Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 64
Found at i:3137296 original size:22 final size:22
Alignment explanation
Indices: 3137270--3137324 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3137260 TTGTGTTTGG
3137270 TCAAAGGTTTGGCATTCGATGC
1 TCAAAGGTTTGGCATTCGATGC
*
3137292 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTCGATGC
3137314 TCAAAGGTTTG
1 TCAAAGGTTTG
3137325 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTCGATGC
Found at i:3137946 original size:15 final size:15
Alignment explanation
Indices: 3137928--3137981 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
3137918 TTTTGTCCCC
3137928 CTTTTTTTATTCTTT
1 CTTTTTTTATTCTTT
* *
3137943 CTTTTTTTGTTTTCTT
1 CTTTTTTTATTCT-TT
**
3137959 CTTTTTTGCTTCTTTT
1 CTTTTTTTATTC-TTT
3137975 CTTTTTT
1 CTTTTTT
3137982 ATTTTTACCC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 11 0.34
16 20 0.62
17 1 0.03
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (15 bp):
CTTTTTTTATTCTTT
Found at i:3137976 original size:16 final size:14
Alignment explanation
Indices: 3137930--3137987 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
3137920 TTGTCCCCCT
* *
3137930 TTTTTTATTCTTTC
1 TTTTTTGTTTTTTC
3137944 TTTTTTTGTTTTCTTC
1 -TTTTTTGTTTT-TTC
3137960 TTTTTTGCTTCTTTTC
1 TTTTTTG-TT-TTTTC
*
3137976 TTTTTTATTTTT
1 TTTTTTGTTTTT
3137988 ACCCTTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.08
15 18 0.49
16 14 0.38
17 2 0.05
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTTTGTTTTTTC
Found at i:3137995 original size:32 final size:30
Alignment explanation
Indices: 3137926--3137996 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 30
3137916 TTTTTTGTCC
*
3137926 CCCTTTTTTTATTCTTTCTTTTTTTGTTTT
1 CCCTTTTTTGATTCTTTCTTTTTTTGTTTT
* *
3137956 CTTCTTTTTTGCTTCTTTTCTTTTTTAT-TTTT
1 C-CCTTTTTTGATTC-TTTCTTTTTT-TGTTTT
3137988 ACCCTTTTT
1 -CCCTTTTT
3137997 GTTCTGATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.03
31 10 0.30
32 20 0.61
33 2 0.06
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (30 bp):
CCCTTTTTTGATTCTTTCTTTTTTTGTTTT
Found at i:3142752 original size:22 final size:22
Alignment explanation
Indices: 3142727--3142780 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3142717 TAATAAGAGC
3142727 AAATAAACTAAA-AATATAATGA
1 AAATAAA-TAAATAATATAATGA
* * *
3142749 AAATAGATAAATAGTATAATTA
1 AAATAAATAAATAATATAATGA
3142771 AAAT-AATAAA
1 AAATAAATAAA
3142781 AAAATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (22 bp):
AAATAAATAAATAATATAATGA
Found at i:3142788 original size:22 final size:23
Alignment explanation
Indices: 3142736--3142806 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 23
3142726 CAAATAAACT
*
3142736 AAAAATATAATGAAAATAGAT-A
1 AAAAATATAATTAAAATAGATAA
* *
3142758 AATAGTATAATTAAAATA-ATAA
1 AAAAATATAATTAAAATAGATAA
*
3142780 AAAAATATATATATAAAA-ATATAA
1 AAAAATATA-AT-TAAAATAGATAA
3142804 AAA
1 AAA
3142807 TGTATGTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 2 0.05
22 23 0.57
23 3 0.08
24 12 0.30
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAAATATAATTAAAATAGATAA
Found at i:3142796 original size:24 final size:24
Alignment explanation
Indices: 3142769--3142827 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
3142759 ATAGTATAAT
3142769 TAAAATAATAAAAAAATATATATA
1 TAAAATAATAAAAAAATATATATA
* * *
3142793 T-AAA-AATATAAAAATGTATGTA
1 TAAAATAATAAAAAAATATATATA
*
3142815 TAATATAATAAAA
1 TAAAATAATAAAA
3142828 TACTAAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 16 0.57
23 5 0.18
24 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (24 bp):
TAAAATAATAAAAAAATATATATA
Found at i:3142974 original size:14 final size:14
Alignment explanation
Indices: 3142951--3143000 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
3142941 ATAATGTTAG
*
3142951 AAAAATATAGTAAA
1 AAAAACATAGTAAA
3142965 AAAAACATAGTAAA
1 AAAAACATAGTAAA
3142979 TAACTAAACATAGATAAA
1 -AA--AAACATAG-TAAA
3142997 AAAA
1 AAAA
3143001 TAATAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 13 0.42
15 4 0.13
17 10 0.32
18 4 0.13
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAACATAGTAAA
Found at i:3143619 original size:37 final size:37
Alignment explanation
Indices: 3143526--3143627 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
3143516 ATGCTTGTAG
* * ** * *
3143526 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
3143563 ATCCTCTTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
3143600 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
3143628 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:3144043 original size:64 final size:64
Alignment explanation
Indices: 3143975--3144110 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 64
3143965 TGCACTAAGG
* *
3143975 GTGCATCGATGCATGAAATGTATTCGATGTTTCAAACA-AGCCTGAGTGCATCGATGCATGGCCT
1 GTGCATCGATGCATAAAATGTATTCGATGTTTCAAA-ATAGCCGGAGTGCATCGATGCATGGCCT
* * * *
3144039 GTGCATCGATGCATAAAATGTATTCGATGTTTTAAAATAGTCGGGGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATAAAATGTATTCGATGTTTCAAAATAGCCGGAGTGCATCGATGCATGGCCT
*
3144103 ATGCATCG
1 GTGCATCG
3144111 GTACACTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
63 1 0.02
64 63 0.98
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGTATTCGATGTTTCAAAATAGCCGGAGTGCATCGATGCATGGCCT
Found at i:3144122 original size:64 final size:64
Alignment explanation
Indices: 3143976--3144129 Score: 177
Period size: 64 Copynumber: 2.4 Consensus size: 64
3143966 GCACTAAGGG
* * * *
3143976 TGCATCGATGCATGAAATGTATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGCCTG
1 TGCATCGATACATAAAATGTATTCGATGTTTCAAACAAGCCGGAGTGCATCGATGCATGGCCTA
* * * * *
3144040 TGCATCGATGCATAAAATGTATTCGATGTTTTAAA-ATAGTCGGGGTGCATCGATGCATGGCTTA
1 TGCATCGATACATAAAATGTATTCGATGTTTCAAACA-AGCCGGAGTGCATCGATGCATGGCCTA
* *
3144104 TGCATCGGTACACT-AAATGCATTCGA
1 TGCATCGATACA-TAAAATGTATTCGA
3144130 AGTTCAATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 76 0.97
65 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (64 bp):
TGCATCGATACATAAAATGTATTCGATGTTTCAAACAAGCCGGAGTGCATCGATGCATGGCCTA
Found at i:3146786 original size:20 final size:20
Alignment explanation
Indices: 3146761--3146812 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3146751 ACCCAATGGA
3146761 TGCATCGATGCATGGCAGTG
1 TGCATCGATGCATGGCAGTG
3146781 TGCATCGATGCATGGCAGTG
1 TGCATCGATGCATGGCAGTG
3146801 TGCATCGATGCA
1 TGCATCGATGCA
3146813 CATTCAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCATGGCAGTG
Found at i:3146830 original size:23 final size:23
Alignment explanation
Indices: 3146800--3146969 Score: 133
Period size: 23 Copynumber: 7.6 Consensus size: 23
3146790 GCATGGCAGT
*
3146800 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAATGA
*
3146823 GTGCATCGGTGCATCA-TC-ATGA
1 GTGCATCGATGCA-CATTCAATGA
* *
3146845 -TGTATTGATGCACATTCAATGA
1 GTGCATCGATGCACATTCAATGA
*
3146867 GTGCATCGGTGCATCA-TC-ATGA
1 GTGCATCGATGCA-CATTCAATGA
* *
3146889 -TGTATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAATGA
* *
3146911 GTGCATCGGTGTATCA-TC-ATGA
1 GTGCATCGATGCA-CATTCAATGA
* * *
3146933 -TGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTCAATGA
3146955 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
3146970 TATTTAGTGT
Statistics
Matches: 113, Mismatches: 21, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
20 6 0.05
21 34 0.30
22 19 0.17
23 36 0.32
24 18 0.16
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAATGA
Found at i:3146856 original size:21 final size:21
Alignment explanation
Indices: 3146827--3146944 Score: 96
Period size: 21 Copynumber: 5.4 Consensus size: 21
3146817 CAAGGAGTGC
*
3146827 ATCGGTGCATCATCATGATGT
1 ATCGATGCATCATCATGATGT
* *
3146848 ATTGATGCA-CATTCAATGAGTGC
1 ATCGATGCATCA-TC-ATGA-TGT
*
3146871 ATCGGTGCATCATCATGATGT
1 ATCGATGCATCATCATGATGT
* *
3146892 ATCGATGCA-CATTCAAGGAGTGC
1 ATCGATGCATCA-TC-ATGA-TGT
* *
3146915 ATCGGTGTATCATCATGATGT
1 ATCGATGCATCATCATGATGT
3146936 ATCGATGCA
1 ATCGATGCA
3146945 CATTCAAAGG
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
20 4 0.05
21 30 0.41
22 14 0.19
23 22 0.30
24 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
ATCGATGCATCATCATGATGT
Found at i:3146863 original size:44 final size:44
Alignment explanation
Indices: 3146804--3146968 Score: 269
Period size: 44 Copynumber: 3.7 Consensus size: 44
3146794 GGCAGTGTGC
3146804 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCATCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCATCATGATGT
* *
3146848 ATTGATGCACATTCAATGAGTGCATCGGTGCATCATCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCATCATGATGT
*
3146892 ATCGATGCACATTCAAGGAGTGCATCGGTGTATCATCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCATCATGATGT
*
3146936 ATCGATGCACATTCAAAGG-GATGCATCGATGCA
1 ATCGATGCACATTC-AAGGAG-TGCATCGGTGCA
3146969 CTATTTAGTG
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
44 98 0.88
45 14 0.12
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGGTGCATCATCATGATGT
Found at i:3152812 original size:19 final size:19
Alignment explanation
Indices: 3152743--3152806 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
3152733 GGAACACTTA
3152743 GTGCATCGGTGCACTAAGG
1 GTGCATCGGTGCACTAAGG
3152762 GTGCATCGGTGCACTAAGG
1 GTGCATCGGTGCACTAAGG
*
3152781 GTGCATCGGTGCACTAATG
1 GTGCATCGGTGCACTAAGG
3152800 GTGCATC
1 GTGCATC
3152807 AATGCATGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.23
Consensus pattern (19 bp):
GTGCATCGGTGCACTAAGG
Found at i:3152916 original size:63 final size:63
Alignment explanation
Indices: 3152801--3152952 Score: 177
Period size: 63 Copynumber: 2.4 Consensus size: 63
3152791 GCACTAATGG
* * *
3152801 TGCATCAATGCATGAATGCATTCGATGTTTCAAACAAGCCTGAGTGCGTCGATGCATGG-TCTA
1 TGCATCGATGCATAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGCT-TA
* *
3152864 TGCATCGATGCATAAAATGCATTCGATGTTT-AAA-ATAGTC-GGGCTGCATCGATGCATGGCTT
1 TGCATCGATGCAT-AAATGCATTCGATGTTTCAAACA-AGCCTGAG-TGCATCGATGCATGGCTT
3152926 A
63 A
*
3152927 TGCATCGATACACTAAATGCATTCGA
1 TGCATCGATGCA-TAAATGCATTCGA
3152953 AGTTCAATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
62 3 0.04
63 57 0.73
64 18 0.23
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (63 bp):
TGCATCGATGCATAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGCTTA
Found at i:3154652 original size:23 final size:23
Alignment explanation
Indices: 3154619--3154738 Score: 93
Period size: 23 Copynumber: 5.3 Consensus size: 23
3154609 AGTCGAGGGT
* *
3154619 TCTATGAGGTCCTTTGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
3154642 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* ** * * *
3154665 TCTTTACGGTTCTTTGGGACAAG
1 TCTATGTGGTCCTTCGGGACAAA
* * *
3154688 CCTATGTGGTACTTCGGGATAAA
1 TCTATGTGGTCCTTCGGGACAAA
* * *
3154711 --TATGTGGTACTTCAGTACAAA
1 TCTATGTGGTCCTTCGGGACAAA
3154732 T-TATGTG
1 TCTATGTG
3154739 AGCAGTGGTG
Statistics
Matches: 77, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
21 18 0.23
22 6 0.08
23 53 0.69
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:3154732 original size:21 final size:22
Alignment explanation
Indices: 3154690--3154738 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
3154680 GGGACAAGCC
* *
3154690 TATGTGGTACTTCGGGATAAA-
1 TATGTGGTACTTCAGGACAAAT
*
3154711 TATGTGGTACTTCAGTACAAAT
1 TATGTGGTACTTCAGGACAAAT
3154733 TATGTG
1 TATGTG
3154739 AGCAGTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (22 bp):
TATGTGGTACTTCAGGACAAAT
Found at i:3154838 original size:19 final size:19
Alignment explanation
Indices: 3154814--3154850 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3154804 ATGTTGGGCT
*
3154814 AATTAAATAAATGGATATA
1 AATTAAACAAATGGATATA
*
3154833 AATTAAACAAATTGATAT
1 AATTAAACAAATGGATAT
3154851 GGAATGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAACAAATGGATATA
Found at i:3158061 original size:45 final size:45
Alignment explanation
Indices: 3157975--3158061 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
3157965 TTTGCCCCTA
* * * *
3157975 TTTACAACAGCAGGCTCAACCCCTCCATCATTTGCCGTTAACTCG
1 TTTACAACAGCAGGCCCAACCACTCAATCATTTACCGTTAACTCG
*
3158020 TTTACACCAGCAGGCCCAACCACTCAATCATTTTACC-TTAAC
1 TTTACAACAGCAGGCCCAACCACTCAATCA-TTTACCGTTAAC
3158062 ACATTTGCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.28, C:0.36, G:0.10, T:0.26
Consensus pattern (45 bp):
TTTACAACAGCAGGCCCAACCACTCAATCATTTACCGTTAACTCG
Found at i:3158816 original size:2 final size:2
Alignment explanation
Indices: 3158811--3158853 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3158801 AAAAATAACA
3158811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3158853 A
1 A
3158854 AACAGTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3159571 original size:14 final size:14
Alignment explanation
Indices: 3159525--3159571 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3159515 TTTCAGAAAC
*
3159525 AAAAAAATAAAATA
1 AAAAAAATGAAATA
*
3159539 TAAAAAATGTAAA-A
1 AAAAAAATG-AAATA
*
3159553 GAAAAAATGAAATA
1 AAAAAAATGAAATA
3159567 AAAAA
1 AAAAA
3159572 GGTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAAAAATGAAATA
Found at i:3160068 original size:3 final size:3
Alignment explanation
Indices: 3160049--3160100 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
3160039 ATATTTTAAA
* *
3160049 TAT TAAT TAT ATAT TAT TAT TAT TAT TAT TAT TAC TAC TAT TAAT T-T
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
3160096 TAT TA
1 TAT TA
3160101 CATAATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 32 0.74
4 9 0.21
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3161841 original size:2 final size:2
Alignment explanation
Indices: 3161836--3161867 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3161826 CATTTTTTTA
3161836 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
3161868 TTTAAATTTT
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):
AT
Found at i:3163924 original size:7 final size:7
Alignment explanation
Indices: 3163912--3163948 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
3163902 GAAAATGAAA
3163912 ATTACAT
1 ATTACAT
3163919 ATTACAT
1 ATTACAT
3163926 ATTACAT
1 ATTACAT
3163933 ATTACAT
1 ATTACAT
3163940 ATTACAT
1 ATTACAT
3163947 AT
1 AT
3163949 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTACAT
Found at i:3164022 original size:37 final size:39
Alignment explanation
Indices: 3163958--3164049 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 39
3163948 TATTTTTAAA
* *
3163958 AAAAGGTTTTCAAAATCATATTATATATATATATCTTCG
1 AAAAGGTTTTCAAAATCATATTATATATATATATATTCC
* * *
3163997 AAAATGTTTTCTAAATTATA-T-TATATATATATATTCC
1 AAAAGGTTTTCAAAATCATATTATATATATATATATTCC
**
3164034 AAAACATTTTCAAAAT
1 AAAAGGTTTTCAAAAT
3164050 GTTTTCAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
37 27 0.60
38 1 0.02
39 17 0.38
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (39 bp):
AAAAGGTTTTCAAAATCATATTATATATATATATATTCC
Found at i:3164110 original size:36 final size:36
Alignment explanation
Indices: 3164051--3164232 Score: 160
Period size: 36 Copynumber: 5.0 Consensus size: 36
3164041 TTTCAAAATG
*
3164051 TTTTCAAAAATGTTTTTTC-AAACTATATAATATATA
1 TTTTCAAAAAT-TGTTTTCAAAACTATATAATATATA
*
3164087 TTTTCAAAAATTATTTTCAAAAC--TATAATATATA
1 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
* * * * *
3164121 TATTC-AAAATTGTTTTTAAAATTATATAATGTGTA
1 TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
* *
3164156 TTTTCAAAAATATTTTTTAAAAAACTATATATTATATATA
1 TTTTCAAAAAT-TGTTTT-CAAAACTATATA--ATATATA
* *
3164196 TTTTTTC-AAAA-TGTTTTCAAAATTATATTATATATA
1 --TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
3164232 T
1 T
3164233 ATATATATAT
Statistics
Matches: 119, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
33 14 0.12
34 16 0.13
35 19 0.16
36 27 0.23
37 5 0.04
38 19 0.16
39 5 0.04
40 5 0.04
41 4 0.03
42 5 0.04
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTTCAAAAATTGTTTTCAAAACTATATAATATATA
Found at i:3164165 original size:69 final size:73
Alignment explanation
Indices: 3164052--3164232 Score: 201
Period size: 69 Copynumber: 2.5 Consensus size: 73
3164042 TTCAAAATGT
* * *
3164052 TTTCAAAAATGTTTTTTCAAACTATATAATATATATTTTCAAAAAT-TATTTT-CAAAACTATA-
1 TTTC-AAAATG-TTTTTAAAATTATATAATATATATTTTCAAAAATATATTTTAAAAAACTATAT
3164114 A-TATATATA
64 ATTATATATA
* * *
3164123 -TTCAAAATTGTTTTTAAAATTATATAATGTGTATTTTCAAAAATATTTTTTAAAAAACTATATA
1 TTTCAAAA-TGTTTTTAAAATTATATAATATATATTTTCAAAAATATATTTTAAAAAACTATATA
3164187 TTATATATA
65 TTATATATA
* *
3164196 TTTTTTCAAAATGTTTTCAAAATTATATTATATATAT
1 ---TTTCAAAATGTTTTTAAAATTATATAATATATAT
3164233 ATATATATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
69 34 0.37
70 10 0.11
71 9 0.10
72 1 0.01
73 8 0.09
76 22 0.24
77 7 0.08
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (73 bp):
TTTCAAAATGTTTTTAAAATTATATAATATATATTTTCAAAAATATATTTTAAAAAACTATATAT
TATATATA
Found at i:3164248 original size:46 final size:49
Alignment explanation
Indices: 3164181--3164278 Score: 141
Period size: 46 Copynumber: 2.1 Consensus size: 49
3164171 TTTAAAAAAC
*
3164181 TATATATTATATATATTTTTTC-AAAAT-GTTTTCAAAA-T-TATATTA
1 TATATATTATATATATATTTTCGAAAATCGTTTTCAAAACTATATATTA
*
3164226 TATATATATATATATATATTTTCGAAAATCTTTTTCAAAACTATATATTA
1 TATATAT-TATATATATATTTTCGAAAATCGTTTTCAAAACTATATATTA
3164276 TAT
1 TAT
3164279 TTTTTTCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
45 7 0.15
46 14 0.30
47 5 0.11
48 9 0.20
49 1 0.02
50 10 0.22
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (49 bp):
TATATATTATATATATATTTTCGAAAATCGTTTTCAAAACTATATATTA
Found at i:3164304 original size:37 final size:39
Alignment explanation
Indices: 3164228--3164301 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 39
3164218 TTATATTATA
* *
3164228 TATATATATATATATATTTTCGAAAATCTTTTTCAAAAC
1 TATATATATATATATATTTTCCAAAATCATTTTCAAAAC
*
3164267 TATATAT-TATAT-TTTTTTCCAAAAT-ATTTTCAAAA
1 TATATATATATATATATTTTCCAAAATCATTTTCAAAA
3164302 ACTCTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.28
37 11 0.34
38 5 0.16
39 7 0.22
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (39 bp):
TATATATATATATATATTTTCCAAAATCATTTTCAAAAC
Found at i:3171217 original size:138 final size:137
Alignment explanation
Indices: 3170933--3171278 Score: 326
Period size: 137 Copynumber: 2.5 Consensus size: 137
3170923 CTATGGGATC
* * * * * * * ** *
3170933 AAACCTAAAATCGTAGGATCTAATATTAATCCAAATCATTTTTAATAAATTGGTGAATCGAATAA
1 AAACCTAAAAT-GAAGGCTCTAATTTTAATCCTAATTAATTTTAATCAATTACTGATTCGAATAA
* * ** * * * *
3170998 TTCAAATGGAACCTCGAGCAAAATTGATGGCCAAATAAAAAATTCCCCTACATTAAAGGATTATT
65 TTAAAATGAAACCTCGAGCAAAAGCGATGACCAAATAAAAAATTCACCTAAATTAAAGGATAATT
3171063 ATGAAATT
130 ATGAAATT
* *
3171071 AAACCTAAAATGGAGGCTCT-ATTAATTAA-CCT-ATTCAATTTTAATCCATTACTGATTCGAAT
1 AAACCTAAAATGAAGGCTCTAATT--TTAATCCTAATT-AATTTTAATCAATTACTGATTCGAAT
* ** *
3171133 AATTAAAATGAAACCTCGAGCAAAAGCGATGACCAAATTAAATTTTCATCTAAATTTAAA-GACT
63 AATTAAAATGAAACCTCGAGCAAAAGCGATGACCAAATAAAAAATTCACCTAAA-TTAAAGGA-T
3171197 AAGTT-TGAAATT
126 AA-TTATGAAATT
* * * *
3171209 AAGCCTAAAGTGAAGGCTCTAATTTTAATCCTAATTAATTTTATTCAATTATTGATTC-AAGTAA
1 AAACCTAAAATGAAGGCTCTAATTTTAATCCTAATTAATTTTAATCAATTACTGATTCGAA-TAA
3171273 TTAAAA
65 TTAAAA
3171279 GCTCTAGGGA
Statistics
Matches: 169, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
136 4 0.02
137 80 0.47
138 77 0.46
139 8 0.05
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (137 bp):
AAACCTAAAATGAAGGCTCTAATTTTAATCCTAATTAATTTTAATCAATTACTGATTCGAATAAT
TAAAATGAAACCTCGAGCAAAAGCGATGACCAAATAAAAAATTCACCTAAATTAAAGGATAATTA
TGAAATT
Found at i:3173173 original size:32 final size:34
Alignment explanation
Indices: 3173110--3173184 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 34
3173100 TCGGGCCGGG
3173110 TATATATA-TTTAAATTAAATATATAAATATT-A
1 TATATATATTTTAAATTAAATATATAAATATTAA
* *
3173142 TATATATATTTTAATTTAAAT-TA-AATTTATTAA
1 TATATATATTTTAAATTAAATATATAA-ATATTAA
3173175 TATTATATAT
1 TA-TATATAT
3173185 ATATAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
31 2 0.05
32 14 0.38
33 14 0.38
34 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TATATATATTTTAAATTAAATATATAAATATTAA
Found at i:3173195 original size:38 final size:37
Alignment explanation
Indices: 3173110--3173195 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
3173100 TCGGGCCGGG
3173110 TATATAT-ATTTAAATTAAATATATAAATATTATATA
1 TATATATAATTTAAATTAAATATATAAATATTATATA
* * *
3173146 TATATTTTAATTTAAATTAAATTTATTAATATTATATA
1 TATA-TATAATTTAAATTAAATATATAAATATTATATA
3173184 TATATAATAATT
1 TATAT-ATAATT
3173196 ATTTTTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 4 0.09
37 3 0.07
38 36 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
TATATATAATTTAAATTAAATATATAAATATTATATA
Found at i:3173196 original size:32 final size:32
Alignment explanation
Indices: 3173110--3173207 Score: 80
Period size: 38 Copynumber: 3.0 Consensus size: 32
3173100 TCGGGCCGGG
* * *
3173110 TATATATAT-TTA-AATTAAATATATAAATAT
1 TATATATATATAATAATTAAATTTATTAATAT
3173140 TATATATATATTTTAATTTAAATTAAATTTATTAATAT
1 TATATATATA---TAA--T-AATTAAATTTATTAATAT
3173178 TATATATATATAATAATT--ATTT-TTAATAT
1 TATATATATATAATAATTAAATTTATTAATAT
3173207 T
1 T
3173208 TATCAGGCCG
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
29 8 0.14
30 13 0.23
32 4 0.07
33 1 0.02
34 2 0.04
35 3 0.05
38 26 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATATATATAATAATTAAATTTATTAATAT
Found at i:3173615 original size:3 final size:3
Alignment explanation
Indices: 3173607--3173676 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
3173597 ATATATTTGA
* *
3173607 AAT AAT AAT AAT AAT AAT AAT AAAT AAG AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
*
3173653 AAT AAT AAT AAAC AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AA
3173677 AAATGACAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
3 54 0.92
4 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3173645 original size:31 final size:28
Alignment explanation
Indices: 3173608--3173676 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 28
3173598 TATATTTGAA
*
3173608 ATAATAATAATAATAATAATAAATAAGAGTA
1 ATAATAATAATAATAATAAT-AATAA-A-CA
3173639 ATAATAATAATAATAATAATAATAAACA
1 ATAATAATAATAATAATAATAATAAACA
3173667 ATAATAATAA
1 ATAATAATAA
3173677 AAATGACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 11 0.30
29 1 0.03
30 5 0.14
31 20 0.54
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (28 bp):
ATAATAATAATAATAATAATAATAAACA
Found at i:3173646 original size:25 final size:25
Alignment explanation
Indices: 3173610--3173680 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
3173600 TATTTGAAAT
3173610 AATAATAATAATAATAATAAATAAG
1 AATAATAATAATAATAATAAATAAG
* *
3173635 AGTAATAATAATAATAAT-AATAAT
1 AATAATAATAATAATAATAAATAAG
*
3173659 AATAAACAATAATAATAA-AAAT
1 AAT-AATAATAATAATAATAAAT
3173681 GACAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.17
25 33 0.82
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (25 bp):
AATAATAATAATAATAATAAATAAG
Found at i:3173687 original size:25 final size:25
Alignment explanation
Indices: 3173616--3173689 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
3173606 AAATAATAAT
* * *
3173616 AATAATAATAATAAATAAGAGT-AAT
1 AATAATAATAA-AAATAACAATAAAC
* *
3173641 AATAATAATAATAATAATAATAAAC
1 AATAATAATAAAAATAACAATAAAC
*
3173666 AATAATAATAAAAATGACAATAAA
1 AATAATAATAAAAATAACAATAAA
3173690 AATGGTGATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 7 0.17
25 34 0.83
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26
Consensus pattern (25 bp):
AATAATAATAAAAATAACAATAAAC
Found at i:3174120 original size:121 final size:118
Alignment explanation
Indices: 3173874--3174235 Score: 519
Period size: 121 Copynumber: 3.0 Consensus size: 118
3173864 AGTGCTGACT
* * * * * *
3173874 CACCTCCTTCTATGATGAATTTGAGCAAAAGGTCGAAGAAATTCTTCTCATTATGAACTTCTTCT
1 CACCTCCTTCTGTGATGGACTTGATCAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * *
3173939 CCCTCTTTGGACGAGTTCTTTTCATTATAAACTATTCCATTGGAAATGTTGATC
66 CCCTCTTTGGATGAGTTCTTTTCATTATGAACTCTTCCATTGGAAATG-TGATC
* * *
3173993 CACCTCCTTATGTGATGGACTTGATCAAAAGGTCGAACAAGTTATTCTCATTATGAACTTATTCT
1 CACCTCCTTCTGTGATGGACTTGATCAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
3174058 CTCTCTCTTTGGATGAGTTCTTCTCATCATGAACTCTTCCATTGGAAATGTCGATC
66 C-C-CTCTTTGGATGAGTTCTTTTCATTATGAACTCTTCCATTGGAAATGT-GATC
*
3174114 CACCTCCTTCTGTGATGGACTTGATCAAAATGTCGAACAAGTTCTTCTCATTATGAACTTCTTC-
1 CACCTCCTTCTGTGATGGACTTGATCAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
3174178 CCCTCTTTGGGTGAGTTCTTTTCATTATGAACCCTTCCATTGGAAATGATGATC
66 CCCTCTTTGGATGAGTTCTTTTCATTATGAACTCTTCCATTGGAAATG-TGATC
3174232 CACC
1 CACC
3174236 ACATTGTTTG
Statistics
Matches: 217, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
118 50 0.23
119 59 0.27
120 3 0.01
121 105 0.48
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (118 bp):
CACCTCCTTCTGTGATGGACTTGATCAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT
CCCTCTTTGGATGAGTTCTTTTCATTATGAACTCTTCCATTGGAAATGTGATC
Found at i:3175371 original size:12 final size:13
Alignment explanation
Indices: 3175356--3175414 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
3175346 CCCCTTTCAA
3175356 TTTTCTTTTCATTTT
1 TTTTCTTTTCA--TT
*
3175371 TTTTGCTTTGCATT
1 TTTT-CTTTTCATT
*
3175385 TTTTCTTTTTA-T
1 TTTTCTTTTCATT
*
3175397 TTTTCTTCT-ATT
1 TTTTCTTTTCATT
3175409 TTTTCT
1 TTTTCT
3175415 CCTTTTAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 1 0.03
12 16 0.42
13 5 0.13
14 6 0.16
15 4 0.11
16 6 0.16
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTCTTTTCATT
Found at i:3184166 original size:20 final size:20
Alignment explanation
Indices: 3184141--3184179 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3184131 AATATTTAAT
*
3184141 GAAAAA-TATAGAAATTGTTG
1 GAAAAAGTAT-GAAAATGTTG
3184161 GAAAAAGTATGAAAATGTT
1 GAAAAAGTATGAAAATGTT
3184180 TAGCTCCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (20 bp):
GAAAAAGTATGAAAATGTTG
Found at i:3184551 original size:20 final size:20
Alignment explanation
Indices: 3184526--3184568 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3184516 AATGTTATGC
3184526 ATTTGAAAATTTTGATATCA
1 ATTTGAAAATTTTGATATCA
*
3184546 ATTTGAAAATTTTGATATTA
1 ATTTGAAAATTTTGATATCA
3184566 ATT
1 ATT
3184569 GTTAGAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (20 bp):
ATTTGAAAATTTTGATATCA
Found at i:3187353 original size:20 final size:20
Alignment explanation
Indices: 3187330--3187381 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3187320 AACGCGATCC
3187330 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
3187350 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
3187370 CCAAAATCGCAA
1 CCAGAATCGCAA
3187382 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:3187398 original size:21 final size:20
Alignment explanation
Indices: 3187371--3187469 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
3187361 AATCAGTTTC
3187371 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3187392 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3187413 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3187433 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3187454 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3187470 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3187498 original size:20 final size:20
Alignment explanation
Indices: 3187436--3187629 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3187426 CGATTTTCCA
* ** *
3187436 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3187456 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3187476 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3187496 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3187516 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3187536 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3187556 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
3187576 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
3187596 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
3187617 AAATCGCAACGCG
1 AAATCGCAACGCG
3187630 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3187520 original size:60 final size:60
Alignment explanation
Indices: 3187436--3187629 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3187426 CGATTTTCCA
* ** * *
3187436 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
3187496 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
3187556 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
3187617 AAATCGCAACGCG
1 AAATCGCAACGCG
3187630 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:3188045 original size:33 final size:33
Alignment explanation
Indices: 3188006--3188076 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3187996 TTCACTTAGA
*
3188006 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3188039 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3188072 TTTCA
1 TTTCA
3188077 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3188216 original size:14 final size:14
Alignment explanation
Indices: 3188197--3188251 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3188187 AGAATGACTG
3188197 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3188211 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
3188230 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3188244 TCGCAACG
1 TCGCAACG
3188252 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3188264 original size:33 final size:33
Alignment explanation
Indices: 3188197--3188267 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3188187 AGAATGACTG
***
3188197 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3188230 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3188263 TCGCA
1 TCGCA
3188268 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:3188285 original size:19 final size:19
Alignment explanation
Indices: 3188263--3188360 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3188253 GAAACCAAAA
*
3188263 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3188282 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3188296 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3188315 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3188329 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3188348 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3188361 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3188304 original size:14 final size:14
Alignment explanation
Indices: 3188285--3188374 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3188275 TTTCATTTCG
3188285 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3188299 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3188318 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3188332 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3188349 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3188365 CGTTGCGATT
1 CGTTGCGATT
3188375 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3188310 original size:33 final size:33
Alignment explanation
Indices: 3188268--3188382 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3188258 CAAAATCGCA
3188268 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3188301 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3188334 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3188367 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3188383 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3190398 original size:93 final size:93
Alignment explanation
Indices: 3190071--3190447 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
3190061 TAGATTGCTT
*
3190071 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3190136 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3190163 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3190227 -TTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3190253 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3190318 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3190346 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3190411 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3190439 AGTAAATTT
1 AGTAAATTT
3190448 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
89 8 0.03
90 79 0.28
91 4 0.01
92 77 0.28
93 112 0.40
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3190530 original size:19 final size:19
Alignment explanation
Indices: 3190490--3190618 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3190480 TAGTTTACTT
* *
3190490 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3190510 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3190529 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3190548 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3190562 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3190581 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3190595 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3190614 TCGCA
1 TCGCA
3190619 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3190569 original size:33 final size:32
Alignment explanation
Indices: 3190526--3190618 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3190516 CGCGAAACCA
**
3190526 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3190558 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3190591 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3190619 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3190616 original size:52 final size:52
Alignment explanation
Indices: 3190490--3190618 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3190480 TAGTTTACTT
**
3190490 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3190542 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3190595 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
3190619 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3190636 original size:19 final size:19
Alignment explanation
Indices: 3190614--3190748 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
3190604 GAAACCAAAA
*
3190614 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3190633 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3190649 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3190666 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3190682 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3190699 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3190718 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3190738 TCGTGTTGCGA
1 TCGCGTTGCGA
3190749 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3190655 original size:14 final size:14
Alignment explanation
Indices: 3190636--3190692 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3190626 TTTCATTTCG
3190636 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3190650 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3190667 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
3190683 CGTTGCGATT
1 CGTTGCGATT
3190693 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3190661 original size:33 final size:33
Alignment explanation
Indices: 3190619--3190711 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
3190609 CAAAATCGCA
*
3190619 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3190652 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3190685 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3190712 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3192589 original size:38 final size:38
Alignment explanation
Indices: 3192541--3192613 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
3192531 TAATGATTGT
*
3192541 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
3192579 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
3192614 GTAAAAGTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:3192600 original size:19 final size:19
Alignment explanation
Indices: 3192536--3192600 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
3192526 TAGTTTAATG
*
3192536 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
3192555 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
3192573 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
3192593 ATTGATTT
1 ATTGATTT
3192601 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:3192625 original size:38 final size:38
Alignment explanation
Indices: 3192545--3192637 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 38
3192535 GATTGTTTTT
* ***
3192545 TGATTGTTTAATTGATTTGTAAAAGTTGATTCAATTTT
1 TGATTGTTTAATTGATTTGTAAAAGATGATTCAATAAG
*
3192583 TGATTGTTTAATTGATTTGTAAAAGATGATTGTAA-AAG
1 TGATTGTTTAATTGATTTGTAAAAGATGATT-CAATAAG
*
3192621 TGATTTGTGTAATTGAT
1 TGA-TTGTTTAATTGAT
3192638 GCGAACATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 33 0.70
39 14 0.30
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.48
Consensus pattern (38 bp):
TGATTGTTTAATTGATTTGTAAAAGATGATTCAATAAG
Found at i:3192628 original size:13 final size:14
Alignment explanation
Indices: 3192595--3192628 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3192585 ATTGTTTAAT
3192595 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
3192609 TGA-TTGTAAAAG-
1 TGATTTGTAAAAGA
3192621 TGATTTGT
1 TGATTTGT
3192629 GTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 13 0.68
14 3 0.16
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3192749 original size:19 final size:19
Alignment explanation
Indices: 3192733--3192834 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3192723 AAAAATGACT
3192733 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3192752 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3192771 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3192785 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3192804 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3192824 ATCGCAATGCG
1 ATCGCAATGCG
3192835 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3192853 original size:19 final size:18
Alignment explanation
Indices: 3192825--3193093 Score: 216
Period size: 19 Copynumber: 15.5 Consensus size: 18
3192815 GAAATGAAAA
* *
3192825 TCGCAATGCGTTTATAATT
1 TCGCATTGCGTTT-TCATT
* *
3192844 TCGCATTGCG-ATT-ATC
1 TCGCATTGCGTTTTCATT
3192860 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
3192877 TCGCATTGCGTTTTCATT
1 TCGCATTGCGTTTTCATT
*
3192895 TCGCATTGCG-ATTC-TT
1 TCGCATTGCGTTTTCATT
3192911 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
3192928 TCGCATTGCGATTTTCA-T
1 TCGCATTGCG-TTTTCATT
* *
3192946 T-GTATTGCGATTTTAATT
1 TCGCATTGCG-TTTTCATT
*
3192964 TCGCATTGCGATTTCATT
1 TCGCATTGCGTTTTCATT
* *
3192982 TCGCATTGCG-ATTC-TC
1 TCGCATTGCGTTTTCATT
3192998 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
3193015 TCGCATTGCGATTTTCA-T
1 TCGCATTGCG-TTTTCATT
* *
3193033 TCGCATTGCG-ATTC-TC
1 TCGCATTGCGTTTTCATT
3193049 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
3193066 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
3193085 TCGCATTGC
1 TCGCATTGC
3193094 TTCTCTCGTT
Statistics
Matches: 207, Mismatches: 20, Indels: 46
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.10
16 31 0.15
17 38 0.18
18 50 0.24
19 68 0.33
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGTTTTCATT
Found at i:3192903 original size:51 final size:51
Alignment explanation
Indices: 3192825--3193093 Score: 220
Period size: 51 Copynumber: 5.2 Consensus size: 51
3192815 GAAATGAAAA
* * *
3192825 TCGCAATGCGTTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGTTT-TCATTTCGCATTGCGATTATTTCGTTGCGATTTTCATT
*
3192877 TCGCATTGCGTTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGTTTTCATTTCGCATTGCGATTATTTCGTTGCGATTTTCATT
*
3192928 TCGCATTGCGATTTTCA-TT-GTATTGCGATTTTAATTTCGCATTGCGA-TTTCATT
1 TCGCATTGCG-TTTTCATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATT
* *
3192982 TCGCATTGCG-ATTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCA-T
1 TCGCATTGCGTTTTCATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATT
* *
3193033 TCGCATTGCG-ATTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGTTTTCATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATT
3193085 TCGCATTGC
1 TCGCATTGC
3193094 TTCTCTCGTT
Statistics
Matches: 198, Mismatches: 9, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
50 8 0.04
51 122 0.62
52 39 0.20
53 6 0.03
54 17 0.09
55 6 0.03
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (51 bp):
TCGCATTGCGTTTTCATTTCGCATTGCGATTATTTCGTTGCGATTTTCATT
Found at i:3192966 original size:87 final size:85
Alignment explanation
Indices: 3192841--3193078 Score: 326
Period size: 87 Copynumber: 2.8 Consensus size: 85
3192831 TGCGTTTATA
* *
3192841 ATTTCGCATTGCGATTATC-TCG-TTGCGATTTTCATTTCGCATTGCGTTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTTTCATTGATTGCGATTTT-ATTTCGCATTGCGTTTTCATTTCGCATTGC
*
3192904 GATTCTTTCGTTGCGATTTTC
65 GATTCTCTCGTTGCGATTTTC
*
3192925 ATTTCGCATTGCGATTTTCATTGTATTGCGATTTTAATTTCGCATTGCGATTTCATTTCGCATTG
1 ATTTCGCATTGCGATTTTCATTG-ATTGCGATTTT-ATTTCGCATTGCGTTTTCATTTCGCATTG
3192990 CGATTCTCTCGTTGCGATTTTC
64 CGATTCTCTCGTTGCGATTTTC
* *
3193012 ATTTCGCATTGCGATTTTCATTCGCATTGCGA--TTCTCTCG--TTGCGATTTTCATTTCGCATT
1 ATTTCGCATTGCGATTTTCATT-G-ATTGCGATTTTATTTCGCATTGCG-TTTTCATTTCGCATT
3193073 GCGATT
63 GCGATT
3193079 TTCATTTCGC
Statistics
Matches: 140, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
83 5 0.04
84 38 0.27
85 6 0.04
86 2 0.01
87 81 0.58
88 8 0.06
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (85 bp):
ATTTCGCATTGCGATTTTCATTGATTGCGATTTTATTTCGCATTGCGTTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTC
Found at i:3193006 original size:14 final size:15
Alignment explanation
Indices: 3192986--3193059 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 15
3192976 TTCATTTCGC
3192986 ATTGCGATTCTCTCG
1 ATTGCGATTCTCTCG
*
3193001 -TTGCGATTTTCATTTCG
1 ATTGCGA--TTC-TCTCG
*
3193018 CATTGCGATTTTCATTCG
1 -ATTGCGATTCTC--TCG
3193036 CATTGCGATTCTCTCG
1 -ATTGCGATTCTCTCG
3193052 -TTGCGATT
1 ATTGCGATT
3193060 TTCATTTCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
14 14 0.29
16 7 0.15
17 6 0.12
18 15 0.31
19 6 0.12
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (15 bp):
ATTGCGATTCTCTCG
Found at i:3193109 original size:31 final size:32
Alignment explanation
Indices: 3192969--3193155 Score: 152
Period size: 31 Copynumber: 5.7 Consensus size: 32
3192959 TAATTTCGCA
3192969 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGC-ATTCTCTCG
*
3193001 TTGCGATTTTCATTTCGCATTGCGATTTTCATTCG
1 TTGCGATTTTCATTTCGCATTGC-ATTCTC--TCG
* * * * *
3193036 CATTGCGATTCTCTCGTTGCG-ATTTTCATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCATTCTCTCG
3193071 TTGCGATTTTCATTTCGCATTGC-TTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCATTCTCTCG
* *
3193102 TTGCGATTTTCATTCCGCATTGCGATT-T-TTG
1 TTGCGATTTTCATTTCGCATTGC-ATTCTCTCG
* *
3193133 TTGGGATTTTCATTTCGCGTTGC
1 TTGCGATTTTCATTTCGCATTGC
3193156 GATTGTATTT
Statistics
Matches: 127, Mismatches: 16, Indels: 25
0.76 0.10 0.15
Matches are distributed among these distances:
30 2 0.02
31 56 0.44
32 9 0.07
33 32 0.25
35 4 0.03
37 10 0.08
38 5 0.04
39 9 0.07
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCATTCTCTCG
Found at i:3193156 original size:31 final size:33
Alignment explanation
Indices: 3192841--3193159 Score: 191
Period size: 33 Copynumber: 9.5 Consensus size: 33
3192831 TGCGTTTATA
*
3192841 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
3192874 ATTTCGCATTGCGTTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCG-ATTC-TCTCG--TTGCGATTTTC
*
3192909 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
* * *
3192944 A-TT-GTATTGCGATTTTAATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TT-CTCTCG--TTGCGATTTTC
3192979 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
3193012 ATTTCGCATTGCGATTTTCATTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTC--TCG--TTGCGATT-T-TC
* * * * *
3193051 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
3193082 ATTTCGCATTGC--TTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
3193113 ATTCCGCATTGCGATT-T-TTGTTGGGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
3193144 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
3193160 GTATTTTCCG
Statistics
Matches: 236, Mismatches: 24, Indels: 54
0.75 0.08 0.17
Matches are distributed among these distances:
30 2 0.01
31 60 0.25
32 14 0.06
33 62 0.26
34 12 0.05
35 23 0.10
36 25 0.11
37 24 0.10
38 5 0.02
39 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:3193159 original size:50 final size:49
Alignment explanation
Indices: 3192914--3193131 Score: 267
Period size: 51 Copynumber: 4.2 Consensus size: 49
3192904 GATTCTTTCG
* * *
3192914 TTGCGATTTTCATTTCGCATTGCGATTTTCATTGTATTGCGATTTTAATTTCGCA
1 TTGCGATTTT--TTTCGCATTGC-ATTCTC-TCG--TTGCGATTTTCATTTCGCA
*
3192969 TTGCGATTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTT-TTTTCGCATTGC-ATTCTCTCGTTGCGATTTTCATTTCGCA
*
3193020 TTGCGATTTTCATTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTT-TTTCGCATTGC-ATTCTCTCGTTGCGATTTTCATTTCGCA
*
3193071 TTGCGATTTTCATTTCGCATTGC-TTCTCTCGTTGCGATTTTCATTCCGCA
1 TTGCGATTTT--TTTCGCATTGCATTCTCTCGTTGCGATTTTCATTTCGCA
3193121 TTGCGATTTTT
1 TTGCGATTTTT
3193132 GTTGGGATTT
Statistics
Matches: 151, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
48 1 0.01
50 36 0.24
51 76 0.50
52 10 0.07
53 2 0.01
54 17 0.11
55 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (49 bp):
TTGCGATTTTTTTCGCATTGCATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:3196234 original size:20 final size:20
Alignment explanation
Indices: 3196206--3196572 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
3196196 AAATTTCAGT
* * * *
3196206 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3196226 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3196246 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3196266 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3196286 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3196306 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3196326 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3196346 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3196366 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3196386 GTTGCGATTTACGGATA--C
1 GTTGCGATTTACGGATACGC
*
3196404 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3196424 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3196444 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3196464 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3196484 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3196504 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3196524 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3196544 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3196564 GTTGCGATT
1 GTTGCGATT
3196573 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
18 17 0.06
19 5 0.02
20 280 0.91
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3197105 original size:28 final size:29
Alignment explanation
Indices: 3197056--3197111 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
3197046 AAACTACAAG
3197056 TTTAGTACCAAAACATCAATTT-TTTCAT
1 TTTAGTACCAAAACATCAATTTGTTTCAT
* * **
3197084 TTTAGTACCTAAACTTTTATTTGTTTCA
1 TTTAGTACCAAAACATCAATTTGTTTCA
3197112 AAATTATACC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTAGTACCAAAACATCAATTTGTTTCAT
Found at i:3212699 original size:6 final size:6
Alignment explanation
Indices: 3212653--3212697 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
3212643 GGGGTTTAGA
* *
3212653 TTGGAGG TTGAGG TTGGGG TTGGGG TTGGGG TTGGGG TTAGGG TT
1 TTGG-GG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TT
3212698 AGAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
6 32 0.91
7 3 0.09
ACGTcount: A:0.07, C:0.00, G:0.58, T:0.36
Consensus pattern (6 bp):
TTGGGG
Found at i:3212736 original size:19 final size:20
Alignment explanation
Indices: 3212713--3212758 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
3212703 TTTTATTTAT
*
3212713 TATTATTA-TTATTATTTAAA
1 TATTATTATTTA-TAATTAAA
3212733 -ATTA-TATTTATAATTAAA
1 TATTATTATTTATAATTAAA
3212751 TATTATTA
1 TATTATTA
3212759 AATTTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.41
19 11 0.50
20 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTATTTATAATTAAA
Found at i:3215276 original size:60 final size:60
Alignment explanation
Indices: 3215141--3215255 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
3215131 TAGTCGAGTG
* * *
3215141 ATCATTTTGCAACTTTTAATAGTCGAGGAACTCAACAAACCAACGTCATATAGTCAGAAT
1 ATCATTTTGTAACTTTTAATAGTCGAAGAACTCAACAAACCAACGCCATATAGTCAGAAT
* ** *
3215201 ATTATTTTGTAACTTTTAATAGTCAGAAG-ACTCAACAAAGTAACGCCCTATAGTC
1 ATCATTTTGTAACTTTTAATAGTC-GAAGAACTCAACAAACCAACGCCATATAGTC
3215256 GTGGAATCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (60 bp):
ATCATTTTGTAACTTTTAATAGTCGAAGAACTCAACAAACCAACGCCATATAGTCAGAAT
Found at i:3215385 original size:14 final size:14
Alignment explanation
Indices: 3215366--3215395 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3215356 ATTCAAGAAA
*
3215366 AGGAGTAGAAAAGT
1 AGGAGTAAAAAAGT
3215380 AGGAGTAAAAAAGT
1 AGGAGTAAAAAAGT
3215394 AG
1 AG
3215396 TGACGAGTTT
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:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (14 bp):
AGGAGTAAAAAAGT
Found at i:3224687 original size:29 final size:31
Alignment explanation
Indices: 3224616--3224689 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
3224606 CCACTCCTAT
3224616 AATTTTTTAAAAAATATTATTAAGACTCTCA
1 AATTTTTTAAAAAATATTATTAAGACTCTCA
* *
3224647 AA-ATTTT-AAAAATTTTAGTT-AGAC-C-CA
1 AATTTTTTAAAAAATATTA-TTAAGACTCTCA
3224674 AATTTTTTAAAAAATA
1 AATTTTTTAAAAAATA
3224690 AATTAAACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 4 0.11
28 5 0.14
29 19 0.53
30 6 0.17
31 2 0.06
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (31 bp):
AATTTTTTAAAAAATATTATTAAGACTCTCA
Found at i:3232984 original size:17 final size:18
Alignment explanation
Indices: 3232962--3232998 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3232952 TCTTATGCAC
3232962 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
3232979 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
3232997 AT
1 AT
3232999 TTATTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:3235190 original size:46 final size:46
Alignment explanation
Indices: 3235137--3235324 Score: 252
Period size: 46 Copynumber: 4.1 Consensus size: 46
3235127 ACCACTATGT
* * * ** *
3235137 ATTTTCATATGTAGCATCCTTTCATGCTAATTATATATTGTTATAC
1 ATTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATAC
* * *
3235183 ATTTTCATTTATGGCATCCTTTCATGACAATTATGCACTGTTATAA
1 ATTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATAC
* * *
3235229 ATTTTCTTTTATGGCATCCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATAC
3235275 ATTTTCATTTAT-GACATCCTTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATAG-CATCCTTTCATGCCAATTATGCACTGTTATAC
3235321 ATTT
1 ATTT
3235325 AGTCTTTTTG
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 125 0.99
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:3235294 original size:92 final size:92
Alignment explanation
Indices: 3235150--3235324 Score: 296
Period size: 92 Copynumber: 1.9 Consensus size: 92
3235140 TTCATATGTA
* * *
3235150 GCATCCTTTCATGCTAATTATATATTGTTATACATTTTCATTTATGGCATCCTTTCATGACAATT
1 GCATCCTTTCATGCCAATTATACATTGTTATACATTTTCATTTATGACATCCTTTCATGACAATT
3235215 ATGCACTGTTATAAATTTTCTTTTATG
66 ATGCACTGTTATAAATTTTCTTTTATG
* *
3235242 GCATCCTTTCATGCCAATTATGCATTGTTATACATTTTCATTTATGACATCCTTTCATGCCAATT
1 GCATCCTTTCATGCCAATTATACATTGTTATACATTTTCATTTATGACATCCTTTCATGACAATT
*
3235307 ATGCACTGTTATACATTT
66 ATGCACTGTTATAAATTT
3235325 AGTCTTTTTG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.46
Consensus pattern (92 bp):
GCATCCTTTCATGCCAATTATACATTGTTATACATTTTCATTTATGACATCCTTTCATGACAATT
ATGCACTGTTATAAATTTTCTTTTATG
Found at i:3235554 original size:54 final size:53
Alignment explanation
Indices: 3235472--3235648 Score: 203
Period size: 54 Copynumber: 3.3 Consensus size: 53
3235462 TTTATTAAGA
* * * * * * *
3235472 TGCACACGTAGTGCCTATACGATCGTTCATCAACCTATGATCAATTATGTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATT-TGTGAGT
3235526 TGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTTCGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTT-GTGAGT
* * * *
3235580 TGCACATATAGTACC-GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGT
1 TGCACACATAGTGCCTG-TACGGTTGTTCATCAACATATGATGAATT-TGTGAGT
*
3235634 TGCACACACAGTGCC
1 TGCACACATAGTGCC
3235649 ATTTGGTAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.02
54 104 0.98
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (53 bp):
TGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTTGTGAGT
Found at i:3236029 original size:19 final size:19
Alignment explanation
Indices: 3236001--3236037 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3235991 GATACTTCTA
* *
3236001 TATTATAGTATTGATACCC
1 TATTACAGTATCGATACCC
3236020 TATTACAGTATCGATACC
1 TATTACAGTATCGATACC
3236038 ATTTCTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
TATTACAGTATCGATACCC
Found at i:3236758 original size:11 final size:11
Alignment explanation
Indices: 3236737--3236778 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3236727 GTGCTGGAAT
3236737 CAAGATAAAAA
1 CAAGATAAAAA
* *
3236748 TAAGATTAAAA
1 CAAGATAAAAA
3236759 CAAGATAAAGAA
1 CAAGATAAA-AA
3236771 -AAGATAAA
1 CAAGATAAA
3236779 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:3241096 original size:10 final size:10
Alignment explanation
Indices: 3241083--3241131 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
3241073 AAATTTTGGC
3241083 TTTTTGTTTT
1 TTTTTGTTTT
3241093 TTTTTGTTTT
1 TTTTTGTTTT
*
3241103 GTTTTTTTTGCCTT
1 -TTTTTGTT---TT
3241117 TTTTTGTTTT
1 TTTTTGTTTT
3241127 TTTTT
1 TTTTT
3241132 AAAAAATAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 17 0.52
11 7 0.21
13 7 0.21
14 2 0.06
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:3241482 original size:11 final size:11
Alignment explanation
Indices: 3241461--3241502 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3241451 GTACTGGAAT
3241461 CAAGATAAAAA
1 CAAGATAAAAA
* *
3241472 TAAGATTAAAA
1 CAAGATAAAAA
3241483 CAAGATAAAGAA
1 CAAGATAAA-AA
3241495 -AAGATAAA
1 CAAGATAAA
3241503 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:3243428 original size:27 final size:27
Alignment explanation
Indices: 3243396--3243447 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3243386 AATAATTTTT
*
3243396 TTAATATAGATTAATTTAAACAATAGC
1 TTAATATAAATTAATTTAAACAATAGC
3243423 TTAATATAAATTAATTTAAACAATA
1 TTAATATAAATTAATTTAAACAATA
3243448 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (27 bp):
TTAATATAAATTAATTTAAACAATAGC
Found at i:3243460 original size:27 final size:27
Alignment explanation
Indices: 3243405--3243460 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
3243395 TTTAATATAG
*** * *
3243405 ATTAATTTAAACAATAGCTTAATATAA
1 ATTAATTTAAACAATAAAATAAAAAAA
3243432 ATTAATTTAAACAATAAAATAAAAAAA
1 ATTAATTTAAACAATAAAATAAAAAAA
3243459 AT
1 AT
3243461 AACAAATAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (27 bp):
ATTAATTTAAACAATAAAATAAAAAAA
Found at i:3243572 original size:25 final size:25
Alignment explanation
Indices: 3243525--3243572 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3243515 CAATAAAATA
* * *
3243525 AAAAACAATATAATTTCATTTAAAC
1 AAAAACAATATAATATAAATTAAAC
*
3243550 AAAAACAATTTAATATAAATTAA
1 AAAAACAATATAATATAAATTAA
3243573 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAACAATATAATATAAATTAAAC
Found at i:3243651 original size:142 final size:146
Alignment explanation
Indices: 3243496--3243822 Score: 391
Period size: 142 Copynumber: 2.2 Consensus size: 146
3243486 TTTTTAACTT
*
3243496 AATTTAAACTATAACAAATCAATAAAATAAAAAACAATATAATTTCATTTAAACAAAAACAATTT
1 AATTTAAACTATAACAAATCAATAAAATAAAAAA-AATATAACTTCA-TTAAA-AAAAACAATTT
* * * *
3243561 AATATAAATTAATTT-AA-A-AAAATAAAA-TAAA-AATCGATAAA-A-AAATAATCTAACTTAA
63 AATATAAATTAATTTAAATAGAAAATAAAATTAAATAAT-AATAAATATAAAAAATCAAACGTAA
3243619 TTTAAACAATAAAA-TAAAA
127 TTTAAACAATAAAATTAAAA
* * * * ***
3243638 ATTTTAAACTATAACAAATCAATAAAATAAAATAAAATCTAACTTCATTCAAATAAATTTTTTAA
1 AATTTAAACTATAACAAATCAATAAAATAAAA-AAAATATAACTTCATTAAAAAAAACAATTTAA
3243703 TATAAATTAATTTAAATAGTAAAATAAAATTTTAAATAATAATAAATTGATAAAAAATCAAACGT
65 TATAAATTAATTTAAATAG-AAAATAAAA--TTAAATAATAATAAA-T-ATAAAAAATCAAACGT
3243768 AATTTAAACAATAAAATTAAAA
125 AATTTAAACAATAAAATTAAAA
*
3243790 AATTAAAACTATAACAAATCAATAAAATAAAAA
1 AATTTAAACTATAACAAATCAATAAAATAAAAA
3243823 GGGTAAGCTA
Statistics
Matches: 157, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
140 22 0.14
141 6 0.04
142 42 0.27
143 2 0.01
144 9 0.06
147 9 0.06
148 3 0.02
150 1 0.01
151 28 0.18
152 35 0.22
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.30
Consensus pattern (146 bp):
AATTTAAACTATAACAAATCAATAAAATAAAAAAAATATAACTTCATTAAAAAAAACAATTTAAT
ATAAATTAATTTAAATAGAAAATAAAATTAAATAATAATAAATATAAAAAATCAAACGTAATTTA
AACAATAAAATTAAAA
Found at i:3245335 original size:180 final size:180
Alignment explanation
Indices: 3244951--3245321 Score: 543
Period size: 186 Copynumber: 2.0 Consensus size: 180
3244941 ATTAAATTTT
*
3244951 AAATTTTAAATATATTATATATAACATATAAGCTCAGCTCAAATCATTTAAAACACAATTAATAA
1 AAATATTAAATATATTATATATAACATATAAGCTCAGCTCAAATCATTTAAAACACAATTAATAA
*
3245016 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAAAAATTATATAAAATTTTTATTT
66 TTTAAGATCAAATAACTTTTAAACCTAAATCAATATTAATTAAAAATTATATAAAATTTTTATTT
*
3245081 TATAATTACATATTATTTAAATTAATTGTAAGCTGTTTTTTGAATTAAAAA
131 TATAATTACATATTATTTAAATTAATTGTAAACTGTTTTTTGAATT-AAAA
** * * *
3245132 AAATATTAAATATATTATATATAACATATTGGCTCAGCTTAAA-CATTTAAACCCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAAGCTCAGCTCAAATCATTTAAAACACAATTAATAA
* *
3245196 TTTAAGATCAAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATGTAAAATTT
66 TTTAAGATCAAATAACTTTTAAACCTAAATC-A-A-T-ATTAATT-AAAAA-TTATATAAAATTT
*
3245261 TTATTTTATAATTATATATTATTTAAATTAATTAG-AAACTGTTTTTT-AATT-AAA
125 TTATTTTATAATTACATATTATTTAAATTAATT-GTAAACTGTTTTTTGAATTAAAA
3245315 AAATATT
1 AAATATT
3245322 TCATTTTTAT
Statistics
Matches: 172, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
180 48 0.28
181 40 0.23
182 1 0.01
183 11 0.06
184 7 0.04
185 9 0.05
186 55 0.32
187 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (180 bp):
AAATATTAAATATATTATATATAACATATAAGCTCAGCTCAAATCATTTAAAACACAATTAATAA
TTTAAGATCAAATAACTTTTAAACCTAAATCAATATTAATTAAAAATTATATAAAATTTTTATTT
TATAATTACATATTATTTAAATTAATTGTAAACTGTTTTTTGAATTAAAA
Found at i:3245843 original size:20 final size:20
Alignment explanation
Indices: 3245818--3245857 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3245808 CATCTACCTT
3245818 GAAGACGTGTAGAAGTCTTG
1 GAAGACGTGTAGAAGTCTTG
* * *
3245838 GAAGACTTTTCGAAGTCTTG
1 GAAGACGTGTAGAAGTCTTG
3245858 AGACTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (20 bp):
GAAGACGTGTAGAAGTCTTG
Found at i:3245863 original size:18 final size:20
Alignment explanation
Indices: 3245829--3245881 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 20
3245819 AAGACGTGTA
3245829 GAAGTCTTGGAAGACTTTTC
1 GAAGTCTTGGAAGACTTTTC
*
3245849 GAAGTCTT-G-AGACTTTTT
1 GAAGTCTTGGAAGACTTTTC
*
3245867 GAAGTCTTTGAAGAC
1 GAAGTCTTGGAAGAC
3245882 CTGTAAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 16 0.53
19 2 0.07
20 12 0.40
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (20 bp):
GAAGTCTTGGAAGACTTTTC
Found at i:3247829 original size:17 final size:17
Alignment explanation
Indices: 3247795--3247829 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3247785 GTTTTAATAA
* *
3247795 TATTAAAATTAAATCTT
1 TATTAAAATGAAAACTT
3247812 TATTAAAATGAAAACTT
1 TATTAAAATGAAAACTT
3247829 T
1 T
3247830 TTTGTTGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (17 bp):
TATTAAAATGAAAACTT
Found at i:3248533 original size:21 final size:21
Alignment explanation
Indices: 3248492--3248534 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3248482 TTCAATAAAT
* *
3248492 CTCTTCATCGAAAGGTTTTAA
1 CTCTTCATCGAAAGATCTTAA
3248513 CTCTTCATCGAAAGATCTTAA
1 CTCTTCATCGAAAGATCTTAA
3248534 C
1 C
3248535 CATTAAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (21 bp):
CTCTTCATCGAAAGATCTTAA
Found at i:3250652 original size:35 final size:35
Alignment explanation
Indices: 3250613--3250684 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
3250603 TAAACTAAAA
3250613 AATAAGTATATCCACCAAGTGACATGACTTATTAT
1 AATAAGTATATCCACCAAGTGACATGACTTATTAT
* *
3250648 AATAAGTCTATTCACCAAGTGACATGACTTATTAT
1 AATAAGTATATCCACCAAGTGACATGACTTATTAT
3250683 AA
1 AA
3250685 ATAGAATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (35 bp):
AATAAGTATATCCACCAAGTGACATGACTTATTAT
Found at i:3252374 original size:35 final size:35
Alignment explanation
Indices: 3252326--3252397 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
3252316 TTGATTCTAT
*
3252326 TTATAATAGGTCATGTCACTTGGTGAATAGACTTA
1 TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
* *
3252361 TTATAATAAGTCATGTCACTTGGTGGATATACTTA
1 TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
3252396 TT
1 TT
3252398 TTTTAGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
Found at i:3254974 original size:26 final size:26
Alignment explanation
Indices: 3254944--3254994 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3254934 ATCCCCCTTT
* *
3254944 CTCCTCCCAGC-CCTTCTCCTTCGTCC
1 CTCCTCCAAGCACCCTCT-CTTCGTCC
3254970 CTCCTCCAAGCACCCTCTCTTCGTC
1 CTCCTCCAAGCACCCTCTCTTCGTC
3254995 TCAATACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.08, C:0.55, G:0.08, T:0.29
Consensus pattern (26 bp):
CTCCTCCAAGCACCCTCTCTTCGTCC
Found at i:3268240 original size:33 final size:32
Alignment explanation
Indices: 3268134--3268229 Score: 111
Period size: 34 Copynumber: 2.9 Consensus size: 32
3268124 TTTTCTAGCT
* *
3268134 TACTAATATTCTAACTTTTATTTTATTTGTTCA
1 TACTAACATACTAACTTTTATTTTA-TTGTTCA
* *
3268167 TACAAACATACTAACTTTTTATTTTTATTGTTCT
1 TACTAACATACTAAC-TTTTA-TTTTATTGTTCA
*
3268201 TACTAACTTACTAACATTTTATTTTATTG
1 TACTAACATACTAAC-TTTTATTTTATTG
3268230 CACAAACTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 20 0.37
34 29 0.54
35 5 0.09
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (32 bp):
TACTAACATACTAACTTTTATTTTATTGTTCA
Found at i:3268416 original size:30 final size:31
Alignment explanation
Indices: 3268381--3268449 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
3268371 TTTTATTTTA
3268381 TTTATTTTCCAGCACTTTAA-ATT-CTAGCAT
1 TTTATTTTCCAGCACTTTAATATTGCTA-CAT
* * * *
3268411 TTTATTTTTCTGCTCTTTAATTTTGCTACAT
1 TTTATTTTCCAGCACTTTAATATTGCTACAT
3268442 TTTATTTT
1 TTTATTTT
3268450 AGTCCTTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.52
31 13 0.39
32 3 0.09
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.58
Consensus pattern (31 bp):
TTTATTTTCCAGCACTTTAATATTGCTACAT
Found at i:3277545 original size:40 final size:40
Alignment explanation
Indices: 3277490--3277651 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
3277480 TGCATGTTTA
*
3277490 TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3277530 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
3277570 TAATACACTTGGGTGTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3277610 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
3277650 TA
1 TA
3277652 GCACTACGGT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:3277820 original size:45 final size:45
Alignment explanation
Indices: 3277756--3277977 Score: 304
Period size: 46 Copynumber: 4.9 Consensus size: 45
3277746 GTAAGCATGC
* * *
3277756 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTGTATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
3277801 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATT-AGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGA-TA
* * *
3277846 AAATAAGCTTAAGAGCTTAAGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGATA
* * *
3277892 AAATAAGGTTACGAGCTTATAGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGATA
*
3277938 AAATAAGCTTACAAGCTTATCGG-ATAAATGGTAAGTATAT
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATAT
3277978 GGGTAAGAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
44 1 0.01
45 78 0.49
46 80 0.50
47 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:3277904 original size:91 final size:91
Alignment explanation
Indices: 3277756--3277983 Score: 327
Period size: 91 Copynumber: 2.5 Consensus size: 91
3277746 GTAAGCATGC
* * * *
3277756 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTGTATTGATAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACAAGCTTAAGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
*
3277821 GGAA-TAAATGGTAAGTATATTAGTA
66 AGAATTAAATGGTAAGTATATTAGTA
*
3277846 AAATAAGCTTA-AGAGCTTAAGGAATTAAATGGTAAGTATATTGGTAAAATAAGGTTACGAGCTT
1 AAATAAGCTTACA-AGCTTAAGGAA-TAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
*
3277910 ATAGAATTAAATGGTAAGTATATTGGTA
64 ATAGAATTAAATGGTAAGTATATTAGTA
* *
3277938 AAATAAGCTTACAAGCTTATCGG-ATAAATGGTAAGTATATGGGTAA
1 AAATAAGCTTACAAGCTTA-AGGAATAAATGGTAAGTATATTGGTAA
3277984 GAAATTTTCT
Statistics
Matches: 124, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
89 1 0.01
90 21 0.17
91 61 0.49
92 38 0.31
93 3 0.02
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (91 bp):
AAATAAGCTTACAAGCTTAAGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
AGAATTAAATGGTAAGTATATTAGTA
Found at i:3277983 original size:45 final size:45
Alignment explanation
Indices: 3277756--3277983 Score: 316
Period size: 45 Copynumber: 5.0 Consensus size: 45
3277746 GTAAGCATGC
* * *
3277756 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTGTATTGATA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
3277801 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
3277846 AAATAAGCTTA-AGAGCTTAAGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACA-AGCTTATGGAA-TAAATGGTAAGTATATTGGTA
* * *
3277892 AAATAAGGTTACGAGCTTATAGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGAA-TAAATGGTAAGTATATTGGTA
*
3277938 AAATAAGCTTACAAGCTTATCGG-ATAAATGGTAAGTATATGGGTA
1 AAATAAGCTTACAAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
3277983 A
1 A
3277984 GAAATTTTCT
Statistics
Matches: 163, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
45 82 0.50
46 80 0.49
47 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:3281581 original size:5 final size:5
Alignment explanation
Indices: 3281555--3281602 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
3281545 AAGTTGTTTT
* *
3281555 TAAAA TAAAA -AAAA TAAGAA TAAAA TAAAA TAAAA -ATAA TTAAA TAAA
1 TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
3281603 CAAATTAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 7 0.19
5 24 0.67
6 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:3281584 original size:19 final size:19
Alignment explanation
Indices: 3281555--3281607 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3281545 AAGTTGTTTT
3281555 TAAAATAAAAAAAATAAGAA
1 TAAAAT-AAAAAAATAAGAA
*
3281575 TAAAATAAAATAAA-AATAA
1 TAAAATAAAA-AAATAAGAA
* *
3281594 TTAAATAAACAAAT
1 TAAAATAAAAAAAT
3281608 TAAAGAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.11
19 16 0.57
20 9 0.32
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAAATAAAAAAATAAGAA
Found at i:3281586 original size:16 final size:15
Alignment explanation
Indices: 3281556--3281593 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
3281546 AGTTGTTTTT
3281556 AAAATAAAAAAAATA
1 AAAATAAAAAAAATA
*
3281571 AGAATAAAATAAAATA
1 AAAATAAAA-AAAATA
3281587 AAAATAA
1 AAAATAA
3281594 TTAAATAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAATAAAAAAAATA
Found at i:3282266 original size:19 final size:19
Alignment explanation
Indices: 3282242--3282364 Score: 60
Period size: 19 Copynumber: 6.5 Consensus size: 19
3282232 ATACCTAAAA
* * *
3282242 AATTAATATTCTAAATCCT
1 AATTAAAATACTAAAACCT
3282261 AATTAAAATACTAAAACCT
1 AATTAAAATACTAAAACCT
* *
3282280 ATTTAAACTA--AAATACCT
1 AATTAAAATACTAAA-ACCT
* * **
3282298 AA-AACAAAGA-TAAAATAT
1 AATTA-AAATACTAAAACCT
*
3282316 AA--AAAATATCCTAAAACTT
1 AATTAAAATA--CTAAAACCT
3282335 AATTAAAATACTAAAAACCT
1 AATTAAAATACT-AAAACCT
*
3282355 ATTTAAAATA
1 AATTAAAATA
3282365 AAATACAAAG
Statistics
Matches: 79, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
16 4 0.05
17 5 0.06
18 12 0.15
19 37 0.47
20 15 0.19
21 6 0.08
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (19 bp):
AATTAAAATACTAAAACCT
Found at i:3289473 original size:17 final size:17
Alignment explanation
Indices: 3289435--3289476 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3289425 TTTTTTAAAA
*
3289435 TAAAAAAAAATAAGAAT
1 TAAATAAAAATAAGAAT
*
3289452 TAAATAAAAATAATAAT
1 TAAATAAAAATAAGAAT
3289469 TAAATAAA
1 TAAATAAA
3289477 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
TAAATAAAAATAAGAAT
Found at i:3295229 original size:35 final size:35
Alignment explanation
Indices: 3295177--3295254 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
3295167 CAACACAATC
3295177 TTCAATTTCATTCTAAACCCCAAATTCCAAAATAA
1 TTCAATTTCATTCTAAACCCCAAATTCCAAAATAA
* * * *
3295212 TTCAATTAT-ATTTTAAACCCTAAATTCTAAAATAC
1 TTCAATT-TCATTCTAAACCCCAAATTCCAAAATAA
3295247 TTCAATTT
1 TTCAATTT
3295255 AGGGTTTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 36 0.95
36 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (35 bp):
TTCAATTTCATTCTAAACCCCAAATTCCAAAATAA
Found at i:3295894 original size:20 final size:20
Alignment explanation
Indices: 3295869--3295906 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3295859 TTATTCATCG
*
3295869 TAAAATAAAATGAATTTAGA
1 TAAAATAAAATCAATTTAGA
3295889 TAAAATAAAATCAATTTA
1 TAAAATAAAATCAATTTA
3295907 TTTCAAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAATAAAATCAATTTAGA
Found at i:3296766 original size:2 final size:2
Alignment explanation
Indices: 3296759--3296784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3296749 CCAGAAATGA
3296759 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3296785 TTGAGAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3297671 original size:12 final size:13
Alignment explanation
Indices: 3297654--3297708 Score: 71
Period size: 12 Copynumber: 4.4 Consensus size: 13
3297644 GCAAGAAGTG
*
3297654 TAATAAATAAT-T
1 TAATAAATAATAA
3297666 TAATAAATAATAA
1 TAATAAATAATAA
3297679 TAAT-AATAATAA
1 TAATAAATAATAA
3297691 TAAT-AATAATTAA
1 TAATAAATAA-TAA
3297704 TAATA
1 TAATA
3297709 TTTTTATAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
12 28 0.72
13 11 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:3297679 original size:3 final size:3
Alignment explanation
Indices: 3297666--3297708 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
3297656 ATAAATAATT
3297666 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
3297709 TTTTTATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3298878 original size:3 final size:3
Alignment explanation
Indices: 3298861--3298898 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
3298851 ATATTATAAA
3298861 TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
3298899 GTATTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3298903 original size:24 final size:24
Alignment explanation
Indices: 3298852--3298907 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3298842 GCTTAAAAAA
* * *
3298852 TATTATAAATATTAATTATATTAT
1 TATTATTATTATTAATTATATTAG
3298876 TATTATTATTATTAATTATTATT-G
1 TATTATTATTATTAATTA-TATTAG
3298900 TATT-TTAT
1 TATTATTAT
3298908 ATTTGTAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 20 0.71
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTATTATTATTAATTATATTAG
Found at i:3313463 original size:3 final size:3
Alignment explanation
Indices: 3313457--3313483 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3313447 TACTTTACCG
3313457 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3313484 GAAGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3313781 original size:20 final size:19
Alignment explanation
Indices: 3313739--3313781 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3313729 TGTTATTCTC
* * *
3313739 AATTTTTTTTAATAAATTT
1 AATTTTTTATAATAAAATA
3313758 AATTTTTTATATATAAAATA
1 AATTTTTTATA-ATAAAATA
3313778 AATT
1 AATT
3313782 CTCTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTTTATAATAAAATA
Found at i:3313891 original size:17 final size:16
Alignment explanation
Indices: 3313865--3313896 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3313855 TTGTTATCCA
3313865 AAACCAACACTTAGAT
1 AAACCAACACTTAGAT
3313881 AAACTCAACACTTAGA
1 AAAC-CAACACTTAGA
3313897 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (16 bp):
AAACCAACACTTAGAT
Done.