Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 72 of 73
Found at i:16611479 original size:26 final size:26
Alignment explanation
Indices: 16611447--16611504 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
16611437 TAGTATTTAT
* * *
16611447 TAATAATATTTATAATAATAATA-CAA
1 TAATAATATATA-AATAACAATATAAA
16611473 TAATAATATATAAATAACAATATAAA
1 TAATAATATATAAATAACAATATAAA
16611499 TAATAA
1 TAATAA
16611505 CGAGACGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATAATATATAAATAACAATATAAA
Found at i:16611863 original size:137 final size:137
Alignment explanation
Indices: 16611651--16612169 Score: 772
Period size: 137 Copynumber: 3.8 Consensus size: 137
16611641 AAATCAAACT
* ** *
16611651 AGTGTATGACATTGTTTATTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACT
1 AGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACA
* * * * * * *
16611716 TGGTTTCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATGCTACTCCTTTATGATGAGGAAT
66 CGGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTTCTTCATGATGAGGAGT
16611781 TCTGATC
131 TCTGATC
* *
16611788 AATGAATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACA
1 AGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACA
* * *
16611853 CAGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGCTTCTTCGTGATGAGGAGT
66 CGGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTTCTTCATGATGAGGAGT
16611918 TCTGATC
131 TCTGATC
* * * * *
16611925 GGTGGATGACATTATTCCTTCATGATAAGGACGTCT-GACCATCTTTAAAGATATTTAAGATAAC
1 AGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAG-CCATCTTTAAAGATATTTGAGATAAC
16611989 ACGGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTTCTTCATGATGAGGAG
65 ACGGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTTCTTCATGATGAGGAG
16612054 TTCTGAT-
130 TTCTGATC
* *
16612061 ATGTGGATGAAATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAAC
1 A-GTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAAC
** *
16612126 ATTGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG
65 ACGGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATG
16612170 TTTCCTAAAA
Statistics
Matches: 345, Mismatches: 34, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
136 1 0.00
137 343 0.99
138 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (137 bp):
AGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACA
CGGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTTCTTCATGATGAGGAGT
TCTGATC
Found at i:16621927 original size:2 final size:2
Alignment explanation
Indices: 16621920--16621953 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16621910 AATAAAGTAA
16621920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16621954 TTTAAACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16623694 original size:14 final size:13
Alignment explanation
Indices: 16623675--16623721 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
16623665 AATAATATTT
16623675 ATAATAATAATACA
1 ATAATAATAATA-A
16623689 ATAATAATATATAA
1 ATAATAATA-ATAA
*
16623703 ATAACAAT-ATAA
1 ATAATAATAATAA
16623715 ATAATAA
1 ATAATAA
16623722 CATGACGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 10 0.33
14 17 0.57
15 3 0.10
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:16623696 original size:26 final size:26
Alignment explanation
Indices: 16623664--16623721 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
16623654 TAGTATTTAT
* * *
16623664 TAATAATATTTATAATAATAATA-CAA
1 TAATAATATATA-AATAACAATATAAA
16623690 TAATAATATATAAATAACAATATAAA
1 TAATAATATATAAATAACAATATAAA
16623716 TAATAA
1 TAATAA
16623722 CATGACGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATAATATATAAATAACAATATAAA
Found at i:16625853 original size:3 final size:3
Alignment explanation
Indices: 16625845--16625933 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
16625835 TTTTTATCCA
16625845 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16625893 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16625934 AATATATATT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16626509 original size:114 final size:113
Alignment explanation
Indices: 16626326--16626982 Score: 877
Period size: 114 Copynumber: 5.7 Consensus size: 113
16626316 ATTAGCTTTT
* *
16626326 CCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
*** * * *** *
16626391 ATTTGTTCAACCTTTT-ACCTGAATTCATCAAATTGATGGATTATTTTTT
65 ATTTGTTCAACCTTTTGGTTTGAATTCATC-ATTTGATGGATCAACATTG
*
16626440 TCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
1 CCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
16626505 ATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
65 ATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
*
16626554 CCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 CCAGG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
16626619 AGAATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
62 AGAATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
* *
16626671 CCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGTAGAAGGAAGAAGAAGTTCATAATGAGA
1 CCAGGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
* * * * * * *** *
16626736 AAAATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTTTT
62 AGAATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
* * *
16626787 CCAAAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CC-AGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
* *
16626852 ACTTGTTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
65 ATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
* *
16626901 CCAGGAAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
1 CCAGGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
* *
16626966 ACTTGTTCAACTTTTTG
65 ATTTGTTCAACCTTTTG
16626983 CATAATTCTA
Statistics
Matches: 485, Mismatches: 48, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
113 54 0.11
114 205 0.42
115 13 0.03
116 45 0.09
117 168 0.35
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
CCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAA
TTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
Found at i:16627307 original size:3 final size:3
Alignment explanation
Indices: 16627299--16627360 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
16627289 TTTTTATCCA
*
16627299 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16627347 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
16627361 AATATATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16627372 original size:11 final size:11
Alignment explanation
Indices: 16627356--16627385 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16627346 TTATTATTAT
16627356 TATTAAATATA
1 TATTAAATATA
16627367 TATTAAATATA
1 TATTAAATATA
16627378 TA-TAAATA
1 TATTAAATA
16627386 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:16628851 original size:13 final size:13
Alignment explanation
Indices: 16628835--16628881 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
16628825 ATATAATAAA
16628835 TAAATATTTATTT
1 TAAATATTTATTT
*
16628848 TAAATAAATTATTT
1 TAAAT-ATTTATTT
16628862 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
16628875 TCAATAT
1 TAAATAT
16628882 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:16632671 original size:12 final size:12
Alignment explanation
Indices: 16632650--16632720 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
16632640 ATATTATGCT
16632650 TGAAGAAAAAAA
1 TGAAGAAAAAAA
16632662 TGAAGGAAAAAAAA
1 TGAA-G-AAAAAAA
*
16632676 AGAA-AAAAAAA
1 TGAAGAAAAAAA
*
16632687 AGAAAGAAAAAAA
1 TG-AAGAAAAAAA
*
16632700 AGAAAGAAAAAAA
1 TG-AAGAAAAAAA
16632713 -GAA-AAAAA
1 TGAAGAAAAA
16632721 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.09
11 11 0.20
12 7 0.13
13 21 0.39
14 10 0.19
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
TGAAGAAAAAAA
Found at i:16632672 original size:1 final size:1
Alignment explanation
Indices: 16632668--16632720 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
16632658 AAAATGAAGG
* * * * * *
16632668 AAAAAAAAAGAAAAAAAAAAGAAAGAAAAAAAAGAAAGAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16632721 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:16632672 original size:13 final size:13
Alignment explanation
Indices: 16632652--16632720 Score: 83
Period size: 12 Copynumber: 5.5 Consensus size: 13
16632642 ATTATGCTTG
*
16632652 AAGAAAAAAATGA
1 AAGAAAAAAAAGA
*
16632665 AGGAAAAAAAA-A
1 AAGAAAAAAAAGA
16632677 GAA-AAAAAAAAGA
1 -AAGAAAAAAAAGA
16632690 AAGAAAAAAAAGA
1 AAGAAAAAAAAGA
16632703 AAG-AAAAAAAGA
1 AAGAAAAAAAAGA
16632715 AA-AAAA
1 AAGAAAA
16632721 GGGGGTCAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
12 25 0.51
13 24 0.49
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:16632695 original size:25 final size:25
Alignment explanation
Indices: 16632655--16632720 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
16632645 ATGCTTGAAG
* *
16632655 AAAAAAATGAAGGAAAAAAAAAGAA
1 AAAAAAAAGAAAGAAAAAAAAAGAA
16632680 AAAAAAAAGAAAG-AAAAAAAAGAA
1 AAAAAAAAGAAAGAAAAAAAAAGAA
16632704 AGAAAAAAAGAAA-AAAA
1 A-AAAAAAAGAAAGAAAA
16632721 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 12 0.32
25 25 0.68
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAAAAAGAAAGAAAAAAAAAGAA
Found at i:16634009 original size:84 final size:84
Alignment explanation
Indices: 16633868--16634759 Score: 1562
Period size: 84 Copynumber: 10.6 Consensus size: 84
16633858 TGGAACAAAT
16633868 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
16633933 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
16633952 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
16634017 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
16634036 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
16634101 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
* *
16634120 ATAATGTGCTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
16634185 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
* * *
16634204 ATAATGTGTTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGACAGAAC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGACAGAAC
*
16634269 CAATCATTGAGTTTGGAAG-
65 CAATCATTGAATTTGGAAGA
*
16634288 ATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 AT-AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
16634352 CAATCATTGAATTTGGAAGA
65 CAATCATTGAATTTGGAAGA
16634372 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
16634437 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
16634456 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
16634521 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
* *
16634540 ATAATGTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGACAGAAC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGACAGAAC
*
16634605 CAATCATTGAGTTTGGAAG-
65 CAATCATTGAATTTGGAAGA
* * *
16634624 ATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
1 AT-AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
16634688 CAATCATTGAATTTGGAAG-
65 CAATCATTGAATTTGGAAGA
* *
16634707 ATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGG
1 AT-AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
16634760 GTTGGTAGGA
Statistics
Matches: 781, Mismatches: 20, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
83 111 0.14
84 603 0.77
85 67 0.09
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (84 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACC
AATCATTGAATTTGGAAGA
Found at i:16635683 original size:114 final size:114
Alignment explanation
Indices: 16635478--16636156 Score: 875
Period size: 114 Copynumber: 5.9 Consensus size: 114
16635468 ATTCAAATCT
* * *
16635478 ATCATTTGATAGATTAGCTTTTCCAGA-AAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTTGATGGATCAACTTTTCCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ***
16635542 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ACCTGAATTC
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
* * ** *
16635591 ATCAAATTGATGGATTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
16635656 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
* * * *
16635706 ATCATTTGATGGATCAACATTGCC-GGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA
1 ATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
16635770 GGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
62 GGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
* * *
16635823 ATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGTAGAA
1 ATCATTTGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * * *
16635887 GGAAGAAGAAGTTCATAATGAGAAAAATTTGTTCAACCTTTT-ATCTGAATTC
62 GGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
* * * ** *
16635939 ATCACTGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAA
1 ATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
16636004 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGGTTTGAATTC
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
* * * *
16636053 ATCATTTGATGGATCAACATTGCCAG-GAAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 ATCATTTGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
16636117 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTG
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTG
16636157 CATAATTCTA
Statistics
Matches: 504, Mismatches: 50, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
113 57 0.11
114 221 0.44
115 13 0.03
116 47 0.09
117 165 0.33
118 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (114 bp):
ATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
Found at i:16636481 original size:3 final size:3
Alignment explanation
Indices: 16636473--16636540 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
16636463 TTTTTATCCA
16636473 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16636521 CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
16636541 AATATATATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16636552 original size:11 final size:11
Alignment explanation
Indices: 16636536--16636565 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16636526 TTATTATTAT
16636536 TATTAAATATA
1 TATTAAATATA
16636547 TATTAAATATA
1 TATTAAATATA
16636558 TA-TAAATA
1 TATTAAATA
16636566 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:16638031 original size:13 final size:13
Alignment explanation
Indices: 16638015--16638061 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
16638005 ATATAATAAA
16638015 TAAATATTTATTT
1 TAAATATTTATTT
*
16638028 TAAATAAATTATTT
1 TAAAT-ATTTATTT
16638042 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
16638055 TCAATAT
1 TAAATAT
16638062 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:16645724 original size:21 final size:21
Alignment explanation
Indices: 16645682--16645731 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
16645672 ATCCGAAAAA
*
16645682 ATCGGATATCCGAAATTTCGG
1 ATCGGATATCCGAAATTCCGG
16645703 ATCGGATATCCG-AATATCCGG
1 ATCGGATATCCGAAAT-TCCGG
16645724 ATCCGGAT
1 AT-CGGAT
16645732 CTGAATCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.69
22 5 0.19
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (21 bp):
ATCGGATATCCGAAATTCCGG
Found at i:16648723 original size:46 final size:45
Alignment explanation
Indices: 16648666--16648754 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 45
16648656 TGATTTAGAT
* *
16648666 AATTATAATTTATTTTAAAATATCTTTTAAAATAAATAATAAATAA
1 AATTATAATTTATTTTAAAAGATATTTT-AAATAAATAATAAATAA
*
16648712 AATTATTATTTATTTTAAAAGATATTTTAAATAAATAATAAAT
1 AATTATAATTTATTTTAAAAGATATTTTAAATAAATAATAAAT
16648755 TAATTAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 15 0.38
46 25 0.62
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (45 bp):
AATTATAATTTATTTTAAAAGATATTTTAAATAAATAATAAATAA
Found at i:16649205 original size:20 final size:20
Alignment explanation
Indices: 16649155--16649226 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
16649145 TTTTCCCAAT
*
16649155 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
16649175 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
16649195 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
16649216 TCGCAATGCGA
1 TCGCAATGCGA
16649227 TACTGACTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:16649239 original size:41 final size:42
Alignment explanation
Indices: 16649194--16649287 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 42
16649184 GAATAAGTAA
* ** * * *
16649194 ATCGCAACGCGAATTG-GGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATAGTACAAAATCACAACGAGATACTGACT
*
16649235 ATCGCAATGCG-ATAGTACAAAATCACAACGAGATACTGACT
1 ATCGCAACGCGAATAGTACAAAATCACAACGAGATACTGACT
*
16649276 TTCGCAACGCGA
1 ATCGCAACGCGA
16649288 TACTGACTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
40 3 0.07
41 39 0.93
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (42 bp):
ATCGCAACGCGAATAGTACAAAATCACAACGAGATACTGACT
Found at i:16649240 original size:20 final size:20
Alignment explanation
Indices: 16649215--16649329 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
16649205 AATTGGGAAA
*
16649215 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
16649235 ATCGCAATGCGATAGT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
16649256 ATCACAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
16649276 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
16649296 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
16649316 TTCGCAACGTGATA
1 ATCGCAACGCGATA
16649330 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:16649545 original size:22 final size:22
Alignment explanation
Indices: 16649517--16649560 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
16649507 CACTCTCTCA
16649517 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
16649539 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
16649561 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:16649567 original size:20 final size:21
Alignment explanation
Indices: 16649517--16649568 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
16649507 CACTCTCTCA
16649517 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
16649538 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
16649560 -CTATCTCCA
1 CCCATCTCCA
16649569 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:16649869 original size:20 final size:20
Alignment explanation
Indices: 16649815--16649873 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
16649805 GCGATTCTCT
**
16649815 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
16649835 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
16649855 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
16649874 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:16651010 original size:18 final size:18
Alignment explanation
Indices: 16650989--16651033 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
16650979 TCCACTTCGG
*
16650989 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
16651007 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
16651025 GAGCCATCA
1 GAGCCATCA
16651034 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:16651503 original size:20 final size:20
Alignment explanation
Indices: 16651480--16651537 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
16651470 TTCACAACAT
16651480 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
* *
16651500 GAAAATGGCTATCGCAATGC
1 GAAAATGACTATCGCAACGC
**
16651520 G-AAATGAAAATCGCAACG
1 GAAAATGACTATCGCAACG
16651538 ACAAAATCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:16651532 original size:19 final size:19
Alignment explanation
Indices: 16651510--16651606 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
16651500 GAAAATGGCT
*
16651510 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
16651529 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
16651543 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATCAAA
16651562 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
* *
16651576 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
16651595 ATCGCAATGCGA
1 ATCGCAATGCGA
16651607 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:16651545 original size:14 final size:14
Alignment explanation
Indices: 16651526--16651584 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
16651516 ATGCGAAATG
16651526 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
16651540 AAAATCGCAATGCGAAATA
1 AAAATCGCAA--CG--A-C
16651559 AAAATCGCAACGAC
1 AAAATCGCAACGAC
16651573 AAAATCGCAACG
1 AAAATCGCAACG
16651585 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:16651552 original size:33 final size:33
Alignment explanation
Indices: 16651510--16651601 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
16651500 GAAAATGGCT
16651510 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
16651543 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
16651576 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
16651602 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:16651678 original size:20 final size:19
Alignment explanation
Indices: 16651644--16651699 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
16651634 TTGCGATTTT
*
16651644 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
16651663 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
16651683 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
16651700 TTTAAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:16652161 original size:41 final size:41
Alignment explanation
Indices: 16652065--16652152 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
16652055 GACTCACCTG
* * *
16652065 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
16652107 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
16652148 TCATC
1 TCATC
16652153 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:16653580 original size:14 final size:14
Alignment explanation
Indices: 16653561--16653596 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16653551 ATTGTTTAAT
16653561 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
16653575 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
16653589 TGATTTGT
1 TGATTTGT
16653597 TTAATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:16653753 original size:19 final size:19
Alignment explanation
Indices: 16653729--16653793 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
16653719 GCAACGAGAG
16653729 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16653748 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16653767 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
16653781 AATCGCAATGCGA
1 AATCGCAATGCGA
16653794 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:16653837 original size:20 final size:20
Alignment explanation
Indices: 16653812--16653869 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
16653802 TCGCATTGCG
*
16653812 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
16653832 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
16653852 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
16653870 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:16654304 original size:41 final size:41
Alignment explanation
Indices: 16654185--16654322 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
16654175 AACTTTGAAA
* * *
16654185 ATCGCATTGTGATTCTGTATTATCTCGTTGCGAAAGTCAGA-
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCA-AT
* ** *
16654226 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAAT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAAT
* * *
16654266 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAAT
16654307 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
16654323 CCCAATTCGC
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.04
40 31 0.38
41 45 0.56
42 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAAT
Found at i:16654319 original size:20 final size:20
Alignment explanation
Indices: 16654205--16654318 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
16654195 GATTCTGTAT
*
16654205 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
16654225 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
16654245 TATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGAAAGTCAG
** *
16654265 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
16654286 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
16654306 TATCGCATTGCGA
1 TATCGCGTTGCGA
16654319 TTTTCCCAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:16654338 original size:41 final size:41
Alignment explanation
Indices: 16654245--16654340 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
16654235 CGAAAGTCAG
* * ** *
16654245 TATCGCGTTGCGAAAGTCAATATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCCAA
*
16654286 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAATATCGCATTGCGATTTT-CCAA
*
16654328 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
16654341 TACTTATTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCCAA
Found at i:16658363 original size:21 final size:20
Alignment explanation
Indices: 16658329--16658371 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
16658319 AAATCCCAAA
*
16658329 AAACTTAAACCCTAAATCTT
1 AAACTTAAACCCTAAACCTT
*
16658349 AAACTTTAAATCCTAAACCTT
1 AAAC-TTAAACCCTAAACCTT
16658370 AA
1 AA
16658372 CTCTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (20 bp):
AAACTTAAACCCTAAACCTT
Found at i:16659251 original size:24 final size:24
Alignment explanation
Indices: 16659219--16659264 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
16659209 TTATTCGATT
*
16659219 AATTTGGTTAATAATTTTCAAAAA
1 AATTCGGTTAATAATTTTCAAAAA
16659243 AATTCGGTTAATAATTTTCAAA
1 AATTCGGTTAATAATTTTCAAA
16659265 TTATTAACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (24 bp):
AATTCGGTTAATAATTTTCAAAAA
Found at i:16660881 original size:14 final size:14
Alignment explanation
Indices: 16660862--16660893 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16660852 TGTTTCAATG
16660862 AAAACATTTTCCAT
1 AAAACATTTTCCAT
*
16660876 AAAACATTTTCCGT
1 AAAACATTTTCCAT
16660890 AAAA
1 AAAA
16660894 TGAATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAACATTTTCCAT
Found at i:16661057 original size:22 final size:23
Alignment explanation
Indices: 16661023--16661065 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
16661013 ATATAATAAA
16661023 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
16661046 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
16661066 TATCAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:16661810 original size:9 final size:8
Alignment explanation
Indices: 16661768--16661807 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
16661758 TCTAATATAT
16661768 TATTTATAA
1 TATTT-TAA
16661777 TTATTTTAA
1 -TATTTTAA
16661786 TATTTTAA
1 TATTTTAA
*
16661794 TAATTTAA
1 TATTTTAA
16661802 TATTTT
1 TATTTT
16661808 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 20 0.71
9 3 0.11
10 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:16667807 original size:168 final size:168
Alignment explanation
Indices: 16667529--16667864 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 168
16667519 AAGATAACGA
16667529 TGACAAGACGGCAACAACCGACCGAGCTAAGAGAATCAGGAGCCAATGTTGAAATCACGGTTTTG
1 TGACAAGACGGCAACAACCGACCGAGCTAAGAGAATCAGGAGCCAATGTTGAAATCACGGTTTTG
16667594 TTGCATAAGCTTATAGAAGCCGAGATTAATAGCTCTGGGGTTATCATGAACAGTTTCCAAGAACT
66 TTGCATAAGCTTATAGAAGCCGAGATTAATAGCTCTGGGGTTATCATGAACAGTTTCCAAGAACT
16667659 GGAACCACTTATGTAGAACACTACAGAAAAACCTTGGG
131 GGAACCACTTATGTAGAACACTACAGAAAAACCTTGGG
16667697 TGACAAGACGGCAACAACCGACCGAGCTAAGAGAATCAGGAGCCAATGTTGAAATCACGGTTTTG
1 TGACAAGACGGCAACAACCGACCGAGCTAAGAGAATCAGGAGCCAATGTTGAAATCACGGTTTTG
16667762 TTGCATAAGCTTATAGAAGCCGAGATTAATAGCTCTGGGGTTATCATGAACAGTTTCCAAGAACT
66 TTGCATAAGCTTATAGAAGCCGAGATTAATAGCTCTGGGGTTATCATGAACAGTTTCCAAGAACT
16667827 GGAACCACTTATGTAGAACACTACAGAAAAACCTTGGG
131 GGAACCACTTATGTAGAACACTACAGAAAAACCTTGGG
16667865 GAGGAAATCA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (168 bp):
TGACAAGACGGCAACAACCGACCGAGCTAAGAGAATCAGGAGCCAATGTTGAAATCACGGTTTTG
TTGCATAAGCTTATAGAAGCCGAGATTAATAGCTCTGGGGTTATCATGAACAGTTTCCAAGAACT
GGAACCACTTATGTAGAACACTACAGAAAAACCTTGGG
Found at i:16671444 original size:18 final size:18
Alignment explanation
Indices: 16671423--16671460 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16671413 TAAAATAAAG
16671423 ATAAGAATTAAATAAATA
1 ATAAGAATTAAATAAATA
* *
16671441 ATAATAATTAATTAAATA
1 ATAAGAATTAAATAAATA
16671459 AT
1 AT
16671461 CTGAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
ATAAGAATTAAATAAATA
Found at i:16676440 original size:25 final size:25
Alignment explanation
Indices: 16676375--16676433 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
16676365 AATTTGCAAA
16676375 GCAATCAACTATCATATACCAAAAG
1 GCAATCAACTATCATATACCAAAAG
16676400 GCAATCAACTATCATATACCAAAAG
1 GCAATCAACTATCATATACCAAAAG
16676425 GCAATCAAC
1 GCAATCAAC
16676434 AAACATAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.19
Consensus pattern (25 bp):
GCAATCAACTATCATATACCAAAAG
Found at i:16688677 original size:19 final size:19
Alignment explanation
Indices: 16688653--16688707 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
16688643 ACAACCCATT
* *
16688653 TTTATTTTTGTTTCTTTTA
1 TTTATTTTTATTTATTTTA
16688672 TTTATTTTTATTTATTTTA
1 TTTATTTTTATTTATTTTA
* *
16688691 TTGAGTATTTATTTATT
1 TTTA-TTTTTATTTATT
16688708 GATTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTATTTTA
Found at i:16688705 original size:15 final size:16
Alignment explanation
Indices: 16688680--16688709 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16688670 TATTTATTTT
16688680 TATTTATTTTATTGAG
1 TATTTATTTTATTGAG
16688696 TATTTA-TTTATTGA
1 TATTTATTTTATTGA
16688710 TTTTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
TATTTATTTTATTGAG
Found at i:16691107 original size:2 final size:2
Alignment explanation
Indices: 16691100--16691173 Score: 70
Period size: 2 Copynumber: 40.0 Consensus size: 2
16691090 AATGTGTTTC
* * * *
16691100 AT AT AT AT AT A- AT AT AT AT TT AT AT TT AT AT TT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16691141 AT -T AT AT A- AT AT AT A- AT AT AT A- AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16691174 TTATTTGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:16691116 original size:7 final size:7
Alignment explanation
Indices: 16691100--16691166 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
16691090 AATGTGTTTC
16691100 ATAT-AT
1 ATATAAT
16691106 ATATAAT
1 ATATAAT
*
16691113 ATATATTT
1 ATATA-AT
*
16691121 ATATTTAT
1 ATA-TAAT
*
16691129 ATTTATAT
1 ATATA-AT
* *
16691137 TTATATT
1 ATATAAT
16691144 ATATAAT
1 ATATAAT
16691151 ATATAAT
1 ATATAAT
16691158 ATATAAT
1 ATATAAT
16691165 AT
1 AT
16691167 TATATATTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
6 4 0.09
7 30 0.64
8 12 0.26
9 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATAAT
Found at i:16691173 original size:12 final size:11
Alignment explanation
Indices: 16691100--16691178 Score: 79
Period size: 12 Copynumber: 7.0 Consensus size: 11
16691090 AATGTGTTTC
*
16691100 ATATATATATA
1 ATATATATATT
16691111 ATATATAT-TT
1 ATATATATATT
*
16691121 ATATTTATATTT
1 ATATATATA-TT
*
16691133 ATATTTATATT
1 ATATATATATT
*
16691144 ATATAATATATA
1 ATAT-ATATATT
16691156 ATATATAATATT
1 ATATAT-ATATT
*
16691168 ATATATTTATT
1 ATATATATATT
16691179 TGGTTCCACG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
10 8 0.14
11 20 0.34
12 30 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATATATT
Found at i:16692490 original size:2 final size:2
Alignment explanation
Indices: 16692483--16692512 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16692473 ACTTTATCAT
*
16692483 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16692513 CTATTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16692752 original size:23 final size:25
Alignment explanation
Indices: 16692726--16692773 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
16692716 TTTTGTGTAC
16692726 GTTT-CATTTTCATTTTTT-TCTTT
1 GTTTGCATTTTCATTTTTTCTCTTT
* *
16692749 GTTTGTATTTTCGTTTTTTCTCTTT
1 GTTTGCATTTTCATTTTTTCTCTTT
16692774 CTTTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.06, C:0.12, G:0.08, T:0.73
Consensus pattern (25 bp):
GTTTGCATTTTCATTTTTTCTCTTT
Found at i:16692784 original size:25 final size:24
Alignment explanation
Indices: 16692731--16692794 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
16692721 TGTACGTTTC
* *
16692731 ATTTTCATTTTTTTCTTTGTTTGT
1 ATTTTCATTTTTTTCTTTCTTTAT
*
16692755 ATTTTCGTTTTTTCTCTTTCTTTAT
1 ATTTTCATTTTTT-TCTTTCTTTAT
* *
16692780 GTTTTTATATTTTTT
1 ATTTTCAT-TTTTTT
16692795 ACCTTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 12 0.38
25 15 0.47
26 5 0.16
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (24 bp):
ATTTTCATTTTTTTCTTTCTTTAT
Found at i:16692849 original size:21 final size:19
Alignment explanation
Indices: 16692799--16692850 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
16692789 TTTTTTACCT
*
16692799 TATTTACTTTATTTTTATTT
1 TATTTA-TTTATTTTTATTG
16692819 TATGTCTATTTATTTTGTCATTG
1 TAT-T-TATTTATTTT-T-ATTG
16692842 TATTTATTT
1 TATTTATTT
16692851 TCCTTATGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 14 0.52
22 4 0.15
23 6 0.22
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (19 bp):
TATTTATTTATTTTTATTG
Found at i:16692880 original size:17 final size:16
Alignment explanation
Indices: 16692812--16692880 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
16692802 TTACTTTATT
*
16692812 TTTATTTTA-TGTCTA
1 TTTATTTTATTATCTA
* * *
16692827 TTTATTTTGTCATTGTA
1 TTTATTTTATTA-TCTA
*
16692844 TTTATTTTCCTTATGCTA
1 TTTATTTT-ATTAT-CTA
16692862 TTTATTTTATTATCATA
1 TTTATTTTATTATC-TA
16692879 TT
1 TT
16692881 CATCTTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
15 8 0.20
16 1 0.02
17 20 0.49
18 12 0.29
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTATTTTATTATCTA
Found at i:16693153 original size:16 final size:17
Alignment explanation
Indices: 16693123--16693155 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16693113 CCCGAATCCG
16693123 ACATATCAGTAGTAAGAC
1 ACATATCAG-AGTAAGAC
16693141 ACATATCAG-GTAAGA
1 ACATATCAGAGTAAGA
16693156 AATAAGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (17 bp):
ACATATCAGAGTAAGAC
Found at i:16704371 original size:85 final size:89
Alignment explanation
Indices: 16704270--16704471 Score: 225
Period size: 95 Copynumber: 2.2 Consensus size: 89
16704260 GCCATTCGGG
* *
16704270 GCTCAACTTCACGACGAAGGGGC-TT-TCTAA-T-TTCAGAGCCAATTTCAACTTCACAGCGAAG
1 GCTCAACTTCACGACGAAGGGGCATTGTCAAATTATTCAGAGCCAATTTCAACTTCACAGCAAAG
* *
16704331 GATATTGGACCCTAGACAACACAA
66 GATATTAGACCCGAGACAACACAA
* *
16704355 GCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAATTCATTCAGAGTCAATTTTAACTTCACA
1 GCTCAACTTCACGACGAA--GG-GGC--ATTGTCAAATT-ATTCAGAGCCAATTTCAACTTCACA
* * *
16704420 GCAAATGATATTAGACTCGAGACAGCACAA
60 GCAAAGGATATTAGACCCGAGACAACACAA
16704450 GCTCAACTTCACAGA-GAAGGGG
1 GCTCAACTTCAC-GACGAAGGGG
16704472 TGGCTGACTG
Statistics
Matches: 97, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
85 18 0.19
87 2 0.02
88 3 0.03
91 2 0.02
92 6 0.06
93 3 0.03
95 61 0.63
96 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (89 bp):
GCTCAACTTCACGACGAAGGGGCATTGTCAAATTATTCAGAGCCAATTTCAACTTCACAGCAAAG
GATATTAGACCCGAGACAACACAA
Found at i:16704469 original size:95 final size:95
Alignment explanation
Indices: 16704301--16704485 Score: 264
Period size: 95 Copynumber: 1.9 Consensus size: 95
16704291 GCTTTCTAAT
* * *
16704301 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCTAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCGAGACAACACAAGCTCAACTTCA
*
16704366 CGACGAAGGGGCGGCTGATTGTCAAATTCA
66 CGACGAAGGGGCGGCTGACTGTCAAATTCA
* * * * *
16704396 TTCAGAGTCAATTTTAACTTCACAGCAAATGATATTAGACTCGAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCGAGACAACACAAGCTCAACTTCA
*
16704461 CAGA-GAAGGGGTGGCTGACTGTCAA
66 C-GACGAAGGGGCGGCTGACTGTCAA
16704486 CAAATAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 77 0.97
96 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (95 bp):
TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCGAGACAACACAAGCTCAACTTCA
CGACGAAGGGGCGGCTGACTGTCAAATTCA
Found at i:16705309 original size:2 final size:2
Alignment explanation
Indices: 16705302--16705371 Score: 89
Period size: 2 Copynumber: 38.0 Consensus size: 2
16705292 AATTTGTTTC
16705302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16705342 TT AT AT -T AT AT -T AT AT -T AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16705372 TTATTTGGTT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
1 6 0.10
2 54 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:16706485 original size:2 final size:2
Alignment explanation
Indices: 16706478--16706514 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16706468 TTATTTGTAT
16706478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16706515 TGTTTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16706945 original size:25 final size:24
Alignment explanation
Indices: 16706892--16706956 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
16706882 TGTACGTTTC
* * *
16706892 ATTTTCGTTTTTTTCTTTGTTTTT
1 ATTTTCATTTTTTTCTTTCTTTAT
16706916 ATTTTCATTTTTTCTCTTTCTTTAT
1 ATTTTCATTTTTT-TCTTTCTTTAT
* *
16706941 GTTTTTATATTTTTTC
1 ATTTTCAT-TTTTTTC
16706957 CCTTATTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 12 0.35
25 17 0.50
26 5 0.15
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (24 bp):
ATTTTCATTTTTTTCTTTCTTTAT
Found at i:16706977 original size:26 final size:26
Alignment explanation
Indices: 16706913--16707032 Score: 68
Period size: 27 Copynumber: 4.4 Consensus size: 26
16706903 TTTCTTTGTT
* *
16706913 TTTATTTTCATTTTTTCTCTTTCTTTA
1 TTTATTTT-ATTTTTTCTCCTTATTTA
16706940 TGTT-TTTATATTTTTTC-CCTTATTTA
1 T-TTATTT-TATTTTTTCTCCTTATTTA
**
16706966 CTTTATTTTATTTTATGTCTATTTATTT-
1 -TTTATTTTATTTT-T-TCTCCTTATTTA
* * *
16706994 TGTCATTGTATTTATTT-TCCTTATGCTA
1 T-TTATTTTATTT-TTTCTCCTTAT-TTA
16707022 TTTATTTTATT
1 TTTATTTTATT
16707033 ATCATATTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
26 20 0.28
27 28 0.39
28 16 0.23
29 7 0.10
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTATTTTATTTTTTCTCCTTATTTA
Found at i:16707040 original size:17 final size:16
Alignment explanation
Indices: 16706972--16707040 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
16706962 TTTACTTTAT
*
16706972 TTTATTTTA-TGTCTA
1 TTTATTTTATTATCTA
* * *
16706987 TTTATTTTGTCATTGTA
1 TTTATTTTATTA-TCTA
*
16707004 TTTATTTTCCTTATGCTA
1 TTTATTTT-ATTAT-CTA
16707022 TTTATTTTATTATCATA
1 TTTATTTTATTATC-TA
16707039 TT
1 TT
16707041 CATCTTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
15 8 0.20
16 1 0.02
17 20 0.49
18 12 0.29
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTATTTTATTATCTA
Found at i:16708936 original size:19 final size:19
Alignment explanation
Indices: 16708900--16708937 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16708890 ATCGGTTTTG
*
16708900 ACCGGTTTGATCGATCTGA
1 ACCGGTTTGACCGATCTGA
*
16708919 ACCGGTTTGACCGGTCTGA
1 ACCGGTTTGACCGATCTGA
16708938 CCCGACCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
ACCGGTTTGACCGATCTGA
Found at i:16708978 original size:22 final size:22
Alignment explanation
Indices: 16708950--16708997 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
16708940 CGACCTGACC
*
16708950 GACCCGACCCGACCCAATCGTT
1 GACCCGACCCGACCCAACCGTT
*
16708972 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCAACCGTT
16708994 GACC
1 GACC
16708998 GTTGACCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCCAACCGTT
Found at i:16711662 original size:29 final size:28
Alignment explanation
Indices: 16711630--16711806 Score: 148
Period size: 29 Copynumber: 6.4 Consensus size: 28
16711620 AAAAAAATAT
16711630 AAAATAACACCATTTTCAAAATAATTACC
1 AAAATAACACCATTTT-AAAATAATTACC
* * *
16711659 AAAATATCACCATTTTAAAAATATTTACT
1 AAAATAACACCATTTT-AAAATAATTACC
* * * *
16711688 AAAATATCA-C-TTTTAAAAAAAGTACG
1 AAAATAACACCATTTTAAAATAATTACC
* * * *
16711714 AAAATAGCA--TTTTTTAAA-AATTACA
1 AAAATAACACCATTTTAAAATAATTACC
* *
16711739 AAAATAGCACCCTTTTCAAAATAATTACC
1 AAAATAACACCATTTT-AAAATAATTACC
*
16711768 AGAATAACACCATTTTAAAATAATTACC
1 AAAATAACACCATTTTAAAATAATTACC
* *
16711796 AAGATACCACC
1 AAAATAACACC
16711807 CGGTCAACGG
Statistics
Matches: 122, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
25 14 0.11
26 23 0.19
27 8 0.07
28 24 0.20
29 53 0.43
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAATAACACCATTTTAAAATAATTACC
Found at i:16711717 original size:26 final size:26
Alignment explanation
Indices: 16711659--16711733 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
16711649 AATAATTACC
** *
16711659 AAAATATCACCATTTTAAAAATATTTACT
1 AAAATATCA-C-TTTTAAAAA-AAGTACG
16711688 AAAATATCACTTTTAAAAAAAGTACG
1 AAAATATCACTTTTAAAAAAAGTACG
* * *
16711714 AAAATAGCATTTTTTAAAAA
1 AAAATATCACTTTTAAAAAA
16711734 TTACAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 21 0.52
27 9 0.22
28 1 0.03
29 9 0.22
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAATATCACTTTTAAAAAAAGTACG
Found at i:16713127 original size:9 final size:9
Alignment explanation
Indices: 16713092--16713142 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
16713082 AGAAAATTAA
16713092 AAATAAAAT
1 AAATAAAAT
*
16713101 -AAT-TAAT
1 AAATAAAAT
*
16713108 CAATAAAAAT
1 AAAT-AAAAT
16713118 AAATAAAAT
1 AAATAAAAT
16713127 AAATAAAAT
1 AAATAAAAT
16713136 AAATAAA
1 AAATAAA
16713143 GAAAGAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 3 0.08
8 6 0.17
9 21 0.58
10 6 0.17
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:16724773 original size:23 final size:22
Alignment explanation
Indices: 16724744--16724820 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 22
16724734 AAATGTCCCC
*
16724744 AAGGACCGCGTAGTATTGTCTCG
1 AAGGACCGCGTAGAATTGTC-CG
* *
16724767 AATGACCGCGTAGAAATGTCCAG
1 AAGGACCGCGTAGAATTGTCC-G
16724790 AAGGACCGCGTAGAATTGTCCCG
1 AAGGACCGCGTAGAATTGT-CCG
16724813 AAGGACCG
1 AAGGACCG
16724821 TGTATAACCC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 44 0.94
24 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.30, T:0.18
Consensus pattern (22 bp):
AAGGACCGCGTAGAATTGTCCG
Found at i:16724783 original size:46 final size:46
Alignment explanation
Indices: 16724731--16724820 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
16724721 AAGTGCCACA
* * * *
16724731 TAGAAATGTCCCCAAGGACCGCGTAGTATTGTCTCGAATGACCGCG
1 TAGAAATGTCCACAAGGACCGCGTAGAATTGTCCCGAAGGACCGCG
*
16724777 TAGAAATGTCCAGAAGGACCGCGTAGAATTGTCCCGAAGGACCG
1 TAGAAATGTCCACAAGGACCGCGTAGAATTGTCCCGAAGGACCG
16724821 TGTATAACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (46 bp):
TAGAAATGTCCACAAGGACCGCGTAGAATTGTCCCGAAGGACCGCG
Found at i:16724955 original size:45 final size:44
Alignment explanation
Indices: 16724897--16725011 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
16724887 TACCATTTAC
*
16724897 ACATTTCACATAGCCTGTATCACATAGACATATAATCACATAGG
1 ACATTTCACATAGCCTATATCACATAGACATATAATCACATAGG
* *** *
16724941 ACATTGTCACATAGCTTATATCACATTTTCATATAGTCACATAGG
1 ACATT-TCACATAGCCTATATCACATAGACATATAATCACATAGG
* ** *
16724986 TCAATACCACATAGCTTATATCACAT
1 AC-ATTTCACATAGCCTATATCACAT
16725012 TTTCATGTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
44 5 0.08
45 53 0.88
46 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (44 bp):
ACATTTCACATAGCCTATATCACATAGACATATAATCACATAGG
Found at i:16725012 original size:45 final size:45
Alignment explanation
Indices: 16724925--16725028 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
16724915 ATCACATAGA
* **
16724925 CATATAATCACATAGGACATTGTCACATAGCTTATATCACATTTT
1 CATATAATCACATAGGACAATACCACATAGCTTATATCACATTTT
* *
16724970 CATATAGTCACATAGGTCAATACCACATAGCTTATATCACATTTT
1 CATATAATCACATAGGACAATACCACATAGCTTATATCACATTTT
*
16725015 CATGTAATCACATA
1 CATATAATCACATA
16725029 TGATGAAATG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (45 bp):
CATATAATCACATAGGACAATACCACATAGCTTATATCACATTTT
Found at i:16741017 original size:21 final size:22
Alignment explanation
Indices: 16740993--16741038 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
16740983 TATCTCTAAT
*
16740993 GACCA-TAGTATTGTCCCGAAG
1 GACCACTAGAATTGTCCCGAAG
*
16741014 GACCACGTAGAATTGTCTCGAAG
1 GACCAC-TAGAATTGTCCCGAAG
16741037 GA
1 GA
16741039 TCGCGTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
23 16 0.76
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
GACCACTAGAATTGTCCCGAAG
Found at i:16741029 original size:23 final size:23
Alignment explanation
Indices: 16741002--16741048 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16740992 TGACCATAGT
16741002 ATTGTCCCGAAGGACCACGTAGA
1 ATTGTCCCGAAGGACCACGTAGA
* * *
16741025 ATTGTCTCGAAGGATCGCGTAGA
1 ATTGTCCCGAAGGACCACGTAGA
16741048 A
1 A
16741049 CCCTCGACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (23 bp):
ATTGTCCCGAAGGACCACGTAGA
Found at i:16741191 original size:40 final size:39
Alignment explanation
Indices: 16741117--16741245 Score: 114
Period size: 45 Copynumber: 3.1 Consensus size: 39
16741107 TTTACTATTT
* * ***
16741117 ACATATTTCACATAGCTTGTAACACATAGACATATAATC
1 ACATATTTCACATAGCTTATATCACATTTTCATATAATC
*
16741156 ACATATTGTCACATAGCTTATATCACATTTTCATATAGTC
1 ACATATT-TCACATAGCTTATATCACATTTTCATATAATC
* * *
16741196 ACATAGGTCAATACCACATAGCTTATATCACTTTTTCATGTAATC
1 ACATA--T---T-TCACATAGCTTATATCACATTTTCATATAATC
16741241 ACATA
1 ACATA
16741246 GGATGAAATG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 7 0.10
40 31 0.42
42 1 0.01
45 34 0.47
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (39 bp):
ACATATTTCACATAGCTTATATCACATTTTCATATAATC
Found at i:16743043 original size:20 final size:21
Alignment explanation
Indices: 16743018--16743065 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
16743008 ATCTAAAAAA
16743018 TAAAAAAATAAAAAAATGA-T
1 TAAAAAAATAAAAAAATGAGT
* * *
16743038 TAAAAACATATAAAAATTAGT
1 TAAAAAAATAAAAAAATGAGT
16743059 TAAAAAA
1 TAAAAAA
16743066 GTGAAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATGAGT
Found at i:16743960 original size:23 final size:23
Alignment explanation
Indices: 16743919--16744000 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
16743909 AGAATTCTTA
*
16743919 AAGGACCACATAG--ATGTCCCG
1 AAGGACCACGTAGAAATGTCCCG
* *
16743940 AATGACCACGTATAAATGTCCCG
1 AAGGACCACGTAGAAATGTCCCG
* *
16743963 AAGGACCATGTAGAATTGTCCCG
1 AAGGACCACGTAGAAATGTCCCG
*
16743986 AAGGACCGCGTAGAA
1 AAGGACCACGTAGAA
16744001 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.20
23 40 0.80
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
AAGGACCACGTAGAAATGTCCCG
Found at i:16744144 original size:30 final size:30
Alignment explanation
Indices: 16744108--16744190 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
16744098 TAGTTCTTTA
* *
16744108 TCACATAGATTATATCACAT-GTTCACGTAG
1 TCACATAGATTATATCACATAG-ACACGTAC
** *
16744138 TCACATAGACCATATCACATAGACATGTAC
1 TCACATAGATTATATCACATAGACACGTAC
*
16744168 TCACATAGCTTATAGTCACATAG
1 TCACATAGATTATA-TCACATAG
16744191 CTTATATCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
30 34 0.79
31 9 0.21
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (30 bp):
TCACATAGATTATATCACATAGACACGTAC
Found at i:16744188 original size:15 final size:15
Alignment explanation
Indices: 16744168--16744196 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16744158 AGACATGTAC
16744168 TCACATAGCTTATAG
1 TCACATAGCTTATAG
16744183 TCACATAGCTTATA
1 TCACATAGCTTATA
16744197 TCATTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
TCACATAGCTTATAG
Found at i:16747220 original size:47 final size:47
Alignment explanation
Indices: 16747169--16747267 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
16747159 TTATGTGCCA
16747169 TAAATAAATTCATCAATCAATTTTAATTTCCCATTTTTTATCCTTCT
1 TAAATAAATTCATCAATCAATTTTAATTTCCCATTTTTTATCCTTCT
16747216 TAAATAAATTCATCAATCAATTTTAATTTCCCATTTTTTATCCTTCT
1 TAAATAAATTCATCAATCAATTTTAATTTCCCATTTTTTATCCTTCT
16747263 TAAAT
1 TAAAT
16747268 CGATTATCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (47 bp):
TAAATAAATTCATCAATCAATTTTAATTTCCCATTTTTTATCCTTCT
Found at i:16748204 original size:2 final size:2
Alignment explanation
Indices: 16748191--16748223 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16748181 CTCATCATTC
*
16748191 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16748224 ATGATCTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16749010 original size:3 final size:3
Alignment explanation
Indices: 16749004--16749083 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
16748994 TTTTTATCCA
* ** *
16749004 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16749052 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16749084 ATTTATATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:16750501 original size:21 final size:20
Alignment explanation
Indices: 16750470--16750508 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
16750460 TTTATATGGT
*
16750470 TAAATATTTTTATATATTCA
1 TAAATATTTTTAAATATTCA
16750490 TAAATAATTTTTAAATATT
1 TAAAT-ATTTTTAAATATT
16750509 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAATATTTTTAAATATTCA
Found at i:16750694 original size:17 final size:18
Alignment explanation
Indices: 16750669--16750721 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
16750659 GGATATTTTT
16750669 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
16750687 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
16750703 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
16750721 A
1 A
16750722 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:16761832 original size:7 final size:7
Alignment explanation
Indices: 16761820--16761853 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
16761810 TATTATGCTT
16761820 GAAAAAA
1 GAAAAAA
16761827 GAAAAAA
1 GAAAAAA
16761834 -AAAAAA
1 GAAAAAA
16761840 GAAAAAA
1 GAAAAAA
16761847 GAAAAAA
1 GAAAAAA
16761854 AGAGGGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:16761839 original size:13 final size:14
Alignment explanation
Indices: 16761820--16761853 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
16761810 TATTATGCTT
16761820 GAAAAAAGAAAAAA
1 GAAAAAAGAAAAAA
16761834 -AAAAAAGAAAAAA
1 GAAAAAAGAAAAAA
16761847 GAAAAAA
1 GAAAAAA
16761854 AGAGGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAAAAAGAAAAAA
Found at i:16762219 original size:18 final size:18
Alignment explanation
Indices: 16762192--16762227 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16762182 GTTCAATGTA
*
16762192 TTTGAGATTCAATTTATT
1 TTTGAAATTCAATTTATT
16762210 TTTGAAATTCAATTTATT
1 TTTGAAATTCAATTTATT
16762228 CTTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTGAAATTCAATTTATT
Found at i:16763177 original size:50 final size:50
Alignment explanation
Indices: 16763118--16763309 Score: 375
Period size: 50 Copynumber: 3.8 Consensus size: 50
16763108 TGAATTTACC
16763118 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
16763168 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
16763218 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
16763268 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
16763310 AGAAGTGTAT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 141 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:16763200 original size:131 final size:131
Alignment explanation
Indices: 16762966--16763208 Score: 486
Period size: 131 Copynumber: 1.9 Consensus size: 131
16762956 GTCCAAACAT
16762966 TAAATGAAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
1 TAAATGAAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
16763031 AGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAACCAATCA
66 AGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAACCAATCA
16763096 G
131 G
16763097 TAAATGAAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
1 TAAATGAAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
16763162 AGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
66 AGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
16763209 ATTAGACAGA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 112 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (131 bp):
TAAATGAAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
AGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAACCAATCA
G
Found at i:16764068 original size:113 final size:112
Alignment explanation
Indices: 16763873--16764409 Score: 783
Period size: 113 Copynumber: 4.8 Consensus size: 112
16763863 TCAAATCCAC
* * *
16763873 TTGATGGATCATTCATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGG
1 TTGATGGATCA-ACATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
16763938 AGTTCATAATGAGAAGAACTTGTTCAA-CTTGTTGTTTAAATTCATCAC
65 AGTTCATAATGAGAAGAACTTGTTCAACCTT-TTGCTTAAATTCATCAT
* *
16763986 TTGATGGATCATTCATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 TTGATGGATCA-ACATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
16764051 AGTTCATAATGAGAAGAACTTGTTCAA-CTTGTTGTTTAAATTCATCAT
65 AGTTCATAATGAGAAGAACTTGTTCAACCTT-TTGCTTAAATTCATCAT
* * *
16764099 TTGATGGATCAACATTTCCAGAGAAGGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTACCAGATAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * * *
16764164 AATTCATAATGAGAAGAATTTTTTCAACCTTTTACCTAAATTCATCAT
65 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAT
* *
16764212 TTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTACCAGAT-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
16764277 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAT
65 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAT
* *
16764325 TTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGA
1 TTGATGGATCAACATTACCAGAT-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-
16764389 AAGTTCATAATGAGAAGAACT
64 AAGTTCATAATGAGAAGAACT
16764410 CATCAAGAGC
Statistics
Matches: 397, Mismatches: 23, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
112 13 0.03
113 379 0.95
114 5 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (112 bp):
TTGATGGATCAACATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAT
Found at i:16764178 original size:24 final size:23
Alignment explanation
Indices: 16764135--16764179 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
16764125 GTTCATAATG
*
16764135 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
16764158 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
16764180 AATTTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:16764670 original size:3 final size:3
Alignment explanation
Indices: 16764664--16764755 Score: 132
Period size: 3 Copynumber: 30.7 Consensus size: 3
16764654 TTTTTATCCA
* ** *
16764664 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16764712 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
16764756 AATATTAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.03
3 74 0.94
4 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:16766352 original size:17 final size:18
Alignment explanation
Indices: 16766327--16766379 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
16766317 GGATATTTTT
16766327 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
16766345 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
16766361 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
16766379 A
1 A
16766380 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:16774855 original size:25 final size:25
Alignment explanation
Indices: 16774798--16774855 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
16774788 AAAAATAGCT
**
16774798 AATGATAAAATCCTAAAAATATTCA
1 AATGATAAAATCCTAAAAATAAACA
* * *
16774823 AATAATAAAATCTTAAAGATAAACA
1 AATGATAAAATCCTAAAAATAAACA
*
16774848 AGTGATAA
1 AATGATAA
16774856 TTCCCAAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (25 bp):
AATGATAAAATCCTAAAAATAAACA
Found at i:16779164 original size:31 final size:31
Alignment explanation
Indices: 16779126--16779191 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
16779116 AGTTACGTAG
16779126 GGGACCATATTGAAAACGGACTAAATGTTGA
1 GGGACCATATTGAAAACGGACTAAATGTTGA
* * * *
16779157 GGGACCATTTTGCAAATGGACTAAATGTTGG
1 GGGACCATATTGAAAACGGACTAAATGTTGA
16779188 GGGA
1 GGGA
16779192 TTATATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGAAAACGGACTAAATGTTGA
Found at i:16779871 original size:31 final size:30
Alignment explanation
Indices: 16779828--16779890 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
16779818 TGAAATATAA
*
16779828 TCCCTAACATTTAGTCCATTTGCAATATGG
1 TCCCTAACATTTAATCCATTTGCAATATGG
**
16779858 TCCCTCAACATTTAATCTGTTTGCAATATGG
1 TCCCT-AACATTTAATCCATTTGCAATATGG
16779889 TC
1 TC
16779891 TTTGACGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (30 bp):
TCCCTAACATTTAATCCATTTGCAATATGG
Found at i:16780681 original size:14 final size:14
Alignment explanation
Indices: 16780662--16780691 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16780652 TTTTTCAATT
*
16780662 TCGAGTTATTTGAG
1 TCGAGTTATTCGAG
16780676 TCGAGTTATTCGAG
1 TCGAGTTATTCGAG
16780690 TC
1 TC
16780692 AACTCGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (14 bp):
TCGAGTTATTCGAG
Found at i:16782552 original size:65 final size:65
Alignment explanation
Indices: 16782441--16782613 Score: 231
Period size: 65 Copynumber: 2.7 Consensus size: 65
16782431 TATACCAAAT
* * * *
16782441 TCATGGCCAAATCTAACTTCT-AGAGACATACCATTTGATATATACCTTTAATGGCCGAACTTAT
1 TCATGGCCAAACCTAACTTCTAAG-GACATACCATTTGGTATGTACCTTTAATGGCCAAACTTAT
16782505 C
65 C
* * * * *
16782506 TCATGGTCAAACCTAACTTCTAAGGACATACCATTCGGTATGTACCTTTAATGGTCAAATTTATT
1 TCATGGCCAAACCTAACTTCTAAGGACATACCATTTGGTATGTACCTTTAATGGCCAAACTTATC
* *
16782571 TCATGGCCAAACCTAACTTCTAAAGACTTACCATTTGGTATGT
1 TCATGGCCAAACCTAACTTCTAAGGACATACCATTTGGTATGT
16782614 TTTTAAACGT
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 92 0.98
66 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (65 bp):
TCATGGCCAAACCTAACTTCTAAGGACATACCATTTGGTATGTACCTTTAATGGCCAAACTTATC
Found at i:16784482 original size:15 final size:15
Alignment explanation
Indices: 16784464--16784494 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16784454 TATTTTTGAA
*
16784464 AAGTTAAAAGTTTTC
1 AAGTTAAAAGGTTTC
16784479 AAGTTAAAAGGTTTC
1 AAGTTAAAAGGTTTC
16784494 A
1 A
16784495 CCTTAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (15 bp):
AAGTTAAAAGGTTTC
Found at i:16786742 original size:413 final size:418
Alignment explanation
Indices: 16786009--16786793 Score: 1165
Period size: 413 Copynumber: 1.9 Consensus size: 418
16785999 AAACTTTTAT
* *
16786009 TATATAACATTTTTGCACCAAAAAATAGAGAGAAATGATTCTGATAGTATAATTTTTCATAATGA
1 TATATAACATTTTTGCACCAAAAAATAGAGAGAAATGATTATAATAGTATAATTTTTCATAATGA
*
16786074 TTAAAATATATAACAACAAAAATAATTGATTACAAAAAAATTAAATTTTATTATCTGATGTGATA
66 TTAAAATATATAACAACAAAAATAATTGATTACAAAAAAATTAAATTTTATTATCTGATGTAATA
*
16786139 ATTTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAATATCACTTTTTGAAACA
131 ATTTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAATATAACTTTTTGAAAC-
16786204 AAAAAAAAAGTGGAGAAAAATATTTATCACAATATATGTCATCACTATAATTAAAATTTAGAACT
195 --AAAAAAAGTGGAGAAAAATATTTATCACAATATATGTCATCACTATAATTAAAATTTAGAACT
* * * *
16786269 ACAAGTATAATTTGTCACAAAAATGTAAATACCATTATTTTTTGTGACAATGTGTTTTTGTAATA
258 ACAAATATAATTTATCACAAAAATGTAAATACAATTATTTTTTATGACAATGTGTTTTTGTAATA
* * * *
16786334 ATTATAAATACTTATAGTTACAAAAATTGTTACTATATGATTTTTTTGGCGTAAAAAATAGGGAG
323 ATTATAAACACTTATAGTTACAAAAATTATCACCATATGATTTTTTTGGCGTAAAAAATAGGGAG
16786399 GAAATTTTTTTATGACATTATATTTTGTTAC
388 GAAATTTTTTTATGACATTATATTTTGTTAC
** *
16786430 TATATAACATTTTTGACATTAAAAAATAGGGAGAAATGATTATAATAGTATAATTTTTCATAATG
1 TATATAACATTTTTG-CACCAAAAAATAGAGAGAAATGATTATAATAGTATAATTTTTCATAATG
** * * *
16786495 ATTAAAATATAT-A-AGTAAAAATAATTTATTACAAAAAAATTTAATTTTATTATTTGATGTAAT
65 ATTAAAATATATAACAACAAAAATAATTGATTACAAAAAAATTAAATTTTATTATCTGATGTAAT
* *
16786558 AATTTTTTCTATATA-AATAACTATAAA-TATAATTATAAAA-TTGTCAATATAAC-TTTTGAAA
130 AATTTTTTCTATA-ACAATAACTATAAATTATAATTACAAAACTTATCAATATAACTTTTTGAAA
* * *
16786619 C-AAAAAAGTGGAGAAAAATATTTATGACAATATATG-CTATCACTATAGTTAAAATTTATAACT
194 CAAAAAAAGTGGAGAAAAATATTTATCACAATATATGTC-ATCACTATAATTAAAATTTAGAACT
* * *
16786682 ACAAATATAATTTATCACAAAAATGTGAATATAATTATTTTTTATGACAACT-TTTTTTTGTAAT
258 ACAAATATAATTTATCACAAAAATGTAAATACAATTATTTTTTATGACAA-TGTGTTTTTGTAAT
* * *
16786746 AATTATTAACGCTTATAGTTACAAAATTTATCACCATATGATTTTTTT
322 AATTATAAACACTTATAGTTACAAAAATTATCACCATATGATTTTTTT
16786794 ACGCCAAAAA
Statistics
Matches: 329, Mismatches: 31, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
412 1 0.00
413 153 0.47
414 1 0.00
417 9 0.03
418 11 0.03
419 12 0.04
420 69 0.21
421 17 0.05
422 56 0.17
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (418 bp):
TATATAACATTTTTGCACCAAAAAATAGAGAGAAATGATTATAATAGTATAATTTTTCATAATGA
TTAAAATATATAACAACAAAAATAATTGATTACAAAAAAATTAAATTTTATTATCTGATGTAATA
ATTTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTATCAATATAACTTTTTGAAACA
AAAAAAGTGGAGAAAAATATTTATCACAATATATGTCATCACTATAATTAAAATTTAGAACTACA
AATATAATTTATCACAAAAATGTAAATACAATTATTTTTTATGACAATGTGTTTTTGTAATAATT
ATAAACACTTATAGTTACAAAAATTATCACCATATGATTTTTTTGGCGTAAAAAATAGGGAGGAA
ATTTTTTTATGACATTATATTTTGTTAC
Found at i:16786842 original size:180 final size:177
Alignment explanation
Indices: 16786618--16787098 Score: 452
Period size: 180 Copynumber: 2.7 Consensus size: 177
16786608 AACTTTTGAA
* * * ** * *
16786618 ACAAAAAAGTGGAGAAAAATATTTATGACAATATATGCTATCACTATAGTTAAAATTTATAACTA
1 ACAAAAAATTGGAG--AAATCTTTGTGACAATATATTTTATCACTATAATTAAAATATATAA-TA
* * *
16786683 CAAATATAATTTATCACAAAAA-TGTGAATATAATTATTTTTTATGACAACTTTTTTTTGTAATA
63 CAAACATAATTTATCACAAAAACTAT-AATATAATTATTTGTTATGACAA-TTTTTTTTGTAATA
* **
16786747 ATTATTA-ACGCTTATAGTTACAAAATTTATCACCATATGATTTT-TTTACG-
126 ATAATTATA-GCTTATAGTTACAAAACATATCACCATATGATTTTGTTTACGT
* *
16786797 CCAAAAAATATGGAGGGAAATCTTTGTGACAATATATTTTATCACTATAATTAAAACA-ATAATG
1 ACAAAAAAT-TGGA--GAAATCTTTGTGACAATATATTTTATCACTATAATTAAAATATATAAT-
** * ** * * *
16786861 ACAAACATTGTTTTTTGCTAAAAACTATAATCTCATTATTTGTTGTGACAATTTTTTTTGTAATA
62 ACAAACATAATTTATCAC-AAAAACTATAATATAATTATTTGTTATGACAATTTTTTTTGTAATA
* **
16786926 ATAATTATAGCTTATAGTTACAAAACATATCACTATATGATTTTGTTTTTGT
126 ATAATTATAGCTTATAGTTACAAAACATATCACCATATGATTTTGTTTACGT
* * *
16786978 ACAAAAAATTGGAGATAATCATTTGTGACTATACATTTTGTCACTATAATTAAAATATATAATTA
1 ACAAAAAATTGGAGA-AATC-TTTGTGACAATATATTTTATCACTATAATTAAAATATATAA-TA
* * * * * * *
16787043 CAAACAAAATTTGTCACAACATAACTA-AATCTCATTATTTATTGTGACAATATTTT
63 CAAACATAATTTATCACAA-A-AACTATAATATAATTATTTGTTATGACAATTTTTT
16787099 CTGTCATAGT
Statistics
Matches: 248, Mismatches: 39, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
178 3 0.01
179 79 0.32
180 105 0.42
181 54 0.22
182 7 0.03
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.40
Consensus pattern (177 bp):
ACAAAAAATTGGAGAAATCTTTGTGACAATATATTTTATCACTATAATTAAAATATATAATACAA
ACATAATTTATCACAAAAACTATAATATAATTATTTGTTATGACAATTTTTTTTGTAATAATAAT
TATAGCTTATAGTTACAAAACATATCACCATATGATTTTGTTTACGT
Found at i:16786946 original size:179 final size:182
Alignment explanation
Indices: 16786715--16787048 Score: 457
Period size: 179 Copynumber: 1.9 Consensus size: 182
16786705 TGTGAATATA
* * **
16786715 ATTATTTTTTATGACAACTTTTTTTTGTAATAATTATTAACGCTTATAGTTACAAAATTTATCAC
1 ATTATTTGTTATGACAACTTTTTTTTGTAATAATAATTAACGCTTATAGTTACAAAACATATCAC
* *
16786780 CATATGATTTT-TTTACG-CCAAAAAATATGGAGGGA-AATC-TTTGTGACAATATATTTTATCA
66 CATATGATTTTGTTTACGTACAAAAAAT-TGGA--GATAATCATTTGTGACAATACATTTTATCA
16786841 CTATAATTAAAACA-ATAATGACAAACATTGTTTTTTGCTAAAAACTATAATCTC
128 CTATAATTAAAACATATAATGACAAACATTGTTTTTTGCTAAAAACTATAATCTC
*
16786895 ATTATTTGTTGTGACAA-TTTTTTTTGTAATAATAATTATA-GCTTATAGTTACAAAACATATCA
1 ATTATTTGTTATGACAACTTTTTTTTGTAATAATAATTA-ACGCTTATAGTTACAAAACATATCA
* ** * *
16786958 CTATATGATTTTGTTTTTGTACAAAAAATTGGAGATAATCATTTGTGACTATACATTTTGTCACT
65 CCATATGATTTTGTTTACGTACAAAAAATTGGAGATAATCATTTGTGACAATACATTTTATCACT
* *
16787023 ATAATTAAAATATATAATTACAAACA
130 ATAATTAAAACATATAATGACAAACA
16787049 AAATTTGTCA
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
178 2 0.01
179 56 0.42
180 56 0.42
181 20 0.15
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (182 bp):
ATTATTTGTTATGACAACTTTTTTTTGTAATAATAATTAACGCTTATAGTTACAAAACATATCAC
CATATGATTTTGTTTACGTACAAAAAATTGGAGATAATCATTTGTGACAATACATTTTATCACTA
TAATTAAAACATATAATGACAAACATTGTTTTTTGCTAAAAACTATAATCTC
Found at i:16787127 original size:181 final size:178
Alignment explanation
Indices: 16786757--16787145 Score: 417
Period size: 181 Copynumber: 2.2 Consensus size: 178
16786747 ATTATTAACG
* * *
16786757 CTTATAGTTACAAAATTTATCACCATATGATTTTTTTACGCCAAAAAATATGGAGGGAAATCTTT
1 CTTATAGTTACAAAACTTATCACTATATGATTTTTTTACGACAAAAAATATGGA-GGAAATCTTT
* *** * **
16786822 GTGACAATATATTTTATCACTATAATTAAAACAATAATGACAAACATTGTTTTTTGCTAAAAACT
65 GTGACAATACATTTTATCACTATAATTAAAACAATAATGACAAACAAAATTTGTCACTAAAAACT
* * * * * *
16786887 ATAATCTCATTATTTGTTGTGACAATTTTTTTTGTAATAATAATTATAG
130 ATAATCTCATTATTTATTGTGACAATATTTTCTGTAATAATAAGTACAA
* **
16786936 CTTATAGTTACAAAACATATCACTATATGATTTTGTTTTTGTACAAAAAAT-TGGA-GATAATCA
1 CTTATAGTTACAAAACTTATCACTATATGATTTT-TTTACG-ACAAAAAATATGGAGGA-AATC-
* * * *
16786999 TTTGTGACTATACATTTTGTCACTATAATTAAAATATATAATTACAAACAAAATTTGTCAC-AAC
62 TTTGTGACAATACATTTTATCACTATAATTAAAACA-ATAATGACAAACAAAATTTGTCACTAA-
* * *
16787063 ATAACTA-AATCTCATTATTTATTGTGACAATATTTTCTGTCATAGTTAGTACAA
125 A-AACTATAATCTCATTATTTATTGTGACAATATTTTCTGTAATAATAAGTACAA
* * *
16787117 CTTTTAGTTACAAAAGTTGTCACTATATG
1 CTTATAGTTACAAAACTTATCACTATATG
16787146 CCTTTAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
178 2 0.01
179 35 0.20
180 42 0.24
181 89 0.51
182 5 0.03
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (178 bp):
CTTATAGTTACAAAACTTATCACTATATGATTTTTTTACGACAAAAAATATGGAGGAAATCTTTG
TGACAATACATTTTATCACTATAATTAAAACAATAATGACAAACAAAATTTGTCACTAAAAACTA
TAATCTCATTATTTATTGTGACAATATTTTCTGTAATAATAAGTACAA
Found at i:16788031 original size:17 final size:18
Alignment explanation
Indices: 16788001--16788038 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16787991 TCTTTGAAAA
16788001 TTTAATATTATTATATAT
1 TTTAATATTATTATATAT
* *
16788019 TTTAAT-TTTTTATGTAT
1 TTTAATATTATTATATAT
16788036 TTT
1 TTT
16788039 CTATTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTAATATTATTATATAT
Found at i:16789538 original size:4 final size:4
Alignment explanation
Indices: 16789531--16789639 Score: 54
Period size: 4 Copynumber: 27.2 Consensus size: 4
16789521 AAAATGAATG
* *
16789531 ATAA ATAA AGTAAA AAAA ATGA ATGAA ATAA ATAA ATAA AT-A A-AA ATAA
1 ATAA ATAA A-T-AA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA
*
16789580 A-AA ATATA GA-AA AT-A A-AA ATAA ATGAA AAAA ATGAA A-AA A-AA
1 ATAA ATA-A -ATAA ATAA ATAA ATAA AT-AA ATAA AT-AA ATAA ATAA
*
16789622 ATAG ATAA AGTAA ATAA A
1 ATAA ATAA A-TAA ATAA A
16789640 ACAAATAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
3 18 0.22
4 44 0.54
5 16 0.20
6 4 0.05
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.18
Consensus pattern (4 bp):
ATAA
Found at i:16789550 original size:31 final size:29
Alignment explanation
Indices: 16789513--16789608 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 29
16789503 TGCGTTAGAT
16789513 AAAAAATGAAAATGAATGATAAATAAAGTAA
1 AAAAAATGAAAATGAAT-ATAAATAAA-TAA
16789544 AAAAAATG--AATGAA-ATAAATAAATAA
1 AAAAAATGAAAATGAATATAAATAAATAA
*
16789570 ATAAAAAT-AAAA--AATATAGA-AAATAA
1 A-AAAAATGAAAATGAATATAAATAAATAA
16789596 AAATAAATGAAAA
1 AAA-AAATGAAAA
16789609 AAATGAAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
25 2 0.03
26 17 0.29
27 23 0.40
28 2 0.03
29 6 0.10
31 8 0.14
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (29 bp):
AAAAAATGAAAATGAATATAAATAAATAA
Found at i:16789561 original size:27 final size:25
Alignment explanation
Indices: 16789511--16789639 Score: 84
Period size: 22 Copynumber: 5.4 Consensus size: 25
16789501 GATGCGTTAG
*
16789511 ATAAA-AAATGAAAATGAATGATAA
1 ATAAATAAATAAAAATGAATGATAA
16789535 ATAAAGTAAA-AAAAATGAATGAAATAA
1 ATAAA-TAAATAAAAATGAATG--ATAA
16789562 ATAAATAAATAAAAAT-AA--A-AA
1 ATAAATAAATAAAAATGAATGATAA
*
16789583 ATATAGA-AAATAAAAATAAATGA-AA
1 ATA-A-ATAAATAAAAATGAATGATAA
*
16789608 A-AAATGAA-AAAAA--AATAGATAA
1 ATAAATAAATAAAAATGAAT-GATAA
16789630 AGTAAATAAA
1 A-TAAATAAA
16789640 ACAAATAAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 30
0.73 0.03 0.25
Matches are distributed among these distances:
20 3 0.03
21 7 0.08
22 21 0.24
23 6 0.07
24 12 0.14
25 14 0.16
26 9 0.10
27 15 0.17
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.19
Consensus pattern (25 bp):
ATAAATAAATAAAAATGAATGATAA
Found at i:16789584 original size:17 final size:17
Alignment explanation
Indices: 16789556--16789609 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
16789546 AAAATGAATG
16789556 AAATAAATAAATAAATAA
1 AAATAAA-AAATAAATAA
16789574 AAATAAAAAAT--ATAGA
1 AAATAAAAAATAAATA-A
16789590 AAAT-AAAAATAAATGAA
1 AAATAAAAAATAAAT-AA
16789607 AAA
1 AAA
16789610 AATGAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
15 9 0.28
16 5 0.16
17 10 0.31
18 8 0.25
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
AAATAAAAAATAAATAA
Found at i:16789599 original size:28 final size:25
Alignment explanation
Indices: 16789542--16789624 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 25
16789532 TAAATAAAGT
* *
16789542 AAAAAAAAT-GAATGAAATAAAT-A
1 AAAAAAAATAAAATGAAAAAAATGA
* *
16789565 AATAAATA-AAAAT-AAAAAATATAGA
1 AAAAAAAATAAAATGAAAAAA-AT-GA
16789590 AAATAAAAAT-AAATGAAAAAAATGA
1 AAA-AAAAATAAAATGAAAAAAATGA
16789615 AAAAAAAATA
1 AAAAAAAATA
16789625 GATAAAGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
22 5 0.11
23 11 0.24
24 6 0.13
25 8 0.17
26 10 0.22
27 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAAAAAATAAAATGAAAAAAATGA
Found at i:16789612 original size:9 final size:9
Alignment explanation
Indices: 16789513--16789620 Score: 53
Period size: 9 Copynumber: 11.7 Consensus size: 9
16789503 TGCGTTAGAT
16789513 AAAAAATGA
1 AAAAAATGA
*
16789522 AAATGAATGA
1 AAA-AAATGA
*
16789532 TAAATAAAGTAA
1 -AAA-AAA-TGA
16789544 AAAAAATGA
1 AAAAAATGA
**
16789553 ATGAAAT-A
1 AAAAAATGA
* *
16789561 AATAAATAA
1 AAAAAATGA
16789570 ATAAAAAT-A
1 A-AAAAATGA
16789579 AAAAATATAGA
1 AAAAA-AT-GA
*
16789590 AAATAA--A
1 AAAAAATGA
*
16789597 AATAAATGA
1 AAAAAATGA
16789606 AAAAAATGA
1 AAAAAATGA
16789615 AAAAAA
1 AAAAAA
16789621 AATAGATAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
7 5 0.07
8 10 0.13
9 31 0.41
10 14 0.18
11 14 0.18
12 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (9 bp):
AAAAAATGA
Found at i:16789637 original size:37 final size:36
Alignment explanation
Indices: 16789542--16789661 Score: 106
Period size: 37 Copynumber: 3.2 Consensus size: 36
16789532 TAAATAAAGT
16789542 AAAAAAAAT-GAATGAAATAAATAAATAAATAAAAAT--
1 AAAAAAAATAG-AT-AAATAAATAAATAAA-AAAAATGA
* *
16789578 AAAAAATATAGA-AAATAAAAATAAATGAAAAAAATGA
1 AAAAAAAATAGATAAAT--AAATAAATAAAAAAAATGA
16789615 AAAAAAAATAGATAAAGTAAATAAA-ACAAATAAAATGA
1 AAAAAAAATAGATAAA-TAAATAAATA-AAA-AAAATGA
16789653 AAGAAAAAA
1 AA-AAAAAA
16789662 GTAATAATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
34 4 0.06
35 6 0.09
36 19 0.27
37 22 0.31
38 12 0.17
39 7 0.10
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (36 bp):
AAAAAAAATAGATAAATAAATAAATAAAAAAAATGA
Found at i:16789771 original size:9 final size:9
Alignment explanation
Indices: 16789759--16789821 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
16789749 AAAAATAAAG
16789759 AATAAAATA
1 AATAAAATA
16789768 AATAAAATTA
1 AATAAAA-TA
* *
16789778 AATTAAATT
1 AATAAAATA
16789787 AATAATAAATA
1 AAT-A-AAATA
16789798 AATAAAATA
1 AATAAAATA
*
16789807 GA-AAAATA
1 AATAAAATA
16789815 AGATAAA
1 A-ATAAA
16789822 TAATAATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
8 6 0.14
9 18 0.42
10 12 0.28
11 7 0.16
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
AATAAAATA
Found at i:16789780 original size:26 final size:25
Alignment explanation
Indices: 16789750--16789830 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
16789740 TAAAAAGATA
16789750 AAAATAAAGAATAAAATAAATAAAAT
1 AAAATAAA-AATAAAATAAATAAAAT
* * *
16789776 TAAATTAAATTAATAATAAAT-AAAT
1 AAAATAAAAATAA-AATAAATAAAAT
*
16789801 AAAATAGAAAAATAAGATAAATAATAAT
1 AAAAT--AAAAATAAAATAAATAA-AAT
16789829 AA
1 AA
16789831 TGATAATAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
25 12 0.28
26 19 0.44
27 7 0.16
28 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (25 bp):
AAAATAAAAATAAAATAAATAAAAT
Found at i:16789888 original size:14 final size:13
Alignment explanation
Indices: 16789869--16789898 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
16789859 CAAATAAATA
16789869 AAAAAGAAATATAG
1 AAAAAGAAATA-AG
16789883 AAAAAGAAATAAG
1 AAAAAGAAATAAG
16789896 AAA
1 AAA
16789899 TATAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAAAGAAATAAG
Found at i:16791023 original size:2 final size:2
Alignment explanation
Indices: 16791016--16791109 Score: 156
Period size: 2 Copynumber: 48.0 Consensus size: 2
16791006 TTTAATAAAA
*
16791016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16791058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16791099 AT AT A- AT AT AT
1 AT AT AT AT AT AT
16791110 GTTTATTTTG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
1 2 0.02
2 84 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16791789 original size:40 final size:40
Alignment explanation
Indices: 16791740--16791819 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
16791730 ATGTCGAGAG
16791740 AGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTT
1 AGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTT
* *
16791780 AGACGAAATTTGTTTAAAGGAAAACATATTCAAAGATTTT
1 AGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTT
16791820 GTTTCAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.31
Consensus pattern (40 bp):
AGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTTT
Found at i:16791869 original size:36 final size:36
Alignment explanation
Indices: 16791817--16792311 Score: 304
Period size: 36 Copynumber: 14.2 Consensus size: 36
16791807 ATTCAAAGAT
* *
16791817 TTTGTTTCAAGGGAAACTTTCTCAAGAGAAACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
16791853 TTTGATTCAAGGGAAACTGTCTCAAGAGAGAGAGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA-AAA
* *
16791890 -TTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
16791925 CTTAGTTCCAAAAGAAACTATCTCAAGGGAGATAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** *
16791962 TTTGTTTAAAGGAAAACAAAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
16791991 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * *
16792027 TTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 TTT-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * **
16792064 TTTGTTTCAAGGAAAACAGAT-TC--CA-AG---ATT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
16792094 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * * *
16792130 CTTAGTTCCAA-AAAAATTGTCTTAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
16792166 TTTGTTTCAAGGAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
16792195 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * *
16792231 TTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 TTT-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
16792268 TTTGTTTTAAGAGG-AACTGTCTCAAGACAGACAAAA
1 TTTGTTTCAAG-GGAAACTGTCTCAAGAGAGACAAAA
16792304 CTTTGTTT
1 -TTTGTTT
16792312 TGAGTAAATT
Statistics
Matches: 345, Mismatches: 79, Indels: 69
0.70 0.16 0.14
Matches are distributed among these distances:
28 2 0.01
29 39 0.11
30 22 0.06
31 2 0.01
32 5 0.01
33 8 0.02
35 13 0.04
36 141 0.41
37 113 0.33
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Done.