Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_pilon, whole genome shotgun sequence
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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:154789 original size:103 final size:104
Alignment explanation
Indices: 154627--154835 Score: 251
Period size: 103 Copynumber: 2.0 Consensus size: 104
154617 TCTCAATGGT
* * * * * *
154627 TTATCAATTTTGTTTCAAATGAAACAATTTCCAATTTTTTGTTTTGAGGGAAAATTGTCTCTAGC
1 TTATCAATTTTGTTTCAAATGAAACAATTTCAAAATTTGTATTTTGAGGGAAAACTGTCTCAAGC
* * **
154692 GAGTCAAAATTTG-TTTTTAAGAAAAATGATCTAAAATG
66 GAGGCAAAATTTGTTTTTTAAAAAAAACAATCTAAAATG
* * *
154730 TTATCAATTTTGTTTCAAGTGAAACAATTTTAAAATTTGTATTTCT-AGGGGAAACTGTCTCAAG
1 TTATCAATTTTGTTTCAAATGAAACAATTTCAAAATTTGTATTT-TGAGGGAAAACTGTCTCAAG
* * *
154794 TGAGGCGAAATTTGTTTTTTAAAAAAAACAATCTCAAATG
65 CGAGGCAAAATTTGTTTTTTAAAAAAAACAATCTAAAATG
154834 TT
1 TT
154836 CGTGTCTTAA
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
103 64 0.73
104 24 0.27
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (104 bp):
TTATCAATTTTGTTTCAAATGAAACAATTTCAAAATTTGTATTTTGAGGGAAAACTGTCTCAAGC
GAGGCAAAATTTGTTTTTTAAAAAAAACAATCTAAAATG
Found at i:154896 original size:37 final size:37
Alignment explanation
Indices: 154855--155035 Score: 172
Period size: 37 Copynumber: 4.9 Consensus size: 37
154845 AGGAAGACTC
** *
154855 TCTCAAGTGAGATGAAATTTGTTTTTAAGAAAAATTA
1 TCTCAAGTGAGACCAAATTTGTTTTTAAGAAAAACTA
*
154892 TCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACTA
1 TCTCAAGTGAGACCAAATTTGTTTTTAAGAAAAACTA
* * * *
154929 TATCAAGCGAGA-CAAATTTTTTTTTTAAG-AAAACAA
1 TCTCAAGTGAGACCAAA-TTTGTTTTTAAGAAAAACTA
* * *
154965 TCTCAAGTGAGATCAATTTTG-TTTCAAGAAAAACTA
1 TCTCAAGTGAGACCAAATTTGTTTTTAAGAAAAACTA
* * * *
155001 TCTCTAGCGAGACGAACA-TTGTTTATAGAGAAAAA
1 TCTCAAGTGAGACCAA-ATTTGTTTTTA-AGAAAAA
155036 ATCTCTAAGG
Statistics
Matches: 117, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
35 6 0.05
36 43 0.37
37 61 0.52
38 7 0.06
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (37 bp):
TCTCAAGTGAGACCAAATTTGTTTTTAAGAAAAACTA
Found at i:155039 original size:72 final size:72
Alignment explanation
Indices: 154873--155040 Score: 196
Period size: 72 Copynumber: 2.3 Consensus size: 72
154863 GAGATGAAAT
*
154873 TTGTTTTTAAGAAAAATTATCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACTATATCAAGCG
1 TTGTTTTTAAGAAAAA--ATCTCAAGTGAGACAAAATTTGTTTTCAAGAAAAACTATATCAAGCG
**
154938 AGACAAATT
64 AGACAAACA
* * * *
154947 TTTTTTTTAAGAAAACAATCTCAAGTGAGATC-AATTTTG-TTTCAAGAAAAACTATCTCTAGCG
1 TTGTTTTTAAGAAAA-AATCTCAAGTGAGA-CAAAATTTGTTTTCAAGAAAAACTATATCAAGCG
*
155010 AGACGAACA
64 AGACAAACA
*
155019 TTGTTTATAGAGAAAAAATCTC
1 TTGTTTTTA-AGAAAAAATCTC
155041 TAAGGTGATA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
72 40 0.49
73 25 0.31
74 15 0.19
75 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (72 bp):
TTGTTTTTAAGAAAAAATCTCAAGTGAGACAAAATTTGTTTTCAAGAAAAACTATATCAAGCGAG
ACAAACA
Found at i:159879 original size:16 final size:18
Alignment explanation
Indices: 159854--159892 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
159844 AATGTCTTTT
159854 AAAATAA-TTTTAAGA-A
1 AAAATAATTTTTAAGACA
*
159870 AAAATCATTTTTAAGACA
1 AAAATAATTTTTAAGACA
159888 AAAAT
1 AAAAT
159893 TGGTTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (18 bp):
AAAATAATTTTTAAGACA
Found at i:160764 original size:16 final size:16
Alignment explanation
Indices: 160739--160774 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
160729 ATAAAGAAAA
*
160739 TAAAAATACATAAATT
1 TAAAAATACATAAAGT
*
160755 TAAAAGTACATAAAGT
1 TAAAAATACATAAAGT
160771 TAAA
1 TAAA
160775 TAGCAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (16 bp):
TAAAAATACATAAAGT
Found at i:160846 original size:16 final size:16
Alignment explanation
Indices: 160805--160847 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
160795 TAGTTAGTAA
* *
160805 TTAGCGGTTCGAAAGG
1 TTAGCGGTTAGAAAAG
**
160821 TTAGATGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
160837 TTAGCGGTTAG
1 TTAGCGGTTAG
160848 TAGAGTCTGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:160940 original size:5 final size:5
Alignment explanation
Indices: 160930--160964 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
160920 ACAAATTAAC
*
160930 AAAAT AAAAT AAAAT AAAAT AAAGT AAATAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAA
160965 AAAGTTAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:161156 original size:131 final size:131
Alignment explanation
Indices: 160832--161235 Score: 511
Period size: 131 Copynumber: 3.1 Consensus size: 131
160822 TAGATGTTAG
** *
160832 AAAAGTTAGCGGTTAGTAGAGTCTGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCA
1 AAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCA
* ***
160897 CAAGGTCGAATCGAATAATT-CAAACAAATTAACA-AAATAAA-ATAA-AATAAAATAAAGT-AA
66 CAAGGTCGAATCGAAT-ATTAGAAAC-AA-TAA-ATAAATAAATA-AACAAT-GGTTAAAGTGAA
160957 ATATAAA-
125 ATA-AAAT
* * *
160964 AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACTCCC-GATCGGGTCACC
1 AAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGTGGATCATAC-CCCGGATCTGGTCACC
* * * *
161028 ACAAGGTCGATTCAAATATTAGAAACAATAAATAAATAAATAAACAATGGTTAGAGTGCAATAAA
65 ACAAGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAAACAATGGTTAAAGTGAAATAAA
161093 AT
130 AT
*
161095 AAAA-TTCAGTAGTTAGCAGAGTCTGAACCATAATAATGTTGATCATACCCCGGATCTGGTCACC
1 AAAAGTT-AGTAGTTAGCAGAGTCTGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACC
* *
161159 ACAAGGTCGAATCGAATATTAGAAACAATAAATATATAAAT-AACAATGGTTAAAGTGTAATAAA
65 ACAAGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAAACAATGGTTAAAGTGAAATAAA
161223 AT
130 AT
161225 AAAAGTTAGTA
1 AAAAGTTAGTA
161236 ATTACCTTGA
Statistics
Matches: 241, Mismatches: 21, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
129 1 0.00
130 56 0.23
131 106 0.44
132 75 0.31
133 3 0.01
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (131 bp):
AAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCA
CAAGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAAACAATGGTTAAAGTGAAATAAAA
T
Found at i:162825 original size:78 final size:79
Alignment explanation
Indices: 162670--162818 Score: 185
Period size: 77 Copynumber: 1.9 Consensus size: 79
162660 ATATAGTAAG
* **
162670 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATCGTTATTTAATTCGAAATAATGA
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATCGACATTTAATTCGAAATAATGA
162735 AATAAGAGTTTAAA
66 AATAAGAGTTTAAA
* * * * * * * *
162749 TAAACGTT-AAAGATTGTAATTTAGATTATAAGTC-TTTAATGGACATTTAATTTGAATTAATTA
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATCGACATTTAATTCGAAATAATGA
162812 AATAAGA
66 AATAAGA
162819 TTTTTAATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 30 0.51
78 22 0.37
79 7 0.12
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATCGACATTTAATTCGAAATAATGA
AATAAGAGTTTAAA
Found at i:164101 original size:139 final size:139
Alignment explanation
Indices: 163904--164606 Score: 852
Period size: 139 Copynumber: 5.1 Consensus size: 139
163894 TCAATTTGAA
* * * * * * *
163904 GATAATTAGGTGACAACACGGTTCCTATGTGATGAGGAAGTCTGATTGTATGAGGATGACACTGC
1 GATAATTTGGAGACAACACGGTTCCTATGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
* * * * * *
163969 TCCTACGCGTTGAGGAGATCTGGTCGGTGGACGACATTATTCCTACGTGATAAGGATGTTTAGCC
66 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
164034 ATCTTTAGG
131 ATCTTTAGG
* * * * * *
164043 GATAATTTGGAGACAACACGATTCATATGTGATAAGAAAGTCTTGTTATCTTAGGATGACGTTGC
1 GATAATTTGGAGACAACACGGTTCCTATGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
** * ** * * * **
164108 TCCTACACGTTGAGGAGATCTGGTTAGTGGAAGACATTATTCCTACGTGATGAGGATGTCTAGTA
66 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
*
164173 ATCTGTAGG
131 ATCTTTAGG
* * * * * *
164182 GATAATTTGGAGATAACTCGATTTCTACGCGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
1 GATAATTTGGAGACAACACGGTTCCTATGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
* * ** **
164247 TCCTACGTGATGAGGAGATCTGGTCGGTTGATGATGTTGTAACTACGTGATGAGGACGTCTAGCC
66 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
*
164312 GTCTTTAGG
131 ATCTTTAGG
* *
164321 GATAATTTAGAGACAACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
1 GATAATTTGGAGACAACACGGTTCCTATGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
* **
164386 TCCTACGTGATGAGGATATCTGGTCGGTGGACGACATTGTTTATACGTGATGAGGACGTCTAGCC
66 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
*
164451 GA-CTTCA-G
131 -ATCTTTAGG
* * * * * *
164459 GATAATTTGGAGAAAACATGGTTCCTATGTGATGAGGAAGTCTGGTTATTTGAGGATGATGTTGC
1 GATAATTTGGAGACAACACGGTTCCTATGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
* * * *
164524 TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACATTGTTCCTACGTGATGAGGACGTCTAGTC
66 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
164589 ATCTTTAGG
131 ATCTTTAGG
164598 GATAATTTG
1 GATAATTTG
164607 TTTCAAGAGA
Statistics
Matches: 480, Mismatches: 81, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
137 1 0.00
138 120 0.25
139 359 0.75
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (139 bp):
GATAATTTGGAGACAACACGGTTCCTATGTGATAAGGAAGTCTGGTTATCTGAGGATGACGCTGC
TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
ATCTTTAGG
Found at i:165141 original size:192 final size:193
Alignment explanation
Indices: 164921--165330 Score: 436
Period size: 194 Copynumber: 2.1 Consensus size: 193
164911 AACTTCATTG
* * * * *
164921 TATACGTGACGAAA-AGAAAATTGTCACATTGTTAGTAACGTAGTAT-ATCGTCACCTAATAGTA
1 TATATGTGACGAAAGAG-ATATTGTCACATTGTTAGTAACATAATATAAT-GTCACCTAATAATA
* *
164984 GCATGGATGACATTTATATATAACGTCACTATATAATTAATATTC-AATGACAACTAATTATAG-
64 GCATGAATGACATTTATACATAACGTCACTATATAATTAATATTCTAATG-CAACTAATTA-AGT
* * * **
165047 CACTAAA-TAATTTAA-ATTTCGTTATTGATGATTTATATCGTCACGGATAATACATTAAAATCA
127 CACTAAATTAA-ATAATATTGCGTTATTGATAATTTATATCGTCACAAATAATACATTAAAATCA
165110 ACC
191 ACC
* * * *
165113 TATATGTGACGAAAGAGATATTGTCACATTTTTAGTGACATAATATAAATGTTACCTAATAATAT
1 TATATGTGACGAAAGAGATATTGTCACATTGTTAGTAACATAATAT-AATGTCACCTAATAATAG
* * * * * * * ** ** *
165178 TATGAATGGCGTTTATGCATAACGTCACTTTATAATTTATATTCTATTGCAGTTGGTTACGTCAC
65 CATGAATGACATTTATACATAACGTCACTATATAATTAATATTCTAATGCAACTAATTAAGTCAC
* * *
165243 TAAATTAAATAATATTGCGTTATTGATAATTTATATTGTCACAAATAATGCATTAAAATCAACT
130 TAAATTAAATAATATTGCGTTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACC
*
165307 TATATGTGACGAAAGATATATTGT
1 TATATGTGACGAAAGAGATATTGT
165331 AGCAAAACAC
Statistics
Matches: 179, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
192 38 0.21
193 66 0.37
194 75 0.42
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (193 bp):
TATATGTGACGAAAGAGATATTGTCACATTGTTAGTAACATAATATAATGTCACCTAATAATAGC
ATGAATGACATTTATACATAACGTCACTATATAATTAATATTCTAATGCAACTAATTAAGTCACT
AAATTAAATAATATTGCGTTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACC
Found at i:167994 original size:11 final size:11
Alignment explanation
Indices: 167978--168005 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
167968 TTAGTTGGGC
167978 GGGCGGATGCG
1 GGGCGGATGCG
167989 GGGCGGATGCG
1 GGGCGGATGCG
168000 GGGCGG
1 GGGCGG
168006 GTAATGTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.18, G:0.68, T:0.07
Consensus pattern (11 bp):
GGGCGGATGCG
Found at i:169879 original size:103 final size:102
Alignment explanation
Indices: 169763--170012 Score: 295
Period size: 103 Copynumber: 2.4 Consensus size: 102
169753 TTGTTGTAGT
* * * *
169763 GAGAAATTTTCTCAAGCGAGACAAAATTTGTTTCGAGATAAACAAACTCAAAGGTTTATGTTTTA
1 GAGAAAATATCTCAAGCGAGACAAAATTTGTTTCGAGAGAAAC-AACTCAAAGGTTTATGTATTA
* * *
169828 AGAGAAATTGTCTCAAGTA-AGACGAAACTTTGTTTCGA
65 AGAGAAACTGTCTCAAG-AGAGACAAAACTTTGTTTCAA
* * * * * * * **
169866 GAGAAACTGTCTCAAGCGAGACAAAGTTTTGTTCCAAGGGAAACAAGTCAATTGTTTATGTATTA
1 GAGAAAATATCTCAAGCGAGACAAA-ATTTGTTTCGAGAGAAACAACTCAAAGGTTTATGTATTA
*
169931 AGAGAAACTGTCTCTAGAGAGACAAAACTTTGTTTCAA
65 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAA
*
169969 GAGAAAATATCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAAC
1 GAGAAAATATCTCAAGCGAGAC-AAAATTTGTTTCGAGAGAAAC
170013 TATCTCAAGC
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
102 1 0.01
103 106 0.86
104 16 0.13
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (102 bp):
GAGAAAATATCTCAAGCGAGACAAAATTTGTTTCGAGAGAAACAACTCAAAGGTTTATGTATTAA
GAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAA
Found at i:170048 original size:36 final size:36
Alignment explanation
Indices: 169930--170160 Score: 208
Period size: 37 Copynumber: 6.5 Consensus size: 36
169920 TTTATGTATT
* * *
169930 AAGAGAAACTGTCTCTAGAGAGACAAAACTTTGTTTC
1 AAGAGAAACTATCTCAAGCGAGAC-AAACTTTGTTTC
*
169967 AAGAGAAAATATCTCAAGCGAGACGAAACTTTGTTTC
1 AAGAGAAACTATCTCAAGCGAGAC-AAACTTTGTTTC
*
170004 GAGAGAAACTATCTCAAGCGAGACACAA-TTTGTTTC
1 AAGAGAAACTATCTCAAGCGAGACA-AACTTTGTTTC
* * ** *
170040 AAGGGAAACAATCTCAA--TTG-----TTTATGTTTC
1 AAGAGAAACTATCTCAAGCGAGACAAACTT-TGTTTC
* *
170070 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTC
1 AAGAGAAACTATCTCAAGCGAGAC-AAACTTTGTTTC
* *
170107 AAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTC
1 AAGAGAAACTATCTCAAGCGAGAC-AAACTTTGTTTC
* *
170144 GAGAGAAACAATCTCAA
1 AAGAGAAACTATCTCAA
170161 CGGTTTATCA
Statistics
Matches: 158, Mismatches: 25, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
29 2 0.01
30 20 0.13
32 1 0.01
34 1 0.01
36 23 0.15
37 109 0.69
38 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (36 bp):
AAGAGAAACTATCTCAAGCGAGACAAACTTTGTTTC
Found at i:170068 original size:103 final size:104
Alignment explanation
Indices: 169961--170160 Score: 296
Period size: 103 Copynumber: 1.9 Consensus size: 104
169951 GACAAAACTT
* * *
169961 TGTTTCAAGAGAAAATATCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAAATATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGCGAG
*
170026 AC-ACAA-TTTGTTTCAAGGGAAACAATCTCAATTGTTTA
66 ACGA-AACTTTGTTTCAAGAGAAACAATCTCAATTGTTTA
* * * *
170064 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAGCGAG
1 TGTTTCAAGAGAAAATATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGCGAG
*
170129 ACGAAACTTTGTTTCGAGAGAAACAATCTCAA
66 ACGAAACTTTGTTTCAAGAGAAACAATCTCAA
170161 CGGTTTATCA
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
103 62 0.72
104 24 0.28
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (104 bp):
TGTTTCAAGAGAAAATATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGCGAG
ACGAAACTTTGTTTCAAGAGAAACAATCTCAATTGTTTA
Found at i:170209 original size:104 final size:101
Alignment explanation
Indices: 170099--170369 Score: 362
Period size: 104 Copynumber: 2.6 Consensus size: 101
170089 GAGACAAAAC
* * * * * *
170099 TTTGTTTCAAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAACGG
1 TTTGTTTTAAGGGAAACTGTCTCAAGCGAGACGAAA-TTTGTTTTGAGAAAAACAATCTCAAAGG
*
170164 TTTATCAATTTTGTTTCAAATGAAACAATTTCCAAATT
65 -TTATCAATTTTGTTTCAAATGAAACAATTTCAAAATT
*
170202 TTGTGTTTTAAGGGAAAACTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAACAATCTCAAA
1 TT-TGTTTTAAGGG-AAACTGTCTCAAGCGAGACGAAATTTG-TTTTGAGAAAAACAATCTCAAA
* *
170267 TGTTATCAATTTTGTTTCAAGTGAAACAATTTCAAAATT
63 GGTTATCAATTTTGTTTCAAATGAAACAATTTCAAAATT
* * *
170306 TTTATTTTTAGGGGAAACTGTCTCAAGTGAGACGAAATTTGTTTTGAAGAAAAACAATCTCAAA
1 TTT-GTTTTAAGGGAAACTGTCTCAAGCGAGACGAAATTTGTTTTG-AGAAAAACAATCTCAAA
170370 TGTTCGTGTC
Statistics
Matches: 149, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
102 4 0.03
103 46 0.31
104 58 0.39
105 41 0.28
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (101 bp):
TTTGTTTTAAGGGAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAGAAAAACAATCTCAAAGGT
TATCAATTTTGTTTCAAATGAAACAATTTCAAAATT
Found at i:170254 original size:140 final size:139
Alignment explanation
Indices: 169821--170246 Score: 547
Period size: 140 Copynumber: 3.0 Consensus size: 139
169811 CAAAGGTTTA
* ** *
169821 TGTTTTAAGAGAAATTGTCTCAAGTAAGACGAAACTTTGTTTCGAGAGAAACTGTCTCAAGCGAG
1 TGTTTCAAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACTATCTCAAGCGAG
* * * *
169886 ACAAAGTTTTGTTCCAAGGGAAACAA-GTCAATTGTTTATGTATTAAGAGAAACTGTCTCTAGAG
66 AC-AA-TTTTGTTTCAAGGGAAACAATCTCAATTGTTTATGTTTTAAGAGAAACTGTCTCAAGAG
169950 AGACAAAACTT
129 AGACAAAACTT
* *
169961 TGTTTCAAGAGAAAATATCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACTATCTCAAGCGAG
* *
170026 ACACAATTTGTTTCAAGGGAAACAATCTCAATTGTTTATGTTTCAAGAGAAACTGTCTCAAGAGA
66 ACA-ATTTTGTTTCAAGGGAAACAATCTCAATTGTTTATGTTTTAAGAGAAACTGTCTCAAGAGA
170091 GACAAAACTT
130 GACAAAACTT
*
170101 TGTTTCAAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAA-CG-G
1 TGTTTCAAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACTATCTCAAGCGAG
** * * * *
170164 TTTATCAATTTTGTTTCAAATGAAACAATTTCCAAAT-TTTGTGTTTTAAGGGAAAACTGTCTCA
66 ---A-CAATTTTGTTTCAAGGGAAACAATCT-CAATTGTTTATGTTTTAAGAG-AAACTGTCTCA
* *
170228 AGCGAGACGAAA-TT
125 AGAGAGACAAAACTT
170242 TGTTT
1 TGTTT
170247 TTAAGAAAAA
Statistics
Matches: 253, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
138 1 0.00
139 21 0.08
140 164 0.65
141 40 0.16
142 27 0.11
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (139 bp):
TGTTTCAAGAGAAATTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACTATCTCAAGCGAG
ACAATTTTGTTTCAAGGGAAACAATCTCAATTGTTTATGTTTTAAGAGAAACTGTCTCAAGAGAG
ACAAAACTT
Found at i:170356 original size:103 final size:104
Alignment explanation
Indices: 170111--170373 Score: 386
Period size: 103 Copynumber: 2.5 Consensus size: 104
170101 TGTTTCAAGA
* * * **
170111 GAAATTGTCTCAAGCGAGACGAAACTTTGTTTCG-AGAGAAACAATCTCAACGGTTTATCAATTT
1 GAAACTGTCTCAAGCGAGACGAAA-TTTGTTTTGAAGAAAAACAATCTCAAATG-TTATCAATTT
* *
170175 TGTTTCAAATGAAACAATTTCCAAATTTTGTGTTTTAAGGG
64 TGTTTCAAATGAAACAATTTCAAAATTTTGTATTTTAAGGG
* *
170216 AAAACTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAACAATCTCAAATGTTATCAATTTTG
1 GAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAAGAAAAACAATCTCAAATGTTATCAATTTTG
* *
170281 TTTCAAGTGAAACAATTTCAAAATTTT-TATTTTTAGGG
66 TTTCAAATGAAACAATTTCAAAATTTTGTATTTTAAGGG
*
170319 GAAACTGTCTCAAGTGAGACGAAATTTGTTTTGAAGAAAAACAATCTCAAATGTT
1 GAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAAGAAAAACAATCTCAAATGTT
170374 CGTGTCTTAA
Statistics
Matches: 143, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
103 61 0.43
104 44 0.31
105 38 0.27
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (104 bp):
GAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAAGAAAAACAATCTCAAATGTTATCAATTTTG
TTTCAAATGAAACAATTTCAAAATTTTGTATTTTAAGGG
Found at i:170368 original size:37 final size:36
Alignment explanation
Indices: 170326--170498 Score: 126
Period size: 37 Copynumber: 4.9 Consensus size: 36
170316 GGGGAAACTG
170326 TCTCAAGTGAGACGAAATTTGTTTTGAAGAAAAACAA
1 TCTCAAGTGAGACGAAATTTGTTTT-AAGAAAAACAA
* ** * * * ***
170363 TCTCAAATG-TTCG-----TGTCTTAAGGAAGATTG
1 TCTCAAGTGAGACGAAATTTGTTTTAAGAAAAACAA
**
170393 TCTCAAGTGAGACGAAATTTGATTTTAAGAAAAACTG
1 TCTCAAGTGAGACGAAATTTG-TTTTAAGAAAAACAA
*
170430 TCTCAAGTGAGACAAAATTTGTTTTTAAG-AAAACAA
1 TCTCAAGTGAGACGAAATTTG-TTTTAAGAAAAACAA
** * *
170466 TCTCAAGTGAGATTAATTTTGTTTCAAGAAAAA
1 TCTCAAGTGAGACGAAATTTGTTTTAAGAAAAA
170499 TATCTCTAGC
Statistics
Matches: 104, Mismatches: 24, Indels: 17
0.72 0.17 0.12
Matches are distributed among these distances:
30 14 0.13
31 7 0.07
35 6 0.06
36 31 0.30
37 46 0.44
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (36 bp):
TCTCAAGTGAGACGAAATTTGTTTTAAGAAAAACAA
Found at i:170470 original size:36 final size:37
Alignment explanation
Indices: 170393--170477 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
170383 AGGAAGATTG
* **
170393 TCTCAAGTGAGACGAAATTTGATTTTAAGAAAAACTG
1 TCTCAAGTGAGACAAAATTTGATTTTAAGAAAAACAA
*
170430 TCTCAAGTGAGACAAAATTTGTTTTTAAG-AAAACAA
1 TCTCAAGTGAGACAAAATTTGATTTTAAGAAAAACAA
170466 TCTCAAGTGAGA
1 TCTCAAGTGAGA
170478 TTAATTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 17 0.39
37 27 0.61
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (37 bp):
TCTCAAGTGAGACAAAATTTGATTTTAAGAAAAACAA
Found at i:172506 original size:37 final size:36
Alignment explanation
Indices: 172462--172586 Score: 175
Period size: 37 Copynumber: 3.5 Consensus size: 36
172452 ATTAATATTG
*
172462 ATTATTAAATATATATGTTATATGTGTAAGTATATAT
1 ATTATT-AATATATATGTTATATGCGTAAGTATATAT
*
172499 ATTATTAATATATATGTTATAAGCGTAAGTTATATAT
1 ATTATTAATATATATGTTATATGCGTAAG-TATATAT
*
172536 ATAATTAATATATATGTTATATGCGTAAGT-TATAT
1 ATTATTAATATATATGTTATATGCGTAAGTATATAT
*
172571 A-T-TTAATATGTATGTT
1 ATTATTAATATATATGTT
172587 GAATTTACAC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
33 13 0.16
35 6 0.07
36 22 0.27
37 40 0.49
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (36 bp):
ATTATTAATATATATGTTATATGCGTAAGTATATAT
Found at i:173728 original size:15 final size:14
Alignment explanation
Indices: 173699--173749 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
173689 CCTTCTATTC
*
173699 TATG-CTTTACTTT
1 TATGTCTTTACATT
*
173712 TATGTCATTTACCTT
1 TATGTC-TTTACATT
173727 TAATG-CTTTACATT
1 T-ATGTCTTTACATT
173741 TATGTCTTT
1 TATGTCTTT
173750 TATTTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 7 0.22
14 13 0.41
15 9 0.28
16 3 0.09
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.57
Consensus pattern (14 bp):
TATGTCTTTACATT
Found at i:174039 original size:14 final size:14
Alignment explanation
Indices: 174029--174055 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
174019 ACATTTCTTG
174029 AAAATATTTTCCGA
1 AAAATATTTTCCGA
174043 AAAATATTTTCCG
1 AAAATATTTTCCG
174056 TAAATGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATATTTTCCGA
Found at i:174455 original size:24 final size:24
Alignment explanation
Indices: 174428--174510 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 24
174418 TTCGATTATT
174428 ATATTA-ATATTAAATATATAAATA
1 ATATTATATATTAAATATATAAA-A
174452 ATATTATTCATTATTAAATATATAAAA
1 ATATTA-T-A-TATTAAATATATAAAA
* * *
174479 A-ATTATATATTTATTAAATAAAA
1 ATATTATATATTAAATATATAAAA
*
174502 ATATAATAT
1 ATATTATAT
174511 CTTATATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 14 0.28
24 13 0.26
25 1 0.02
26 4 0.08
27 3 0.06
28 15 0.30
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATTATATATTAAATATATAAAA
Found at i:174473 original size:28 final size:27
Alignment explanation
Indices: 174435--174498 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
174425 ATTATATTAA
174435 TATTAAATATATAAATAATATTAT-TCA-T
1 TATTAAATATATAAA-AA-ATTATAT-ATT
174463 TATTAAATATATAAAAAATTATATATT
1 TATTAAATATATAAAAAATTATATATT
174490 TATTAAATA
1 TATTAAATA
174499 AAAATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 6 0.18
27 13 0.38
28 15 0.44
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTAAATATATAAAAAATTATATATT
Found at i:174486 original size:40 final size:40
Alignment explanation
Indices: 174411--174487 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
174401 TCTTTATTAA
* **
174411 AATATTATTCGATTATTATATTAATATTAAATATATAAAT
1 AATATTATTCGATTATTAAATTAATAAAAAATATATAAAT
174451 AATATTATTC-ATTATTAAA-TATATAAAAAATTATATA
1 AATATTATTCGATTATTAAATTA-ATAAAAAA-TATATA
174488 TTTATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.06
39 14 0.44
40 16 0.50
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (40 bp):
AATATTATTCGATTATTAAATTAATAAAAAATATATAAAT
Found at i:174566 original size:22 final size:22
Alignment explanation
Indices: 174536--174584 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
174526 TATAATTGAT
*
174536 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
174558 TATTATATTATATTATTATAAA
1 TATTATATTATAATATTAAAAA
174580 TATTA
1 TATTA
174585 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:174574 original size:30 final size:32
Alignment explanation
Indices: 174534--174592 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
174524 AATATAATTG
*
174534 ATTATTTTATTAT-AATATTAA-AAATATTAT
1 ATTATATTATTATAAATATTAATAAATATTAT
174564 ATTATATTATTATAAATATTAATAAATAT
1 ATTATATTATTATAAATATTAATAAATAT
174593 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 12 0.46
31 8 0.31
32 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTATATTATTATAAATATTAATAAATATTAT
Found at i:174592 original size:22 final size:21
Alignment explanation
Indices: 174548--174604 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
174538 TTTTATTATA
* *
174548 ATATTAAAAATATTATATTAT
1 ATATTATAAATATTATATAAT
174569 ATTATTATAAATATTA-ATAAAT
1 A-TATTATAAATATTATAT-AAT
*
174591 ATATTTTAAATATT
1 ATATTATAAATATT
174605 TTATTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTATAAATATTATATAAT
Found at i:174594 original size:77 final size:75
Alignment explanation
Indices: 174462--174603 Score: 166
Period size: 79 Copynumber: 1.9 Consensus size: 75
174452 ATATTATTCA
**
174462 TTATTAAATATATAAAAAATTATATATTTATTAAATAAAAATATAATATCTTATATTATTATAAT
1 TTATTAAATATATAAAAAATTATATATTTATT-AATAAAAATATAATATAATATATT-TTA-AAT
174527 ATAATTGATTATT
63 ATAATTGATTATT
*
174540 TTATTATAATAT-TAAAAATATTATATTATATTATT-ATAAATAT-TAATA-AATATATTTTAAA
1 TTATTA-AATATATAAAAA-ATTATA-TAT-TTATTAATAAAAATATAATATAATATATTTTAAA
174601 TAT
62 TAT
174604 TTTATTAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
75 5 0.09
76 3 0.05
77 6 0.11
78 17 0.30
79 18 0.32
80 3 0.05
81 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (75 bp):
TTATTAAATATATAAAAAATTATATATTTATTAATAAAAATATAATATAATATATTTTAAATATA
ATTGATTATT
Found at i:174879 original size:42 final size:42
Alignment explanation
Indices: 174818--174909 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
174808 TCCCTCCAAC
* *
174818 CAAACACTGGAAAAAATTTTCCGGAAAACGAATTACGTAAAA
1 CAAACACGGGAAAAAATTTTCCGGAAAACGAATTACATAAAA
* *
174860 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
1 CAAACACGGGAAAAAATTTTCCGGAAAACGAATTACATAAAA
174902 CAAACACG
1 CAAACACG
174910 TAATTTCGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.16
Consensus pattern (42 bp):
CAAACACGGGAAAAAATTTTCCGGAAAACGAATTACATAAAA
Found at i:175087 original size:32 final size:32
Alignment explanation
Indices: 175045--175141 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 32
175035 CATATATTTA
*
175045 AATTATTTTATGGTATGTTAATGTCATTTGTG
1 AATTACTTTATGGTATGTTAATGTCATTTGTG
* * *
175077 AATTACTTTATAGCATGTTAATGTAATTTGTG
1 AATTACTTTATGGTATGTTAATGTCATTTGTG
* * * * **
175109 ATTTACTTTAGGGTTTCTTAGCGTCATTTGTG
1 AATTACTTTATGGTATGTTAATGTCATTTGTG
175141 A
1 A
175142 TTCTATGCTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (32 bp):
AATTACTTTATGGTATGTTAATGTCATTTGTG
Found at i:176501 original size:3 final size:3
Alignment explanation
Indices: 176493--176616 Score: 248
Period size: 3 Copynumber: 41.3 Consensus size: 3
176483 TTCCGACACC
176493 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
176541 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
176589 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
176617 ATTTGTGCAT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:178222 original size:62 final size:61
Alignment explanation
Indices: 178097--178235 Score: 140
Period size: 62 Copynumber: 2.2 Consensus size: 61
178087 ACTTTTCCAC
* * *
178097 TTTATTTTAAATTTTTGACATGATGGTTTGTTTGTTTTTATTTTAGTCCTATTTGCATGTTGT
1 TTTATTTT-AATTTTTGACATGATGCTTTGTATGTTTTTATTTTAGTCCTATTAG-ATGTTGT
* *
178160 TTTATTTTAATTTTTG-CATGTTGCTTT-TATGTTATTTCATTTTAGTCACTCATTAG-TTTTGT
1 TTTATTTTAATTTTTGACATGATGCTTTGTATGTT-TTT-ATTTTAGTC-CT-ATTAGATGTTGT
* *
178222 TCTATATTAATTTT
1 TTTATTTTAATTTT
178236 CATGATACCC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
60 5 0.08
61 12 0.18
62 34 0.52
63 10 0.15
64 4 0.06
ACGTcount: A:0.19, C:0.08, G:0.12, T:0.61
Consensus pattern (61 bp):
TTTATTTTAATTTTTGACATGATGCTTTGTATGTTTTTATTTTAGTCCTATTAGATGTTGT
Found at i:178889 original size:131 final size:129
Alignment explanation
Indices: 178655--179022 Score: 441
Period size: 131 Copynumber: 2.8 Consensus size: 129
178645 TTAATTTTGA
* * * * * * *
178655 AAATAGTAATATCTTTTCATTTCAGTTGGAGTAATAAATTATTGGTTTAAGGAACGAGAGGTCTT
1 AAATAGTGATATC-TTTCATTTGA-TTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
* * * *
178720 TTATCCTCGA-TTGCAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGA
64 TTATTCTCGATTTG-AAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTAAAGA
178784 CG
128 CG
* *
178786 AAATAGTGATATCTCTTCATTTGGATTGGAGAAATAAGTGATTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCT-TTCATTT-GATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
* * *
178851 TTATTTTCAATTTGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTAAAGAT
64 TTATTCTCGATTTGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTAAAGAC
178916 G
129 G
** * * * * *
178917 AAATAGTGATATCTTCTCATTTCGATCAGCGTAATAAATGACTACTTTATGGCATTAGAGGTCAT
1 AAATAGTGATATCTT-TCATTT-GATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
* *
178982 TTATTCTCGATTGGAAATAATTAGATATTATTGTTTTCTCT
64 TTATTCTCGATTTGAAATAATTAGATATTATCGTTTTCTCT
179023 TAGAATTATT
Statistics
Matches: 203, Mismatches: 30, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
130 2 0.01
131 197 0.97
132 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (129 bp):
AAATAGTGATATCTTTCATTTGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTT
ATTCTCGATTTGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTAAAGACG
Found at i:189839 original size:1 final size:1
Alignment explanation
Indices: 189833--189915 Score: 58
Period size: 1 Copynumber: 83.0 Consensus size: 1
189823 CTGAAGAAAT
* ** * * * * * * *
189833 AAAAAAATAAAAAATGAAAAAAAATAAAAAAAAATAAAAAAAATATAAAAGAGAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
189898 AAAATAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAA
189916 GAGAATAAAT
Statistics
Matches: 59, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (1 bp):
A
Found at i:189868 original size:35 final size:34
Alignment explanation
Indices: 189829--189929 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 34
189819 TTGCCTGAAG
189829 AAATAAAAAAATAAAAAATGAAAAAAAATAAAAAA
1 AAATAAAAAAATAAAAAA-GAAAAAAAATAAAAAA
* *
189864 AAATAAAAAAAATATAAAAGAGAAAAAATAAAAAA
1 AAAT-AAAAAAATAAAAAAGAAAAAAAATAAAAAA
* * *
189899 AAATAAAAAAA-AGAAAAGAGAATAAATAAAA
1 AAATAAAAAAATAAAAAAGAAAAAAAATAAAA
189930 GAGGGTTCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 18 0.30
34 7 0.11
35 23 0.38
36 13 0.21
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (34 bp):
AAATAAAAAAATAAAAAAGAAAAAAAATAAAAAA
Found at i:189910 original size:9 final size:9
Alignment explanation
Indices: 189829--189929 Score: 84
Period size: 9 Copynumber: 11.2 Consensus size: 9
189819 TTGCCTGAAG
189829 AAAT-AAAA
1 AAATAAAAA
189837 AAAT--AAA
1 AAATAAAAA
189844 AAATGAAAAA
1 AAAT-AAAAA
189854 AAATAAAAAA
1 AAAT-AAAAA
189864 AAATAAAAA
1 AAATAAAAA
*
189873 AAATATAAA
1 AAATAAAAA
* *
189882 AGAGAAAAA
1 AAATAAAAA
*
189891 ATA-AAAAA
1 AAATAAAAA
189899 AAATAAAAA
1 AAATAAAAA
*
189908 AAAGAAAAGA
1 AAATAAAA-A
*
189918 GAATAAATAA
1 AAATAAA-AA
189928 AA
1 AA
189930 GAGGGTTCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
7 7 0.09
8 11 0.14
9 33 0.43
10 24 0.32
11 1 0.01
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (9 bp):
AAATAAAAA
Found at i:189922 original size:19 final size:18
Alignment explanation
Indices: 189830--189931 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 18
189820 TGCCTGAAGA
189830 AATAAAAAAATA-AAAAATG
1 AATAAAAAAA-AGAAAAA-G
189849 AA-AAAAAATAA-AAAAA-
1 AATAAAAAA-AAGAAAAAG
*
189865 AATAAAAAAAATATAAAAG
1 AATAAAAAAAAGA-AAAAG
*
189884 AGA-AAAAATAA-AAAAA-
1 A-ATAAAAAAAAGAAAAAG
189900 AATAAAAAAAAGAAAAGAG
1 AATAAAAAAAAGAAAA-AG
*
189919 AATAAATAAAAGA
1 AATAAAAAAAAGA
189932 GGGTTCAAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
15 1 0.01
16 12 0.17
17 15 0.21
18 18 0.26
19 23 0.33
20 1 0.01
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (18 bp):
AATAAAAAAAAGAAAAAG
Found at i:191454 original size:134 final size:134
Alignment explanation
Indices: 191197--191454 Score: 320
Period size: 134 Copynumber: 1.9 Consensus size: 134
191187 GCAAATCAAA
* * * * *
191197 CTCGATTCAATCTTCCCTGAAGAACAGTTGAATGAATCAATGTCTCCAGATCTGATTTTCCCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAAAGACTACAAATCTGATTTTCCCTGA
* * * * * *
191262 AGAAGCAGTAGAACAGACCCCCTATTTCCAGACTTGATCTTCCCTAAATAGCAGTGGAATTTAGT
66 AGAAGCAGCAGAACAAACCCCCTATTTCCAAACTTGATCTTCACTAAATAACAATGGAATTTAGT
191327 CTGC
131 CTGC
*
191331 CTCGATTCAATCATT-CCTGAAGAATAGTGGAATGAATCAAAGACTACAAATCTGATTTTCCCTG
1 CTCGATTCAATC-TTCCCTGAAGAACAGTGGAATGAATCAAAGACTACAAATCTGATTTTCCCTG
* * * * * * * *
191395 AAGAAGCAGCGGAACAAATCCCCTCTTTCTAAATTTGATCTTCATTGAGTAACAATGGAA
65 AAGAAGCAGCAGAACAAACCCCCTATTTCCAAACTTGATCTTCACTAAATAACAATGGAA
191455 CAAGTCTTCC
Statistics
Matches: 103, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
134 101 0.98
135 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAAAGACTACAAATCTGATTTTCCCTGA
AGAAGCAGCAGAACAAACCCCCTATTTCCAAACTTGATCTTCACTAAATAACAATGGAATTTAGT
CTGC
Found at i:191733 original size:3 final size:3
Alignment explanation
Indices: 191725--191830 Score: 184
Period size: 3 Copynumber: 36.7 Consensus size: 3
191715 TCACAATACC
191725 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
191772 ATT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
191818 ATT ATT ATT -TT AT
1 ATT ATT ATT ATT AT
191831 GCAGGCCTAT
Statistics
Matches: 99, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
2 8 0.08
3 91 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:193125 original size:75 final size:75
Alignment explanation
Indices: 193020--193163 Score: 177
Period size: 75 Copynumber: 1.9 Consensus size: 75
193010 CCATGGTAAG
* * **
193020 GGTATCGATACCAGTAAACATCGAATCTAA-TTTATGTATCGATACCT-AAGGGGGGTATCGGTA
1 GGTATCGATACCAGTAAACATCGAAGCTAATTTTA-GTATCGATA-CTAAAAGGGGGTATCAATA
193083 CCATAACATAGT
64 CCATAACATAGT
* * *
193095 GGTATCGATACCAG-ACTACATTGAAGCTAATTTTAGTATTGATACTAAAAGGGGGTATCAATAC
1 GGTATCGATACCAGTA-AACATCGAAGCTAATTTTAGTATCGATACTAAAAGGGGGTATCAATAC
193159 CATAA
65 CATAA
193164 TAGGGTAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
74 3 0.05
75 52 0.88
76 4 0.07
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (75 bp):
GGTATCGATACCAGTAAACATCGAAGCTAATTTTAGTATCGATACTAAAAGGGGGTATCAATACC
ATAACATAGT
Found at i:193697 original size:45 final size:44
Alignment explanation
Indices: 193646--193953 Score: 316
Period size: 45 Copynumber: 6.9 Consensus size: 44
193636 GAAAGGATGA
* *
193646 TATAGTTGAAATGTATATGGGTACATTATCAACAGAAAATCATAT
1 TATAGTTGAAATGTATATGGGTACATTATCAAAAGAAAAT-ATAC
* * *
193691 TTTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGC
1 TATAGTTGAAATGTATATGGGTACATTATCAAAAGAAAA-TATAC
* * * * * * *
193736 TAGAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTGTGC
1 TATAGTTGAAATGTATATGGGTACATTATCAAAAGAAAA-TATAC
* * * * *
193781 TAGAGTTGAAATGCATATGGGTGCATTATCAAAAGAATAACATGC
1 TATAGTTGAAATGTATATGGGTACATTATCAAAAGAA-AATATAC
* *
193826 T-TGAGTTGAAATGTATATGGGTACATTATCAAAAGAAATGTCTAC
1 TAT-AGTTGAAATGTATATGGGTACATTATCAAAAGAAA-ATATAC
*
193871 TAT-GCTTGAAATGTATATGGGTACATTATCAATAAAAAAATATAC
1 TATAG-TTGAAATGTATATGGGTACATTATCAA-AAGAAAATATAC
* *
193916 TATAGTTGAAAT-TCATATGGGTGCATTATCAATAGAAA
1 TATAGTTGAAATGT-ATATGGGTACATTATCAAAAGAAA
193954 GATGTTATGG
Statistics
Matches: 228, Mismatches: 26, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
44 7 0.03
45 211 0.93
46 10 0.04
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (44 bp):
TATAGTTGAAATGTATATGGGTACATTATCAAAAGAAAATATAC
Found at i:193833 original size:135 final size:135
Alignment explanation
Indices: 193615--193953 Score: 405
Period size: 135 Copynumber: 2.5 Consensus size: 135
193605 ATATTAATTA
* * * * * * *
193615 ATATGGGTGCATTATTAGCATGAAAG-GATGATATAGTTGAAATGTATATGGGTACATTATCAAC
1 ATATGGGTGCATTATCAACATAAAAGTG-TGCTATAGTTGAAATGCATATGGGTGCATTATCAAA
* * * * *
193679 AGAAAATCATATTTTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTA-GAGTT
65 AGAAAATCATACTTGAGTTGAAATGTATATGGGTACATTATCAAAAGAAAAGTATACTATG-CTT
193743 GAAATGC
129 GAAATGC
*
193750 ATATGGGTGCATTATCAACATAAAAGTGTGCTAGAGTTGAAATGCATATGGGTGCATTATCAAAA
1 ATATGGGTGCATTATCAACATAAAAGTGTGCTATAGTTGAAATGCATATGGGTGCATTATCAAAA
* * *
193815 GAATAA-CATGCTTGAGTTGAAATGTATATGGGTACATTATCAAAAGAAATGTCTACTATGCTTG
66 GAA-AATCATACTTGAGTTGAAATGTATATGGGTACATTATCAAAAGAAAAGTATACTATGCTTG
*
193879 AAATGT
130 AAATGC
* * * * * * * *
193885 ATATGGGTACATTATCAATAAAAAAATATACTATAGTTGAAATTCATATGGGTGCATTATCAATA
1 ATATGGGTGCATTATCAACATAAAAGTGTGCTATAGTTGAAATGCATATGGGTGCATTATCAAAA
193950 GAAA
66 GAAA
193954 GATGTTATGG
Statistics
Matches: 175, Mismatches: 26, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
134 1 0.01
135 170 0.97
136 4 0.02
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (135 bp):
ATATGGGTGCATTATCAACATAAAAGTGTGCTATAGTTGAAATGCATATGGGTGCATTATCAAAA
GAAAATCATACTTGAGTTGAAATGTATATGGGTACATTATCAAAAGAAAAGTATACTATGCTTGA
AATGC
Found at i:196124 original size:22 final size:22
Alignment explanation
Indices: 196096--196151 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
196086 TATTCTAGGC
196096 ATGGATTGGTTGTCTTCACATT
1 ATGGATTGGTTGTCTTCACATT
196118 ATGGATTGGTTGTCTTCACATT
1 ATGGATTGGTTGTCTTCACATT
*
196140 ATGGATGGGTTG
1 ATGGATTGGTTG
196152 ATTGTCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.43
Consensus pattern (22 bp):
ATGGATTGGTTGTCTTCACATT
Found at i:200277 original size:22 final size:22
Alignment explanation
Indices: 200246--200339 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
200236 CTGGAAGGGG
*
200246 GTATCAATACCATAATAGGGTA
1 GTATCGATACCATAATAGGGTA
* * *
200268 GTATTGATACTATAGTAGGG--
1 GTATCGATACCATAATAGGGTA
*
200288 GTATCAATACCATAATAGGGTA
1 GTATCGATACCATAATAGGGTA
* *
200310 GTATCGATACTATAGTAGGG--
1 GTATCGATACCATAATAGGGTA
200330 GTATCGATAC
1 GTATCGATAC
200340 TGAAGGGTCA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 26 0.44
22 33 0.56
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATAATAGGGTA
Found at i:200297 original size:42 final size:42
Alignment explanation
Indices: 200243--200339 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
200233 ATACTGGAAG
*
200243 GGGGTATCAATACCATAATAGGGTAGTATTGATACTATAGTA
1 GGGGTATCAATACCATAATAGGGTAGTATCGATACTATAGTA
200285 GGGGTATCAATACCATAATAGGGTAGTATCGATACTATAGTA
1 GGGGTATCAATACCATAATAGGGTAGTATCGATACTATAGTA
*
200327 GGGGTATCGATAC
1 GGGGTATCAATAC
200340 TGAAGGGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (42 bp):
GGGGTATCAATACCATAATAGGGTAGTATCGATACTATAGTA
Found at i:200883 original size:90 final size:88
Alignment explanation
Indices: 200753--201043 Score: 363
Period size: 90 Copynumber: 3.2 Consensus size: 88
200743 AATATTAATT
* * *
200753 CATATGGGTGCATTATTAGCATGAAA-GAATGCTATAGTTGAAATGTATATGGGTACATTATCAA
1 CATATGGGTGCATTATCAACA-GAAATG--TGCTAGAGTTGAAATGTATATGGGTACATTATCAA
200817 CAGAAAAGTATGCTAGAGTTGAAATG
63 CAGAAAAGTATGCTAGAGTTGAAATG
* * *
200843 CATATGGGTGCATTATCAACAGAAAATTGTGCTAGAGTTGAAATGCATATGGGTGCATTATCAAA
1 CATATGGGTGCATTATCAACAG-AAA-TGTGCTAGAGTTGAAATGTATATGGGTACATTATCAAC
* *
200908 AGAAGAGCATGCTAGAGTTGAAATG
64 AGAAAAGTATGCTAGAGTTGAAATG
* * * *
200933 AATATGGGTACATTATCAATAGAAATGTCAACTATG-GTTGAAATGTAT-TGGGTACATTATCAA
1 CATATGGGTGCATTATCAACAGAAATGT--GCTA-GAGTTGAAATGTATATGGGTACATTATCAA
* *
200996 CAGAAAAGTATACTATAGTTGAAATG
63 CAGAAAAGTATGCTAGAGTTGAAATG
201022 CATATGGGTGCATTATCAACAG
1 CATATGGGTGCATTATCAACAG
201044 GAAAGTATAC
Statistics
Matches: 173, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
88 3 0.02
89 58 0.34
90 110 0.64
91 1 0.01
92 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (88 bp):
CATATGGGTGCATTATCAACAGAAATGTGCTAGAGTTGAAATGTATATGGGTACATTATCAACAG
AAAAGTATGCTAGAGTTGAAATG
Found at i:201049 original size:45 final size:45
Alignment explanation
Indices: 200753--201060 Score: 327
Period size: 45 Copynumber: 6.9 Consensus size: 45
200743 AATATTAATT
* * * *
200753 CATATGGGTGCATTATTAGCATGAAAGAATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACAGGAAAGTATGCTATAGTTGAAATG
* * * *
200798 TATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGAAATG
1 CATATGGGTGCATTATCAACAGGAAAGTATGCTATAGTTGAAATG
* * * *
200843 CATATGGGTGCATTATCAACAGAAAATTGTGCTAGAGTTGAAATG
1 CATATGGGTGCATTATCAACAGGAAAGTATGCTATAGTTGAAATG
* * *
200888 CATATGGGTGCATTATCAA-AAGAAGAGCATGCTAGAGTTGAAATG
1 CATATGGGTGCATTATCAACAGGAA-AGTATGCTATAGTTGAAATG
* * * * *
200933 AATATGGGTACATTATCAATA-GAAATGTCA-ACTATGGTTGAAATG
1 CATATGGGTGCATTATCAACAGGAAA-GT-ATGCTATAGTTGAAATG
* * * *
200978 TAT-TGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATG
1 CATATGGGTGCATTATCAACAGGAAAGTATGCTATAGTTGAAATG
* *
201022 CATATGGGTGCATTATCAACAGGAAAGTATACTCTAGTT
1 CATATGGGTGCATTATCAACAGGAAAGTATGCTATAGTT
201061 ACCTTAGAGT
Statistics
Matches: 225, Mismatches: 31, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
43 1 0.00
44 38 0.17
45 184 0.82
46 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (45 bp):
CATATGGGTGCATTATCAACAGGAAAGTATGCTATAGTTGAAATG
Found at i:202085 original size:62 final size:63
Alignment explanation
Indices: 201954--202092 Score: 162
Period size: 62 Copynumber: 2.2 Consensus size: 63
201944 ATTAAAAATG
* *
201954 TTCATTTTAGTCACTTTTGCACTTTATTTTGTTTTAATTTTTGACATGATGATTTGTTTGTTT
1 TTCATTTTAGTCACTTTTGCACTTTATTTTATTTTAATTTTTGACATGATGATTTGTATGTTT
* * * *
202017 AT-ATTTTAGTC-CTATTTGCA-TGTTGTTTTATTTTAATTTTTG-CATGTTGCTTT-TATGTTA
1 TTCATTTTAGTCACT-TTTGCACT-TTATTTTATTTTAATTTTTGACATGATGATTTGTATGTT-
202077 T
63 T
202078 TTCATTTTAGTCACT
1 TTCATTTTAGTCACT
202093 AATTAATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
60 5 0.08
61 14 0.22
62 42 0.66
63 3 0.05
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.60
Consensus pattern (63 bp):
TTCATTTTAGTCACTTTTGCACTTTATTTTATTTTAATTTTTGACATGATGATTTGTATGTTT
Found at i:202767 original size:131 final size:130
Alignment explanation
Indices: 202531--202900 Score: 445
Period size: 131 Copynumber: 2.8 Consensus size: 130
202521 ATTAATTTTG
* * * * * * * *
202531 AAAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGACTTCATTAAGACACGAGAGATCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCA
* * * * * *
202596 TTTATCCTCGATTGAAAATAATTAGATATTATTGTATTCTCTCGCATCAATATTGATTTTTAAAA
66 TTTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGA-ATTTAAAA
202661 C
130 C
* *
202662 AAAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAGTGACTACTTTAAGGCATGCA-AGGTC
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATG-AGAGGTC
* * * *
202726 ATTTATTCTAAATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGAATTTAAGA
65 ATTTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTAAAA
202791 C
130 C
** * * * *
202792 AAAATAGTGATATCTCTTCATTTCGATCAGAGTAATAAATTATTGCTTTTAAGGCATGAGATGTC
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTAC-TTTAAGGCATGAGAGGTC
* * *
202857 ATTTATTCTCAGTTGTAAATAATTAGATATTATCGTTTTATCTC
65 ATTTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTC
202901 TTAAAATTAT
Statistics
Matches: 203, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
130 47 0.23
131 155 0.76
132 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (130 bp):
AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCA
TTTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTAAAAC
Found at i:204512 original size:13 final size:13
Alignment explanation
Indices: 204494--204532 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
204484 TCCTCAAACC
204494 TTTTTTTAAAAGG
1 TTTTTTTAAAAGG
204507 TTTTTTTAAAAGG
1 TTTTTTTAAAAGG
204520 TTTTTTTAAAAGG
1 TTTTTTTAAAAGG
204533 AAAGATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTTTTTAAAAGG
Found at i:205049 original size:18 final size:18
Alignment explanation
Indices: 205015--205078 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
205005 TGTACTTAGG
205015 TAAAT-TTTAATTCATAAT
1 TAAATATTTAATT-ATAAT
205033 TAAATATTTAATTATAAT
1 TAAATATTTAATTATAAT
* * *
205051 GAATTAGTTTATTTA-AAT
1 TAAATA-TTTAATTATAAT
205069 TAAATTATTT
1 TAAA-TATTT
205079 TTATACAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 22 0.58
19 16 0.42
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (18 bp):
TAAATATTTAATTATAAT
Found at i:208214 original size:3 final size:3
Alignment explanation
Indices: 208206--208239 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
208196 CATAAATTTG
*
208206 TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
208240 TTTTTTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:209079 original size:136 final size:136
Alignment explanation
Indices: 208605--209090 Score: 657
Period size: 136 Copynumber: 3.6 Consensus size: 136
208595 GACTTGAAAG
* ** *
208605 GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CCT-T-TAAGACGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* ** ** *
208665 CTT--TTGGAAATATCAATCCCTCTAA-CAAGGCATCACTGATTCAAAATATCGTGAATCGAGTG
66 CTTCACTGGAAATATTGATCCCTC-AAGCAAGGTGTCACTGATTCGAAATATCGTGAATCGAGTG
208727 ATAGGTC
130 ATAGGTC
208734 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * ** *
208799 CTCCATTGGAAATACTGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTTCACTGGAAATATTGATCCCTCAAGCAAGGTGTCACTGATTCGAAATATCGTGAATCGAGTGA
208864 TAGGTC
131 TAGGTC
* *
208870 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTGTCGGATAAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* *
208935 CTTCACTGGAAATGTTGATCCCTCAAGCAAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGA
66 CTTCACTGGAAATATTGATCCCTCAAGCAAGGTGTCACTGATTCGAAATATCGTGAATCGAGTGA
209000 TAGGTC
131 TAGGTC
* * * *
209006 AAACAAGCTCTTCTCATTATGAACTTCATCTCCCTCTATTGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* *
209071 -TTGTACTGGAAATGTTGATC
66 CTT-CACTGGAAATATTGATC
209091 TGTTTATCTT
Statistics
Matches: 317, Mismatches: 31, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
129 23 0.07
130 1 0.00
131 4 0.01
132 3 0.01
133 1 0.00
134 26 0.08
135 4 0.01
136 255 0.80
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTTCACTGGAAATATTGATCCCTCAAGCAAGGTGTCACTGATTCGAAATATCGTGAATCGAGTGA
TAGGTC
Found at i:209473 original size:76 final size:72
Alignment explanation
Indices: 209393--209543 Score: 176
Period size: 76 Copynumber: 2.0 Consensus size: 72
209383 ATCTCAAGTA
* * * ** *
209393 AGACGAAGTAAGTTTTAAGAAAAACTATCTCAAGTGAGATTCAATTTCTTGTTTCAAGGGAAAGT
1 AGACGAAGTAAGTTTTAAGAAAAACCATATCAAGGGAGA--CAAAAT-TTGTTTCAAGGGAAA-C
*
209458 TGTCTTAAGCG
62 TGTCTAAAGCG
* **
209469 AGACGAATTTGGTTTTAAGAAAAACCATATCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
1 AGACGAAGTAAGTTTTAAGAAAAACCATATCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
209534 TAAAGCG
66 TAAAGCG
209541 AGA
1 AGA
209544 TAAAATCTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 13 0.20
73 15 0.23
74 4 0.06
76 33 0.51
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (72 bp):
AGACGAAGTAAGTTTTAAGAAAAACCATATCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
TAAAGCG
Found at i:209560 original size:39 final size:40
Alignment explanation
Indices: 209515--209633 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 40
209505 AGACAAAATT
* **
209515 TGTTTCAAGG-GAAACTGTCTAAAGCGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTAAAGCGAGATAAAATCTTC
** *
209554 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTAAAGCGAGATAAAATCTTC
** *
209594 TGTTTCAAGGAAAAACAATCTCGAGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTAAAGCGAGATAAAATCTTC
209634 CGTATTAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 10 0.14
40 62 0.86
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (40 bp):
TGTTTCAAGGAAAAACAATCTAAAGCGAGATAAAATCTTC
Found at i:209573 original size:23 final size:23
Alignment explanation
Indices: 209547--209614 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
209537 AGCGAGATAA
209547 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
** * *
209570 AATC-T-TGAGT-GA-G-ATAA-
1 AATCTTCTGTTTCAAGGAAAAAC
209587 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
209610 AATCT
1 AATCT
209615 CGAGTGAGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 12
0.61 0.16 0.24
Matches are distributed among these distances:
17 4 0.13
18 4 0.13
19 4 0.13
20 2 0.06
21 4 0.13
22 4 0.13
23 9 0.29
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:209589 original size:40 final size:40
Alignment explanation
Indices: 209540--209633 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
209530 TGTCTAAAGC
*
209540 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTCGAGT
209580 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTCGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTCGAGT
209620 GAGATAAAATCTTC
1 GAGATAAAATCTTC
209634 CGTATTAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTCGAGT
Found at i:211874 original size:9 final size:9
Alignment explanation
Indices: 211860--211924 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
211850 TCTTGTTTTG
211860 TTTTTTCTT
1 TTTTTTCTT
211869 TTTTTTACTT
1 TTTTTT-CTT
*
211879 TTTTTGCTT
1 TTTTTTCTT
211888 TTTGTTT-TT
1 TTT-TTTCTT
211897 TTTGTTT-TT
1 TTT-TTTCTT
* *
211906 TGTTTACTT
1 TTTTTTCTT
211915 TTTTTT-TT
1 TTTTTTCTT
211923 TT
1 TT
211925 ACAAAATATC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 6 0.13
9 31 0.66
10 10 0.21
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:211880 original size:16 final size:18
Alignment explanation
Indices: 211860--211917 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 18
211850 TCTTGTTTTG
*
211860 TTTTTTCTTTTT-TTTAC
1 TTTTTGCTTTTTGTTTAC
211877 TTTTTTTGCTTTTTGTTT--
1 --TTTTTGCTTTTTGTTTAC
*
211895 TTTTTGTTTTTTGTTTAC
1 TTTTTGCTTTTTGTTTAC
211913 TTTTT
1 TTTTT
211918 TTTTTTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 15 0.44
18 5 0.15
19 11 0.32
20 3 0.09
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (18 bp):
TTTTTGCTTTTTGTTTAC
Found at i:211884 original size:25 final size:25
Alignment explanation
Indices: 211855--211926 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
211845 CTTCTTCTTG
*
211855 TTTTGTTTTTTCTTTTTTTTACTTT
1 TTTTGTTTTTTCTTTTTTTTACGTT
* *
211880 TTTTGCTTTTTGTTTTTTTT--GTT
1 TTTTGTTTTTTCTTTTTTTTACGTT
*
211903 TTTTGTTTACTTTTTTTTTTTTAC
1 TTTTGTTT--TTTCTTTTTTTTAC
211927 AAAATATCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.24
25 29 0.76
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.82
Consensus pattern (25 bp):
TTTTGTTTTTTCTTTTTTTTACGTT
Found at i:211920 original size:16 final size:16
Alignment explanation
Indices: 211841--211922 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
211831 ACATCTGATC
*
211841 TTTGCTTCTTCTTGTTT
1 TTTGTTTCTT-TTGTTT
*
211858 TGTTTTTTC-TTT-TTT
1 T-TTGTTTCTTTTGTTT
** *
211873 TTACTTT-TTTTGCTT
1 TTTGTTTCTTTTGTTT
*
211888 TTTGTTTTTTTTGTTT
1 TTTGTTTCTTTTGTTT
211904 TTTGTTTACTTTT-TTT
1 TTTGTTT-CTTTTGTTT
211920 TTT
1 TTT
211923 TTACAAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
14 7 0.14
15 11 0.22
16 22 0.43
17 6 0.12
18 5 0.10
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (16 bp):
TTTGTTTCTTTTGTTT
Found at i:213408 original size:2 final size:2
Alignment explanation
Indices: 213401--213442 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
213391 ACAACAAGGG
*
213401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
213443 GGATAAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213936 original size:15 final size:15
Alignment explanation
Indices: 213916--213945 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
213906 AATTAAAAGA
213916 ATCCTTAATTCATTC
1 ATCCTTAATTCATTC
213931 ATCCTTAATTCATTC
1 ATCCTTAATTCATTC
213946 TATATTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
ATCCTTAATTCATTC
Found at i:218150 original size:3 final size:3
Alignment explanation
Indices: 218142--218168 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
218132 CATAAATTTG
218142 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
218169 AATAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:218173 original size:3 final size:3
Alignment explanation
Indices: 218167--218193 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
218157 TATTATTATT
218167 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
218194 TTTTTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:218488 original size:24 final size:24
Alignment explanation
Indices: 218449--218538 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
218439 CGTTCGATTA
* *
218449 TATGTTCGTTTCTGTTCATTCATT
1 TATGTTCATTTATGTTCATTCATT
*
218473 TATGTTCATTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCATTCATT
* *
218497 TATGTTCATTTATG-TCTGTTTATT
1 TATGTTCATTTATGTTC-ATTCATT
*
218521 TATGTTCATTTATCTTCA
1 TATGTTCATTTATGTTCA
218539 AACAGAGGGC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (24 bp):
TATGTTCATTTATGTTCATTCATT
Found at i:218516 original size:14 final size:13
Alignment explanation
Indices: 218461--218526 Score: 57
Period size: 14 Copynumber: 5.1 Consensus size: 13
218451 TGTTCGTTTC
* *
218461 TGTTCATTCATTT
1 TGTTCATTTATGT
218474 ATGTTCATTTATGT
1 -TGTTCATTTATGT
218488 TCGTTCATTTA---
1 T-GTTCATTTATGT
218499 TGTTCATTTATGT
1 TGTTCATTTATGT
*
218512 CTGTTTATTTATGT
1 -TGTTCATTTATGT
218526 T
1 T
218527 CATTTATCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
10 9 0.20
11 1 0.02
13 2 0.05
14 32 0.73
ACGTcount: A:0.17, C:0.11, G:0.12, T:0.61
Consensus pattern (13 bp):
TGTTCATTTATGT
Found at i:218533 original size:10 final size:10
Alignment explanation
Indices: 218467--218511 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
218457 TTTCTGTTCA
218467 TTCATTTATG
1 TTCATTTATG
218477 TTCATTTATGTTCG
1 TTCATTTA---T-G
218491 TTCATTTATG
1 TTCATTTATG
218501 TTCATTTATG
1 TTCATTTATG
218511 T
1 T
218512 CTGTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
13 1 0.03
14 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (10 bp):
TTCATTTATG
Found at i:218935 original size:16 final size:16
Alignment explanation
Indices: 218914--218946 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
218904 AAAAAAAATT
218914 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
218930 TGTTCGTTTTTGTTCG
1 TGTTCGTTTATGTTCG
218946 T
1 T
218947 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:220363 original size:2 final size:2
Alignment explanation
Indices: 220356--220393 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
220346 CAAAATAGCA
220356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
220394 TTAAACTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220881 original size:25 final size:23
Alignment explanation
Indices: 220852--220897 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
220842 CGTATAGTAT
220852 AATATAATATGCACAACATGGGTG
1 AATA-AATATGCACAACATGGGTG
220876 ---AAATATGCACAACATGGGTG
1 AATAAATATGCACAACATGGGTG
220896 AA
1 AA
220898 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (23 bp):
AATAAATATGCACAACATGGGTG
Found at i:220882 original size:20 final size:20
Alignment explanation
Indices: 220857--220899 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
220847 AGTATAATAT
220857 AATATGCACAACATGGGTGA
1 AATATGCACAACATGGGTGA
220877 AATATGCACAACATGGGTGA
1 AATATGCACAACATGGGTGA
220897 AAT
1 AAT
220900 TTAAATATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (20 bp):
AATATGCACAACATGGGTGA
Found at i:221207 original size:15 final size:15
Alignment explanation
Indices: 221187--221219 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
221177 TAGTGTGACT
221187 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
221202 AAAATAAAATACTTA
1 AAAATAAAATACTTA
221217 AAA
1 AAA
221220 CAAAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:222542 original size:42 final size:42
Alignment explanation
Indices: 222483--222644 Score: 216
Period size: 43 Copynumber: 3.8 Consensus size: 42
222473 AATTGTCACT
* *
222483 AAGGAACCCCTATATATCACGTTGGTCCCTCAAGTGTTCATC
1 AAGGAACCCCTACATATCACGTTGGTCCCTCAAGTTTTCATC
* *
222525 AAGGAACCCCTACATATCACGTTGGTTCCTCATGTTTGTCATC
1 AAGGAACCCCTACATATCACGTTGGTCCCTCAAGTTT-TCATC
* * *
222568 AATGAACCCCTACATATCACGCTGGTTCCTCAAGCTTTTCATC
1 AAGGAACCCCTACATATCACGTTGGTCCCTCAAG-TTTTCATC
* * *
222611 AAGAAACCCCTACATATCACGATGGTCCTTCAAG
1 AAGGAACCCCTACATATCACGTTGGTCCCTCAAG
222645 CTTAGTTTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
42 33 0.31
43 70 0.66
44 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (42 bp):
AAGGAACCCCTACATATCACGTTGGTCCCTCAAGTTTTCATC
Found at i:222720 original size:39 final size:39
Alignment explanation
Indices: 222659--222867 Score: 242
Period size: 39 Copynumber: 5.3 Consensus size: 39
222649 GTTTCTTATT
* * *
222659 AAATCTTTTGTTTCGAAAGAAACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTTGAAGGAAACTATCTCAAGCGAGACA
*
222698 AAATCTTCTGTTTTGAAGGAAACTATCTCAAGAGAGACA
1 AAATCTTCTGTTTTGAAGGAAACTATCTCAAGCGAGACA
* * *
222737 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCAAGACA
1 AAATCTTCTGTTTTGAAGGAAACTATCTCAAGCGAGACA
* *
222776 AAATCTTTCTG-TTTCAAGGGAAACTATCTCAAGCGAGATA
1 AAATC-TTCTGTTTTGAA-GGAAACTATCTCAAGCGAGACA
* * * *
222816 AAATCTTTTG-TTTCAAGGAAAATTATCTCAAGCGAGATA
1 AAATCTTCTGTTTTGAAGG-AAACTATCTCAAGCGAGACA
* *
222855 AAATATTTTGTTT
1 AAATCTTCTGTTT
222868 CAAGAAAAAA
Statistics
Matches: 150, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
38 2 0.01
39 116 0.77
40 32 0.21
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (39 bp):
AAATCTTCTGTTTTGAAGGAAACTATCTCAAGCGAGACA
Found at i:222828 original size:79 final size:79
Alignment explanation
Indices: 222659--222871 Score: 288
Period size: 79 Copynumber: 2.7 Consensus size: 79
222649 GTTTCTTATT
** *
222659 AAATCTTTTGTTTCGAAAGAAACTATCTCAAGCGAGACAAAATC-TTCTGTTTTGAA-GGAAACT
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTTCTG-TTTCAAGGGAAACT
222722 ATCTCAAGAGAGACA
65 ATCTCAAGAGAGACA
* *
222737 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCAAGACAAAATCTTTCTGTTTCAAGGGAAACTA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTTCTGTTTCAAGGGAAACTA
* *
222802 TCTCAAGCGAGATA
66 TCTCAAGAGAGACA
* * * * *
222816 AAATCTTTTGTTTCAAGGAAAATTATCTCAAGCGAGATAAAATATTT-TGTTTCAAG
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTTCTGTTTCAAG
222872 AAAAAACAAC
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
78 54 0.45
79 65 0.55
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (79 bp):
AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTTCTGTTTCAAGGGAAACTA
TCTCAAGAGAGACA
Found at i:222932 original size:40 final size:40
Alignment explanation
Indices: 222692--223259 Score: 571
Period size: 40 Copynumber: 14.3 Consensus size: 40
222682 TATCTCAAGC
* * * ** *
222692 GAGACAAAATCTTCTGTTTTGAAGG--AAACTATCTCAAGA
1 GAGATAAAATCTTCTG-TTTCAAGGAAAAACAATCTTGAGT
* * * * ** *
222731 GAGACAAAATCTTCTGTTTCGAGG-GAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * * * ** *
222770 AAGACAAAATCTTTCTGTTTCAAGG-GAAACTATCTCAAGC
1 GAGATAAAATC-TTCTGTTTCAAGGAAAAACAATCTTGAGT
* ** ** *
222810 GAGATAAAATCTTTTGTTTCAAGG-AAAATTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * * **
222849 GAGATAAAATATTTTGTTTCAAGAAAAAACAA-CTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
222888 GAGATAAAATCTTCAGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
222928 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * **
222968 GAG-TTAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
223007 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
223047 GAGATAAAATCTTCTGTTTCAAGGAAAAAAAAAATCTTAAAT
1 GAGATAAAATCTTCTGTTTCAAGG--AAAAACAATCTTGAGT
* * **
223089 GAGATAAAATCTTCTGTTTTAAGTG--AAA-TATCTCAAGT
1 GAGATAAAATCTTCTGTTTCAAG-GAAAAACAATCTTGAGT
* * *
223127 GAGATAAAATCTTTTGTTACAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
223167 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTTAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
223207 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
223247 GAAATAAAATCTT
1 GAGATAAAATCTT
223260 TCTTTTCTTT
Statistics
Matches: 463, Mismatches: 55, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
37 1 0.00
38 33 0.07
39 158 0.34
40 235 0.51
42 35 0.08
43 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:223200 original size:23 final size:23
Alignment explanation
Indices: 223174--223242 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
223164 AATGAGATAA
223174 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
* *
223197 AATCTT-TAG--T-GA-G-ATAA-
1 AATCTTCT-GTTTCAAGGAAAAAC
223214 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
223237 AATCTT
1 AATCTT
223243 GAATGAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 2 0.06
20 2 0.06
21 2 0.06
22 4 0.12
23 13 0.38
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:223273 original size:10 final size:9
Alignment explanation
Indices: 223258--223366 Score: 106
Period size: 10 Copynumber: 12.3 Consensus size: 9
223248 AAATAAAATC
223258 TTTCTTTTCT
1 TTTCTTTT-T
223268 TTTC--TTT
1 TTTCTTTTT
223275 TTTC-TTTT
1 TTTCTTTTT
223283 TTTCTTCTTT
1 TTTCTT-TTT
223293 TTTCTTTTT
1 TTTCTTTTT
*
223302 CTTT-TTTTC
1 -TTTCTTTTT
223311 TTTCTTTTT
1 TTTCTTTTT
223320 TTTC--TTT
1 TTTCTTTTT
*
223327 TCTC-TTTT
1 TTTCTTTTT
223335 TTTCTTTTT
1 TTTCTTTTT
223344 TTTCTCTTTT
1 TTTCT-TTTT
223354 TTTCCTTTTT
1 TTT-CTTTTT
223364 TTT
1 TTT
223367 TCTCTGATGG
Statistics
Matches: 86, Mismatches: 4, Indels: 18
0.80 0.04 0.17
Matches are distributed among these distances:
7 11 0.13
8 18 0.21
9 25 0.29
10 30 0.35
11 2 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:223283 original size:1 final size:1
Alignment explanation
Indices: 223262--223367 Score: 59
Period size: 1 Copynumber: 106.0 Consensus size: 1
223252 AAAATCTTTC
* * * * * * * * * *
223262 TTTTCTTTTCTTTTTTCTTTTTTTCTTCTTTTTTCTTTTTCTTTTTTTCTTTCTTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * **
223327 TCTCTTTTTTTCTTTTTTTTCTCTTTTTTTCCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
223368 CTCTGATGGA
Statistics
Matches: 73, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:223292 original size:28 final size:27
Alignment explanation
Indices: 223259--223369 Score: 133
Period size: 28 Copynumber: 4.1 Consensus size: 27
223249 AATAAAATCT
223259 TTCTTTTCTTTTCTTTTTTCTTTTTTTC
1 TTCTTTT-TTTTCTTTTTTCTTTTTTTC
223287 TTC--TTTTTTC-TTTTTCTTTTTTTC
1 TTCTTTTTTTTCTTTTTTCTTTTTTTC
*
223311 TTTCTTTTTTTTCTTTTCTCTTTTTTTC
1 -TTCTTTTTTTTCTTTTTTCTTTTTTTC
*
223339 TT-TTTTTTCTCTTTTTTTCCTTTTTTT-
1 TTCTTTTTTTTC-TTTTTT-CTTTTTTTC
223366 TTCT
1 TTCT
223370 CTGATGGATG
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
24 14 0.19
25 8 0.11
26 10 0.14
27 16 0.22
28 25 0.34
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (27 bp):
TTCTTTTTTTTCTTTTTTCTTTTTTTC
Found at i:223300 original size:24 final size:24
Alignment explanation
Indices: 223258--223369 Score: 115
Period size: 24 Copynumber: 4.6 Consensus size: 24
223248 AAATAAAATC
223258 TTTCTT-TTCTTTTCTTTTTTCTTTT
1 TTTCTTCTT-TTTTC-TTTTTCTTTT
223283 TTTCTTCTTTTTTCTTTTTCTTTT
1 TTTCTTCTTTTTTCTTTTTCTTTT
* *
223307 TTTCTTTCTTTTTTTTCTTTTCTCTT
1 TTTC-TTCTTTTTTCT-TTTTCTTTT
*
223333 TTT-TTC-TTTTT-TTTCTCTTTT
1 TTTCTTCTTTTTTCTTTTTCTTTT
*
223354 TTTCCTTTTTTTTTCT
1 TTT-CTTCTTTTTTCT
223370 CTGATGGATG
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
21 10 0.13
22 1 0.01
23 7 0.09
24 22 0.29
25 22 0.29
26 13 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTCTTCTTTTTTCTTTTTCTTTT
Found at i:223370 original size:21 final size:20
Alignment explanation
Indices: 223272--223371 Score: 111
Period size: 19 Copynumber: 5.0 Consensus size: 20
223262 TTTTCTTTTC
223272 TTTTTTCTTTTTTTCTTCT-T
1 TTTTTTCTTTTTTT-TTCTCT
223292 TTTTCTT-TTTCTTTTTT-TCT
1 TTTT-TTCTTT-TTTTTTCTCT
*
223312 TTCTTTT-TTTTCTTTTCTCT
1 TT-TTTTCTTTTTTTTTCTCT
223332 TTTTTTC-TTTTTTTTCTCT
1 TTTTTTCTTTTTTTTTCTCT
223351 TTTTTTCCTTTTTTTTTCTCT
1 TTTTTT-CTTTTTTTTTCTCT
223372 GATGGATGAG
Statistics
Matches: 70, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
19 27 0.39
20 23 0.33
21 20 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTCTCT
Found at i:226226 original size:37 final size:37
Alignment explanation
Indices: 226174--226252 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
226164 TTTAAAGGAA
*
226174 GTCTTCAATCGGCTTTAGATTTCTTCATTCA-TCGGAT
1 GTCTTCAATCAGCTTTAGATTTCTTCATTCACT-GGAT
*
226211 GTCTTCTATCAGCTTTAGATTTCTTCATTCACTGGAT
1 GTCTTCAATCAGCTTTAGATTTCTTCATTCACTGGAT
226248 GTCTT
1 GTCTT
226253 TCTTAATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 38 0.97
38 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.46
Consensus pattern (37 bp):
GTCTTCAATCAGCTTTAGATTTCTTCATTCACTGGAT
Found at i:227585 original size:16 final size:18
Alignment explanation
Indices: 227564--227603 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
227554 AGCAACTTTT
227564 AAAAACA-ATTTTAAGA-
1 AAAAACATATTTTAAGAC
*
227580 AAAAACATTTTTTAAGAC
1 AAAAACATATTTTAAGAC
227598 AAAAAC
1 AAAAAC
227604 TGGTATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAAACATATTTTAAGAC
Found at i:227883 original size:2 final size:2
Alignment explanation
Indices: 227876--227961 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
227866 ATATCAATAA
227876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227960 AT
1 AT
227962 TTAAACTTAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228026 original size:22 final size:22
Alignment explanation
Indices: 227978--228019 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
227968 TTATAAAGAC
*
227978 CAAAATAAAAAACATTAGGAAT
1 CAAAATAAAAAACATTAGAAAT
*
228000 CAAAATAACAAA-ATTAGAAA
1 CAAAATAAAAAACATTAGAAA
228020 ATTAAAAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (22 bp):
CAAAATAAAAAACATTAGAAAT
Found at i:228443 original size:25 final size:23
Alignment explanation
Indices: 228414--228459 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
228404 CGTATAGTAT
228414 AATATAATATGCACAACATGGGTG
1 AATA-AATATGCACAACATGGGTG
228438 ---AAATATGCACAACATGGGTG
1 AATAAATATGCACAACATGGGTG
228458 AA
1 AA
228460 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (23 bp):
AATAAATATGCACAACATGGGTG
Found at i:228444 original size:20 final size:20
Alignment explanation
Indices: 228419--228461 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
228409 AGTATAATAT
228419 AATATGCACAACATGGGTGA
1 AATATGCACAACATGGGTGA
228439 AATATGCACAACATGGGTGA
1 AATATGCACAACATGGGTGA
228459 AAT
1 AAT
228462 TTAAATATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (20 bp):
AATATGCACAACATGGGTGA
Found at i:228769 original size:15 final size:15
Alignment explanation
Indices: 228749--228781 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
228739 TAGTGTGACT
228749 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
228764 AAAATAAAATACTTA
1 AAAATAAAATACTTA
228779 AAA
1 AAA
228782 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:230423 original size:89 final size:89
Alignment explanation
Indices: 230272--230490 Score: 327
Period size: 89 Copynumber: 2.5 Consensus size: 89
230262 ATGTTGAAAG
* ***
230272 CATCTTGC-CCGAAGGTCTTAT-GATGGATTGAAGGACTTAAAAAAATCAAGAAACCTCGAAGGC
1 CATCTTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTT--AAAAATCAAGAAACCTCGAAGGC
230335 TCAGTTTCTTAGATCTCAATTAAAAA
64 TCAGTTTCTTAGATCTCAATTAAAAA
230361 CATCTTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAACCAT-GAAGGCT
1 CATCTTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAACC-TCGAAGGCT
* *
230425 CAGTTTCTTAGATCTCATTTGAAAA
65 CAGTTTCTTAGATCTCAATTAAAAA
*
230450 CATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTA
1 CATCTTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTA
230491 TCATCTTGCT
Statistics
Matches: 120, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
89 93 0.77
90 13 0.11
91 14 0.12
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (89 bp):
CATCTTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAACCTCGAAGGCTC
AGTTTCTTAGATCTCAATTAAAAA
Found at i:230580 original size:42 final size:41
Alignment explanation
Indices: 230467--230580 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
230457 CACTGAAGGT
* * *
230467 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* *
230508 CTTATAGATGGCCCGAAGAACTTACGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTA-TCATCATGCTCGAAAGA
* *
230550 CTTACT-GATGGCCCAAAGGACTCATTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
230581 AGAAACTCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 22 0.36
42 38 0.62
43 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:230864 original size:43 final size:43
Alignment explanation
Indices: 230625--230872 Score: 274
Period size: 43 Copynumber: 5.8 Consensus size: 43
230615 TGTCACTAAG
* * *
230625 GAACCCCTACATATCACGTTGGTCCCTCAAG--TGTTCATCAAG
1 GAACCCCTACATATCACGATGGTCCTTCAAGCTTG-TCATCAAA
* * *
230667 GAACCCCTACATATCACGTTGGTTCC-TCAAGTTTGTCATCAAT
1 GAACCCCTACATATCACGATGG-TCCTTCAAGCTTGTCATCAAA
* * * * *
230710 GAAACCGTACATATCACGCTGGTTCCTT-AGGCTTTTCATC-AA
1 GAACCCCTACATATCACGATGG-TCCTTCAAGCTTGTCATCAAA
*
230752 GAAACCCCTACATATCACGATGGT-TTCTCAAGCTTGTCATCAAA
1 G-AACCCCTACATATCACGATGGTCCT-TCAAGCTTGTCATCAAA
* *
230796 GAACCCCTACATGTCACGATGGTCCTTTAAGCTTGTCATCAAA
1 GAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAA
*
230839 GAACCCCTACATATCACGATAGTCCTTCAAGCTT
1 GAACCCCTACATATCACGATGGTCCTTCAAGCTT
230873 AGTTTCTTAT
Statistics
Matches: 177, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.01
42 31 0.18
43 138 0.78
44 7 0.04
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (43 bp):
GAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAA
Found at i:231134 original size:40 final size:40
Alignment explanation
Indices: 231035--231589 Score: 753
Period size: 40 Copynumber: 13.9 Consensus size: 40
231025 TATCTCAAGC
* * ** * *
231035 GAGATAAAATATTTTGTTTCAAGG-AAAATTATC-TCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAA-T
* * *
231074 GAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
231114 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
231154 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
231194 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
231234 GAGATAAAATCTTCTGTTTCAAGGAAAACCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
231274 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* * *
231314 GAGATAAAATCTTCTGTTTCAAGTG--AAA-TATC-TCAAGC
1 GAGATAAAATCTTCTGTTTCAAG-GAAAAACAATCTTGAA-T
* *
231352 GAGATAAAATCTTTTGTTACAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* * *
231392 GAGATAAAATCTTATGTTTTAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* * *
231432 GAGATAAAATCTTATGTTTTAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
231472 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
231512 GAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* * *
231552 GAAATAAAATATTATGTTTCAAGGAAAAACAATCTTGA
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGA
231590 GTCAAATGAA
Statistics
Matches: 471, Mismatches: 37, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
37 4 0.01
38 24 0.05
39 30 0.06
40 406 0.86
41 7 0.01
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
Found at i:231425 original size:23 final size:23
Alignment explanation
Indices: 231399--231467 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
231389 AATGAGATAA
231399 AATCTTATGTTTTAAGGAAAAAC
1 AATCTTATGTTTTAAGGAAAAAC
* *
231422 AATCTTGA-G---TGA-G-ATAA-
1 AATCTT-ATGTTTTAAGGAAAAAC
231439 AATCTTATGTTTTAAGGAAAAAC
1 AATCTTATGTTTTAAGGAAAAAC
231462 AATCTT
1 AATCTT
231468 GAGTGAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
16 1 0.03
17 7 0.21
18 3 0.09
19 1 0.03
20 4 0.12
21 1 0.03
22 3 0.09
23 13 0.38
24 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (23 bp):
AATCTTATGTTTTAAGGAAAAAC
Found at i:234511 original size:13 final size:12
Alignment explanation
Indices: 234497--234572 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 12
234487 TTCAATTTCA
234497 TTTTTTTTCTTC
1 TTTTTTTTCTTC
*
234509 ATTTTTCTTTATT-
1 -TTTTT-TTTCTTC
*
234522 TTCTTTCTT-TTC
1 TT-TTTTTTCTTC
*
234534 TTTCTTTTC-TC
1 TTTTTTTTCTTC
234545 TTTTTTTT-TTC
1 TTTTTTTTCTTC
234556 TTTTTTTTCTT-
1 TTTTTTTTCTTC
234567 TTTTTT
1 TTTTTT
234573 CCTTTTTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
11 31 0.60
12 8 0.15
13 8 0.15
14 5 0.10
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:234523 original size:9 final size:8
Alignment explanation
Indices: 234498--234583 Score: 77
Period size: 9 Copynumber: 10.1 Consensus size: 8
234488 TCAATTTCAT
234498 TTTTTTTC
1 TTTTTTTC
234506 TTCATTTTTC
1 TT--TTTTTC
234516 TTTATTTTC
1 TTT-TTTTC
234525 TTTCTTTTC
1 TTT-TTTTC
234534 TTTCTTTTC
1 TTT-TTTTC
*
234543 TCTTTTT-
1 TTTTTTTC
*
234550 TTTTTCT-
1 TTTTTTTC
234557 TTTTTTTC
1 TTTTTTTC
234565 TTTTTTTTCC
1 -TTTTTTT-C
234575 TTTTTTTC
1 TTTTTTTC
234583 T
1 T
234584 CTGATGGATG
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
7 11 0.16
8 9 0.13
9 38 0.57
10 9 0.13
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:234558 original size:31 final size:30
Alignment explanation
Indices: 234520--234581 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
234510 TTTTTCTTTA
234520 TTTTCTTTCTTTTCTTTCTTTTCTCTTTTTT
1 TTTTCTTTCTTTTCTTTCTTTTC-CTTTTTT
* *
234551 TTTTCTTTTTTTTCTTTTTTTTCCTTTTTT
1 TTTTCTTTCTTTTCTTTCTTTTCCTTTTTT
234581 T
1 T
234582 CTCTGATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (30 bp):
TTTTCTTTCTTTTCTTTCTTTTCCTTTTTT
Found at i:234559 original size:10 final size:10
Alignment explanation
Indices: 234492--234581 Score: 78
Period size: 10 Copynumber: 9.1 Consensus size: 10
234482 ATTGATTCAA
*
234492 TTTCATTTTT
1 TTTCTTTTTT
**
234502 TTTCTTCATT
1 TTTCTTTTTT
*
234512 TTTC-TTTAT
1 TTTCTTTTTT
*
234521 TTTC-TTTCT
1 TTTCTTTTTT
234530 TTTCTTTCTTT
1 TTTCTTT-TTT
*
234541 TCTCTTTTTT
1 TTTCTTTTTT
234551 TTT-TCTTTTT
1 TTTCT-TTTTT
234561 TTTCTTTTTT
1 TTTCTTTTTT
*
234571 TTCCTTTTTT
1 TTTCTTTTTT
234581 T
1 T
234582 CTCTGATGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
9 15 0.23
10 41 0.63
11 9 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:234564 original size:40 final size:40
Alignment explanation
Indices: 234510--234585 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
234500 TTTTTCTTCA
234510 TTTTTCTTTATTTTCTTTCTTTT-CTTTCTTTTCTCTTTTT
1 TTTTTCTTTATTTTCTTTCTTTTCCTTT-TTTTCTCTTTTT
* *
234550 TTTTTCTTTTTTTTCTTTTTTTTCCTTTTTTTCTCT
1 TTTTTCTTTATTTTCTTTCTTTTCCTTTTTTTCTCT
234586 GATGGATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (40 bp):
TTTTTCTTTATTTTCTTTCTTTTCCTTTTTTTCTCTTTTT
Found at i:240363 original size:21 final size:21
Alignment explanation
Indices: 240342--240479 Score: 181
Period size: 21 Copynumber: 6.5 Consensus size: 21
240332 CCAATGACGA
*
240342 GAAGACCATTCACAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
*
240363 GAAGACCATTCACAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
*
240384 GAAGACCATTCATGAAGACAT
1 GAAGACCATTCATAAAGACAT
*
240405 GAAGACCATTCATGAAGACAT
1 GAAGACCATTCATAAAGACAT
240426 GAAGACCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
* *
240447 TAAGACCATTAATAAAGACAT
1 GAAGACCATTCATAAAGACAT
240468 GAAGACCCATTC
1 GAAGA-CCATTC
240480 GCATTTGAGG
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
20 1 0.01
21 102 0.94
22 5 0.05
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:244911 original size:16 final size:16
Alignment explanation
Indices: 244845--244910 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 16
244835 GAAAAAGGAA
*
244845 AGAAAATAAGAAAAAT
1 AGAAAATGAGAAAAAT
*
244861 --AAATTGA-AAAAAT
1 AGAAAATGAGAAAAAT
*
244874 TGAAAATGAG-AAAAT
1 AGAAAATGAGAAAAAT
244889 GAGAAAATGAGAAAAAT
1 -AGAAAATGAGAAAAAT
244906 A-AAAA
1 AGAAAA
244911 AAAAGAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.15
14 5 0.12
15 15 0.37
16 10 0.24
17 5 0.12
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
AGAAAATGAGAAAAAT
Found at i:246169 original size:16 final size:17
Alignment explanation
Indices: 246150--246182 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
246140 AAAAATATTT
246150 TATTCAAATA-TAAAAA
1 TATTCAAATATTAAAAA
*
246166 TATTCTAATATTAAAAA
1 TATTCAAATATTAAAAA
246183 ATAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTCAAATATTAAAAA
Found at i:246795 original size:34 final size:34
Alignment explanation
Indices: 246757--246826 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
246747 TTCAGATGAT
*
246757 TCTTAATTATATTTTGATACAAAACTCATAAGTC
1 TCTTAATTATATTTAGATACAAAACTCATAAGTC
246791 TCTTAATTATATTTAGATACAAAACTCATAAGTC
1 TCTTAATTATATTTAGATACAAAACTCATAAGTC
246825 TC
1 TC
246827 GACCAATCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.40
Consensus pattern (34 bp):
TCTTAATTATATTTAGATACAAAACTCATAAGTC
Found at i:247939 original size:21 final size:21
Alignment explanation
Indices: 247888--247974 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 21
247878 AAATTTAAAT
*
247888 TAAAAAATCAAATATTAAAAA
1 TAAAAAATAAAATATTAAAAA
**
247909 GT-AAATTTAAAATATTAAAAA
1 -TAAAAAATAAAATATTAAAAA
* ** *
247930 TAAAAATTAAGTTACTAAAAA
1 TAAAAAATAAAATATTAAAAA
247951 TATTAAAAATAATAA-ATTAAAAA
1 TA--AAAAATAA-AATATTAAAAA
247974 T
1 T
247975 TATTTTAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.66
22 1 0.02
23 15 0.30
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAAAATAAAATATTAAAAA
Found at i:247971 original size:23 final size:24
Alignment explanation
Indices: 247945--247998 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
247935 ATTAAGTTAC
247945 TAAAAA-TA-TTAAAAATAATAAAT
1 TAAAAATTATTTAAAAATAA-AAAT
*
247968 TAAAAATTATTTTAAAAATAAATAT
1 TAAAAATTA-TTTAAAAATAAAAAT
247993 TAAAAA
1 TAAAAA
247999 AACATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 2 0.07
25 9 0.33
26 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAATTATTTAAAAATAAAAAT
Found at i:247991 original size:39 final size:39
Alignment explanation
Indices: 247902--248009 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 39
247892 AAATCAAATA
247902 TTAAAAAGTAAAT-TTAAAATATTAA-AAA-TAAAAATTAAG
1 TTAAAAA-TAAATATTAAAA-A-TAATAAATTAAAAATTAAG
** **
247941 TTACTAA-AAATATTAAAAATAATAAATTAAAAATTATT
1 TTAAAAATAAATATTAAAAATAATAAATTAAAAATTAAG
*
247979 TTAAAAATAAATATTAAAAAAACATAAATTA
1 TTAAAAATAAATATTAAAAATA-ATAAATTA
248010 TACATAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
36 3 0.05
37 8 0.14
38 20 0.35
39 18 0.32
40 8 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (39 bp):
TTAAAAATAAATATTAAAAATAATAAATTAAAAATTAAG
Found at i:248852 original size:16 final size:17
Alignment explanation
Indices: 248834--248869 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
248824 TTCTTGAATA
248834 TTTAAATATTTTTATAT
1 TTTAAATATTTTTATAT
248851 TTTAAATATTTTTAT-T
1 TTTAAATATTTTTATAT
248867 TTT
1 TTT
248870 CTAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTAAATATTTTTATAT
Found at i:251555 original size:22 final size:22
Alignment explanation
Indices: 251528--251592 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
251518 TGTTCACGGC
*
251528 ACTGTTCACGGTATTGTTCATT
1 ACTGTTCACGGTACTGTTCATT
*
251550 ACTGTTTACGGTACTGTTCATT
1 ACTGTTCACGGTACTGTTCATT
251572 ACTGTTCACGGTACTGTTCAT
1 ACTGTTCACGGTACTGTTCAT
251593 ACCATATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (22 bp):
ACTGTTCACGGTACTGTTCATT
Found at i:251590 original size:12 final size:12
Alignment explanation
Indices: 251516--251591 Score: 79
Period size: 12 Copynumber: 6.7 Consensus size: 12
251506 TACATTCGAC
*
251516 ACTGTTCACGGC
1 ACTGTTCACGGT
251528 ACTGTTCACGGT
1 ACTGTTCACGGT
* *
251540 ATTGTTCA--TT
1 ACTGTTCACGGT
*
251550 ACTGTTTACGGT
1 ACTGTTCACGGT
*
251562 ACTGTTCA--TT
1 ACTGTTCACGGT
251572 ACTGTTCACGGT
1 ACTGTTCACGGT
251584 ACTGTTCA
1 ACTGTTCA
251592 TACCATATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
10 16 0.31
12 35 0.69
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (12 bp):
ACTGTTCACGGT
Found at i:256074 original size:3 final size:3
Alignment explanation
Indices: 256066--256118 Score: 81
Period size: 3 Copynumber: 17.3 Consensus size: 3
256056 ATTATGTTTA
256066 ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT A-T ATAT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
256112 ATT ATT A
1 ATT ATT A
256119 AATAAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:257533 original size:14 final size:14
Alignment explanation
Indices: 257514--257542 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
257504 TTATAATACT
257514 TCGAATAAGGGCCA
1 TCGAATAAGGGCCA
257528 TCGAATAAGGGCCA
1 TCGAATAAGGGCCA
257542 T
1 T
257543 TAACTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (14 bp):
TCGAATAAGGGCCA
Found at i:257613 original size:17 final size:17
Alignment explanation
Indices: 257581--257628 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
257571 TAACAGTTTG
*
257581 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
257597 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
257614 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
257629 TTCTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:257671 original size:21 final size:20
Alignment explanation
Indices: 257637--257676 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
257627 ATTTCTTTAA
257637 TTTTGATTATTATTATTTTG
1 TTTTGATTATTATTATTTTG
*
257657 TTTTGTTTAATTATTATTTT
1 TTTTGATT-ATTATTATTTT
257677 TGATATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTGATTATTATTATTTTG
Found at i:260866 original size:16 final size:16
Alignment explanation
Indices: 260845--260876 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
260835 ATGATGGGTT
260845 TTGTAACAGTAAAATC
1 TTGTAACAGTAAAATC
260861 TTGTAACAGTAAAATC
1 TTGTAACAGTAAAATC
260877 GAGACCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
TTGTAACAGTAAAATC
Found at i:263454 original size:9 final size:9
Alignment explanation
Indices: 263440--263475 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
263430 ATTTGAAGAA
263440 GAAAAAAAG
1 GAAAAAAAG
263449 GAAAAAAAG
1 GAAAAAAAG
263458 GAAAAAAAAG
1 G-AAAAAAAG
263468 GAAAAAAA
1 GAAAAAAA
263476 TTGAATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:263456 original size:10 final size:10
Alignment explanation
Indices: 263441--263475 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
263431 TTTGAAGAAG
263441 AAAAAAAGG-
1 AAAAAAAGGA
263450 AAAAAAAGGA
1 AAAAAAAGGA
263460 AAAAAAAGGA
1 AAAAAAAGGA
263470 AAAAAA
1 AAAAAA
263476 TTGAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGA
Found at i:266529 original size:75 final size:75
Alignment explanation
Indices: 266440--266597 Score: 237
Period size: 75 Copynumber: 2.1 Consensus size: 75
266430 CAAATTCTGA
* * * * *
266440 GGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACGTATTTTGAATGTTTGTATC-A
1 GGCATGCTAAAAGCCCATTTCAATCAGAATCAGGAATATTGACGCATTTTGAACGCTTGTATCGA
266504 GCAAATGTTGG
66 -CAAATGTTGG
* *
266515 GGCATGCTAAAAGCCCATTTCAATCAGAATGAGGAATGTTGACGCATTTTGAACGCTTGTATCGA
1 GGCATGCTAAAAGCCCATTTCAATCAGAATCAGGAATATTGACGCATTTTGAACGCTTGTATCGA
266580 CAAATGTTGG
66 CAAATGTTGG
266590 GGCATGCT
1 GGCATGCT
266598 GAAGGCCTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
75 74 0.99
76 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (75 bp):
GGCATGCTAAAAGCCCATTTCAATCAGAATCAGGAATATTGACGCATTTTGAACGCTTGTATCGA
CAAATGTTGG
Done.