Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1573213 original size:3 final size:3
Alignment explanation
Indices: 1573193--1573244 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1573183 CAAGTGTTTA
* * * * *
1573193 CTT CTT CCT CCT CCT CTT CTT CTT CTT CTT TTT CTT CTT CTT CAT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1573241 CTT C
1 CTT C
1573245 ATCATCATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:1574960 original size:21 final size:22
Alignment explanation
Indices: 1574919--1574961 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1574909 TATTTACCCA
*
1574919 GATTATAAAAAAATCTTATTTT
1 GATTATAAAAAAATCTGATTTT
1574941 GATTA-AAAAAAAT-TAGATTTT
1 GATTATAAAAAAATCT-GATTTT
1574962 AAAAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (22 bp):
GATTATAAAAAAATCTGATTTT
Found at i:1579030 original size:14 final size:14
Alignment explanation
Indices: 1578996--1579039 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1578986 TATTTTGTTT
1578996 GTCAAAGTCAACAG
1 GTCAAAGTCAACAG
* * *
1579010 GTTAAAGTTAACGG
1 GTCAAAGTCAACAG
1579024 GTCAAAGTCAACAG
1 GTCAAAGTCAACAG
1579038 GT
1 GT
1579040 TGACTCAGAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (14 bp):
GTCAAAGTCAACAG
Found at i:1581246 original size:18 final size:18
Alignment explanation
Indices: 1581223--1581266 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1581213 AACTTTGACT
*
1581223 AAAAAGTCAACCT-TTTCG
1 AAAAAGGCAA-CTGTTTCG
1581241 AAAAAGGCAACTGTTTCG
1 AAAAAGGCAACTGTTTCG
*
1581259 AAGAAGGC
1 AAAAAGGC
1581267 CTATTTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (18 bp):
AAAAAGGCAACTGTTTCG
Found at i:1584330 original size:60 final size:59
Alignment explanation
Indices: 1584144--1584331 Score: 209
Period size: 60 Copynumber: 3.1 Consensus size: 59
1584134 GCATCGTATG
* *
1584144 TTCTCAAACTATGATCCTCATTTTAAATTAGTCCCTAAAATTTTGAATATTCTAATTTCA
1 TTCTCAAACTA-AATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
* * * *
1584204 -TCATCAAACTAATATACTCATTTTAAACTAGTCCTTAAACTTTTGAACATTCTAATTTCA
1 TTC-TCAAACTAA-ATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
* * * * * *
1584264 TCCTCAAACTACAACCCTTATTCTAAATTGGTCCCTAAACTTTTAAATATT-TCAATTTCA
1 TTCTCAAACTA-AATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCT-AATTTCA
1584324 TTCTCAAA
1 TTCTCAAA
1584332 TTTATTCAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
59 3 0.03
60 101 0.95
61 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (59 bp):
TTCTCAAACTAAATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
Found at i:1590390 original size:2 final size:2
Alignment explanation
Indices: 1590383--1590410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1590373 CTTCGTGATC
1590383 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
1590411 GTAATTAAAG
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:1595955 original size:94 final size:94
Alignment explanation
Indices: 1595829--1596006 Score: 320
Period size: 94 Copynumber: 1.9 Consensus size: 94
1595819 ATTTTGATTA
* * *
1595829 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAATTCACTCTTCTTCTTATTCTTTTAATCGTT
1 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
1595894 AGAGTTCCTTTATTGGGTGTTTCAGACTC
66 AGAGTTCCTTTATTGGGTGTTTCAGACTC
1595923 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
1 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
*
1595988 AGGGTTCCTTTATTGGGTG
66 AGAGTTCCTTTATTGGGTG
1596007 CTTCTCGTTA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 80 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (94 bp):
TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
AGAGTTCCTTTATTGGGTGTTTCAGACTC
Found at i:1599982 original size:43 final size:43
Alignment explanation
Indices: 1599924--1600258 Score: 505
Period size: 43 Copynumber: 7.9 Consensus size: 43
1599914 AGGTCTTATA
* *
1599924 CTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* *
1599967 ATTGCACACAACAAAAGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
*
1600009 CTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * *
1600052 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
1600095 CTTGCACACAGCAAAAGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* *
1600137 CTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
* * * * *
1600180 CTTGCACACAGCAAAGGGACATGGGGGAATTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
*
1600223 CTTGCACACAGCAAAAGAA-CTTGGGAAACTGTAAGG
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGG
1600259 AACCTGGGGA
Statistics
Matches: 265, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
42 91 0.34
43 174 0.66
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACC
Found at i:1600014 original size:85 final size:86
Alignment explanation
Indices: 1599924--1600258 Score: 505
Period size: 85 Copynumber: 3.9 Consensus size: 86
1599914 AGGTCTTATA
* * *
1599924 CTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCATTGCACACAACAAAAGAACCT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
1599989 -GGGAAACTGTAAGGCTTACC
66 GGGGAAACTGTAAGGCTTACC
* * * *
1600009 CTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
*
1600074 GGGGGAACTGTAAGGCTTACC
66 GGGGAAACTGTAAGGCTTACC
*
1600095 CTTGCACACAGCAAAAGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
1600159 GGGGAAACTGTAAGGCTTACC
66 GGGGAAACTGTAAGGCTTACC
* * * * * *
1600180 CTTGCACACAGCAAAGGGACATGGGGGAATTGTAAGGCTTACCCTTGCACACAGCAAAAGAA-CT
1 CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
*
1600244 TGGGAAACTGTAAGG
66 GGGGAAACTGTAAGG
1600259 AACCTGGGGA
Statistics
Matches: 228, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
85 153 0.67
86 75 0.33
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (86 bp):
CTTGCACACAGCAAAAGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAAGAACCT
GGGGAAACTGTAAGGCTTACC
Found at i:1600152 original size:128 final size:128
Alignment explanation
Indices: 1599924--1600258 Score: 573
Period size: 128 Copynumber: 2.6 Consensus size: 128
1599914 AGGTCTTATA
* * * * *
1599924 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCATTGCACACAACAAAAGAACC
1 CTTGCACACAGCAAAGGGA-CCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACC
*
1599988 TGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACC
65 TGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
1600052 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCT
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCT
1600117 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
66 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
* * *
1600180 CTTGCACACAGCAAAGGGACATGGGGGAATTGTAAGGCTTACCCTTGCACACAGCAAAAGAACTT
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCT
1600245 GGGAAACTGTAAGG
66 GGGAAACTGTAAGG
1600259 AACCTGGGGA
Statistics
Matches: 197, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
128 195 0.99
129 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (128 bp):
CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCT
GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACC
Found at i:1600321 original size:43 final size:43
Alignment explanation
Indices: 1600255--1600362 Score: 198
Period size: 43 Copynumber: 2.5 Consensus size: 43
1600245 GGGAAACTGT
* *
1600255 AAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCA
1 AAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCA
1600298 AAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCA
1 AAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCA
1600341 AAGGGACCTGGGGGAACTGTAA
1 AAGGGACCTGGGGGAACTGTAA
1600363 CGGTAATTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.16
Consensus pattern (43 bp):
AAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCA
Found at i:1600332 original size:105 final size:105
Alignment explanation
Indices: 1600150--1600342 Score: 368
Period size: 105 Copynumber: 1.8 Consensus size: 105
1600140 GCACACAACA
*
1600150 AAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACATGGGGGAATTGTAA
1 AAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACATGGGGGAACTGTAA
1600215 GGCTTACCCTTGCACACAGCAAAAGAACTTGGGAAACTGT
66 GGCTTACCCTTGCACACAGCAAAAGAACTTGGGAAACTGT
*
1600255 AAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
1 AAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACATGGGGGAACTGTAA
1600320 GGCTTACCCTTGCACACAGCAAA
66 GGCTTACCCTTGCACACAGCAAA
1600343 GGGACCTGGG
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 86 1.00
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (105 bp):
AAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACATGGGGGAACTGTAA
GGCTTACCCTTGCACACAGCAAAAGAACTTGGGAAACTGT
Found at i:1601771 original size:26 final size:26
Alignment explanation
Indices: 1601707--1601764 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1601697 TTCATTTCAG
*
1601707 AGCTCGAGGATATCCAATCATTCCTA
1 AGCTTGAGGATATCCAATCATTCCTA
*
1601733 AGCTTGAGAATATCCAATCATTCCTA
1 AGCTTGAGGATATCCAATCATTCCTA
1601759 AGCTTG
1 AGCTTG
1601765 GTGATATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (26 bp):
AGCTTGAGGATATCCAATCATTCCTA
Found at i:1603208 original size:18 final size:18
Alignment explanation
Indices: 1603200--1603257 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
1603190 GGGTCAGGTT
1603200 GGGTAAACGGATCGGGTC
1 GGGTAAACGGATCGGGTC
1603218 GGGTAAACGGATCGGGTC
1 GGGTAAACGGATCGGGTC
*
1603236 GGGTAAACGGGTCGGGTC
1 GGGTAAACGGATCGGGTC
1603254 GGGT
1 GGGT
1603258 TATGACCGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.19, C:0.16, G:0.48, T:0.17
Consensus pattern (18 bp):
GGGTAAACGGATCGGGTC
Found at i:1603227 original size:36 final size:36
Alignment explanation
Indices: 1603187--1603257 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
1603177 AACGCCAGTC
* *
1603187 AACGGGTCAGGTTGGGTAAACGGATCGGGTCGGGTA
1 AACGGATCAGGTCGGGTAAACGGATCGGGTCGGGTA
* *
1603223 AACGGATCGGGTCGGGTAAACGGGTCGGGTCGGGT
1 AACGGATCAGGTCGGGTAAACGGATCGGGTCGGGT
1603258 TATGACCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.46, T:0.18
Consensus pattern (36 bp):
AACGGATCAGGTCGGGTAAACGGATCGGGTCGGGTA
Found at i:1603596 original size:20 final size:20
Alignment explanation
Indices: 1603573--1603620 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1603563 ATTTATCTAT
*
1603573 TTTAAGATTCA-ATTATTTTA
1 TTTAAAATTCAGA-TATTTTA
*
1603593 TTTAAAATTTAGATATTTTA
1 TTTAAAATTCAGATATTTTA
1603613 TTTAAAAT
1 TTTAAAAT
1603621 GTATAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTAAAATTCAGATATTTTA
Found at i:1603666 original size:29 final size:28
Alignment explanation
Indices: 1603634--1603689 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1603624 TAATTTAAGT
1603634 TTTAAATTTTAGA-ATTTAGAAATTAAAAA
1 TTTAAATTTTA-ATATTTA-AAATTAAAAA
*
1603663 TTTAGATTTTAATATTTAAAATTAAAA
1 TTTAAATTTTAATATTTAAAATTAAAA
1603690 TAATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
TTTAAATTTTAATATTTAAAATTAAAAA
Found at i:1603683 original size:21 final size:21
Alignment explanation
Indices: 1603591--1603685 Score: 88
Period size: 21 Copynumber: 4.5 Consensus size: 21
1603581 TCAATTATTT
1603591 TATTTAAAATTTAGATATTT--
1 TATTTAAAATTTAGA-ATTTAA
* *
1603611 TATTTAAAATGTATAATTTAA
1 TATTTAAAATTTAGAATTTAA
*
1603632 GT-TTTAAATTTTAGAATTTAGA
1 -TATTTAAAATTTAGAATTTA-A
* * *
1603654 AATTAAAAATTTAGATTTTAA
1 TATTTAAAATTTAGAATTTAA
1603675 TATTTAAAATT
1 TATTTAAAATT
1603686 AAAATAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.07
20 13 0.22
21 25 0.42
22 17 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (21 bp):
TATTTAAAATTTAGAATTTAA
Found at i:1605103 original size:15 final size:16
Alignment explanation
Indices: 1605085--1605114 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1605075 ATTTAATAGT
1605085 TAAATTA-ATAAAATA
1 TAAATTATATAAAATA
1605100 TAAATTATATAAAAT
1 TAAATTATATAAAAT
1605115 TATGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTATATAAAATA
Found at i:1606973 original size:42 final size:42
Alignment explanation
Indices: 1606921--1607005 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1606911 CGTTATTACA
1606921 TAAATTTTAACAATTTTTGTGTCATATTTGTATTTATTTATT
1 TAAATTTTAACAATTTTTGTGTCATATTTGTATTTATTTATT
1606963 TAAATTTTAACAATTTTTGTGTCATATTTGTATTTATTTATT
1 TAAATTTTAACAATTTTTGTGTCATATTTGTATTTATTTATT
1607005 T
1 T
1607006 CGCGTTATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (42 bp):
TAAATTTTAACAATTTTTGTGTCATATTTGTATTTATTTATT
Found at i:1608233 original size:3 final size:3
Alignment explanation
Indices: 1608214--1608262 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1608204 TAAAAGATTA
*
1608214 TTC TTT TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1608261 TT
1 TT
1608263 GTTTTCTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:1613358 original size:628 final size:623
Alignment explanation
Indices: 1611958--1614842 Score: 3129
Period size: 628 Copynumber: 4.7 Consensus size: 623
1611948 ATATAATACA
** * *
1611958 GTATTAATTGATTATTTTTGATTTTATTTGGATACTAATTAATAGCTCGAATATATTATTTTCAA
1 GTATTAATTGATTATTTCCGATTTTATTTGGATACTAATTAATAGCCCGAATATATTATTTCCAA
* *
1612023 TTCGTCTCTCTTGTGAAATACTATAAATATCGTGCTAACCTACTAGGTTAAATAC-GTTCAAAAA
66 TTCGTCTCCCTTGTGAAACACTATAAATATCGTGCTAACCTACTAGGTTAAATACGGTTCAAAAA
* *
1612087 CTCTCTCTTTCTCTCTTATTTTCGGTGATAGTCTCTAATAAGATTTGGTTCGTGATCTCGCAAGT
131 CTCTCTCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCGCAAGT
* * * *
1612152 TGTGC-AATAGTGCGCTAATCGTATCGTTGTTGTATCTTGGGAAACATACGGCCAAGATATCTCG
196 TGTGCTACT-GTGCGCTGATCGTATCGTTGTTGTATCCTGGGAAACATACGACCAAGATATCTCG
* * * * *
1612216 AGCACCAAAGAGTGACTGAAAATTTGTCTTAAGGAAATTACGTAATTGCAGGCATCAACCAGATT
260 AGCACCAAGGAGTGGCTGAAAATTTGTCTTAAGGAAACTGCGTAATTGCAGGCCTCAACCAGATT
* * * *
1612281 CAAGTTCGATTTCATCTTATTATTCAAGTTCTTTATTCTAATATGTTCCTCCTCATTCATTAATA
325 CAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTCTAATATGTTCCTCCTCATTTATTAATA
*
1612346 AAGTTCGATCTTTTATTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTGGAAAC
390 AAGTTTGATCTTTTATTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTGGAAAC
* * * * ** * *
1612411 ACACGTGGGCGACGTA-AATGTC-CGGACCGGTCGGGGCTTGCGGATATTTTACCTACT-ATG-A
455 AAACGT---C-AC-AACAATG-CACGGACCGGTCGGAGC-T-CGAATATTGAACC-CCTCACGTA
* * * *
1612472 ATTAAATATG-GTATGACTTGCAATTCATGAATATATTCGATATAAAACAATATTAATTGATTAT
511 ATTAAATA-GCGTATGACTTGCAATTCACGAATATATTCGATATGATACAATACTAATTGATTAT
* * * *
1612536 TTCCAATTTTATTCATATACTTATTAACTGTA--GAAATATTTTTCAGGCA
575 TTCCGATTTTATTCAGATACTTATTAAC-G-ACCGAAATATTTTTAAGGCG
*
1612585 GTATTAATTGATTATTT-CGATTTTATTCT-GATACTGATTAATAGCCCGAATATATTATTTCCA
1 GTATTAATTGATTATTTCCGATTTTATT-TGGATACTAATTAATAGCCCGAATATATTATTTCCA
* * * *
1612648 ATTCTTCTCCCTTGTGAAAAACTATAAATAAT-GTGCTAA--TACATTAGGTTAAATATGGTTAA
65 ATTCGTCTCCCTTGTGAAACACTATAAAT-ATCGTGCTAACCTAC--TAGGTTAAATACGGTTCA
* *
1612710 AAAACTCTCTTCTTTTTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGCGATCTCG
127 AAAACTCTC-TCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCG
* ** *
1612775 TAAGTTGTGCTACTGTGCGCTGATTATATCGTTGTTGTATCCTGGGAAACATACGATCAAGATAT
191 CAAGTTGTGCTACTGTGCGCTGATCGTATCGTTGTTGTATCCTGGGAAACATACGACCAAGATAT
* * * ** *
1612840 CTCGAGCACCAAAGAGTAGCCGAAAATCCGTCTTAAGGAAACTGTGTAATTGCAGGCCTCAACCA
256 CTCGAGCACCAAGGAGTGGCTGAAAATTTGTCTTAAGGAAACTGCGTAATTGCAGGCCTCAACCA
* *
1612905 GATTCAAGTTCGATTTCCTCTTATTATTCAGGTTATTTATTCTAATATGTTCCTCCTCATTTATT
321 GATTCAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTCTAATATGTTCCTCCTCATTTATT
1612970 AATAAAGTTTGATCTTTTATTTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTG
386 AATAAAGTTTGATCTTTTA-TTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTG
** * **
1613035 GAAACAAACGTGGCAACGCGAATGTC-CGGACCGGTCGGGGCCTGCGAATATTTTACCCACT-AC
450 GAAACAAACGTCACAA--C-AATG-CACGGACCGGTCGGAG-CT-CGAATATTGAACCC-CTCAC
* *
1613098 G-AATTAAATATG-GTATGACTTGCAATTCATGAATATATTCGGTATGATACAATACTAATTGAT
508 GTAATTAAATA-GCGTATGACTTGCAATTCACGAATATATTCGATATGATACAATACTAATTGAT
* * *
1613161 TATTTTCGATTTTATTCAGATACTTATTAACGACCAAAATATTTTTTAGGCG
572 TATTTCCGATTTTATTCAGATACTTATTAACGACCGAAATATTTTTAAGGCG
* * *
1613213 GTATTAATTGATTATTTCCAATTTTATTTGGATACTAATTAATAGACTGAATATATTATTTCCAA
1 GTATTAATTGATTATTTCCGATTTTATTTGGATACTAATTAATAGCCCGAATATATTATTTCCAA
* * *
1613278 TTCGTCTCCCCTTTTGAAACACTATAAATACCATGCTAACCTACTAGGTTAAATACGGTTCAAAA
66 TTCGTCT-CCCTTGTGAAACACTATAAATATCGTGCTAACCTACTAGGTTAAATACGGTTCAAAA
* * *
1613343 ACTCTCTTCTTTCTCTCTTGTTTTTGGTGATGGTCTCTAACAAGATTTGGTTCATGATCTCGCAA
130 ACTCTC-TCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCGCAA
* * * * * *
1613408 GTTGTGCTATTGTGTGTTGATCGTATCGTTGTTGTATCCT--G-TAGAT--GACCAAGATATTTC
194 GTTGTGCTACTGTGCGCTGATCGTATCGTTGTTGTATCCTGGGAAACATACGACCAAGATATCTC
* * * *
1613468 GAGCACCAAGGAGTGGATGAAAATTTGTCTTAAGGAAACTGCGTAATTTCATGCCTCAACCATAT
259 GAGCACCAAGGAGTGGCTGAAAATTTGTCTTAAGGAAACTGCGTAATTGCAGGCCTCAACCAGAT
* *
1613533 TCAAATTCGATTTCCTGTTATTATTC-GAGTTCTTTATTCTAATTTGTTCCTCCTCATTTATTAA
324 TCAAGTTCGATTTCCTGTTATTATTCAG-GTTCTTTATTCTAATATGTTCCTCCTCATTTATTAA
* * * *
1613597 TAAAGTTTAATCTTTTATTTTTCTTTTATTTATGTCTCGGATTTTATAACACATCTTACCTGGAA
388 TAAAGTTTGATCTTTTATTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTGGAA
* * *** ** ** * * * * * **
1613662 ACAAACTTCACAACAATGCAAGTTGCATTTTGAG-TAGAATGATATGAACTCTTCATGTATTTGC
453 ACAAACGTCACAACAATGCACGGACCGGTCGGAGCTCGAAT-AT-TGAACCCCTCACGTAATTAA
* * *** *
1613726 ATAGCGTA--AATGTGATCAATTCACGAATATATTTGATATGATATGGTGCTAATTGATTATTTC
516 ATAGCGTATGACT-TG--CAATTCACGAATATATTCGATATGATACAATACTAATTGATTATTTC
* * * *
1613789 CGATTTTATTCGGATACTTATTAAAGGCCGAAATA-TTTTAAGGCT
578 CGATTTTATTCAGATACTTATTAACGACCGAAATATTTTTAAGGCG
* * * *
1613834 ATATTAATTGATTATTTCCGATTTTATTCGGATACTGATTAATAGTCCGAATATATTATTTCCAA
1 GTATTAATTGATTATTTCCGATTTTATTTGGATACTAATTAATAGCCCGAATATATTATTTCCAA
1613899 TTCGTCTCCCTTGTGAAACACTATAAATATCGTGCTAACCTACTAGGTTAAATACGGTTCAAAAA
66 TTCGTCTCCCTTGTGAAACACTATAAATATCGTGCTAACCTACTAGGTTAAATACGGTTCAAAAA
*
1613964 CTCTCCTCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTTGTGATCTCGCAAG
131 CTCT-CTCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCGCAAG
* * * * * * * *
1614029 TTATGCTACTGTACGTTGATCGTATCGTTATTGTATCCTGGGAGACAGACAACCAAGATATCTCA
195 TTGTGCTACTGTGCGCTGATCGTATCGTTGTTGTATCCTGGGAAACATACGACCAAGATATCTCG
* * * * * * * *
1614094 AACACCAAGGAGTGGCT-AAAA-ATGTCTTAAAGAAACTGTGTAGTTACAAGCCTCAACCAAATT
260 AGCACCAAGGAGTGGCTGAAAATTTGTCTTAAGGAAACTGCGTAATTGCAGGCCTCAACCAGATT
* * ** *
1614157 CAGGTACGATTTATTGTTATTATTCGGGTTCTTTATTCTAATATGTTCCTCCTCATTTATTAATA
325 CAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTCTAATATGTTCCTCCTCATTTATTAATA
* * * * *
1614222 AAGTTCGATATTTTATTTTTCTTTTATTTACGTCTCGGATTGTATAACACATCTTACATAGAAAC
390 AAGTTTGATCTTTTATTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTGGAAAC
* ** **** * * * * ** **
1614287 AAACTTCACAACAATGCAGCTTATATTTTTAGTAGCAT-G-ATA-TGAACTCTTCACGTGTTTGC
455 AAACGTCACAACAATGCA-C--GGACCGGTCGGAGC-TCGAATATTGAACCCCTCACGTAATTAA
* *** * * * ** *
1614349 GTAGCGTAAATGGGAT-CAATTCACGAATGTATTCAATATGATACGATGTTAATTGATTATTTTC
516 ATAGCGT--ATGACTTGCAATTCACGAATATATTCGATATGATACAATACTAATTGATTATTTCC
*
1614413 GATTTTATTCAGATACTTATTAGC-AGCCGAAATATTTTTAAGGCG
579 GATTTTATTCAGATACTTATTAACGA-CCGAAATATTTTTAAGGCG
* * * *
1614458 TTATTGATTGATTATTTCCGATTTTATTTGGATACTAATTAATAGCCCAAATATATTATTTTCAA
1 GTATTAATTGATTATTTCCGATTTTATTTGGATACTAATTAATAGCCCGAATATATTATTTCCAA
* *
1614523 TTAGTCTCCATTGTGAAACACTAT-AA-A------T-A-C--C---G-----T----TTCAAAAA
66 TTCGTCTCCCTTGTGAAACACTATAAATATCGTGCTAACCTACTAGGTTAAATACGGTTCAAAAA
* *
1614564 ---------T-TATCTTATTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCGCAAGT
131 CTCTCTCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCGCAAGT
* * * * *
1614619 TGTGCTACTGTGCGCTGATCGTATCATTGTTGTATCATAGGAGACAAACGACCAAGATATCTCGA
196 TGTGCTACTGTGCGCTGATCGTATCGTTGTTGTATCCTGGGAAACATACGACCAAGATATCTCGA
* * * * * *
1614684 ACACCAAGGAGTGGC-CAACAATTTGTCTTAAGAAAATTGCGTAGTTGCAGGTCTCAACCAGATT
261 GCACCAAGGAGTGGCTGAA-AATTTGTCTTAAGGAAACTGCGTAATTGCAGGCCTCAACCAGATT
*
1614748 CAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTCTAATATGTTCGTCCTCATTTATTAATA
325 CAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTCTAATATGTTCCTCCTCATTTATTAATA
1614813 AAGTTTGATCTTTTATTTTTCTTTTATTTA
390 AAGTTTGATCTTTTATTTTTCTTTTATTTA
1614843 TGTCCTCATT
Statistics
Matches: 1961, Mismatches: 244, Indels: 142
0.84 0.10 0.06
Matches are distributed among these distances:
589 123 0.06
590 3 0.00
591 120 0.06
600 8 0.00
604 1 0.00
609 1 0.00
612 1 0.00
614 1 0.00
615 1 0.00
616 1 0.00
618 4 0.00
619 6 0.00
620 158 0.08
621 93 0.05
622 73 0.04
623 266 0.14
624 154 0.08
625 171 0.09
626 93 0.05
627 38 0.02
628 398 0.20
629 106 0.05
630 138 0.07
632 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (623 bp):
GTATTAATTGATTATTTCCGATTTTATTTGGATACTAATTAATAGCCCGAATATATTATTTCCAA
TTCGTCTCCCTTGTGAAACACTATAAATATCGTGCTAACCTACTAGGTTAAATACGGTTCAAAAA
CTCTCTCTTTCTCTCTTGTTTTCGGTGATAGTCTCTAACAAGATTTGGTTCGTGATCTCGCAAGT
TGTGCTACTGTGCGCTGATCGTATCGTTGTTGTATCCTGGGAAACATACGACCAAGATATCTCGA
GCACCAAGGAGTGGCTGAAAATTTGTCTTAAGGAAACTGCGTAATTGCAGGCCTCAACCAGATTC
AAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTCTAATATGTTCCTCCTCATTTATTAATAA
AGTTTGATCTTTTATTTTTCTTTTATTTACGTCTCAGATTGTATAACACATCTTACCTGGAAACA
AACGTCACAACAATGCACGGACCGGTCGGAGCTCGAATATTGAACCCCTCACGTAATTAAATAGC
GTATGACTTGCAATTCACGAATATATTCGATATGATACAATACTAATTGATTATTTCCGATTTTA
TTCAGATACTTATTAACGACCGAAATATTTTTAAGGCG
Found at i:1614849 original size:48 final size:48
Alignment explanation
Indices: 1614796--1614890 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
1614786 TAATATGTTC
1614796 GTCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTAT
1 GTCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTAT
1614844 GTCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTA
1 GTCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTA
1614891 CGTCTCGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (48 bp):
GTCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTAT
Found at i:1614962 original size:639 final size:637
Alignment explanation
Indices: 1614206--1615488 Score: 1903
Period size: 639 Copynumber: 2.0 Consensus size: 637
1614196 AATATGTTCC
*
1614206 TCCTCATTTATTAATAAAGTTCGATATTTTATTTTTCTTTTATTTACGTCTCGGATTGTATAACA
1 TCCTCATTTATTAATAAAGTTCGATATTTTATTTTTCTTTTATTTACGTCTCGAATTGTATAACA
* *
1614271 CATCTTACATAGAAACAAACTTCACAACAATGCAGCTTATATTTTTAGTAGCATGATATGAACTC
66 CATCTTACATAGAAACAAACTTCACAACAATGCAGCTTACATTTTGAGTAGCATGATATGAACTC
* * * * *
1614336 TTCACGTGTTTGCGTAGCGTAAATGGGATCAATTCACGAATGTATTCAATATGATACGATGTTAA
131 TTCACGTATTTGCGTAGCATAAATGAGATCAATTCACGAATATATTCAATATCATACGATGTTAA
* * *
1614401 TTGATTATTTTCGATTTTATTCAGATACTTATTAGCAGCCGAAATATTTTTAAGGCGTTATTGAT
196 TTGATTATTTTCG-TTTTATTCAGATACTTATTAACAGCCGAAATATTTTTAAGGCGATATTAAT
* *
1614466 TGATTATTTCCGA-TTTTATTTGGATACTAATTAATAGCCCAAATATATTATTTTCAATTAGTCT
260 TGATTATTTCCAATTTTTATTCGGATACTAATTAATAG-CCAAATATATTATTTTCAATTAGTCT
1614530 CCATTGTGAAACACTATAAATACCGTTTCAAAAA-T-TATCTTATTTTCGGTGATAGTCTCTAAC
324 CCATTGTGAAACACTATAAATACCGTTTCAAAAATTCTATCTTATTTTCGGTGATAGTCTCTAAC
* *
1614593 AAGATTTGGTTCGTGATCTCGCAAGTTGTGCTACTGTGCGCTGATCGTATCATTGTTGTATCATA
389 AAGATTTGGTTCGTGATCTCGCAAGTTGTGCTACTATGCACTGATCGTATCATTGTTGTATCATA
* * *
1614658 GGAGACAAACGACCAAGATATCTCGAA-CACCAAGGAGTGGCC-AACAATTTGTCTTAAGAAAAT
454 GGAGACAAACAACCAAGATATCTC-AAGCACCAAGGAGTGACCGAA-AATTTGTCTTAAGAAAAC
* *
1614721 TGCGTAGTTGCAGGTCTCAACCAGATTCAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTC
517 TGCGTAGTTGCAGGCCTCAACCAGATTCAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTA
*
1614786 TAATATGTTCGTCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTATG
582 TAATATG---GTCCTCATTTATTAATAAAGTTCGATCTTTTATTTTTCTTTTATTTATG
* * *
1614845 TCCTCATTTATTAATAAAGTTTGATCTTTTATTTTTCTTTTATTTACGTCTCGAATTGTATAATA
1 TCCTCATTTATTAATAAAGTTCGATATTTTATTTTTCTTTTATTTACGTCTCGAATTGTATAACA
* * * *
1614910 CATCTTACCTGGAAACAAACTTCACAACAATGCGGGC-TGCATTTTGAGTAGCATGATATGAACT
66 CATCTTACATAGAAACAAACTTCACAACAATGC-AGCTTACATTTTGAGTAGCATGATATGAACT
* **
1614974 CTTCATGTATTTGCGTAGCATAAATGAGATCAATTCACGAATATATTTTATATCATACGATGTTA
130 CTTCACGTATTTGCGTAGCATAAATGAGATCAATTCACGAATATATTCAATATCATACGATGTTA
* *
1615039 ATTGATTATTTTCGTTTTATTCAGATACTTATTAACGGCCGAAATATTTTTAAGGTGATATTAAT
195 ATTGATTATTTTCGTTTTATTCAGATACTTATTAACAGCCGAAATATTTTTAAGGCGATATTAAT
* * *
1615104 TGATTATTTCTAATTTTTATTCGGATACTAATTAATAGCCGAATATATTATTTTCAATTCGTCTC
260 TGATTATTTCCAATTTTTATTCGGATACTAATTAATAGCCAAATATATTATTTTCAATTAGTCTC
* * *
1615169 CCTTGTGAAACACTATAAATACCGTTTCAAAAACTCTCTTCTTTCTCTCTTGTTTTCGGTGATAG
325 CATTGTGAAACACTATAAATACCGTTTCAAAAA---------TTCTATCTTATTTTCGGTGATAG
* * *
1615234 TCTCTAACAAGATTTGGTTCGTGATCTCGCAAGTTGTGCTATTATGCACTGATTGTATCGTTGTT
381 TCTCTAACAAGATTTGGTTCGTGATCTCGCAAGTTGTGCTACTATGCACTGATCGTATCATTGTT
* * * *
1615299 GTATCTTGGGAGACATACAACCAAGATATCTCAAGCACGAAGGAGTGACCGAAAATTTGTCTTAA
446 GTATCATAGGAGACAAACAACCAAGATATCTCAAGCACCAAGGAGTGACCGAAAATTTGTCTTAA
* * * * **
1615364 GGAAACTGCGTAGTTTCAGGCCTTAACCAGATTCAAGTTCGATTTCTTGTTATTATTTGGGTTCT
511 GAAAACTGCGTAGTTGCAGGCCTCAACCAGATTCAAGTTCGATTTCCTGTTATTATTCAGGTTCT
1615429 TTATTATAATATGGTCCTCATTTATTAATAAAGTTCGATCTTTTATTTTTCTTTTATTTA
576 TTATTATAATATGGTCCTCATTTATTAATAAAGTTCGATCTTTTATTTTTCTTTTATTTA
1615489 CGTATCGGAT
Statistics
Matches: 577, Mismatches: 52, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
638 114 0.20
639 210 0.36
640 2 0.00
646 46 0.08
648 3 0.01
649 200 0.35
650 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (637 bp):
TCCTCATTTATTAATAAAGTTCGATATTTTATTTTTCTTTTATTTACGTCTCGAATTGTATAACA
CATCTTACATAGAAACAAACTTCACAACAATGCAGCTTACATTTTGAGTAGCATGATATGAACTC
TTCACGTATTTGCGTAGCATAAATGAGATCAATTCACGAATATATTCAATATCATACGATGTTAA
TTGATTATTTTCGTTTTATTCAGATACTTATTAACAGCCGAAATATTTTTAAGGCGATATTAATT
GATTATTTCCAATTTTTATTCGGATACTAATTAATAGCCAAATATATTATTTTCAATTAGTCTCC
ATTGTGAAACACTATAAATACCGTTTCAAAAATTCTATCTTATTTTCGGTGATAGTCTCTAACAA
GATTTGGTTCGTGATCTCGCAAGTTGTGCTACTATGCACTGATCGTATCATTGTTGTATCATAGG
AGACAAACAACCAAGATATCTCAAGCACCAAGGAGTGACCGAAAATTTGTCTTAAGAAAACTGCG
TAGTTGCAGGCCTCAACCAGATTCAAGTTCGATTTCCTGTTATTATTCAGGTTCTTTATTATAAT
ATGGTCCTCATTTATTAATAAAGTTCGATCTTTTATTTTTCTTTTATTTATG
Found at i:1617191 original size:21 final size:22
Alignment explanation
Indices: 1617158--1617198 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1617148 TTAAAAATTA
*
1617158 TAAAGGTAGTACCGATACTCAT
1 TAAAGGTAGTACCAATACTCAT
1617180 TAAAGG-AGTACCAATACTC
1 TAAAGGTAGTACCAATACTC
1617199 CCTGTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
TAAAGGTAGTACCAATACTCAT
Found at i:1618402 original size:20 final size:20
Alignment explanation
Indices: 1618361--1618408 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1618351 AATGATTTTC
* *
1618361 TTTTGAAAGCAAAATTGGAT
1 TTTTAAAAGCAAAATTGAAT
1618381 TTTTAAAAGCAAAA-TGAAAT
1 TTTTAAAAGCAAAATTG-AAT
*
1618401 TTTGAAAA
1 TTTTAAAA
1618409 TGATTTTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTTAAAAGCAAAATTGAAT
Found at i:1629357 original size:26 final size:26
Alignment explanation
Indices: 1629328--1629380 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1629318 AGAGTAACTT
1629328 GTAATGCGATGGCATGGCTCATCTTA
1 GTAATGCGATGGCATGGCTCATCTTA
1629354 GTAATGCGATGGCATGGCTCATCTTA
1 GTAATGCGATGGCATGGCTCATCTTA
1629380 G
1 G
1629381 GAGAGCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (26 bp):
GTAATGCGATGGCATGGCTCATCTTA
Found at i:1634979 original size:23 final size:23
Alignment explanation
Indices: 1634949--1634998 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1634939 CGAACCTACA
1634949 TTACTTGGACTTAGGTATGAGTT
1 TTACTTGGACTTAGGTATGAGTT
1634972 TTACTTGGACTTAGGTATGAGTT
1 TTACTTGGACTTAGGTATGAGTT
1634995 TTAC
1 TTAC
1634999 ATATACAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (23 bp):
TTACTTGGACTTAGGTATGAGTT
Found at i:1635997 original size:28 final size:29
Alignment explanation
Indices: 1635959--1636018 Score: 113
Period size: 28 Copynumber: 2.1 Consensus size: 29
1635949 AAAATGGGTT
1635959 AAAATCTGAAACTTGAAAAGGGAATAAAA
1 AAAATCTGAAACTTGAAAAGGGAATAAAA
1635988 AAAAT-TGAAACTTGAAAAGGGAATAAAA
1 AAAATCTGAAACTTGAAAAGGGAATAAAA
1636016 AAA
1 AAA
1636019 TGTACCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17
Consensus pattern (29 bp):
AAAATCTGAAACTTGAAAAGGGAATAAAA
Found at i:1638166 original size:32 final size:32
Alignment explanation
Indices: 1638123--1638184 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1638113 TAACTTTGGT
*
1638123 TTTTTCATGTTGTCAAAGAGTTGAATAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
1638155 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
1638185 AAAATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:1655664 original size:19 final size:20
Alignment explanation
Indices: 1655629--1655668 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1655619 ATTTTAGTTT
*
1655629 GGGAAGATGATAAGATGAGA
1 GGGAAGAGGATAAGATGAGA
1655649 GGGAAGAGGA-AAGATGAGA
1 GGGAAGAGGATAAGATGAGA
1655668 G
1 G
1655669 TAAAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.10
Consensus pattern (20 bp):
GGGAAGAGGATAAGATGAGA
Found at i:1661226 original size:15 final size:15
Alignment explanation
Indices: 1661207--1661273 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 15
1661197 ATCAAGTGTG
1661207 CTGCTATCTGGTCTA
1 CTGCTATCTGGTCTA
* *
1661222 TTGCTATCTGGTTTA
1 CTGCTATCTGGTCTA
*
1661237 CTGCTATCTCGTCTA
1 CTGCTATCTGGTCTA
* *
1661252 CTACTATCTGGTTTA
1 CTGCTATCTGGTCTA
*
1661267 TTGCTAT
1 CTGCTAT
1661274 TTTGTTTACT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (15 bp):
CTGCTATCTGGTCTA
Found at i:1661241 original size:30 final size:30
Alignment explanation
Indices: 1661207--1661273 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1661197 ATCAAGTGTG
* * *
1661207 CTGCTATCTGGTCTATTGCTATCTGGTTTA
1 CTGCTATCTCGTCTACTACTATCTGGTTTA
1661237 CTGCTATCTCGTCTACTACTATCTGGTTTA
1 CTGCTATCTCGTCTACTACTATCTGGTTTA
*
1661267 TTGCTAT
1 CTGCTAT
1661274 TTTGTTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (30 bp):
CTGCTATCTCGTCTACTACTATCTGGTTTA
Found at i:1665479 original size:2 final size:2
Alignment explanation
Indices: 1665472--1665510 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1665462 ATAGAAAAGA
1665472 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
1665511 AAGAGAGAGA
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:1669329 original size:16 final size:15
Alignment explanation
Indices: 1669300--1669360 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
1669290 ATTATAGTTT
*
1669300 AACCGAAATCAACCTG
1 AACCGAAAT-AACCCG
1669316 AACCGAAAGTAACCCG
1 AACCGAAA-TAACCCG
* *
1669332 AACTC-AAAGCAACCCA
1 AAC-CGAAA-TAACCCG
1669348 AACCGAAATAACC
1 AACCGAAATAACC
1669361 ATCCGAAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 5 0.13
16 31 0.82
17 2 0.05
ACGTcount: A:0.48, C:0.33, G:0.11, T:0.08
Consensus pattern (15 bp):
AACCGAAATAACCCG
Found at i:1669469 original size:3 final size:3
Alignment explanation
Indices: 1669461--1669490 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1669451 AAATAGTTTT
1669461 TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
1669491 TTAGTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1669916 original size:2 final size:2
Alignment explanation
Indices: 1669911--1669950 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1669901 AATTAAATTG
1669911 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
1669951 GATAAATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1670401 original size:24 final size:23
Alignment explanation
Indices: 1670374--1670423 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1670364 CGACTCGAAC
1670374 ACCAACCGA-TCCGATTTTGACCAA
1 ACCAACCGACT-CGA-TTTGACCAA
* *
1670398 ACCAATCGACTCGATTTGACCCA
1 ACCAACCGACTCGATTTGACCAA
1670421 ACC
1 ACC
1670424 TGATACCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 11 0.48
25 1 0.04
ACGTcount: A:0.32, C:0.36, G:0.12, T:0.20
Consensus pattern (23 bp):
ACCAACCGACTCGATTTGACCAA
Found at i:1672828 original size:28 final size:28
Alignment explanation
Indices: 1672783--1672844 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
1672773 AAATTACAAT
*
1672783 AAAA-AATATAAAAGATAAAATAAAAAG
1 AAAATAATATAAAAGATAAAAGAAAAAG
1672810 AAAATAATATAACAA-ATAAAAGAAAAAG
1 AAAATAATATAA-AAGATAAAAGAAAAAG
1672838 AAAATAA
1 AAAATAA
1672845 CAAAAGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 4 0.12
28 26 0.81
29 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (28 bp):
AAAATAATATAAAAGATAAAAGAAAAAG
Found at i:1672836 original size:23 final size:22
Alignment explanation
Indices: 1672800--1672883 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 22
1672790 ATAAAAGATA
1672800 AAATAAAAAGAAAATAATATAAC
1 AAATAAAAA-AAAATAATATAAC
* *
1672823 AAATAAAAGAAAAAGAAAATAAC
1 AAATAAAA-AAAAATAATATAAC
1672846 AAA-AGAAACTAAAAATAATAATAAC
1 AAATA-AAA--AAAAATAAT-ATAAC
*
1672871 AAA-AATAAAAAAT
1 AAATAAAAAAAAAT
1672884 CAGAAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 7 0.14
23 25 0.49
24 10 0.20
25 9 0.18
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (22 bp):
AAATAAAAAAAAATAATATAAC
Found at i:1683374 original size:22 final size:22
Alignment explanation
Indices: 1683347--1683399 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
1683337 ACTCGTACAA
1683347 AAATATACAAATCGAG-GTTTAC
1 AAATATACAAATC-AGTGTTTAC
1683369 AAATATACAAATCAGTGTTTAC
1 AAATATACAAATCAGTGTTTAC
1683391 AAATATACA
1 AAATATACA
1683400 CGCACTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.28
Consensus pattern (22 bp):
AAATATACAAATCAGTGTTTAC
Found at i:1691673 original size:3 final size:3
Alignment explanation
Indices: 1691665--1691754 Score: 89
Period size: 3 Copynumber: 30.7 Consensus size: 3
1691655 TTGGTTTTAC
1691665 TAT TAT TAT TAT TAT TAT TAT TAT TATT TATT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT
* * * * *
1691711 TAT TA- TAT TAT AAT T-T AAT TA- TAA TAA TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1691755 CAGGCCCAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
2 7 0.09
3 63 0.82
4 7 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1691701 original size:11 final size:10
Alignment explanation
Indices: 1691667--1691721 Score: 69
Period size: 11 Copynumber: 5.4 Consensus size: 10
1691657 GGTTTTACTA
1691667 TTATTATTA-
1 TTATTATTAT
1691676 TTATTATTA-
1 TTATTATTAT
1691685 TTATTATTTAT
1 TTATTA-TTAT
1691696 TTATTATTATT
1 TTATTATTA-T
1691707 TTATTATTAT
1 TTATTATTAT
1691717 ATTAT
1 -TTAT
1691722 AATTTAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.36
10 7 0.17
11 20 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTATTAT
Found at i:1691701 original size:14 final size:14
Alignment explanation
Indices: 1691670--1691716 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1691660 TTTACTATTA
1691670 TTATTATTA-TTA-
1 TTATTATTATTTAT
1691682 TTATTATTATTTAT
1 TTATTATTATTTAT
1691696 TTATTATTATTT-T
1 TTATTATTATTTAT
1691709 ATTATTAT
1 -TTATTAT
1691717 ATTATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.28
13 4 0.12
14 19 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:1693604 original size:15 final size:14
Alignment explanation
Indices: 1693584--1693618 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1693574 TTTAATATAT
*
1693584 ATATATATATATTAA
1 ATATATAGATATT-A
1693599 ATATATAGATATTA
1 ATATATAGATATTA
1693613 ATATAT
1 ATATAT
1693619 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
ATATATAGATATTA
Found at i:1697511 original size:15 final size:15
Alignment explanation
Indices: 1697491--1697537 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1697481 GATCAATACC
1697491 TTTTGCATACATTCA
1 TTTTGCATACATTCA
*
1697506 TTTTGCATACAATCA
1 TTTTGCATACATTCA
1697521 TTTTGCATACATTCA
1 TTTTGCATACATTCA
1697536 TT
1 TT
1697538 GCATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:1704907 original size:19 final size:19
Alignment explanation
Indices: 1704873--1704921 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1704863 ATTATGCTTG
*
1704873 AAGAA-AAAAA-AAGAAAGA
1 AAGAAGAAAAAGATGAAA-A
1704891 AA-AAGAAAAAGATGAAAA
1 AAGAAGAAAAAGATGAAAA
*
1704909 AAGAAGAATAAGA
1 AAGAAGAAAAAGA
1704922 AAATAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 10 0.38
19 14 0.54
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (19 bp):
AAGAAGAAAAAGATGAAAA
Found at i:1704923 original size:16 final size:16
Alignment explanation
Indices: 1704873--1704935 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
1704863 ATTATGCTTG
*
1704873 AAGAAAAAAAAAG-A-
1 AAGAAAAAAGAAGAAT
* *
1704887 AAG-AAAAAGAAAAAG
1 AAGAAAAAAGAAGAAT
*
1704902 ATGAAAAAAGAAGAAT
1 AAGAAAAAAGAAGAAT
*
1704918 AAGAAAATAGAA-AAT
1 AAGAAAAAAGAAGAAT
1704933 AAG
1 AAG
1704936 GGTCAAGATG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 7 0.18
14 4 0.10
15 8 0.21
16 20 0.51
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
AAGAAAAAAGAAGAAT
Found at i:1705314 original size:18 final size:18
Alignment explanation
Indices: 1705277--1705314 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1705267 CAAGTTTATC
**
1705277 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAAAATA
1705295 TTTTCGAAATTCAAAATA
1 TTTTCGAAATTCAAAATA
1705313 TT
1 TT
1705315 CTTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTTCGAAATTCAAAATA
Found at i:1705854 original size:61 final size:61
Alignment explanation
Indices: 1705779--1705954 Score: 282
Period size: 61 Copynumber: 2.9 Consensus size: 61
1705769 CTAATGAGGC
* *
1705779 ATCTGATCAGAAACCATAGGAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATTGAAA
1 ATCTGATCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATTGAAA
*
1705840 ATCTGATCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGCTTTATGAACATTGAAA
1 ATCTGATCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATTGAAA
* * *
1705901 ATCT-AGGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGA-TCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1705955 CAATAATTAT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 1 0.01
61 106 0.99
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (61 bp):
ATCTGATCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATTGAAA
Found at i:1706342 original size:22 final size:22
Alignment explanation
Indices: 1706319--1706416 Score: 135
Period size: 22 Copynumber: 4.5 Consensus size: 22
1706309 ACATCTACAT
*
1706319 TCTTCAAAGATGATATATACAT-
1 TCTTCAAAGATGATAGATAC-TC
*
1706341 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATACTC
*
1706363 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATACTC
*
1706385 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATACTC
*
1706407 TTTTCAAAGA
1 TCTTCAAAGA
1706417 AGAAATATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
21 1 0.01
22 71 0.99
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATACTC
Found at i:1706376 original size:44 final size:44
Alignment explanation
Indices: 1706319--1706416 Score: 153
Period size: 44 Copynumber: 2.2 Consensus size: 44
1706309 ACATCTACAT
*
1706319 TCTTCAAAGATGATATATACAT-TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATAC-TCTCTTCAAAGATGATAGATTCTC
*
1706363 TCTTCAAAGATGATAGATTCTCTCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATACTCTCTTCAAAGATGATAGATTCTC
*
1706407 TTTTCAAAGA
1 TCTTCAAAGA
1706417 AGAAATATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (44 bp):
TCTTCAAAGATGATAGATACTCTCTTCAAAGATGATAGATTCTC
Found at i:1707033 original size:123 final size:123
Alignment explanation
Indices: 1706796--1707608 Score: 1076
Period size: 123 Copynumber: 6.7 Consensus size: 123
1706786 CACTCGATGG
* *
1706796 ATCAACATTTCCA-A-AAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCA
1 ATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCA
* * *
1706858 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAGC
64 TAATGAGAAGAATTTGTTCAACCTTTTGCTTAATTATATCACAGAAGGAGATAGATCAGC
* * *
1706918 ATTAACATTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
1706983 ATGAGAAGAATTTGTTCAACCTTTTGCTTAATTCTATCACAGAAGAAGATAAATCAAC
66 ATGAGAAGAATTTGTTCAACCTTTTGCTTAATTATATCACAGAAGGAGATAGATCAGC
* *
1707041 ATCAACATTTCCAGAGAAAGTTCATAATGAAAAGAACTTATCTGAAGATGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
1707106 ATAAGAAGAATTTGTTCAACCTTTTGC-TAGACTCTATCACAGAAGAAGATAGATCAGC
66 ATGAGAAGAATTTGTTCAACCTTTTGCTTA-ATTATATCACAGAAGGAGATAGATCAGC
*
1707164 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAATAAGTTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1707229 ATGAGAAGAATTTGTTCAACCTTTTGCTTGATTATATCACATAAGGAGATAGATCATC
66 ATGAGAAGAATTTGTTCAACCTTTTGCTTAATTATATCACAGAAGGAGATAGATCAGC
* * *
1707287 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAAAACTTAACTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* *
1707352 ATGAGAAGAATTTGTTCAACCTTTTGCTTGATTATATCACAGAAGGAGATAGATTAGC
66 ATGAGAAGAATTTGTTCAACCTTTTGCTTAATTATATCACAGAAGGAGATAGATCAGC
** * *
1707410 ATCAACATTTCCAGA-AGTGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
* * * *
1707473 AATGAGAAGAATTTGTTCAACTTTTTGC-TAGATTATTTCACAGAAGGAGATAAAT-TGTC
65 AATGAGAAGAATTTGTTCAACCTTTTGCTTA-ATTATATCACAGAAGGAGATAGATCAG-C
* * * * ** * *
1707532 ATC-CCA-AT--GGA-AAAGTTCATAATGAGAAGAACTAATCCCAAAGAAGAAGATGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTAT-CTGAAGAGGAAGAAGAAGTTCAT
*
1707592 ACTGAGAAGAATTTGTT
65 AATGAGAAGAATTTGTT
1707609 TAACATTTAC
Statistics
Matches: 621, Mismatches: 60, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
118 25 0.04
119 32 0.05
120 1 0.00
121 4 0.01
122 107 0.17
123 449 0.72
124 3 0.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (123 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTGCTTAATTATATCACAGAAGGAGATAGATCAGC
Found at i:1707245 original size:20 final size:20
Alignment explanation
Indices: 1707183--1707246 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1707173 TCCAGAGAAA
*
1707183 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAATTT
* **
1707203 -ATC-TGAA-GAGGAAGAATAA
1 GTTCAT-AATGA-GAAGAATTT
1707222 GTTCATAATGAGAAGAATTT
1 GTTCATAATGAGAAGAATTT
1707242 GTTCA
1 GTTCA
1707247 ACCTTTTGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
18 3 0.09
19 10 0.31
20 16 0.50
21 3 0.09
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (20 bp):
GTTCATAATGAGAAGAATTT
Found at i:1707749 original size:3 final size:3
Alignment explanation
Indices: 1707743--1707802 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1707733 TCATTTGGTT
1707743 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1707791 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1707803 CAGGCCTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1709897 original size:17 final size:17
Alignment explanation
Indices: 1709875--1709922 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
1709865 ATGGCGATTC
1709875 TCAAAATATTTTTTTAA
1 TCAAAATATTTTTTTAA
* *
1709892 TCAAAATCATTTATTTAT
1 TCAAAAT-ATTTTTTTAA
**
1709910 TCATTATATTTTT
1 TCAAAATATTTTT
1709923 CCCGCCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TCAAAATATTTTTTTAA
Found at i:1712078 original size:148 final size:148
Alignment explanation
Indices: 1711810--1712112 Score: 606
Period size: 148 Copynumber: 2.0 Consensus size: 148
1711800 TATTTCTTTT
1711810 AAGAAAGTATATTATGTTTAATTTAGATATTTTATTTTATTAAATTTTAAACATGAACTATCAGC
1 AAGAAAGTATATTATGTTTAATTTAGATATTTTATTTTATTAAATTTTAAACATGAACTATCAGC
1711875 TAACGTGTTAACATTTTTAAGTGAACTTGATTTTACGTTTTAAATCTGGTGTTTTCATTCAAATT
66 TAACGTGTTAACATTTTTAAGTGAACTTGATTTTACGTTTTAAATCTGGTGTTTTCATTCAAATT
1711940 TTAGTAAATTAATTAAAG
131 TTAGTAAATTAATTAAAG
1711958 AAGAAAGTATATTATGTTTAATTTAGATATTTTATTTTATTAAATTTTAAACATGAACTATCAGC
1 AAGAAAGTATATTATGTTTAATTTAGATATTTTATTTTATTAAATTTTAAACATGAACTATCAGC
1712023 TAACGTGTTAACATTTTTAAGTGAACTTGATTTTACGTTTTAAATCTGGTGTTTTCATTCAAATT
66 TAACGTGTTAACATTTTTAAGTGAACTTGATTTTACGTTTTAAATCTGGTGTTTTCATTCAAATT
1712088 TTAGTAAATTAATTAAAG
131 TTAGTAAATTAATTAAAG
1712106 AAGAAAG
1 AAGAAAG
1712113 GGGTGGATAT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 155 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (148 bp):
AAGAAAGTATATTATGTTTAATTTAGATATTTTATTTTATTAAATTTTAAACATGAACTATCAGC
TAACGTGTTAACATTTTTAAGTGAACTTGATTTTACGTTTTAAATCTGGTGTTTTCATTCAAATT
TTAGTAAATTAATTAAAG
Found at i:1714618 original size:7 final size:7
Alignment explanation
Indices: 1714603--1714655 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
1714593 ACATAGGCAT
1714603 AGGGGAA
1 AGGGGAA
*
1714610 AGGGTAA
1 AGGGGAA
1714617 AGGGGAA
1 AGGGGAA
1714624 AGGGGAA
1 AGGGGAA
*
1714631 AGGGGGA
1 AGGGGAA
*
1714638 AGGGAAA
1 AGGGGAA
*
1714645 AGGGGGA
1 AGGGGAA
1714652 AGGG
1 AGGG
1714656 TGGTTAGGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.58, T:0.02
Consensus pattern (7 bp):
AGGGGAA
Found at i:1724323 original size:14 final size:13
Alignment explanation
Indices: 1724301--1724339 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1724291 AATGAGAAGT
*
1724301 AATCCCTGCAAATA
1 AATCTCTGCAAA-A
1724315 AATCTCTGCATAAA
1 AATCTCTGCA-AAA
1724329 AATCTCTGCAA
1 AATCTCTGCAA
1724340 CATAGACAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (13 bp):
AATCTCTGCAAAA
Found at i:1725630 original size:20 final size:20
Alignment explanation
Indices: 1725593--1725631 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1725583 AAAAAGTAAA
*
1725593 TTAAAATTTTAGACCCACTC
1 TTAAAATTTTAAACCCACTC
* *
1725613 TTAAATTTTTAAATCCACT
1 TTAAAATTTTAAACCCACT
1725632 GATACAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAAAATTTTAAACCCACTC
Found at i:1735203 original size:14 final size:14
Alignment explanation
Indices: 1735180--1735231 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
1735170 AACTCACATA
1735180 AACGAACATAAACG
1 AACGAACATAAACG
* *
1735194 AATGACCATAAACG
1 AACGAACATAAACG
*
1735208 AACGAACATAAATG
1 AACGAACATAAACG
1735222 AACGAACATA
1 AACGAACATA
1735232 TTATCGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.56, C:0.19, G:0.13, T:0.12
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1747693 original size:15 final size:15
Alignment explanation
Indices: 1747669--1747702 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1747659 CCGTAGGACC
*
1747669 ACTACATCCCGAAGG
1 ACTACATCCCGAAAG
*
1747684 ACTACGTCCCGAAAG
1 ACTACATCCCGAAAG
1747699 ACTA
1 ACTA
1747703 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAAG
Found at i:1747834 original size:29 final size:29
Alignment explanation
Indices: 1747774--1747852 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1747764 CATTATATGT
1747774 TCATGTA-CTCATGTCA-TT-TCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1747800 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1747829 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1747853 ATATCACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
26 7 0.14
27 9 0.18
28 2 0.04
29 26 0.53
30 5 0.10
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1748302 original size:64 final size:63
Alignment explanation
Indices: 1748233--1748395 Score: 170
Period size: 64 Copynumber: 2.6 Consensus size: 63
1748223 TAATGAAGGT
* **
1748233 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
1748296 G
63 G
* * * * * *
1748297 ATGCATCGATGTA-TGCCTTATGCATCGATGTACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
1748360 AGTGCATCGATGCACTACCTGTGCATCGATGCACTA
1 A-TGCATCGATGCACTACTTGTGCATCGATGCACTA
1748396 CCTGTGCATC
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.85
65 9 0.11
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:1748385 original size:19 final size:19
Alignment explanation
Indices: 1748361--1748408 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1748351 TTTTAAAAGA
1748361 GTGCATCGATGCACTACCT
1 GTGCATCGATGCACTACCT
1748380 GTGCATCGATGCACTACCT
1 GTGCATCGATGCACTACCT
1748399 GTGCATCGAT
1 GTGCATCGAT
1748409 ACACCTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCACTACCT
Found at i:1754400 original size:15 final size:15
Alignment explanation
Indices: 1754376--1754409 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1754366 CCGTAGGACC
1754376 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
1754391 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1754406 ACTA
1 ACTA
1754410 TTATACCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1754536 original size:29 final size:29
Alignment explanation
Indices: 1754494--1754661 Score: 320
Period size: 29 Copynumber: 5.8 Consensus size: 29
1754484 TTTTATATGT
1754494 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1754522 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1754551 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1754580 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1754609 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1754638 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1754662 ATATCACATA
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
28 7 0.05
29 126 0.91
30 5 0.04
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1755111 original size:64 final size:63
Alignment explanation
Indices: 1755042--1755198 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 63
1755032 TAATGAAGGT
* **
1755042 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
1755105 G
63 G
* * * * *
1755106 ATGCATCGATGTA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
* *
1755169 AGTGCATCGATACACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
1755199 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
63 3 0.04
64 63 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:1760326 original size:20 final size:20
Alignment explanation
Indices: 1760301--1760340 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1760291 GCCATTGATC
1760301 AATAATAGAAACAACACTTG
1 AATAATAGAAACAACACTTG
1760321 AATAATAGAAACAACACTTG
1 AATAATAGAAACAACACTTG
1760341 TGAGAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (20 bp):
AATAATAGAAACAACACTTG
Found at i:1761730 original size:42 final size:41
Alignment explanation
Indices: 1761641--1761760 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 41
1761631 AAATCTATTG
**
1761641 TCGTCACAAATCACCAACTAAGACTAGTG-AAAAACGATTA
1 TCGTCACAAATCACCAACTAAGACTAGTGAAAAAATAATTA
* *
1761681 TCATCACAAATCATCAACTAAGACTAGTGACAAAAATAATTA
1 TCGTCACAAATCACCAACTAAGACTAGTGA-AAAAATAATTA
*
1761723 TCGTCACAAATCACCAGCTAAGACTAGTGATAAAAATA
1 TCGTCACAAATCACCAACTAAGACTAGTGA-AAAAATA
1761761 TTTCTTCGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
40 27 0.39
42 43 0.61
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.22
Consensus pattern (41 bp):
TCGTCACAAATCACCAACTAAGACTAGTGAAAAAATAATTA
Found at i:1768374 original size:24 final size:23
Alignment explanation
Indices: 1768345--1768406 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 23
1768335 TTCTTTTCCT
1768345 TTCGATTTTTTTTCTGGTATTT-GG
1 TTCGATTTTTTTTCT-GT-TTTGGG
1768369 TTCGATATTTTTTTTCTGTTTTGGG
1 TTCG--ATTTTTTTTCTGTTTTGGG
1768394 TT-GATGTTTTTTT
1 TTCGAT-TTTTTTT
1768407 TCTAAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 2 0.06
23 7 0.21
24 8 0.24
25 6 0.18
26 11 0.32
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.66
Consensus pattern (23 bp):
TTCGATTTTTTTTCTGTTTTGGG
Found at i:1768407 original size:24 final size:26
Alignment explanation
Indices: 1768349--1768409 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 26
1768339 TTTCCTTTCG
1768349 ATTTTTTTTCTGGTATTTGGTTCGAT
1 ATTTTTTTTCTGGTATTTGGTTCGAT
1768375 ATTTTTTTTCT-GT-TTTGGGTT-GAT
1 ATTTTTTTTCTGGTATTT-GGTTCGAT
*
1768399 GTTTTTTTTCT
1 ATTTTTTTTCT
1768410 AAAAAACCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 16 0.48
25 6 0.18
26 11 0.33
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.67
Consensus pattern (26 bp):
ATTTTTTTTCTGGTATTTGGTTCGAT
Found at i:1768944 original size:3 final size:3
Alignment explanation
Indices: 1768932--1768964 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1768922 TAGTCAAAAT
1768932 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1768965 TAGAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1769236 original size:40 final size:42
Alignment explanation
Indices: 1769138--1769243 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 42
1769128 GGTGGGGGAC
** *
1769138 GACACTGCTCATACGTGATGAAGGGTTCTGGTCGTCTAAGGGT
1 GACACTGCTCATACGTGATGAAGGAATCTGGTCGTCT-AGGAT
* *
1769181 GACAC-GACTCCTACGTGAT-AAGGAAATCTGGTCG-GT-GGAT
1 GACACTG-CTCATACGTGATGAAGG-AATCTGGTCGTCTAGGAT
1769221 GACACTGCTCATACGTGATGAAG
1 GACACTGCTCATACGTGATGAAG
1769244 AGTTCTTGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
40 19 0.36
41 4 0.08
42 6 0.11
43 24 0.45
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
GACACTGCTCATACGTGATGAAGGAATCTGGTCGTCTAGGAT
Found at i:1769768 original size:65 final size:63
Alignment explanation
Indices: 1769693--1769831 Score: 192
Period size: 65 Copynumber: 2.2 Consensus size: 63
1769683 CAAAGATGGT
1769693 AAATTTTGTTTCCAAAGAAACATAATCAAAGATTTTTCTTAAAAGAAAATGT-C-TTAAAAGAGA
1 AAATTTTGTTTCCAAAGAAACATAATCAAAGATTTTTC--AAAAG-AAAT-TACTTTAAAAGAGA
1769756 CA
62 CA
* * *
1769758 AAATTTTGTTTCCAAAGAAACATATTCAATGATTTTTCAAAAGAAATTACTTTAAGAGAGACA
1 AAATTTTGTTTCCAAAGAAACATAATCAAAGATTTTTCAAAAGAAATTACTTTAAAAGAGACA
*
1769821 AAACTTTGTTT
1 AAATTTTGTTT
1769832 TTCAGAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
61 1 0.01
62 5 0.07
63 26 0.38
65 36 0.53
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (63 bp):
AAATTTTGTTTCCAAAGAAACATAATCAAAGATTTTTCAAAAGAAATTACTTTAAAAGAGACA
Found at i:1770049 original size:32 final size:31
Alignment explanation
Indices: 1770010--1770209 Score: 92
Period size: 29 Copynumber: 6.4 Consensus size: 31
1770000 AAGGGAAGCG
1770010 ACTCAAAGATGGTTT-TATTTCAAGAGAAACAA
1 ACTCAAAGAT--TTTGTATTTCAAGAGAAACAA
* **
1770042 ACTCAAAGATTTTGTATTTCTAGAGAAACTG
1 ACTCAAAGATTTTGTATTTCAAGAGAAACAA
* * *
1770073 CCTCAAGGGAGACAAAATTTGT-TTT-AATAGAAACAA
1 ACTCAA---AG----ATTTTGTATTTCAAGAGAAACAA
* * ** *
1770109 TCTCAAAG-GTGGGTATTTCAAGAGAAACTA
1 ACTCAAAGATTTTGTATTTCAAGAGAAACAA
** * * *
1770139 ACTCAAAGA-TAGGTGTTTCAAAAGAAAC-G
1 ACTCAAAGATTTTGTATTTCAAGAGAAACAA
* * *
1770168 ACTCAAAGATTTT-TGTTTCAAAAGAAACGA
1 ACTCAAAGATTTTGTATTTCAAGAGAAACAA
1770198 A-TCAAAGATTTT
1 ACTCAAAGATTTT
1770210 TTTACGAAAA
Statistics
Matches: 132, Mismatches: 23, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.02
29 38 0.29
30 37 0.28
31 19 0.14
32 10 0.08
33 2 0.02
34 2 0.02
36 12 0.09
37 3 0.02
38 6 0.05
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (31 bp):
ACTCAAAGATTTTGTATTTCAAGAGAAACAA
Found at i:1770135 original size:30 final size:29
Alignment explanation
Indices: 1770101--1770206 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
1770091 TTGTTTTAAT
* * *
1770101 AGAAACAATCTCAAAGGTGGGTATTTCAAG
1 AGAAACAA-CTCAAAGATAGGTATTTCAAA
*
1770131 AGAAACTAACTCAAAGATAGGTGTTTCAAA
1 AGAAAC-AACTCAAAGATAGGTATTTCAAA
* *** *
1770161 AGAAACGACTCAAAGATTTTTGTTTCAAA
1 AGAAACAACTCAAAGATAGGTATTTCAAA
1770190 AGAAACGAA-TCAAAGAT
1 AGAAAC-AACTCAAAGAT
1770207 TTTTTTACGA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
29 33 0.51
30 30 0.46
31 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (29 bp):
AGAAACAACTCAAAGATAGGTATTTCAAA
Found at i:1770184 original size:29 final size:29
Alignment explanation
Indices: 1770124--1770404 Score: 135
Period size: 29 Copynumber: 9.4 Consensus size: 29
1770114 AAGGTGGGTA
* * ***
1770124 TTTCAAGAGAAACTAACTCAAAGATAGGTG
1 TTTCAAAAGAAAC-GACTCAAAGATTTTTG
1770154 TTTCAAAAGAAACGACTCAAAGATTTTTG
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
*
1770183 TTTCAAAAGAAACGAATCAAAGATTTTT-
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
* * * * **
1770211 TTAC-GAA-AAACTGTCTCATGAGAAACAAAACTTTG
1 TTTCAAAAGAAAC-GACTC------AA-AGATTTTTG
* *
1770246 TTTCAAAATAAACAGACTTAAAGA-TTTT-
1 TTTCAAAAGAAAC-GACTCAAAGATTTTTG
* *
1770274 TTTCAAAAGAAACAACTCAAAGATTTTTA
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
* ** *
1770303 TTTCAAACGAAATAACTC--AGACTTTTG
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
*
1770330 TTTCAAGAGAAACAGACTCAAAGATAGGTTTTG
1 TTTCAAAAGAAAC-GACTCAAAGAT---TTTTG
** * * *
1770363 TTTCAAGGGAAACAATCTTAAAGATGTTTG
1 TTTCAAAAGAAACGA-CTCAAAGATTTTTG
*
1770393 TTTTAAAAGAAA
1 TTTCAAAAGAAA
1770405 TTGTCTCAAA
Statistics
Matches: 192, Mismatches: 39, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
26 4 0.02
27 30 0.16
28 23 0.12
29 58 0.30
30 30 0.16
31 2 0.01
32 1 0.01
33 27 0.14
34 5 0.03
35 3 0.02
36 2 0.01
37 7 0.04
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTCAAAAGAAACGACTCAAAGATTTTTG
Found at i:1770286 original size:28 final size:29
Alignment explanation
Indices: 1770246--1770353 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 29
1770236 CAAAACTTTG
* *
1770246 TTTCAAAATAAACAGACTTAAAGA-TTTT-
1 TTTCAAAAGAAACA-ACTCAAAGACTTTTA
*
1770274 TTTCAAAAGAAACAACTCAAAGATTTTTA
1 TTTCAAAAGAAACAACTCAAAGACTTTTA
* * *
1770303 TTTCAAACGAAATAACTC--AGACTTTTG
1 TTTCAAAAGAAACAACTCAAAGACTTTTA
*
1770330 TTTCAAGAGAAACAGACTCAAAGA
1 TTTCAAAAGAAACA-ACTCAAAGA
1770354 TAGGTTTTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
27 26 0.39
28 21 0.32
29 16 0.24
30 3 0.05
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (29 bp):
TTTCAAAAGAAACAACTCAAAGACTTTTA
Found at i:1770479 original size:66 final size:65
Alignment explanation
Indices: 1770382--1770590 Score: 269
Period size: 64 Copynumber: 3.2 Consensus size: 65
1770372 AAACAATCTT
* * * * *
1770382 AAAGATGTTTGTTTTAAAAGAAATTGTCTCAAAAGAGACAAAACTTTGTTTTCATAA-AAATAGA
1 AAAGAT-TTT-TTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCA-AAGAAACATA
1770446 CTC
63 CTC
* * *
1770449 AAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGACAAAATTTTCTTTCCAAAGAAACATACT
1 AAAGATTTTT-TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACT
1770514 C
65 C
* * *
1770515 AAAGA-TTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTC
1 AAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTC
1770579 AAAGATTTTTTT
1 AAAGATTTTTTT
1770591 TTTGTGTTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
64 55 0.44
65 11 0.09
66 52 0.42
67 6 0.05
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (65 bp):
AAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTC
Found at i:1770525 original size:27 final size:27
Alignment explanation
Indices: 1770493--1770544 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1770483 AGACAAAATT
*
1770493 TTCTTTCCAAAGAAACATACTCAAAGA
1 TTCTTTCAAAAGAAACATACTCAAAGA
* *
1770520 TTCTTTCAAAAGAAACTTTCTCAAA
1 TTCTTTCAAAAGAAACATACTCAAA
1770545 AGAGACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (27 bp):
TTCTTTCAAAAGAAACATACTCAAAGA
Found at i:1770656 original size:100 final size:101
Alignment explanation
Indices: 1770504--1770684 Score: 260
Period size: 100 Copynumber: 1.8 Consensus size: 101
1770494 TCTTTCCAAA
*
1770504 GAAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATC-AAA
1 GAAACAGACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTT-TCAAAA
*
1770568 GAAACATACTCAAAGATTTTTTTTTTGTGTTTTAAGT
65 GAAACAGACTCAAAGATTTTTTTTTTGTGTTTTAAGT
* * * *
1770605 GAAACAGACTCAAAGATT-TTTCAAGA-AAATTTGTCTCAAGAGAGACGAAATTTTGTTTCAAAA
1 GAAACAGACTCAAAGATTCTTTCAAAAGAAACTT-TCTCAAAAGAGACAAAATTTTGTTTCAAAA
*
1770668 GAAATAGACTCAAAGAT
65 GAAACAGACTCAAAGAT
1770685 CCTTTGTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
99 7 0.10
100 47 0.66
101 17 0.24
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (101 bp):
GAAACAGACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTTCAAAAG
AAACAGACTCAAAGATTTTTTTTTTGTGTTTTAAGT
Found at i:1770710 original size:30 final size:31
Alignment explanation
Indices: 1770656--1770714 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1770646 GAGACGAAAT
1770656 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
1770687 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
1770715 GACGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:1770871 original size:36 final size:35
Alignment explanation
Indices: 1770752--1770860 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 35
1770742 ATAATTTGTA
* *
1770752 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAAAG
1 AAATTGTCTCAAGCGAGACAA-ATTTGTTTTTAGAG
* *
1770788 AAATTGTCTCAAACGAGACAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAATTTGTTTTTAGAG
1770823 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAAA-TTTGTTTTTAGAG
1770858 AAA
1 AAA
1770861 ACGATCTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
35 39 0.59
36 27 0.41
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAAATTTGTTTTTAGAG
Found at i:1771122 original size:36 final size:36
Alignment explanation
Indices: 1771026--1771122 Score: 117
Period size: 36 Copynumber: 2.7 Consensus size: 36
1771016 TATATCAAAG
* *
1771026 GAAAAA-TGTCTCAAGTGAGACGAAATTTGTTTTGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
* *
1771061 -AAGAAATTGTCTCAAGCGACACAAAATTTGTTTTTA
1 GAA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
* *
1771097 GAAAAATTATCTCAAGCGAGGCAAAA
1 GAAAAATTGTCTCAAGCGAGACAAAA
1771123 ATTTATTTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 2 0.04
35 3 0.06
36 45 0.87
37 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
Found at i:1771137 original size:37 final size:36
Alignment explanation
Indices: 1771064--1771139 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
1771054 GTTTTGAAAG
* * **
1771064 AAATTGTCTCAAGCGACACAAAATTTGTTTTTAGAA
1 AAATTATCTCAAGCGACACAAAATTTATTTCCAGAA
1771100 AAATTATCTCAAGCGAGGCA-AAAATTTATTTCCAGAA
1 AAATTATCTCAAGCGA--CACAAAATTTATTTCCAGAA
1771137 AAA
1 AAA
1771140 CAACTCAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 15 0.44
37 17 0.50
38 2 0.06
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (36 bp):
AAATTATCTCAAGCGACACAAAATTTATTTCCAGAA
Found at i:1771475 original size:26 final size:26
Alignment explanation
Indices: 1771419--1771477 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
1771409 TATTATGTAT
* * * *
1771419 CATGTATGTGTATGCATGTATGTATA
1 CATGTATATATATGCATGCATGCATA
* *
1771445 TATGTATATATATGCATGCATGCATG
1 CATGTATATATATGCATGCATGCATA
1771471 CATGTAT
1 CATGTAT
1771478 GTATGCACGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (26 bp):
CATGTATATATATGCATGCATGCATA
Found at i:1771489 original size:4 final size:4
Alignment explanation
Indices: 1771482--1771552 Score: 61
Period size: 4 Copynumber: 17.8 Consensus size: 4
1771472 ATGTATGTAT
* * * ** * *
1771482 GCAC GCAC GCAC GCAC GCAC ACAC GCAC GCAT GCAT ATAT GCAA GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
* *
1771530 GCAC GAAC GCAC GCAT GCAC GCA
1 GCAC GCAC GCAC GCAC GCAC GCA
1771553 TGTATGTATG
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.31, C:0.39, G:0.23, T:0.07
Consensus pattern (4 bp):
GCAC
Found at i:1771523 original size:40 final size:40
Alignment explanation
Indices: 1771470--1771554 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
1771460 ATGCATGCAT
* * * *
1771470 GCATGTATGTATGCACGCACGCACGCACGCACACACGCAC
1 GCATGCATATATGCAAGCACGCACGAACGCACACACGCAC
* *
1771510 GCATGCATATATGCAAGCACGCACGAACGCACGCATGCAC
1 GCATGCATATATGCAAGCACGCACGAACGCACACACGCAC
1771550 GCATG
1 GCATG
1771555 TATGTATGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.34, G:0.24, T:0.13
Consensus pattern (40 bp):
GCATGCATATATGCAAGCACGCACGAACGCACACACGCAC
Found at i:1771553 original size:8 final size:8
Alignment explanation
Indices: 1771456--1771554 Score: 54
Period size: 8 Copynumber: 12.4 Consensus size: 8
1771446 ATGTATATAT
*
1771456 ATGCATGC
1 ATGCACGC
*
1771464 ATGCATGC
1 ATGCACGC
* * *
1771472 ATGTATGT
1 ATGCACGC
1771480 ATGCACGC
1 ATGCACGC
*
1771488 ACGCACGC
1 ATGCACGC
* *
1771496 ACGCACAC
1 ATGCACGC
*
1771504 ACGCACGC
1 ATGCACGC
***
1771512 ATGCATAT
1 ATGCACGC
*
1771520 ATGCAAGC
1 ATGCACGC
* *
1771528 ACGCACGA
1 ATGCACGC
*
1771536 ACGCACGC
1 ATGCACGC
1771544 ATGCACGC
1 ATGCACGC
1771552 ATG
1 ATG
1771555 TATGTATGTA
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 71 1.00
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.15
Consensus pattern (8 bp):
ATGCACGC
Found at i:1771563 original size:8 final size:8
Alignment explanation
Indices: 1771550--1771699 Score: 246
Period size: 8 Copynumber: 18.8 Consensus size: 8
1771540 ACGCATGCAC
1771550 GCATGTAT
1 GCATGTAT
*
1771558 GTATGTAT
1 GCATGTAT
*
1771566 GTATGTAT
1 GCATGTAT
*
1771574 GTATGTAT
1 GCATGTAT
1771582 GCATGTAT
1 GCATGTAT
1771590 GCATGTAT
1 GCATGTAT
1771598 GCATGTAT
1 GCATGTAT
1771606 GCATGTAT
1 GCATGTAT
1771614 GCATGTAT
1 GCATGTAT
1771622 GCATGTAT
1 GCATGTAT
1771630 GCATGTAT
1 GCATGTAT
1771638 GCATGTAT
1 GCATGTAT
*
1771646 GTATGTAT
1 GCATGTAT
1771654 GCATGTAT
1 GCATGTAT
1771662 GCATGTAT
1 GCATGTAT
1771670 GCATGTAT
1 GCATGTAT
1771678 GCATGTAT
1 GCATGTAT
*
1771686 GTATGTAT
1 GCATGTAT
*
1771694 GTATGT
1 GCATGT
1771700 GTGTGTTGAT
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 137 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (8 bp):
GCATGTAT
Found at i:1772939 original size:21 final size:20
Alignment explanation
Indices: 1772914--1772970 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1772904 TGTTCTGATT
1772914 TCTTTGATTTTTCTTTCTTT-
1 TCTTTG-TTTTTCTTTCTTTC
*
1772934 TACTTTGCTTTTT-TCTCTTTGC
1 T-CTTTG-TTTTTCTTTCTTT-C
1772956 TCTTTGTTTTTCTTT
1 TCTTTGTTTTTCTTT
1772971 GCTTCTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.40
21 17 0.57
22 1 0.03
ACGTcount: A:0.04, C:0.18, G:0.07, T:0.72
Consensus pattern (20 bp):
TCTTTGTTTTTCTTTCTTTC
Found at i:1772971 original size:17 final size:19
Alignment explanation
Indices: 1772944--1772978 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1772934 TACTTTGCTT
1772944 TTTTCTCTTTGC-TCTTTG
1 TTTTCTCTTTGCTTCTTTG
1772962 TTTT-TCTTTGCTTCTTT
1 TTTTCTCTTTGCTTCTTT
1772979 TCTCTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.20, G:0.09, T:0.71
Consensus pattern (19 bp):
TTTTCTCTTTGCTTCTTTG
Found at i:1772971 original size:31 final size:32
Alignment explanation
Indices: 1772925--1772986 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
1772915 CTTTGATTTT
1772925 TCTTTCTTTTACTTTGCTT-TTTTCTCTTTGC
1 TCTTTCTTTTACTTTGCTTCTTTTCTCTTTGC
* *
1772956 TCTTTGTTTTTCTTTGCTTCTTTTCTCTTTG
1 TCTTTCTTTTACTTTGCTTCTTTTCTCTTTG
1772987 TTTTGATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.02, C:0.21, G:0.08, T:0.69
Consensus pattern (32 bp):
TCTTTCTTTTACTTTGCTTCTTTTCTCTTTGC
Found at i:1772996 original size:25 final size:25
Alignment explanation
Indices: 1772949--1772996 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1772939 TGCTTTTTTC
**
1772949 TCTTTGCTCTTTGTTTTTCTTTGCT
1 TCTTTGCTCTTTGTTTTGATTTGCT
*
1772974 TCTTTTCTCTTTGTTTTGATTTG
1 TCTTTGCTCTTTGTTTTGATTTG
1772997 ATCTTCGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.12, T:0.69
Consensus pattern (25 bp):
TCTTTGCTCTTTGTTTTGATTTGCT
Found at i:1774310 original size:14 final size:13
Alignment explanation
Indices: 1774265--1774307 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1774255 CTTAAAAATG
*
1774265 AAATGTAGATGCA
1 AAATGCAGATGCA
1774278 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
1774292 AAATGCAGATGCA
1 AAATGCAGATGCA
1774305 AAA
1 AAA
1774308 ATGTTGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 6 0.23
15 6 0.23
ACGTcount: A:0.51, C:0.12, G:0.21, T:0.16
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:1775977 original size:39 final size:40
Alignment explanation
Indices: 1775848--1776032 Score: 182
Period size: 41 Copynumber: 4.6 Consensus size: 40
1775838 TACATATAAC
1775848 GGCGTTTTTGA-ACAAACGCCGC-AAAATACTA-TACTT-TAGT
1 GGCGTTTTT-ATACAAACGCCGCTAAAA-A-TAGTA-TTGTAGT
* * * * *
1775888 GGCGTTTGTATACAAATGCCGCTAAATAATTGTACTATAGT
1 GGCGTTTTTATACAAACGCCGCTAAA-AATAGTATTGTAGT
* *
1775929 GGCGGTTTTATACAAACGCC-ATAAAAATAGTATTGTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAAATAGTATTGTAGT
* *
1775968 GGCGTTTTTATACAAATGCCGCTATAAACTAGTATTGTAGT
1 GGCGTTTTTATACAAACGCCGCTA-AAAATAGTATTGTAGT
* *
1776009 GGTGTTTTTATAAAAACGCCGCTA
1 GGCGTTTTTATACAAACGCCGCTA
1776033 TAGACTCATA
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
39 30 0.25
40 26 0.22
41 63 0.52
42 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (40 bp):
GGCGTTTTTATACAAACGCCGCTAAAAATAGTATTGTAGT
Found at i:1776050 original size:41 final size:41
Alignment explanation
Indices: 1775848--1776128 Score: 179
Period size: 41 Copynumber: 6.9 Consensus size: 41
1775838 TACATATAAC
*
1775848 GGCGTTTTTGA-ACAAACGCCGC-AAAATACT-ATACTTTAGT
1 GGCGTTTTT-ATACAAACGCCGCTATAA-ACTCATACTTTAGT
* * * ** *
1775888 GGCGTTTGTATACAAATGCCGCTA-AATAATTGTACTATAGT
1 GGCGTTTTTATACAAACGCCGCTATAA-ACTCATACTTTAGT
* * *
1775929 GGCGGTTTTATACAAACGCC-ATA-AAAAT-AGTA-TTGTAGT
1 GGCGTTTTTATACAAACGCCGCTATAAACTCA-TACTT-TAGT
*
1775968 GGCGTTTTTATACAAATGCCGCTATAAACT-AGTA-TTGTAGT
1 GGCGTTTTTATACAAACGCCGCTATAAACTCA-TACTT-TAGT
* * *
1776009 GGTGTTTTTATAAAAACGCCGCTATAGACTCATACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAAACTCATACTTTAGT
* *** * * *
1776050 GGCGTTTTTACACAAATTTCGTTATAGACACATACTTTTA-T
1 GGCGTTTTTATACAAACGCCGCTATAAACTCATAC-TTTAGT
* ** *
1776091 GGTGTTTCAATACCAAACGCCGCTTTAAACTCATACTT
1 GGCGTTTTTATA-CAAACGCCGCTATAAACTCATACTT
1776129 AACAAACGCT
Statistics
Matches: 192, Mismatches: 38, Indels: 21
0.76 0.15 0.08
Matches are distributed among these distances:
38 1 0.01
39 28 0.15
40 29 0.15
41 111 0.58
42 23 0.12
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTATAAACTCATACTTTAGT
Found at i:1777963 original size:81 final size:84
Alignment explanation
Indices: 1777854--1778011 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 84
1777844 CTAGAGTTGA
* *
1777854 ATATGCTAAGATTTAAAAGGAAATTTGTAACCAGAGCCTGT-GGTTTTGTGCTGGAATCTTGCAG
1 ATATGCTAAGATTCAAAAGGAAATTTGTAACCAGAGCCTATGGGTTTTGTGCTGGAATCTTGCAG
* *
1777918 GAGTTTACATTTGATTTGG
66 AAGTTAACATTTGATTTGG
** ** * *
1777937 ATATGCT-A-ATTCAAAAGGAAATTTGTAGTCATTGTCTATGGGTTTTGTGCTGGAGTCTTGCAG
1 ATATGCTAAGATTCAAAAGGAAATTTGTAACCAGAGCCTATGGGTTTTGTGCTGGAATCTTGCAG
1778000 AAGTTAACATTT
66 AAGTTAACATTT
1778012 CTAAGTATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 24 0.38
82 33 0.52
83 7 0.11
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (84 bp):
ATATGCTAAGATTCAAAAGGAAATTTGTAACCAGAGCCTATGGGTTTTGTGCTGGAATCTTGCAG
AAGTTAACATTTGATTTGG
Found at i:1780041 original size:42 final size:43
Alignment explanation
Indices: 1779953--1780078 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 43
1779943 GGTATAGTTA
* * **
1779953 TGACCTTTTGCGGCGTTTATGTTC-AAAAACACCGCTATAGGTC
1 TGACCTTTTGCGGCATTT-TGTTCTAAAAACGCCGCTATAGACC
* *
1779996 TGACCTTTTGCAGC-TTTTGTTCTAAAAATGCCGCTATAGACC
1 TGACCTTTTGCGGCATTTTGTTCTAAAAACGCCGCTATAGACC
* *
1780038 TGACATTTTGCGGCATTTTTTTCTAAAAACGCCGCTATAGA
1 TGACCTTTTGCGGCATTTTGTTCTAAAAACGCCGCTATAGA
1780079 TCATGGCTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
41 5 0.07
42 30 0.42
43 37 0.51
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (43 bp):
TGACCTTTTGCGGCATTTTGTTCTAAAAACGCCGCTATAGACC
Found at i:1780101 original size:43 final size:43
Alignment explanation
Indices: 1780010--1780119 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 43
1780000 CTTTTGCAGC
* * * *
1780010 TTTTGTTCTAAAAATGCCGCTATAGACCTGACATTTTGCGGCA
1 TTTTTTTCTAAAAACGCCGCTATAGACATGACATTTTACGGCA
* * *
1780053 TTTTTTTCTAAAAACGCCGCTATAGATCATGGCTTTTTACGGTA
1 TTTTTTTCTAAAAACGCCGCTATAGA-CATGACATTTTACGGCA
*
1780097 TTTTTTGTTCT-CAAACGCCGCTA
1 -TTTTT-TTCTAAAAACGCCGCTA
1780120 ACTTTAGCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 24 0.43
44 12 0.21
45 16 0.29
46 4 0.07
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (43 bp):
TTTTTTTCTAAAAACGCCGCTATAGACATGACATTTTACGGCA
Found at i:1781415 original size:30 final size:30
Alignment explanation
Indices: 1781373--1781508 Score: 93
Period size: 30 Copynumber: 4.6 Consensus size: 30
1781363 AAATACAAAT
*
1781373 ATTTACAA-GACTAAAATAA-AATTAACATAA
1 ATTTA-AAGGACTAAAATAATAA-AAACATAA
1781403 ATTTAAAGGACTAAAATAATAAAAACATAA
1 ATTTAAAGGACTAAAATAATAAAAACATAA
* * * *
1781433 A-CTAAAGGGACTAAAATGGA-AAAAATAAAA
1 ATTTAAA-GGACTAAAAT-AATAAAAACATAA
* * * *
1781463 ACTT-ATGGACTAAAATAGTAAAAACAAAA
1 ATTTAAAGGACTAAAATAATAAAAACATAA
** *
1781492 ACCTAGAGGACTAAAAT
1 ATTTAAAGGACTAAAAT
1781509 GTCAAGAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
29 28 0.33
30 54 0.63
31 4 0.05
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAATAAAAACATAA
Found at i:1781455 original size:29 final size:30
Alignment explanation
Indices: 1781396--1781508 Score: 106
Period size: 30 Copynumber: 3.8 Consensus size: 30
1781386 AAATAAAATT
** *
1781396 AACATAAATTTAAAGGACTAAAATAATAAA
1 AACATAAACCTAAAGGACTAAAATAGTAAA
*
1781426 AACATAAA-CTAAAGGGACTAAAAT-GGAAA
1 AACATAAACCTAAA-GGACTAAAATAGTAAA
* * *
1781455 AA-ATAAAAACTTATGGACTAAAATAGTAAA
1 AACAT-AAACCTAAAGGACTAAAATAGTAAA
* *
1781485 AACAAAAACCTAGAGGACTAAAAT
1 AACATAAACCTAAAGGACTAAAAT
1781509 GTCAAGAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
28 2 0.03
29 22 0.33
30 42 0.63
31 1 0.01
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (30 bp):
AACATAAACCTAAAGGACTAAAATAGTAAA
Found at i:1784422 original size:15 final size:14
Alignment explanation
Indices: 1784393--1784425 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1784383 TATTTGACAA
1784393 TTTA-AATCTTAAT
1 TTTATAATCTTAAT
1784406 TTTATAATCTATAAT
1 TTTATAATCT-TAAT
1784421 TTTAT
1 TTTAT
1784426 CTCATCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 5 0.28
15 9 0.50
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATAATCTTAAT
Found at i:1784543 original size:15 final size:16
Alignment explanation
Indices: 1784523--1784553 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1784513 CTCGTTCGTC
1784523 ATACATTTTT-TATAA
1 ATACATTTTTATATAA
1784538 ATACATTTTTATATAA
1 ATACATTTTTATATAA
1784554 TATAGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
ATACATTTTTATATAA
Found at i:1793783 original size:25 final size:24
Alignment explanation
Indices: 1793732--1793780 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
1793722 TACTTTTTTT
*
1793732 AATTTAAATATAATTTAATTATTTA
1 AATTTAAATATAATTTAATGA-TTA
1793757 AATTTAAATAATAATTTTAATGAT
1 AATTTAAAT-ATAA-TTTAATGAT
1793781 AAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 5 0.24
27 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTAAATATAATTTAATGATTA
Found at i:1796145 original size:22 final size:21
Alignment explanation
Indices: 1796115--1796156 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1796105 ATAGAATTAA
*
1796115 AAAATATGTCATAAAATATAAG
1 AAAACATGTCATAAAA-ATAAG
1796137 AAAACATGTCATAAAAATAA
1 AAAACATGTCATAAAAATAA
1796157 AATTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAACATGTCATAAAAATAAG
Found at i:1796791 original size:10 final size:10
Alignment explanation
Indices: 1796776--1796814 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1796766 TTTTTTTAAT
1796776 GATTAAATTA
1 GATTAAATTA
1796786 GATTAAATTA
1 GATTAAATTA
* *
1796796 GATTGAAGTA
1 GATTAAATTA
*
1796806 TATTAAATT
1 GATTAAATT
1796815 GTAAGATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (10 bp):
GATTAAATTA
Found at i:1797099 original size:126 final size:127
Alignment explanation
Indices: 1796786--1797142 Score: 626
Period size: 126 Copynumber: 2.8 Consensus size: 127
1796776 GATTAAATTA
* * *
1796786 GATTAAATTAGATTGAAGTATATTAAATTGTAAGATAAATAAAAATATATTGAAATTAGATAAAT
1 GATTAAATTAGATTGAAGTAGATTAAATTGCAAGATAGATAAAAATATATTGAAATTAGATAAAT
*
1796851 AAACATACTAATTTTTTGAAACATAAAAATACAACAAACATAAAAACATATAATTTTTTTAAT
66 AAACATACTAATTTTTTGAAACATAAAAATACAACAAACATAAAAACA-AGAATTTTTTTAAT
*
1796914 GATTAAATTAGATTGAAGTAGATTAAATTGCAAGATAGATAAAAATATATTAAAATTAGATAAAT
1 GATTAAATTAGATTGAAGTAGATTAAATTGCAAGATAGATAAAAATATATTGAAATTAGATAAAT
1796979 AAACATACTAATTTTTTGAAACATAAAAATACAACAAACATAAAAAC-AGAATTTTTTTAAT
66 AAACATACTAATTTTTTGAAACATAAAAATACAACAAACATAAAAACAAGAATTTTTTTAAT
* *
1797040 GATTAAATTAGATTAAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAAT
1 GATTAAATTAGATTGAAGTAGATTAAATTGCAAGATAGATAAAAATATATTGAAATTAGATAAAT
*
1797105 AAACATACTAATTTTTTGAAACATTAAAATACAACAAA
66 AAACATACTAATTTTTTGAAACATAAAAATACAACAAA
1797143 TGTCGAATAT
Statistics
Matches: 220, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
126 112 0.51
128 108 0.49
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.32
Consensus pattern (127 bp):
GATTAAATTAGATTGAAGTAGATTAAATTGCAAGATAGATAAAAATATATTGAAATTAGATAAAT
AAACATACTAATTTTTTGAAACATAAAAATACAACAAACATAAAAACAAGAATTTTTTTAAT
Found at i:1797470 original size:13 final size:15
Alignment explanation
Indices: 1797452--1797484 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1797442 TTTATGAATG
1797452 TTTTAT-TT-ATATT
1 TTTTATCTTGATATT
1797465 TTTTATCTTGATATT
1 TTTTATCTTGATATT
1797480 TTTTA
1 TTTTA
1797485 GAAATGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 2 0.11
15 10 0.56
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTATCTTGATATT
Found at i:1797631 original size:22 final size:22
Alignment explanation
Indices: 1797605--1797654 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1797595 TATTTCATCT
* *
1797605 CTAGAGTATAGATAGAGATGCA
1 CTAGAGTAGAGATAGAAATGCA
1797627 CTAGAGTAGAGATAGAAATGCA
1 CTAGAGTAGAGATAGAAATGCA
1797649 CTAGAG
1 CTAGAG
1797655 ATGGCCTAAG
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:0.42, C:0.10, G:0.28, T:0.20
Consensus pattern (22 bp):
CTAGAGTAGAGATAGAAATGCA
Found at i:1799773 original size:15 final size:15
Alignment explanation
Indices: 1799753--1799782 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1799743 GTGTAATATT
*
1799753 AATTTAATTTATAAA
1 AATTTAAATTATAAA
1799768 AATTTAAATTATAAA
1 AATTTAAATTATAAA
1799783 TTAGTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAAATTATAAA
Found at i:1799804 original size:14 final size:15
Alignment explanation
Indices: 1799785--1799814 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1799775 ATTATAAATT
1799785 AGTTAAAT-ATTTAA
1 AGTTAAATAATTTAA
1799799 AGTTAAATAATTTAA
1 AGTTAAATAATTTAA
1799814 A
1 A
1799815 ATAAAGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
AGTTAAATAATTTAA
Found at i:1799816 original size:24 final size:25
Alignment explanation
Indices: 1799757--1799817 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
1799747 AATATTAATT
* *
1799757 TAATTTATAAAAATTTAAATTATAAA
1 TAATTTA-AAATATTTAAAGTATAAA
* *
1799783 TTAGTT-AAATATTTAAAGT-TAAA
1 TAATTTAAAATATTTAAAGTATAAA
1799806 TAATTTAAAATA
1 TAATTTAAAATA
1799818 AAGAGTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
26 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
TAATTTAAAATATTTAAAGTATAAA
Found at i:1800401 original size:8 final size:8
Alignment explanation
Indices: 1800388--1800413 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1800378 ACAGTATTCC
1800388 TTTAAAAT
1 TTTAAAAT
1800396 TTTAAAAT
1 TTTAAAAT
1800404 TTTAAAAT
1 TTTAAAAT
1800412 TT
1 TT
1800414 CATTTCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1800991 original size:22 final size:21
Alignment explanation
Indices: 1800962--1801002 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1800952 TATTTTAATC
1800962 TTTATTTTAACTAATTTATTT
1 TTTATTTTAACTAATTTATTT
*
1800983 TTTATTTTTAATTAATTTAT
1 TTTA-TTTTAACTAATTTAT
1801003 AATTATACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTTAACTAATTTATTT
Found at i:1802023 original size:31 final size:31
Alignment explanation
Indices: 1801987--1802046 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1801977 AACTTAAAAG
* * *
1801987 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1802018 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1802047 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1802558 original size:20 final size:20
Alignment explanation
Indices: 1802510--1802571 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1802500 AACTTAAATC
*
1802510 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1802530 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1802548 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1802567 AAAAT
1 AAAAT
1802572 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:1802666 original size:38 final size:35
Alignment explanation
Indices: 1802587--1802669 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 35
1802577 ATCTATAATA
* **
1802587 TAATATTAAAAATTAATATTTAATTTATTTGAAAAT
1 TAATATT-AAAATTAATATCTAATTTATTAAAAAAT
1802623 TAATATTAAAATTAATATCTAATATAATATTAAAAAAT
1 TAATATTAAAATTAATATCTAAT-T--TATTAAAAAAT
1802661 TAATATTAA
1 TAATATTAA
1802670 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
35 15 0.37
36 8 0.20
38 18 0.44
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
TAATATTAAAATTAATATCTAATTTATTAAAAAAT
Found at i:1802706 original size:59 final size:60
Alignment explanation
Indices: 1802566--1802711 Score: 199
Period size: 59 Copynumber: 2.4 Consensus size: 60
1802556 TTATATGATA
*
1802566 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTGAAAATTAATAT
1 TAAAATTAAA-ATC-A-AATATAATATTAAAAATTAATATTTAATTTATTTAAAAATTAATAT
* *
1802629 TAAAATTAATATCTAATATAATATTAAAAAATTAATA-TTAA-TTATTTAAAAAATT-ATAT
1 TAAAATTAAAATCAAATATAATATT-AAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1802688 TAAAATTAAAATCAAATATAATAT
1 TAAAATTAAAATCAAATATAATAT
1802712 AGATTTAAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
59 32 0.42
60 21 0.28
61 11 0.14
62 3 0.04
63 9 0.12
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (60 bp):
TAAAATTAAAATCAAATATAATATTAAAAATTAATATTTAATTTATTTAAAAATTAATAT
Done.