TCCTGCTCAA
Statistics
Matches: 133, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.02
41 129 0.97
42 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (41 bp):
CAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATCATAG
Found at i:28680184 original size:43 final size:43
Alignment explanation
Indices: 28680063--28680245 Score: 246
Period size: 43 Copynumber: 4.3 Consensus size: 43
28680053 ATTTGTTAAT
* * * * * *
28680063 TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGACCAT-GTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGAACATGGTC
* *
28680105 TTTAGCGGCGTTTGTGAG-AAAGCG-CTGCTAAAGAACATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGTC-ACTAAAGAACATGGTC
28680147 TTTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGAACATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGAACATGGTC
* *
28680190 TTTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGAACATGGTC
28680233 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
28680246 TTTCAAATAA
Statistics
Matches: 128, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
40 1 0.01
41 17 0.13
42 34 0.27
43 75 0.59
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGAACATGGTC
Found at i:28680649 original size:23 final size:23
Alignment explanation
Indices: 28680623--28680699 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
28680613 ATTTAAAATA
* *
28680623 AAACATTATGGTAGGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
28680646 AAACATAATGGCAGGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
* * *
28680669 AAATATAATGACAAGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
28680692 AAA-ATAAT
1 AAACATAAT
28680700 AATTACTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 5 0.10
23 44 0.90
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (23 bp):
AAACATAATGGCAGGAGAGTTAC
Found at i:28682504 original size:21 final size:21
Alignment explanation
Indices: 28682477--28682527 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28682467 GGATTATGTA
28682477 ATTTGGATTTATAAACATTAT
1 ATTTGGATTTATAAACATTAT
* * *
28682498 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACATTAT
*
28682519 ATTTAGATT
1 ATTTGGATT
28682528 ATGCTACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (21 bp):
ATTTGGATTTATAAACATTAT
Found at i:28693180 original size:43 final size:43
Alignment explanation
Indices: 28693133--28693447 Score: 402
Period size: 43 Copynumber: 7.3 Consensus size: 43
28693123 GTTGTTATAA
* * *
28693133 AACATGATCTTTAGCGACGCTTTTCCCATAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG
* * * *
28693176 AACATGGTCTTTAGTGGCACTTTT-TCATAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG
* * * * *
28693218 ACCATGTTCGTTAGCGGCGCTTTCCCCACAAACGCTGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG
*
28693261 AACATGGTCTTTAGCGGCGTTTTTCCCACAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG
* *
28693304 AACATGGTCTTTAGCGGCGCTTTTACCACAAATGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG
* *
28693347 AACATGGTCTTTAGTGGCGC-TTCCCTCACAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCC-CACAAACGCCGCTAAAG
* * *
28693390 AACATGGTCTTTAGCAGCGC-TTCCCTCACAAACGTCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTCC-CACAAACGCCGCTAAAG
*
28693433 ATCATGGTCTTTAGC
1 AACATGGTCTTTAGC
28693448 AGTGCTTCCC
Statistics
Matches: 239, Mismatches: 31, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
42 38 0.16
43 201 0.84
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (43 bp):
AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG
Found at i:28699655 original size:34 final size:34
Alignment explanation
Indices: 28699616--28699734 Score: 123
Period size: 34 Copynumber: 3.4 Consensus size: 34
28699606 TAACTTATTA
28699616 AATAATTAAATAATTAAATATTTGAGTTATTTTT
1 AATAATTAAATAATTAAATATTTGAGTTATTTTT
* ** * * ***
28699650 AATAATTAAATAGTTTGAT-TTAGGGTTTAATAAAT
1 AATAATTAAATAATTAAATATTTGAG-TT-ATTTTT
*
28699685 AACTAATTAAATAATTAAATATTTGAGTTGTTTTT
1 AA-TAATTAAATAATTAAATATTTGAGTTATTTTT
28699720 AATAATTAAATAATT
1 AATAATTAAATAATT
28699735 TGGTTTAGGG
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
33 4 0.06
34 31 0.48
35 9 0.14
36 16 0.25
37 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (34 bp):
AATAATTAAATAATTAAATATTTGAGTTATTTTT
Found at i:28699670 original size:78 final size:75
Alignment explanation
Indices: 28699575--28699816 Score: 270
Period size: 70 Copynumber: 3.2 Consensus size: 75
28699565 AAATATTTTG
28699575 AATTAAATATTTGGATTTAGGGTTCAATAAATAACTTATTAAATAATTAAATAATTAAATATTTG
1 AATTAAATATTT-GATTTAGGGTT-AATAAATAAC-TATTAAATAATTAAATAATTAAATATTTG
28699640 AGTTATTTTTAAT
63 AGTTATTTTTAAT
*
28699653 AATTAAATAGTTTGATTTAGGGTT--T-AATAA--A-TAACTAATTAAATAATTAAATATTTGAG
1 AATTAAATA-TTTGATTTAGGGTTAATAAATAACTATTAAATAATTAAATAATTAAATATTTGAG
*
28699712 TTGTTTTTAAT
65 TTATTTTTAAT
* * * *
28699723 AATTAAATAATTTGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTCAAT-TCTT
1 AATTAAAT-ATTTGATTTAGGG-TTAATAAATAACT-ATTAAATAATTAAATAATTAAATAT-TT
28699787 --GTTATGTTTTAAT
62 GAGTTAT-TTTTAAT
*
28699800 AATTTAATATTT-ATTTA
1 AATTAAATATTTGATTTA
28699817 AATATAATTA
Statistics
Matches: 142, Mismatches: 10, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
70 56 0.39
71 4 0.03
73 1 0.01
74 10 0.07
75 5 0.04
76 8 0.06
77 16 0.11
78 39 0.27
79 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.47
Consensus pattern (75 bp):
AATTAAATATTTGATTTAGGGTTAATAAATAACTATTAAATAATTAAATAATTAAATATTTGAGT
TATTTTTAAT
Found at i:28699705 original size:70 final size:70
Alignment explanation
Indices: 28699618--28699778 Score: 286
Period size: 70 Copynumber: 2.3 Consensus size: 70
28699608 ACTTATTAAA
*
28699618 TAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATAGTTTGATTTAGGGTTTAATAA
1 TAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATAATTTGATTTAGGGTTTAATAA
28699683 ATAAC
66 ATAAC
* *
28699688 TAATTAAATAATTAAATATTTGAGTTGTTTTTAATAATTAAATAATTTGGTTTAGGGTTTAATAA
1 TAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATAATTTGATTTAGGGTTTAATAA
28699753 ATAAC
66 ATAAC
*
28699758 TAATTAAATAATTAATTATTT
1 TAATTAAATAATTAAATATTT
28699779 CAATTCTTGT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 87 1.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (70 bp):
TAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATAATTTGATTTAGGGTTTAATAA
ATAAC
Found at i:28703930 original size:15 final size:15
Alignment explanation
Indices: 28703910--28703944 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
28703900 TAGGTCAAAA
28703910 AGAACAAATATGATC
1 AGAACAAATATGATC
28703925 AGAACAAATATGATC
1 AGAACAAATATGATC
28703940 AGAAC
1 AGAAC
28703945 TATAACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.17
Consensus pattern (15 bp):
AGAACAAATATGATC
Found at i:28704650 original size:41 final size:41
Alignment explanation
Indices: 28704582--28704915 Score: 388
Period size: 41 Copynumber: 8.1 Consensus size: 41
28704572 AAATAAATTT
* * * *
28704582 GCGGCGCTTTCCCAAAAATGCCACTAATGCTCTGACTTTTA
1 GCGGCGCTTTCACAAAAACGCCGCTAATGCTCTGACCTTTA
* *
28704623 GCAGCGCTTTCACATAAACGCCGCTAATGCTCTGACCTTTA
1 GCGGCGCTTTCACAAAAACGCCGCTAATGCTCTGACCTTTA
* * * *
28704664 GCGACGC-TTCTTCAAAAACGCCGCTAGTGCTTTGACCTTTA
1 GCGGCGCTTTC-ACAAAAACGCCGCTAATGCTCTGACCTTTA
*
28704705 GCGGCGCTTTCACATAAACGCCGCTAATGCTCTGACCTTTA
1 GCGGCGCTTTCACAAAAACGCCGCTAATGCTCTGACCTTTA
* ** *
28704746 GCGGCG-TTTCTCCAAAAATTCCGCTAATGCTTTGACCTTTA
1 GCGGCGCTTTC-ACAAAAACGCCGCTAATGCTCTGACCTTTA
* * * *
28704787 GCGGTGCTTTCCCAAAAACGCCACTAATGCTCTAACCTTTA
1 GCGGCGCTTTCACAAAAACGCCGCTAATGCTCTGACCTTTA
* * *
28704828 GCGGTGCTTCTC-CTAAAACGCTGCTAATGCTCTGACCTTTA
1 GCGGCGCTT-TCACAAAAACGCCGCTAATGCTCTGACCTTTA
*
28704869 GCGGCGCTTCTC-CAAAAATGCCGCTAATGCTCTGACCTTTA
1 GCGGCGCTT-TCACAAAAACGCCGCTAATGCTCTGACCTTTA
*
28704910 GTGGCG
1 GCGGCG
28704916 TTTTTTCTAC
Statistics
Matches: 251, Mismatches: 37, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
40 7 0.03
41 235 0.94
42 9 0.04
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGCTTTCACAAAAACGCCGCTAATGCTCTGACCTTTA
Found at i:28704723 original size:82 final size:82
Alignment explanation
Indices: 28704582--28704915 Score: 429
Period size: 82 Copynumber: 4.1 Consensus size: 82
28704572 AAATAAATTT
* * * * *
28704582 GCGGCGCTT-TCCCAAAAATGCCACTAATGCTCTGACTTTTAGCAGCGCTTTCACATAAACGCCG
1 GCGGCGCTTCT-CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACGCCG
28704646 CTAATGCTCTGACCTTTA
65 CTAATGCTCTGACCTTTA
* * * * *
28704664 GCGACGCTTCTTCAAAAACGCCGCTAGTGCTTTGACCTTTAGCGGCGCTTTCACATAAACGCCGC
1 GCGGCGCTTCTCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACGCCGC
28704729 TAATGCTCTGACCTTTA
66 TAATGCTCTGACCTTTA
* ** * * * *
28704746 GCGGCGTTTCTCCAAAAATTCCGCTAATGCTTTGACCTTTAGCGGTGCTTTCCCAAAAACGCCAC
1 GCGGCGCTTCTCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACGCCGC
*
28704811 TAATGCTCTAACCTTTA
66 TAATGCTCTGACCTTTA
* * * *
28704828 GCGGTGCTTCTCCTAAAACGCTGCTAATGCTCTGACCTTTAGCGGCGCTTCTC-CAAAAATGCCG
1 GCGGCGCTTCTCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTT-TCACAAAAACGCCG
28704892 CTAATGCTCTGACCTTTA
65 CTAATGCTCTGACCTTTA
*
28704910 GTGGCG
1 GCGGCG
28704916 TTTTTTCTAC
Statistics
Matches: 218, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
82 215 0.99
83 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (82 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACGCCGC
TAATGCTCTGACCTTTA
Found at i:28704977 original size:39 final size:40
Alignment explanation
Indices: 28704933--28705030 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
28704923 TACAAACACT
*
28704933 GCTATTGCTTTACCTTTTGC-ACATTTATGAAAAAACGTC
1 GCTATTGCTTTACCTTTTGCGACATTTATGAAAAAACGCC
* * * *
28704972 GCTATTGCTTTACCTTTTACGGCGTTTATGGAAAAACGCC
1 GCTATTGCTTTACCTTTTGCGACATTTATGAAAAAACGCC
28705012 GCTATTGCTTTACCTTTTG
1 GCTATTGCTTTACCTTTTG
28705031 TGCCGTTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 19 0.37
40 33 0.63
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (40 bp):
GCTATTGCTTTACCTTTTGCGACATTTATGAAAAAACGCC
Found at i:28706644 original size:28 final size:28
Alignment explanation
Indices: 28706596--28706694 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
28706586 CAAATGATTT
*
28706596 TAAAATTATTAAAATTATTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAATA
* * *
28706624 T-AATTTTTTTAAATTATTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTTAAATA
28706651 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTA-TTTTTT-AAAT-A
28706682 TAAAATTATTAAA
1 TAAAATTATTAAA
28706695 TAATTTTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.38
28 13 0.22
29 6 0.10
30 4 0.07
31 14 0.23
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTAAATA
Found at i:28707062 original size:197 final size:195
Alignment explanation
Indices: 28706741--28707167 Score: 701
Period size: 197 Copynumber: 2.2 Consensus size: 195
28706731 TCATTTCAAT
*
28706741 TTTCAGATTTTCTTACATTTTCCCATCAACCAAACACCCAAAAAAACTTGTTTTTCTTGCATACG
1 TTTCAGATTTTCCTACATTTTCCCATCAACCAAACACCCAAAAAAACTTGTTTTTCTTGCATACG
*
28706806 ACTGAGATTCTTGCATAGATAGCAAATGGGTTATCATAGTTCAAATTTCAAACACAAACCCATCA
66 ACTGAGATTCTTGCATAGATAGCAAATGGGTTATCATAGTTCAAATTTAAAACACAAACCCATCA
** *
28706871 ATCTTTTTTTCCCTAAGACCCAATCACAGTTCAAAACCAAGTGCAAATTCTTCAGCAACAAGAAA
131 ATCTTTCCTTCCCTAAGACCCAATCACAATTCAAAACCAAGTGCAAATTCTTCAGCAACAAGAAA
*
28706936 TTTCTAGATTTTCCTACATTTTCCCATCAACCAAACACCCAAAAAAATTTGTTTTTTCTTGCATA
1 TTTC-AGATTTTCCTACATTTTCCCATCAACCAAACACCCAAAAAAACTTG-TTTTTCTTGCATA
* * * *
28707001 TGATTGAGATTCTTGCATAGATATCAAATGGGTTATCATAGTTCAAATTTAAAAGACAAACCCAT
64 CGACTGAGATTCTTGCATAGATAGCAAATGGGTTATCATAGTTCAAATTTAAAACACAAACCCAT
* * *
28707066 CAATCTTTCCTTCCCTAAGACCCAATTACAATTCAAAACCAAGTGTAAATTCTTCAGGAACAAGA
129 CAATCTTTCCTTCCCTAAGACCCAATCACAATTCAAAACCAAGTGCAAATTCTTCAGCAACAAGA
28707131 AA
194 AA
*
28707133 TTTCCAGATTTTCGTACATTTTCCCATCAACCAAA
1 TTT-CAGATTTTCCTACATTTTCCCATCAACCAAA
28707168 TAGGACTGGT
Statistics
Matches: 215, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
195 4 0.02
196 44 0.20
197 166 0.77
198 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (195 bp):
TTTCAGATTTTCCTACATTTTCCCATCAACCAAACACCCAAAAAAACTTGTTTTTCTTGCATACG
ACTGAGATTCTTGCATAGATAGCAAATGGGTTATCATAGTTCAAATTTAAAACACAAACCCATCA
ATCTTTCCTTCCCTAAGACCCAATCACAATTCAAAACCAAGTGCAAATTCTTCAGCAACAAGAAA
Found at i:28707745 original size:11 final size:11
Alignment explanation
Indices: 28707729--28707803 Score: 69
Period size: 11 Copynumber: 7.6 Consensus size: 11
28707719 GATGATGATT
28707729 ATAATTTTAAA
1 ATAATTTTAAA
28707740 ATAATTTT--A
1 ATAATTTTAAA
28707749 ATAATTTT---
1 ATAATTTTAAA
28707757 AT-ATTTTAAA
1 ATAATTTTAAA
28707767 A-AA-TTTAAA
1 ATAATTTTAAA
*
28707776 TTAATTTTAAA
1 ATAATTTTAAA
*
28707787 ATAAATTTAAA
1 ATAATTTTAAA
28707798 A-AATTT
1 ATAATTT
28707804 ATATTTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 15 0.28
10 8 0.15
11 24 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:28707754 original size:20 final size:20
Alignment explanation
Indices: 28707729--28707837 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
28707719 GATGATGATT
28707729 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
28707749 ATAATTTT---AT-ATTTTA
1 ATAATTTTAAAATAATTTTA
* * *
28707765 AAAAATTTAAATTAATTTTAAA
1 ATAATTTTAAAATAATTTT--A
*
28707787 ATAAATTTAAAA-AA-TTT-
1 ATAATTTTAAAATAATTTTA
* *
28707804 ATATTTTTAAAAATAAATTTA
1 ATAATTTT-AAAATAATTTTA
28707825 ATAATTTTAAAAT
1 ATAATTTTAAAAT
28707838 CATTCGTTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
16 12 0.17
17 8 0.11
18 4 0.06
19 3 0.04
20 24 0.34
21 9 0.13
22 11 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:28707798 original size:29 final size:28
Alignment explanation
Indices: 28707765--28707831 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
28707755 TTATATTTTA
*
28707765 AAAAATTTAAATTAATTTTAAAATAAATTT
1 AAAAATTTAAATT--TTTAAAAATAAATTT
*
28707795 AAAAAATTTATATTTTTAAAAATAAATTT
1 -AAAAATTTAAATTTTTAAAAATAAATTT
*
28707824 AATAATTT
1 AAAAATTT
28707832 TAAAATCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.21
29 14 0.42
31 12 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAAATTTAAATTTTTAAAAATAAATTT
Found at i:28707834 original size:21 final size:20
Alignment explanation
Indices: 28707798--28707836 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28707788 TAAATTTAAA
*
28707798 AAATTTATATTTTTAAAAAT
1 AAATTTATAATTTTAAAAAT
28707818 AAATTTAATAATTTTAAAA
1 AAATTT-ATAATTTTAAAA
28707837 TCATTCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTTATAATTTTAAAAAT
Found at i:28708884 original size:42 final size:43
Alignment explanation
Indices: 28708823--28708946 Score: 184
Period size: 42 Copynumber: 3.0 Consensus size: 43
28708813 CGAAACGAGC
* *
28708823 ATGAGGATAT-ATTTAAGGAAGACTCATGTCTCAAG-ATGAGA
1 ATGAGAATATGATTAAAGGAAGACTCATGTCTCAAGAATGAGA
*
28708864 ATGAGAATATGATTAAAGGAAGACTCATGTCT-TAGAATGAGA
1 ATGAGAATATGATTAAAGGAAGACTCATGTCTCAAGAATGAGA
*
28708906 ATGAGAATATGATTAAAGGAAGACTCATGACTC-AGAATGAG
1 ATGAGAATATGATTAAAGGAAGACTCATGTCTCAAGAATGAG
28708947 CTTGGGATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
41 11 0.14
42 65 0.86
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (43 bp):
ATGAGAATATGATTAAAGGAAGACTCATGTCTCAAGAATGAGA
Found at i:28708964 original size:42 final size:42
Alignment explanation
Indices: 28708823--28708982 Score: 180
Period size: 42 Copynumber: 3.8 Consensus size: 42
28708813 CGAAACGAGC
* * *
28708823 ATGAGGATAT-ATTTAAGGAAGACTCATGTCTCA-AGATGAGA
1 ATGAGAATATGATTAAAGGAAGACTCATGACTCAGA-ATGAGA
* *
28708864 ATGAGAATATGATTAAAGGAAGACTCATGTCTTAGAATGAGA
1 ATGAGAATATGATTAAAGGAAGACTCATGACTCAGAATGAGA
*
28708906 ATGAGAATATGATTAAAGGAAGACTCATGACTCAGAATGAGC
1 ATGAGAATATGATTAAAGGAAGACTCATGACTCAGAATGAGA
* * * * *
28708948 TTGGGATTATGTTTAAAAAGGAAGACTTATGACTC
1 ATGAGAATATGATT--AAAGGAAGACTCATGACTC
28708983 GGTAGAGCAT
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 9 0.09
42 76 0.73
43 1 0.01
44 18 0.17
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (42 bp):
ATGAGAATATGATTAAAGGAAGACTCATGACTCAGAATGAGA
Found at i:28717265 original size:117 final size:117
Alignment explanation
Indices: 28717059--28717294 Score: 454
Period size: 117 Copynumber: 2.0 Consensus size: 117
28717049 ACAAGGTTGG
*
28717059 AAAGAAACTATGCTTACTGAAATGAGCATGATTCATAAGAATCCGACCTGGGAACTAGTTGAAAG
1 AAAGAAACTATGCTTACTAAAATGAGCATGATTCATAAGAATCCGACCTGGGAACTAGTTGAAAG
28717124 ACCAGTCCATAAGAAAGTTATTGGGGTGAAATGGGTATTTAGAGCCAAGCAC
66 ACCAGTCCATAAGAAAGTTATTGGGGTGAAATGGGTATTTAGAGCCAAGCAC
*
28717176 AAAGAAACTATGCTTACTAAAATGAGCATGATTCATAAGAATCCGACTTGGGAACTAGTTGAAAG
1 AAAGAAACTATGCTTACTAAAATGAGCATGATTCATAAGAATCCGACCTGGGAACTAGTTGAAAG
28717241 ACCAGTCCATAAGAAAGTTATTGGGGTGAAATGGGTATTTAGAGCCAAGCAC
66 ACCAGTCCATAAGAAAGTTATTGGGGTGAAATGGGTATTTAGAGCCAAGCAC
28717293 AA
1 AA
28717295 TGCTGATGGA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (117 bp):
AAAGAAACTATGCTTACTAAAATGAGCATGATTCATAAGAATCCGACCTGGGAACTAGTTGAAAG
ACCAGTCCATAAGAAAGTTATTGGGGTGAAATGGGTATTTAGAGCCAAGCAC
Found at i:28720544 original size:13 final size:13
Alignment explanation
Indices: 28720526--28720551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28720516 ACAGGTGCGT
28720526 CGATAAATTTATC
1 CGATAAATTTATC
28720539 CGATAAATTTATC
1 CGATAAATTTATC
28720552 GGGACAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
CGATAAATTTATC
Found at i:28726768 original size:18 final size:18
Alignment explanation
Indices: 28726745--28726798 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
28726735 TGCATTTGAG
*
28726745 TATATGGCTGTATCTGAT
1 TATATGACTGTATCTGAT
* *
28726763 TATATGACTGTATTTGAG
1 TATATGACTGTATCTGAT
* *
28726781 TATGTGACTGCATCTGAT
1 TATATGACTGTATCTGAT
28726799 CAGGCTGCGC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (18 bp):
TATATGACTGTATCTGAT
Found at i:28731084 original size:31 final size:28
Alignment explanation
Indices: 28731023--28731088 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
28731013 CAAAATTATG
*
28731023 TTTTTTTTTTTATTTTTAAGGTGCCCAA
1 TTTTTTTTTTTATTTTTAAGGTGCCAAA
28731051 TTTTATTTTTTTAGTTTTTAAGG-GTCCAAA
1 TTTT-TTTTTTTA-TTTTTAAGGTG-CCAAA
*
28731081 ATTTTTTT
1 TTTTTTTT
28731089 ACCGACTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 4 0.12
29 13 0.39
30 16 0.48
ACGTcount: A:0.20, C:0.08, G:0.11, T:0.62
Consensus pattern (28 bp):
TTTTTTTTTTTATTTTTAAGGTGCCAAA
Found at i:28735530 original size:2 final size:2
Alignment explanation
Indices: 28735525--28735554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28735515 GAAAAAATAA
28735525 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
28735555 CATAAAATGA
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:28737436 original size:20 final size:21
Alignment explanation
Indices: 28737399--28737438 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28737389 GAACGTTGGC
**
28737399 AACAATGCAGCATTAGCATGA
1 AACAATGCAGCAGCAGCATGA
28737420 AACAA-GCAGCAGCAGCATG
1 AACAATGCAGCAGCAGCATG
28737439 GAGCAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (21 bp):
AACAATGCAGCAGCAGCATGA
Found at i:28742520 original size:17 final size:17
Alignment explanation
Indices: 28742485--28742523 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28742475 AGGTGGAGAA
** *
28742485 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAAAGAATT
28742502 CTTGTTCGTAAAGAATT
1 CTTGTTCGTAAAGAATT
28742519 CTTGT
1 CTTGT
28742524 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAAAGAATT
Found at i:28745760 original size:14 final size:14
Alignment explanation
Indices: 28745741--28745770 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28745731 AAGCTGATGT
28745741 TACAGCTTGGATAC
1 TACAGCTTGGATAC
28745755 TACAGCTTGGATAC
1 TACAGCTTGGATAC
28745769 TA
1 TA
28745771 GCACAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (14 bp):
TACAGCTTGGATAC
Found at i:28749391 original size:30 final size:30
Alignment explanation
Indices: 28749357--28749425 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
28749347 TTTATATTCG
28749357 TTTATTTAAAATTATGTGTATTCATGTTCA
1 TTTATTTAAAATTATGTGTATTCATGTTCA
* *
28749387 TTTATTTAAAATTATGTGTGTTCATGTTCG
1 TTTATTTAAAATTATGTGTATTCATGTTCA
*
28749417 TTTGTTTAA
1 TTTATTTAA
28749426 TGTTCACGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (30 bp):
TTTATTTAAAATTATGTGTATTCATGTTCA
Found at i:28749483 original size:24 final size:26
Alignment explanation
Indices: 28749450--28749509 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
28749440 TTCATTTAAC
*
28749450 TTAATCGAATATGTTAACGAAC-ATA
1 TTAATTGAATATGTTAACGAACAATA
*
28749475 -TAATTGAATATGTTCACGAACAATA
1 TTAATTGAATATGTTAACGAACAATA
28749500 TTAA-TGAATA
1 TTAATTGAATA
28749510 ATAAACAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 19 0.61
25 9 0.29
26 3 0.10
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (26 bp):
TTAATTGAATATGTTAACGAACAATA
Found at i:28749623 original size:12 final size:12
Alignment explanation
Indices: 28749608--28749669 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
28749598 AAACAAGTCA
28749608 ATAAACGAGCTT
1 ATAAACGAGCTT
* **
28749620 ATAAATGAGCCA
1 ATAAACGAGCTT
28749632 ATAAACGAGCTT
1 ATAAACGAGCTT
* **
28749644 ATAAATGAGCCA
1 ATAAACGAGCTT
28749656 ATAAACGAGCTT
1 ATAAACGAGCTT
28749668 AT
1 AT
28749670 TCGTGAACAT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:28749633 original size:24 final size:24
Alignment explanation
Indices: 28749606--28749669 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
28749596 ATAAACAAGT
28749606 CAATAAACGAGCTTATAAATGAGC
1 CAATAAACGAGCTTATAAATGAGC
28749630 CAATAAACGAGCTTATAAATGAGC
1 CAATAAACGAGCTTATAAATGAGC
28749654 CAATAAACGAGCTTAT
1 CAATAAACGAGCTTAT
28749670 TCGTGAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (24 bp):
CAATAAACGAGCTTATAAATGAGC
Found at i:28758104 original size:2 final size:2
Alignment explanation
Indices: 28758091--28758122 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28758081 GTTTATTGTC
*
28758091 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28758123 CTTTTTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28758778 original size:17 final size:17
Alignment explanation
Indices: 28758733--28758780 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
28758723 ACTACAATGC
* *
28758733 AAATGTGATAACAAGTA
1 AAATGTAATGACAAGTA
* * *
28758750 AAATGCATTGACAATTA
1 AAATGTAATGACAAGTA
28758767 AAATGTAATGACAA
1 AAATGTAATGACAA
28758781 CTAGATAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (17 bp):
AAATGTAATGACAAGTA
Found at i:28759202 original size:15 final size:14
Alignment explanation
Indices: 28759182--28759239 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
28759172 TCAAAACAAC
28759182 TTCTTCTCGTTCTTT
1 TTCTTCTC-TTCTTT
*
28759197 TTCTTCTCTTCTCT
1 TTCTTCTCTTCTTT
28759211 TTCTTCATCTTCTCTT
1 TTCTTC-TCTTCT-TT
28759227 TTC-TCTTCTTCTT
1 TTCTTC-TCTTCTT
28759240 CAACACCCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
14 12 0.32
15 22 0.58
16 4 0.11
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.66
Consensus pattern (14 bp):
TTCTTCTCTTCTTT
Found at i:28759208 original size:20 final size:20
Alignment explanation
Indices: 28759183--28759226 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28759173 CAAAACAACT
**
28759183 TCTTCTCGTTCTTTTTCTTC
1 TCTTCTCGTTCTTCATCTTC
*
28759203 TCTTCTCTTTCTTCATCTTC
1 TCTTCTCGTTCTTCATCTTC
28759223 TCTT
1 TCTT
28759227 TTCTCTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (20 bp):
TCTTCTCGTTCTTCATCTTC
Found at i:28761030 original size:24 final size:25
Alignment explanation
Indices: 28760995--28761042 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
28760985 TACAGAAACT
*
28760995 AAAGAAACAAATTAA-AGTAAAATA
1 AAAGAAACAAATTAACAGAAAAATA
28761019 AAAGACAA-AAATTAACAGAAAAAT
1 AAAGA-AACAAATTAACAGAAAAAT
28761043 TTGCAATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (25 bp):
AAAGAAACAAATTAACAGAAAAATA
Found at i:28768827 original size:12 final size:12
Alignment explanation
Indices: 28768810--28768840 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28768800 AAATACACTT
28768810 ATAAACATTAAA
1 ATAAACATTAAA
28768822 ATAAACATTAAA
1 ATAAACATTAAA
*
28768834 AAAAACA
1 ATAAACA
28768841 AATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAACATTAAA
Found at i:28768985 original size:20 final size:22
Alignment explanation
Indices: 28768962--28769059 Score: 83
Period size: 23 Copynumber: 4.3 Consensus size: 22
28768952 AAAACGCATA
*
28768962 AAAAATAACATCCAAA-A-AAC
1 AAAAATAACATCAAAACACAAC
*
28768982 AAAAACAACAATCAAAACAGCAAC
1 AAAAATAAC-ATCAAAACA-CAAC
*
28769006 AAAAATAACAACAAAACAACAAC
1 AAAAATAACATCAAAAC-ACAAC
* *
28769029 AAAAATAATAACAAAAGCAGCAAC
1 AAAAATAACATCAAAA-CA-CAAC
*
28769053 CAAAATA
1 AAAAATA
28769060 GCAAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
20 8 0.12
21 6 0.09
22 1 0.02
23 27 0.42
24 23 0.35
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.07
Consensus pattern (22 bp):
AAAAATAACATCAAAACACAAC
Found at i:28769027 original size:44 final size:45
Alignment explanation
Indices: 28768962--28769068 Score: 114
Period size: 44 Copynumber: 2.4 Consensus size: 45
28768952 AAAACGCATA
*
28768962 AAAAATAACATCCAAAAAACAA-AAACAACAAT-CAAAA-CAGCAAC
1 AAAAATAACA-ACAAAAAACAACAAA-AACAATACAAAAGCAGCAAC
*
28769006 AAAAATAACAACAAAACAACAACAAAAATAATAACAAAAGCAGCAAC
1 AAAAATAACAACAAAA-AACAACAAAAACAAT-ACAAAAGCAGCAAC
* *
28769053 CAAAATAGCAA-AAAAA
1 AAAAATAACAACAAAAA
28769069 TACACCAGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 5 0.09
44 20 0.37
45 4 0.07
46 9 0.17
47 16 0.30
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (45 bp):
AAAAATAACAACAAAAAACAACAAAAACAATACAAAAGCAGCAAC
Found at i:28769033 original size:12 final size:12
Alignment explanation
Indices: 28768979--28769044 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
28768969 ACATCCAAAA
28768979 AACAAAAACAAC
1 AACAAAAACAAC
*
28768991 AATC-AAAACAGC
1 AA-CAAAAACAAC
*
28769003 AACAAAAATAAC
1 AACAAAAACAAC
28769015 AAC-AAAACAAC
1 AACAAAAACAAC
* *
28769026 AACAAAAATAAT
1 AACAAAAACAAC
28769038 AACAAAA
1 AACAAAA
28769045 GCAGCAACCA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 11 0.24
12 33 0.73
13 1 0.02
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.06
Consensus pattern (12 bp):
AACAAAAACAAC
Found at i:28769063 original size:12 final size:12
Alignment explanation
Indices: 28768983--28769057 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
28768973 CCAAAAAACA
*
28768983 AAAACAACAATC
1 AAAACAACAACC
* *
28768995 AAAACAGCAACA
1 AAAACAACAACC
*
28769007 AAAATAACAA-C
1 AAAACAACAACC
*
28769018 AAAACAACAACA
1 AAAACAACAACC
* *
28769030 AAAATAATAA-C
1 AAAACAACAACC
*
28769041 AAAAGCAGCAACC
1 AAAA-CAACAACC
28769054 AAAA
1 AAAA
28769058 TAGCAAAAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 5
0.71 0.22 0.08
Matches are distributed among these distances:
11 13 0.28
12 28 0.61
13 5 0.11
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.05
Consensus pattern (12 bp):
AAAACAACAACC
Found at i:28770412 original size:16 final size:16
Alignment explanation
Indices: 28770393--28770443 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
28770383 TTTTCATTTT
28770393 TTTAATTTTTATAAAA
1 TTTAATTTTTATAAAA
*
28770409 TTTATATTTTT-TAAATT
1 TTTA-ATTTTTATAAA-A
28770426 TTGTAATTTTTA-AAAA
1 TT-TAATTTTTATAAAA
28770442 TT
1 TT
28770444 ACATATAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 10 0.34
17 17 0.59
18 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTAATTTTTATAAAA
Found at i:28770437 original size:25 final size:24
Alignment explanation
Indices: 28770376--28770437 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
28770366 CGGGATTTTT
* *
28770376 TTTTAT-ATTTTCATTTTTTTAAT
1 TTTTATAATTTTTATTTTTTTAAA
**
28770399 TTTTATAAAATTTATATTTTTTAAA
1 TTTTATAATTTTTAT-TTTTTTAAA
*
28770424 TTTTGTAATTTTTA
1 TTTTATAATTTTTA
28770438 AAAATTACAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 6 0.20
24 5 0.17
25 19 0.63
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTATAATTTTTATTTTTTTAAA
Found at i:28770777 original size:20 final size:20
Alignment explanation
Indices: 28770731--28770782 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
28770721 ATTTTGCACA
*
28770731 TAATTATAATTTTAAAGTAT
1 TAATTATAATTTTAAAGAAT
**
28770751 TTTTTATAATTTTAAA-AAT
1 TAATTATAATTTTAAAGAAT
28770770 TAAATTATGAATT
1 T-AATTAT-AATT
28770783 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.12
20 18 0.72
21 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTATAATTTTAAAGAAT
Found at i:28777979 original size:30 final size:30
Alignment explanation
Indices: 28777800--28778154 Score: 264
Period size: 29 Copynumber: 12.0 Consensus size: 30
28777790 TCCAGTAGAT
* **
28777800 CCCTAAACTTTT-CAGAAATCATGTTTTAAC
1 CCCTAAACTTTTCCA-AAATTACATTTTAAC
* * * *
28777830 CTC-AAACTTTTCTAAAATTATATTTTGA-
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
28777858 CCTTAAACTTTTTCAAAATTACATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
28777888 CTC-AAACTTTTTCAAAATTACATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
** ** * *
28777917 CTCC-AAGTTTTTCCAAAAACAAATTTTTAC
1 C-CCTAAACTTTTCCAAAATTACATTTTAAC
*
28777947 CCCTAAACTTTTCCAAAATCACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
28777977 CCCTAAAC-TCTCATAAAATCACATTTTAA-
1 CCCTAAACTTTTC-CAAAATTACATTTTAAC
*
28778006 CCCTAAAAC--TTCCTAAAATCACATTTTAAC
1 CCCT-AAACTTTTCC-AAAATTACATTTTAAC
* * * *
28778036 CCTTAAACCTTTCTAAAATTATATTTTAA-
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * * *
28778065 CCCTAACCTTCTCTAAGATTACATTTTAA-
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
28778094 CCCTAAACTTTCCCAAAAATACATTTTTAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
*
28778124 CCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
28778154 C
1 C
28778155 TCGAATTCTC
Statistics
Matches: 263, Mismatches: 50, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.00
29 143 0.54
30 116 0.44
31 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:28778025 original size:59 final size:57
Alignment explanation
Indices: 28777941--28778154 Score: 202
Period size: 59 Copynumber: 3.6 Consensus size: 57
28777931 AAAAACAAAT
*
28777941 TTTTACCCCTAAACTTTTCC-AAAATCACATTTTAACCCCTAAACTCTCATAAAATCACA
1 TTTTAACCCTAAAC--TTCCTAAAATCACATTTTAACCCCTAAACTCTCATAAAAT-ACA
* * *
28778000 TTTTAACCCTAAAACTTCCTAAAATCACATTTTAACCCTTAAACCTTTC-TAAAATTATA
1 TTTTAACCCT-AAACTTCCTAAAATCACATTTTAACCCCTAAA-CTCTCATAAAA-TACA
* * * *
28778059 TTTTAACCCTAACCTTCTCTAAGATTACATTTTAA-CCCTAAACTTTCCCA-AAAATACA
1 TTTTAACCCTAAACTTC-CTAAAATCACATTTTAACCCCTAAAC--TCTCATAAAATACA
* * *
28778117 TTTTTACCCCTAAACTTTTCTAAAATTACATTTTAACC
1 -TTTTAACCCTAAAC-TTCCTAAAATCACATTTTAACC
28778155 TCGAATTCTC
Statistics
Matches: 129, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
57 1 0.01
58 19 0.15
59 97 0.75
60 12 0.09
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (57 bp):
TTTTAACCCTAAACTTCCTAAAATCACATTTTAACCCCTAAACTCTCATAAAATACA
Found at i:28782541 original size:15 final size:15
Alignment explanation
Indices: 28782521--28782560 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
28782511 GACGTGTTAT
28782521 CAAAAAGAAAAAAAA
1 CAAAAAGAAAAAAAA
28782536 CAAAAA-AAAAAAAA
1 CAAAAAGAAAAAAAA
* *
28782550 GAAGAAGAAAA
1 CAAAAAGAAAA
28782561 GATGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (15 bp):
CAAAAAGAAAAAAAA
Found at i:28783508 original size:22 final size:22
Alignment explanation
Indices: 28783465--28783530 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
28783455 CCCGGATTCG
*
28783465 ATAAAGAAAAATAAATA-AAAA
1 ATAAAGAAAAATAAAGAGAAAA
*
28783486 AGAAAAGAAAAATAAAGAGAAAA
1 A-TAAAGAAAAATAAAGAGAAAA
28783509 ATAAA-AATAAA-AAAGAGAAAA
1 ATAAAGAA-AAATAAAGAGAAAA
28783530 A
1 A
28783531 AGGAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 14 0.36
22 20 0.51
23 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (22 bp):
ATAAAGAAAAATAAAGAGAAAA
Found at i:28783529 original size:7 final size:6
Alignment explanation
Indices: 28783467--28783572 Score: 60
Period size: 6 Copynumber: 18.2 Consensus size: 6
28783457 CGGATTCGAT
* * * * *
28783467 AAAGAA AAATAA ATA-AA AAAG-A AAAGAA AAATAA AGAGAA AAATAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * * **
28783513 AAATAA AAA-AGA GAA-AA AAGGAA AAAGAA AATAGAA AAA-AA AGGGAA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA
*
28783560 AAAGAA AAGGAA A
1 AAAGAA AAAGAA A
28783573 GGTCGAGGTG
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
5 15 0.19
6 56 0.73
7 6 0.08
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:28783531 original size:23 final size:22
Alignment explanation
Indices: 28783467--28783567 Score: 73
Period size: 23 Copynumber: 4.4 Consensus size: 22
28783457 CGGATTCGAT
28783467 AAAGAAAAATA-AATAAAAAAG-A
1 AAAGAAAAA-AGAA-AAAAAAGAA
*
28783489 AAAGAAAAATA-AAGAGAAAAATAA
1 AAAGAAAAA-AGAA-A-AAAAAGAA
* *
28783513 AAATAAAAAAGAGAAAAAAGGAA
1 AAAGAAAAAAGA-AAAAAAAGAA
*
28783536 AAAGAAAATAGAAAAAAAAGGGAA
1 AAAGAAAAAAGAAAAAAAA--GAA
28783560 AAAGAAAA
1 AAAGAAAA
28783568 GGAAAGGTCG
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
22 20 0.31
23 22 0.34
24 22 0.34
25 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (22 bp):
AAAGAAAAAAGAAAAAAAAGAA
Found at i:28783551 original size:36 final size:36
Alignment explanation
Indices: 28783477--28783551 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
28783467 AAAGAAAAAT
* * *
28783477 AAATAAAAAAGAAAAGAAAAATAAAGAGAAAAATAA
1 AAATAAAAAAGAAAAGAAAAAGAAAAAGAAAAAGAA
* *
28783513 AAATAAAAAAGAGAA-AAAAGGAAAAAGAAAATAGAA
1 AAATAAAAAAGAAAAGAAAAAGAAAAAGAAAA-AGAA
28783549 AAA
1 AAA
28783552 AAAGGGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (36 bp):
AAATAAAAAAGAAAAGAAAAAGAAAAAGAAAAAGAA
Found at i:28783572 original size:23 final size:23
Alignment explanation
Indices: 28783511--28783567 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
28783501 AGAGAAAAAT
* * *
28783511 AAAAATAAAAAAGAGAAAAAAGG
1 AAAAAGAAAATAGAAAAAAAAGG
28783534 AAAAAGAAAATAGAAAAAAAAGGG
1 AAAAAGAAAATAGAAAAAAAA-GG
28783558 AAAAAGAAAA
1 AAAAAGAAAA
28783568 GGAAAGGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAAAGAAAATAGAAAAAAAAGG
Found at i:28783822 original size:32 final size:32
Alignment explanation
Indices: 28783784--28783847 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
28783774 TCATCAAGTT
28783784 TGCTTAGTGAAGCTCATACTTTGATATATGGG
1 TGCTTAGTGAAGCTCATACTTTGATATATGGG
*
28783816 TGCTTAGTGAAGCTCATACTTTGATATCTGGG
1 TGCTTAGTGAAGCTCATACTTTGATATATGGG
28783848 GGCACTTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (32 bp):
TGCTTAGTGAAGCTCATACTTTGATATATGGG
Found at i:28784595 original size:49 final size:49
Alignment explanation
Indices: 28784534--28784704 Score: 182
Period size: 49 Copynumber: 3.5 Consensus size: 49
28784524 AGAAAATATG
* * *
28784534 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATG
1 AAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATA
* * * *
28784583 AAGATTTAAAGGGAAAGGTTGAGGCCACAACGGCAAACCTGGTACCTTAA
1 AAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCAT-A
* * * *** * *
28784633 AAGATGTGATGGG-AAGGATTGAGGCCGTAACAATAAACCCGATACTATA
1 AAGATTTGAAGGGAAAGG-TTGAGGCCGCAACGGCAAACCCGGTACCATA
28784682 AAGATTTGAAGGGAAAGGTTGAG
1 AAGATTTGAAGGGAAAGGTTGAG
28784705 TCTGCAATGG
Statistics
Matches: 98, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
49 63 0.64
50 35 0.36
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.18
Consensus pattern (49 bp):
AAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATA
Found at i:28785149 original size:39 final size:39
Alignment explanation
Indices: 28785102--28785552 Score: 270
Period size: 39 Copynumber: 11.6 Consensus size: 39
28785092 CAGCCATTGC
* * *
28785102 TTACCCCGAGCCTGGGGCAGATTGCAGCCATCCGATCTT
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
** * *
28785141 TTACCCCGAGCTTGGGGCAGATCACAATCAGCCAATCTT
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
* * * *
28785180 TTACCCCGAGCTTGGGGCAGATTACAATCGTCCGATCTT
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
* * ** * * * *
28785219 TTACCCCGAGCTTAGGACAGATCACCATCAACCAATCTC
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
* * *
28785258 TTACCCCAAGCTTGGGGCACATTGCAACCATCCGATCTT
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
* * ** * * * *
28785297 TTATCCTGAGCTTGGGGCAGATCACCATCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
* ** *
28785336 TTACCCCGAGCTTGAGGCAGATTGCATTCATCCGATCTT
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
* * * * *
28785375 TTACCCCGATCATGAGGCAGA-T-C-ACCGTCAGTCAATCTC
1 TTACCCCGAGCTTGGGGCAGATTGCAACCATC---CAATCTT
* ** * *
28785414 TTACCCCGCGGC-AAGGGCAGATTGTAGCCATCCAATCTT
1 TTACCCCG-AGCTTGGGGCAGATTGCAACCATCCAATCTT
* * * * *
28785453 TTACCTCGATCATGGGGCAG-TT-C-ACTGTCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATTGCAAC---CATCCAATCTT
** ** *
28785492 TTACCCC-ATAATAAGGGCAGATTGCAACCATCCTATCTT
1 TTACCCCGA-GCTTGGGGCAGATTGCAACCATCCAATCTT
* *
28785531 TTACCCCGATCATGGGGCAGAT
1 TTACCCCGAGCTTGGGGCAGAT
28785553 CACCGTCAGT
Statistics
Matches: 306, Mismatches: 90, Indels: 32
0.71 0.21 0.07
Matches are distributed among these distances:
36 4 0.01
37 1 0.00
38 5 0.02
39 284 0.93
40 5 0.02
41 1 0.00
42 6 0.02
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATTGCAACCATCCAATCTT
Found at i:28785217 original size:78 final size:78
Alignment explanation
Indices: 28785058--28785751 Score: 643
Period size: 78 Copynumber: 8.9 Consensus size: 78
28785048 TGAAGATTCT
* * *
28785058 GATCTCTTACCCCGAGTC-TGGGGTAGATCACCATCAGCC-AT-TGCTTACCCCGAGCCTGGGGC
1 GATCTTTTACCCCGAG-CATGGGGCAGATCACCATCAGCCAATCT-CTTACCCCGAGCTTGGGGC
*
28785120 AGATTGCAGCCATCC
64 AGATTGCAACCATCC
* * *
28785135 GATCTTTTACCCCGAGCTTGGGGCAGATCACAATCAGCCAATCTTTTACCCCGAGCTTGGGGCAG
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
* * *
28785200 ATTACAATCGTCC
66 ATTGCAACCATCC
* * * * * *
28785213 GATCTTTTACCCCGAGCTTAGGACAGATCACCATCAACCAATCTCTTACCCCAAGCTTGGGGCAC
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
28785278 ATTGCAACCATCC
66 ATTGCAACCATCC
* * * *
28785291 GATCTTTTATCCTGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGCAG
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
**
28785356 ATTGCATTCATCC
66 ATTGCAACCATCC
* * * * * **
28785369 GATCTTTTACCCCGATCATGAGGCAGATCACCGTCAGTCAATCTCTTACCCCGCGGC-AAGGGCA
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCG-AGCTTGGGGCA
* *
28785433 GATTGTAGCCATCC
65 GATTGCAACCATCC
* * * * ** ** **
28785447 AATCTTTTACCTCGATCATGGGGCAGTTCACTGTCAGCCAATCTCTTACCCC-ATAATAAGGGCA
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGA-GCTTGGGGCA
28785511 GATTGCAACCATCC
65 GATTGCAACCATCC
* * * * * **
28785525 TATCTTTTACCCCGATCATGGGGCAGATCACCGTCAGTCAATCTCTTACCTCGCGA-C-AGGGTT
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACC-C-CGAGCTTGGGGC
*
28785588 AGATTGCAATCATCC
64 AGATTGCAACCATCC
* * * *
28785603 GATCTTTTACCCTGATCATGGGGCAGATCACCGTCAGCCAATCTCTTACCCC-A-CAATAGGGGC
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC--TTGGGGC
* *
28785666 AGATTGCAGCCACCC
64 AGATTGCAACCATCC
* * * * * * * * * * *
28785681 GATCTCTTACCCCGACCATGAGGTAGATCA-CAGCCATCTAATCTCTTACCCCAATCATAGGGCA
1 GATCTTTTACCCCGAGCATGGGGCAGATCACCA-TCAGCCAATCTCTTACCCCGAGCTTGGGGCA
28785745 GATTGCA
65 GATTGCA
28785752 GTTATCCAAA
Statistics
Matches: 518, Mismatches: 84, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
75 2 0.00
76 2 0.00
77 36 0.07
78 470 0.91
79 5 0.01
80 2 0.00
81 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (78 bp):
GATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
ATTGCAACCATCC
Found at i:28785574 original size:39 final size:39
Alignment explanation
Indices: 28785059--28785747 Score: 239
Period size: 39 Copynumber: 17.7 Consensus size: 39
28785049 GAAGATTCTG
* *
28785059 ATCTCTTACCCCGAGTC-TGGGGTAGATCACCA-TCAG-CC
1 ATCTCTTACCCCGAG-CATGGGGCAGATCA-CAGTCAGTCA
* ** * *
28785097 AT-TGCTTACCCCGAGCCTGGGGCAGATTGCAGCCA-TCCG
1 ATCT-CTTACCCCGAGCATGGGGCAGATCACAGTCAGT-CA
* * * *
28785136 ATCTTTTACCCCGAGCTTGGGGCAGATCACAATCAGCCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTCA
* * * * *
28785175 ATCTTTTACCCCGAGCTTGGGGCAGATTACAATC-GTCCG
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGT-CA
* * * * **
28785214 ATCTTTTACCCCGAGCTTAGGACAGATCACCA-TCAACCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCAGTCA
* * * ** ** *
28785253 ATCTCTTACCCCAAGCTTGGGGCACATTGCAACCA-TCCG
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGT-CA
* * * * *
28785292 ATCTTTTATCCTGAGCTTGGGGCAGATCACCA-TCAGCCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCAGTCA
* * ** * *
28785331 ATCTCTTACCCCGAGCTTGAGGCAGATTGCATTCA-TCCG
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGT-CA
* * * *
28785370 ATCTTTTACCCCGATCATGAGGCAGATCACCGTCAGTCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTCA
* * *** *
28785409 ATCTCTTACCCCGCGGCA-AGGGCAGATTGTAGCCA-TCCA
1 ATCTCTTACCCCG-AGCATGGGGCAGATCACAGTCAGT-CA
* * * * * *
28785448 ATCTTTTACCTCGATCATGGGGCAGTTCACTGTCAGCCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTCA
** * ** ** *
28785487 ATCTCTTACCCC-ATAATAAGGGCAGATTGCAACCA-TCCT
1 ATCTCTTACCCCGAGCAT-GGGGCAGATCACAGTCAGT-CA
* * *
28785526 ATCTTTTACCCCGATCATGGGGCAGATCACCGTCAGTCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTCA
** ** * *
28785565 ATCTCTTACCTCGCGA-CA-GGGTTAGATTGCAATCA-TCCG
1 ATCTCTTACC-C-CGAGCATGGGGCAGATCACAGTCAGT-CA
* * * * *
28785604 ATCTTTTACCCTGATCATGGGGCAGATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTCA
** * ** *
28785643 ATCTCTTACCCC-A-CAATAGGGGCAGATTGCAGCCACCCG
1 ATCTCTTACCCCGAGC-AT-GGGGCAGATCACAGTCAGTCA
* * * *
28785682 ATCTCTTACCCCGACCATGAGGTAGATCACAGCCA-TCTA
1 ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTC-A
* * *
28785721 ATCTCTTACCCCAATCATAGGGCAGAT
1 ATCTCTTACCCCGAGCATGGGGCAGAT
28785748 TGCAGTTATC
Statistics
Matches: 477, Mismatches: 138, Indels: 71
0.70 0.20 0.10
Matches are distributed among these distances:
37 7 0.01
38 44 0.09
39 403 0.84
40 19 0.04
41 4 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCATGGGGCAGATCACAGTCAGTCA
Found at i:28787612 original size:30 final size:29
Alignment explanation
Indices: 28787572--28788165 Score: 464
Period size: 30 Copynumber: 20.1 Consensus size: 29
28787562 GTAAGTCCCT
* * *
28787572 AAACTTTTCAAAAATCATATTTTGACCTC
1 AAACTTTTCCAAAATCACATTTTGACCCC
* * * **
28787601 AAACTTTTTCAAAATTACATTTTAACCTT
1 AAACTTTTCCAAAATCACATTTTGACCCC
28787630 AAACTTTTCCAAAATCACA-TTTGACCCCC
1 AAACTTTTCCAAAATCACATTTTGA-CCCC
** * *
28787659 AAGTTTTTCCAAAATCACATTTTTACCCTT
1 AAACTTTTCCAAAATCACATTTTGACCC-C
* *
28787689 AAACTTTTCTAAAATCAAATTTTGACCCC
1 AAACTTTTCCAAAATCACATTTTGACCCC
* * *
28787718 TAAACTTCT-CAAAATCATATTTTAACCCC
1 -AAACTTTTCCAAAATCACATTTTGACCCC
* *
28787747 TAAA-TTTTCCTAAAATCATATTTTGACCCTA
1 -AAACTTTTCC-AAAATCACATTTTGACCC-C
*
28787778 AAACTTTTCCAAAATTACATTTTGACCCC
1 AAACTTTTCCAAAATCACATTTTGACCCC
* *
28787807 TAAACTTCTCCAAAATCACATTTTAACCCC
1 -AAACTTTTCCAAAATCACATTTTGACCCC
*
28787837 TAAACCTTTCCAAAATCACATTTTGACCCC
1 -AAACTTTTCCAAAATCACATTTTGACCCC
* **
28787867 TAAACCTTTCCAAAATCACATTTTGACCTT
1 -AAACTTTTCCAAAATCACATTTTGACCCC
* * * **
28787897 AAAC-TTTCCTAAATTTACATTTTTACACTT
1 AAACTTTTCC-AAAATCACATTTTGAC-CCC
* *
28787927 AAACTTTTCCAAAATAACATTTTGACCCTT
1 AAACTTTTCCAAAATCACATTTTGACCC-C
* * *
28787957 AAAC-TTCCCAAAATCACATTTTAAACCCA
1 AAACTTTTCCAAAATCACATTTT-GACCCC
* * * *
28787986 AAACATTTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATCACATTTTGACCC-C
* * * *
28788016 AAAATTCTCCAAAATCACATTTTGATCGCT
1 AAACTTTTCCAAAATCACATTTTGA-CCCC
* *
28788046 AAACCTTTCCAAAATCACATTTTGACCCT
1 AAACTTTTCCAAAATCACATTTTGACCCC
* * **
28788075 AAACTTCTT-TAAAATCACATTTTAACCTT
1 AAACTT-TTCCAAAATCACATTTTGACCCC
* * * *
28788104 AAACTTTCCCAAAATTACATTTTTACCCTT
1 AAACTTTTCCAAAATCACATTTTGACCC-C
* * *
28788134 AATA-TTTTCCAAAATTACATTTTAACCTC
1 AA-ACTTTTCCAAAATCACATTTTGACCCC
28788163 AAA
1 AAA
28788166 TTCTCTAAAA
Statistics
Matches: 468, Mismatches: 76, Indels: 43
0.80 0.13 0.07
Matches are distributed among these distances:
28 14 0.03
29 175 0.37
30 265 0.57
31 14 0.03
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
AAACTTTTCCAAAATCACATTTTGACCCC
Found at i:28787693 original size:59 final size:60
Alignment explanation
Indices: 28787571--28788156 Score: 520
Period size: 59 Copynumber: 9.9 Consensus size: 60
28787561 AGTAAGTCCC
* * * * *
28787571 TAAACTTTTCAAAAATCATATTTTGA-CCTCAAACTTTTT-CAAAATTACA-TTTTAACCT
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAA-TTTTTCCAAAATCACATTTTTACCCT
** *
28787629 TAAACTTTTCCAAAATCACA-TTTGACCCCCAAGTTTTTCCAAAATCACATTTTTACCCT
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTTTACCCT
* * * * * * * *
28787688 TAAACTTTTCTAAAATCAAATTTTGACCCCTAAACTTCT-CAAAATCATATTTTAACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTTTACCCT
* * * * * *
28787747 TAAA-TTTTCCTAAAATCATATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCC
1 TAAACTTTTCC-AAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTTTACCCT
* * * ** * *
28787807 TAAACTTCTCCAAAATCACATTTTAACCCCTAAACCTTTCCAAAATCACATTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTTTACCCT
* * * * *
28787867 TAAACCTTTCCAAAATCACATTTTGA-CCTTAAA-CTTTCCTAAATTTACATTTTTACACT
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCC-AAAATCACATTTTTACCCT
* * * *
28787926 TAAACTTTTCCAAAATAACATTTTGACCCTTAAA-CTTCCCAAAATCACATTTTAAACCC-
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTT-TACCCT
* * * * * * * *
28787985 AAAACATTTCCAAAATTACATTTTAACCCTTAAAATTCTCCAAAATCACATTTTGATCGC-
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTTTA-CCCT
* *
28788045 TAAACCTTTCCAAAATCACATTTTGACCC-TAAACTTCTTT--AAAATCACA-TTTTAACCT
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAA-TT-TTTCCAAAATCACATTTTTACCCT
* * * *
28788103 TAAACTTTCCCAAAATTACATTTTTACCCTT-AATATTTTCCAAAATTACATTTT
1 TAAACTTTTCCAAAATCACATTTTGACCCTTAAAT-TTTTCCAAAATCACATTTT
28788157 AACCTCAAAT
Statistics
Matches: 439, Mismatches: 69, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
57 15 0.03
58 75 0.17
59 179 0.41
60 163 0.37
61 7 0.02
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (60 bp):
TAAACTTTTCCAAAATCACATTTTGACCCTTAAATTTTTCCAAAATCACATTTTTACCCT
Found at i:28787782 original size:89 final size:87
Alignment explanation
Indices: 28787568--28788156 Score: 582
Period size: 89 Copynumber: 6.6 Consensus size: 87
28787558 TCCAGTAAGT
* * * * * *
28787568 CCCTAAACTTTTCAAAAATCATATTTTGA-CCTCAAACTTTTTCAAAATTACATTTTAACCTTAA
1 CCCTAAA-TTTTCCAAAATCACATTTTGACCCT-AAACTTTTCCAAAATCACATTTTGACCCTAA
* *
28787632 ACTTTTCCAAAATCACA-TTTGAC
64 ACTTCTCCAAAATCACATTTTAAC
* * * * *
28787655 CCCCAAGTTTTTCCAAAATCACATTTTTACCCTTAAACTTTTCTAAAATCAAATTTTGACCCCTA
1 CCCTAA-ATTTTCCAAAATCACATTTTGACCC-TAAACTTTTCCAAAATCACATTTTGA-CCCTA
*
28787720 AACTTCT-CAAAATCATATTTTAAC
63 AACTTCTCCAAAATCACATTTTAAC
* *
28787744 CCCTAAATTTTCCTAAAATCATATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCTA
1 CCCTAAATTTTCC-AAAATCACATTTTGACCCT-AAACTTTTCCAAAATCACATTTTGA-CCCTA
28787809 AACTTCTCCAAAATCACATTTTAAC
63 AACTTCTCCAAAATCACATTTTAAC
* * *
28787834 CCCTAAACCTTTCCAAAATCACATTTTGACCCCTAAACCTTTCCAAAATCACATTTTGACCTTAA
1 CCCTAAA-TTTTCCAAAATCACATTTTGA-CCCTAAACTTTTCCAAAATCACATTTTGACCCTAA
* * *
28787899 ACTT-TCCTAAATTTACATTTTTAC
64 ACTTCTCC-AAAATCACATTTTAAC
* * * * * *
28787923 ACTTAAACTTTTCCAAAATAACATTTTGACCCTTAAAC-TTCCCAAAATCACATTTTAAACCCAA
1 CCCTAAA-TTTTCCAAAATCACATTTTGACCC-TAAACTTTTCCAAAATCACATTTT-GACCCTA
*
28787987 AACATT-TCCAAAATTACATTTTAAC
63 AAC-TTCTCCAAAATCACATTTTAAC
* * * *
28788012 CCTTAAAATTCTCCAAAATCACATTTTGATCGCTAAACCTTTCCAAAATCACATTTTGACCCTAA
1 CCCT-AAATTTTCCAAAATCACATTTTGA-CCCTAAACTTTTCCAAAATCACATTTTGACCCTAA
**
28788077 ACTTCTTTAAAATCACATTTTAA-
64 ACTTCTCCAAAATCACATTTTAAC
* * * * *
28788100 CCTTAAACTTTCCCAAAATTACATTTTTACCCTTAATA-TTTTCCAAAATTACATTTT
1 CCCTAAA-TTTTCCAAAATCACATTTTGACCC-TAA-ACTTTTCCAAAATCACATTTT
28788157 AACCTCAAAT
Statistics
Matches: 424, Mismatches: 57, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
87 28 0.07
88 104 0.25
89 196 0.46
90 87 0.21
91 9 0.02
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (87 bp):
CCCTAAATTTTCCAAAATCACATTTTGACCCTAAACTTTTCCAAAATCACATTTTGACCCTAAAC
TTCTCCAAAATCACATTTTAAC
Found at i:28793088 original size:2 final size:2
Alignment explanation
Indices: 28793081--28793118 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28793071 AGCTGTCTTT
*
28793081 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28793119 AAATCTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28795285 original size:27 final size:27
Alignment explanation
Indices: 28795228--28795285 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
28795218 GACTATCTTT
* * *
28795228 GTGGTGTATTATGAATGAACTGCTTTT
1 GTGGTGTACTATGAATGAACTGCCTTA
*
28795255 GTGGTGTACTCTGAAT-AGACTGCCTTA
1 GTGGTGTACTATGAATGA-ACTGCCTTA
28795282 GTGG
1 GTGG
28795286 CATACCATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (27 bp):
GTGGTGTACTATGAATGAACTGCCTTA
Found at i:28797399 original size:24 final size:23
Alignment explanation
Indices: 28797371--28797423 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 23
28797361 AGTTTTAATT
28797371 TTTTTTGATGATTTGTCATTGTTCA
1 TTTTTTGAT-ATTTGTCA-TGTTCA
*
28797396 TTTTTTTGATATTTTTCATGTTCA
1 -TTTTTTGATATTTGTCATGTTCA
28797420 TTTT
1 TTTT
28797424 ATAATCATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 6 0.23
25 7 0.27
26 9 0.35
ACGTcount: A:0.15, C:0.08, G:0.11, T:0.66
Consensus pattern (23 bp):
TTTTTTGATATTTGTCATGTTCA
Found at i:28797409 original size:25 final size:25
Alignment explanation
Indices: 28797370--28797423 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
28797360 TAGTTTTAAT
28797370 TTTTTTTGATGATTTGTCATTGTTCA
1 TTTTTTTGATGATTTGTCA-TGTTCA
*
28797396 TTTTTTTGAT-ATTTTTCATGTTCA
1 TTTTTTTGATGATTTGTCATGTTCA
28797420 TTTT
1 TTTT
28797424 ATAATCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 10 0.37
25 7 0.26
26 10 0.37
ACGTcount: A:0.15, C:0.07, G:0.11, T:0.67
Consensus pattern (25 bp):
TTTTTTTGATGATTTGTCATGTTCA
Found at i:28799194 original size:28 final size:30
Alignment explanation
Indices: 28799143--28799234 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 30
28799133 AATTTTTTAA
*
28799143 ATTTTAAAAACTTAAGAAATTATAAAAA-AT
1 ATTTTTAAAA-TTAAGAAATTATAAAAATAT
*
28799173 ATTTTTTAAAATTAA-AAA-TATAAAAATGT
1 A-TTTTTAAAATTAAGAAATTATAAAAATAT
* *
28799202 ATTTTTAAATATTAATAAAGTTTTAAAAATAT
1 ATTTTTAAA-ATTAAGAAA-TTATAAAAATAT
28799234 A
1 A
28799235 ATTAAATGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
28 16 0.31
29 10 0.19
30 8 0.15
31 8 0.15
32 10 0.19
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTTTTAAAATTAAGAAATTATAAAAATAT
Found at i:28801937 original size:21 final size:22
Alignment explanation
Indices: 28801888--28801938 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
28801878 TATTGTTTTT
28801888 TAATTTT-TTTAAATATTTATA
1 TAATTTTATTTAAATATTTATA
* *
28801909 TTATTTTATTTTAATATTTA-A
1 TAATTTTATTTAAATATTTATA
28801930 TAATTTTAT
1 TAATTTTAT
28801939 ACATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TAATTTTATTTAAATATTTATA
Found at i:28805394 original size:18 final size:17
Alignment explanation
Indices: 28805367--28805430 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
28805357 TTTTTTAATA
*
28805367 AATTTGATAATTTATTAG
1 AATTTTATAATTT-TTAG
*
28805385 AATTTTATAAGTTTTATG
1 AATTTTATAATTTTTA-G
*
28805403 AATTTTTTATAATTTTTAT
1 AA--TTTTATAATTTTTAG
*
28805422 AAGTTTATA
1 AATTTTATA
28805431 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 9 0.24
18 14 0.37
19 2 0.05
20 13 0.34
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (17 bp):
AATTTTATAATTTTTAG
Found at i:28805505 original size:9 final size:9
Alignment explanation
Indices: 28805358--28805539 Score: 82
Period size: 10 Copynumber: 18.8 Consensus size: 9
28805348 TAAATGAATT
28805358 TTTTTAATAA
1 TTTTT-ATAA
* *
28805368 ATTTGATAA
1 TTTTTATAA
*
28805377 TTTATTAGAA
1 TTT-TTATAA
28805387 -TTTTATAA
1 TTTTTATAA
*
28805395 GTTTTATGAA
1 TTTTTAT-AA
28805405 TTTTTTATAA
1 -TTTTTATAA
28805415 TTTTTATAA
1 TTTTTATAA
*
28805424 GTTTATATAAA
1 -TTTTTAT-AA
** *
28805435 AATTTAAATA
1 TTTTTATA-A
28805445 TTTTTA-ATA
1 TTTTTATA-A
28805454 TGTTTTAT-A
1 T-TTTTATAA
*
28805463 TGTTTATATA
1 TTTTTATA-A
* *
28805473 TTCATTATGA
1 TT-TTTATAA
*
28805483 TTTTTATAGG
1 TTTTTATA-A
28805493 TTTTTATAA
1 TTTTTATAA
28805502 TTTTTATAA
1 TTTTTATAA
28805511 CTTTTTATAAAA
1 -TTTTTAT--AA
*
28805523 TTTTTAATAT
1 TTTTT-ATAA
28805533 TTTTTAT
1 TTTTTAT
28805540 TAGAAAAATG
Statistics
Matches: 132, Mismatches: 23, Indels: 35
0.69 0.12 0.18
Matches are distributed among these distances:
8 10 0.08
9 45 0.34
10 56 0.42
11 17 0.13
12 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:28805515 original size:19 final size:19
Alignment explanation
Indices: 28805477--28805520 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28805467 TATATATTCA
* **
28805477 TTATGATTTTTATAGGTTT
1 TTATAATTTTTATAACTTT
28805496 TTATAATTTTTATAACTTT
1 TTATAATTTTTATAACTTT
28805515 TTATAA
1 TTATAA
28805521 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATAATTTTTATAACTTT
Found at i:28808001 original size:41 final size:41
Alignment explanation
Indices: 28807944--28808026 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
28807934 GCTTGAAGAA
28807944 CAGACTTTATGAAAACCATCTTACCCCATTGTGATAGCCAT
1 CAGACTTTATGAAAACCATCTTACCCCATTGTGATAGCCAT
*
28807985 CAGACTTTATGAAAACCATCTTACCCCGTTGTGATAGCCAT
1 CAGACTTTATGAAAACCATCTTACCCCATTGTGATAGCCAT
28808026 C
1 C
28808027 CATTGCACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (41 bp):
CAGACTTTATGAAAACCATCTTACCCCATTGTGATAGCCAT
Found at i:28810925 original size:12 final size:13
Alignment explanation
Indices: 28810908--28810937 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28810898 TTGTTTCAAT
28810908 TTTTCATTT-TTC
1 TTTTCATTTCTTC
28810920 TTTTCATTTCTTC
1 TTTTCATTTCTTC
28810933 TTTTC
1 TTTTC
28810938 GTCCTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTCTTC
Found at i:28812103 original size:47 final size:47
Alignment explanation
Indices: 28812034--28812133 Score: 191
Period size: 47 Copynumber: 2.1 Consensus size: 47
28812024 TTTAAGAATA
*
28812034 TAAGAACCAGGATTTAGATACATGATGAGGATTGTTAGTCCTAATTT
1 TAAGAACCAGGATTTAGATACATGATGAGGATTGCTAGTCCTAATTT
28812081 TAAGAACCAGGATTTAGATACATGATGAGGATTGCTAGTCCTAATTT
1 TAAGAACCAGGATTTAGATACATGATGAGGATTGCTAGTCCTAATTT
28812128 TAAGAA
1 TAAGAA
28812134 TATAAGTAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (47 bp):
TAAGAACCAGGATTTAGATACATGATGAGGATTGCTAGTCCTAATTT
Found at i:28813934 original size:48 final size:48
Alignment explanation
Indices: 28813879--28813980 Score: 177
Period size: 48 Copynumber: 2.1 Consensus size: 48
28813869 TTCTTCTTTT
*
28813879 TAAAATTCTAATCTTTTTGTATATCAGCTGCCTCTTTTAAAGACAAAA
1 TAAAATTCTAATCTTTTTGTATATCAGCTGCCCCTTTTAAAGACAAAA
* *
28813927 TAAAATTCTAATCTTTTTGTATTTCAGCTGCCCCTTTTAAAGCCAAAA
1 TAAAATTCTAATCTTTTTGTATATCAGCTGCCCCTTTTAAAGACAAAA
28813975 TAAAAT
1 TAAAAT
28813981 GTTACCTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (48 bp):
TAAAATTCTAATCTTTTTGTATATCAGCTGCCCCTTTTAAAGACAAAA
Found at i:28818539 original size:48 final size:48
Alignment explanation
Indices: 28818485--28818586 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 48
28818475 TTCTTCTTTT
*
28818485 TAAAATTCTAATCTTTTTGAATATCAGTTGCCCCTTTTAAAGCCAAAA
1 TAAAATTCTAATCTTTTTGAATATCAGCTGCCCCTTTTAAAGCCAAAA
*
28818533 TAAAATTCTAATCTTTTTGTATATCAGCTGCCCCTTTTAAAGCCAAAA
1 TAAAATTCTAATCTTTTTGAATATCAGCTGCCCCTTTTAAAGCCAAAA
28818581 TAAAAT
1 TAAAAT
28818587 GTTACCTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (48 bp):
TAAAATTCTAATCTTTTTGAATATCAGCTGCCCCTTTTAAAGCCAAAA
Done.