Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001976.1 Hibiscus syriacus cultivar Beakdansim tig00004004_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: 915387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:262802 original size:20 final size:20
Alignment explanation
Indices: 262747--262803 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
262737 ATTTTGACAA
* *
262747 TTTCGCAACACGAATTTCTT
1 TTTCGCAACATGATTTTCTT
*
262767 TTTCGCAAC-TCAATTTTCTT
1 TTTCGCAACAT-GATTTTCTT
262787 TTTCGCAACATGATTTT
1 TTTCGCAACATGATTTT
262804 TTTGGGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (20 bp):
TTTCGCAACATGATTTTCTT
Found at i:262976 original size:14 final size:15
Alignment explanation
Indices: 262957--262994 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
262947 TCCCCATCTC
262957 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
262971 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
262987 TAATTTTT
1 TAATTTTT
262995 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:263195 original size:23 final size:23
Alignment explanation
Indices: 263161--263213 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
263151 CGGTAATTAC
*
263161 TGATTCAGCAAAACAATGTTGAA
1 TGATTCAACAAAACAATGTTGAA
* *
263184 TGATTCAACAAAATAGTGTTGAA
1 TGATTCAACAAAACAATGTTGAA
263207 TGATTCA
1 TGATTCA
263214 GCACAGAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (23 bp):
TGATTCAACAAAACAATGTTGAA
Found at i:263903 original size:12 final size:12
Alignment explanation
Indices: 263882--263915 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
263872 ACCACATTTC
*
263882 CAATACCAAACA
1 CAATATCAAACA
263894 CAATATCAAACA
1 CAATATCAAACA
*
263906 CAATCTCAAA
1 CAATATCAAA
263916 ATCTATAACT
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:266710 original size:20 final size:20
Alignment explanation
Indices: 266672--266712 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
266662 ACTCGAATTC
*
266672 CAAATTCGCAACTCAAAAAT
1 CAAATTCGCAACACAAAAAT
* *
266692 CAAATTCGTAACACGAAAAT
1 CAAATTCGCAACACAAAAAT
266712 C
1 C
266713 GCAACTCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACAAAAAT
Found at i:266826 original size:34 final size:34
Alignment explanation
Indices: 266759--266827 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
266749 TTCACTTTTC
* *
266759 ATTTTCGCGTTGCGAATTTAAATATCGAGTTGCG
1 ATTTTCGCATTGCGAATTTAAATATCGAATTGCG
* * * *
266793 ATTTTCGTATTGCGAATTTGATTTTCGAATTGCG
1 ATTTTCGCATTGCGAATTTAAATATCGAATTGCG
266827 A
1 A
266828 AATCGATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (34 bp):
ATTTTCGCATTGCGAATTTAAATATCGAATTGCG
Found at i:266826 original size:54 final size:54
Alignment explanation
Indices: 266759--266887 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
266749 TTCACTTTTC
** * * * *
266759 ATTTTCGCGTTGCGAATTTAAATATCGAGTTGCGATTTTCGTATTGCGAATTTG
1 ATTTTCGAATTGCGAAATCAAATATCGAGTTACGATTTTCGTATTACGAATTTG
* * * *
266813 ATTTTCGAATTGCGAAATCGATTTTCGAGTTACGATTTTCGTGTTACGAATTTG
1 ATTTTCGAATTGCGAAATCAAATATCGAGTTACGATTTTCGTATTACGAATTTG
**
266867 ATTTTCGAATTGTAAAATCAA
1 ATTTTCGAATTGCGAAATCAA
266888 TTTTCGCGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (54 bp):
ATTTTCGAATTGCGAAATCAAATATCGAGTTACGATTTTCGTATTACGAATTTG
Found at i:266850 original size:14 final size:14
Alignment explanation
Indices: 266831--266861 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
266821 ATTGCGAAAT
266831 CGATTTTCGAGTTA
1 CGATTTTCGAGTTA
*
266845 CGATTTTCGTGTTA
1 CGATTTTCGAGTTA
266859 CGA
1 CGA
266862 ATTTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (14 bp):
CGATTTTCGAGTTA
Found at i:266891 original size:54 final size:54
Alignment explanation
Indices: 266783--266893 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
266773 AATTTAAATA
* * * *
266783 TCGAGTTGCGATTTTCGTATTGCGAATTTGATTTTCGAATTGCGAAATCGATTT
1 TCGAGTTACGATTTTCGTATTACGAATTTGATTTTCGAATTGCAAAATCAATTT
* *
266837 TCGAGTTACGATTTTCGTGTTACGAATTTGATTTTCGAATTGTAAAATCAATTT
1 TCGAGTTACGATTTTCGTATTACGAATTTGATTTTCGAATTGCAAAATCAATTT
266891 TCG
1 TCG
266894 CGTTGCAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (54 bp):
TCGAGTTACGATTTTCGTATTACGAATTTGATTTTCGAATTGCAAAATCAATTT
Found at i:266892 original size:40 final size:40
Alignment explanation
Indices: 266847--266952 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
266837 TCGAGTTACG
* *
266847 ATTTTCGTGTTACGAATTTGATTTTCGAATTGTAAAATCA
1 ATTTTCGTGTTGCGAATTTGATTTTCGAATTGCAAAATCA
* * * * ** * * *
266887 ATTTTCGCGTTGCAAATTCGATTTTTGCGTTGCGAATTCG
1 ATTTTCGTGTTGCGAATTTGATTTTCGAATTGCAAAATCA
*
266927 ATTTTTGTGTTGCGAATTTGATTTTC
1 ATTTTCGTGTTGCGAATTTGATTTTC
266953 TTAAACTTAT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (40 bp):
ATTTTCGTGTTGCGAATTTGATTTTCGAATTGCAAAATCA
Found at i:266910 original size:20 final size:20
Alignment explanation
Indices: 266791--266952 Score: 93
Period size: 20 Copynumber: 8.4 Consensus size: 20
266781 TATCGAGTTG
**
266791 CGATTTTCGTATTGCGAATT
1 CGATTTTCGCGTTGCGAATT
* ** *
266811 TGATTTTCGAATTGCGAAAT
1 CGATTTTCGCGTTGCGAATT
*
266831 CGATTTTCGAGTT----A--
1 CGATTTTCGCGTTGCGAATT
* *
266845 CGATTTTCGTGTTACGAATT
1 CGATTTTCGCGTTGCGAATT
* ** ** *
266865 TGATTTTCGAATTGTAAAAT
1 CGATTTTCGCGTTGCGAATT
* *
266885 CAATTTTCGCGTTGCAAATT
1 CGATTTTCGCGTTGCGAATT
*
266905 CGATTTTTGCGTTGCGAATT
1 CGATTTTCGCGTTGCGAATT
* *
266925 CGATTTTTGTGTTGCGAATT
1 CGATTTTCGCGTTGCGAATT
*
266945 TGATTTTC
1 CGATTTTC
266953 TTAAACTTAT
Statistics
Matches: 111, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
14 12 0.11
16 1 0.01
18 1 0.01
20 97 0.87
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (20 bp):
CGATTTTCGCGTTGCGAATT
Found at i:268570 original size:21 final size:20
Alignment explanation
Indices: 268520--268571 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
268510 TTAAACGATG
*
268520 AGAGGTGAATCCTGAACAAT
1 AGAGGTGGATCCTGAACAAT
*
268540 AGAAGTGGATCCTGAACAAT
1 AGAGGTGGATCCTGAACAAT
*
268560 TGTAGGTGGATC
1 AG-AGGTGGATC
268572 AGGCTTCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (20 bp):
AGAGGTGGATCCTGAACAAT
Found at i:268936 original size:42 final size:41
Alignment explanation
Indices: 268845--268937 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 41
268835 TAGAGCACCG
* ** *
268845 ACCTTATCACGTAAAGTAGCTATCTCACCACGTAAAGCATA
1 ACCTCATCACGTAAAACAGCTACCTCACCACGTAAAGCATA
**
268886 ATTGTCATCACGTAAAACAGCTACCTCACCACGTAAAGACCAT-
1 A-CCTCATCACGTAAAACAGCTACCTCACCACGTAAAG--CATA
268929 ACCTCATCA
1 ACCTCATCA
268938 AGCCATACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.02
42 36 0.88
43 1 0.02
44 3 0.07
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.23
Consensus pattern (41 bp):
ACCTCATCACGTAAAACAGCTACCTCACCACGTAAAGCATA
Found at i:269021 original size:21 final size:21
Alignment explanation
Indices: 268953--269006 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
268943 TACATCATTG
268953 TCATCACGTAAAGCACTGACC
1 TCATCACGTAAAGCACTGACC
268974 TCATCACGTAAAGCACTGACC
1 TCATCACGTAAAGCACTGACC
*
268995 TTATCACGTAAA
1 TCATCACGTAAA
269007 ACACCTAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (21 bp):
TCATCACGTAAAGCACTGACC
Found at i:269163 original size:39 final size:39
Alignment explanation
Indices: 269120--269232 Score: 127
Period size: 39 Copynumber: 2.8 Consensus size: 39
269110 GTGATAGAAT
* * *
269120 AAGTGATGGATCTCGGTGTCGAGGTGTAGAGTCGGTTAG
1 AAGTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTAG
* * *
269159 AAGTGATGGCTCTCGGTGTCAAGGTGTAGAATCAGCTCG
1 AAGTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTAG
* *
269198 ATCAGGTGATGGATCTCGGTGTCGAAGTGGAGAAT
1 A--A-GTGATGGATCTCGGTGTCGAGGTGTAGAAT
269233 TGACTCGATG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 34 0.56
41 1 0.02
42 26 0.43
ACGTcount: A:0.23, C:0.13, G:0.37, T:0.27
Consensus pattern (39 bp):
AAGTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTAG
Found at i:269217 original size:42 final size:41
Alignment explanation
Indices: 269122--269262 Score: 137
Period size: 42 Copynumber: 3.4 Consensus size: 41
269112 GATAGAATAA
* * * * *
269122 GTGATGGATCTCGGTGTCGAGGTGTAGAGTCGGTTAGA-A-
1 GTGATGGATCTCGGTGTCAAGGTGTAGAATCAGCTCGATAG
*
269161 GTGATGGCTCTCGGTGTCAAGGTGTAGAATCAGCTCGATCAG
1 GTGATGGATCTCGGTGTCAAGGTGTAGAATCAGCTCGAT-AG
* *
269203 GTGATGGATCTCGGTGTCGAA-GTGGAGAAT-TGACTCGATGAG
1 GTGATGGATCTCGGTGTC-AAGGTGTAGAATCAG-CTCGAT-AG
*
269245 GTGATGAATCTCGGTGTC
1 GTGATGGATCTCGGTGTC
269263 GAACTGAAGA
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
39 32 0.37
41 2 0.02
42 50 0.58
43 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.37, T:0.28
Consensus pattern (41 bp):
GTGATGGATCTCGGTGTCAAGGTGTAGAATCAGCTCGATAG
Found at i:269263 original size:42 final size:42
Alignment explanation
Indices: 269169--269285 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
269159 AAGTGATGGC
* * * *
269169 TCTCGGTGTC-AAGGTGTAGAA-TCAGCTCGATCAGGTGATGGA
1 TCTCGGTGTCGAA-GTGAAGAATTGA-CTCGATGAGGTGATGAA
*
269211 TCTCGGTGTCGAAGTGGAGAATTGACTCGATGAGGTGATGAA
1 TCTCGGTGTCGAAGTGAAGAATTGACTCGATGAGGTGATGAA
* *
269253 TCTCGGTGTCGAACTGAAGAATCGACTCGATGA
1 TCTCGGTGTCGAAGTGAAGAATTGACTCGATGA
269286 AAAAGTAGGG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (42 bp):
TCTCGGTGTCGAAGTGAAGAATTGACTCGATGAGGTGATGAA
Found at i:275865 original size:34 final size:34
Alignment explanation
Indices: 275813--275877 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
275803 CGATTTTAGT
*
275813 TTTCGCGTTGCGAATTTCATGTTACGAATTTCAC
1 TTTCGAGTTGCGAATTTCATGTTACGAATTTCAC
* * *
275847 TTTCGAGTTGTGATTTTCATGTTGCGAATTT
1 TTTCGAGTTGCGAATTTCATGTTACGAATTT
275878 AAGTTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.46
Consensus pattern (34 bp):
TTTCGAGTTGCGAATTTCATGTTACGAATTTCAC
Found at i:276138 original size:15 final size:15
Alignment explanation
Indices: 276113--276150 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
276103 ATGTAATAAT
*
276113 AATACAAAAAATTTAA
1 AATA-AAAAAAATTAA
276129 AATAAAAAAAATTAA
1 AATAAAAAAAATTAA
276144 AA-AAAAA
1 AATAAAAA
276151 TTAACCCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 12 0.57
16 4 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAAAAAAATTAA
Found at i:276258 original size:22 final size:22
Alignment explanation
Indices: 276233--276282 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
276223 TGGAGGGAGA
* * *
276233 TCGTCGGATATGGGGACTGATG
1 TCGTCGAAGATGGGGACGGATG
276255 TCGTCGAAGATGGGGACGGATG
1 TCGTCGAAGATGGGGACGGATG
276277 TCGTCG
1 TCGTCG
276283 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.42, T:0.24
Consensus pattern (22 bp):
TCGTCGAAGATGGGGACGGATG
Found at i:279200 original size:22 final size:22
Alignment explanation
Indices: 279168--279211 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
279158 AGAAAATTTC
*
279168 AACATTTATTAAACATAACCTA
1 AACATTAATTAAACATAACCTA
* *
279190 AACATTAATTAACCATTACCTA
1 AACATTAATTAAACATAACCTA
279212 CCGTCACAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (22 bp):
AACATTAATTAAACATAACCTA
Found at i:293961 original size:14 final size:15
Alignment explanation
Indices: 293927--293962 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
293917 GCCCCTTAAA
293927 TTAAATTAAATGCAC
1 TTAAATTAAATGCAC
293942 TT-AATTAAAT-CAC
1 TTAAATTAAATGCAC
293955 TTAAATTA
1 TTAAATTA
293963 CACATGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (15 bp):
TTAAATTAAATGCAC
Found at i:294159 original size:19 final size:19
Alignment explanation
Indices: 294135--294179 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
294125 CTGGTCAACG
294135 GTTAACGATTTGTGTCAAA
1 GTTAACGATTTGTGTCAAA
294154 GTTAACGATTTGTGTCAAA
1 GTTAACGATTTGTGTCAAA
*
294173 GTCAACG
1 GTTAACG
294180 GTTCATGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (19 bp):
GTTAACGATTTGTGTCAAA
Found at i:294188 original size:19 final size:19
Alignment explanation
Indices: 294147--294196 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
294137 TAACGATTTG
* **
294147 TGTCAAAGTTAACGATTTG
1 TGTCAAAGTCAACGATTCA
*
294166 TGTCAAAGTCAACGGTTCA
1 TGTCAAAGTCAACGATTCA
*
294185 TGTCAAATTCAA
1 TGTCAAAGTCAA
294197 TGGGTCAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
TGTCAAAGTCAACGATTCA
Found at i:294233 original size:20 final size:20
Alignment explanation
Indices: 294208--294263 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
294198 GGGTCAAACT
*
294208 GATTTGGGTTTACTCAGGCC
1 GATTTGGGTTGACTCAGGCC
294228 GATTTGGGTTGACTCAGGCC
1 GATTTGGGTTGACTCAGGCC
*
294248 GATTTGAGTTGACTCA
1 GATTTGGGTTGACTCA
294264 ATTTGGTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (20 bp):
GATTTGGGTTGACTCAGGCC
Found at i:294296 original size:20 final size:20
Alignment explanation
Indices: 294253--294299 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
294243 AGGCCGATTT
* *
294253 GAGTTGACTCAATTTGGTTT
1 GAGTTGACTCAACTTGGTTC
294273 GAGTTGACTCAAACTT-GTTC
1 GAGTTGACTC-AACTTGGTTC
294293 GAGTTGA
1 GAGTTGA
294300 TTCGAACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (20 bp):
GAGTTGACTCAACTTGGTTC
Found at i:294307 original size:20 final size:20
Alignment explanation
Indices: 294253--294312 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
294243 AGGCCGATTT
** * *
294253 GAGTTGACTCAATTTGGTTT
1 GAGTTGACTCAAACTAGTTC
*
294273 GAGTTGACTCAAACTTGTTC
1 GAGTTGACTCAAACTAGTTC
* *
294293 GAGTTGATTCGAACTAGTTC
1 GAGTTGACTCAAACTAGTTC
294313 TAGGATGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (20 bp):
GAGTTGACTCAAACTAGTTC
Found at i:304460 original size:13 final size:13
Alignment explanation
Indices: 304437--304474 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
304427 ATTTCAGAAG
304437 ATTTG-TTTTCTC
1 ATTTGCTTTTCTC
304449 ATTTGCTTTTCTC
1 ATTTGCTTTTCTC
304462 ATTTGCTTTTCTC
1 ATTTGCTTTTCTC
304475 TGTTCTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.08, C:0.21, G:0.08, T:0.63
Consensus pattern (13 bp):
ATTTGCTTTTCTC
Found at i:313187 original size:32 final size:33
Alignment explanation
Indices: 313129--313194 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
313119 TTAAGATTTT
* * *
313129 AAATATTTTTATTTAATTATTAAAAATATTATA
1 AAATATATTTATTTAATAATTAAAAATATAATA
*
313162 AAATATATTT-TTTAATAATTTAAAATATAATA
1 AAATATATTTATTTAATAATTAAAAATATAATA
313194 A
1 A
313195 TGATTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATATATTTATTTAATAATTAAAAATATAATA
Found at i:313224 original size:15 final size:15
Alignment explanation
Indices: 313155--313228 Score: 59
Period size: 14 Copynumber: 5.3 Consensus size: 15
313145 TTATTAAAAA
313155 TATTATAAAATATAT
1 TATTATAAAATATAT
* *
313170 T-TTTTAATA-AT-T
1 TATTATAAAATATAT
** *
313182 TAAAATATAATA-AT
1 TATTATAAAATATAT
*
313196 GATTAT-AAATATAT
1 TATTATAAAATATAT
313210 TATTATAAAATATAT
1 TATTATAAAATATAT
313225 TATT
1 TATT
313229 TTAATTATTT
Statistics
Matches: 42, Mismatches: 12, Indels: 10
0.66 0.19 0.16
Matches are distributed among these distances:
12 2 0.05
13 9 0.21
14 18 0.43
15 13 0.31
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TATTATAAAATATAT
Found at i:314027 original size:20 final size:20
Alignment explanation
Indices: 314002--314039 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
313992 TTTGGTTCAC
314002 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
314022 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
314040 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:314049 original size:16 final size:18
Alignment explanation
Indices: 314002--314051 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
313992 TTTGGTTCAC
314002 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
314022 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
314040 GGAA-TAAGATTA
1 GGAAGTAAGATTA
314052 TTGTGAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.27
18 5 0.17
20 17 0.57
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:315555 original size:23 final size:23
Alignment explanation
Indices: 315525--315569 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
315515 TCGTCGGTTG
315525 GTGATTTTCTAT-AGTAAGAGATA
1 GTGATTTTCTATGA-TAAGAGATA
*
315548 GTGATTTTTTATGATAAGAGAT
1 GTGATTTTCTATGATAAGAGAT
315570 GAAAGCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.42
Consensus pattern (23 bp):
GTGATTTTCTATGATAAGAGATA
Found at i:321669 original size:31 final size:31
Alignment explanation
Indices: 321633--321691 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
321623 AACTTAAAAG
* *
321633 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
*
321664 AGTTTTATAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
321692 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:321743 original size:22 final size:22
Alignment explanation
Indices: 321715--321989 Score: 354
Period size: 22 Copynumber: 12.5 Consensus size: 22
321705 ATAATATTTT
*
321715 TTTTAAAATAAATCCATCCATA
1 TTTTAAAATAAATCAATCCATA
321737 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
321759 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
321781 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
321803 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
***
321825 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
321847 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
** *
321869 TTTTAAAATAAAT-TTTCTATA
1 TTTTAAAATAAATCAATCCATA
321890 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** **
321912 TTTTAAAATAAATTTTTTTATA
1 TTTTAAAATAAATCAATCCATA
*
321934 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *
321956 TTTTAAAATAAATCATTTCATA
1 TTTTAAAATAAATCAATCCATA
321978 TTTTAAAATAAA
1 TTTTAAAATAAA
321990 ATTTTAAAAT
Statistics
Matches: 219, Mismatches: 33, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
21 19 0.09
22 200 0.91
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:321995 original size:13 final size:13
Alignment explanation
Indices: 321977--322002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
321967 ATCATTTCAT
321977 ATTTTAAAATAAA
1 ATTTTAAAATAAA
321990 ATTTTAAAATAAA
1 ATTTTAAAATAAA
322003 TTTAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTTAAAATAAA
Found at i:326985 original size:23 final size:23
Alignment explanation
Indices: 326959--327007 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
326949 TATTTGCTTA
*
326959 TAAATTGATTTTTTAATT-TAATT
1 TAAATTGA-TTTTAAATTGTAATT
326982 TAAATTGATTTTAAATTGTAATT
1 TAAATTGATTTTAAATTGTAATT
327005 TAA
1 TAA
327008 TAAATTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (23 bp):
TAAATTGATTTTAAATTGTAATT
Found at i:328991 original size:16 final size:16
Alignment explanation
Indices: 328970--329001 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
328960 ACTATTTACA
*
328970 TGAATAGTAAATTTTG
1 TGAATAGTAAAATTTG
328986 TGAATAGTAAAATTTG
1 TGAATAGTAAAATTTG
329002 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
TGAATAGTAAAATTTG
Found at i:333253 original size:22 final size:21
Alignment explanation
Indices: 333199--333262 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
333189 AGTCGAGGGT
333199 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
333220 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
333242 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
333263 AATTTCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:333808 original size:22 final size:22
Alignment explanation
Indices: 333776--333821 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
333766 TGTAGCAGTA
*
333776 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGATTCC
*
333798 CTGTAGTAGGGGAATCGATTCC
1 CTGTAGCAGGGGAATCGATTCC
333820 CT
1 CT
333822 ATTTGTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.26
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGATTCC
Found at i:334249 original size:25 final size:24
Alignment explanation
Indices: 334207--334256 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
334197 CTGGTATGGT
*
334207 AATGAGTATGTTGGTTTTGCTAATAG
1 AATGAGTATGTTGATTTT--TAATAG
*
334233 AATGA-TATGTTTATTTTTAATAG
1 AATGAGTATGTTGATTTTTAATAG
334256 A
1 A
334257 TGTCCGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (24 bp):
AATGAGTATGTTGATTTTTAATAG
Found at i:340111 original size:22 final size:21
Alignment explanation
Indices: 340057--340120 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
340047 AGTCGAGGGT
340057 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
340078 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
340100 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
340121 AATTTCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:341658 original size:18 final size:18
Alignment explanation
Indices: 341635--341674 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
341625 AGTTTCTTGG
341635 AAGAGTTAGGCAAGAAAC
1 AAGAGTTAGGCAAGAAAC
341653 AAGAGTTAGGCAAGAAAC
1 AAGAGTTAGGCAAGAAAC
341671 AAGA
1 AAGA
341675 AAACAATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.28, T:0.10
Consensus pattern (18 bp):
AAGAGTTAGGCAAGAAAC
Found at i:346833 original size:25 final size:23
Alignment explanation
Indices: 346785--346834 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 23
346775 TAAACTTTAT
346785 TTAATTTTTTTCAAATCTAAATTA
1 TTAATTTTTTTCAAA-CTAAATTA
346809 TTAAGTTTTTATTCAAA-TAATATTA
1 TTAA-TTTTT-TTCAAACTAA-ATTA
346834 T
1 T
346835 GAAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 10 0.43
26 6 0.26
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAATTTTTTTCAAACTAAATTA
Found at i:354516 original size:42 final size:42
Alignment explanation
Indices: 354452--354571 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
354442 TTTTACTGAA
354452 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTT
* *
354494 TTCCTGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTT
*
354536 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAA
354572 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTT
Found at i:354763 original size:24 final size:24
Alignment explanation
Indices: 354696--354774 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
354686 TTTTCATCAA
354696 AATATTAATTATTAAAATATTTAAAAT
1 AATA-TAA-TATT-AAATATTTAAAAT
*
354723 -ATAT-TTATT-AATATTTAAAAT
1 AATATAATATTAAATATTTAAAAT
* *
354744 AATATAATATTAAATTTTTAATAT
1 AATATAATATTAAATATTTAAAAT
*
354768 TATATAA
1 AATATAA
354775 AATAATCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
21 12 0.27
22 4 0.09
23 8 0.18
24 16 0.36
25 1 0.02
26 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATAATATTAAATATTTAAAAT
Found at i:354766 original size:22 final size:22
Alignment explanation
Indices: 354696--354771 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
354686 TTTTCATCAA
*
354696 AATATTAATTATTAAAATATTTAA-
1 AATA-TAA-TATT-AAATTTTTAAT
* **
354720 AATATATTTATTAATATTTAAAAT
1 AATATA-ATATTAA-ATTTTTAAT
354744 AATATAATATTAAATTTTTAAT
1 AATATAATATTAAATTTTTAAT
*
354766 ATTATA
1 AATATA
354772 TAAAATAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 14 0.34
23 17 0.41
24 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATAATATTAAATTTTTAAT
Found at i:354824 original size:29 final size:29
Alignment explanation
Indices: 354787--354888 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
354777 TAATCAATTA
*
354787 TATTATAATAATATA-AGAT-ATTATATTTT
1 TATTTTAATAATATATA-ATAATTAT-TTTT
*
354816 TATTTTAATAATATATAATAATTCTTTTT
1 TATTTTAATAATATATAATAATTATTTTT
*
354845 TATATTTAATAATGA-ATAAT-ATTATTTATA
1 TAT-TTTAATAAT-ATATAATAATTATTT-TT
*
354875 TATTTCAATAATAT
1 TATTTTAATAATAT
354889 TTTAGTAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
28 1 0.02
29 37 0.60
30 23 0.37
31 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
TATTTTAATAATATATAATAATTATTTTT
Found at i:355260 original size:20 final size:20
Alignment explanation
Indices: 355203--355252 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
355193 TCATAAAACG
355203 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
355223 TTTCCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
355243 TTTTCCAGAA
1 TTTTCCAGAA
355253 TTCAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:355271 original size:15 final size:15
Alignment explanation
Indices: 355251--355301 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
355241 CATTTTCCAG
355251 AATTCAAATTTTAGT
1 AATTCAAATTTTAGT
*
355266 AATTC--ATTTTCCAGA
1 AATTCAAATTTT--AGT
*
355281 AATTCAAATTTCAGT
1 AATTCAAATTTTAGT
355296 AATTCA
1 AATTCA
355302 TTTTCTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 5 0.17
15 20 0.69
17 4 0.14
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTCAAATTTTAGT
Found at i:355277 original size:29 final size:30
Alignment explanation
Indices: 355235--355306 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
355225 TCCCAGAAAT
*
355235 GTAATTCATTTTCCAG-AATTCAAATTTTA
1 GTAATTCATTTTCCAGAAATTCAAATTTCA
355264 GTAATTCATTTTCCAGAAATTCAAATTTCA
1 GTAATTCATTTTCCAGAAATTCAAATTTCA
355294 GTAATTCATTTTC
1 GTAATTCATTTTC
355307 TGAAAAATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTCCAGAAATTCAAATTTCA
Found at i:355616 original size:42 final size:42
Alignment explanation
Indices: 355554--355670 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
355544 TTTTCCTGAA
* * * *
355554 TTCTCGTGTTTGTTTTACGTAATTTGTTTTTCGAAAAATGTT
1 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTC
355596 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTC
1 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTC
* *
355638 TTC-CTATGTTTGTTTCACGTAATTGGTTTTCCG
1 TTCTC-GTGTTTGTTTCACGTAATTCGTTTTCCG
355671 GAATTTAATT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.01
42 67 0.99
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (42 bp):
TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTC
Found at i:355867 original size:17 final size:18
Alignment explanation
Indices: 355847--355889 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
355837 TTTTCATCAA
* *
355847 AATATTATTTATTAAT-T
1 AATATTATATAATAATAT
355864 AATATT-TATAATAATAT
1 AATATTATATAATAATAT
355881 AATATTATA
1 AATATTATA
355890 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 13 0.59
18 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTATATAATAATAT
Found at i:355888 original size:16 final size:16
Alignment explanation
Indices: 355859--355912 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
355849 TATTATTTAT
355859 TAAT-TAATATTTATAA
1 TAATATAATA-TTATAA
355875 TAATATAATATTATAA
1 TAATATAATATTATAA
*
355891 T--TTTAATATTAT-A
1 TAATATAATATTATAA
*
355904 TAAAATAAT
1 TAATATAAT
355913 CAATTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
15 4 0.12
16 11 0.34
17 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATATAATATTATAA
Found at i:355919 original size:31 final size:30
Alignment explanation
Indices: 355862--356021 Score: 80
Period size: 31 Copynumber: 5.6 Consensus size: 30
355852 TATTTATTAA
355862 TTAATATTTATAATAATATAATATTATAATT
1 TTAATATTTATAATAATATAATATTAT-ATT
* *
355893 TTAATA-TTAT-ATAAAAT-A-ATCA-A--
1 TTAATATTTATAATAATATAATATTATATT
*
355916 TT-ATA-TTATAATAATACAAGATATTATATT
1 TTAATATTTATAATAATA-TA-ATATTATATT
* ** *
355946 TTTAT-TTTAATAAT-ATATAATAAAATTTT
1 TTAATATTT-ATAATAATATAATATTATATT
*
355975 TTATATATTTAATAATGA-ATAATATTAT-TT
1 TTA-ATATTT-ATAATAATATAATATTATATT
*
356005 AT-ATATTTA-AATAATAT
1 TTAATATTTATAATAATAT
356022 TTTAATAAAG
Statistics
Matches: 100, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
22 7 0.07
23 7 0.07
25 1 0.01
26 5 0.05
27 9 0.09
28 8 0.08
29 15 0.15
30 12 0.12
31 30 0.30
32 6 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TTAATATTTATAATAATATAATATTATATT
Found at i:355930 original size:18 final size:19
Alignment explanation
Indices: 355898--355943 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
355888 TAATTTTAAT
*
355898 ATTATA-TAAAATAAT-CA
1 ATTATATTATAATAATACA
355915 ATTATATTATAATAATACA
1 ATTATATTATAATAATACA
*
355934 A-GATATTATA
1 ATTATATTATA
355944 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTATATTATAATAATACA
Found at i:355987 original size:28 final size:28
Alignment explanation
Indices: 355956--356019 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
355946 TTTATTTTAA
*
355956 TAATATAT-AATAAAATTTTTTATATATT
1 TAATA-ATGAATAAAATTATTTATATATT
*
355984 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAAAATTATTTATATATT
356012 TAAATAAT
1 T-AATAAT
356020 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TAATAATGAATAAAATTATTTATATATT
Found at i:355999 original size:19 final size:19
Alignment explanation
Indices: 355977--356029 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
355967 AAAATTTTTT
*
355977 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
355996 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
356018 ATAT-TTTAATAA
1 ATATATTTAATAA
356030 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:356050 original size:23 final size:23
Alignment explanation
Indices: 356024--356068 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
356014 AATAATATTT
356024 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
356047 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
356069 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:356200 original size:20 final size:20
Alignment explanation
Indices: 356164--356203 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
356154 TAATAAAATT
356164 ATAAAAAATAATATTTAATA
1 ATAAAAAATAATATTTAATA
*
356184 ATAAATAAATTAT-TTTAATA
1 ATAAA-AAATAATATTTAATA
356204 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAATAATATTTAATA
Found at i:356391 original size:14 final size:14
Alignment explanation
Indices: 356372--356405 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
356362 AAATGTAATT
356372 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
356386 CATTTTTCGGAAAA
1 CATTTTACGGAAAA
*
356400 CGTTTT
1 CATTTT
356406 CCAGAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:356450 original size:15 final size:15
Alignment explanation
Indices: 356424--356481 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 15
356414 ATAATTTATT
356424 TTCCAG-AATTCAAA
1 TTCCAGTAATTCAAA
356438 TTCCAGTAATTCATCCAA
1 TTCCAGTAATTCA---AA
356456 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
*
356471 TTCCAATAATT
1 TTCCAGTAATT
356482 TATTTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
14 6 0.15
15 18 0.46
18 15 0.38
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:360604 original size:2 final size:2
Alignment explanation
Indices: 360597--360632 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
360587 CGTCCATTTA
360597 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
360633 TTGGATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:365823 original size:9 final size:9
Alignment explanation
Indices: 365785--365840 Score: 71
Period size: 9 Copynumber: 6.3 Consensus size: 9
365775 CAGCTGGAAA
365785 ACCGGTTTG
1 ACCGGTTTG
365794 A-CGG-TTG
1 ACCGGTTTG
365801 ACCGGTTTG
1 ACCGGTTTG
365810 AACCGGTTTG
1 -ACCGGTTTG
365820 ACCGGTTTG
1 ACCGGTTTG
* *
365829 AACGGTCTG
1 ACCGGTTTG
365838 ACC
1 ACC
365841 CAACCCGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 4 0.10
8 6 0.15
9 22 0.54
10 9 0.22
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:365834 original size:18 final size:18
Alignment explanation
Indices: 365785--365840 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 18
365775 CAGCTGGAAA
365785 ACCGGTTTG-ACGG-TTG
1 ACCGGTTTGAACGGTTTG
365801 ACCGGTTTGAACCGGTTTG
1 ACCGGTTTGAA-CGGTTTG
*
365820 ACCGGTTTGAACGGTCTG
1 ACCGGTTTGAACGGTTTG
365838 ACC
1 ACC
365841 CAACCCGACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 9 0.25
17 1 0.03
18 12 0.33
19 14 0.39
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (18 bp):
ACCGGTTTGAACGGTTTG
Found at i:374338 original size:18 final size:19
Alignment explanation
Indices: 374314--374364 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
374304 TTGCGGTTAT
374314 AATTTAATATTATTCATT-
1 AATTTAATATTATTCATTA
* * *
374332 TATTTAATTTTATTTATTA
1 AATTTAATATTATTCATTA
374351 AATTTAATAATTAT
1 AATTTAAT-ATTAT
374365 AAGATTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.58
19 7 0.27
20 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTAATATTATTCATTA
Found at i:374924 original size:23 final size:23
Alignment explanation
Indices: 374888--374932 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
374878 ACAATTCAAT
374888 TATAATATGATTGTATTTAAAAA
1 TATAATATGATTGTATTTAAAAA
* *
374911 TATAATGTGGTTGTATTTAAAA
1 TATAATATGATTGTATTTAAAA
374933 TACATAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (23 bp):
TATAATATGATTGTATTTAAAAA
Found at i:394222 original size:60 final size:61
Alignment explanation
Indices: 394158--394287 Score: 176
Period size: 60 Copynumber: 2.1 Consensus size: 61
394148 TAAATGTTTT
* * * * *
394158 AATTTCATCCCTAAGA-TATGAT-TGTCATTCTAAATTAGTTCTCAAAC-TTTTGAACATTTC
1 AATTTCATCCCTAA-ACTATGATCT-TCATTCTAAACTAGTCCCCAAACGTGTTGAACATTCC
394218 AATTTCATCCCTAAACTATGATCTTCATTCTAAACTAGTCCCCAAACGTGTTGAACATTCC
1 AATTTCATCCCTAAACTATGATCTTCATTCTAAACTAGTCCCCAAACGTGTTGAACATTCC
394279 AATTTCATC
1 AATTTCATC
394288 ACAACTATAC
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
59 1 0.02
60 40 0.65
61 21 0.34
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (61 bp):
AATTTCATCCCTAAACTATGATCTTCATTCTAAACTAGTCCCCAAACGTGTTGAACATTCC
Found at i:406659 original size:22 final size:22
Alignment explanation
Indices: 406632--406681 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
406622 TTGCGATTTT
406632 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
406654 TTGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
406676 TCGTTG
1 TCGTTG
406682 TGATTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:406711 original size:76 final size:76
Alignment explanation
Indices: 406579--406720 Score: 230
Period size: 76 Copynumber: 1.9 Consensus size: 76
406569 TTGCATTTCG
* ***
406579 TGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCTAAATTCGTTGCGATTTTTCGTTGCGATAG
1 TGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGAAAATTCGTTGCGATAG
406644 TCTACAGTTGT
66 TCTACAGTTGT
* *
406655 TGTTGCGATAGTCTACAGTTGTCGTTGTGATTTTCCAAATTCGTTGCGAAAATTCGTTGTGATAG
1 TGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGAAAATTCGTTGCGATAG
406720 T
66 T
406721 TAAAAAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (76 bp):
TGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGAAAATTCGTTGCGATAG
TCTACAGTTGT
Found at i:407324 original size:6 final size:6
Alignment explanation
Indices: 407313--407339 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
407303 TCTCGTCTCG
407313 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
407340 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:407480 original size:22 final size:22
Alignment explanation
Indices: 407452--407543 Score: 102
Period size: 22 Copynumber: 4.3 Consensus size: 22
407442 AATTTGGAAA
407452 ATCGCAACGAAAACTGTAGACT
1 ATCGCAACGAAAACTGTAGACT
407474 ATCGCAAC-AACAACTGTAGACT
1 ATCGCAACGAA-AACTGTAGACT
* * **
407496 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGAAAACTGTAGACT
*
407515 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGAAAACTGTAGACT
407537 ATCGCAA
1 ATCGCAA
407544 TGCGAAATGC
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
21 4 0.07
22 38 0.67
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (22 bp):
ATCGCAACGAAAACTGTAGACT
Found at i:411152 original size:6 final size:6
Alignment explanation
Indices: 411141--411166 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
411131 TTGATTTTTT
411141 TTATAA TTATAA TTATAA TTATAA TT
1 TTATAA TTATAA TTATAA TTATAA TT
411167 TATTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:420011 original size:2 final size:2
Alignment explanation
Indices: 420004--420036 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
419994 AGATATCTTC
420004 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 A
420037 CATTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:427430 original size:20 final size:21
Alignment explanation
Indices: 427405--427456 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
427395 TTTTCCCAAT
*
427405 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
427425 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
427446 TCGCAATGCGA
1 TCGCAATGCGA
427457 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:427470 original size:20 final size:20
Alignment explanation
Indices: 427445--427558 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
427435 AATTGGGAAA
*
427445 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
427465 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
427485 ATCGCAATGTGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
427506 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
427526 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
427546 TTCGCAACGCGAT
1 ATCGCAACGCGAT
427559 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:427489 original size:61 final size:61
Alignment explanation
Indices: 427442--427558 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
427432 GCGAATTGGG
* * * * * *
427442 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGTGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
427503 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
427559 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:428156 original size:19 final size:19
Alignment explanation
Indices: 428134--428318 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
428124 GAAACCAAAA
*
428134 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
428153 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
428172 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
428191 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
428211 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
428227 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
428244 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
428258 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
428277 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
428297 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
428317 TC
1 TC
428319 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:428211 original size:39 final size:38
Alignment explanation
Indices: 428134--428318 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
428124 GAAACCAAAA
*
428134 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
428172 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
428211 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
428244 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
428277 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
428317 TC
1 TC
428319 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:428295 original size:20 final size:20
Alignment explanation
Indices: 428261--428318 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
428251 GCGATTCTCT
**
428261 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
428281 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
428301 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
428319 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:430370 original size:42 final size:42
Alignment explanation
Indices: 430310--430432 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
430300 GCCCGACTCG
* * *
430310 CCTATCATCACTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCACTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
430352 CCTATCATTC-CTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCA-TCACTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
430394 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCACTCAAGA-GTCCACTCCCACCGTTCAAGAG
430433 CCTGATTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 59 0.88
43 6 0.09
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCACTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:430390 original size:21 final size:21
Alignment explanation
Indices: 430366--430432 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
430356 TCATTCCTCG
430366 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
430387 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
430408 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
430429 AGAG
1 AGAG
430433 CCTGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:431810 original size:14 final size:14
Alignment explanation
Indices: 431791--431826 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
431781 ATTGTTTAAT
431791 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
431805 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
431819 TGATTTGT
1 TGATTTGT
431827 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:432056 original size:20 final size:19
Alignment explanation
Indices: 432006--432059 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
431996 CGAAATTAAA
** *
432006 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTAAT
*
432025 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATAGTAAT
432044 TTCCGCGTTGCGATAG
1 TT-CGCGTTGCGATAG
432060 ACATTAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTAAT
Found at i:434343 original size:12 final size:12
Alignment explanation
Indices: 434326--434350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
434316 TCTTCGGGGA
434326 CTTTTTCTTCTT
1 CTTTTTCTTCTT
434338 CTTTTTCTTCTT
1 CTTTTTCTTCTT
434350 C
1 C
434351 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:434577 original size:24 final size:25
Alignment explanation
Indices: 434525--434579 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
434515 CTGAAACATC
* *
434525 ATCAAAATCCGTGTATTTGACCAAT
1 ATCAAAATCCGGGTATTTGACCAAG
*
434550 ATCAAAGTCCGGGTA-TTGACCAAG
1 ATCAAAATCCGGGTATTTGACCAAG
434574 ATCAAA
1 ATCAAA
434580 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (25 bp):
ATCAAAATCCGGGTATTTGACCAAG
Found at i:435664 original size:20 final size:20
Alignment explanation
Indices: 435639--435696 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
435629 ATTCATTTGA
435639 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
435659 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
435679 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
435697 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:435885 original size:14 final size:14
Alignment explanation
Indices: 435866--435902 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
435856 CATCAATTAA
435866 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
435880 ACAAATCATCTTTT
1 ACAAATCAACATTT
435894 ACAAATCAA
1 ACAAATCAA
435903 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:437837 original size:19 final size:19
Alignment explanation
Indices: 437745--437848 Score: 84
Period size: 19 Copynumber: 5.4 Consensus size: 19
437735 TAGTTTACTT
* *
437745 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* * **
437765 TCACAACGCGAAATTACTA
1 TCGCAACGCGAAATGAAAA
***
437784 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
**
437804 TCGCAATTCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
437823 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
437841 TCGCAACG
1 TCGCAACG
437849 ACAAAATCGC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
18 11 0.16
19 32 0.46
20 26 0.38
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:437855 original size:19 final size:19
Alignment explanation
Indices: 437814--437855 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
437804 TCGCAATTCG
*
437814 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCA
437833 AAATG-AAATCGCAACGACA
1 AAATGAAAATCGCAACG-CA
437852 AAAT
1 AAAT
437856 CGCAACGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCA
Found at i:437896 original size:19 final size:19
Alignment explanation
Indices: 437874--437955 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
437864 GAAACACAAA
437874 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
437893 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
437911 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
437927 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
437944 TCGCATTGCGAT
1 TCGCATTGCGAT
437956 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:437974 original size:20 final size:19
Alignment explanation
Indices: 437940--437994 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
437930 TTGCGATTTT
*
437940 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
437959 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
437979 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
437995 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:437983 original size:39 final size:34
Alignment explanation
Indices: 437874--437975 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
437864 GAAACACAAA
437874 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
437911 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
437944 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
437976 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:438496 original size:18 final size:18
Alignment explanation
Indices: 438470--438514 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
438460 GTCGATCAGA
*
438470 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
438488 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
438506 TGATGGCTC
1 TGATGGCTC
438515 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:439859 original size:20 final size:20
Alignment explanation
Indices: 439834--439871 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
439824 AATAGTTTCT
439834 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
439854 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
439872 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:440391 original size:20 final size:20
Alignment explanation
Indices: 440366--440418 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
440356 GATTATGTAT
*
440366 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
440386 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
440406 TATCTCGTTGCGA
1 TATCGCGTTGCGA
440419 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:452284 original size:5 final size:5
Alignment explanation
Indices: 452274--452299 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
452264 TGACTTAGAA
452274 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
452300 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:455629 original size:28 final size:31
Alignment explanation
Indices: 455569--455630 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
455559 CGTAATTTTA
*
455569 TTTTAATATTTATTATTATAGGTTCATATTT
1 TTTTAATATTTATTATTATAGGGTCATATTT
*
455600 TTTTAATATTTATTA-T-TAGGGTCTTATTT
1 TTTTAATATTTATTATTATAGGGTCATATTT
455629 TT
1 TT
455631 ATAGTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.45
30 1 0.03
31 15 0.52
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (31 bp):
TTTTAATATTTATTATTATAGGGTCATATTT
Found at i:455641 original size:31 final size:29
Alignment explanation
Indices: 455566--455641 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
455556 GTGCGTAATT
* *
455566 TTATTTTAATATTTA-TTATTATAGGTTC
1 TTATTTTTATATTTATTTATTATAGGGTC
* * *
455594 ATATTTTTTTA-ATATTTATTATTAGGGTC
1 TTATTTTTATATTTATTTATTA-TAGGGTC
455623 TTATTTTTATAGTTTATTT
1 TTATTTTTATA-TTTATTT
455642 TTTCCTAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
27 2 0.06
28 14 0.39
29 15 0.42
31 5 0.14
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (29 bp):
TTATTTTTATATTTATTTATTATAGGGTC
Found at i:455644 original size:43 final size:43
Alignment explanation
Indices: 455578--455709 Score: 108
Period size: 43 Copynumber: 3.0 Consensus size: 43
455568 ATTTTAATAT
* *
455578 TTATTATTATAGGTTCATATTTTTTTAATATTTATTATTAGGGTC
1 TTATTTTTATA-GTTTAT-TTTTTTTAATATTTATTATTAGGGTC
* * **
455623 TTATTTTTATAGTTTATTTTTTCCTAATATTT-GTATTAGTATC
1 TTATTTTTATAGTTTATTTTTT-TTAATATTTATTATTAGGGTC
* * *
455666 TAATTATTTACCA--ATATTTTTTTTAATATTTATTATTAAGGGTC
1 TTATT-TTTA-TAGTTTATTTTTTTTAATATTTATTATT-AGGGTC
455710 CAATTTTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
42 8 0.12
43 29 0.42
44 21 0.30
45 11 0.16
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.58
Consensus pattern (43 bp):
TTATTTTTATAGTTTATTTTTTTTAATATTTATTATTAGGGTC
Found at i:459315 original size:31 final size:31
Alignment explanation
Indices: 459279--459338 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
459269 AAATTAAAAG
* * *
459279 AGTTTTGCAGTACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
459310 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
459339 CATACAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:459853 original size:20 final size:20
Alignment explanation
Indices: 459805--459866 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
459795 AACTTAAATC
*
459805 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
459825 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
459843 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
459862 AAAAT
1 AAAAT
459867 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:459899 original size:14 final size:14
Alignment explanation
Indices: 459882--459930 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
459872 ATCTATAATA
459882 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
459896 TAATATT---TAAT
1 TAATATTAAAAAAT
*
459907 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
459920 TAATATTAAAA
1 TAATATTAAAA
459931 TTAAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 6 0.22
13 6 0.22
14 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:459900 original size:28 final size:24
Alignment explanation
Indices: 459862--459926 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 24
459852 TATATGATAT
459862 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATAT-T-TAAT-TAAT-TTAA
*
459891 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
459915 AAAATTAATATT
1 AAAATTAATATT
459927 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 16 0.46
25 3 0.09
26 4 0.11
27 1 0.03
28 5 0.14
29 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:459960 original size:12 final size:12
Alignment explanation
Indices: 459915--459965 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
459905 ATTTATTTAA
459915 AAAATT-AATATT
1 AAAATTAAATA-T
459927 AAAATTAAA-AT
1 AAAATTAAATAT
*
459938 CAAA-TATAATAT
1 AAAATTA-AATAT
459950 AAAATTAAATAT
1 AAAATTAAATAT
459962 AAAA
1 AAAA
459966 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:462122 original size:15 final size:15
Alignment explanation
Indices: 462078--462156 Score: 72
Period size: 15 Copynumber: 5.1 Consensus size: 15
462068 AAAAAAAATT
*
462078 AATAAT-TTTAAATA
1 AATAATATTTTAATA
*
462092 AATAATA-ATTATATA
1 AATAATATTTTA-ATA
*
462107 AATATTATTTTAATA
1 AATAATATTTTAATA
*
462122 AAAAATAATATTTACATA
1 AATAAT-AT-TTTA-ATA
462140 AATAATATTTTAATA
1 AATAATATTTTAATA
462155 AA
1 AA
462157 AAAATAATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
14 8 0.15
15 21 0.40
16 9 0.17
17 6 0.12
18 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATATTTTAATA
Found at i:462133 original size:18 final size:18
Alignment explanation
Indices: 462106--462168 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
462096 ATAATTATAT
*
462106 AAATATTATTTTAATAAA
1 AAATAATATTTTAATAAA
462124 AAATAATA-TTTACAT---
1 AAATAATATTTTA-ATAAA
462139 AAATAATATTTTAATAAAA
1 AAATAATATTTTAAT-AAA
462158 AAATAATATTT
1 AAATAATATTT
462169 ACATAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
15 10 0.26
16 4 0.11
17 4 0.11
18 9 0.24
19 11 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAATATTTTAATAAA
Found at i:462164 original size:34 final size:34
Alignment explanation
Indices: 462086--462195 Score: 147
Period size: 33 Copynumber: 3.3 Consensus size: 34
462076 TTAATAATTT
* * * *
462086 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATATTTACATAAATAATATTTTAA
462120 T-AAAAAATAATATTTACATAAATAATATTTTAA
1 TAAAAAAATAATATTTACATAAATAATATTTTAA
462153 TAAAAAAATAATATTTACATAAAT-ATA--TTAA
1 TAAAAAAATAATATTTACATAAATAATATTTTAA
462184 TATAAAAAATAA
1 TA-AAAAAATAA
462196 GAACTATTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
31 6 0.09
32 9 0.13
33 32 0.46
34 23 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAAATAATATTTACATAAATAATATTTTAA
Found at i:462174 original size:19 final size:19
Alignment explanation
Indices: 462121--462175 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 19
462111 TTATTTTAAT
462121 AAAAAATAATATTTACAT-
1 AAAAAATAATATTTACATA
*
462139 AAATAAT-AT-TTTA-ATA
1 AAAAAATAATATTTACATA
462155 AAAAAATAATATTTACATA
1 AAAAAATAATATTTACATA
462174 AA
1 AA
462176 TATATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
17 4 0.13
18 10 0.32
19 5 0.16
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATAATATTTACATA
Found at i:463866 original size:54 final size:54
Alignment explanation
Indices: 463803--463917 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 54
463793 CGGAGTGCAC
* *
463803 ACTTGTTTGAATTTATTTTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
1 ACTTGTTTGAATTTATTCTGATTTGAACTGTTAAGTGGTGGTTTTGTAACTGCT
463857 ACTTGTTTGAATTTATTCTGATTTGAACTGTTAAGTGGTGGTTTTGTAACTGCT
1 ACTTGTTTGAATTTATTCTGATTTGAACTGTTAAGTGGTGGTTTTGTAACTGCT
*
463911 ATTTGTT
1 ACTTGTT
463918 AGTTTTCGTC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.51
Consensus pattern (54 bp):
ACTTGTTTGAATTTATTCTGATTTGAACTGTTAAGTGGTGGTTTTGTAACTGCT
Found at i:466008 original size:18 final size:18
Alignment explanation
Indices: 465985--466036 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
465975 ATATAACACA
*
465985 TATGTCCCGAATGACCAC
1 TATGTCCCGAAGGACCAC
*
466003 TATGTCCCAAAGGACCAC
1 TATGTCCCGAAGGACCAC
466021 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
466037 GCGTAGACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:466863 original size:24 final size:20
Alignment explanation
Indices: 466810--466867 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
466800 TTCCCCTTGA
*
466810 AGTGCATAGATGCATTCTTC
1 AGTGCATCGATGCATTCTTC
466830 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
466853 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
466868 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:466926 original size:65 final size:63
Alignment explanation
Indices: 466855--466996 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 63
466845 TCTTTAACAT
*
466855 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTTAAAG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTTAAAG
*
466918 G
63 A
* * * * *
466919 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTTGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
*
466983 GTGCATTGATGCAC
1 GTGCATCGATGCAC
466997 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
63 14 0.21
64 15 0.22
65 38 0.57
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:467336 original size:17 final size:18
Alignment explanation
Indices: 467303--467342 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
467293 TCTTTCAAGA
*
467303 TTTCTTTTATTCATCTCT
1 TTTCTTTAATTCATCTCT
467321 TTTCTTTAATTC-TCTCT
1 TTTCTTTAATTCATCTCT
*
467338 ATTCT
1 TTTCT
467343 CTTCATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTTTAATTCATCTCT
Found at i:486041 original size:35 final size:35
Alignment explanation
Indices: 486001--486142 Score: 212
Period size: 35 Copynumber: 4.0 Consensus size: 35
485991 AAAAGATGAA
*
486001 CATTTGAATCGAAAGTGTTGATGCTTCCTTCCGTT
1 CATTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* *
486036 CATTTGAATCGAAAGTGCCGATGCTTCCTTTCGTT
1 CATTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
*
486071 CTTCTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
1 CAT-TTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* * *
486107 CACTTGAATCGAAAGTGTCGATGCTTCATTTCGTT
1 CATTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
486142 C
1 C
486143 TTCTTATTCA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 65 0.68
36 31 0.32
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (35 bp):
CATTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
Found at i:486120 original size:71 final size:71
Alignment explanation
Indices: 486004--486147 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
485994 AGATGAACAT
* * *
486004 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCATTTCG
486069 TTCTTC
66 TTCTTC
*
486075 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCATTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCATTTCG
486140 TTCTTC
66 TTCTTC
486146 TT
1 TT
486148 ATTCACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (71 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCATTTCG
TTCTTC
Found at i:492443 original size:20 final size:20
Alignment explanation
Indices: 492406--492443 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
492396 TCTCAGTCAT
*
492406 TCCTTCCTCCAAGGTCTGTA
1 TCCTTCCTCCAAGCTCTGTA
492426 TCCTTCCCTCC-AGCTCTG
1 TCCTT-CCTCCAAGCTCTG
492444 CTTTCTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.11, C:0.42, G:0.13, T:0.34
Consensus pattern (20 bp):
TCCTTCCTCCAAGCTCTGTA
Found at i:497951 original size:160 final size:161
Alignment explanation
Indices: 497684--498006 Score: 459
Period size: 160 Copynumber: 2.0 Consensus size: 161
497674 TGATATTAAA
*
497684 ATCTATAAGGTCTCACAAAAGCGATAATAGTTTGCTGAAATTCATATCTACACAAACATCTTAAA
1 ATCTATAAGGTCTCACAAAAGCAATAATAGTTTGCTGAAATTCATATCTACACAAACATCTTAAA
* * * * *
497749 CGGCACAAATAGACAGACATTGATCATTCAACAGACGACCACATTTTATATGCAGATTTTT-CTA
66 CAGCACAAACAGACAGACATTAATCATTCAACAGAAGACCACATTTTATATGCAGATTTTTCCAA
*
497813 AATAAACAAAGCAAAGGAAGCACTTTCATGT
131 AAAAAACAAAGCAAAGGAAGCACTTTCATGT
* * * *
497844 ATCTATAGGGTCTCACAAAAGCAATAATAGTTTGCTGATATTCATATCTATACAAACATCTTAAT
1 ATCTATAAGGTCTCACAAAAGCAATAATAGTTTGCTGAAATTCATATCTACACAAACATCTTAAA
* * * *
497909 CATCACAACCAGACAGGCATTAATCGTTCAACAGAAGACCACATTTTATATGCAGATTTTTCCAA
66 CAGCACAAACAGACAGACATTAATCATTCAACAGAAGACCACATTTTATATGCAGATTTTTCCAA
* * * * *
497974 AAAAAACATAGCGACGGGATCACTTTCATGT
131 AAAAAACAAAGCAAAGGAAGCACTTTCATGT
498005 AT
1 AT
498007 ATTCCATTCA
Statistics
Matches: 142, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
160 113 0.80
161 29 0.20
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (161 bp):
ATCTATAAGGTCTCACAAAAGCAATAATAGTTTGCTGAAATTCATATCTACACAAACATCTTAAA
CAGCACAAACAGACAGACATTAATCATTCAACAGAAGACCACATTTTATATGCAGATTTTTCCAA
AAAAAACAAAGCAAAGGAAGCACTTTCATGT
Found at i:502602 original size:24 final size:24
Alignment explanation
Indices: 502574--502621 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
502564 CACCTCTGGC
502574 ACCCTCTTCATGATGATCACCATG
1 ACCCTCTTCATGATGATCACCATG
* *
502598 ACCCTCTTCCTTATGATCACCATG
1 ACCCTCTTCATGATGATCACCATG
502622 GCCACCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.31
Consensus pattern (24 bp):
ACCCTCTTCATGATGATCACCATG
Found at i:508196 original size:25 final size:25
Alignment explanation
Indices: 508168--508215 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
508158 TAGGTAGTAT
*
508168 AAGTTTGTTCATAATATTTTTGTCG
1 AAGTATGTTCATAATATTTTTGTCG
*
508193 AAGTATGTTCATGATATTTTTGT
1 AAGTATGTTCATAATATTTTTGT
508216 ATTTCCGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (25 bp):
AAGTATGTTCATAATATTTTTGTCG
Done.