Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 19 of 290
Found at i:6129828 original size:47 final size:47
Alignment explanation
Indices: 6129717--6129892 Score: 316
Period size: 47 Copynumber: 3.7 Consensus size: 47
6129707 GCCCTTCGAG
*
6129717 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
6129767 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6129814 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6129861 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
6129893 ATAGTATCAT
Statistics
Matches: 125, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
47 87 0.70
49 34 0.27
50 4 0.03
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:6132943 original size:140 final size:138
Alignment explanation
Indices: 6132573--6133130 Score: 768
Period size: 141 Copynumber: 4.0 Consensus size: 138
6132563 ACATAGATAA
* * * * *
6132573 AATTAATAAATGAAATTGATTCATATAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
6132638 TGAATAATTATATTAATAAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
*
6132703 AAAAATAT
131 AAGAATAT
*
6132711 AATT-A-ATATGAATTTGATTCATACAAAATATTAATTGTATA-CTTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* ** *
6132773 TAAACAATTATATTAATTAATTTTGGTCAAAATATAAAATCCATGGAAATTAGTATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
6132838 AAGAATAT
131 AAGAATAT
* * *
6132846 AATTAGTATATGAATTTAATTCATACAAAATATTATTTGTTTATATATTTTACCGAATTTATTAA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTG--TATATATTTTACCGAATTTATTAA
* * *
6132911 TATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATAGAAATTAATATACTTTTT
64 TATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTC-TTTT
6132976 GGAAAGAATAT
128 GGAAAGAATAT
* **
6132987 AATTAACATATATGAATTTTATTCATA-AAAATTATTAATTGTATATATTTTACTAAATTTATTA
1 AATT-A-ATATATGAATTTGATTCATACAAAA-TATTAATTGTATATATTTTACCGAATTTATTA
*
6133051 ATATAAA-AAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACAT-GATAATTAATATTCTT
63 ATATAAACAA-TTATATTAATTAATTTTGATCAAAATATAAAAGACATGGA-AATTAATATTCTT
*
6133114 TTAGAAAGAATAT
126 TTGGAAAGAATAT
6133127 AATT
1 AATT
6133131 CCTTTTTCTA
Statistics
Matches: 374, Mismatches: 35, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
135 87 0.23
136 32 0.09
137 31 0.08
138 4 0.01
139 4 0.01
140 92 0.25
141 93 0.25
142 5 0.01
143 26 0.07
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:6133233 original size:75 final size:75
Alignment explanation
Indices: 6133106--6133252 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 75
6133096 ATGATAATTA
* * * * *
6133106 ATATTCTTTTAGAAAGAATATAATTCCTTTTTCTAACTTTTCATTTGTCTTCTCTATTAATAAGG
1 ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
6133171 GAATAATCTT
66 GAATAATCTT
* * *
6133181 ATATTATTTTGGAAAGAATATAATTTATTTTTCTAACTTTCCATTTGCCTTCTCTATTAGTAAGA
1 ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
6133246 GAATAAT
66 GAATAAT
6133253 AATGGTTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (75 bp):
ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
GAATAATCTT
Found at i:6138128 original size:30 final size:30
Alignment explanation
Indices: 6138094--6138292 Score: 163
Period size: 30 Copynumber: 6.7 Consensus size: 30
6138084 AGCCAAAGCT
*
6138094 ATCCCTTTCCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * *
6138124 ATCCCTTTCCATT-GTTGATGGTCCTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * * *
6138153 ATCCCTTTTCATAATTTGATAGCCG-AAGCTC
1 ATCCCTTTTCATTATTTGATGGTCGTCA-C-C
** * * *** *
6138184 -TCCCTTTTCACAATTCGATAG-CCAAAGTC
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CC
* *
6138213 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
6138243 ATCCCTTTTCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* *
6138273 ATCCTTTTTCATAATTTGAT
1 ATCCCTTTTCATTATTTGAT
6138293 AGCCTAGGCT
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
29 28 0.20
30 107 0.78
31 3 0.02
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGTCGTCACC
Found at i:6138151 original size:29 final size:30
Alignment explanation
Indices: 6138094--6138160 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
6138084 AGCCAAAGCT
* *
6138094 ATCCCTTTCCATTATTTGATGGTCGTCACC
1 ATCCCTTTCCATTAGTTGATGGTCCTCACC
6138124 ATCCCTTTCCATT-GTTGATGGTCCTCACC
1 ATCCCTTTCCATTAGTTGATGGTCCTCACC
6138153 ATCCCTTT
1 ATCCCTTT
6138161 TCATAATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.15, C:0.33, G:0.12, T:0.40
Consensus pattern (30 bp):
ATCCCTTTCCATTAGTTGATGGTCCTCACC
Found at i:6138279 original size:119 final size:120
Alignment explanation
Indices: 6138079--6138296 Score: 343
Period size: 119 Copynumber: 1.8 Consensus size: 120
6138069 TTTTCATAGC
*
6138079 TCGATAGCCAAAGCTATCCCTTTCCATTATTTGATGGTCGTCACCATCCCTTTCCATTGTTGATG
1 TCGATAGCCAAAGCTATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTCCATTGTTGATG
6138144 GTCCTCACCATCCC-TTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
66 GTCCTCACCATCCCTTTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
* * * *
6138198 TCGATAGCCAAAG-TCATCCCTTTTCATTGTTCGATGGTCGTCACCATCCCTTTTCATTATTTGA
1 TCGATAGCCAAAGCT-ATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTCCATT-GTTGA
*
6138262 TGGTCGTCACCAT-CCTTTTTCATAATTTGATAGCC
64 TGGTCCTCACCATCCCTTTTTCATAATTTGATAGCC
6138297 TAGGCTATCC
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
118 1 0.01
119 54 0.60
120 35 0.39
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (120 bp):
TCGATAGCCAAAGCTATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTCCATTGTTGATG
GTCCTCACCATCCCTTTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
Found at i:6138323 original size:31 final size:31
Alignment explanation
Indices: 6138279--6138348 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
6138269 CACCATCCTT
* *
6138279 TTTCA-TAATTTGATAGCCTAGGCTATCCCA
1 TTTCATTAATTTGATAGCCGAAGCTATCCCA
* * **
6138309 TTTCATTATTTTGATTGCCGAAGCTATCCTT
1 TTTCATTAATTTGATAGCCGAAGCTATCCCA
6138340 TTTCATTAA
1 TTTCATTAA
6138349 CCGATGATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTCATTAATTTGATAGCCGAAGCTATCCCA
Found at i:6139880 original size:6 final size:6
Alignment explanation
Indices: 6139869--6139899 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6139859 CGATTTTTTG
*
6139869 CTTCCC CTTCCC CTTTCC CTTCCC CTTCCC C
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC C
6139900 CATCCTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:6143028 original size:19 final size:20
Alignment explanation
Indices: 6143004--6143045 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
6142994 CAAACACCAT
6143004 AAAAGTAAATCA-TTTCCAG
1 AAAAGTAAATCATTTTCCAG
6143023 AAAAGTAAATCATTTTCCAG
1 AAAAGTAAATCATTTTCCAG
6143043 AAA
1 AAA
6143046 TCATTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAGTAAATCATTTTCCAG
Found at i:6143048 original size:14 final size:14
Alignment explanation
Indices: 6143029--6143066 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
6143019 CCAGAAAAGT
6143029 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
6143043 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
6143057 AAAACATTTT
1 AAATCATTTT
6143067 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:6152390 original size:20 final size:20
Alignment explanation
Indices: 6152351--6152392 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6152341 AAGTTGTAGG
*
6152351 TTTGCTTACCAAAAATGTTA
1 TTTGCTTACCAAAAACGTTA
*
6152371 TTTGCTTACCAAAACCGTTA
1 TTTGCTTACCAAAAACGTTA
6152391 TT
1 TT
6152393 ATTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTGCTTACCAAAAACGTTA
Found at i:6152756 original size:27 final size:26
Alignment explanation
Indices: 6152694--6152757 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
6152684 GAGCCCTATT
* *
6152694 CAATATCAGTACAGTTTGGCCTTAGCC
1 CAATA-CAGTACAGTGTGGCCTAAGCC
6152721 CTTAA-ACAGTAGCAGTGTGGCCTAAGCC
1 C--AATACAGTA-CAGTGTGGCCTAAGCC
6152749 CAATACAGT
1 CAATACAGT
6152758 TTCAGTATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 2 0.06
27 11 0.35
28 16 0.52
29 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (26 bp):
CAATACAGTACAGTGTGGCCTAAGCC
Found at i:6153195 original size:24 final size:24
Alignment explanation
Indices: 6153163--6153239 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
6153153 AAGTCTGTCA
*
6153163 GGAGAGGATTTATGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
6153187 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
6153211 GGAGAGGATTTAGGAGCTAATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
6153235 GGAGA
1 GGAGA
6153240 ACAGTGTTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:6154725 original size:27 final size:26
Alignment explanation
Indices: 6154655--6154755 Score: 103
Period size: 27 Copynumber: 3.8 Consensus size: 26
6154645 CTAGTGGCTA
* *
6154655 TGCCACAATTATCTGATCTGGTGCCTC
1 TGCCAC-ATTATCTGTTCTGGTGACTC
* * * *
6154682 TGCAACATATTTTTGTTCTGGTGGCTC
1 TGCCACAT-TATCTGTTCTGGTGACTC
*
6154709 TGCCGCGATTATCTGTTCTGGTGACTC
1 TGCCAC-ATTATCTGTTCTGGTGACTC
*
6154736 TGTCACATTATCTGTTCTGG
1 TGCCACATTATCTGTTCTGG
6154756 CAGCCATACT
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
26 16 0.27
27 42 0.70
28 2 0.03
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.40
Consensus pattern (26 bp):
TGCCACATTATCTGTTCTGGTGACTC
Found at i:6160853 original size:11 final size:11
Alignment explanation
Indices: 6160837--6160861 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6160827 TCATACTGTA
6160837 AATAATAAAAT
1 AATAATAAAAT
6160848 AATAATAAAAT
1 AATAATAAAAT
6160859 AAT
1 AAT
6160862 TATTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:6184363 original size:22 final size:22
Alignment explanation
Indices: 6184338--6184387 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6184328 TTTGGCGACG
*
6184338 TCATGAAAT-GAAGGAAGTGGCA
1 TCATGAAATAG-AGGAAGTGACA
**
6184360 TCATGACGTAGAGGAAGTGACA
1 TCATGAAATAGAGGAAGTGACA
6184382 TCATGA
1 TCATGA
6184388 TGTCGACCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (22 bp):
TCATGAAATAGAGGAAGTGACA
Found at i:6186691 original size:28 final size:26
Alignment explanation
Indices: 6186635--6186691 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
6186625 AGCATGGCTG
**
6186635 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAACCA
*
6186661 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGACAGAACCA
6186689 CCA
1 CCA
6186692 AGACGCTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 9 0.35
28 12 0.46
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.14
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAACCA
Found at i:6187127 original size:16 final size:16
Alignment explanation
Indices: 6187106--6187149 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
6187096 CCCAAAATAC
6187106 CAACTTTTCGGCATTT
1 CAACTTTTCGGCATTT
6187122 CAACTTTTCGGCATTT
1 CAACTTTTCGGCATTT
*
6187138 CAGCTTTTCGGC
1 CAACTTTTCGGC
6187150 TTTTGCCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (16 bp):
CAACTTTTCGGCATTT
Found at i:6188140 original size:24 final size:24
Alignment explanation
Indices: 6188126--6188196 Score: 133
Period size: 24 Copynumber: 3.0 Consensus size: 24
6188116 CTAGATTTTC
*
6188126 TCCCTTATCTACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
6188150 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
6188174 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
6188197 CTCCTGACAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:6189302 original size:54 final size:54
Alignment explanation
Indices: 6189235--6189396 Score: 288
Period size: 54 Copynumber: 3.0 Consensus size: 54
6189225 GCTACAGGTA
* *
6189235 TGTATGGAAAACTATTCAAGTATTGAGCTAATGGAAGTTAAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
6189289 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
* *
6189343 TGTACGGAAAACTATTCAAGTATTGAACAAATGGAAGTTGAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
6189397 ATTTAGTGAT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (54 bp):
TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
Found at i:6191480 original size:33 final size:33
Alignment explanation
Indices: 6191441--6191509 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
6191431 TCTAGAGTTG
6191441 AAATAATTTGTCATTCTAGTTGAAAGGGCTTGT
1 AAATAATTTGTCATTCTAGTTGAAAGGGCTTGT
6191474 AAATAATTTGTCATTCTAGTTGAAAGGGCTTGT
1 AAATAATTTGTCATTCTAGTTGAAAGGGCTTGT
6191507 AAA
1 AAA
6191510 GCTAAGGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (33 bp):
AAATAATTTGTCATTCTAGTTGAAAGGGCTTGT
Found at i:6199870 original size:20 final size:18
Alignment explanation
Indices: 6199837--6199873 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
6199827 TATGATGTTG
6199837 ATATGATTAATTTAATTA
1 ATATGATTAATTTAATTA
6199855 ATATGACTTAAATTTAATT
1 ATATGA-TT-AATTTAATT
6199874 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATGATTAATTTAATTA
Found at i:6208533 original size:18 final size:18
Alignment explanation
Indices: 6208510--6208544 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6208500 GTTTCATTCC
6208510 CGATACTTTGTGCACTAT
1 CGATACTTTGTGCACTAT
6208528 CGATACTTTGTGCACTA
1 CGATACTTTGTGCACTA
6208545 AGTGTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (18 bp):
CGATACTTTGTGCACTAT
Found at i:6209894 original size:46 final size:45
Alignment explanation
Indices: 6209844--6210015 Score: 161
Period size: 46 Copynumber: 3.7 Consensus size: 45
6209834 TGAGCATCCA
*
6209844 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCTG
*** * * *
6209890 AACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCTG
* *
6209937 AGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCT-G
* *
6209983 AGCTCGTTGAGTTAAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6210016 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 60 0.59
47 30 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCTG
Found at i:6212771 original size:15 final size:15
Alignment explanation
Indices: 6212727--6212801 Score: 78
Period size: 15 Copynumber: 5.0 Consensus size: 15
6212717 GTACCGTATC
* *
6212727 TTGGGTTTCTTTATC
1 TTGGATTTCTTTATT
* *
6212742 CTGGATCTCTTTATT
1 TTGGATTTCTTTATT
6212757 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
* * * *
6212772 TCGGGTTTCTCTATC
1 TTGGATTTCTTTATT
6212787 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
6212802 CGGTTTTCTT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.11, C:0.15, G:0.16, T:0.59
Consensus pattern (15 bp):
TTGGATTTCTTTATT
Found at i:6225171 original size:22 final size:24
Alignment explanation
Indices: 6225126--6225171 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
6225116 TAATCTTTAA
6225126 TATATAATTATATCTATTATAATT
1 TATATAATTATATCTATTATAATT
6225150 TATAT-ATTA-ATCT-TTATCAATT
1 TATATAATTATATCTATTAT-AATT
6225172 AGCATAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 4 0.19
24 5 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATAATTATATCTATTATAATT
Found at i:6228976 original size:63 final size:63
Alignment explanation
Indices: 6228877--6229001 Score: 250
Period size: 63 Copynumber: 2.0 Consensus size: 63
6228867 ACCGAGAAGC
6228877 AATTTGAAGTTTTGGGGCACATTAATTTCCAGCCTAAGACGGTCCAGAAACGTGTATTAATTA
1 AATTTGAAGTTTTGGGGCACATTAATTTCCAGCCTAAGACGGTCCAGAAACGTGTATTAATTA
6228940 AATTTGAAGTTTTGGGGCACATTAATTTCCAGCCTAAGACGGTCCAGAAACGTGTATTAATT
1 AATTTGAAGTTTTGGGGCACATTAATTTCCAGCCTAAGACGGTCCAGAAACGTGTATTAATT
6229002 CATAATTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (63 bp):
AATTTGAAGTTTTGGGGCACATTAATTTCCAGCCTAAGACGGTCCAGAAACGTGTATTAATTA
Found at i:6229537 original size:25 final size:23
Alignment explanation
Indices: 6229482--6229537 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
6229472 TTTTTCCATC
6229482 CCATTTC-CCTTTTGTTCAAGTG
1 CCATTTCTCCTTTTGTTCAAGTG
*
6229504 CCTTCTTCTCCTTATTGTTCAAGTG
1 CCAT-TTCTCCTT-TTGTTCAAGTG
*
6229529 TCGATTTCT
1 -CCATTTCT
6229538 TCTATTGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 4 0.15
25 15 0.56
26 2 0.07
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.48
Consensus pattern (23 bp):
CCATTTCTCCTTTTGTTCAAGTG
Found at i:6231324 original size:18 final size:17
Alignment explanation
Indices: 6231297--6231330 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6231287 TCTTCTCTTC
*
6231297 TCTTCTCTCTTTCGCAAT
1 TCTTCCCTCTTT-GCAAT
6231315 TCTTCCCTCTTTGCAA
1 TCTTCCCTCTTTGCAA
6231331 CTTGTGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTTCCCTCTTTGCAAT
Found at i:6243872 original size:32 final size:32
Alignment explanation
Indices: 6243836--6243906 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
6243826 TACTTAATTG
** *
6243836 AAATATTTTCAAATTTTAGTTG-CTCTTTTTGT
1 AAATATTTT-AAAAATTAGATGTCTCTTTTTGT
6243868 AAATA--TTAAAAATTAGATGTCTCTTTTTGT
1 AAATATTTTAAAAATTAGATGTCTCTTTTTGT
6243898 AAATATTTT
1 AAATATTTT
6243907 TAAAGGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 9 0.27
30 17 0.52
32 7 0.21
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.52
Consensus pattern (32 bp):
AAATATTTTAAAAATTAGATGTCTCTTTTTGT
Found at i:6243996 original size:16 final size:15
Alignment explanation
Indices: 6243969--6244002 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
6243959 ATAACTAGTA
*
6243969 TATAATTATATTTAT
1 TATAATTATATTAAT
6243984 TATAATATATATTAAT
1 TATAAT-TATATTAAT
6244000 TAT
1 TAT
6244003 TATAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:6245954 original size:41 final size:41
Alignment explanation
Indices: 6245872--6245955 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
6245862 TCGATGCCAC
* **
6245872 TGTCCCAGACAGGGTCTTACACGAATCAAATACGATGTCGA
1 TGTCCCAGACAGGGTCTTACACGAACCAAATACGAAATCGA
* * *
6245913 TGTCCCAGACATGGTCTTACACGTAACCATATA-TAAATCGA
1 TGTCCCAGACAGGGTCTTACACG-AACCAAATACGAAATCGA
6245954 TG
1 TG
6245956 CCAACATCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 29 0.81
42 7 0.19
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
TGTCCCAGACAGGGTCTTACACGAACCAAATACGAAATCGA
Found at i:6249535 original size:40 final size:40
Alignment explanation
Indices: 6249491--6249675 Score: 298
Period size: 40 Copynumber: 4.6 Consensus size: 40
6249481 AACCCAATTA
* * ** *
6249491 CCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
6249531 CCTTCGGGACTTAACCCGGAAATAGCAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
6249571 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
6249611 CCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
6249651 CCTTCGGGACTTAACCCGGATATAA
1 CCTTCGGGACTTAACCCGGAAATAA
6249676 TCCTCAATTG
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 136 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
Found at i:6257210 original size:103 final size:103
Alignment explanation
Indices: 6257031--6257236 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 103
6257021 TGGATCTCCC
* *
6257031 AAGTCTGATAGTTCACGAACAAAATCTATAAAACAGGGAATGAAGGCAAAAATAGTAACCATTTC
1 AAGTCTGATAGTTCACGAACAAAATCTATAAAACAGGGAATGAAAGCAAAAAGAGTAACCATTTC
6257096 GATGCTTAGTAAGTCTTAAGTAATGAAATCATTTATAA
66 GATGCTTAGTAAGTCTTAAGTAATGAAATCATTTATAA
*
6257134 AAGTCTGATAGTTCACGAACAAAATCTATAAAACAGGGAATGAAAGCAAAAAGAGTAAGCATTTC
1 AAGTCTGATAGTTCACGAACAAAATCTATAAAACAGGGAATGAAAGCAAAAAGAGTAACCATTTC
6257199 GATGCTTAGTAAGTCTTAAGTAATGAAATCATTTATAA
66 GATGCTTAGTAAGTCTTAAGTAATGAAATCATTTATAA
6257237 CTAAAGCATA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (103 bp):
AAGTCTGATAGTTCACGAACAAAATCTATAAAACAGGGAATGAAAGCAAAAAGAGTAACCATTTC
GATGCTTAGTAAGTCTTAAGTAATGAAATCATTTATAA
Found at i:6257651 original size:46 final size:46
Alignment explanation
Indices: 6257583--6257673 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
6257573 AAATTATTAC
*
6257583 GACAAGATCGCACATTTTCAACCCAATTGCCTTCGGGATTTAGCCT
1 GACAAGATCGCACATTTCCAACCCAATTGCCTTCGGGATTTAGCCT
6257629 GACAAGATCGCACATTTCCAACCCAATTGCCTTCGGGATTTAGCC
1 GACAAGATCGCACATTTCCAACCCAATTGCCTTCGGGATTTAGCC
6257674 CGGATGTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (46 bp):
GACAAGATCGCACATTTCCAACCCAATTGCCTTCGGGATTTAGCCT
Found at i:6257700 original size:40 final size:40
Alignment explanation
Indices: 6257656--6257798 Score: 189
Period size: 40 Copynumber: 3.6 Consensus size: 40
6257646 CCAACCCAAT
* * * *
6257656 TGCCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
* *
6257696 TGCCTTCGGAACTTAACCCGGGA-ATAGCAACCAGCACGAA
1 TGCCTTCGGGACTTAACCC-GGATATAACAACCAGCACGAA
* *
6257736 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
*
6257776 TGCCTGCGGGACTTAACCCGGAT
1 TGCCTTCGGGACTTAACCCGGAT
6257799 GTAGTCCTCA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 3 0.03
40 84 0.93
41 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.23, T:0.18
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
Found at i:6258538 original size:48 final size:48
Alignment explanation
Indices: 6258486--6258580 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
6258476 CTCATATATA
6258486 TTTTATCCATAAAATTTTCAGAATTTTTAGTTTGGCCAATCAATACCC
1 TTTTATCCATAAAATTTTCAGAATTTTTAGTTTGGCCAATCAATACCC
* *
6258534 TTTTATTCATAAAATTTTCATAATTTTTAGTTTGGCCAATCAATACC
1 TTTTATCCATAAAATTTTCAGAATTTTTAGTTTGGCCAATCAATACC
6258581 AGATTTTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (48 bp):
TTTTATCCATAAAATTTTCAGAATTTTTAGTTTGGCCAATCAATACCC
Found at i:6259411 original size:131 final size:131
Alignment explanation
Indices: 6259177--6259435 Score: 491
Period size: 131 Copynumber: 2.0 Consensus size: 131
6259167 TGTACTACGC
*
6259177 CGAACCTTTAGGAAATCAAGCACCTAATTTATCCATTTCAAAACACCTAATCGGCCTTTCTTCAA
1 CGAACCTTTAGGAAATCAAGCACCTAATTTATCCATTTCAAAACACCTAATCGGCATTTCTTCAA
6259242 GACATTAAGCAAAGTCTACGTTCGGCTATTACACATATGAGTATTAGAAATTATAGTTTTTAATG
66 GACATTAAGCAAAGTCTACGTTCGGCTATTACACATATGAGTATTAGAAATTATAGTTTTTAATG
6259307 T
131 T
*
6259308 CGAACCTTTAGGAAATCAAGCACCTAATTTATCCATTTCAAAACACCTAATCGGCATTTGTTCAA
1 CGAACCTTTAGGAAATCAAGCACCTAATTTATCCATTTCAAAACACCTAATCGGCATTTCTTCAA
*
6259373 GACATTAAGCAAAGTCTAGGTTCGGCTATTACACATATGAGTATTAGAAATTATAGTTTTTAA
66 GACATTAAGCAAAGTCTACGTTCGGCTATTACACATATGAGTATTAGAAATTATAGTTTTTAA
6259436 CAAGATCAAC
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (131 bp):
CGAACCTTTAGGAAATCAAGCACCTAATTTATCCATTTCAAAACACCTAATCGGCATTTCTTCAA
GACATTAAGCAAAGTCTACGTTCGGCTATTACACATATGAGTATTAGAAATTATAGTTTTTAATG
T
Found at i:6262446 original size:17 final size:19
Alignment explanation
Indices: 6262409--6262447 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
6262399 TTTCTCCTAA
*
6262409 ATTTCAATTTTATTTAATT
1 ATTTCAATTTTATTGAATT
6262428 ATTT-AATTTT-TTGAATT
1 ATTTCAATTTTATTGAATT
6262445 ATT
1 ATT
6262448 AATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTTCAATTTTATTGAATT
Found at i:6271794 original size:23 final size:23
Alignment explanation
Indices: 6271762--6271812 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6271752 CATGTGAACC
* *
6271762 AATGACAATGACACTTCGGTGCA
1 AATGAAAATGACACTTCAGTGCA
* *
6271785 AATGAAAATGGCACTTTAGTGCA
1 AATGAAAATGACACTTCAGTGCA
6271808 AATGA
1 AATGA
6271813 TAGTGGCCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (23 bp):
AATGAAAATGACACTTCAGTGCA
Found at i:6272898 original size:17 final size:17
Alignment explanation
Indices: 6272876--6272909 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6272866 TAGGGTTACG
*
6272876 GAGCATTACCGAACATA
1 GAGCATTACCAAACATA
6272893 GAGCATTACCAAACATA
1 GAGCATTACCAAACATA
6272910 TTATACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (17 bp):
GAGCATTACCAAACATA
Found at i:6287376 original size:43 final size:43
Alignment explanation
Indices: 6287328--6287443 Score: 159
Period size: 43 Copynumber: 2.7 Consensus size: 43
6287318 GATTTTGTGG
6287328 AAGACCATGTCTAGGACATTGGCATCGATATGA-GATTACGTGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGATGATTA-GTGT
6287371 AAGACCATGTCTAGGACATTGGCATCG-TAT-ATGATTAGTGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGATGATTAGTGT
* **
6287412 AAGATCC-TGTCTGGGACAGAGGCATCGATATG
1 AAGA-CCATGTCTAGGACATTGGCATCGATATG
6287444 TGAAAACATC
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
41 26 0.39
42 13 0.20
43 27 0.41
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (43 bp):
AAGACCATGTCTAGGACATTGGCATCGATATGATGATTAGTGT
Found at i:6290063 original size:20 final size:20
Alignment explanation
Indices: 6290034--6290078 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6290024 AGCACATGTA
* *
6290034 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
6290054 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
6290074 TTCAT
1 TTCAT
6290079 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:6290326 original size:47 final size:47
Alignment explanation
Indices: 6290273--6290369 Score: 169
Period size: 47 Copynumber: 2.1 Consensus size: 47
6290263 CCCATTTTTC
6290273 ATACCTTGATTAA-TTTTCAAATTAATCCCTCAAATAGAGAGATTAAG
1 ATACCTTGA-TAACTTTTCAAATTAATCCCTCAAATAGAGAGATTAAG
*
6290320 ATACCTTGATAACTTTTCAAATTAATCCCTCCAATAGAGAGATTAAG
1 ATACCTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTAAG
6290367 ATA
1 ATA
6290370 TCCCAGTTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 3 0.06
47 45 0.94
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (47 bp):
ATACCTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTAAG
Found at i:6291204 original size:66 final size:66
Alignment explanation
Indices: 6291098--6291231 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
6291088 ACATTTTCAA
*
6291098 ATTTCATGTAATCAACATTTACATTCATTCACATCATTCCTAATATAAGCCTACGAGGCCCAAAA
1 ATTTCATATAATCAACATTTACATTCATTCACATCATTCCTAATATAAGCCTACGAGGCCCAAAA
6291163 T
66 T
6291164 ATTTCATATAATCAACATTTACATTCATTCACATCATTCCTAATATAAGCCTACGAGGCCCAAAA
1 ATTTCATATAATCAACATTTACATTCATTCACATCATTCCTAATATAAGCCTACGAGGCCCAAAA
6291229 T
66 T
6291230 AT
1 AT
6291232 ACATTCGGGG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (66 bp):
ATTTCATATAATCAACATTTACATTCATTCACATCATTCCTAATATAAGCCTACGAGGCCCAAAA
T
Found at i:6292680 original size:39 final size:39
Alignment explanation
Indices: 6292614--6292742 Score: 170
Period size: 39 Copynumber: 3.3 Consensus size: 39
6292604 GGTAAACTAT
6292614 TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
1 TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
* * * * *
6292653 TGTATTGAATAATTGATAATTATTGAATTACTAAACTAC
1 TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
* * *
6292692 TGCACTGAAT-ATCTGATAGTTACTGAATGACTAAATTAT
1 TGTACTGAATAAT-TGATAGTTACTGAATAACTAAATTAC
6292731 TGTACTGAATAA
1 TGTACTGAATAA
6292743 CTAATTGTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
38 2 0.03
39 72 0.96
40 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
Found at i:6292753 original size:39 final size:39
Alignment explanation
Indices: 6292606--6292755 Score: 165
Period size: 39 Copynumber: 3.8 Consensus size: 39
6292596 TTAATAGGGG
* *
6292606 TAAACTATTGTACTGAATAATTGATAGTTACTGAATAAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * * * * *
6292645 TAAATTACTGTATTGAATAATTGATAATTATTGAATTAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * *
6292684 TAAACTACTGCACTGAATATCTGATAGTTACTGAATGAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * * *
6292723 TAAATTATTGTACTGAATAACTAATTGTTACTG
1 TAAACTACTGTACTGAATAACTGATAGTTACTG
6292756 GTTAAATATG
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (39 bp):
TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
Found at i:6303800 original size:79 final size:82
Alignment explanation
Indices: 6303689--6303873 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
6303679 GCTACTCGTT
* *
6303689 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
6303752 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
6303769 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
6303832 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
6303849 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6303874 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:6303873 original size:40 final size:40
Alignment explanation
Indices: 6303670--6303873 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
6303660 CGGAATTTAA
** *
6303670 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6303710 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
6303750 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6303789 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
6303829 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
6303869 CCGGA
1 CCGGA
6303874 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:6311788 original size:79 final size:82
Alignment explanation
Indices: 6311677--6311861 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
6311667 GCTACTCGTT
* *
6311677 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
6311740 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
6311757 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
6311820 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
6311837 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6311862 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:6311861 original size:40 final size:40
Alignment explanation
Indices: 6311658--6311861 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
6311648 CGGAATTTAA
** *
6311658 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6311698 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
6311738 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6311777 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
6311817 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
6311857 CCGGA
1 CCGGA
6311862 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:6316513 original size:23 final size:23
Alignment explanation
Indices: 6316487--6316532 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6316477 TTCATGAATG
6316487 TTTGATAGTTACTGAATGACTAA
1 TTTGATAGTTACTGAATGACTAA
6316510 TTTGATAGTTACTGAATGACTAA
1 TTTGATAGTTACTGAATGACTAA
6316533 ATTACTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (23 bp):
TTTGATAGTTACTGAATGACTAA
Found at i:6329059 original size:40 final size:40
Alignment explanation
Indices: 6328989--6329206 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
6328979 AAGCCAGGTA
* * * *
6328989 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
6329028 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
6329068 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
6329108 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
6329148 CCTTTGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
6329188 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
6329207 TTATCATCCG
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 13 0.08
40 148 0.92
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:6331194 original size:25 final size:25
Alignment explanation
Indices: 6331166--6331230 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
6331156 TTCTTATGCA
*
6331166 TGTATGCTCATACGAGCTATGAATC
1 TGTATGCTCATACGAGCTATAAATC
*
6331191 TGTATGCTC-TAACGAGCTGTAAATC
1 TGTATGCTCAT-ACGAGCTATAAATC
*
6331216 GGTATGCTCATACGA
1 TGTATGCTCATACGA
6331231 ACTGAGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (25 bp):
TGTATGCTCATACGAGCTATAAATC
Found at i:6331250 original size:50 final size:49
Alignment explanation
Indices: 6331167--6331294 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 49
6331157 TCTTATGCAT
* *
6331167 GTATGCTCATACGAGCT-ATGAATCTGTATGCTCTAACGAGCTGTAAATCG
1 GTATGCTCATACGAACTGA-GAATCTGTAAGCTCTAACGAGCTG-AAATCG
* *
6331217 GTATGCTCATACGAACTGAGAAT-TGATAAGCTCTCACGAGCTGCAATCG
1 GTATGCTCATACGAACTGAGAATCTG-TAAGCTCTAACGAGCTGAAATCG
* *
6331266 GTAAGCTCATAC-AAGCTGAGAATCGGTAA
1 GTATGCTCATACGAA-CTGAGAATCTGTAA
6331295 TCCCTAGTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
48 2 0.03
49 29 0.43
50 36 0.53
51 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (49 bp):
GTATGCTCATACGAACTGAGAATCTGTAAGCTCTAACGAGCTGAAATCG
Found at i:6331282 original size:24 final size:25
Alignment explanation
Indices: 6331212--6331294 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
6331202 ACGAGCTGTA
*
6331212 AATCGGTATGCTCATACGAA-CTGAG
1 AATCGGTAAGCTCATAC-AAGCTGAG
* * * *
6331237 AATTGATAAGCTC-TCACGAGCTG-C
1 AATCGGTAAGCTCAT-ACAAGCTGAG
6331261 AATCGGTAAGCTCATACAAGCTGAG
1 AATCGGTAAGCTCATACAAGCTGAG
6331286 AATCGGTAA
1 AATCGGTAA
6331295 TCCCTAGTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
24 20 0.44
25 25 0.56
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
AATCGGTAAGCTCATACAAGCTGAG
Found at i:6334812 original size:41 final size:41
Alignment explanation
Indices: 6334737--6334818 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
6334727 TGATATCAGC
6334737 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
1 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
6334778 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
1 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
6334819 AAGATTCAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (41 bp):
TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
Found at i:6341702 original size:26 final size:25
Alignment explanation
Indices: 6341647--6341702 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
6341637 ATTTTAATCC
* *
6341647 TTTTAATTTTTTTATAATTTATTTT
1 TTTTAAATATTTTATAATTTATTTT
6341672 TTTTAAATATTTTAT-ATATTATTTAT
1 TTTTAAATATTTTATAAT-TTATTT-T
6341698 TTTTA
1 TTTTA
6341703 CTATAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 19 0.70
26 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTAAATATTTTATAATTTATTTT
Found at i:6341748 original size:12 final size:12
Alignment explanation
Indices: 6341731--6341874 Score: 97
Period size: 12 Copynumber: 12.0 Consensus size: 12
6341721 TATGTAAAAA
6341731 ATTATTATATAT
1 ATTATTATATAT
* *
6341743 ATTATTTTTATTT
1 ATTA-TTATATAT
6341756 ATGTATTATTTATCAT
1 AT-TATTA--TAT-AT
6341772 ATTATT-TATAT
1 ATTATTATATAT
*
6341783 TTTATTATATAT
1 ATTATTATATAT
*
6341795 TTTATT-TATAT
1 ATTATTATATAT
6341806 ATT-TTAT-TAT
1 ATTATTATATAT
6341816 A-TATTATATCAT
1 ATTATTATAT-AT
* *
6341828 TTTACTATATAT
1 ATTATTATATAT
6341840 ATTATTCAT-TAT
1 ATTATT-ATATAT
*
6341852 ATTATT-TTTAT
1 ATTATTATATAT
6341863 -TCTATTATATAT
1 AT-TATTATATAT
6341875 TATATTATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 30
0.72 0.07 0.20
Matches are distributed among these distances:
9 1 0.01
10 12 0.11
11 23 0.22
12 39 0.37
13 19 0.18
14 2 0.02
15 7 0.07
16 3 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:6341764 original size:17 final size:18
Alignment explanation
Indices: 6341732--6341801 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 18
6341722 ATGTAAAAAA
6341732 TTATTATATATATTATTT
1 TTATTATATATATTATTT
*
6341750 TTATT-TATGTATTA--T
1 TTATTATATATATTATTT
*
6341765 TTATCATAT-TATTTATATT
1 TTATTATATATA-TTAT-TT
*
6341784 TTATTATATATTTTATTT
1 TTATTATATATATTATTT
6341802 ATATATTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.17
16 6 0.14
17 8 0.19
18 7 0.17
19 13 0.31
20 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (18 bp):
TTATTATATATATTATTT
Found at i:6341780 original size:23 final size:22
Alignment explanation
Indices: 6341731--6341882 Score: 95
Period size: 23 Copynumber: 6.9 Consensus size: 22
6341721 TATGTAAAAA
6341731 ATTA-TTATATA-TA-TTAT-T
1 ATTATTTATATATTATTTATAT
* *
6341749 TTTATTTATGTATTATTTATCAT
1 ATTATTTATATATTATTTAT-AT
*
6341772 ATTATTTATATTTTATTATATAT
1 ATTATTTATATATTATT-TATAT
* *
6341795 TTTATTTATATATTTTATTATAT
1 ATTATTTATATATTAT-TTATAT
* *
6341818 ATTA--TATCATTTTACTATATAT
1 ATTATTTAT-ATATTA-TTTATAT
*
6341840 ATTATTCATTATATTATTT-T-T
1 ATTATTTA-TATATTATTTATAT
*
6341861 ATTCTATTATATATTATATTAT
1 ATTAT-TTATATATTAT-TTAT
6341883 TTTGTTTTTT
Statistics
Matches: 102, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.03
19 6 0.06
20 2 0.02
21 20 0.20
22 18 0.18
23 42 0.41
24 10 0.10
25 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (22 bp):
ATTATTTATATATTATTTATAT
Found at i:6341821 original size:32 final size:33
Alignment explanation
Indices: 6341740--6341885 Score: 73
Period size: 31 Copynumber: 4.5 Consensus size: 33
6341730 AATTATTATA
* *
6341740 TATATTATT-TTTA-TTTATGTAT-TA-TTTAT
1 TATATTATTATATATTTTATTTATATATTTTAT
*
6341769 CATATTATT-TATATTTTA-TTATATATTTTAT
1 TATATTATTATATATTTTATTTATATATTTTAT
* *
6341800 T-TATATATT-T-TATTATATATTATATCATTTTAC
1 TATAT-TATTATATATTTTAT-TTATAT-ATTTTAT
* *
6341833 TATATATATTATTCATTATATTATTT-T-TATTCTAT
1 TATAT-TATTA-T-A-TATTTTATTTATATATTTTAT
6341868 TATA-TATTATATTATTTT
1 TATATTATTATA-TATTTT
6341886 GTTTTTTATT
Statistics
Matches: 93, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
29 14 0.15
30 15 0.16
31 17 0.18
32 7 0.08
33 12 0.13
34 8 0.09
35 9 0.10
36 2 0.02
37 1 0.01
38 2 0.02
39 6 0.06
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (33 bp):
TATATTATTATATATTTTATTTATATATTTTAT
Found at i:6343203 original size:18 final size:19
Alignment explanation
Indices: 6343180--6343217 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6343170 TGGAAAGATA
*
6343180 AAAATTTGAAAGA-AAAGG
1 AAAATTAGAAAGATAAAGG
*
6343198 AAAATTAGAAGGATAAAGG
1 AAAATTAGAAAGATAAAGG
6343217 A
1 A
6343218 TAAGTGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (19 bp):
AAAATTAGAAAGATAAAGG
Found at i:6345182 original size:39 final size:39
Alignment explanation
Indices: 6345117--6345219 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 39
6345107 AATAGCACAC
* * *
6345117 CAGT-TTGTGGACAAGCCTCTAATAATACAGATAAACT-G
1 CAGTATTGTGGACAAG-CACTAGTAATACAAATAAACTAG
*
6345155 CGGTATTGTGGACAAGTCACTAGTAATACAAATAAACTAG
1 CAGTATTGTGGACAAG-CACTAGTAATACAAATAAACTAG
*
6345195 TAGTATTGTGGACAAGCTACTAGTA
1 CAGTATTGTGGACAAGC-ACTAGTA
6345220 TTGTAGACAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.05
39 30 0.55
40 22 0.40
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (39 bp):
CAGTATTGTGGACAAGCACTAGTAATACAAATAAACTAG
Found at i:6348417 original size:16 final size:16
Alignment explanation
Indices: 6348383--6348433 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
6348373 AATGAATCGC
* *
6348383 AAAAGCCGAAATGCCG
1 AAAAGCCGAAAAGCTG
*
6348399 AAAAGCCAAAAAGCTG
1 AAAAGCCGAAAAGCTG
* *
6348415 AAATGCTGAAAAGCTG
1 AAAAGCCGAAAAGCTG
6348431 AAA
1 AAA
6348434 GTTAGGCTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.51, C:0.18, G:0.22, T:0.10
Consensus pattern (16 bp):
AAAAGCCGAAAAGCTG
Found at i:6348417 original size:24 final size:24
Alignment explanation
Indices: 6348383--6348428 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
6348373 AATGAATCGC
6348383 AAAAGCCGAAATGCCGAAAAGCCA
1 AAAAGCCGAAATGCCGAAAAGCCA
* *
6348407 AAAAGCTGAAATGCTGAAAAGC
1 AAAAGCCGAAATGCCGAAAAGC
6348429 TGAAAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.22, T:0.09
Consensus pattern (24 bp):
AAAAGCCGAAATGCCGAAAAGCCA
Found at i:6348714 original size:29 final size:29
Alignment explanation
Indices: 6348649--6348763 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
6348639 GCATGAGTAT
* *
6348649 AATATGATTTGGGCCTAATGGGCCATATG
1 AATATGAATTGGGCCTAGTGGGCCATATG
** *
6348678 AAGGTGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAATTGGGCCTAGTGGGCCATATG
* * * *
6348707 AATATGAACTAGGCC-AGATGGGTCATTTG
1 AATATGAATTGGGCCTAG-TGGGCCATATG
* *
6348736 AATAAG-ATTGGGCCTAGTGGGCTATATG
1 AATATGAATTGGGCCTAGTGGGCCATATG
6348764 CATGTATGTA
Statistics
Matches: 66, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
28 16 0.24
29 50 0.76
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (29 bp):
AATATGAATTGGGCCTAGTGGGCCATATG
Found at i:6356115 original size:16 final size:16
Alignment explanation
Indices: 6356094--6356124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6356084 ATGAATTGGC
6356094 AAATGCCGAAAAGCCG
1 AAATGCCGAAAAGCCG
*
6356110 AAATGCCGAGAAGCC
1 AAATGCCGAAAAGCC
6356125 AAAAAGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.26, T:0.06
Consensus pattern (16 bp):
AAATGCCGAAAAGCCG
Found at i:6356281 original size:19 final size:18
Alignment explanation
Indices: 6356259--6356295 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6356249 AGAATTGACC
6356259 AAATGGGCCGGAATGGGCT
1 AAATGGGCCGG-ATGGGCT
*
6356278 AAATGGGCCTGATGGGCT
1 AAATGGGCCGGATGGGCT
6356296 GTTGGGCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.19
Consensus pattern (18 bp):
AAATGGGCCGGATGGGCT
Found at i:6356418 original size:29 final size:27
Alignment explanation
Indices: 6356376--6356482 Score: 99
Period size: 29 Copynumber: 3.8 Consensus size: 27
6356366 ATAATATAAT
*
6356376 TTGGGCCTAATGGGCCATATGAAGGTGAA
1 TTGGGCCTAGTGGGCCATATGAA--TGAA
*
6356405 TTGGGCCTAGTGGGCCATAAGAATATGAA
1 TTGGGCCTAGTGGGCCATATG-A-ATGAA
* * *
6356434 TTGGGCC-AGATGGGTCATTTGAATAAGA
1 TTGGGCCTAG-TGGGCCATATGAATGA-A
*
6356462 TTGGGCCTAGTGGGCTATATG
1 TTGGGCCTAGTGGGCCATATG
6356483 CATGTATGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.05
28 19 0.30
29 40 0.62
30 1 0.02
31 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.27
Consensus pattern (27 bp):
TTGGGCCTAGTGGGCCATATGAATGAA
Found at i:6371226 original size:34 final size:34
Alignment explanation
Indices: 6371183--6371251 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
6371173 ATTTCTTTCA
6371183 TAAGTATGTTTTAATAATGAATGTTTAAAGTTTT
1 TAAGTATGTTTTAATAATGAATGTTTAAAGTTTT
6371217 TAAGTATGTTTTAATAATGAATGTTTAAAGTTTT
1 TAAGTATGTTTTAATAATGAATGTTTAAAGTTTT
6371251 T
1 T
6371252 TTTTTGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (34 bp):
TAAGTATGTTTTAATAATGAATGTTTAAAGTTTT
Found at i:6374720 original size:53 final size:53
Alignment explanation
Indices: 6374526--6374732 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 53
6374516 ATTAGGGTTT
* * * * *
6374526 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTT-TTACAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATA-AA-GC
* * * * * * * *
6374580 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAAGC
* * * *
6374635 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAAGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAAGC
* *
6374688 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
6374733 TAAAAAGGAA
Statistics
Matches: 121, Mismatches: 29, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
53 45 0.37
54 37 0.31
55 36 0.30
56 1 0.01
57 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAAGC
Found at i:6377525 original size:20 final size:18
Alignment explanation
Indices: 6377478--6377526 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
6377468 CAAGATAAAC
6377478 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
6377495 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
6377515 ATTAAATTAATA
1 ATTAAATTAATA
6377527 AAATGCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:6384143 original size:36 final size:36
Alignment explanation
Indices: 6384102--6384185 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 36
6384092 TACTCTCTAT
*
6384102 TTTGGTGTGTTTCGGATGGA-TGAGCTCTTATGAGCA
1 TTTGGTGTGTTTCGAATGGACT-AGCTCTTATGAGCA
6384138 TTTGGTGTGTTTCGAATGGACTAGCTCTTATGAGCA
1 TTTGGTGTGTTTCGAATGGACTAGCTCTTATGAGCA
*
6384174 TCTGGTGTGTTT
1 TTTGGTGTGTTT
6384186 TGGTAGGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 44 0.98
37 1 0.02
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.42
Consensus pattern (36 bp):
TTTGGTGTGTTTCGAATGGACTAGCTCTTATGAGCA
Found at i:6386149 original size:29 final size:29
Alignment explanation
Indices: 6386116--6386210 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
6386106 ACATAGTACC
* * *
6386116 TGATAAATATAACACCGACACAGAGTGCT
1 TGATAAATGTAACACTGACACAAAGTGCT
* ** *
6386145 TGATAACTGTAACACTGGTACAAAGTACT
1 TGATAAATGTAACACTGACACAAAGTGCT
* *
6386174 TGATAAATGTAATCACTGACACATAGTGCC
1 TGATAAATGTAA-CACTGACACAAAGTGCT
6386204 TGATAAA
1 TGATAAA
6386211 CCCTAATAAC
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
29 33 0.63
30 19 0.37
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (29 bp):
TGATAAATGTAACACTGACACAAAGTGCT
Found at i:6386927 original size:33 final size:33
Alignment explanation
Indices: 6386885--6386952 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
6386875 ACTTTACAAA
6386885 ATAGTCCTATTTAACAATTGAGCTTATAAACCT
1 ATAGTCCTATTTAACAATTGAGCTTATAAACCT
6386918 ATAGTCCTATTTAACAATTGAGCTTATAAACCT
1 ATAGTCCTATTTAACAATTGAGCTTATAAACCT
6386951 AT
1 AT
6386953 CATTTAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (33 bp):
ATAGTCCTATTTAACAATTGAGCTTATAAACCT
Found at i:6396438 original size:47 final size:47
Alignment explanation
Indices: 6396378--6396612 Score: 470
Period size: 47 Copynumber: 5.0 Consensus size: 47
6396368 GATATATAAT
6396378 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
6396425 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
6396472 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
6396519 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
6396566 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
6396613 TAATATAATT
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 188 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (47 bp):
ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
Found at i:6397127 original size:21 final size:21
Alignment explanation
Indices: 6397103--6397158 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
6397093 TTATATTATT
6397103 TATAAAATTTTA-TATATGAAA
1 TATAAAATTTTATTATAT-AAA
6397124 TATAAAATTAATTATTATATAAA
1 TATAAAATT--TTATTATATAAA
6397147 TAATTAAAATTT
1 T-A-TAAAATTT
6397159 ACTATTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.30
23 8 0.27
24 6 0.20
25 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAAATTTTATTATATAAA
Found at i:6397671 original size:45 final size:44
Alignment explanation
Indices: 6397622--6397727 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 44
6397612 TATTTTCATT
6397622 TAATATTAAAATAAATATAAATATTTAATTTTAATTTAATT-TTAA
1 TAATATTAAAATAAATATAAA-ATTTAATTTTAATTT-ATTCTTAA
** * *
6397667 TAATAATT-ATTTACAATTTCAAATTTAATTTTAATTTATTCTTAA
1 TAAT-ATTAAAATA-AATATAAAATTTAATTTTAATTTATTCTTAA
* *
6397712 TAATTTTAAAAAAAAT
1 TAATATTAAAATAAAT
6397728 TGTATAATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
44 8 0.16
45 32 0.65
46 9 0.18
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (44 bp):
TAATATTAAAATAAATATAAAATTTAATTTTAATTTATTCTTAA
Found at i:6400911 original size:17 final size:17
Alignment explanation
Indices: 6400881--6400921 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6400871 AGATTATTGG
*
6400881 AAGCTTGATCGGGTTGA
1 AAGCTCGATCGGGTTGA
* *
6400898 AAGCTCGATTGGGTTGG
1 AAGCTCGATCGGGTTGA
6400915 AAGCTCG
1 AAGCTCG
6400922 CCGGAGATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.27
Consensus pattern (17 bp):
AAGCTCGATCGGGTTGA
Found at i:6401065 original size:20 final size:20
Alignment explanation
Indices: 6401042--6401088 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
6401032 AGCTCCGTCC
* *
6401042 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAACTCAGTTG
* *
6401062 AGCTCATTTCAACTCGGTTG
1 AGCTCAATTCAACTCAGTTG
6401082 AGCTCAA
1 AGCTCAA
6401089 CCGAAATTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (20 bp):
AGCTCAATTCAACTCAGTTG
Found at i:6401347 original size:15 final size:16
Alignment explanation
Indices: 6401327--6401359 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6401317 ATTATATGAA
6401327 TAATTATAT-TTTATT
1 TAATTATATGTTTATT
*
6401342 TAATTATGTGTTTATT
1 TAATTATATGTTTATT
6401358 TA
1 TA
6401360 TTTGTAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TAATTATATGTTTATT
Found at i:6406914 original size:33 final size:33
Alignment explanation
Indices: 6406872--6406937 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6406862 GATAATATCG
6406872 GTTCAACTTGTTCTTAGGACCAACCTTACCATA
1 GTTCAACTTGTTCTTAGGACCAACCTTACCATA
6406905 GTTCAACTTGTTCTTAGGACCAACCTTACCATA
1 GTTCAACTTGTTCTTAGGACCAACCTTACCATA
6406938 CTTTTGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (33 bp):
GTTCAACTTGTTCTTAGGACCAACCTTACCATA
Found at i:6408359 original size:19 final size:20
Alignment explanation
Indices: 6408327--6408367 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
6408317 GAATGAAATC
6408327 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
6408347 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
6408366 GA
1 GA
6408368 AAGTGAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:6408410 original size:30 final size:31
Alignment explanation
Indices: 6408353--6408412 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
6408343 AAAAGAGAGA
*
6408353 AAAACAAAGAAAAGAAAGTGAACAAGAAAAT
1 AAAACAAAGAAAAGAAAGTGAAAAAGAAAAT
* * *
6408384 AAAATAAA-AAAAGACATTGAAAAAGAAAA
1 AAAACAAAGAAAAGAAAGTGAAAAAGAAAA
6408413 AGAATGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.08
Consensus pattern (31 bp):
AAAACAAAGAAAAGAAAGTGAAAAAGAAAAT
Found at i:6410434 original size:10 final size:10
Alignment explanation
Indices: 6410421--6410456 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6410411 GAGCTCCGTC
*
6410421 CAGCTCAATT
1 CAGCTCATTT
6410431 CAGCTCATTT
1 CAGCTCATTT
*
6410441 GAGCTCATTT
1 CAGCTCATTT
6410451 CAGCTC
1 CAGCTC
6410457 GGTTGAGCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (10 bp):
CAGCTCATTT
Found at i:6410445 original size:20 final size:20
Alignment explanation
Indices: 6410422--6410468 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
6410412 AGCTCCGTCC
*
6410422 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCAGTTG
* *
6410442 AGCTCATTTCAGCTCGGTTG
1 AGCTCAATTCAGCTCAGTTG
6410462 AGCTCAA
1 AGCTCAA
6410469 CCGAGCTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (20 bp):
AGCTCAATTCAGCTCAGTTG
Found at i:6415977 original size:43 final size:43
Alignment explanation
Indices: 6415920--6416067 Score: 153
Period size: 43 Copynumber: 3.4 Consensus size: 43
6415910 AATGCCAACA
* *
6415920 TCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTG
1 TCCCAGACGTGGTCTTACACGTAATTAAATATCGATGCCACTG
*
6415963 TCCCAGACAG-GGTCTTACACGAAATTAAATA-CGATGCCAACAT-
1 TCCCAGAC-GTGGTCTTACACGTAATTAAATATCGATGCC-AC-TG
* *
6416006 T-CCAGACGTGGTCTTACACGTAAATTATAA-GTCGATGCCAATG
1 TCCCAGACGTGGTCTTACACGT-AATTA-AATATCGATGCCACTG
* *
6416049 TCCCAGACTTGGTCATACA
1 TCCCAGACGTGGTCTTACA
6416068 GGATAACACA
Statistics
Matches: 88, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
41 1 0.01
42 25 0.28
43 36 0.41
44 26 0.30
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
TCCCAGACGTGGTCTTACACGTAATTAAATATCGATGCCACTG
Found at i:6420339 original size:22 final size:21
Alignment explanation
Indices: 6420314--6420383 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
6420304 TAGTTCATTA
6420314 AATGTTAAATATTAATTATTCC
1 AATGTTAAA-ATTAATTATTCC
* * * *
6420336 AATGGCTAAAATCAGTTCATT-A
1 AAT-GTTAAAATTAATT-ATTCC
*
6420358 AATGTTAGAGATTAATTATTCC
1 AATGTTA-AAATTAATTATTCC
6420380 AATG
1 AATG
6420384 CCTAAAATCT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
21 6 0.17
22 21 0.60
23 8 0.23
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (21 bp):
AATGTTAAAATTAATTATTCC
Found at i:6420372 original size:44 final size:44
Alignment explanation
Indices: 6420305--6420392 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
6420295 AACCCTACAT
* *
6420305 AGTTCATTAAATGTTAAATATTAATTATTCCAATGGCTAAAATC
1 AGTTCATTAAATGTTAAAGATTAATTATTCCAATGCCTAAAATC
*
6420349 AGTTCATTAAATGTTAGAGATTAATTATTCCAATGCCTAAAATC
1 AGTTCATTAAATGTTAAAGATTAATTATTCCAATGCCTAAAATC
6420393 TCCAGCAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (44 bp):
AGTTCATTAAATGTTAAAGATTAATTATTCCAATGCCTAAAATC
Found at i:6427957 original size:5 final size:5
Alignment explanation
Indices: 6427923--6427954 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
6427913 TACGGTTGCA
*
6427923 CACCT CACCT CACCT CACCT CACCT CATCT CA
1 CACCT CACCT CACCT CACCT CACCT CACCT CA
6427955 TCTTTTTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.22, C:0.56, G:0.00, T:0.22
Consensus pattern (5 bp):
CACCT
Found at i:6431126 original size:20 final size:21
Alignment explanation
Indices: 6431101--6431143 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
6431091 AATTGAAGTG
6431101 AATGTGATATTGAG-TTATGA
1 AATGTGATATTGAGATTATGA
6431121 AATGTGATATTGAGATTATGA
1 AATGTGATATTGAGATTATGA
6431142 AA
1 AA
6431144 AGTAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (21 bp):
AATGTGATATTGAGATTATGA
Found at i:6432550 original size:50 final size:52
Alignment explanation
Indices: 6432443--6432559 Score: 143
Period size: 50 Copynumber: 2.3 Consensus size: 52
6432433 AACAAATGAA
* * *
6432443 TTACTTAATGCATGATTTAATTTGATGATACAAACATTAACTAATATGGGAG
1 TTACATAATGCATGATATAATTTGATGATACAAACATTAACTAACATGGGAG
* *
6432495 TTACATAATGCATG-TCATAATTT-ATGATGCAAAC-TTAACTTACA-GGAGAG
1 TTACATAATGCATGAT-ATAATTTGATGATACAAACATTAACTAACATGG-GAG
6432545 TTACATAATGCATGA
1 TTACATAATGCATGA
6432560 CTTTATTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
49 2 0.04
50 25 0.44
51 11 0.19
52 19 0.33
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (52 bp):
TTACATAATGCATGATATAATTTGATGATACAAACATTAACTAACATGGGAG
Found at i:6432623 original size:39 final size:39
Alignment explanation
Indices: 6432579--6432654 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
6432569 ATGCAGAACA
6432579 CATATTAATAATGTTCAAACTATGACATAATTAAAGATT
1 CATATTAATAATGTTCAAACTATGACATAATTAAAGATT
*
6432618 CATATTAATGATGTTCAAACTATGACATAATTAAAGA
1 CATATTAATAATGTTCAAACTATGACATAATTAAAGA
6432655 CACAAACTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (39 bp):
CATATTAATAATGTTCAAACTATGACATAATTAAAGATT
Found at i:6435177 original size:25 final size:25
Alignment explanation
Indices: 6435123--6435177 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
6435113 AATCATTAAA
*
6435123 TTTAATTTAATATTAAGACAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
6435148 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
6435172 TATTAA
1 T-TTAA
6435178 GATAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:6435348 original size:67 final size:67
Alignment explanation
Indices: 6435215--6435350 Score: 175
Period size: 67 Copynumber: 2.0 Consensus size: 67
6435205 AAATATATTA
* * ** * *
6435215 AAATAATATTATTTTTAGGATACTTAATCTAAAATTAAATTCTTTGATAGAGTCCTAATAGGAGT
1 AAATAATAATATTTTAAAAATACTTAATCTAAAATCAAATTCTTTGATAGAGTCCTAATAGAAGT
6435280 GT
66 GT
* * *
6435282 AAATAATAATATTTTAAAAATACTTAATTTAAAATCAAATTCTTTGGTAGAGT-CTCGATAGAAG
1 AAATAATAATATTTTAAAAATACTTAATCTAAAATCAAATTCTTTGATAGAGTCCT-AATAGAAG
6435346 TGT
65 TGT
6435349 AA
1 AA
6435351 CTCTTTTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 2 0.03
67 57 0.97
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (67 bp):
AAATAATAATATTTTAAAAATACTTAATCTAAAATCAAATTCTTTGATAGAGTCCTAATAGAAGT
GT
Found at i:6435508 original size:60 final size:60
Alignment explanation
Indices: 6435442--6435560 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
6435432 ACCCCGAGCT
*
6435442 GGTTTGGTTGTTGTTGGTTCGGTTCGAGCCAGTGATGGGCCAACCGATCTGGTCTAGCCC
1 GGTTTGGTTGTTGTTGGTTCGGTTCGAGCCAGTGATGGCCCAACCGATCTGGTCTAGCCC
6435502 GGTTTGGTTGTTGTTGGTTCGGTTCGAGCCAGTGATGGCCCAACCGATCTGGTCTAGCC
1 GGTTTGGTTGTTGTTGGTTCGGTTCGAGCCAGTGATGGCCCAACCGATCTGGTCTAGCC
6435561 ATTGGTTGGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.12, C:0.22, G:0.34, T:0.32
Consensus pattern (60 bp):
GGTTTGGTTGTTGTTGGTTCGGTTCGAGCCAGTGATGGCCCAACCGATCTGGTCTAGCCC
Found at i:6435661 original size:19 final size:19
Alignment explanation
Indices: 6435637--6435674 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6435627 TCGGTTTTGG
*
6435637 GCCAGGTCTAATTTACTAT
1 GCCAGGCCTAATTTACTAT
6435656 GCCAGGCCTAATTTACTAT
1 GCCAGGCCTAATTTACTAT
6435675 CTTAGGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (19 bp):
GCCAGGCCTAATTTACTAT
Found at i:6444195 original size:14 final size:14
Alignment explanation
Indices: 6444176--6444205 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6444166 GATAATGTTA
6444176 GATCAAATAAAACT
1 GATCAAATAAAACT
6444190 GATCAAATAAAACT
1 GATCAAATAAAACT
6444204 GA
1 GA
6444206 ATGTGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (14 bp):
GATCAAATAAAACT
Found at i:6450130 original size:25 final size:25
Alignment explanation
Indices: 6450102--6450151 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
6450092 AAATGCATGG
*
6450102 TTTAATTAATATGCAAACTAAATGA
1 TTTAATTAAGATGCAAACTAAATGA
6450127 TTTAATTAAGATGCAAACTAAATGA
1 TTTAATTAAGATGCAAACTAAATGA
6450152 ACAAATGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (25 bp):
TTTAATTAAGATGCAAACTAAATGA
Found at i:6450418 original size:31 final size:33
Alignment explanation
Indices: 6450342--6450430 Score: 121
Period size: 31 Copynumber: 2.8 Consensus size: 33
6450332 AAATGCTACT
6450342 CACATAATGCAAGACATAATTTAAA-GATTCAAA
1 CACATAATGCAAGACATAA-TTAAATGATTCAAA
*
6450375 CACATAATGCAAGTCATAATTAAATG-TT-AAA
1 CACATAATGCAAGACATAATTAAATGATTCAAA
* *
6450406 CATATAACGCAAGACATAATTAAAT
1 CACATAATGCAAGACATAATTAAAT
6450431 AAGCAAGCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 25 0.49
32 7 0.14
33 19 0.37
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (33 bp):
CACATAATGCAAGACATAATTAAATGATTCAAA
Found at i:6459269 original size:50 final size:50
Alignment explanation
Indices: 6459145--6459386 Score: 238
Period size: 50 Copynumber: 4.8 Consensus size: 50
6459135 AGCTGAAGCT
* * * * * *
6459145 ATCTGATACGCATAGTAGCCTGCACTTTGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * *
6459194 ATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * * *
6459244 ATCTGATACACGTAGTATCCTGCACTTAGTACTACACACGTGATCGAAGTC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CC
* * * * * *
6459295 AT-TGAGTACGCATAGTAGTCTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGA-TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * *
6459344 AGTATGGTACACGTAGTAGCCTGCACTTAGTACTACAAACGTG
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
6459387 TATTCACAAT
Statistics
Matches: 156, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 40 0.26
50 78 0.50
51 38 0.24
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:6461198 original size:26 final size:26
Alignment explanation
Indices: 6461164--6461216 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6461154 TCAAACATGC
6461164 ATTTAGGTAAATTTAACC-CTAGGGGT
1 ATTTAGGT-AATTTAACCACTAGGGGT
* *
6461190 ATTTCGGTAATTTATCCACTAGGGGT
1 ATTTAGGTAATTTAACCACTAGGGGT
6461216 A
1 A
6461217 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (26 bp):
ATTTAGGTAATTTAACCACTAGGGGT
Found at i:6462674 original size:26 final size:26
Alignment explanation
Indices: 6462643--6462750 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
6462633 TGAAATGCCC
*
6462643 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
6462669 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
6462695 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
6462721 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6462747 ATCA
1 ATCA
6462751 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6466731 original size:44 final size:43
Alignment explanation
Indices: 6466667--6466754 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 43
6466657 ACCTGAGTGT
*
6466667 GATCAATGTGGAAGACGACATTTTGGAGAGTGCTGGGGAAAGA
1 GATCAATGTGGAAGACGACATTTTGGAAAGTGCTGGGGAAAGA
*
6466710 GNATCAATGTGGAAGATGACATTTTGGAAAGTGCTGGGGAAAGA
1 G-ATCAATGTGGAAGACGACATTTTGGAAAGTGCTGGGGAAAGA
6466754 G
1 G
6466755 TAATAACCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.33, C:0.08, G:0.36, T:0.22
Consensus pattern (43 bp):
GATCAATGTGGAAGACGACATTTTGGAAAGTGCTGGGGAAAGA
Found at i:6477057 original size:40 final size:40
Alignment explanation
Indices: 6476959--6477064 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
6476949 TGCGAGTACC
* * *
6476959 TGTCAACTTGTGTGAGCAACCCGTGTTGTTATGTCTTGAT
1 TGTCAACTTGTGTGAGCAGCCCGTGTTGTTACGTCCTGAT
* *
6476999 TGTCAGCTTGTGTGAGCAGCCTGTGTTGTTACGTCCTGAT
1 TGTCAACTTGTGTGAGCAGCCCGTGTTGTTACGTCCTGAT
6477039 TGTCAACTTGTGTGAGCAGGCCCGTG
1 TGTCAACTTGTGTGAGCA-GCCCGTG
6477065 ATTAGCTCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 52 0.90
41 6 0.10
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (40 bp):
TGTCAACTTGTGTGAGCAGCCCGTGTTGTTACGTCCTGAT
Found at i:6479834 original size:49 final size:47
Alignment explanation
Indices: 6479774--6480132 Score: 540
Period size: 47 Copynumber: 7.6 Consensus size: 47
6479764 GATAATTGTG
* *
6479774 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
6479821 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
6479868 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
6479917 ATGTGAAAGTGTATATATATGTGCTAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
6479966 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
6480013 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
6480060 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
*
6480107 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
6480133 TCCCGAAGGG
Statistics
Matches: 289, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
46 2 0.01
47 192 0.66
48 2 0.01
49 93 0.32
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:6479844 original size:96 final size:96
Alignment explanation
Indices: 6479738--6480130 Score: 385
Period size: 96 Copynumber: 4.1 Consensus size: 96
6479728 TACATGATAG
**
6479738 TATATGTGATATGTGAAGTATATTTGGATAAT-TG-TG-ATGTGAATGTATATATATGTGATAAG
1 TATATGTGATATGTGAAG-ATA--TGGCCAATGTGATGAATGTGAATGTATATATATGTGATAAG
6479800 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
63 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
* **
6479834 TATATGTGATAAG-GCCGA-ATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATGTGATATGTGAAGATATGGCCAATGTGATGAATGTG-AA-TGTATATATATGTGATAAGG
6479897 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
64 CCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
* * *** * * *
6479932 TATATGTGCTAAG-GCCTA-ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TATATGTGATATGTGAAGATATGGCCAATGTGATGAATGTGAATGTATATATATGTGATAAGGCC
*
6479995 TAATAGCCGATGTGATGAATGTGAAAGTGTA
66 TAATGGCCGATGTGATGAATGTGAAAGTGTA
*** * * * *
6480026 TATATGTGATGA-G-GCCTA-ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA-CAGAG
1 TATATGTGAT-ATGTGAAGATATGGCCAATGTGATGAATGTGAATGTATATATATGTGATAAG-G
* * * * *
6480087 CCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
64 CCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
6480120 TAAATGTGATA
1 TATATGTGATA
6480131 AGTCCCGAAG
Statistics
Matches: 268, Mismatches: 20, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
91 6 0.02
92 2 0.01
93 6 0.02
94 98 0.37
95 5 0.02
96 111 0.41
97 2 0.01
98 38 0.14
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.31
Consensus pattern (96 bp):
TATATGTGATATGTGAAGATATGGCCAATGTGATGAATGTGAATGTATATATATGTGATAAGGCC
TAATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:6488733 original size:54 final size:54
Alignment explanation
Indices: 6488669--6488773 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
6488659 GGCCATGCGA
*
6488669 CTTGACACACAGGCCTGTGAGGTTATTTCGAGTGTTACACGGCCTAGCACACGG
1 CTTGACACACAGGCCTGTGAGGTCATTTCGAGTGTTACACGGCCTAGCACACGG
*
6488723 CTTGACACACAGGCCTGTGAGGTCATTTCGAGTGTTACACGGCCTGGCACA
1 CTTGACACACAGGCCTGTGAGGTCATTTCGAGTGTTACACGGCCTAGCACA
6488774 TAGTTGTGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.24
Consensus pattern (54 bp):
CTTGACACACAGGCCTGTGAGGTCATTTCGAGTGTTACACGGCCTAGCACACGG
Found at i:6492575 original size:9 final size:9
Alignment explanation
Indices: 6492548--6492584 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6492538 TGAGTTTTCG
6492548 AATTCGAAT
1 AATTCGAAT
* *
6492557 AACTCAAAT
1 AATTCGAAT
6492566 AATTCGAAT
1 AATTCGAAT
6492575 AATTCGAAT
1 AATTCGAAT
6492584 A
1 A
6492585 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6492931 original size:17 final size:17
Alignment explanation
Indices: 6492904--6492945 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
6492894 ACTCACCCTA
*
6492904 TTTATTTCCCCTCAAACT
1 TTTATTTCCCC-AAAACT
6492922 TTTA-TTCCCCAAAACTT
1 TTTATTTCCCCAAAAC-T
6492939 TTTATTT
1 TTTATTT
6492946 TTCCTCAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATTTCCCCAAAACT
Found at i:6493479 original size:5 final size:5
Alignment explanation
Indices: 6493469--6493494 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6493459 GAACAAATAT
6493469 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
6493495 ATTCCTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:6498795 original size:20 final size:20
Alignment explanation
Indices: 6498772--6498834 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
6498762 TACTTCGATC
6498772 CCCTAAATTGCACTTACGTG
1 CCCTAAATTGCACTTACGTG
* * * ** *
6498792 CCCTTATTTGTACTTTGGTA
1 CCCTAAATTGCACTTACGTG
*
6498812 CCCTGAATTGCACTTACGTG
1 CCCTAAATTGCACTTACGTG
6498832 CCC
1 CCC
6498835 CTGTCTGTAC
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (20 bp):
CCCTAAATTGCACTTACGTG
Found at i:6498955 original size:40 final size:40
Alignment explanation
Indices: 6498729--6498961 Score: 218
Period size: 40 Copynumber: 5.8 Consensus size: 40
6498719 CACTTAATTA
* ** *
6498729 TACCCTTGAATTGCGCTTACGTGCCTATGTTTGTACTTCGA
1 TACCC-TGAATTGCACTTACGTGCCCCTGTTTGTACTTCGG
* * * * *
6498770 TCCCCTAAATTGCACTTACGTGCCCTTATTTGTACTTTGG
1 TACCCTGAATTGCACTTACGTGCCCCTGTTTGTACTTCGG
* *
6498810 TACCCTGAATTGCACTTACGTGCCCCTGTCTGTACTTCAG
1 TACCCTGAATTGCACTTACGTGCCCCTGTTTGTACTTCGG
* * * * **
6498850 TACCCCTGAATTTCACTTATGT-TCCCT-ATTGTACTTCAA
1 TA-CCCTGAATTGCACTTACGTGCCCCTGTTTGTACTTCGG
* * *
6498889 CACCCCCTGAATTGTAGTTACGTGCCCCTGTTTGTACTTCGG
1 TA--CCCTGAATTGCACTTACGTGCCCCTGTTTGTACTTCGG
* *
6498931 TACCCTAAATTGCACATACGTGCCCCTGTTT
1 TACCCTGAATTGCACTTACGTGCCCCTGTTT
6498962 ACACTCCAAT
Statistics
Matches: 153, Mismatches: 35, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
39 10 0.07
40 108 0.71
41 25 0.16
42 10 0.07
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.36
Consensus pattern (40 bp):
TACCCTGAATTGCACTTACGTGCCCCTGTTTGTACTTCGG
Found at i:6511167 original size:41 final size:41
Alignment explanation
Indices: 6511108--6511190 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
6511098 TATCCCATAC
*
6511108 AATGAACCATGTTCGATACATATGAACAATAGGAATGACAA
1 AATGAACCATGTTCGATACATATGAACAACAGGAATGACAA
*
6511149 AATGAACCATGTTTGATACATATGAACAACAGGAATGACAA
1 AATGAACCATGTTCGATACATATGAACAACAGGAATGACAA
6511190 A
1 A
6511191 CGATTCGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (41 bp):
AATGAACCATGTTCGATACATATGAACAACAGGAATGACAA
Found at i:6511175 original size:20 final size:20
Alignment explanation
Indices: 6511104--6511175 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
6511094 AGAATATCCC
*
6511104 ATACA-ATGAACCATGTTCG
1 ATACATATGAACCATGTTTG
* **
6511123 ATACATATGAACAATAGGAATG
1 ATACATATGAACCAT--GTTTG
* *
6511145 ACA-AAATGAACCATGTTTG
1 ATACATATGAACCATGTTTG
6511164 ATACATATGAAC
1 ATACATATGAAC
6511176 AACAGGAATG
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
19 10 0.26
20 15 0.39
21 9 0.24
22 4 0.11
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
ATACATATGAACCATGTTTG
Found at i:6513498 original size:46 final size:45
Alignment explanation
Indices: 6513448--6513623 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 45
6513438 TGGTTGAGCA
6513448 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
6513494 TCCGAACTCGTTGAGTTGAGTTCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
6513541 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
6513587 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6513624 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 66 0.61
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:6513604 original size:93 final size:93
Alignment explanation
Indices: 6513445--6513615 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
6513435 GGATGGTTGA
*
6513445 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
*
6513510 TGAGTTCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
6513538 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
6513602 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
6513616 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:6517670 original size:49 final size:48
Alignment explanation
Indices: 6517567--6517919 Score: 182
Period size: 46 Copynumber: 7.5 Consensus size: 48
6517557 ATGCCGACGC
* ** * * *
6517567 CATGTCCCAGACATGGTCTTACACTGGCTAGC--ACATCAAAGTCGATG
1 CATGTCCCAGACA-GGTCTTACACTGACTTTCATATATCGAGGTCGATG
*
6517614 CCATGTCCCAGACAAGTCTTACACTGACTTTCATATATCGAGGTCGATG
1 -CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGTCGATG
* * * * * *
6517663 CCATGTCCCAGGCAGGTCTTATAGTGGCTCTCATCTATC-AGTGTCGATG
1 -CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG-GTCGATG
* * * * * *
6517712 CCATGT-CCAAACAGGTCTTACACTGAC--ACAGA-A-CAAGCT-TATG
1 -CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGTCGATG
* * *
6517755 ACATGTCCTAGACAGGTCTTACACT-AGCTTGT-ATATCTTGAGGTCGATG
1 -CATGTCCCAGACAGGTCTTACACTGA-CTT-TCATATATCGAGGTCGATG
* * * * *
6517804 CATGTCCCAGACATGTCTTACGCT-AGCTTTC--ATCTC-ACTGCCGATG
1 CATGTCCCAGACAGGTCTTACACTGA-CTTTCATATATCGA-GGTCGATG
* * * * * *
6517850 CATGTCCCAGACATGTCTTACACTGGCTCTCATA-GT-GTGGCCGATG
1 CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGTCGATG
* *
6517896 CATGTCCCAAACATGTCTTACACT
1 CATGTCCCAGACAGGTCTTACACT
6517920 AGCACACATA
Statistics
Matches: 240, Mismatches: 47, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
43 9 0.04
44 19 0.08
45 4 0.02
46 71 0.30
47 16 0.07
48 61 0.25
49 60 0.25
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGTCGATG
Found at i:6526643 original size:29 final size:29
Alignment explanation
Indices: 6526610--6526683 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
6526600 GTTGTGAGAT
* *
6526610 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
6526639 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
6526668 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
6526684 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Done.