Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001983.1 Hibiscus syriacus cultivar Beakdansim tig00004041_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: 530088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:12107 original size:2 final size:2
Alignment explanation
Indices: 12100--12145 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12090 ACTGTAAATA
12100 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
12142 AT AT
1 AT AT
12146 CGAAATTCGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12520 original size:22 final size:22
Alignment explanation
Indices: 12492--12789 Score: 445
Period size: 22 Copynumber: 13.5 Consensus size: 22
12482 ATTTTAAAAT
12492 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
12514 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
* *
12536 TTTATTTTAAAACATGAATTGA
1 TTTATTTTAAAATATGGATTGA
12558 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
12580 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
12601 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
*
12624 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
12646 TTTATTTTTAAATATGGAAAAA
1 TTTATTTTAAAATATGGATTGA
12668 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
***
12690 TTTATTTTAAAATATGGAAAAA
1 TTTATTTTAAAATATGGATTGA
*
12712 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
12734 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
12756 TTTATTTTAAAATGTGGATTGA
1 TTTATTTTAAAATATGGATTGA
12778 TTTATTTTAAAA
1 TTTATTTTAAAA
12790 AAAATTATTA
Statistics
Matches: 247, Mismatches: 27, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
21 1 0.00
22 245 0.99
23 1 0.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:16928 original size:2 final size:2
Alignment explanation
Indices: 16921--16962 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
16911 TAGGTGAGAT
16921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16963 ATTATTTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17497 original size:2 final size:2
Alignment explanation
Indices: 17490--17515 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17480 TTTTAATTCA
17490 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
17516 TACTTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28441 original size:99 final size:97
Alignment explanation
Indices: 28119--28434 Score: 278
Period size: 99 Copynumber: 3.2 Consensus size: 97
28109 CTTGACTAGC
* * * *
28119 ATGTGTCGGTGGCGGATACAGTCCGCCATGCCCCATAGATGGCAAAATAGGTTTCTCCG-G-AGT
1 ATGTGTTGGTGGCGGATACAGTCCGCCGTGCCTCATAGATGGCAGAATAGGTTTCT-CGAGAAG-
*
28182 ACCTCAACGGTCAAGTCATGATCAACTTGATTTGG
64 ACC-CAACGTTCAAGTCATGATCAACTTGATTTGG
** ** ** ** * * *
28217 ATGTGTTGGTGGCGGATTTAGTCCGCCGCCACCAATGTTAGAAAGC-GAATCGAGTTCCTCAAGA
1 ATGTGTTGGTGGCGGATACAGTCCGCCG-TGCC--TCATAGATGGCAGAATAG-GTTTCTCGAGA
* ** * *
28281 ATTGACCTAACGTTCAAGTCACCATCAACTTGACTTGC
62 A--GACCCAACGTTCAAGTCATGATCAACTTGATTTGG
* *
28319 AAGCGTTGGTGGCGGATACAGTCCGCCGTGCCTCATAGATGGCAGAATAGGTTTCTCGAGAAGCA
1 ATGTGTTGGTGGCGGATACAGTCCGCCGTGCCTCATAGATGGCAGAATAGGTTTCTCGAGAAG-A
* *
28384 CCGCAACATTCAAATCATGATCAACTTGATTTGG
65 CC-CAACGTTCAAGTCATGATCAACTTGATTTGG
*
28418 GTGTGTTGGTGGCGGAT
1 ATGTGTTGGTGGCGGAT
28435 TTAGTCCTCC
Statistics
Matches: 163, Mismatches: 44, Indels: 21
0.71 0.19 0.09
Matches are distributed among these distances:
97 1 0.01
98 27 0.17
99 57 0.35
100 10 0.06
101 14 0.09
102 50 0.31
103 3 0.02
104 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (97 bp):
ATGTGTTGGTGGCGGATACAGTCCGCCGTGCCTCATAGATGGCAGAATAGGTTTCTCGAGAAGAC
CCAACGTTCAAGTCATGATCAACTTGATTTGG
Found at i:29377 original size:108 final size:108
Alignment explanation
Indices: 29185--30621 Score: 2168
Period size: 108 Copynumber: 13.4 Consensus size: 108
29175 GCGCAACCGG
* * * *
29185 AACCGGTTTATTTCCGCCGTGACCGGGCGAAGATGGTGGTACAGATGCCTTG-GGAAGTACCCCA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCC-TGAGGAAGTACACCA
* * * * * *
29249 AAGTTCAAAGCAAGACCGGCTTGACTGACATGGGATGGAGGCGC
65 AAGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* * * *
29293 AACCGGTTTATTTCCACCGTGACCGGGCGAAGACGGTGGCACGGGTGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
* * * * * * *
29358 AGTTCAAAGCACGAACGGCTTGACTGACATAGGA---CGGAG-
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
*
29397 -A-CGGTTTATTTCCACCGTGACCAGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
29460 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* * * *
29503 AATCGGTTTATTTCCACCATGACCGGGTGAAGAAGGTGGTACAGGTACCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
* * * *
29568 AGTTCAAGGCTCGACCAGATTGGCCTACATGGGACGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
*
29611 AACCGGTTTATTTCCACCGTGACCGGGTGAAGAAGGTGGTACAGGTGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
29676 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* * *
29719 AACTGGTTTATTTCCACCATGACCGGGTGAAGATGGTGGTACAGGTACCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
** * * * *
29784 AGTTCAAGGTTCGACCAGATTGGCCTACGTGGGACGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* *
29827 AACCGGTTTATTTCCACCGTGACCGGGTGAAGAAGGTGGTACAGGCGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
29892 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* * *
29935 AAACGGTTTATTTCCACCATGACCGGGTGAAGATGGTGGTACAGGTACCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
* * * *
30000 AGTTCAAGGCTCGACCAGATTGGCCTACATGGGACGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* *
30043 AACCGGTTTATTTCCACCGTGACCGGGTGAAGAAGGTGGTACAGGCGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
30108 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
*
30151 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGCGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
30216 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* *
30259 AACCGGTTTATTTCCACCATGACCGGGTGAAGATGGTGGTACAGGTACCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
* * * *
30324 AGTTCAAGGCTCGACCAGATTGGCCTACATGGGACGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* *
30367 AACCGGTTTATTTCCACCGTGACCGGGTGAAGAAGGTGGTACAGGCGCCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
* *
30432 AGTTCAAGGCTCGACCGGATTGGCTTACATGTGATGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* * * *
30475 AAACGGTTTATTTCCACCATGACCGGGTGAAGATGGTGGTACAAGTACCTGAGGAAGTACACCAA
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
* * * *
30540 AGTTCAAGGCTCGACCAGATTGGCCTACATGGGACGGCGGCGC
66 AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
* *
30583 AACCGGTTTATTTCCACCGTGACCGGGGGAAGACGGTGG
1 AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGG
30622 AACGGGGACT
Statistics
Matches: 1215, Mismatches: 107, Indels: 14
0.91 0.08 0.01
Matches are distributed among these distances:
102 85 0.07
103 1 0.00
105 7 0.01
107 3 0.00
108 1119 0.92
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.19
Consensus pattern (108 bp):
AACCGGTTTATTTCCACCGTGACCGGGTGAAGATGGTGGTACAGGTGCCTGAGGAAGTACACCAA
AGTTCAAGGCACGACCGGATTGGCTTACATGGGATGGCGGCGC
Found at i:34275 original size:60 final size:60
Alignment explanation
Indices: 34204--34373 Score: 236
Period size: 60 Copynumber: 2.8 Consensus size: 60
34194 AGTCCTTGAT
*
34204 TATAGAGCATTGCTTTGTTGAGTCCCATGACTATTAAAAGTTACAAAATGGTACCCTAAC
1 TATAGAGCATTGCTTTGTTGAGTCCCATGACTATTAAAAGTTACAAAATGGTACCCCAAC
* * * *
34264 TATAGAACATTGATTTGTTGAGT-CCATTGACTATTAAAAGTTACAAAATGGTCCCCCGAC
1 TATAGAGCATTGCTTTGTTGAGTCCCA-TGACTATTAAAAGTTACAAAATGGTACCCCAAC
* * *
34324 CATAGAGCATTGCTTTGTTGAG-CCTCCTGACTATCAAAAGTTACAAAATG
1 TATAGAGCATTGCTTTGTTGAGTCC-CATGACTATTAAAAGTTACAAAATG
34374 ACCATCCAAC
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
59 3 0.03
60 93 0.96
61 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (60 bp):
TATAGAGCATTGCTTTGTTGAGTCCCATGACTATTAAAAGTTACAAAATGGTACCCCAAC
Found at i:41097 original size:154 final size:155
Alignment explanation
Indices: 40779--41763 Score: 1006
Period size: 154 Copynumber: 6.2 Consensus size: 155
40769 GTGTAATGTA
* * * * *
40779 GAGTCTATGAATCTTCTTTAGGACTATTTTGATAGCTGATAGAAATGGTTTTGTTTACTGCCTGT
1 GAGTCGATGAATCTTGTTTAGGACTA--TTGGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGT
* * * *
40844 TTAATTAGAATTGTTGTTCTCTATGATGGGATTGCTAATTCGTTGTTGAGTT--A-T-AA-ATTG
64 TTAAGTAGAATTGTT-CTCTCTATGATGGCATTGCTAATTCGTTGTT--GTTGAATTCAATATCG
* *
40904 ATCTCGTTCTTCCTCTCGAGGTATGGTACG
126 ATCTCGTTCTTCCTCTTGAAGTATGGTACG
* * * **
40934 GGGTCGATGAATCTTGTTTAGGACTATTGGTAGCTGATTGAAATGGTTTTGTTTGCTGCCCATTT
1 GAGTCGATGAATCTTGTTTAGGACTATTGGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGTTT
*
40999 AAGTAGAATTGTT-TCTCTATGATGGCATTGCTAATTCATTGTTGTTGAATTCAATATCGATCTC
66 AAGTAGAATTGTTCTCTCTATGATGGCATTGCTAATTCGTTGTTGTTGAATTCAATATCGATCTC
*
41063 GTTCTTCCTCTTGAAATATGGTACG
131 GTTCTTCCTCTTGAAGTATGGTACG
* * * * **
41088 GAGTCGATGAATCTTGTTTAGGACTGTTTTGTAGCTGATTGAAAGGGTTCTGCTTACTGCCTGGC
1 GAGTCGATGAATCTTGTTTAGGACT-ATTGGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGTT
* * * *
41153 TAAGTAAAATTGTTGCTCTCTATGATGGAATTGTTATTTCGTTGTTGTTGAACTAAATTTACGTT
65 TAAGTAGAATTGTT-CTCTCTATGATGGCATTGCTAATTCGTTGTTGTTG------A---A--TT
* **
41218 CGATATCGATCTCCGTTCTTCCTCTCAAAGTATGATGTA--
118 CAATATCGATCT-CGTTCTTCCTCTTGAAGTATG--GTACG
* * *
41257 GTGTCGATGAATCTTGTTTAGGACTATTTTGGTAGCTGAATGAAATGGTTCTGTTTACTGCTTGT
1 GAGTCGATGAATCTTGTTTAGGACTA--TTGGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGT
* * * * *
41322 TTAAGTAGAATCGTTGCTCTCTAAGATGGCATTGCTAATTCGTTGTTGTTGAATACGATATAGAT
64 TTAAGTAGAATTGTT-CTCTCTATGATGGCATTGCTAATTCGTTGTTGTTGAATTCAATATCGAT
*
41387 CTCGTTCTTCCTCTCGAAGTATGGTACG
128 CTCGTTCTTCCTCTTGAAGTATGGTACG
* * * * **
41415 G-GATCAATGAATCTTGTTTACGACTATTGGTAGCTGATTAAAATGGTTTTGTTTACTGCCCATT
1 GAG-TCGATGAATCTTGTTTAGGACTATTGGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGTT
* *
41479 TAAGTAGAATTGTTTCTCTCTATGATGGCATTGCTAATTCGTTGTTATTGAATTCGATATCGATC
65 TAAGTAGAATTG-TTCTCTCTATGATGGCATTGCTAATTCGTTGTTGTTGAATTCAATATCGATC
*
41544 TCTTTCTT--TC--GAAGTATGGTACG
129 TCGTTCTTCCTCTTGAAGTATGGTACG
* *
41567 GAGTCGATGAATCTTGTTTGGGACTATTTAGGTAGCTGATTGAAAGGGTTCTGTTTACTGCCTGT
1 GAGTCGATGAATCTTGTTTAGGACTA-TT-GGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGT
* * * * *
41632 CTAAGTAAAATTGTTGCTCTCTATGATGGAATTGCTAATTCGCTGTTGTTGAACTAAATTTATGT
64 TTAAGTAGAATTGTT-CTCTCTATGATGGCATTGCTAATTCGTTGTTGTTG-----AATTCA---
41697 TTGATATCGATCTCGTTCTTCCTCTTGAAGTATGGTACG
120 ---ATATCGATCTCGTTCTTCCTCTTGAAGTATGGTACG
*
41736 GAGTTGATGAATCTTGTTTAGGACTATT
1 GAGTCGATGAATCTTGTTTAGGACTATT
41764 TTGGTATCTG
Statistics
Matches: 698, Mismatches: 85, Indels: 81
0.81 0.10 0.09
Matches are distributed among these distances:
149 3 0.00
151 29 0.04
152 35 0.05
153 53 0.08
154 129 0.18
155 65 0.09
156 99 0.14
157 33 0.05
158 42 0.06
159 16 0.02
161 1 0.00
163 1 0.00
164 1 0.00
165 16 0.02
166 1 0.00
167 2 0.00
168 15 0.02
169 79 0.11
170 75 0.11
171 3 0.00
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (155 bp):
GAGTCGATGAATCTTGTTTAGGACTATTGGTAGCTGATTGAAATGGTTCTGTTTACTGCCTGTTT
AAGTAGAATTGTTCTCTCTATGATGGCATTGCTAATTCGTTGTTGTTGAATTCAATATCGATCTC
GTTCTTCCTCTTGAAGTATGGTACG
Found at i:45821 original size:138 final size:135
Alignment explanation
Indices: 45549--45822 Score: 433
Period size: 138 Copynumber: 2.0 Consensus size: 135
45539 TATCGAGTTA
* *
45549 TTTCGAGTTCAGATCTTGATTGTTTATGTTTAAATCGAATCGAGTTCGGTTTGAGTATGATGATG
1 TTTCGAGATCAGATCTTGATTGTTTATGTTTAAATCGAATCGAGTTCAGTTTGAGTATGATGATG
* *
45614 TTTAGCATGATAATGTTGTACCTTGGTTCTGGACTGTATAGGAGGAATTAGATGAGTATGCCGAA
66 TTTAGCATGATAATGTTGTACCTTGGTTCTGGACTGTATAGGAGGAATTAGAGGAGTATACCGAA
45679 AAAGC
131 AAAGC
*
45684 TTTCGAGATCAGATCTTGATTGTTTATGTTTAAATCGAGTCGAGTTCAGTTTGAGTATATGATGA
1 TTTCGAGATCAGATCTTGATTGTTTATGTTTAAATCGAATCGAGTTCAGTTTGAG--TATGATGA
* *
45749 TGTTTTAGTATGATAATGTTGTACCTTGGTTCCT-GACTGTATAGGAGGAATTCGAGGAGTATAC
64 TG-TTTAGCATGATAATGTTGTACCTTGGTT-CTGGACTGTATAGGAGGAATTAGAGGAGTATAC
*
45813 CGAGAAAGC
127 CGAAAAAGC
45822 T
1 T
45823 AAGACCCTCC
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
135 52 0.41
137 10 0.08
138 63 0.50
139 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.37
Consensus pattern (135 bp):
TTTCGAGATCAGATCTTGATTGTTTATGTTTAAATCGAATCGAGTTCAGTTTGAGTATGATGATG
TTTAGCATGATAATGTTGTACCTTGGTTCTGGACTGTATAGGAGGAATTAGAGGAGTATACCGAA
AAAGC
Found at i:55763 original size:60 final size:60
Alignment explanation
Indices: 55660--55834 Score: 201
Period size: 60 Copynumber: 2.9 Consensus size: 60
55650 TTTGAATGAA
* * * * *
55660 TTTGGGGATGAAATTGAAA-GATCTAAAAGTTTAGGGACCAATTTATAATGAGATTCATAG
1 TTTGGGGATGAAATTGAAATG-TTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
* *
55720 TTTGGGGATGAAATTCAAATGTTTAAAAGTCTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
** * * * *
55780 TTTAAGGATGAAATTGAAGTATTTAAAAGTTTAAAGACTAATAT-GAAATGAGAGT
1 TTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAG-AATGAGAGT
55835 TTTAATTTAA
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.01
60 96 0.98
61 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (60 bp):
TTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
Found at i:68907 original size:19 final size:20
Alignment explanation
Indices: 68883--68926 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
68873 TATCCGAAAA
68883 AAAAATCCGGT-AGGGGTTT
1 AAAAATCCGGTCAGGGGTTT
* *
68902 AAAAATCTGGTCTGGGGTTT
1 AAAAATCCGGTCAGGGGTTT
68922 AAAAA
1 AAAAA
68927 ATTGGATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCAGGGGTTT
Found at i:68972 original size:17 final size:17
Alignment explanation
Indices: 68941--68975 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
68931 GATTACCGGA
**
68941 TTAAAAACCGGTTTTTT
1 TTAAAAACCAATTTTTT
68958 TTAAAAACCAATTTTTT
1 TTAAAAACCAATTTTTT
68975 T
1 T
68976 CAAACCGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (17 bp):
TTAAAAACCAATTTTTT
Found at i:75008 original size:15 final size:17
Alignment explanation
Indices: 74977--75008 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
74967 CTATAACTCT
74977 TGAAACAACATTAAAGC
1 TGAAACAACATTAAAGC
74994 TGAAA-AACA-TAAAGC
1 TGAAACAACATTAAAGC
75009 ATTGCTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (17 bp):
TGAAACAACATTAAAGC
Found at i:77068 original size:14 final size:15
Alignment explanation
Indices: 77027--77068 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
77017 GTACTTAAAT
77027 TTTTAATTTTGTTCAA
1 TTTTAATTTT-TTCAA
*
77043 TTTTAATATTTT-AA
1 TTTTAATTTTTTCAA
77057 TTTTAATTTTTT
1 TTTTAATTTTTT
77069 TCAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 2 0.08
16 9 0.38
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTAATTTTTTCAA
Found at i:77323 original size:48 final size:49
Alignment explanation
Indices: 77253--77347 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 49
77243 TGAATATAAT
* * *
77253 AACATTTTAAGTTAAAATCGAAAATGTTGT-TTATTCATAATATTTTCG
1 AACATTTTAAGTTAAAACCGAAAATGATATATTATTCATAATATTTTCG
** * *
77301 AACATTTTCTGTTACAACCGAAAATGATATATTATTTATAATATTTT
1 AACATTTTAAGTTAAAACCGAAAATGATATATTATTCATAATATTTT
77348 TAGTTGTAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 24 0.62
49 15 0.38
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.44
Consensus pattern (49 bp):
AACATTTTAAGTTAAAACCGAAAATGATATATTATTCATAATATTTTCG
Found at i:77547 original size:14 final size:14
Alignment explanation
Indices: 77528--77583 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
77518 AAATAAAATG
77528 TATTTATATTTATT
1 TATTTATATTTATT
* **
77542 TATTTATCTTTAAA
1 TATTTATATTTATT
77556 TATTTCATATTTAATT
1 TATTT-ATATTT-ATT
77572 TATGTT-TATTTA
1 TAT-TTATATTTA
77584 AATTTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 17 0.52
15 10 0.30
16 4 0.12
17 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (14 bp):
TATTTATATTTATT
Found at i:77584 original size:30 final size:28
Alignment explanation
Indices: 77528--77591 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
77518 AAATAAAATG
*
77528 TATTTATATTTATTTATTTATCTTTAAA
1 TATTTATATTTATTTATTTATATTTAAA
77556 TATTTCATATTTAATTTATGTT-TATTTAAA
1 TATTT-ATATTT-ATTTAT-TTATATTTAAA
*
77586 TTTTTA
1 TATTTA
77592 ATATCGTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 5 0.16
29 7 0.23
30 17 0.55
31 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTTATATTTATTTATTTATATTTAAA
Found at i:79900 original size:22 final size:21
Alignment explanation
Indices: 79859--79901 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
79849 CGAAAAAAGA
*
79859 AAAAAATAATCAAAGGTAAAT
1 AAAAAATAATCAAAGATAAAT
79880 AAAAAATGAATCGAAA-ATAAAT
1 AAAAAAT-AATC-AAAGATAAAT
79902 TTAGACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAAAATAATCAAAGATAAAT
Found at i:85319 original size:29 final size:29
Alignment explanation
Indices: 85286--85341 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
85276 TCCCAACACA
85286 TAGGTCGCCATGCCCTCCAGGCGACCTTG
1 TAGGTCGCCATGCCCTCCAGGCGACCTTG
*
85315 TAGGTCGCCATGCCCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCAGGCGACCT
85342 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.39, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCAGGCGACCTTG
Found at i:85386 original size:33 final size:33
Alignment explanation
Indices: 85345--85413 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
85335 GCGACCTACC
* *
85345 CTCGCTCGGCTT-CTCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
85378 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
85411 CTC
1 CTC
85414 ATTCGGATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.09, C:0.41, G:0.23, T:0.28
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:85430 original size:33 final size:33
Alignment explanation
Indices: 85360--85438 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
85350 TCGGCTTCTC
* * * *
85360 TCGGATTCCCTCGCATAGCTCGCTCGGTTGCCC
1 TCGGATGCCCTCGCATAGCTCACTCGGATGCCA
* *
85393 TCGGATGCCCTCGCATAGCTCATTCGGATGGCA
1 TCGGATGCCCTCGCATAGCTCACTCGGATGCCA
*
85426 TCGGATGCTCTCG
1 TCGGATGCCCTCG
85439 GATGGCCTCG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.34, G:0.27, T:0.27
Consensus pattern (33 bp):
TCGGATGCCCTCGCATAGCTCACTCGGATGCCA
Found at i:86735 original size:31 final size:30
Alignment explanation
Indices: 86662--86735 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
86652 CCCGTGTTAA
*
86662 AAATTTAGGTACTAAAATGAAATAAAAAAT
1 AAATTTAGGTATTAAAATGAAATAAAAAAT
* ** *
86692 AAACGTCGGGTATTAAAATGAAATAAAAAGT
1 AAA-TTTAGGTATTAAAATGAAATAAAAAAT
86723 AAATATTAGGTAT
1 AAAT-TTAGGTAT
86736 GATTTTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (30 bp):
AAATTTAGGTATTAAAATGAAATAAAAAAT
Found at i:88763 original size:9 final size:9
Alignment explanation
Indices: 88750--88791 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
88740 TTGGATACAA
*
88750 AATAAAATA
1 AATAAAATT
88759 AATAAAATT
1 AATAAAATT
88768 AATAAAATT
1 AATAAAATT
88777 AATAAAATT
1 AATAAAATT
88786 AATAAA
1 AATAAA
88792 TATACTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AATAAAATT
Found at i:89487 original size:31 final size:31
Alignment explanation
Indices: 89452--89538 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 31
89442 GAACTCCGGA
89452 TATCAAATTGAACCTTAAAGTCAAGTTTAAG
1 TATCAAATTGAACCTTAAAGTCAAGTTTAAG
* *** * *
89483 TATCAAATTGGACAAAAAAATC--G--TAGG
1 TATCAAATTGAACCTTAAAGTCAAGTTTAAG
*
89510 TACCAAATTGAACCTTAAAGTCAAGTTTA
1 TATCAAATTGAACCTTAAAGTCAAGTTTA
89539 CGTACATAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
27 19 0.47
29 2 0.05
31 19 0.47
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (31 bp):
TATCAAATTGAACCTTAAAGTCAAGTTTAAG
Found at i:89517 original size:58 final size:55
Alignment explanation
Indices: 89455--89573 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 55
89445 CTCCGGATAT
89455 CAAATTGAACCTTAAAGTCAAGTTTAAGTATCA-AATTGGACAAAAAAATCGTAGGTAC
1 CAAATTGAACCTTAAAGTCAAGTTTAAGTA-CATAATTGGAC--AAAAAT-GTAGGTAC
*
89513 CAAATTGAACCTTAAAGTCAAGTTTACGTACATAATTGGACAAAAATGTAGGTAC
1 CAAATTGAACCTTAAAGTCAAGTTTAAGTACATAATTGGACAAAAATGTAGGTAC
89568 CAAATT
1 CAAATT
89574 AAATCTTGAA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
55 14 0.24
56 6 0.10
57 2 0.03
58 37 0.63
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (55 bp):
CAAATTGAACCTTAAAGTCAAGTTTAAGTACATAATTGGACAAAAATGTAGGTAC
Found at i:93979 original size:14 final size:14
Alignment explanation
Indices: 93960--93986 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
93950 TTTCCCTAAA
93960 GACCGAGTTAAGCG
1 GACCGAGTTAAGCG
93974 GACCGAGTTAAGC
1 GACCGAGTTAAGC
93987 AGACAAGGAT
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:0.30, C:0.22, G:0.33, T:0.15
Consensus pattern (14 bp):
GACCGAGTTAAGCG
Found at i:96678 original size:23 final size:24
Alignment explanation
Indices: 96652--96720 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
96642 TTTATGTGTA
* *
96652 TATGTTCAAAATGCAATTTCT-TT
1 TATGTTCAATATGCAATTTCTCCT
*
96675 TATGTTCAATATGCACTGGTT-TCCT
1 TATGTTCAATATGCAAT--TTCTCCT
96700 TATGTTCAATATGCAATTTCT
1 TATGTTCAATATGCAATTTCT
96721 ATGAGTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 17 0.45
24 2 0.05
25 19 0.50
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (24 bp):
TATGTTCAATATGCAATTTCTCCT
Found at i:101173 original size:35 final size:36
Alignment explanation
Indices: 101134--101210 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
101124 GTTCTAAATT
*
101134 TTAATTTATTTTGATTTT-T-CCCTCATTTTCTA-TG
1 TTAATTTATTAT-ATTTTGTCCCCTCATTTTCTATTG
*
101168 ATTAATTTATTATATTTTGTCCCCTCGTTTTCTATTG
1 -TTAATTTATTATATTTTGTCCCCTCATTTTCTATTG
101205 TTAATT
1 TTAATT
101211 ATGTTCCCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.14
35 12 0.32
36 18 0.49
37 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.60
Consensus pattern (36 bp):
TTAATTTATTATATTTTGTCCCCTCATTTTCTATTG
Found at i:101235 original size:44 final size:43
Alignment explanation
Indices: 101185--101268 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 43
101175 TATTATATTT
* *
101185 TGTCCCCTCGTTTTCTATTGTTAATTATGTTCCCCCCTTAATTA
1 TGTCCCCTCATTTTCTATGGTTAATTATGTT-CCCCCTTAATTA
101229 TGTCCCCTCATTTTCTATGGTTAATTATGTTCCCCCTTAA
1 TGTCCCCTCATTTTCTATGGTTAATTATGTTCCCCCTTAA
101269 ATTGATTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 9 0.24
44 29 0.76
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.46
Consensus pattern (43 bp):
TGTCCCCTCATTTTCTATGGTTAATTATGTTCCCCCTTAATTA
Found at i:105699 original size:29 final size:31
Alignment explanation
Indices: 105653--105714 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
105643 TATAATTATG
* * *
105653 TTATTATTTTATTCCAATTTAAATATA-GTT
1 TTATAATTATATTCCAATATAAATATATGTT
*
105683 TTATAATTATATT-CAATATATATATATGTT
1 TTATAATTATATTCCAATATAAATATATGTT
105713 TT
1 TT
105715 TTCATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.56
Consensus pattern (31 bp):
TTATAATTATATTCCAATATAAATATATGTT
Found at i:108103 original size:2 final size:2
Alignment explanation
Indices: 108058--108086 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108048 TGCGTGTGTG
108058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
108087 TTCTCAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:116875 original size:32 final size:34
Alignment explanation
Indices: 116833--116907 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
116823 CGAAAAACCC
* *
116833 TAAACCCTAACTTAAAACCGTAAATCCTAA-ATA
1 TAAACCCTAACTTAAAACCCTAAACCCTAACATA
*
116866 TAAA-CCTAACTTAACACCCTAAACCCTAACATA
1 TAAACCCTAACTTAAAACCCTAAACCCTAACATA
*
116899 -AAATCCTAA
1 TAAACCCTAA
116908 ATAATAGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 25 0.68
33 12 0.32
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23
Consensus pattern (34 bp):
TAAACCCTAACTTAAAACCCTAAACCCTAACATA
Found at i:121545 original size:5 final size:5
Alignment explanation
Indices: 121521--121568 Score: 69
Period size: 5 Copynumber: 9.2 Consensus size: 5
121511 TCCACTTTGC
*
121521 TTCTCT TTCATT TTCTT TTCCT TTCTT TTCTT TTCTT TTCTT TTCTT T
1 TTCT-T TTC-TT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT T
121569 GTCAATAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
5 31 0.79
6 7 0.18
7 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (5 bp):
TTCTT
Found at i:126489 original size:12 final size:12
Alignment explanation
Indices: 126472--126501 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
126462 TTCCTGCCCT
126472 AGAAATTTGTGA
1 AGAAATTTGTGA
126484 AGAAATTTGTGA
1 AGAAATTTGTGA
126496 ACGAAA
1 A-GAAA
126502 ATCTCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (12 bp):
AGAAATTTGTGA
Found at i:131360 original size:25 final size:25
Alignment explanation
Indices: 131342--131402 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
131332 TAAAGAAAAC
131342 AAAATGTAATATAGGTAAATGGAAT
1 AAAATGTAATATAGGTAAATGGAAT
131367 AAAATGTAATATAGGTAAATGGAAT
1 AAAATGTAATATAGGTAAATGGAAT
131392 AAAATGTAATA
1 AAAATGTAATA
131403 ATAATAGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (25 bp):
AAAATGTAATATAGGTAAATGGAAT
Found at i:132416 original size:22 final size:21
Alignment explanation
Indices: 132391--132443 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
132381 CATGATTCAT
*
132391 ATTAAAAATGAAATATT-AATTA
1 ATTAAAAATCAAAT-TTCAA-TA
132413 ATTAAGAAATCAAATTTCAATA
1 ATTAA-AAATCAAATTTCAATA
132435 ATTATAAAA
1 ATTA-AAAA
132444 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
ATTAAAAATCAAATTTCAATA
Found at i:132449 original size:22 final size:24
Alignment explanation
Indices: 132393--132450 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
132383 TGATTCATAT
*
132393 TAAAAATGAAATATTAATTAATTA
1 TAAAAATCAAATATTAATTAATTA
*
132417 -AGAAATCAAAT-TTCAA-TAATTA
1 TAAAAATCAAATATT-AATTAATTA
132439 TAAAAAT-AAATA
1 TAAAAATCAAATA
132451 AATAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (24 bp):
TAAAAATCAAATATTAATTAATTA
Found at i:133833 original size:17 final size:17
Alignment explanation
Indices: 133808--133840 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
133798 TTGATTAATA
133808 TAAATAATAATTTAAAAT
1 TAAATAATAA-TTAAAAT
133826 TAAA-AATAATTAAAA
1 TAAATAATAATTAAAA
133841 AATGCCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATAATAATTAAAAT
Found at i:133841 original size:17 final size:18
Alignment explanation
Indices: 133808--133841 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
133798 TTGATTAATA
*
133808 TAAATAATAATTTAAAAT
1 TAAATAATAATTAAAAAT
133826 TAAA-AATAATTAAAAA
1 TAAATAATAATTAAAAA
133842 ATGCCACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATAATAATTAAAAAT
Found at i:137457 original size:24 final size:24
Alignment explanation
Indices: 137424--137469 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
137414 GTCAATTGAA
*
137424 ACTTTTGTTTTGT-TTGTTGTTTCT
1 ACTTTGGTTTTGTCTT-TTGTTTCT
137448 ACTTTGGTTTTGTCTTTTGTTT
1 ACTTTGGTTTTGTCTTTTGTTT
137470 GTTACTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.04, C:0.09, G:0.17, T:0.70
Consensus pattern (24 bp):
ACTTTGGTTTTGTCTTTTGTTTCT
Found at i:141916 original size:60 final size:60
Alignment explanation
Indices: 141845--142006 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 60
141835 TATATGACAC
* * *
141845 TCATTTCAAATTGGTCACT-AAACTTTTAAACATTTTAATTTCATCATTAAACTATGAT-T
1 TCATTTTAAATTGGTC-CTCAAACTTTTAAACATTTCAATTTCATCATCAAACTATGATCT
* * *
141904 ATCATTTTAAATTAGTCCTCAAACTTTTAAACATTTCATTTTCATCCTCAAACTATGATCT
1 -TCATTTTAAATTGGTCCTCAAACTTTTAAACATTTCAATTTCATCATCAAACTATGATCT
* * * * *
141965 TCATTCTAAATTGGTCCCCAATCTTTTTGAATATTTCAATTT
1 TCATTTTAAATTGGTCCTCAAAC-TTTTAAACATTTCAATTT
142007 TATCCTAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.02
60 68 0.79
61 16 0.19
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (60 bp):
TCATTTTAAATTGGTCCTCAAACTTTTAAACATTTCAATTTCATCATCAAACTATGATCT
Found at i:151459 original size:60 final size:59
Alignment explanation
Indices: 151387--151515 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 59
151377 TCAACTGGTA
* * * *
151387 ATTTTATAACTTTTAATAGTCGAGGGACTCAAC-AAAGCAATGTCTTATAGTCGGAGGAAC
1 ATTTTATAACTTTTAATAGTCGAGGGAATCAACTAAA-CAATATCCTATAATCGG-GGAAC
* * * *
151447 ATTTTGTAACTTTTGATAGTCGATGGAATCAACTAAACAATATCCTATAATCGGGGACC
1 ATTTTATAACTTTTAATAGTCGAGGGAATCAACTAAACAATATCCTATAATCGGGGAAC
151506 ATTTTTATAA
1 A-TTTTATAA
151516 TTTACCCTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
59 5 0.09
60 50 0.86
61 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAGTCGAGGGAATCAACTAAACAATATCCTATAATCGGGGAAC
Found at i:166224 original size:18 final size:18
Alignment explanation
Indices: 166201--166235 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
166191 ATTTTTATTG
166201 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
166219 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
166236 GGGTCGAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:170362 original size:4 final size:4
Alignment explanation
Indices: 170353--170381 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
170343 TCTTCACTTC
170353 CATT CATT CATT CATT CATT CATT CATT C
1 CATT CATT CATT CATT CATT CATT CATT C
170382 CCAGCAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:182673 original size:158 final size:157
Alignment explanation
Indices: 182391--182696 Score: 382
Period size: 158 Copynumber: 1.9 Consensus size: 157
182381 GAATTTATCA
* * *
182391 TTTTACGGGGGCTTAAATCCAATTTTATCATGTATAAAACTAATAATTGTTTAATTTCCAAAAAG
1 TTTTACGGGGGCCTAAATCCAATTTTACCATGTATAAAACTAACAA-TGTTTAATTTCCAAAAAG
* * * ** * *
182456 TCTATATGCAATTTTATAACTATAGGGTGTGCCTATGGTAACATGCATAGATAATTAGATATGCT
65 TCAATATACAAATTTATAACTATAGGGACTGCCTATGGCAACATGCATAGATAACTAGATATGCT
182521 CTGGCATGAAATAAATATAATTTTATTG
130 CTGGCATGAAATAAATATAATTTTATTG
* * * *
182549 TTTTACGGGGGCCTATATTCAATTTTACCATGTAT-AAATTTACAA-GTATTAGATTTCCAAATA
1 TTTTACGGGGGCCTAAATCCAATTTTACCATGTATAAAACTAACAATGT-TTA-ATTTCCAAA-A
* * * *
182612 AGTCAATATACAAATTTATCATTGTAGGGACTGCTTATGGCAACATGCATAGATAACTAGATATG
63 AGTCAATATACAAATTTATAACTATAGGGACTGCCTATGGCAACATGCATAGATAACTAGATATG
* *
182677 CTCTGTCATGAATTAAATAT
128 CTCTGGCATGAAATAAATAT
182697 GTTAAATTTT
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
155 2 0.02
156 3 0.02
157 16 0.13
158 104 0.83
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (157 bp):
TTTTACGGGGGCCTAAATCCAATTTTACCATGTATAAAACTAACAATGTTTAATTTCCAAAAAGT
CAATATACAAATTTATAACTATAGGGACTGCCTATGGCAACATGCATAGATAACTAGATATGCTC
TGGCATGAAATAAATATAATTTTATTG
Found at i:183145 original size:2 final size:2
Alignment explanation
Indices: 183138--183176 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
183128 TTCGAAAAGA
183138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
183177 GTTTAATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:183518 original size:59 final size:59
Alignment explanation
Indices: 183434--183558 Score: 193
Period size: 59 Copynumber: 2.2 Consensus size: 59
183424 TTAAATCCAT
* *
183434 AAAATAATTAAC---TTATTGGGTATGTTTTAGTCCAAACCCAAAACATTAAAAGTAAA
1 AAAATAATTAACTTATTATTAGGTATGTTTTAGTCCAAACCCAAAACATTAAAAATAAA
* *
183490 AAATTAATTAACTTATTATTAGGTATGTTTTGGTCCAAACCCAAAACATTAAAAATAAA
1 AAAATAATTAACTTATTATTAGGTATGTTTTAGTCCAAACCCAAAACATTAAAAATAAA
183549 AAAATAATTA
1 AAAATAATTA
183559 TTTAAAACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
56 11 0.18
59 50 0.82
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (59 bp):
AAAATAATTAACTTATTATTAGGTATGTTTTAGTCCAAACCCAAAACATTAAAAATAAA
Found at i:184233 original size:21 final size:21
Alignment explanation
Indices: 184209--184253 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
184199 TGATTTTGAA
184209 AAAATTAAAAGTTT-AGATACT
1 AAAATTAAAAGTTTAAG-TACT
* *
184230 AAAATTGATAGTTTAAGTACT
1 AAAATTAAAAGTTTAAGTACT
184251 AAA
1 AAA
184254 TGCATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (21 bp):
AAAATTAAAAGTTTAAGTACT
Found at i:186629 original size:12 final size:12
Alignment explanation
Indices: 186612--186645 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
186602 TTTAATAATA
186612 AAATTTTTAAAT
1 AAATTTTTAAAT
186624 AAATTTTTAAAT
1 AAATTTTTAAAT
**
186636 TTATTTTTAA
1 AAATTTTTAA
186646 TAATTTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTTTTAAAT
Found at i:187712 original size:31 final size:30
Alignment explanation
Indices: 187639--187727 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
187629 GATGAATTTT
* *
187639 GGGATGAAATTA-AAATATTTAAAAGTTTG
1 GGGATGAAATTAGAAAAATTTAAAAGTTTA
* * *
187668 GGGATCAATTTAGAAAGAATATTATAAG-TTA
1 GGGATGAAATTAGAAA-AAT-TTAAAAGTTTA
*
187699 GGGATGAAATTAG-AATATTTAAAAGTTTA
1 GGGATGAAATTAGAAAAATTTAAAAGTTTA
187728 AGTATTAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
28 6 0.13
29 15 0.32
30 5 0.11
31 15 0.32
32 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.20, T:0.34
Consensus pattern (30 bp):
GGGATGAAATTAGAAAAATTTAAAAGTTTA
Found at i:191326 original size:2 final size:2
Alignment explanation
Indices: 191319--191345 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
191309 TTTATTATGC
191319 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
191346 GTTAGCATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:199243 original size:21 final size:21
Alignment explanation
Indices: 199219--199264 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
199209 TGATTTTGAA
199219 AAAATTAAAAGTTTAAATACT
1 AAAATTAAAAGTTTAAATACT
* * **
199240 AAAATTGATAGTTTATGTACT
1 AAAATTAAAAGTTTAAATACT
199261 AAAA
1 AAAA
199265 GTAATTTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (21 bp):
AAAATTAAAAGTTTAAATACT
Found at i:200831 original size:21 final size:21
Alignment explanation
Indices: 200805--200847 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
200795 ATTAAATAAT
200805 AGGAACGGGAGACAAAGGGTA
1 AGGAACGGGAGACAAAGGGTA
200826 AGGAACGGGAGACAAAGGGTA
1 AGGAACGGGAGACAAAGGGTA
200847 A
1 A
200848 AAGGCAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.42, T:0.05
Consensus pattern (21 bp):
AGGAACGGGAGACAAAGGGTA
Found at i:205573 original size:27 final size:27
Alignment explanation
Indices: 205516--205574 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
205506 CTAAATCAAG
**
205516 TTTATCATATCGGATTTCGACAGTAGT
1 TTTATCATATCGGATTTCGACAGTAAC
* *
205543 TTTATCATGTCGGATTTCAGGC-GTAAC
1 TTTATCATATCGGATTTC-GACAGTAAC
205570 TTTAT
1 TTTAT
205575 AATTGGGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (27 bp):
TTTATCATATCGGATTTCGACAGTAAC
Found at i:208790 original size:23 final size:23
Alignment explanation
Indices: 208760--208807 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
208750 CTAGTGAACC
*
208760 AACCAGAACCGCTTAACCGTTCG
1 AACCAGAACCGCTGAACCGTTCG
208783 AACCAGAACCGCTGAACCGTTCG
1 AACCAGAACCGCTGAACCGTTCG
208806 AA
1 AA
208808 TTGGACCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (23 bp):
AACCAGAACCGCTGAACCGTTCG
Found at i:213365 original size:21 final size:22
Alignment explanation
Indices: 213340--213383 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
213330 TAAAGCTGCT
*
213340 AAAACTAATCC-AATTTAAACA
1 AAAACTAAACCGAATTTAAACA
*
213361 AAAACTAAACCGAATTTACACA
1 AAAACTAAACCGAATTTAAACA
213383 A
1 A
213384 TTCTAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAACTAAACCGAATTTAAACA
Found at i:214674 original size:3 final size:3
Alignment explanation
Indices: 214666--214712 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
214656 TATGACATGT
214666 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
214713 TGACGTGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:218276 original size:15 final size:15
Alignment explanation
Indices: 218258--218310 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
218248 CCGGTTTCGG
218258 TTTTAAAAAAACCGA
1 TTTTAAAAAAACCGA
* *
218273 TTTTTTTAAAAAACCGG
1 --TTTTAAAAAAACCGA
*
218290 TTATAAAAAAACCGA
1 TTTTAAAAAAACCGA
218305 TTTTAA
1 TTTTAA
218311 TATTCCAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (15 bp):
TTTTAAAAAAACCGA
Found at i:218728 original size:13 final size:13
Alignment explanation
Indices: 218707--218761 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
218697 AAGTTCGATA
*
218707 AATTCAAATACTT
1 AATTGAAATACTT
218720 AATTGAAATACTT
1 AATTGAAATACTT
* *
218733 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
218747 AATTGAAATACTT
1 AATTGAAATACTT
218760 AA
1 AA
218762 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:218843 original size:32 final size:33
Alignment explanation
Indices: 218747--218845 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
218737 AACTCAACAT
* * *
218747 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
218780 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
218813 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
218845 A
1 A
218846 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:218864 original size:21 final size:21
Alignment explanation
Indices: 218840--218879 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
218830 ACTTCAAGTT
218840 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
218861 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
218880 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:221189 original size:12 final size:12
Alignment explanation
Indices: 221172--221217 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
221162 TTCGGATAAA
221172 AACCGGTTTTTT
1 AACCGGTTTTTT
221184 AACCGGTTTTTTT
1 AACCGG-TTTTTT
221197 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
221211 ATCCGGT
1 AACCGGT
221218 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:221202 original size:15 final size:14
Alignment explanation
Indices: 221171--221210 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
221161 TTTCGGATAA
221171 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
221184 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
221197 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
221211 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:224543 original size:94 final size:93
Alignment explanation
Indices: 224367--224552 Score: 232
Period size: 94 Copynumber: 2.0 Consensus size: 93
224357 AACTGTGTCG
* * * *
224367 GTATATGGAATATACAAGTACTTGATATGCTTATTCTGAGATAACATCTTCCTACAAGCAAAGAG
1 GTATATGGAATATACAAGTACTTCACATGCTTATTC-GAGACAACATCTTCCTACAAGAAAAGAG
* ***
224432 GTAAGATGCTTTTAATGTTTGAGAATCCA
65 GTAAGAAGCTCACAATGTTTGAGAATCCA
* *
224461 GTATATGGAATGTACAAGTACTTCACGTGCTTACATTC-AGACAACATCTTCCTACAAGAAAAGA
1 GTATATGGAATATACAAGTACTTCACATGCTT--ATTCGAGACAACATCTTCCTACAAGAAAAGA
224525 GGTATA-AAGCTCACAATGTTTGAGAATC
64 GGTA-AGAAGCTCACAATGTTTGAGAATC
224553 AAATTCTTCA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
94 74 0.94
95 1 0.01
96 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (93 bp):
GTATATGGAATATACAAGTACTTCACATGCTTATTCGAGACAACATCTTCCTACAAGAAAAGAGG
TAAGAAGCTCACAATGTTTGAGAATCCA
Found at i:226770 original size:60 final size:59
Alignment explanation
Indices: 226654--226770 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 59
226644 TCATATATCT
* * * * *
226654 TCAAACTATGATCCTTGTTTTAAATTGCCCCTAAACTTTTGAATATTTCAATTTCATAC
1 TCAAACTATGATACTTATTCTAAATTGCCCCTAAACTTTTAAATATTCCAATTTCATAC
* * *
226713 TCAAACTATGATACTTATTCTAAATTGGTCTCTAAACTTTTAAATCTTCCAATTTCAT
1 TCAAACTATGATACTTATTCTAAATT-GCCCCTAAACTTTTAAATATTCCAATTTCAT
226771 CCCTAAATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 23 0.47
60 26 0.53
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.43
Consensus pattern (59 bp):
TCAAACTATGATACTTATTCTAAATTGCCCCTAAACTTTTAAATATTCCAATTTCATAC
Found at i:227933 original size:30 final size:30
Alignment explanation
Indices: 227886--227976 Score: 148
Period size: 31 Copynumber: 3.0 Consensus size: 30
227876 AAATTTTGAA
*
227886 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
227915 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAA-CATTTTG
227946 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATTCAAGTCCAAAAAC-ATTTTG
227977 CCTTAAATTG
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 36 0.62
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTG
Found at i:229373 original size:17 final size:18
Alignment explanation
Indices: 229336--229373 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
229326 GTGTTAGAGG
*
229336 AAAAAAATGAATAAATGA
1 AAAAAAATGAATAAATAA
*
229354 AAAAAAATGAA-GAATAA
1 AAAAAAATGAATAAATAA
229371 AAA
1 AAA
229374 TAAGTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (18 bp):
AAAAAAATGAATAAATAA
Found at i:229425 original size:2 final size:2
Alignment explanation
Indices: 229418--229446 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
229408 AATAAATGAA
229418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
229447 AATGAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229540 original size:19 final size:17
Alignment explanation
Indices: 229505--229545 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
229495 ACGAAAATAT
229505 AATATAATATAAACAAA
1 AATATAATATAAACAAA
*
229522 AATATATATATAAAC-CA
1 AATATA-ATATAAACAAA
229539 AATATAA
1 AATATAA
229546 AAGTATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.59
18 8 0.36
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (17 bp):
AATATAATATAAACAAA
Found at i:229654 original size:2 final size:2
Alignment explanation
Indices: 229647--229691 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
229637 GATAATTACA
229647 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
229689 AT A
1 AT A
229692 GTAATACACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:229771 original size:19 final size:19
Alignment explanation
Indices: 229740--229777 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
229730 ATATATATAT
*
229740 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
229759 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
229778 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:230364 original size:37 final size:37
Alignment explanation
Indices: 230323--230418 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
230313 GGATCCTATC
* * *
230323 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
* *
230360 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
230397 TTTAGGAGTTTGAATCCTAGTA
1 TTTAGGAGTTTGAATCCTAGTA
230419 TGACGAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
Found at i:231515 original size:106 final size:106
Alignment explanation
Indices: 231150--232825 Score: 2253
Period size: 106 Copynumber: 16.0 Consensus size: 106
231140 GCATTGTTCC
* *** * *
231150 GAGTCCAATATCC-TCTG-TCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC
* * *
231213 AACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
231256 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
231315 TCAATC-GCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 -CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* *
231357 G-G-----TATCTTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
231416 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
231457 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
**
231522 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTAACTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * *
231563 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTAAGATGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
231628 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
231669 GAGTCTAATATCCTTCACTGTGAAATTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
231734 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCAT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
231775 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
231840 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
231881 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
231946 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
231987 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
232052 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
232093 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
232158 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
232199 GGGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
232264 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
232305 GAGTCCAATATCCCTCACTGTGAAGTTGAAATTGG----G--A-----AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
232358 CCAACGTTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
232399 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
232464 CCAGCGGTCCCTTCGTCATGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
232505 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
232570 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
232611 GAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
232676 CCAACGATCCCTTCGTCATGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * * *
232717 GAGTTCAATATCCTTCGTTGTGAACTTGAAATTGGCTCCGAAATTGGAAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
232781 CTAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
232822 GAGT
1 GAGT
232826 GGCACGATAT
Statistics
Matches: 1402, Mismatches: 136, Indels: 65
0.87 0.08 0.04
Matches are distributed among these distances:
94 81 0.06
95 31 0.02
96 2 0.00
97 1 0.00
98 1 0.00
99 3 0.00
100 51 0.04
101 46 0.03
102 4 0.00
105 49 0.03
106 1129 0.81
107 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:234167 original size:22 final size:22
Alignment explanation
Indices: 234139--234185 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
234129 GATTTCTGGG
* *
234139 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
234161 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
234182 CAAG
1 CAAG
234186 CGAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:235973 original size:22 final size:22
Alignment explanation
Indices: 235900--235965 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
235890 TATGGACATC
*
235900 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
235922 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
235944 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
235966 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:237498 original size:15 final size:15
Alignment explanation
Indices: 237478--237512 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
237468 CGAGGGTATT
237478 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
237493 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
237508 GTAGT
1 GTAGT
237513 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:244170 original size:27 final size:27
Alignment explanation
Indices: 244116--244180 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
244106 GATATGACCA
*
244116 ATATGAAATGAAATAAGCTATGTGAAT
1 ATATGAAATGAAATAAGATATGTGAAT
* *
244143 ATATGAAATGACATATGAATATGT-AAT
1 ATATGAAATGAAATAAG-ATATGTGAAT
* *
244170 ATGTGATATGA
1 ATATGAAATGA
244181 TATGAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.32
Consensus pattern (27 bp):
ATATGAAATGAAATAAGATATGTGAAT
Found at i:246442 original size:22 final size:21
Alignment explanation
Indices: 246417--246499 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 21
246407 CTTTTTGTCC
*
246417 CTTTTTCTTTTGATTTTTGCTT
1 CTTTTTTTTTTG-TTTTTGCTT
* *
246439 CTTTTCTTTTTTGTTCTTGATT
1 CTTTT-TTTTTTGTTTTTGCTT
246461 CTTTTTTTTATTTGTTTTTTGCTT
1 C-TTTTTTT-TTTG-TTTTTGCTT
*
246485 CTTTGCTTTTTTGTT
1 CTTT-TTTTTTTGTT
246500 CTTGATTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 18 0.36
23 21 0.42
24 11 0.22
ACGTcount: A:0.04, C:0.12, G:0.10, T:0.75
Consensus pattern (21 bp):
CTTTTTTTTTTGTTTTTGCTT
Found at i:246455 original size:15 final size:15
Alignment explanation
Indices: 246430--246502 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 15
246420 TTTCTTTTGA
246430 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
246446 TTTTTGTTCTTGATTCT
1 TTTTTGTTCTT--TTCT
* *
246463 TTTTT-TT-ATTTGT
1 TTTTTGTTCTTTTCT
*
246476 TTTTTGCTTCTTTGCT
1 TTTTTG-TTCTTTTCT
246492 TTTTTGTTCTT
1 TTTTTGTTCTT
246503 GATTGGATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.17
15 13 0.28
16 17 0.36
17 9 0.19
ACGTcount: A:0.03, C:0.12, G:0.10, T:0.75
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:246498 original size:23 final size:23
Alignment explanation
Indices: 246424--246499 Score: 91
Period size: 22 Copynumber: 3.3 Consensus size: 23
246414 TCCCTTTTTC
*
246424 TTTTGATTTTTGCTTCTTTTCTT
1 TTTTGTTTTTTGCTTCTTTTCTT
* * *
246447 TTTTG-TTCTTGATTCTTTTTTT
1 TTTTGTTTTTTGCTTCTTTTCTT
*
246469 TATTTGTTTTTTGCTTCTTTGCTT
1 T-TTTGTTTTTTGCTTCTTTTCTT
246493 TTTTGTT
1 TTTTGTT
246500 CTTGATTGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 15 0.34
23 15 0.34
24 14 0.32
ACGTcount: A:0.04, C:0.11, G:0.11, T:0.75
Consensus pattern (23 bp):
TTTTGTTTTTTGCTTCTTTTCTT
Found at i:251093 original size:2 final size:2
Alignment explanation
Indices: 251086--251126 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
251076 CCCTGCTCTA
251086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
251127 GTAATAATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:251191 original size:19 final size:19
Alignment explanation
Indices: 251169--251259 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
251159 AAAAGTATGT
251169 ATATATATATAAATAATAA
1 ATATATATATAAATAATAA
* *
251188 ATATAGTATTAAAAAATAACCAA
1 ATATA-TA-T-ATAAATAA-TAA
* *
251211 ATGAATATAAATAAATAAAAA
1 AT--ATATATATAAATAATAA
* *
251232 ATATATTTATATATAAT-A
1 ATATATATATAAATAATAA
251250 ATA-ATATATA
1 ATATATATATA
251260 GTGTAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 4 0.07
19 16 0.29
20 2 0.04
21 5 0.09
22 14 0.25
23 4 0.07
24 2 0.04
25 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
ATATATATATAAATAATAA
Found at i:251304 original size:67 final size:66
Alignment explanation
Indices: 251147--251317 Score: 167
Period size: 67 Copynumber: 2.6 Consensus size: 66
251137 GCTTATAAGT
* *
251147 AAAATATTTAAAAAAAGTATGTATATATATATA-AATAATAAATATAGTATTAAAAAATAACCAA
1 AAAATATTTAAAAAAAATATGTATATATATATATAATAATAAATATAGTAGTAAAAAAT-A-CAA
251211 ATG
64 ATG
* ** *
251214 AATATAAATAAATAAAAA-A--TATATTTATATATAATAATAATATATAGT-GTAAAAAAT-CAA
1 AAAATATTTAAA-AAAAATATGTATATATATATATAATAATAA-ATATAGTAGTAAAAAATACAA
*
251274 TTG
64 ATG
*
251277 AAAATCATTTAAAAAAACATATGTATATATATTTAT-ATAAT
1 AAAAT-ATTTAAAAAAA-ATATGTATATATATATATAATAAT
251318 GAAAATAATG
Statistics
Matches: 84, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
63 13 0.15
64 6 0.07
65 12 0.14
66 21 0.25
67 28 0.33
68 4 0.05
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (66 bp):
AAAATATTTAAAAAAAATATGTATATATATATATAATAATAAATATAGTAGTAAAAAATACAAAT
G
Found at i:251760 original size:37 final size:37
Alignment explanation
Indices: 251719--251822 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
251709 GTGCTTGTGG
* * * *
251719 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* *
251756 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
251793 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
251823 TGACGAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:259560 original size:59 final size:58
Alignment explanation
Indices: 259440--259620 Score: 213
Period size: 59 Copynumber: 3.1 Consensus size: 58
259430 CATATATTTA
* * * * *
259440 CAAATTATGATCCTTATTTTAAATTGCCCCTAAACTTTTAAATATTTCAATTGCATCCT
1 CAAACTATGATCCTTATTATAAATTGTCCCTAAACTTTTAAATATTCCAATTTCAT-CT
* * *
259499 CAAACTATGATACTTATTATAAATTAGT-CCTCAAATTTTTGAATATTCCAATTTCATCT
1 CAAACTATGATCCTTATTATAAATT-GTCCCT-AAACTTTTAAATATTCCAATTTCATCT
* *
259558 CAAACTATG-TCCCTTATTCTAAATTTGTCCCTAAACTTTTAAATATTCCAATTTCATCC
1 CAAACTATGAT-CCTTATTATAAA-TTGTCCCTAAACTTTTAAATATTCCAATTTCATCT
259617 CAAA
1 CAAA
259621 ATCCATCCAA
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
58 1 0.01
59 76 0.73
60 27 0.26
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (58 bp):
CAAACTATGATCCTTATTATAAATTGTCCCTAAACTTTTAAATATTCCAATTTCATCT
Found at i:259797 original size:30 final size:29
Alignment explanation
Indices: 259748--259804 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
259738 ATACATATAA
* * *
259748 TTTGGGATGAAATTGAAATGTTGAAAATG
1 TTTGGGATGAAACTAAAATGTTCAAAATG
259777 TTTGGGAATGAAACTAAAATGTTCAAAA
1 TTTGGG-ATGAAACTAAAATGTTCAAAA
259805 ATTTAAAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (29 bp):
TTTGGGATGAAACTAAAATGTTCAAAATG
Found at i:261705 original size:42 final size:42
Alignment explanation
Indices: 261646--261729 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
261636 AATCCAAGAG
* *
261646 ATGAACTGGTTCTCCTTCCTGTTCCAGTGGTTGTTCCATATC
1 ATGAACTGGTTCTCCTTCATGTTCCAGTGGTTGTTCAATATC
261688 ATGAACTGGTTCTCCTTCATGTTCCAGTGGTTGTTCAATATC
1 ATGAACTGGTTCTCCTTCATGTTCCAGTGGTTGTTCAATATC
261730 TGTTGGGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (42 bp):
ATGAACTGGTTCTCCTTCATGTTCCAGTGGTTGTTCAATATC
Found at i:265339 original size:35 final size:35
Alignment explanation
Indices: 265285--265395 Score: 188
Period size: 35 Copynumber: 3.2 Consensus size: 35
265275 TATAAAAATA
265285 ATCATACT-AAAAAATATTAGGACTACAAAGACGG
1 ATCATACTAAAAAAATATTAGGACTACAAAGACGG
265319 ATCATACTAAAAAAATATTAGGACTACAAAGACGG
1 ATCATACTAAAAAAATATTAGGACTACAAAGACGG
* * *
265354 ATCATACTAAAAAAATATTAGGACTATAAAAAGGG
1 ATCATACTAAAAAAATATTAGGACTACAAAGACGG
265389 ATCATAC
1 ATCATAC
265396 AAATGATCCC
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 8 0.11
35 65 0.89
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.22
Consensus pattern (35 bp):
ATCATACTAAAAAAATATTAGGACTACAAAGACGG
Found at i:266542 original size:59 final size:58
Alignment explanation
Indices: 266406--266561 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 58
266396 TTTAAAATGC
* * * * *
266406 CCCTAAACTTTTAAATATTTCAATTTCATCCTCAAACTATGATACTTTTTTTAAATTAG
1 CCCTAAACTTTTAAATATTCCAATTTCAT-CTCAAAATATGACACTTATTCTAAATTAG
* ** * * * * *
266465 ACCTCGGATTTTTTAATATTCCAATTTCATCTCAAAATATGGCCCTTATTCTAAATTTG
1 CCCT-AAACTTTTAAATATTCCAATTTCATCTCAAAATATGACACTTATTCTAAATTAG
*
266524 TCCCTAAACTTTTAAATATTCCAATTTCATCCCAAAAT
1 -CCCTAAACTTTTAAATATTCCAATTTCATCTCAAAAT
266562 CCATCCAAAC
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
59 53 0.70
60 23 0.30
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (58 bp):
CCCTAAACTTTTAAATATTCCAATTTCATCTCAAAATATGACACTTATTCTAAATTAG
Found at i:269502 original size:29 final size:29
Alignment explanation
Indices: 269468--269536 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
269458 CGATTTAGTC
269468 ATTAAATTTTAAAATGAATCATTTTTATG
1 ATTAAATTTTAAAATGAATCATTTTTATG
269497 ATTAAATTTTAAAATGAATCATTTTTATG
1 ATTAAATTTTAAAATGAATCATTTTTATG
269526 ATTAAATTTTA
1 ATTAAATTTTA
269537 GTTTTCGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (29 bp):
ATTAAATTTTAAAATGAATCATTTTTATG
Found at i:269522 original size:16 final size:16
Alignment explanation
Indices: 269474--269523 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
269464 AGTCATTAAA
269474 TTTTAAAATGAATCAT
1 TTTTAAAATGAATCAT
* * *
269490 TTTT---ATGATTAAA
1 TTTTAAAATGAATCAT
269503 TTTTAAAATGAATCAT
1 TTTTAAAATGAATCAT
269519 TTTTA
1 TTTTA
269524 TGATTAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 10 0.40
16 15 0.60
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTAAAATGAATCAT
Found at i:270162 original size:89 final size:89
Alignment explanation
Indices: 270011--270190 Score: 281
Period size: 89 Copynumber: 2.0 Consensus size: 89
270001 AAAAGGTAAA
* *
270011 AAAATAAAGAATAGTGAAATATGAATGTTTTGATATCGATCTTGTTGCAAACAATGACCGATGAC
1 AAAATAAAGAATAGTGAAATATGAATGTTTTGATATCGATCTTGCTGCAAACAACGACCGATGAC
*
270076 ACGCAACAAATGGTCAATAGAGAC
66 ACACAACAAATGGTCAATAGAGAC
*
270100 AAAATAAAGAGTAGTGAAATATGAATGTTTT-AGTATCGATCTTGCTGCAAACAACGACCGATGA
1 AAAATAAAGAATAGTGAAATATGAATGTTTTGA-TATCGATCTTGCTGCAAACAACGACCGATGA
* * *
270164 CACACGACAATTGGTCGATAGAGAC
65 CACACAACAAATGGTCAATAGAGAC
270189 AA
1 AA
270191 TAAGTGAAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 1 0.01
89 82 0.99
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (89 bp):
AAAATAAAGAATAGTGAAATATGAATGTTTTGATATCGATCTTGCTGCAAACAACGACCGATGAC
ACACAACAAATGGTCAATAGAGAC
Found at i:271769 original size:2 final size:2
Alignment explanation
Indices: 271762--271789 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
271752 GATTTTCTGA
271762 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
271790 TAAGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:271867 original size:23 final size:22
Alignment explanation
Indices: 271829--271872 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
271819 TGTTTTTTTC
271829 TCTTAAAAATTGTATAAGTTCA
1 TCTTAAAAATTGTATAAGTTCA
*
271851 TCTTCAAAAATTTTATAAGTTC
1 TCTT-AAAAATTGTATAAGTTC
271873 TCTCCTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
TCTTAAAAATTGTATAAGTTCA
Found at i:275561 original size:19 final size:19
Alignment explanation
Indices: 275537--275584 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
275527 GAATATTTTT
* *
275537 AATTAAAAAAATAGTTTAC
1 AATTAAAAAAATAATATAC
* * *
275556 AATTAATATAATAATATAT
1 AATTAAAAAAATAATATAC
275575 AATTAAAAAA
1 AATTAAAAAA
275585 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATTAAAAAAATAATATAC
Found at i:279364 original size:43 final size:40
Alignment explanation
Indices: 279274--279369 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
279264 AGTTCGCTTA
*
279274 TGTTCGTTTATTT-ATTAAATGAACGAACATGAACAAGAT
1 TGTTCGTTCATTTAATTAAATGAACGAACATGAACAAGAT
*
279313 T-TTGCGTTCGTTTAATTAAATGAACGAACATGAACAAAGAGCT
1 TGTT-CGTTCATTTAATTAAATGAACGAACATGAAC-AAGA--T
279356 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
279370 CGTTCGTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 2 0.04
39 8 0.17
40 21 0.44
41 4 0.08
43 11 0.23
44 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (40 bp):
TGTTCGTTCATTTAATTAAATGAACGAACATGAACAAGAT
Found at i:279674 original size:10 final size:10
Alignment explanation
Indices: 279659--279732 Score: 103
Period size: 10 Copynumber: 7.1 Consensus size: 10
279649 AGTTTTTTTT
279659 TGTTCGTTTA
1 TGTTCGTTTA
279669 TGTTCGTTTA
1 TGTTCGTTTA
279679 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
**
279692 TGTTCGTTCG
1 TGTTCGTTTA
279702 TGTTCGTTTA
1 TGTTCGTTTA
279712 TGTTCGTTTA
1 TGTTCGTTTA
279722 TGTTCGTTTA
1 TGTTCGTTTA
279732 T
1 T
279733 TTATTCAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
10 47 0.82
13 10 0.18
ACGTcount: A:0.08, C:0.11, G:0.22, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:279676 original size:43 final size:43
Alignment explanation
Indices: 279628--279722 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
279618 CTTTTTTACA
* ** **
279628 TTCGTTTGTTGTGTTCGAATAAGTTTTTTTTTGTTCGTTTATG
1 TTCGTTTATTGTGTTCGAATAAGTTCGTTCGTGTTCGTTTATG
** *
279671 TTCGTTTATTGTGTTCGTTTATGTTCGTTCGTGTTCGTTTATG
1 TTCGTTTATTGTGTTCGAATAAGTTCGTTCGTGTTCGTTTATG
279714 TTCGTTTAT
1 TTCGTTTAT
279723 GTTCGTTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.60
Consensus pattern (43 bp):
TTCGTTTATTGTGTTCGAATAAGTTCGTTCGTGTTCGTTTATG
Found at i:279914 original size:43 final size:40
Alignment explanation
Indices: 279824--279919 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
279814 TGTTCGTTTA
* * *
279824 TGTTCGTTTATTT-ATTAAATGAATGAACATGAACTAGAT
1 TGTTCGTTCATTTAATTAAATGAACGAACATGAACAAGAT
*
279863 T-TTGCGTTCGTTTAATTAAATGAACGAACATGAACAAAGAGCT
1 TGTT-CGTTCATTTAATTAAATGAACGAACATGAAC-AAGA--T
279906 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
279920 CGTTCGTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
38 2 0.04
39 8 0.17
40 20 0.43
41 3 0.07
43 11 0.24
44 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (40 bp):
TGTTCGTTCATTTAATTAAATGAACGAACATGAACAAGAT
Found at i:280344 original size:16 final size:16
Alignment explanation
Indices: 280323--280355 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
280313 AAAAAAAATT
280323 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
280339 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
280355 T
1 T
280356 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:281966 original size:33 final size:35
Alignment explanation
Indices: 281908--281982 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 35
281898 ATAAAAATGA
* *
281908 ATCATACTAAAAAAATATTAGGACTACAAAGACGG
1 ATCATACTAAAAAAATATTAAGACTACAAAAACGG
*
281943 ATCATACT-AAAAAA-ATTAAGACTATAAAAACGG
1 ATCATACTAAAAAAATATTAAGACTACAAAAACGG
281976 ATCATAC
1 ATCATAC
281983 AAATGGTCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 23 0.62
34 6 0.16
35 8 0.22
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (35 bp):
ATCATACTAAAAAAATATTAAGACTACAAAAACGG
Found at i:283521 original size:13 final size:13
Alignment explanation
Indices: 283503--283531 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
283493 TTTCACTTCT
283503 AAATGCAAGGCCC
1 AAATGCAAGGCCC
283516 AAATGCAAGGCCC
1 AAATGCAAGGCCC
283529 AAA
1 AAA
283532 ATCGTCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.28, G:0.21, T:0.07
Consensus pattern (13 bp):
AAATGCAAGGCCC
Found at i:288204 original size:16 final size:17
Alignment explanation
Indices: 288183--288224 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
288173 ATCCGACCCG
*
288183 AAATAACATATTTA-TA
1 AAATAACATATTGAGTA
*
288199 AAATAATATATTGAGTA
1 AAATAACATATTGAGTA
288216 AAA-AACATA
1 AAATAACATA
288225 ATCCGATCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (17 bp):
AAATAACATATTGAGTA
Found at i:290772 original size:37 final size:37
Alignment explanation
Indices: 290696--290772 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
290686 TTTTTATATT
*
290696 TTTAATTTTGTAAAAATAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAATAATTATATAAATATTATCAA
* *
290733 TTTAATTTTTTAAAGAA-AA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AATAATTATATAAATATTAT-CAA
290770 TTT
1 TTT
290773 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAATAATTATATAAATATTATCAA
Found at i:297283 original size:19 final size:19
Alignment explanation
Indices: 297246--297376 Score: 156
Period size: 19 Copynumber: 6.7 Consensus size: 19
297236 AACACAGAAG
297246 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
297267 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
297286 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
297305 TCAAATTCACAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
297325 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
* *
297345 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
297365 T-AATTTCGCAAC
1 TCAAATTCGCAAC
297377 AGGTTTTAGT
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
19 49 0.49
20 41 0.41
21 10 0.10
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:297355 original size:59 final size:59
Alignment explanation
Indices: 297246--297357 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
297236 AACACAGAAG
*
297246 TCAAATTCGCAACACTGAATTTCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCACAACACTGAATTTCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
* * * *
297305 TCAAATTCACAACTC-GATTTTCAAATTCGCAACTCGATTTTCGAATTCGCAAC
1 TCAAATTCACAACACTGAATTTCAAATTCGCAACT-GAATTTCAAATTCGCAAC
297358 ACGAATTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 18 0.38
59 29 0.62
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (59 bp):
TCAAATTCACAACACTGAATTTCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
Found at i:297377 original size:19 final size:20
Alignment explanation
Indices: 297087--297377 Score: 215
Period size: 20 Copynumber: 14.7 Consensus size: 20
297077 AAATGACCAA
* * *
297087 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* * *
297107 CAATTTCGCAAC-CTAGTTT
1 CAAATTCGCAACACGAATTT
*
297126 CCAAATTCGCAACGCGAATATGT
1 -CAAATTCGCAACACGAAT-T-T
*
297149 -AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* *
297167 GTAAA-TCGCAACACTG-ATGT
1 -CAAATTCGCAACAC-GAATTT
* **
297187 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACGAATTT
*
297207 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* *
297227 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACAC-GAATTT
297247 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
297268 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
297287 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* * *
297306 CAAATTCACAACTCGATTTT
1 CAAATTCGCAACACGAATTT
* *
297326 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
297346 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
297366 -AATTTCGCAACA
1 CAAATTCGCAACA
297378 GGTTTTAGTT
Statistics
Matches: 224, Mismatches: 33, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.00
19 56 0.25
20 139 0.62
21 26 0.12
22 1 0.00
23 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:298333 original size:24 final size:24
Alignment explanation
Indices: 298306--298359 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
298296 GTATTCGAAA
**
298306 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTCATCAATACCCGGAC
* *
298330 TTTGATCTTCATCAATACTCGGAT
1 TTTGATCTTCATCAATACCCGGAC
298354 TTTGAT
1 TTTGAT
298360 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTCATCAATACCCGGAC
Found at i:300636 original size:18 final size:18
Alignment explanation
Indices: 300613--300648 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
300603 AAGCAAAAGG
*
300613 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
300631 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
300649 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:300971 original size:27 final size:27
Alignment explanation
Indices: 300941--301037 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
300931 AATTTAAAAC
300941 AACAAATCAACTTTTACAAATCAATTA
1 AACAAATCAACTTTTACAAATCAATTA
* *
300968 AACAAGCAATAAATAATTCTATTTACACATCAAATTA
1 AAC-A--AAT---CAA--CT-TTTACAAATCAA-TTA
*
301005 AACAAATCAACTTTTACAAATAAATTA
1 AACAAATCAACTTTTACAAATCAATTA
301032 AACAAA
1 AACAAA
301038 CAAAAAATTC
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
27 12 0.22
28 11 0.20
29 2 0.04
30 3 0.05
31 2 0.04
33 2 0.04
34 3 0.05
35 2 0.04
36 12 0.22
37 6 0.11
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (27 bp):
AACAAATCAACTTTTACAAATCAATTA
Found at i:301091 original size:61 final size:64
Alignment explanation
Indices: 300941--301079 Score: 205
Period size: 64 Copynumber: 2.2 Consensus size: 64
300931 AATTTAAAAC
* *
300941 AACAAATCAACTTTTACAAATCAATTAAACAAGCAATAAATAATTCTATTTACACATCAAATTA
1 AACAAATCAACTTTTACAAATAAATTAAACAAACAATAAATAATTCTATTTACACATCAAATTA
* *
301005 AACAAATCAACTTTTACAAATAAATTAAACAAAC-A-AAA-AATTCTTATTTCCTCATC-AATTA
1 AACAAATCAACTTTTACAAATAAATTAAACAAACAATAAATAATTC-TATTTACACATCAAATTA
301066 AACAAATCAACTTT
1 AACAAATCAACTTT
301080 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
61 24 0.34
62 13 0.19
63 1 0.01
64 32 0.46
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATAAATTAAACAAACAATAAATAATTCTATTTACACATCAAATTA
Found at i:302462 original size:21 final size:20
Alignment explanation
Indices: 302438--302509 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
302428 GAGGGACCCA
* *
302438 TTGAACGATGACTATGGCCTC
1 TTGAACGATGA-GAAGGCCTC
* * *
302459 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGA-AGGCCTC
302480 TTGAACGATGAGAAGAGCCTC
1 TTGAACGATGAGAAG-GCCTC
302501 TTGAACGAT
1 TTGAACGAT
302510 AGGAGATGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (20 bp):
TTGAACGATGAGAAGGCCTC
Found at i:302473 original size:42 final size:42
Alignment explanation
Indices: 302414--302507 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
302404 GTGAATCGGG
* *
302414 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGACTATG-GC
1 CTCTTGAACGGTGGGAGGGACCTC-TTGAACGATGA-GAAGAGC
*
302456 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAAGAGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGAGAAGAGC
302498 CTCTTGAACG
1 CTCTTGAACG
302508 ATAGGAGATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 2 0.04
42 44 0.94
43 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGAGAAGAGC
Found at i:302520 original size:21 final size:20
Alignment explanation
Indices: 302454--302527 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
302444 GATGACTATG
* * *
302454 GCCTCTTGAACGGTGGGAGGG
1 GCCTCTTGAACGATAGGA-GA
*
302475 GCCTCTTGAACGATGAGAAGA
1 GCCTCTTGAACGAT-AGGAGA
302496 GCCTCTTGAACGATAGGAGA
1 GCCTCTTGAACGATAGGAGA
*
302516 TGCCTATTGAAC
1 -GCCTCTTGAAC
302528 AATGACAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.11
21 38 0.84
22 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (20 bp):
GCCTCTTGAACGATAGGAGA
Found at i:302526 original size:42 final size:42
Alignment explanation
Indices: 302414--302533 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
302404 GTGAATCGGG
* * * * *
302414 CTCTTGAACGGTGGGAG-GGACCCATTGAACGATGACTATGGC
1 CTCTTGAACGATAGGAGAGG-CCTATTGAACGATGACGAAGGC
* * * *
302456 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGA-GAAGAGC
1 CTCTTGAACGATAGGAGAGGCCTATTGAACGATGACGAAG-GC
* *
302498 CTCTTGAACGATAGGAGATGCCTATTGAACAATGAC
1 CTCTTGAACGATAGGAGAGGCCTATTGAACGATGAC
302534 AGGTGAATCA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATAGGAGAGGCCTATTGAACGATGACGAAGGC
Found at i:305043 original size:22 final size:22
Alignment explanation
Indices: 305013--305069 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
305003 GATGGAGATA
* * *
305013 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGAG
*
305035 GACGGATTTCGTCAGAGATGAG
1 GACGGATTTCGCCAGAGATGAG
*
305057 GACGGATGTCGCC
1 GACGGATTTCGCC
305070 CTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGAG
Found at i:305248 original size:20 final size:20
Alignment explanation
Indices: 305223--305474 Score: 198
Period size: 20 Copynumber: 12.6 Consensus size: 20
305213 TAAACGCGCT
305223 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATTGCG
305243 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATTGCG
* *
305263 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATTGCG
* *
305283 TTGCGAATTTGA-AATTCAGTG
1 TTGCGAATTTGACTATT--GCG
* **
305304 TTGCGAATTTGACTATCGTT
1 TTGCGAATTTGACTATTGCG
* *
305324 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATTGCG
*
305344 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TATT-GCG
* *
305364 TTGCGAATTTGACT-TCAGTG
1 TTGCGAATTTGACTAT-TGCG
**
305384 TTGCGAATTTGACTACCGCG
1 TTGCGAATTTGACTATTGCG
*
305404 TTGCGAATTTGACT-TATGTG
1 TTGCGAATTTGACTAT-TGCG
*
305424 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC-TATT-GCG
*
305444 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TATT-GCG
305464 TTGCGAATTTG
1 TTGCGAATTTG
305475 TTGGTCATTT
Statistics
Matches: 192, Mismatches: 25, Indels: 28
0.78 0.10 0.11
Matches are distributed among these distances:
18 4 0.02
19 13 0.07
20 148 0.77
21 23 0.12
22 4 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTATTGCG
Found at i:305314 original size:61 final size:62
Alignment explanation
Indices: 305223--305416 Score: 231
Period size: 60 Copynumber: 3.2 Consensus size: 62
305213 TAAACGCGCT
* * *
305223 TTGCGAATTTGAC-TATT-GCGTTGCGAATTTGACTATTGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACAGATTCGCGTTGCGAATTTGACTATAGTGTTGCGAATTTGACTTTTGTG
* * *
305283 TTGCGAATTTGA-A-ATTCAGTGTTGCGAATTTGACTATCGTTTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACAGATTC-GCGTTGCGAATTTGACTATAGTGTTGCGAATTTGACTTTTGTG
*** *
305344 TTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGACT-TCAGTGTTGCGAATTTGACTACCGCG
1 TTGCGAATTTGACAGATTCGCGTTGCGAATTTGACTAT-AGTGTTGCGAATTTGACTTTTGTG
305404 TTGCGAATTTGAC
1 TTGCGAATTTGAC
305417 TTATGTGTTG
Statistics
Matches: 115, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
59 5 0.04
60 56 0.49
61 52 0.45
62 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (62 bp):
TTGCGAATTTGACAGATTCGCGTTGCGAATTTGACTATAGTGTTGCGAATTTGACTTTTGTG
Found at i:305415 original size:80 final size:80
Alignment explanation
Indices: 305223--305474 Score: 307
Period size: 80 Copynumber: 3.1 Consensus size: 80
305213 TAAACGCGCT
* * * * * *
305223 TTGCGAATTTGACTATTGCGTTGCGAATTTGACTATTGCGTTGCGAATTTGAC-TTTTGTGTTGC
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCG-ATTT-ACAATTCGCGTTGC
305287 GAATTTGAAATTCAGTG
64 GAATTTGAAATTCAGTG
**
305304 TTGCGAATTTGACTATCGTTTTGCGAATTTGACTTTTGTGTTGCGATTTACAGATTCGCGTTGCG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACA-ATTCGCGTTGCG
*
305369 AATTTG-ACTTCAGTG
65 AATTTGAAATTCAGTG
* *
305384 TTGCGAATTTGACTACCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAC-AATTCGCGTTGCG
*
305449 -ATTT-ACAGATTC-GCG
65 AATTTGA-A-ATTCAGTG
305464 TTGCGAATTTG
1 TTGCGAATTTG
305475 TTGGTCATTT
Statistics
Matches: 150, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
79 6 0.04
80 85 0.57
81 59 0.39
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (80 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAATTCGCGTTGCGA
ATTTGAAATTCAGTG
Found at i:321676 original size:2 final size:2
Alignment explanation
Indices: 321669--321696 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
321659 AACCAGAATA
321669 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
321697 GATTTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.