Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008733.1 Hibiscus syriacus cultivar Beakdansim tig00111806_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: 774200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:152854 original size:20 final size:20
Alignment explanation
Indices: 152825--152869 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
152815 CCTATCTCAT
* * *
152825 TCTTCTTCTTGTTTTTCTTC
1 TCTTCATCTTCTTTATCTTC
152845 TCTTCATCTTCTTTATCTTC
1 TCTTCATCTTCTTTATCTTC
152865 T-TTCA
1 TCTTCA
152870 CCATCAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.07, C:0.27, G:0.02, T:0.64
Consensus pattern (20 bp):
TCTTCATCTTCTTTATCTTC
Found at i:154243 original size:20 final size:21
Alignment explanation
Indices: 154213--154252 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
154203 AGCTGTTAGG
154213 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
154234 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
154253 CTATATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:155826 original size:17 final size:16
Alignment explanation
Indices: 155804--155853 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
155794 ATTTCAAAAA
155804 TTTTATTTTCTTTTTT
1 TTTTATTTTCTTTTTT
155820 CTTTTATTTTCTTTATTT
1 -TTTTATTTTCTTT-TTT
*
155838 TCTT-TTTTCTTTTTT
1 TTTTATTTTCTTTTTT
155853 T
1 T
155854 CATTTCTCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 16 0.52
18 3 0.10
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTCTTTTTT
Found at i:155836 original size:9 final size:8
Alignment explanation
Indices: 155809--155854 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
155799 AAAAATTTTA
155809 TTTTC-TT
1 TTTTCTTT
155816 TTTTCTTTT
1 TTTTC-TTT
155825 ATTTTCTTT
1 -TTTTCTTT
155834 ATTTTC-TT
1 -TTTTCTTT
155842 TTTTCTTT
1 TTTTCTTT
155850 TTTTC
1 TTTTC
155855 ATTTCTCCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 10 0.29
8 9 0.26
9 11 0.31
10 5 0.14
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:184108 original size:8 final size:8
Alignment explanation
Indices: 184096--184163 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 8
184086 AAGCATAATT
*
184096 AAAATAAT
1 AAAATAAA
184104 AAAATAACA
1 AAAATAA-A
*
184113 ATAATTAAA
1 A-AAATAAA
184122 AAAATAAA
1 AAAATAAA
184130 AAACTATAAA
1 AAA--ATAAA
* *
184140 AACATAAT
1 AAAATAAA
*
184148 AGAATAAA
1 AAAATAAA
184156 AAAATAAA
1 AAAATAAA
184164 TACAAGTTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
8 32 0.68
9 3 0.06
10 12 0.26
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (8 bp):
AAAATAAA
Found at i:184118 original size:23 final size:23
Alignment explanation
Indices: 184090--184154 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
184080 ATTAACAAGC
184090 ATAATTAAAATAATAAAATAACA
1 ATAATTAAAATAATAAAATAACA
* *
184113 ATAATTAAAAAAATAAAA-AACT
1 ATAATTAAAATAATAAAATAACA
*
184135 ATAA--AAACATAATAGAATAA
1 ATAATTAAA-ATAATAAAATAA
184155 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.08
21 7 0.19
22 9 0.25
23 17 0.47
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (23 bp):
ATAATTAAAATAATAAAATAACA
Found at i:185744 original size:3 final size:3
Alignment explanation
Indices: 185736--185800 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
185726 AGTTGTAAAT
* * * * *
185736 TAA TAA TAA TAA TAA AAA TAA TAT TAC TAT TAA TAA -AA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
185783 AAA TAA TATA TATA TAA T
1 TAA TAA TA-A TA-A TAA T
185801 TTGAAAAATG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 41 0.82
4 7 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:188803 original size:16 final size:16
Alignment explanation
Indices: 188782--188824 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
188772 TTGTATTCCC
188782 GGGTCTGGATCAATCT
1 GGGTCTGGATCAATCT
*
188798 GGGTCTGGATTAATCT
1 GGGTCTGGATCAATCT
*
188814 GGGCCTGGATC
1 GGGTCTGGATC
188825 TGCTTGGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.30
Consensus pattern (16 bp):
GGGTCTGGATCAATCT
Found at i:188925 original size:3 final size:3
Alignment explanation
Indices: 188919--188998 Score: 65
Period size: 3 Copynumber: 26.0 Consensus size: 3
188909 TAATATTATT
* * *
188919 TAA TAA TATA TAA TAA TAA -CA TATA TAA CAA TAG T-A TAA TATA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA
* *
188965 TTA TATA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
188999 GTAAGATCGA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
2 2 0.03
3 47 0.77
4 12 0.20
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:189333 original size:20 final size:20
Alignment explanation
Indices: 189280--189321 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
189270 TTTACAGATG
*
189280 ACCCGGAGGATTTACGAATT
1 ACCCAGAGGATTTACGAATT
189300 ACCCAGAGGATTTACGAATT
1 ACCCAGAGGATTTACGAATT
189320 AC
1 AC
189322 TCGAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
ACCCAGAGGATTTACGAATT
Found at i:189408 original size:139 final size:139
Alignment explanation
Indices: 189184--189438 Score: 420
Period size: 139 Copynumber: 1.8 Consensus size: 139
189174 ACTATTCACC
*
189184 CGAAGGATTTAATTTTCTAGAACATTAAACGAGAAGCTTTGAAAATCGCTATCTCATTTTCATGC
1 CGAAGGATTTAATTTTCTAGAACATTAAACGAGAAACTTTGAAAATCGCTATCTCATTTTCATGC
** * * *
189249 GAAAACATCATACCTTGAGGTTTTACAGATGACCCGGAGGATTTACGAATTACCCAGAGGATTTA
66 GAAAACATCATACCCCGAGGTTGTACAGATGACCCAGAGGATTTACAAATTACCCAGAGGATTTA
189314 CGAATTACT
131 CGAATTACT
* *
189323 CGAAGGATTTATTTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGC
1 CGAAGGATTTAATTTTCTAGAACATTAAACGAGAAACTTTGAAAATCGCTATCTCATTTTCATGC
* *
189388 GAAAACATCCTACCCCGAGGTTGTACATATGACCCAGAGGATTTACAAATT
66 GAAAACATCATACCCCGAGGTTGTACAGATGACCCAGAGGATTTACAAATT
189439 CGTGGGAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 106 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (139 bp):
CGAAGGATTTAATTTTCTAGAACATTAAACGAGAAACTTTGAAAATCGCTATCTCATTTTCATGC
GAAAACATCATACCCCGAGGTTGTACAGATGACCCAGAGGATTTACAAATTACCCAGAGGATTTA
CGAATTACT
Found at i:198062 original size:3 final size:3
Alignment explanation
Indices: 198056--198157 Score: 77
Period size: 3 Copynumber: 34.0 Consensus size: 3
198046 TAATATTATT
* * * *
198056 TAA TAA TAC TAA TAC TAA TATA TAA TAA TAA -CA TATA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
* *
198102 T-A TAA TATA TAA TTA TATA TAA TAA TAT TAA TAA T-A TAA TAA T-A
1 TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
198146 TAT TAA TAA TAA
1 TAA TAA TAA TAA
198158 GTAAGACCGG
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
2 6 0.08
3 59 0.77
4 12 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:198084 original size:25 final size:25
Alignment explanation
Indices: 198056--198157 Score: 101
Period size: 25 Copynumber: 4.2 Consensus size: 25
198046 TAATATTATT
*
198056 TAATAATACTA-ATACTAATATATAA
1 TAATAATA-TATATAATAATATATAA
*
198081 TAATAACATATATAATAATAGTATAA
1 TAATAATATATATAATAATA-TATAA
*
198107 TATATAAT-TATAT-ATAATA-ATAT
1 TA-ATAATATATATAATAATATATAA
198130 TAATAATATA-ATAAT-ATAT-TAA
1 TAATAATATATATAATAATATATAA
198152 TAATAA
1 TAATAA
198158 GTAAGACCGG
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
22 18 0.27
23 9 0.14
24 2 0.03
25 21 0.32
26 12 0.18
27 4 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (25 bp):
TAATAATATATATAATAATATATAA
Found at i:198098 original size:37 final size:34
Alignment explanation
Indices: 198055--198157 Score: 97
Period size: 37 Copynumber: 2.9 Consensus size: 34
198045 GTAATATTAT
*
198055 TTAATAATACTAATACTAATATATAATAATAACATA
1 TTAATAATA-TAATAATAATATATAATAATAA-ATA
198091 TATAATAATAGT-ATAATATATAATTATATATAAT-AATA
1 T-TAATAATA-TAATAATA-AT-A-TATA-ATAATAAATA
198129 TTAATAATATAATAAT-ATAT-TAATAATAA
1 TTAATAATATAATAATAATATATAATAATAA
198158 GTAAGACCGG
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
31 5 0.09
32 3 0.05
33 1 0.02
34 1 0.02
35 2 0.03
36 7 0.12
37 24 0.41
38 5 0.09
39 5 0.09
40 5 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (34 bp):
TTAATAATATAATAATAATATATAATAATAAATA
Found at i:198105 original size:28 final size:29
Alignment explanation
Indices: 198056--198157 Score: 90
Period size: 28 Copynumber: 3.7 Consensus size: 29
198046 TAATATTATT
* *
198056 TAATAATA-CTAATACTAATATATAATAA
1 TAATAATATATAATAATAATATATAATAA
* *
198084 TAA-CATATATAATAAT-A-GTATAATATA
1 TAATAATATATAATAATAATATATAATA-A
* *
198111 TAATTATATATAATAATATTA-ATAAT-A
1 TAATAATATATAATAATAATATATAATAA
198138 TAATAATATATTAATAATAA
1 TAATAATATA-TAATAATAA
198158 GTAAGACCGG
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
26 7 0.12
27 18 0.31
28 29 0.49
29 5 0.08
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
TAATAATATATAATAATAATATATAATAA
Found at i:198108 original size:8 final size:8
Alignment explanation
Indices: 198065--198153 Score: 77
Period size: 8 Copynumber: 11.6 Consensus size: 8
198055 TTAATAATAC
198065 TAATACTAA
1 TAATA-TAA
198074 T-ATATAA
1 TAATATAA
198081 TAATA-ACA
1 TAATATA-A
198089 T-ATATAA
1 TAATATAA
198096 TAATAGT-A
1 TAATA-TAA
198104 TAATAT-A
1 TAATATAA
198111 TAAT-T-A
1 TAATATAA
198117 T-ATATAA
1 TAATATAA
198124 TAATATTAA
1 TAATA-TAA
198133 TAATATAA
1 TAATATAA
*
198141 TAATATAT
1 TAATATAA
198149 TAATA
1 TAATA
198154 ATAAGTAAGA
Statistics
Matches: 70, Mismatches: 1, Indels: 19
0.78 0.01 0.21
Matches are distributed among these distances:
5 2 0.03
6 4 0.06
7 18 0.26
8 36 0.51
9 10 0.14
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (8 bp):
TAATATAA
Found at i:198155 original size:31 final size:31
Alignment explanation
Indices: 198065--198157 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
198055 TTAATAATAC
*
198065 TAATACTAAT-ATATAATAATAACATATATAA
1 TAATACTAATAATATAATAAT-ATATATATAA
*
198096 TAATAGT-ATAATAT-ATAAT-TATATATAA
1 TAATACTAATAATATAATAATATATATATAA
*
198124 TAATATTAATAATATAATAATATAT-TAATAA
1 TAATACTAATAATATAATAATATATAT-ATAA
198155 TAA
1 TAA
198158 GTAAGACCGG
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
28 14 0.26
29 7 0.13
30 13 0.24
31 20 0.37
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (31 bp):
TAATACTAATAATATAATAATATATATATAA
Found at i:199097 original size:2 final size:2
Alignment explanation
Indices: 199080--199114 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
199070 TTTTCCAAAC
199080 TA TA TA CTA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
199115 TTTATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:209246 original size:60 final size:60
Alignment explanation
Indices: 209153--209338 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 60
209143 ATCATGTGTT
** * * * * * **
209153 CTCAAACTATGATTTTTATTTTAAATTGGTCCTTAAGCTTTTGAATATTTTAATTTCATC
1 CTCAAACTATGATAATCATTTTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATC
*
209213 CTCAAACTATGATAATCATTTTAAATTATTCCTTAAACTTTTAAACATTCCAATTTCATC
1 CTCAAACTATGATAATCATTTTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATC
* *** * * *
209273 CTCAAACTACGACCCTCATTCTAAATTAGTCCTCAAACTTTTAAATC-TTCCAATTTTATC
1 CTCAAACTATGATAATCATTTTAAATTAGTCCTTAAACTTTTAAA-CATTCCAATTTCATC
*
209333 CCCAAA
1 CTCAAA
209339 TTCATCCAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 105 0.99
61 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (60 bp):
CTCAAACTATGATAATCATTTTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATC
Found at i:213013 original size:131 final size:130
Alignment explanation
Indices: 212807--213174 Score: 538
Period size: 131 Copynumber: 2.8 Consensus size: 130
212797 TCGATATTGA
* * * *
212807 AAATAGTAATATCTCTTCGTTTCGGTTGGAGTAAAAAATACTGCTTTAAGGCATGAGAGGTCATT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATACTGCTTTAAGGCATGAGAGGTCATT
* **
212872 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGACG
66 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAACATTGAAGTTTAAGACG
* * * *
212937 GAATAGTGATATTTCTTCATTTCGATTGGAGTAATAAATGATTACTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAAT-ACTGCTTTAAGGCATGAGAGGTCAT
* * * *
213002 TTATTCACGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCAACATTGAAGTTTAATAC
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAACATTGAAGTTTAAGAC
213067 G
130 G
* * * * *
213068 AAACAATGATATCTCTTCATTTCGATTGGAGTGATAAAATACCGCTTTAAGGCGTGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAAT-AAATACTGCTTTAAGGCATGAGAGGTCAT
213133 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTC
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTC
213175 TTAAATTTTG
Statistics
Matches: 209, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
130 33 0.16
131 172 0.82
132 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (130 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATACTGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAACATTGAAGTTTAAGACG
Found at i:214796 original size:20 final size:20
Alignment explanation
Indices: 214771--214816 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
214761 AACCAATGAA
214771 TGAAGAAATTTGAAGCTGAT
1 TGAAGAAATTTGAAGCTGAT
*
214791 TGAAGAAATTTGAAGTTGAT
1 TGAAGAAATTTGAAGCTGAT
214811 TGAAGA
1 TGAAGA
214817 TTTCCTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.26, T:0.30
Consensus pattern (20 bp):
TGAAGAAATTTGAAGCTGAT
Found at i:214979 original size:18 final size:18
Alignment explanation
Indices: 214956--214993 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
214946 CAACAACAAA
214956 CAATTTAAGGACACCAAG
1 CAATTTAAGGACACCAAG
214974 CAATTTAAGGACACCAAG
1 CAATTTAAGGACACCAAG
214992 CA
1 CA
214994 TCATCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (18 bp):
CAATTTAAGGACACCAAG
Found at i:215798 original size:31 final size:31
Alignment explanation
Indices: 215748--215808 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
215738 ACTACATTTA
*
215748 TTCGAGACTCCAAAGTCATACCTTTACCTTT
1 TTCGAGACACCAAAGTCATACCTTTACCTTT
* * * *
215779 TTCGAGACACTAAATTCATACTTTTGCCTT
1 TTCGAGACACCAAAGTCATACCTTTACCTT
215809 CTCGGGTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (31 bp):
TTCGAGACACCAAAGTCATACCTTTACCTTT
Found at i:216043 original size:19 final size:19
Alignment explanation
Indices: 216019--216063 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
216009 CTGAAGAGAG
*
216019 GCTCGAATAATTGGGGCAT
1 GCTCGAATAATTAGGGCAT
216038 GCTCGAATAATTAGGGCAT
1 GCTCGAATAATTAGGGCAT
216057 GCTCGAA
1 GCTCGAA
216064 GCAAGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
GCTCGAATAATTAGGGCAT
Found at i:216926 original size:41 final size:41
Alignment explanation
Indices: 216827--217014 Score: 225
Period size: 41 Copynumber: 4.6 Consensus size: 41
216817 TAAATACTTG
* * * *
216827 TACTTTAGTGGTGTTTTTATATAAACGCCGCTAAAGCCT-A
1 TACTTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCA
* * *
216867 TACTTTAGTGGCGTTTTTATACCAATGCCGCTATAGAGTCA
1 TACTTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCA
* * * *
216908 TACTTTATTGGCGGTTTTATACAAACGCCGCTAAAGATTCA
1 TACTTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCA
* * *
216949 TACTTTAGTGGCATTTTTATACAAATGCCACTAAAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCA
* *
216990 TACTTTGGTGGCATTTTTATACAAA
1 TACTTTAGTGGCGTTTTTATACAAA
217015 CTCTGCTATA
Statistics
Matches: 126, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 32 0.25
41 94 0.75
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCA
Found at i:218159 original size:20 final size:20
Alignment explanation
Indices: 218134--218185 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
218124 ATCTTGAAAA
218134 TGGTATCGATACCATCCTTC
1 TGGTATCGATACCATCCTTC
*
218154 TGGTATTGATACCATCCTTC
1 TGGTATCGATACCATCCTTC
218174 TGGTATCGATAC
1 TGGTATCGATAC
218186 TACCCATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (20 bp):
TGGTATCGATACCATCCTTC
Found at i:218199 original size:20 final size:19
Alignment explanation
Indices: 218176--218246 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 19
218166 CATCCTTCTG
218176 GTATCGATACTACCCATATA
1 GTATCGATACTACCCATA-A
*
218196 GTATCGATAC--CCCTTCAA
1 GTATCGATACTACCCAT-AA
218214 CCGGTATCGATACTACCCATACA
1 ---GTATCGATACTACCCATA-A
218237 GTATCGATAC
1 GTATCGATAC
218247 CCCTTCAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
18 5 0.12
19 1 0.02
20 20 0.48
21 10 0.24
22 1 0.02
23 5 0.12
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.27
Consensus pattern (19 bp):
GTATCGATACTACCCATAA
Found at i:218222 original size:21 final size:21
Alignment explanation
Indices: 218196--218267 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
218186 TACCCATATA
218196 GTATCGATACCCCTTCAACCG
1 GTATCGATACCCCTTCAACCG
* *
218217 GTATCGATACTACC--CATA-CA
1 GTATCGATAC-CCCTTCA-ACCG
218237 GTATCGATACCCCTTCAACCG
1 GTATCGATACCCCTTCAACCG
218258 GTATCGATAC
1 GTATCGATAC
218268 TACCCTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 24 0.57
22 2 0.05
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (21 bp):
GTATCGATACCCCTTCAACCG
Found at i:218225 original size:41 final size:41
Alignment explanation
Indices: 218175--218272 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
218165 CCATCCTTCT
*
218175 GGTATCGATACTACCCATATAGTATCGATACCCCTTCAACC
1 GGTATCGATACTACCCATACAGTATCGATACCCCTTCAACC
218216 GGTATCGATACTACCCATACAGTATCGATACCCCTTCAACC
1 GGTATCGATACTACCCATACAGTATCGATACCCCTTCAACC
218257 GGTATCGATACTACCC
1 GGTATCGATACTACCC
218273 TTAATAATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.26
Consensus pattern (41 bp):
GGTATCGATACTACCCATACAGTATCGATACCCCTTCAACC
Found at i:221354 original size:5 final size:5
Alignment explanation
Indices: 221344--221378 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
221334 TTAGTCCTAT
*
221344 TTTTA TTTTA TTTTA TTTTA TTTTAA TTTAA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT
221379 TGCATGTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:221355 original size:11 final size:11
Alignment explanation
Indices: 221341--221379 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
221331 ATTTTAGTCC
221341 TATTTTTATTT
1 TATTTTTATTT
221352 TA-TTTTATTT
1 TATTTTTATTT
*
221362 TATTTTAATTT
1 TATTTTTATTT
*
221373 AATTTTT
1 TATTTTT
221380 GCATGTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:222044 original size:131 final size:129
Alignment explanation
Indices: 221852--222211 Score: 531
Period size: 131 Copynumber: 2.7 Consensus size: 129
221842 GAAAATAGTA
* * *
221852 ATATCTCTTCATTTCGGTTTGAGTAATAAACGATTGCTTTAAGGTATGAGTGGTCATTTATTCTC
1 ATATCTCTTCATTTC-GATTGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTC
* *
221917 GATTGAAAATAATTAGATATTACCGTTTTCTCTCGAATCAATATTGAATTTTAAGACGGAATAAT
65 GATTG-AAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAAT
221982 G
129 G
*
221983 ATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATTG-AGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTC
* * ** *
222048 GATTGGAAATCATTAGATATTTTCGTTTTCAATCGAATCAATATTGAATTTTAAGACGAAATAGT
65 GATT-GAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAAT
222113 G
129 G
* *
222114 ATATATCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATT-GAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTC
* *
222179 AATTTGAAATAATTAGATATTATCATTTTCTCT
65 GA-TTGAAATAATTAGATATTATCGTTTTCTCT
222212 GTTAATATTA
Statistics
Matches: 205, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
130 4 0.02
131 197 0.96
132 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (129 bp):
ATATCTCTTCATTTCGATTGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCG
ATTGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAATAATG
Found at i:222999 original size:7 final size:7
Alignment explanation
Indices: 222987--223013 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
222977 AATTAATTAA
222987 AAATATT
1 AAATATT
222994 AAATATT
1 AAATATT
223001 AAATATT
1 AAATATT
223008 AAATAT
1 AAATAT
223014 GTATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:227352 original size:134 final size:134
Alignment explanation
Indices: 226938--228983 Score: 2049
Period size: 134 Copynumber: 15.2 Consensus size: 134
226928 GCAAGTCAAA
* * * *
226938 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCATCTCCCCCAGATCTAATATTCCCTCC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* * *** * * * * *
227003 GGAGGAAGAAAAACAAATACCTCTTTTTCAA-ATTTTGATATTCCCTAATTGACAGTGGAACAAG
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGA-TTTGATATTCCCTGAGTGACAGTGGAACAAG
* *
227067 TTTAC
130 TCTGC
* * * * *
227072 CTCGATTAAATCTTTCTTGAGTGACATTGGAATGGATCAACTCCCTCAGATCTGATATTCCCTTC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* * ** * * ** *
227137 AGAAGAAGTAGAAAATATCTTTTTTTTTTTCAAGATTTGATATTCCCCAAGTGGCAGTGGAACAA
66 AGAAGAAGTGGAACATATC--CCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAA
227202 GTCTGC
129 GTCTGC
* * * * * *
227208 CTCGATTCAATCTTTCCTGAATAATAGTAGAATGGATCAACTCCCCCAGATTTGATATTTCCTCC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* * * * * * * *
227273 AAAATAAATGGAACAAATCCCTCTATTTCTAGATTTGATATTCCTTGAGTGACAGTAGAACAAGT
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGT
*
227338 CTAC
131 CTGC
* * *
227342 CTCGATTCAATC-TTCCTTAAGAGACAG-GTGAATGGATCAACGT-CCTCAGATCTGATATTCCC
1 CTCGATTCAATCTTTCC-TGAGTGACAGTG-GAATGGATCAAC-TCCCCCAGATCTGATATTCCC
* * * * *
227404 TCTAGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTAATATTCCCTGAGTGACAGTGGAACA
63 TCCAGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACA
227469 AGTCTGC
128 AGTCTGC
* * ** * * *
227476 CTCGATTTAATC-TTCCTTAAGTGTTAATGGAATGGATCAACGT-CCTCAGATCTTATATTCCCT
1 CTCGATTCAATCTTTCC-TGAGTGACAGTGGAATGGATCAAC-TCCCCCAGATCTGATATTCCCT
* * * * *
227539 CCAGAAGAAGCGTAACATATCCCTATCTTTCAAGATTTAATATTCCCTGAGTGACAGTGGAATAA
64 CCAGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAA
* *
227604 TTCTAC
129 GTCTGC
* * * * * *
227610 CTCGATTCAATATTTCCTCAGTGACATTGGAATGGATCAACTCCCCCAAATATGATATTCCCTCT
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
** * * * * *
227675 AGAAGAAGTAAAATATATACCTCTTTTTCAAGATTTGATATTACCTGAGTGAAAGT-GAGACAAG
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGA-ACAAG
*
227739 TCTCC
130 TCTGC
* * *** **
227744 CTCAATTCAATCTTCCCTGAGTGACAGTGGAATGGATCAACTCCTATAGATCTGATATTCATTCC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* * * * * * *
227809 AGAAGAAGAGGAACAAATCTCTCTCTTTCAAGATTTGATATTCTCTTAGTAATAGTGGAACAAGT
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGT
*
227874 CTAC
131 CTGC
* * *
227878 CTCGATTCAATCTTTCCTGAGTGACATTGGAATGGATCAACTCCCCCAGATATGATATTCCCTCT
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* ** * * *
227943 AGAAAAAGCAGAACAAATCCCTCTTTTTCAAGATTTGATATT-CCTCGAGTGACAGTGGAGCAAG
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCT-GAGTGACAGTGGAACAAG
228007 TCTGC
130 TCTGC
* * * * ** * * * *
228012 CTCGATTC-ATCTTCCCTGAGTGACAATAGAATTGATCAACTCCCAATATATATGATGTTCCTTC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCC-CCAGATCTGATATTCCCTC
* * * * * * * * *
228076 AAAAAGAAGCGGAACAAACCCCTCTCTTTCAAGATTTAATATTCTCTGAGTGATATTGGAACAAG
65 CAGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
228141 TCTGC
130 TCTGC
* * * * * * *
228146 CTCGATTCAATC-TTCCTTGAATAATAGTAGAATGGATCAACTCCCCCAAATATGATTTTCCCTC
1 CTCGATTCAATCTTTCC-TGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTC
* * * * *
228210 CAAAAAAAGTGGAACATATCCCTCTATTTCTAGATTTGATATTCCTTGAGTGACAGTGGAACAAG
65 CAGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
228275 TCTGC
130 TCTGC
* * * *
228280 CTCGATTCAATC-TTCCTTAATTGACAGTGGAATGGATCAACGT-CCTCAGATATGATATTCCCT
1 CTCGATTCAATCTTTCC-TGAGTGACAGTGGAATGGATCAAC-TCCCCCAGATCTGATATTCCCT
* * *
228343 CCAGAAGAAGCT-GAACATATCTCTCTCTCTTTCAAGATTTAATATTCCCTAAGTGATAGTGGAA
64 CCAGAAGAAG-TGGAACATATC-C-CTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAA
*
228407 CATGTCTGC
126 CAAGTCTGC
* * * * * *
228416 CTCGATTCAATC-TTCCTTGAGTGAAAATGGAATGGATTAA-TGTCCCTAGATCTTATATTCCCT
1 CTCGATTCAATCTTTCC-TGAGTGACAGTGGAATGGATCAACT-CCCCCAGATCTGATATTCCCT
* * **
228479 CCAGAAGAAGTGG-ACTAGATCCCTCTCTTACAAGATTTGATATTCCCTGAGTGGTAGTGGAACA
64 CCAGAAGAAGTGGAAC-ATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACA
228543 AGTCTGC
128 AGTCTGC
* * * * * * *
228550 CTCGATTGAATATTCCCTGAGTGGCAGTGGAATGGATCAACGT-CCCTAGATTTGATATTACCTC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAAC-TCCCCCAGATCTGATATTCCCTC
* * * * *
228614 CAGAAGAAGCGGAACATATCCATTTCTTTCAATATTTGATATTCCCTAAGTGACAGTGGAACAAG
65 CAGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
*
228679 TCTTC
130 TCTGC
* ** * * * *
228684 CTCAATTCAATCTCCCCTGAGTGATAGTGGAATGTATCAACTCCTCCAGATCTGATATTCCCTCT
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* * *
228749 AGAAGAAGCGAAACATATCACTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAA-AATG
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAA-G
**
228813 TCTAT
130 TCTGC
* * * * *
228818 CTCGATTCAATATTCCCTGAGAGACAGTGGAATGTATCAACTCCCCCAGATCTGATATTCCCTTC
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
* * * *
228883 AGAATAAGTGGAACATATCCCTCTTTTTCAAGATTTGATATTGCTTGAGTGACAGTGGAACAAGT
66 AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGT
*
228948 CTTC
131 CTGC
* *
228952 CTCGATTCAATCTTCCCTAAGTGACAGTGGAA
1 CTCGATTCAATCTTTCCTGAGTGACAGTGGAA
228984 CAAGTCTTCC
Statistics
Matches: 1586, Mismatches: 295, Indels: 62
0.82 0.15 0.03
Matches are distributed among these distances:
133 44 0.03
134 1275 0.80
135 50 0.03
136 216 0.14
137 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (134 bp):
CTCGATTCAATCTTTCCTGAGTGACAGTGGAATGGATCAACTCCCCCAGATCTGATATTCCCTCC
AGAAGAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGT
CTGC
Found at i:228977 original size:175 final size:175
Alignment explanation
Indices: 228789--229144 Score: 502
Period size: 175 Copynumber: 2.0 Consensus size: 175
228779 AGATTTGATA
*
228789 TTCCCTGAGTGACAGTGGAA-AATGTCTAT-CTCGATTCAATATTCCCTGAGAGACAGTGGAATG
1 TTCCCTAAGTGACAGTGGAACAA-GTCT-TCCTCGATTCAATATTCCCTGAGAGACAGTGGAATG
* * * * *
228852 TATCAACTCCCCCAGATCTGATATTCCCT-TCAGAATAAGTGGAACATATCCCTCTTTTTCAAGA
64 GATCAACTCCCCCAGATCTGATATTCCCTCT-AGAATAAGCGGAACAGATCCATCTCTTTCAAGA
* * * * * *
228916 TTTGATATTGCTTGAGTGACAGTGGAACAAGTCTTCCTCGATTCAATC
128 TTTGATATTCCCTGAGTAACAATGGAACAAATCTGCCTCGATTCAATC
* * *
228964 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTTGATTCAATCTTCCCTGAGTGACAGTGGAATGGA
1 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTCGATTCAATATTCCCTGAGAGACAGTGGAATGGA
* * *
229029 TCAACTCCCCCAGATTTGATATTTCCTCTAGAATAAGCGGAACAGGTCCATCTCTTTCAAGATTT
66 TCAACTCCCCCAGATCTGATATTCCCTCTAGAATAAGCGGAACAGATCCATCTCTTTCAAGATTT
229094 GATATTCCCTGAGTAACAATGGAACAAATCTGCCTCGATTCAATC
131 GATATTCCCTGAGTAACAATGGAACAAATCTGCCTCGATTCAATC
229139 TTCCCT
1 TTCCCT
229145 GAGTTATAGT
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
174 1 0.01
175 156 0.98
176 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (175 bp):
TTCCCTAAGTGACAGTGGAACAAGTCTTCCTCGATTCAATATTCCCTGAGAGACAGTGGAATGGA
TCAACTCCCCCAGATCTGATATTCCCTCTAGAATAAGCGGAACAGATCCATCTCTTTCAAGATTT
GATATTCCCTGAGTAACAATGGAACAAATCTGCCTCGATTCAATC
Found at i:228987 original size:41 final size:41
Alignment explanation
Indices: 228930--229024 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
228920 ATATTGCTTG
228930 AGTGACAGTGGAACAAGTCTTCCTCGATTCAATCTTCCCTA
1 AGTGACAGTGGAACAAGTCTTCCTCGATTCAATCTTCCCTA
* *
228971 AGTGACAGTGGAACAAGTCTTCCTTGATTCAATCTTCCCTG
1 AGTGACAGTGGAACAAGTCTTCCTCGATTCAATCTTCCCTA
229012 AGTGACAGTGGAA
1 AGTGACAGTGGAA
229025 TGGATCAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
AGTGACAGTGGAACAAGTCTTCCTCGATTCAATCTTCCCTA
Found at i:228994 original size:309 final size:309
Alignment explanation
Indices: 228655--229214 Score: 829
Period size: 309 Copynumber: 1.8 Consensus size: 309
228645 ATATTTGATA
* *
228655 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTCAATTCAATCTCCCCTGAGTGATAGTGGAATGTA
1 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTCAATTCAATCTCCCCTGAGTGACAGTGGAATGGA
* *
228720 TCAACTCCTCCAGATCTGATATTCCCTCTAGAAGAAGCGAAACATAT-CACTCTCTTTCAAGATT
66 TCAACTCCCCCAGATCTGATATTCCCTCTAGAAGAAGCGAAACAGATCCA-TCTCTTTCAAGATT
* * * * *
228784 TGATATTCCCTGAGTGACAGTGGAA-AATGTCTATCTCGATTCAATATTCCCTGAGAGACAGTGG
130 TGATATTCCCTGAGTAACAATGGAACAA-ATCTACCTCGATTCAATATTCCCTGAGAGACAGTAG
* * * * *
228848 AATGTATCAAC-TCCCCCAGATCTGATATTCCCTTCAGAATAAGTGGAACATATCCCTCTTTTTC
194 AATGAATCAACGT-CCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAGATCCCTCTTTTTC
228912 AAGATTTGATATTGCTTGAGTGACAGTGGAACAAGTCTTCCTCGATTCAATC
258 AAGATTTGATATTGCTTGAGTGACAGTGGAACAAGTCTTCCTCGATTCAATC
** *
228964 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTTGATTCAATCTTCCCTGAGTGACAGTGGAATGGA
1 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTCAATTCAATCTCCCCTGAGTGACAGTGGAATGGA
* * * * *
229029 TCAACTCCCCCAGATTTGATATTTCCTCTAGAATAAGCGGAACAGGTCCATCTCTTTCAAGATTT
66 TCAACTCCCCCAGATCTGATATTCCCTCTAGAAGAAGCGAAACAGATCCATCTCTTTCAAGATTT
* * ** *
229094 GATATTCCCTGAGTAACAATGGAACAAATCTGCCTCGATTCAATCTTCCCTGAGTTATAGTAGAA
131 GATATTCCCTGAGTAACAATGGAACAAATCTACCTCGATTCAATATTCCCTGAGAGACAGTAGAA
229159 TGAATCAACGTCCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAGATCCCTC
196 TGAATCAACGTCCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAGATCCCTC
229215 ATAATATTCC
Statistics
Matches: 221, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
309 216 0.98
310 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (309 bp):
TTCCCTAAGTGACAGTGGAACAAGTCTTCCTCAATTCAATCTCCCCTGAGTGACAGTGGAATGGA
TCAACTCCCCCAGATCTGATATTCCCTCTAGAAGAAGCGAAACAGATCCATCTCTTTCAAGATTT
GATATTCCCTGAGTAACAATGGAACAAATCTACCTCGATTCAATATTCCCTGAGAGACAGTAGAA
TGAATCAACGTCCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAGATCCCTCTTTTTCAAG
ATTTGATATTGCTTGAGTGACAGTGGAACAAGTCTTCCTCGATTCAATC
Found at i:229102 original size:134 final size:134
Alignment explanation
Indices: 228964--229207 Score: 346
Period size: 134 Copynumber: 1.8 Consensus size: 134
228954 CGATTCAATC
* * * * * * *
228964 TTCCCTAAGTGACAGTGGAACAAGTCTTCCTTGATTCAATCTTCCCTGAGTGACAGTGGAATGGA
1 TTCCCTAAGTAACAATGGAACAAATCTGCCTCGATTCAATCTTCCCTGAGTGACAGTAGAATGAA
* * * *
229029 TCAAC-TCCCCCAGATTTGATATTTCCTCTAGAATAAGCGGAACAGGTCCATCTCTTTCAAGATT
66 TCAACGT-CCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAGGTCCATCTCTTTCAAGATT
229093 TGATA
130 TGATA
* * *
229098 TTCCCTGAGTAACAATGGAACAAATCTGCCTCGATTCAATCTTCCCTGAGTTATAGTAGAATGAA
1 TTCCCTAAGTAACAATGGAACAAATCTGCCTCGATTCAATCTTCCCTGAGTGACAGTAGAATGAA
229163 TCAACGTCCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAG
66 TCAACGTCCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAG
229208 ATCCCTCATA
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
134 94 0.99
135 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (134 bp):
TTCCCTAAGTAACAATGGAACAAATCTGCCTCGATTCAATCTTCCCTGAGTGACAGTAGAATGAA
TCAACGTCCCCAGATCTGATATTCCCTCCAGAAAAAGCGGAACAGGTCCATCTCTTTCAAGATTT
GATA
Found at i:237264 original size:23 final size:23
Alignment explanation
Indices: 237213--237281 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
237203 ACATTTTATA
* *
237213 TGGCACTTCGGTGCAATTCTACA
1 TGGCACTTCGGTGCAATTATACG
**
237236 CAGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
* *
237259 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
237282 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:239737 original size:51 final size:50
Alignment explanation
Indices: 239674--239775 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 50
239664 TGTAATTTTA
239674 ATTTGTTTTAATTTAGCCCCATGTTTTATTTATTTTTTTGTTATCCCTTGT
1 ATTTGTTTTAATTTAGCCCCATGTTTTATTTA-TTTTTTGTTATCCCTTGT
239725 ATTTGTTTTAATTTAGCCCCATGTTTTATTTATTTTTTGTTATCCCTTGT
1 ATTTGTTTTAATTTAGCCCCATGTTTTATTTATTTTTTGTTATCCCTTGT
239775 A
1 A
239776 ATTTTAGCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 19 0.37
51 32 0.63
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.60
Consensus pattern (50 bp):
ATTTGTTTTAATTTAGCCCCATGTTTTATTTATTTTTTGTTATCCCTTGT
Found at i:241469 original size:3 final size:3
Alignment explanation
Indices: 241461--241520 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
241451 CATTTTCATT
* * *
241461 TTA TTA TTA TTA TTAA TAA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
241506 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
241521 AATAATTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:243332 original size:26 final size:25
Alignment explanation
Indices: 243294--243348 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
243284 TGATATTTCT
* *
243294 AAATAAAATAAATGTCTCATTTATAA
1 AAATAAAATAAATATAT-ATTTATAA
243320 AAATATAAA-AAATATATATTTATAA
1 AAATA-AAATAAATATATATTTATAA
243345 AAAT
1 AAAT
243349 TAATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 11 0.42
27 3 0.12
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATAAAATAAATATATATTTATAA
Found at i:243343 original size:17 final size:18
Alignment explanation
Indices: 243323--243358 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
243313 TTTATAAAAA
243323 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
243340 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
243358 T
1 T
243359 TCTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:243355 original size:20 final size:19
Alignment explanation
Indices: 243330--243369 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
243320 AAATATAAAA
243330 AATATATATTTATAAAAATT
1 AATATAT-TTTATAAAAATT
* *
243350 AATATATTTTCTAATAATT
1 AATATATTTTATAAAAATT
243369 A
1 A
243370 TACTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATATTTTATAAAAATT
Found at i:247262 original size:19 final size:18
Alignment explanation
Indices: 247238--247274 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
247228 CAAGAAATTC
*
247238 GAGAATTTATTGATAAATG
1 GAGAATTAATTGA-AAATG
247257 GAGAATTAATTGAAAATG
1 GAGAATTAATTGAAAATG
247275 TGATCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (18 bp):
GAGAATTAATTGAAAATG
Found at i:252680 original size:43 final size:45
Alignment explanation
Indices: 252540--252693 Score: 224
Period size: 45 Copynumber: 3.5 Consensus size: 45
252530 CTATTTCCCA
*
252540 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCCATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*** *
252585 CATTTGTAAGCCCTTCAGAGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCCATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
252630 CAT-CATAAGCCCTTCAGTGCATGAT-TTTTCAAAGCCTT-GGGT
1 CATCCATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
252672 CATCCATAAGACCTACAGTGCA
1 CATCCATAAGCCCTTCAGTGCA
252694 GGGTTTTCAA
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 7 0.07
43 29 0.29
44 19 0.19
45 45 0.45
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (45 bp):
CATCCATAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
Found at i:252793 original size:45 final size:45
Alignment explanation
Indices: 252723--252832 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
252713 GGGAGCTTTT
* * * ** *
252723 TGATATTTTCAAAGCCTTCGGGTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
252768 TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
252813 TGATGTTTTCAAAAGCCTTC
1 TGATGTTTTC-AAAGCCTTC
252833 AGGAGCTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 49 0.84
46 9 0.16
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGAGTCATCCGTAAGACCTACAGTGCA
Found at i:252952 original size:45 final size:45
Alignment explanation
Indices: 252849--253121 Score: 358
Period size: 45 Copynumber: 6.2 Consensus size: 45
252839 TTTTTGATAG
* * *
252849 TTTCAAAGCCTTCGAGTCATCTGTAAGCCTTTCA--G--TGATGT
1 TTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
*
252890 TTTCAAA-ACCTCTGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAGCCCTC-GGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* *
252935 TTTCAAAGCCCGCGGGTCATCTGTAAGCTCTTCAGTGCATGATGT
1 TTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* *
252980 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGT
1 TTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* *
253025 TTTCAAAGCCCTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGT
1 TTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* * * * * *
253070 TTTCAAAGCCTTCGGGTCATCCGTAAGACCTACAATGCAGGATGT
1 TTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
253115 TTTCAAA
1 TTTCAAA
253122 AAGCCTTCGG
Statistics
Matches: 205, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 3 0.01
41 26 0.13
43 1 0.00
45 172 0.84
46 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (45 bp):
TTTCAAAGCCCTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
Found at i:253042 original size:135 final size:131
Alignment explanation
Indices: 252849--253480 Score: 462
Period size: 135 Copynumber: 5.0 Consensus size: 131
252839 TTTTTGATAG
*
252849 TTTCAAAGCCTTCGAGTCATCTGTAAGCCTTTCAGTGATGTTTTCAAAACCTCTGGGTCATCTGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGATGTTTTCAAAACCTCTGGGTCATCTGT
* * * *
252914 AAGCCCTTCAGTGCATGATGTTTTCAAAGCCCGCGGGTCATCTGTAAG-CTCTTCAGTGCATGAT
66 AAGCCCTTCAGTGCATGATGTTTTCAAAGCCCGCGGGTCATCCGTAAGAC-CTACAATGCAGGAT
252978 GT
130 GT
*
252980 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTT-AGTGCATGATGTTTTCAAAGCC-CTCGGGTC
1 TTTCAAAGCCTTCGGGTCATCTGTAAG-CCTTTCA--G--TGATGTTTTCAAAACCTCT-GGGTC
* * **
253043 ATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGACCTACAATGC
60 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCCGCGGGTCATCCGTAAGACCTACAATGC
253108 AGGATGT
125 AGGATGT
* * *
253115 TTTCAAAAAGCCTTCGGG--A---G---G-ATTT---TGATATTTTCAAAGCCT-TCGGGTCATC
1 TTTC--AAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGATGTTTTCAAAACCTCT-GGGTCATC
** * *
253167 TGTAAGCCCTTCAGTGCATGA--TTTTCAAAGCCTTCGGATCATCCGTAAGACCTACAGTGCAGG
63 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCCGCGGGTCATCCGTAAGACCTACAATGCAGG
*
253230 ATAT
128 ATGT
*
253234 TTTCAAAAAGCCTTC-GG------G--AG-CTTT---TGATAG-TTTCAAAGCCT-TCGGGTCAT
1 TTTC--AAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGAT-GTTTTCAAAACCTCT-GGGTCAT
* * * * * ** *
253284 CTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTC-CGGGTCATCTGTAAGCCCTTTAGTGCA
62 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCC-CGCGGGTCATCCGTAAGACCTACAATGCA
*
253348 TGATGT
126 GGATGT
* * *
253354 TTTCAAAGACCTT---GCCATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAGCCT-TCGGGAT
1 TTTCAAAG-CCTTCGGGTCATCTGTAAGCCTTTCAGTG----ATGTTTTCAAAACCTCT-GGG-T
* * * *
253415 -ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTC-CAGGTCATCTGTAAGACCTACAGT
59 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCC-CGCGGGTCATCCGTAAGACCTACAAT
253478 GCA
123 GCA
253481 AGATAATAAG
Statistics
Matches: 430, Mismatches: 37, Indels: 66
0.81 0.07 0.12
Matches are distributed among these distances:
117 2 0.00
118 54 0.13
119 62 0.14
120 40 0.09
121 44 0.10
123 1 0.00
125 2 0.00
126 3 0.01
127 3 0.01
129 3 0.01
131 27 0.06
132 7 0.02
133 79 0.18
134 3 0.01
135 87 0.20
136 1 0.00
137 12 0.03
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (131 bp):
TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGATGTTTTCAAAACCTCTGGGTCATCTGT
AAGCCCTTCAGTGCATGATGTTTTCAAAGCCCGCGGGTCATCCGTAAGACCTACAATGCAGGATG
T
Found at i:253209 original size:43 final size:44
Alignment explanation
Indices: 253144--253250 Score: 135
Period size: 43 Copynumber: 2.4 Consensus size: 44
253134 GGATTTTGAT
* * * * *
253144 ATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG-
1 ATTTTCAAAGCCTTCGGATCATCCGTAAGACCTACAGTGCAGGA
253187 ATTTTCAAAGCCTTCGGATCATCCGTAAGACCTACAGTGCAGGA
1 ATTTTCAAAGCCTTCGGATCATCCGTAAGACCTACAGTGCAGGA
253231 TATTTTCAAAAAGCCTTCGG
1 -ATTTTC--AAAGCCTTCGG
253251 GAGCTTTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 38 0.69
45 6 0.11
47 11 0.20
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
ATTTTCAAAGCCTTCGGATCATCCGTAAGACCTACAGTGCAGGA
Found at i:253237 original size:119 final size:119
Alignment explanation
Indices: 253019--253360 Score: 506
Period size: 119 Copynumber: 2.9 Consensus size: 119
253009 CTTTAGTGCA
* *
253019 TGATGTTTTCAAAGCCCTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGA-GTTTTCAAAGCCTTCG
*
253084 GGTCATCCGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGGATTT
65 GGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGA-GATTT
* *
253140 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA-TTTTCAAAGCCTTCGG
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGAGTTTTCAAAGCCTTCGG
* * *
253204 ATCATCCGTAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTTCGGGAGCTTT
66 GTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTT
* * *
253258 TGATAGTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTCCG
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGA-GTTTTCAAAGCCTTCG
* * ** *
253323 GGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAA
65 GGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAA
253361 GACCTTGCCA
Statistics
Matches: 199, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
118 49 0.25
119 62 0.31
120 44 0.22
121 44 0.22
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (119 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGAGTTTTCAAAGCCTTCGG
GTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTT
Found at i:253315 original size:45 final size:45
Alignment explanation
Indices: 253264--253480 Score: 280
Period size: 45 Copynumber: 4.9 Consensus size: 45
253254 CTTTTGATAG
* *
253264 TTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTTAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* * *
253309 TTTCAAAACCTCCGGGTCATCTGTAAGCCCTTTAGTGCATGATGT
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* *
253354 TTTCAAAGACCTT---GCCATCTGTAAGCCCTTCAGTGCATTATGT
1 TTTCAAAG-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
253397 TTTCAAAGCCTTCGGGAT-ATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAGCCTTCGGG-TCATCTGTAAGCCCTTCAGTGCATGATGT
* * * * *
253442 TTTCAAAACCTCCAGGTCATCTGTAAGACCTACAGTGCA
1 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
253481 AGATAATAAG
Statistics
Matches: 151, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
42 4 0.03
43 35 0.23
44 1 0.01
45 108 0.72
46 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (45 bp):
TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
Found at i:253434 original size:88 final size:87
Alignment explanation
Indices: 253281--253452 Score: 265
Period size: 88 Copynumber: 2.0 Consensus size: 87
253271 GCCTTCGGGT
* * *
253281 CATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTTTAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTTCAGTG
253346 CATGATGTTTTCAAAGACCTTGC
66 CATGATGTTTTCAAA-ACCTTGC
* * *
253369 CATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAGCCTTCGGGAT-ATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGG-TCATCTGTAAGCCCTTCAGT
253433 GCATGATGTTTTCAAAACCT
65 GCATGATGTTTTCAAAACCT
253453 CCAGGTCATC
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
87 4 0.05
88 72 0.94
89 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (87 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAACCTTGC
Found at i:253685 original size:3 final size:3
Alignment explanation
Indices: 253679--253735 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
253669 AATAATAATA
* * *
253679 ATT ATT AAT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
253727 A-T ATT ATT A
1 ATT ATT ATT A
253736 ATAAATAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:253691 original size:9 final size:9
Alignment explanation
Indices: 253660--253738 Score: 61
Period size: 9 Copynumber: 8.2 Consensus size: 9
253650 ATTTTCATTT
253660 TATTA-TAA
1 TATTATTAA
* *
253668 TAATAATAA
1 TATTATTAA
253677 TAATTATTAA
1 T-ATTATTAA
253687 TATTATTATTA
1 TATTATTA--A
*
253698 TTATTATAAA
1 -TATTATTAA
*
253708 TATTATTAT
1 TATTATTAA
253717 TATTATTATTA
1 TATTATTA--A
253728 TATTATTAA
1 TATTATTAA
253737 TA
1 TA
253739 AATAATTACA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.07
9 29 0.51
10 8 0.14
11 9 0.16
12 7 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATTAA
Found at i:255043 original size:25 final size:27
Alignment explanation
Indices: 255015--255066 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
255005 TGTTAGTCAT
*
255015 TGTTTAGTT-ATATTTTAATT-TTATA
1 TGTTTAATTAATATTTTAATTATTATA
255040 TGTTTAATTCAATATTTTAATTATTAT
1 TGTTTAATT-AATATTTTAATTATTAT
255067 TATTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
27 11 0.48
28 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (27 bp):
TGTTTAATTAATATTTTAATTATTATA
Found at i:255047 original size:14 final size:13
Alignment explanation
Indices: 255022--255066 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
255012 CATTGTTTAG
255022 TTATATTTTAATT
1 TTATATTTTAATT
255035 TTATATGTTTAATT
1 TTATAT-TTTAATT
**
255049 CAATATTTTAATT
1 TTATATTTTAATT
255062 ATTAT
1 -TTAT
255067 TATTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:255311 original size:139 final size:138
Alignment explanation
Indices: 255121--255484 Score: 371
Period size: 140 Copynumber: 2.6 Consensus size: 138
255111 TATAAGTTGA
**
255121 TAATATTTATTTATTTTAAAAATATTAAGAAA-ATGCAGTCTTAAAGCAACTAGATGTC-TTATT
1 TAATATTTATTTATTTT-TTAATATTAAGAAAGA--CAGTCTTAAAGCAACTAGATGTCATT-TT
* *
255184 CTGGTATTTTAAAGAATAATAAATATCATGC-TTATA-AAAAAT-ATATATTTTGCT-TTAATTT
62 CTGATATTTTAAA-AA-AATAAATATCATACTTTATATAAAAATAATATATTTT-CTATTAATTT
* *
255245 TATATAAATCATGTTTT
124 TATAGAAAT-AT-TTAT
255262 TAATATTTATTTATTTTTTAATATTAAGAAAGACAGTCTTAAAGCAACTAGATGTCATTTTCTGA
1 TAATATTTATTTATTTTTTAATATTAAGAAAGACAGTCTTAAAGCAACTAGATGTCATTTTCTGA
* * * * ** * * * *
255327 TATTTTAAATAAATTAATATCCTACTTTATATTAATTTAATTTATTTTTTATTATTTTTATGGAA
66 TATTTTAAAAAAATAAATATCATACTTTATATAAAAATAATATATTTTCTATTAATTTTATAGAA
255392 ATATTTAT
131 ATATTTAT
* * * * * *
255400 TAATATTTATTTATTTTTTAATATTAAGAAAGGGGCTGTCTTAAAGCAACTAGAAGGCCTTTTGT
1 TAATATTTATTTATTTTTTAATATTAAGAAA--GACAGTCTTAAAGCAACTAGATGTCATTTTCT
255465 GATATTTCTAAATAAAATAA
64 GATATTT-TAAA-AAAATAA
255485 TGTCTTATTT
Statistics
Matches: 189, Mismatches: 24, Indels: 19
0.81 0.10 0.08
Matches are distributed among these distances:
137 11 0.06
138 40 0.21
139 43 0.23
140 68 0.36
141 22 0.12
142 5 0.03
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (138 bp):
TAATATTTATTTATTTTTTAATATTAAGAAAGACAGTCTTAAAGCAACTAGATGTCATTTTCTGA
TATTTTAAAAAAATAAATATCATACTTTATATAAAAATAATATATTTTCTATTAATTTTATAGAA
ATATTTAT
Found at i:255524 original size:18 final size:18
Alignment explanation
Indices: 255501--255537 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
255491 ATTTATAAAA
255501 TATAAAAA-TATATATATT
1 TATAAAAATTA-ATATATT
255519 TATAAAAATTAATATATT
1 TATAAAAATTAATATATT
255537 T
1 T
255538 TCTAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAAAATTAATATATT
Found at i:255533 original size:138 final size:137
Alignment explanation
Indices: 255261--255526 Score: 297
Period size: 140 Copynumber: 1.9 Consensus size: 137
255251 AATCATGTTT
* *
255261 TTAATATTTATTTATTTTTTAATATTAAGAAAGACAGTCTTAAAGCAACTAGATGTCATTTTCTG
1 TTAATATTTATTTATTTTTTAATATTAAGAAAGACAGTCTTAAAGCAACTAGAAGGCATTTTCTG
* * * * * * * * ***
255326 ATATTTTAAATAAATTAATATCCTACTTTATATTAATTTAATTTATTTTTTATTATTTTTATGGA
66 ATATTTTAAATAAAATAATATCCTACTTTATATAAATATAA-TAAATATATATTATTTATAAAAA
255391 AATATTTA
130 AATATTTA
* * * *
255399 TTAATATTTATTTATTTTTTAATATTAAGAAAGGGGCTGTCTTAAAGCAACTAGAAGGCCTTTTG
1 TTAATATTTATTTATTTTTTAATATTAAGAAA--GACAGTCTTAAAGCAACTAGAAGGCATTTTC
* *
255464 TGATATTTCTAAATAAAATAATGTCTTA-TTTATA-AAATATAA-AAATATATA-TATTTATAAA
64 TGATATTT-TAAATAAAATAATATCCTACTTTATATAAATATAATAAATATATATTATTTATAAA
255525 AA
128 AA
255527 TTAATATATT
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
136 8 0.08
137 5 0.05
138 32 0.30
139 6 0.06
140 39 0.37
141 16 0.15
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.46
Consensus pattern (137 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAAGACAGTCTTAAAGCAACTAGAAGGCATTTTCTG
ATATTTTAAATAAAATAATATCCTACTTTATATAAATATAATAAATATATATTATTTATAAAAAA
ATATTTA
Found at i:265540 original size:5 final size:5
Alignment explanation
Indices: 265532--265670 Score: 191
Period size: 5 Copynumber: 28.2 Consensus size: 5
265522 TAAAACTATC
265532 TTATA TTATA TTATA -TATA -TATA TTATA -T-TA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
265578 TTATA -TATA TTATA -TATA TTATATA TTATA TATATA TTATA TTATA
1 TTATA TTATA TTATA TTATA -T-TATA TTATA T-TATA TTATA TTATA
*
265624 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTTATT TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA T
265671 ATGTTTATTT
Statistics
Matches: 123, Mismatches: 2, Indels: 18
0.86 0.01 0.13
Matches are distributed among these distances:
3 2 0.02
4 18 0.15
5 89 0.72
6 10 0.08
7 4 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:265556 original size:18 final size:19
Alignment explanation
Indices: 265532--265664 Score: 195
Period size: 18 Copynumber: 7.1 Consensus size: 19
265522 TAAAACTATC
265532 TTATATTATATTATATATA
1 TTATATTATATTATATATA
265551 -TATATTATATTAT-TATA
1 TTATATTATATTATATATA
265568 TTATATTATATTATATATA
1 TTATATTATATTATATATA
265587 TTATA-TATA-T-TATATA
1 TTATATTATATTATATATA
265603 TTATATATATATTATATTATA
1 TTATAT-TATATTATA-TATA
265624 TTATATTATATTATATTATA
1 TTATATTATATTATA-TATA
*
265644 TTATATTATATTATATTTA
1 TTATATTATATTATATATA
265663 TT
1 TT
265665 TTATATATGT
Statistics
Matches: 106, Mismatches: 1, Indels: 14
0.88 0.01 0.12
Matches are distributed among these distances:
16 11 0.10
17 5 0.05
18 34 0.32
19 15 0.14
20 31 0.29
21 10 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATTATATTATATATA
Found at i:265592 original size:41 final size:41
Alignment explanation
Indices: 265532--265672 Score: 198
Period size: 41 Copynumber: 3.4 Consensus size: 41
265522 TAAAACTATC
265532 TTATATTATAT-TATATATATATATTATATTATTATATTATA
1 TTATATTATATATAT-TATATATATTATATTATTATATTATA
265573 TTATATTATATATATTATATATATTATA-TATTATATATATA
1 TTATATTATATATATTATATATATTATATTATTATAT-TATA
265614 TTATATTATATTATATTATATTATATTATATTATATTATATTATA
1 TTATATTATA-TATATTATA-TATATTATA-T-TATTATATTATA
*
265659 TT-TATTTTATATAT
1 TTATATTATATATAT
265673 GTTTATTTGA
Statistics
Matches: 92, Mismatches: 1, Indels: 12
0.88 0.01 0.11
Matches are distributed among these distances:
40 8 0.09
41 38 0.41
42 12 0.13
43 14 0.15
44 6 0.07
45 6 0.07
46 8 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (41 bp):
TTATATTATATATATTATATATATTATATTATTATATTATA
Found at i:265680 original size:15 final size:16
Alignment explanation
Indices: 265532--265670 Score: 173
Period size: 16 Copynumber: 8.7 Consensus size: 16
265522 TAAAACTATC
265532 TTATATTATATTATAT
1 TTATATTATATTATAT
265548 ATATATATTATATTATTAT
1 -T-TATATTATATTA-TAT
265567 ATTATATTATATTATA-
1 -TTATATTATATTATAT
265583 -TATATTATA-TATAT
1 TTATATTATATTATAT
265597 TATATATTATA-TATAT
1 T-TATATTATATTATAT
265613 ATTATATTATATTATA-
1 -TTATATTATATTATAT
265629 TTATATTATATTATA-
1 TTATATTATATTATAT
265644 TTATATTATATTATAT
1 TTATATTATATTATAT
*
265660 TTATTTTATAT
1 TTATATTATAT
265671 ATGTTTATTT
Statistics
Matches: 113, Mismatches: 1, Indels: 17
0.86 0.01 0.13
Matches are distributed among these distances:
13 4 0.04
14 9 0.08
15 30 0.27
16 33 0.29
17 8 0.07
18 24 0.21
19 5 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTATATTATAT
Found at i:268990 original size:18 final size:17
Alignment explanation
Indices: 268967--269000 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
268957 AAAATGATAC
268967 AACTAAAAAAATAAAAAG
1 AACT-AAAAAATAAAAAG
*
268985 AACTAAATAATAAAAA
1 AACTAAAAAATAAAAA
269001 CAATTATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AACTAAAAAATAAAAAG
Found at i:269000 original size:26 final size:26
Alignment explanation
Indices: 268971--269027 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
268961 TGATACAACT
268971 AAAAAAATAAAAAG-AACTAAATAATA
1 AAAAAAAT-AAAAGCAACTAAATAATA
* * * *
268997 AAAACAATTATAGCAATTAAATAATA
1 AAAAAAATAAAAGCAACTAAATAATA
269023 AAAAA
1 AAAAA
269028 TTAAGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.19
Consensus pattern (26 bp):
AAAAAAATAAAAGCAACTAAATAATA
Found at i:271576 original size:157 final size:159
Alignment explanation
Indices: 271290--271607 Score: 604
Period size: 157 Copynumber: 2.0 Consensus size: 159
271280 AGGTTGTGTT
271290 TGAGGGAAGAGGGGAGAGGGTAGAAGGGGTTCCCATAAATGTGGTAGGTGGACGGTTGGGGTATT
1 TGAGGGAAGAGGGGAGAGGGTAGAAGGGGTTCCCATAAATGTGGTAGGTGGACGGTTGGGGTATT
271355 AAAGGAAAGGCGTGGATCATTATCCGCACCTTACGTACGTGTCAGAATTCCCGCACAGGCATGGA
66 AAAGGAAAGGCGTGGATCATTATCCGCACCTTACGTACGTGTCAGAATTCCCGCACAGGCATGGA
271420 TGACCAT-C-CCTTTCTTGACATGGCGCC
131 TGACCATCCACCTTTCTTGACATGGCGCC
271447 TGAGGGAAGAGGGGAGAGGGTAGAAGGGGTTCCCATAAATGTGGTAGGTGGACGGTTGGGGTATT
1 TGAGGGAAGAGGGGAGAGGGTAGAAGGGGTTCCCATAAATGTGGTAGGTGGACGGTTGGGGTATT
271512 AAAGGAAAGGCGTGGATCATTATCCGCACCTTACGTACGTGTCAGAATTCCCGCACAGGCATGGA
66 AAAGGAAAGGCGTGGATCATTATCCGCACCTTACGTACGTGTCAGAATTCCCGCACAGGCATGGA
271577 TGACCATCCAAGCCTTTCTTGACATGGCGCC
131 TGACCATCC-A-CCTTTCTTGACATGGCGCC
271608 AACTCGGTTA
Statistics
Matches: 157, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
157 137 0.87
158 1 0.01
161 19 0.12
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (159 bp):
TGAGGGAAGAGGGGAGAGGGTAGAAGGGGTTCCCATAAATGTGGTAGGTGGACGGTTGGGGTATT
AAAGGAAAGGCGTGGATCATTATCCGCACCTTACGTACGTGTCAGAATTCCCGCACAGGCATGGA
TGACCATCCACCTTTCTTGACATGGCGCC
Found at i:272390 original size:2 final size:2
Alignment explanation
Indices: 272383--272409 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
272373 TACATTTTTA
272383 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
272410 GGTTAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:274336 original size:22 final size:22
Alignment explanation
Indices: 274311--274403 Score: 123
Period size: 22 Copynumber: 4.2 Consensus size: 22
274301 ACATTGATCG
274311 TTGACCGGTCTGACCGTTGACT
1 TTGACCGGTCTGACCGTTGACT
*
274333 TTGACCGGTCTGACCGTTGATT
1 TTGACCGGTCTGACCGTTGACT
** *
274355 TTGATAGGTCTGGCCGTTGACT
1 TTGACCGGTCTGACCGTTGACT
* * *
274377 TTGACCAGTATGACCATTGACT
1 TTGACCGGTCTGACCGTTGACT
274399 TTGAC
1 TTGAC
274404 AAAAAAGTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (22 bp):
TTGACCGGTCTGACCGTTGACT
Found at i:276455 original size:30 final size:30
Alignment explanation
Indices: 276421--276479 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
276411 GATTTATTTA
*
276421 GTGACTAAATTA-TAAATTTGGTAAAGTTTG
1 GTGACTAAAGTATTAAATTTGG-AAAGTTTG
*
276451 GTGACTAAAGTATTAACTTTGGAAAGTTT
1 GTGACTAAAGTATTAAATTTGGAAAGTTT
276480 AGGGACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (30 bp):
GTGACTAAAGTATTAAATTTGGAAAGTTTG
Found at i:278475 original size:44 final size:45
Alignment explanation
Indices: 278425--278554 Score: 172
Period size: 46 Copynumber: 2.9 Consensus size: 45
278415 GTAAGCATGC
* * *
278425 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTAATA
1 AAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATATTAATA
* * * *
278469 AAATAAGCGTACAAGTTTATGGTATTAAATGGTAAGTATATTGATA
1 AAATAAGCCTACAAGCTTATGG-AATAAATGGTAAGTATATTAATA
*
278515 AAATAAGCCTACAAGCTTATGGAATGAATGGTAAGTATAT
1 AAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATAT
278555 GGTAAAATAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
44 19 0.26
45 18 0.24
46 37 0.50
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (45 bp):
AAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATATTAATA
Found at i:280317 original size:45 final size:46
Alignment explanation
Indices: 280234--280324 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 46
280224 AATGATCGAG
280234 AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
1 AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
280280 AAGCATCTAAGGTTGCACG-TTTCAAGACCAAAACTCTCAGATAAT
1 AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
280325 GACAAGTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 26 0.58
46 19 0.42
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (46 bp):
AAGCATCTAAGGTTGCACGCTTTCAAGACCAAAACTCTCAGATAAT
Found at i:281401 original size:21 final size:21
Alignment explanation
Indices: 281362--281401 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
281352 GATAAATCTG
**
281362 AGAAATCTTCGAATTGAAGCA
1 AGAAATCTTCGAAGAGAAGCA
*
281383 AGAAGTCTTCGAAGAGAAG
1 AGAAATCTTCGAAGAGAAG
281402 GCCCCACCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.20
Consensus pattern (21 bp):
AGAAATCTTCGAAGAGAAGCA
Found at i:281786 original size:13 final size:14
Alignment explanation
Indices: 281762--281791 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
281752 ATATATTAGA
281762 AATAATAATTTTAT
1 AATAATAATTTTAT
281776 AATAA-AATTTTAT
1 AATAATAATTTTAT
281789 AAT
1 AAT
281792 GTTTAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATTTTAT
Found at i:282708 original size:12 final size:12
Alignment explanation
Indices: 282693--282731 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
282683 TACTATGAAT
282693 AGTAACTGCTAC
1 AGTAACTGCTAC
*
282705 AGTACCTGCTAC
1 AGTAACTGCTAC
282717 AGT-ACTGCTAC
1 AGTAACTGCTAC
282728 AGTA
1 AGTA
282732 CTTCCGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (12 bp):
AGTAACTGCTAC
Found at i:282726 original size:11 final size:11
Alignment explanation
Indices: 282697--282733 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
282687 ATGAATAGTA
282697 ACTGCTACAGT
1 ACTGCTACAGT
282708 ACCTGCTACAGT
1 A-CTGCTACAGT
282720 ACTGCTACAGT
1 ACTGCTACAGT
282731 ACT
1 ACT
282734 TCCGTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (11 bp):
ACTGCTACAGT
Found at i:283334 original size:23 final size:23
Alignment explanation
Indices: 283268--283353 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
283258 TCATATAAAT
*
283268 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
283291 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
283316 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
283338 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
283354 TATAATATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.60
24 17 0.33
25 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:289769 original size:21 final size:22
Alignment explanation
Indices: 289743--289786 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
289733 GAATGCAAAT
*
289743 AGGGAATCG-TTACTCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
*
289764 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
289786 A
1 A
289787 ATACTGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (22 bp):
AGGGAATCGATTACCCTGCTAC
Found at i:290401 original size:23 final size:23
Alignment explanation
Indices: 290335--290420 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
290325 TCATATAAAT
290335 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
290358 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
290383 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
290405 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
290421 TATAATATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.58
24 18 0.34
25 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:293341 original size:19 final size:18
Alignment explanation
Indices: 293311--293347 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
293301 ATTTTTATGT
293311 ATTTTAATTTTAATTTGG
1 ATTTTAATTTTAATTTGG
*
293329 ATTTTAGATTTTATTTTGG
1 ATTTTA-ATTTTAATTTGG
293348 TTATATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (18 bp):
ATTTTAATTTTAATTTGG
Found at i:300522 original size:80 final size:82
Alignment explanation
Indices: 300357--300644 Score: 386
Period size: 82 Copynumber: 3.5 Consensus size: 82
300347 AAATTAATCC
* * *
300357 TCAAGTCTGATCTCCCCTG-AAGAATAGTGGAGCATACCTATCTTCCAAAATTGATCTGAATACT
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATACC
300421 CGAAAAAGAGGAACATA
66 CGAAAAAGAGGAACATA
* * * * * * *
300438 TCAAGTTTGATCTCCCCTGAAAAAATAGTGAAGCATA-TTGTCTTCC-AAAGTGATCTGATTACC
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATACC
*
300501 CGAAAAAGAGGAACAAA
66 CGAAAAAGAGGAACATA
* * * *
300518 TCAAGTCTAATCTCCCCTGAAAGAATCGTGGAGCAAACCCGTCTTCCAAAATTCATCT-AACTAC
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAA-TAC
300582 CCGAAAAAGAGGAACATA
65 CCGAAAAAGAGGAACATA
* *
300600 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCAGACCCGTCTT
1 TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTT
300645 TGGTCACTGA
Statistics
Matches: 180, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
80 61 0.34
81 33 0.18
82 86 0.48
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (82 bp):
TCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCATACCTGTCTTCCAAAATTGATCTGAATACC
CGAAAAAGAGGAACATA
Found at i:300772 original size:31 final size:31
Alignment explanation
Indices: 300737--300795 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
300727 TTAATTATTT
* *
300737 TTAATTTAATTACTTAACTTTC-AATTTACTC
1 TTAATTTAATCAC-TAACATTCAAATTTACTC
300768 TTAATTTAATCACTAACATTCAAATTTA
1 TTAATTTAATCACTAACATTCAAATTTA
300796 TTTTTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAATTTAATCACTAACATTCAAATTTACTC
Found at i:301100 original size:26 final size:24
Alignment explanation
Indices: 301057--301110 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
301047 AGTATAATTT
301057 TAAAACAAATAAAAATTTAAATAC
1 TAAAACAAATAAAAATTTAAATAC
**
301081 TAAAACAAAACTAAAAATTTGGATAC
1 TAAAAC-AAA-TAAAAATTTAAATAC
301107 TAAA
1 TAAA
301111 CGTAGTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 3 0.12
26 17 0.65
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (24 bp):
TAAAACAAATAAAAATTTAAATAC
Found at i:302441 original size:266 final size:266
Alignment explanation
Indices: 301919--302447 Score: 902
Period size: 266 Copynumber: 2.0 Consensus size: 266
301909 CCAATTCACT
* * *
301919 AGTCTGTAATGGGCTAGAATCGGAGGTAACCTTAGCAGGTTGTAAAGATGGCTTGGGAACCTTTA
1 AGTCTGTAATGGGCCAGAATCGGAGGCAACCTTAGCAGGTTGTAAAGAGGGCTTGGGAACCTTTA
* * *
301984 GTAGAACCTAGCCTCATATAGAGAATTTAGTAAACCTACCCTACTAGAGCCTTGTGGATAACTAG
66 GTAGAACCCAACCTCATATAGAGAATTTAGTAAACATACCCTACTAGAGCCTTGTGGATAACTAG
302049 GAGAACTAGAACACATGCGGTTAGGATTATTAATTCTCTTTGTATGCCTTTTTCAGTCTCAACTT
131 GAGAACTAGAACACATGCGGTTAGGATTATTAATTCTCTTTGTATGCCTTTTTCAGTCTCAACTT
* *
302114 TGAGTCGCATTTATTTATTGTTGCTAAGATTACATTTCTTTGACTAATCATTTCAACAAACTTGA
196 TGAGTCGCATTTATTTATTATTGCTAAGATTACATTTCTGTGACTAATCATTTCAACAAACTTGA
302179 TTCGCA
261 TTCGCA
* *
302185 AGTCTGTAATGGGCCAGAATCTGAGGCAACCTTATCAGGTAT-TAAAGAGGGCTTGGGAACC-TT
1 AGTCTGTAATGGGCCAGAATCGGAGGCAACCTTAGCAGGT-TGTAAAGAGGGCTTGGGAACCTTT
*
302248 AGCTAGAACCCAACCTCATATAGAGAATTTAGTGAACATACCCTACTAGAGCCTTGTGGATAACT
65 AG-TAGAACCCAACCTCATATAGAGAATTTAGTAAACATACCCTACTAGAGCCTTGTGGATAACT
302313 AGGAGAACTAGAACACATGCGGTTAGGATTATTAATTCTCTTTGTATGCCTTTTTTCAGTCTCAA
129 AGGAGAACTAGAACACATGCGGTTAGGATTATTAATTCTCTTTGTATGCC-TTTTTCAGTCTCAA
*
302378 CTTTGAGTTGCATTTATTTATTATTGCTAAGATTACATTTCTGTGACTAATCATTTC-ACAAACT
193 CTTTGAGTCGCATTTATTTATTATTGCTAAGATTACATTTCTGTGACTAATCATTTCAACAAACT
302442 TGATTC
258 TGATTC
302448 TTTATTTCTA
Statistics
Matches: 248, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
265 4 0.02
266 175 0.71
267 69 0.28
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (266 bp):
AGTCTGTAATGGGCCAGAATCGGAGGCAACCTTAGCAGGTTGTAAAGAGGGCTTGGGAACCTTTA
GTAGAACCCAACCTCATATAGAGAATTTAGTAAACATACCCTACTAGAGCCTTGTGGATAACTAG
GAGAACTAGAACACATGCGGTTAGGATTATTAATTCTCTTTGTATGCCTTTTTCAGTCTCAACTT
TGAGTCGCATTTATTTATTATTGCTAAGATTACATTTCTGTGACTAATCATTTCAACAAACTTGA
TTCGCA
Found at i:302959 original size:14 final size:15
Alignment explanation
Indices: 302940--302976 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
302930 CATTGTTGCA
302940 TTTGCATCTCACA-T
1 TTTGCATCTCACATT
*
302954 TTTGCA-CTCCCATT
1 TTTGCATCTCACATT
302968 TTTGCATCT
1 TTTGCATCT
302977 TTACATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.16, C:0.30, G:0.08, T:0.46
Consensus pattern (15 bp):
TTTGCATCTCACATT
Found at i:305301 original size:76 final size:76
Alignment explanation
Indices: 305172--305360 Score: 224
Period size: 76 Copynumber: 2.5 Consensus size: 76
305162 ATCTCACTTG
* * * * * *
305172 AGATTGTTTTTCTTTAAAAC-TGATTTTGTCTCACTTGAGACAGTTTTTTCTCGAAATAAGATAT
1 AGATTGTTTTTC-TTAAAACAAGATTTT-TCTCACTTGAGACAATTTTTACTCGAAAGAAAACAT
305236 TTCATTTCACTCA
64 TTCATTTCACTCA
* *
305249 ATATTGTTTTTCTTAAAACAAGATTTTTCTCTCTTGAGACAATTTTTACTCGAAAGAAAACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTTTCTCACTTGAGACAATTTTTACTCGAAAGAAAACATTT
* *
305314 TATTTTACTCA
66 CATTTCACTCA
* *
305325 AGATTG--TTT-TTAAAACAAGATTTATCTCGCTTGAGA
1 AGATTGTTTTTCTTAAAACAAGATTTTTCTCACTTGAGA
305361 TTGTTTCACT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
73 25 0.26
74 3 0.03
76 53 0.54
77 17 0.17
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTTTCTCACTTGAGACAATTTTTACTCGAAAGAAAACATTT
CATTTCACTCA
Found at i:305396 original size:39 final size:39
Alignment explanation
Indices: 305341--305630 Score: 392
Period size: 39 Copynumber: 7.5 Consensus size: 39
305331 TTTTTAAAAC
305341 AAGA-TTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * * *
305379 AATATTTCATCTTGCTTGAG-TTAGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATT-GTTTCACTCGAAACAG
* *
305418 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
305457 AATATTTTATCTCGCTTGAGATTATTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
305496 AAGATTTTATCTCACTTGAGATTGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
305535 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAATAA
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
305574 AAGATTTTATCTAGCTTGAGATAT-TTTCACTTGAAACA-
1 AAGATTTTATCTCGCTTGAGAT-TGTTTCACTCGAAACAG
*
305612 AAGA-TTTATCTCACTTGAG
1 AAGATTTTATCTCGCTTGAG
305631 GTGTTTTTTT
Statistics
Matches: 223, Mismatches: 25, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
37 13 0.06
38 9 0.04
39 199 0.89
40 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
Found at i:306005 original size:135 final size:133
Alignment explanation
Indices: 305659--306007 Score: 405
Period size: 134 Copynumber: 2.6 Consensus size: 133
305649 ACTTCCTCAA
* * * * * *
305659 TTGAGGGATTAACATTTCAAATGGAGAGTTTATAATGAGAAGAGCTCATACGATAGAGGGAGAAA
1 TTGAGGGATTAA-ATTTCAAATGGAGAGTTCATAATAAAAAGAACTCATCCGATAGAGGGAGAAG
* * * * * **
305724 AAGTTCATAATGAGAAGAGCTTGTTCGACCTATCGCTTGAGTCACGACATTTCGAATCAGAGATG
65 AAGTTCATAAT--GAAGACCTTGTTCGACCTATCGATCGAGTCACAACACTTCGAATCAGAGACA
305789 CCTCGC
128 CCTCGC
* * * *
305795 TTGAGGGATTAGCATTTCAAATGGAGAGTTCATAATGAGAAA-AACTCATCCGATAGAGGCAGAG
1 TTGAGGGATTA-AATTTCAAATGGAGAGTTCATAAT-AAAAAGAACTCATCCGATAGAGGGAGAA
* * * *
305859 GATGTTCATAATGAAGACCTTGTTCGACCTATTGATCGATTCACAACACTTCGAATTAGTA-ACA
64 GAAGTTCATAATGAAGACCTTGTTCGACCTATCGATCGAGTCACAACACTTCGAATCAG-AGACA
305923 CCTCGC
128 CCTCGC
**
305929 TTGAGGGATTGAAATTTTCAAATGGAGAGTTCATAATAAAAAGAACTCATCCGACCGAGGGAGAA
1 TTGAGGGATT-AAA-TTTCAAATGGAGAGTTCATAATAAAAAGAACTCATCCGATAGAGGGAGAA
305994 GAAGTTCATAATGA
64 GAAGTTCATAATGA
306008 GAAGAACTCA
Statistics
Matches: 179, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
134 61 0.34
135 55 0.31
136 61 0.34
137 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (133 bp):
TTGAGGGATTAAATTTCAAATGGAGAGTTCATAATAAAAAGAACTCATCCGATAGAGGGAGAAGA
AGTTCATAATGAAGACCTTGTTCGACCTATCGATCGAGTCACAACACTTCGAATCAGAGACACCT
CGC
Found at i:306046 original size:40 final size:40
Alignment explanation
Indices: 305956--306052 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
305946 TCAAATGGAG
* *
305956 AGTTCATAATAAAAAGAACTCATCCGACCGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
305996 AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
306036 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
306053 GCTTGTTCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.16
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCCGACCGAGGGAGAAGA
Found at i:307771 original size:17 final size:18
Alignment explanation
Indices: 307749--307793 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
307739 GTCTTTGTAC
*
307749 TTGTTTTTATTTTTA-TT
1 TTGTTTTTATTTTTACTG
*
307766 TTG-TTTTGTTTTTACTG
1 TTGTTTTTATTTTTACTG
307783 TT-TTTTTATTT
1 TTGTTTTTATTT
307794 AATTATGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (18 bp):
TTGTTTTTATTTTTACTG
Found at i:308787 original size:74 final size:72
Alignment explanation
Indices: 308650--308789 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 72
308640 CGTGTCCTCG
* ** *
308650 TTGAAATCCGAATTTTTACGTTAGTTGTTTATTTTTTAATGGTACCCACCCTGAAATTATATTTG
1 TTGAAATCCGAATTTTTACGTTAGCTGTACATTTTTTAATGGTAACCACCCTGAAATTATATTTG
308715 TGTCACC
66 TGTCACC
* * * *
308722 TTGAAATCTGAATTTCTTTATGTTAGCTGTACATTTTATTAATGGTAACCA-CCTTAAATTTTAT
1 TTGAAATCCGAA-TT-TTTACGTTAGCTGTACATTTT-TTAATGGTAACCACCCTGAAATTATAT
308786 TTGT
63 TTGT
308790 ATTTGTCTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
72 11 0.19
73 2 0.04
74 32 0.56
75 12 0.21
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (72 bp):
TTGAAATCCGAATTTTTACGTTAGCTGTACATTTTTTAATGGTAACCACCCTGAAATTATATTTG
TGTCACC
Found at i:315408 original size:23 final size:23
Alignment explanation
Indices: 315382--315426 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
315372 TATGGGTCGA
*
315382 GTTTGGTTTGGGCTCTGGGTTTG
1 GTTTGGTTTGGGCTCTAGGTTTG
315405 GTTTGGTTTGGGCTCTAGGTTT
1 GTTTGGTTTGGGCTCTAGGTTT
315427 TAGGTGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.02, C:0.09, G:0.40, T:0.49
Consensus pattern (23 bp):
GTTTGGTTTGGGCTCTAGGTTTG
Found at i:316107 original size:41 final size:43
Alignment explanation
Indices: 316062--316153 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 43
316052 AAGGTCATAC
* * *
316062 AGATGGCCC-GAAGGACTT-ATCATCTTGCTCAAAAGACTTA-T
1 AGATGGCCCAG-AGGACTTAAGCACCATGCTCAAAAGACTTACT
* *
316103 AGATGACCCAGAGGATTTAAGCACCATGCTCAAAAGACTTACT
1 AGATGGCCCAGAGGACTTAAGCACCATGCTCAAAAGACTTACT
316146 -GATGGCCC
1 AGATGGCCC
316154 TAATAACTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
41 14 0.33
42 27 0.64
43 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (43 bp):
AGATGGCCCAGAGGACTTAAGCACCATGCTCAAAAGACTTACT
Found at i:316576 original size:42 final size:43
Alignment explanation
Indices: 316483--316587 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 43
316473 TCTTATGAAT
*
316483 AGCCCGAAGGATTT-ATCATCTTGCTCAAAAGACTTATAGATG
1 AGCCCGAAGGATTTAATCATCATGCTCAAAAGACTTATAGATG
*** ** *
316525 AG-AAAAAGGATTTAATCATCATGCTTGAAAGACTTATTGATG
1 AGCCCGAAGGATTTAATCATCATGCTCAAAAGACTTATAGATG
* *
316567 -GCCCGAAGGACTTACTCATCA
1 AGCCCGAAGGATTTAATCATCA
316588 AGAAACCCTT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
41 9 0.18
42 40 0.82
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (43 bp):
AGCCCGAAGGATTTAATCATCATGCTCAAAAGACTTATAGATG
Found at i:316593 original size:177 final size:177
Alignment explanation
Indices: 316234--316582 Score: 509
Period size: 177 Copynumber: 2.0 Consensus size: 177
316224 GATTTAAATG
* * *
316234 AGAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAAATATCCTGCCCGAAGGTCT
1 AGAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAAACATCCTACCCAAAGGTCT
* * *** * *
316299 TATGGATAGACTGAAGGACTTATCATCTTGCTCAAAAGAATTATAGATGACCCGAATGATTTTAG
66 TATGAATAGACCGAAGGACTTATCATCTTGCTCAAAAGAATTATAGATGACAAAAAGGATTTAAG
*
316364 CGTCATGCTCGAAAGAATTACTGATGGCCCAAAGGACTTACTAAGTA
131 CATCATGCTCGAAAGAATTACTGATGGCCCAAAGGACTTACTAAGTA
*
316411 AGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAACATCCTACCCAAAGGTCT
1 AGAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAAACATCCTACCCAAAGGTCT
* * * * *
316476 TATGAATAGCCCGAAGGATTTATCATCTTGCTCAAAAGACTTATAGATGAGAAAAAGGATTTAAT
66 TATGAATAGACCGAAGGACTTATCATCTTGCTCAAAAGAATTATAGATGACAAAAAGGATTTAAG
* * * *
316541 CATCATGCTTGAAAGACTTATTGATGGCCCGAAGGACTTACT
131 CATCATGCTCGAAAGAATTACTGATGGCCCAAAGGACTTACT
316583 CATCAAGAAA
Statistics
Matches: 151, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
177 151 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (177 bp):
AGAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAAACATCCTACCCAAAGGTCT
TATGAATAGACCGAAGGACTTATCATCTTGCTCAAAAGAATTATAGATGACAAAAAGGATTTAAG
CATCATGCTCGAAAGAATTACTGATGGCCCAAAGGACTTACTAAGTA
Found at i:316715 original size:56 final size:56
Alignment explanation
Indices: 316582--316787 Score: 236
Period size: 56 Copynumber: 3.6 Consensus size: 56
316572 AAGGACTTAC
* * * * **
316582 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTC-TTAAAAATGTTCGTTTACAGCT-A
1 TCATCAAGAAACCCTT-AAAATCAGGCTTAGCTTCTTTAAAAA--TTC-ATTAGAAATAA
* * *
316640 TCATCAAGAAACCCCTAAAAACAGGCTTAGCTTCTTTAAAAATTCATTGGAAATAA
1 TCATCAAGAAACCCTTAAAATCAGGCTTAGCTTCTTTAAAAATTCATTAGAAATAA
*
316696 TCATTAAGAAACCCTTAAAATCAGGCTTAGCTTCTTTAAAAATTCATTAGAAATAA
1 TCATCAAGAAACCCTTAAAATCAGGCTTAGCTTCTTTAAAAATTCATTAGAAATAA
** *
316752 TCATCAAGAAACCTCTGCAAATCAGGCTTAGTTTCT
1 TCATCAAGAAACC-CTTAAAATCAGGCTTAGCTTCT
316788 AAAAAAAATG
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
55 4 0.03
56 68 0.53
57 34 0.27
58 22 0.17
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (56 bp):
TCATCAAGAAACCCTTAAAATCAGGCTTAGCTTCTTTAAAAATTCATTAGAAATAA
Found at i:316794 original size:113 final size:113
Alignment explanation
Indices: 316582--316794 Score: 252
Period size: 113 Copynumber: 1.9 Consensus size: 113
316572 AAGGACTTAC
* * **
316582 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAAATGTTCGTTTACAGCTATCATCAA
1 TCATCAAGAAACCCTTGAAAATCAAGCTTAGCTTCTTAAAAA-GTTCGATTACAAATATCATCAA
**
316647 GAAACCCCTAAAAACAGGCTTAGCTTCTTTAAAAATTCATTGGAAATAA
65 GAAACCCCTAAAAACAGGCTTAGCTTCTAAAAAAATTCATTGGAAATAA
* * *
316696 TCATTAAGAAACCCTT-AAAATCAGGCTTAGCTTCTTTAAAAA-TTC-ATTAGAAATAATCATCA
1 TCATCAAGAAACCCTTGAAAATCAAGCTTAGCTTC-TTAAAAAGTTCGATTACAAAT-ATCATCA
* * * *
316758 AGAAACCTCTGCAAATCAGGCTTAGTTTCTAAAAAAA
64 AGAAACCCCT-AAAAACAGGCTTAGCTTCTAAAAAAA
316795 ATGCGTCAGC
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
111 5 0.06
112 19 0.23
113 37 0.45
114 22 0.27
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (113 bp):
TCATCAAGAAACCCTTGAAAATCAAGCTTAGCTTCTTAAAAAGTTCGATTACAAATATCATCAAG
AAACCCCTAAAAACAGGCTTAGCTTCTAAAAAAATTCATTGGAAATAA
Found at i:318390 original size:2 final size:2
Alignment explanation
Indices: 318383--318414 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
318373 TCAGCTTTAT
318383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318415 ATTGCCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:322844 original size:14 final size:13
Alignment explanation
Indices: 322823--322882 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 13
322813 ATAAAAAGGG
322823 AAAT-ATAATAAT
1 AAATAATAATAAT
322835 AAAATAATAAATAAT
1 -AAATAAT-AATAAT
**
322850 AAATAATAATTTT
1 AAATAATAATAAT
322863 CAAGATAATAATAA-
1 -AA-ATAATAATAAT
322877 AAATAA
1 AAATAA
322883 AAGGGGGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 4 0.10
13 10 0.26
14 11 0.28
15 14 0.36
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:322848 original size:7 final size:7
Alignment explanation
Indices: 322824--322858 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
322814 TAAAAAGGGA
322824 AATATAAT
1 AATA-AAT
322832 AATAAAAT
1 AAT-AAAT
322840 AATAAAT
1 AATAAAT
322847 AATAAAT
1 AATAAAT
322854 AATAA
1 AATAA
322859 TTTTCAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 16 0.62
8 9 0.35
9 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:325960 original size:24 final size:25
Alignment explanation
Indices: 325913--325960 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
325903 TTGATTTAGA
* *
325913 AAAAGATAGAATTTCATATTAATATG
1 AAAAGATAGAA-TTAATATAAATATG
325939 AAAAGATAGAA-TAATATAAATA
1 AAAAGATAGAATTAATATAAATA
325961 AAAATAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
26 11 0.55
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.29
Consensus pattern (25 bp):
AAAAGATAGAATTAATATAAATATG
Found at i:326900 original size:83 final size:81
Alignment explanation
Indices: 326802--326969 Score: 241
Period size: 83 Copynumber: 2.0 Consensus size: 81
326792 AATAAAGAAA
* *
326802 TAAATCCTAATTAAAATACTTAAAACTACTTAAACTAAAATACCTAAAACAATATAAGATAAAAT
1 TAAATCCGAATTAAAACACTTAAAACTACTTAAACTAAAATACCTAAAAC---A-AAGATAAAAT
326867 ATA-A-TAAAAATAATATCC
62 ATATATTAAAAATAATATCC
* *
326885 TAAATCCGAATTAAAACACTTAAAACTATTTAAACTAAAATTCCTAAAACAAAGATAAAATATAT
1 TAAATCCGAATTAAAACACTTAAAACTACTTAAACTAAAATACCTAAAACAAAGATAAAATATAT
*
326950 ATTTAAAATAATATCC
66 ATTAAAAATAATATCC
326966 TAAA
1 TAAA
326970 ACATGAGTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
79 13 0.17
80 2 0.03
81 17 0.22
83 46 0.59
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.29
Consensus pattern (81 bp):
TAAATCCGAATTAAAACACTTAAAACTACTTAAACTAAAATACCTAAAACAAAGATAAAATATAT
ATTAAAAATAATATCC
Found at i:330724 original size:45 final size:43
Alignment explanation
Indices: 330660--330746 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
330650 CGTTTGGTCT
*
330660 AGATATTTAACGGTGTTTTTTGGATACAAACACTGCAAAAGGTTA
1 AGATATTTAACGGCG-TTTTTGGATACAAA-ACTGCAAAAGGTTA
* * *
330705 AGATATTTACCGGCGTTTTTGGATACAAATCTGCAACAGGTT
1 AGATATTTAACGGCGTTTTTGGATACAAAACTGCAAAAGGTT
330747 TGGTATATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 11 0.29
44 14 0.37
45 13 0.34
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (43 bp):
AGATATTTAACGGCGTTTTTGGATACAAAACTGCAAAAGGTTA
Found at i:330800 original size:44 final size:43
Alignment explanation
Indices: 330748--330873 Score: 162
Period size: 44 Copynumber: 2.9 Consensus size: 43
330738 CAACAGGTTT
* * *
330748 GGTATATAGAGGCGCTTTTCGGATACAAACGCCATAAAATGTGA
1 GGTATATAGCGGCG-TTTTAGGATACAAACGCCATAAAATGTCA
* *
330792 GGTATATAGCGGCGTTTTTAGGATACAAACGCCACAAAATGTCT
1 GGTATATAGCGGCG-TTTTAGGATACAAACGCCATAAAATGTCA
* * *
330836 GGTATATAGCGGCGTTTTATGTTACAAACACCATAAAA
1 GGTATATAGCGGCGTTTTAGGATACAAACGCCATAAAA
330874 AATCAGAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 20 0.28
44 52 0.72
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (43 bp):
GGTATATAGCGGCGTTTTAGGATACAAACGCCATAAAATGTCA
Found at i:340109 original size:83 final size:81
Alignment explanation
Indices: 340000--340266 Score: 286
Period size: 82 Copynumber: 3.2 Consensus size: 81
339990 ATAAGATTGT
* * *
340000 GGCGTTTGTAAAAAACGCCTCTATAGTGCTAA-TATATCGCGGCGTTTACTTAAAAAACGCCACT
1 GGCGTTTGTACAAAACGCCTCTATAGTAC-AACTCTATCGCGGCGTTTACTT-AAAAACGCCACT
*
340064 ACTGTCCAACTCTATAGC
64 AATGTCCAACTCTATAGC
* * * *
340082 GGCGTTTGTACGAAAACGGCTCTATAGTACAACTCTATCACGGTGTTTACTTAAAATCGCCACTA
1 GGCGTTTGTAC-AAAACGCCTCTATAGTACAACTCTATCGCGGCGTTTACTTAAAAACGCCACTA
*
340147 ATGTCCAACTCTATAGT
65 ATGTCCAACTCTATAGC
* * * **
340164 AGCGTTTGTACAAAATCGCCTCTATAGTTCAACTCTATCGCGGCATTTTGTTTAAAAACGCCACT
1 GGCGTTTGTACAAAA-CGCCTCTATAGTACAACTCTATCGCGGC-GTTTACTTAAAAACGCCACT
* *** *
340229 AACGTATGACTCTTTAGC
64 AATGTCCAACTCTATAGC
340247 GGCGTTTTGGTA-AAAACGCC
1 GGCG-TTT-GTACAAAACGCC
340267 GCTAACGTAC
Statistics
Matches: 154, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
81 4 0.03
82 73 0.47
83 67 0.44
84 7 0.05
85 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (81 bp):
GGCGTTTGTACAAAACGCCTCTATAGTACAACTCTATCGCGGCGTTTACTTAAAAACGCCACTAA
TGTCCAACTCTATAGC
Found at i:340115 original size:41 final size:41
Alignment explanation
Indices: 340000--340207 Score: 128
Period size: 41 Copynumber: 5.1 Consensus size: 41
339990 ATAAGATTGT
* * * *
340000 GGCGTTTGTA-AAAAACGCCTCTATAGTGCTAA-TATATCGC
1 GGCGTTTGTACAAAATCGCCTCTATAGTAC-AACTCTATAGC
* * * *
340040 GGCGTTTACTTA-AAAAACGCCACTACT-GTCCAACTCTATAGC
1 GGCGTTT--GTACAAAATCGCCTCTA-TAGTACAACTCTATAGC
*
340082 GGCGTTTGTACGAAAA-CGGCTCTATAGTACAACTCTATCA-C
1 GGCGTTTGTAC-AAAATCGCCTCTATAGTACAACTCTAT-AGC
* * * *
340123 GGTG-TT-TACTTAAAATCGCCACTA-ATGTCCAACTCTATAGT
1 GGCGTTTGTAC--AAAATCGCCTCTATA-GTACAACTCTATAGC
* * *
340164 AGCGTTTGTACAAAATCGCCTCTATAGTTCAACTCTATCGC
1 GGCGTTTGTACAAAATCGCCTCTATAGTACAACTCTATAGC
340205 GGC
1 GGC
340208 ATTTTGTTTA
Statistics
Matches: 131, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
39 3 0.02
40 18 0.14
41 68 0.52
42 38 0.29
43 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (41 bp):
GGCGTTTGTACAAAATCGCCTCTATAGTACAACTCTATAGC
Found at i:340241 original size:42 final size:41
Alignment explanation
Indices: 340195--340275 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
340185 CTATAGTTCA
* *
340195 ACTCTATCGCGGCATTTTGTTTAAAAACGCCACTAACGTATG
1 ACTCTATAGCGGCATTTTG-GTAAAAACGCCACTAACGTATG
* * *
340237 ACTCTTTAGCGGCGTTTTGGTAAAAACGCCGCTAACGTA
1 ACTCTATAGCGGCATTTTGGTAAAAACGCCACTAACGTA
340276 CATCTATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 18 0.53
42 16 0.47
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
ACTCTATAGCGGCATTTTGGTAAAAACGCCACTAACGTATG
Found at i:340856 original size:25 final size:25
Alignment explanation
Indices: 340825--340906 Score: 155
Period size: 25 Copynumber: 3.3 Consensus size: 25
340815 CTCATACCTC
340825 TGGTTCACCAAGAAGACTCCTTGCT
1 TGGTTCACCAAGAAGACTCCTTGCT
*
340850 TGGTTCACCAAGAAGACTCATTGCT
1 TGGTTCACCAAGAAGACTCCTTGCT
340875 TGGTTCACCAAGAAGACTCCTTGCT
1 TGGTTCACCAAGAAGACTCCTTGCT
340900 TGGTTCA
1 TGGTTCA
340907 ATGCTTCACT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
TGGTTCACCAAGAAGACTCCTTGCT
Found at i:342066 original size:82 final size:82
Alignment explanation
Indices: 341980--342171 Score: 228
Period size: 82 Copynumber: 2.3 Consensus size: 82
341970 ACTATTTATG
341980 AACCCTATTATGGA-GTTTATCTAAAAACACCGCTAAAGTACA-CTTTATTCCAGCCTT-TGTTA
1 AACCCTATTAT-GACGTTTATCTAAAAACACCGCTAAAGTA-ATCTTTATTCCAGCCTTAT-TTA
**
342042 AAAAAATGCCACTATAAACT
63 AAAAAACACCACTATAAACT
* * * * * **
342062 AACCCTATTATGACATTTTTCTAAAAACACCGCTAAAGTAATCTTTATTGCGGCGTTATTTGGAA
1 AACCCTATTATGACGTTTATCTAAAAACACCGCTAAAGTAATCTTTATTCCAGCCTTATTTAAAA
342127 AAACACCACTATAAACT
66 AAACACCACTATAAACT
* *
342144 AACCATATTACGACGTTTATGCTAAAAA
1 AACCCTATTATGACGTTTAT-CTAAAAA
342172 TGTCCCTAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
81 3 0.03
82 82 0.88
83 8 0.09
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (82 bp):
AACCCTATTATGACGTTTATCTAAAAACACCGCTAAAGTAATCTTTATTCCAGCCTTATTTAAAA
AAACACCACTATAAACT
Found at i:342452 original size:11 final size:11
Alignment explanation
Indices: 342418--342474 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
342408 ACTAGGGCTA
*
342418 GGGTTAGGTTT
1 GGGTTGGGTTT
* *
342429 AGGGTAGGCTTT
1 -GGGTTGGGTTT
342441 GGGTTGGGTTT
1 GGGTTGGGTTT
* *
342452 GGTTTGGGCTCT
1 GGGTTGGG-TTT
342464 GGGTTGGGTTT
1 GGGTTGGGTTT
342475 TGTTTGGGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.05, C:0.05, G:0.47, T:0.42
Consensus pattern (11 bp):
GGGTTGGGTTT
Found at i:342461 original size:23 final size:23
Alignment explanation
Indices: 342435--342540 Score: 97
Period size: 23 Copynumber: 4.6 Consensus size: 23
342425 GTTTAGGGTA
*
342435 GGCTTTGGGTTGGGT-TTGGTTTG
1 GGCTTTGGGTTGGGTACT-GTTTG
* **
342458 GGCTCTGGGTTGGGTTTTGTTTG
1 GGCTTTGGGTTGGGTACTGTTTG
* *
342481 GGCTCTGGGTCGGGTACTGTTTG
1 GGCTTTGGGTTGGGTACTGTTTG
* * *
342504 GGTTTTAGGTTGGGTCCTGTTTG
1 GGCTTTGGGTTGGGTACTGTTTG
* *
342527 GGTTTTAGGTTGGG
1 GGCTTTGGGTTGGG
342541 GCATGTTTGG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
23 71 0.97
24 2 0.03
ACGTcount: A:0.03, C:0.08, G:0.44, T:0.44
Consensus pattern (23 bp):
GGCTTTGGGTTGGGTACTGTTTG
Found at i:342547 original size:23 final size:23
Alignment explanation
Indices: 342498--342552 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
342488 GGTCGGGTAC
* *
342498 TGTTTGGGTTTTAGGTTGGGTCC
1 TGTTTGGGTTTTAGGTTGGGGCA
342521 TGTTTGGGTTTTAGGTTGGGGCA
1 TGTTTGGGTTTTAGGTTGGGGCA
342544 TGTTTGGGT
1 TGTTTGGGT
342553 ATTTCGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.47
Consensus pattern (23 bp):
TGTTTGGGTTTTAGGTTGGGGCA
Found at i:344280 original size:23 final size:23
Alignment explanation
Indices: 344250--344301 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
344240 TTTGGCTTGG
*
344250 TTTGGGCT-CAAGGTCAGGTTCAA
1 TTTGGGCTCCAA-GTCAAGTTCAA
*
344273 TTTGGGCTCCAAGTCAAGTTCTA
1 TTTGGGCTCCAAGTCAAGTTCAA
344296 TTTGGG
1 TTTGGG
344302 TTTTAGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (23 bp):
TTTGGGCTCCAAGTCAAGTTCAA
Found at i:352249 original size:57 final size:57
Alignment explanation
Indices: 352028--352250 Score: 322
Period size: 57 Copynumber: 3.9 Consensus size: 57
352018 ATAATGTCAT
*
352028 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATCA-GCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTAT-AGGCAC
* * *
352085 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGGATTTCAGTATGGGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAGGCAC
* * *
352142 TAAATGTGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCTGTATAGGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAGGCAC
* ** * *
352199 TGAGTGTTCAAAATTTTAAGAAATTAATAATTTGTTTATGAATTTTTGTATA
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATA
352251 AGAACTTTAT
Statistics
Matches: 149, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
57 149 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (57 bp):
TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAGGCAC
Found at i:352268 original size:57 final size:57
Alignment explanation
Indices: 352028--352295 Score: 306
Period size: 57 Copynumber: 4.7 Consensus size: 57
352018 ATAATGTCAT
* * *
352028 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATCAGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTAATAATTTGTTTATGAATTTCTGTATAAGCAC
* * * **
352085 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGGATTTCAGTATGGGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTAATAATTTGTTTATGAATTTCTGTATAAGCAC
* * * *
352142 TAAATGTGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCTGTATAGGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTAATAATTTGTTTATGAATTTCTGTATAAGCAC
* ** * *
352199 TGAGTGTTCAAAATTTTAAGAAATTAATAATTTGTTTATGAATTTTTGTATAAGAAC
1 TGAGTGTGCAAAAAGTTAAGAAATTAATAATTTGTTTATGAATTTCTGTATAAGCAC
* * * *
352256 TTTA-TATGCAAAAA-CTAAGAAATTATATGAATTTCTTTAT
1 -TGAGTGTGCAAAAAGTTAAGAAATTA-AT-AATTTGTTTAT
352296 TGGTATTATG
Statistics
Matches: 183, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
56 10 0.05
57 161 0.88
58 12 0.07
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (57 bp):
TGAGTGTGCAAAAAGTTAAGAAATTAATAATTTGTTTATGAATTTCTGTATAAGCAC
Found at i:352526 original size:67 final size:67
Alignment explanation
Indices: 352452--352907 Score: 646
Period size: 67 Copynumber: 6.8 Consensus size: 67
352442 TAAAAGTTTA
*
352452 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTTCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
352517 TT
66 TT
* * ** * *
352519 TGAGGCCTAACTATGCATTGACAAAAATATGTCAATTATGCCAGTTAGATGAAATGCTAAGCGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
352584 TT
66 TT
* * * * *
352586 TCAGGCCTAACTGTGCATTGACAGAAAGGTATTAATTATGCTAGTTAGATGAAAGGCTAAGTTCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
352651 TT
66 TT
* *
352653 TGAGGGCTAATTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
352718 TT
66 TT
* * *
352720 TTAGGCCTAATTGTGCATTCG-CAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCATT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGC
352784 CTT
65 CTT
* * *
352787 TGAGGTCTAACTGTGCATTGACAGATAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
352852 TT
66 TT
* * * * *
352854 TGAGACCTAGA-TGTTCATTTGGCAGAAAGGTGTCAATTATGCAAGTAAGATGAA
1 TGAGGCCTA-ACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
352908 CGGTTAAAGA
Statistics
Matches: 343, Mismatches: 42, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
66 1 0.00
67 309 0.90
68 33 0.10
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (67 bp):
TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
TT
Found at i:352996 original size:81 final size:80
Alignment explanation
Indices: 352876--353146 Score: 327
Period size: 81 Copynumber: 3.4 Consensus size: 80
352866 GTTCATTTGG
* * * *
352876 CAGAAAGGTGTCAATTATGCAAGTAAGATGAACGGTTAAAGACCATTGAGTAAAAGTTAAATGGC
1 CAGAAAGGTGTCAATTATGCAAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGC
352941 CTAGCTGTGCATTTGA
66 CTAGCTGTGCATTT-A
* * *
352957 TAGAAAGGAT-TCAATTATGCCAGTTAGATGAACGATTAAAGATCGTTGAGTAAAAGATAAATGG
1 CAGAAAGG-TGTCAATTATGCAAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGG
*
353021 CCTAGCTGTTCATTT-
65 CCTAGCTGTGCATTTA
* * *
353036 -TG-CAGGTGTCAATTATATC-AGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGG
1 CAGAAAGGTGTCAATTAT-GCAAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGG
* *
353098 CCTAACTATGCATTTA
65 CCTAGCTGTGCATTTA
* * *
353114 GCAGAAAAGTATCAATCATGCAAGTTAGATGAA
1 -CAGAAAGGTGTCAATTATGCAAGTTAGATGAA
353147 AGGTTAAATG
Statistics
Matches: 161, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
76 1 0.01
77 65 0.40
78 2 0.01
80 2 0.01
81 90 0.56
82 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (80 bp):
CAGAAAGGTGTCAATTATGCAAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGC
CTAGCTGTGCATTTA
Found at i:353169 original size:158 final size:159
Alignment explanation
Indices: 352881--353176 Score: 377
Period size: 158 Copynumber: 1.9 Consensus size: 159
352871 TTTGGCAGAA
* * *
352881 AGGTGTCAATTATGCAAGTAAGATGAACGGTTAAAGACCATTGAGTAAAAGTTAAATGGCCTAGC
1 AGGTGTCAATTATGCAAGTAAGATGAACGATTAAAGACCATTGAGTAAAAGATAAATGGCCTAAC
* * * * * *
352946 TGTGCATTTGATAGAAAGGATTCAATTATGCCAGTTAGATGAACGATTAAAGATCGTTGAGTAAA
66 TATGCATTTGAGAGAAAGGATTCAATCATGCAAGTTAGATGAAAGATTAAAGACCGTTGAGTAAA
353011 AGA-TAAATGGCCTAGCTGTTCATTTTGC
131 AGACTAAATGGCCTAGCTGTTCATTTTGC
* * *
353039 AGGTGTCAATTATATC-AGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGCCTAA
1 AGGTGTCAATTAT-GCAAGTAAGATGAACGATTAAAGACCATTGAGTAAAAGATAAATGGCCTAA
* * * *
353103 CTATGCATTT-AGCAGAAAAG-TATCAATCATGCAAGTTAGATGAAAGGTTAAATG-CCTTTGGG
65 CTATGCATTTGAG-AGAAAGGAT-TCAATCATGCAAGTTAGATGAAAGATTAAA-GACCGTTGAG
353165 TAAAAGACTAAA
127 TAAAAGACTAAA
353177 GGAATTATAA
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
157 2 0.02
158 109 0.93
159 6 0.05
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (159 bp):
AGGTGTCAATTATGCAAGTAAGATGAACGATTAAAGACCATTGAGTAAAAGATAAATGGCCTAAC
TATGCATTTGAGAGAAAGGATTCAATCATGCAAGTTAGATGAAAGATTAAAGACCGTTGAGTAAA
AGACTAAATGGCCTAGCTGTTCATTTTGC
Found at i:353396 original size:43 final size:45
Alignment explanation
Indices: 353337--353422 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
353327 GTGTATAAAA
* *
353337 GGCATGAAAGGATGCCATCAATG-AAATGCAT-ATGGTGCATTTT
1 GGCATGAAAGAATGCCATAAATGAAAATGCATAATGGTGCATTTT
353380 GGCATGAAAGAATGCCATAAATGAAAATGCATAATGGTGCATT
1 GGCATGAAAGAATGCCATAAATGAAAATGCATAATGGTGCATT
353423 ATAAGTATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 21 0.54
44 8 0.21
45 10 0.26
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (45 bp):
GGCATGAAAGAATGCCATAAATGAAAATGCATAATGGTGCATTTT
Found at i:355828 original size:4 final size:4
Alignment explanation
Indices: 355819--355874 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
355809 TTAATATTCT
* *
355819 TTTA TTTA TTTA TTTTA TTTG TTTCCT TTTA TTTA TTTA -TTA TTTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTTA TTTA
355869 -TTA TTT
1 TTTA TTT
355875 CTCATCTAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
3 6 0.14
4 31 0.70
5 4 0.09
6 3 0.07
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Done.