Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 130 of 138
Found at i:18185822 original size:15 final size:15
Alignment explanation
Indices: 18185765--18185843 Score: 72
Period size: 15 Copynumber: 5.1 Consensus size: 15
18185755 TTATTTAATA
18185765 TTTTTTATCTTTATCT
1 TTTTTTATCTTTAT-T
* *
18185781 TATTTTTATTTTTGTT
1 T-TTTTTATCTTTATT
*
18185797 TTACTTT-TCTTTATT
1 TT-TTTTATCTTTATT
18185812 TTTTTTATCTTTATT
1 TTTTTTATCTTTATT
*
18185827 TATTTTCAT-TTTATT
1 T-TTTTTATCTTTATT
18185842 TT
1 TT
18185844 GTTCTATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
14 4 0.08
15 25 0.48
16 12 0.23
17 11 0.21
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTTTTATCTTTATT
Found at i:18185832 original size:40 final size:41
Alignment explanation
Indices: 18185772--18185858 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
18185762 ATATTTTTTA
* **
18185772 TCTTTATCTTATTTTTATTTTTGTTTTACTTTTCTT-TATTT
1 TCTTTATCTTATATTTATTTTCATTTTA-TTTTCTTCTATTT
* *
18185813 TTTTTATCTT-TATTTATTTTCATTTTATTTTGTTCTATTT
1 TCTTTATCTTATATTTATTTTCATTTTATTTTCTTCTATTT
18185853 TCTTTA
1 TCTTTA
18185859 AATAAAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 6 0.15
40 24 0.62
41 9 0.23
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (41 bp):
TCTTTATCTTATATTTATTTTCATTTTATTTTCTTCTATTT
Found at i:18185837 original size:6 final size:5
Alignment explanation
Indices: 18185754--18185853 Score: 55
Period size: 5 Copynumber: 19.6 Consensus size: 5
18185744 TTAGATTAGA
* * * *
18185754 TTTAT TTAAT ATT-T TTTAT CTTTAT CTTATT TTTATT TTTGT TTTACT
1 TTTAT TTTAT TTTAT TTTAT -TTTAT TTTA-T TTTA-T TTTAT TTTA-T
* * *
18185802 TTT-C TTTAT TTT-T TTTAT CTTTA- TTTAT TTTCAT TTTAT TTTGT TCTAT
1 TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT
18185851 TTT
1 TTT
18185854 CTTTAAATAA
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
4 14 0.19
5 31 0.43
6 27 0.38
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:18185837 original size:10 final size:9
Alignment explanation
Indices: 18185708--18185858 Score: 71
Period size: 9 Copynumber: 16.0 Consensus size: 9
18185698 AAAAATTTTT
*
18185708 TTTTATTTG
1 TTTTATTTA
18185717 TTTTATTTA
1 TTTTATTTA
18185726 -TTTATTTA
1 TTTTATTTA
18185734 -TTTATTT-
1 TTTTATTTA
*
18185741 TTATTAGATTA
1 TT-TTA-TTTA
*
18185752 GATTTATTTAA
1 -TTTTATTT-A
18185763 TATTT-TTTA
1 T-TTTATTTA
18185772 TCTTTATCTTA
1 T-TTTAT-TTA
18185783 TTTTTATTT-
1 -TTTTATTTA
*
18185792 TTGT-TTTA
1 TTTTATTTA
*
18185800 CTTTTCTTTA
1 -TTTTATTTA
*
18185810 TTTTTTTTA
1 TTTTATTTA
18185819 TCTTTATTTA
1 T-TTTATTTA
18185829 TTTTCATTTTA
1 TTTT-A-TTTA
*
18185840 TTTTGTTCTA
1 TTTTATT-TA
*
18185850 TTTTCTTTA
1 TTTTATTTA
18185859 AATAAAAATC
Statistics
Matches: 113, Mismatches: 12, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
7 3 0.03
8 19 0.17
9 35 0.31
10 31 0.27
11 23 0.20
12 2 0.02
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:18185840 original size:21 final size:20
Alignment explanation
Indices: 18185774--18185857 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
18185764 ATTTTTTATC
* *
18185774 TTTATCTTATTTTTATTTTTGT
1 TTTATCTT-TATTTA-TTTTCT
*
18185796 TTTA-CTTTTCTTTATTTT-T
1 TTTATC-TTTATTTATTTTCT
18185815 TTTATCTTTATTTATTTTCAT
1 TTTATCTTTATTTATTTTC-T
*
18185836 TTTAT-TTTGTTCTATTTTCT
1 TTTATCTTTATT-TATTTTCT
18185856 TT
1 TT
18185858 AAATAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
19 16 0.30
20 13 0.24
21 19 0.35
22 6 0.11
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTATCTTTATTTATTTTCT
Found at i:18185997 original size:58 final size:58
Alignment explanation
Indices: 18185870--18186086 Score: 332
Period size: 58 Copynumber: 3.7 Consensus size: 58
18185860 ATAAAAATCC
18185870 AAAAAATATTTTTA-GGAAAAGTTG-AAGTATCAATTTTCCTTAAAAATAAATTTTCA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
*
18185926 AAAAATATTTTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
* *
18185985 AAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
1 AAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC--A
*
18186046 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
18186087 CTACACAAGA
Statistics
Matches: 148, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
56 5 0.03
57 9 0.06
58 50 0.34
59 44 0.30
61 40 0.27
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (58 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
Found at i:18186846 original size:25 final size:25
Alignment explanation
Indices: 18186798--18186846 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
18186788 TTTGATTGTG
*
18186798 GGCTTTAAACATTTGGGCCTTATTA
1 GGCTTTAAACATTTGGGCCATATTA
** *
18186823 GGCTTTAGCCATTTGGGTCATATT
1 GGCTTTAAACATTTGGGCCATATT
18186847 GGACTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (25 bp):
GGCTTTAAACATTTGGGCCATATTA
Found at i:18187851 original size:22 final size:22
Alignment explanation
Indices: 18187821--18187880 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
18187811 AAAAGCAAGT
18187821 CATTCGACTA-CTTCAACTAAGA
1 CATTCGACTACCTT-AACTAAGA
* *
18187843 CATTTGACTACCTTAACTAAGG
1 CATTCGACTACCTTAACTAAGA
* *
18187865 CATTCAACTACGTTAA
1 CATTCGACTACCTTAA
18187881 TAAAGCCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 29 0.91
23 3 0.09
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (22 bp):
CATTCGACTACCTTAACTAAGA
Found at i:18190065 original size:50 final size:49
Alignment explanation
Indices: 18189812--18190237 Score: 239
Period size: 50 Copynumber: 8.6 Consensus size: 49
18189802 GGTCAAGTAG
* * * * * * * * *
18189812 ACTTGTTCTTGAATTAAAGGAATATTGACTTTGCTTCAAGTTCTTTGAT
1 ACTTGTTCTTGAATTGAAGAAATATGGACTTCGTTTAAAGGTCGTTGAA
* * * * * * * **
18189861 ACTTATTCTTAAAATGAATG-AATATGGACTTTGCTTCAAGAGTCATTGGG
1 ACTTGTTCTTGAATTGAA-GAAATATGGACTTCGTTTAAAG-GTCGTTGAA
* * * * * * *
18189911 ACTTATTCTTAAACTAAAGAAATATGGACTTCATTTCAAGGGTCATT-AA
1 ACTTGTTCTTGAATTGAAGAAATATGGACTTCGTTT-AAAGGTCGTTGAA
* * * * * * *
18189960 GACTTGTTATTGAATTCAAGAAATATGGACTTCTCTTTTAGGGTC-ATAAA
1 -ACTTGTTCTTGAATTGAAGAAATATGGACTTC-GTTTAAAGGTCGTTGAA
* **
18190010 GACTTGTTCTTGAATTGAAAAAATATGGACTTCGCTTTAACA-GTTTTTGAA
1 -ACTTGTTCTTGAATTGAAGAAATATGGACTTCG-TTTAA-AGGTCGTTGAA
* * * * * * *
18190061 ACTTGTTCTTGAATGGAAGAGATTTGGATTTCATTTTAAGGATCGTTGAG
1 ACTTGTTCTTGAATTGAAGAAATATGGACTTCGTTTAAAGG-TCGTTGAA
* * * * * *
18190111 ACTTGTTCTTGAATTGAAAAAATGTGAACTTCGATTCAAAGGTCATTAAA
1 ACTTGTTCTTGAATTGAAGAAATATGGACTTCG-TTTAAAGGTCGTTGAA
* * * * *
18190161 ACTTGTTCTTGAATTGAAGAAGTATGAACTTTGTTTAAAGGGTTGTTGAG
1 ACTTGTTCTTGAATTGAAGAAATATGGACTTCGTTTAAA-GGTCGTTGAA
*
18190211 ACTTGTTCTTGAATTGAAGAAACATGG
1 ACTTGTTCTTGAATTGAAGAAATATGG
18190238 TGTTTCTATG
Statistics
Matches: 294, Mismatches: 69, Indels: 27
0.75 0.18 0.07
Matches are distributed among these distances:
48 1 0.00
49 45 0.15
50 234 0.80
51 14 0.05
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (49 bp):
ACTTGTTCTTGAATTGAAGAAATATGGACTTCGTTTAAAGGTCGTTGAA
Found at i:18190065 original size:100 final size:99
Alignment explanation
Indices: 18189810--18190237 Score: 321
Period size: 100 Copynumber: 4.3 Consensus size: 99
18189800 AGGGTCAAGT
* * * * * * * * * *
18189810 AGACTTGTTCTTGAATT-AAAGGAATATTGACTTTGCTTC-AAGTTCTTTGATACTTATTCTTAA
1 AGACTTGTTCTTGAATTGAAA-AAATATGGACTTCGATTCAAAGGTCATTAAAACTTGTTCTTGA
* ** * *
18189873 AATGAATG-AATATGGACTTTGCTTCAAGAGTCATTG
65 ATTGAA-GAAATATGGACTTT-CTTTTAGGGTCGTTG
* * * * * * *
18189909 GGACTTATTCTTAAACT-AAAGAAATATGGACTTC-ATTTCAAGGGTCATTAAGACTTGTTATTG
1 AGACTTGTTCTTGAATTGAAA-AAATATGGACTTCGA-TTCAAAGGTCATTAAAACTTGTTCTTG
* * **
18189972 AATTCAAGAAATATGGACTTCTCTTTTAGGGTCATAA
64 AATTGAAGAAATATGGACTT-TCTTTTAGGGTCGTTG
* * ** *
18190009 AGACTTGTTCTTGAATTGAAAAAATATGGACTTCGCTTTAACA-GTTTTTGAAACTTGTTCTTGA
1 AGACTTGTTCTTGAATTGAAAAAATATGGACTTCGATTCAA-AGGTCATTAAAACTTGTTCTTGA
* * * *
18190073 ATGGAAGAGATTTGGA-TTTCATTTTAAGGATCGTTG
65 ATTGAAGAAATATGGACTTTC-TTTT-AGGGTCGTTG
* *
18190109 AGACTTGTTCTTGAATTGAAAAAATGTGAACTTCGATTCAAAGGTCATTAAAACTTGTTCTTGAA
1 AGACTTGTTCTTGAATTGAAAAAATATGGACTTCGATTCAAAGGTCATTAAAACTTGTTCTTGAA
* * * * *
18190174 TTGAAGAAGTATGAACTTTGTTTAAAGGGTTGTTG
66 TTGAAGAAATATGGACTTTCTTT-TAGGGTCGTTG
* *
18190209 AGACTTGTTCTTGAATTGAAGAAACATGG
1 AGACTTGTTCTTGAATTGAAAAAATATGG
18190238 TGTTTCTATG
Statistics
Matches: 254, Mismatches: 63, Indels: 23
0.75 0.19 0.07
Matches are distributed among these distances:
98 2 0.01
99 38 0.15
100 207 0.81
101 7 0.03
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (99 bp):
AGACTTGTTCTTGAATTGAAAAAATATGGACTTCGATTCAAAGGTCATTAAAACTTGTTCTTGAA
TTGAAGAAATATGGACTTTCTTTTAGGGTCGTTG
Found at i:18190113 original size:150 final size:149
Alignment explanation
Indices: 18189935--18190230 Score: 344
Period size: 150 Copynumber: 2.0 Consensus size: 149
18189925 TAAAGAAATA
* * * ** **
18189935 TGGACTTCATTTCAAGGGTCATTAAGACTTGTTATTGAATTCAAGAAATATGGACTTCTCTTTTA
1 TGGACTTCATTTCAAGGATCATTAAGACTTGTTATTGAATTCAAAAAATATGAACTTCGATTCAA
* * *
18190000 GGGTCA-TAAAGACTTGTTCTTGAATTGAAAAAATATGGACTTCGCTTTAACA-GTTTTTGAAAC
66 AGGTCATTAAA-ACTTGTTCTTGAATTGAAAAAATATGAACTTCG-TTTAA-AGGTTGTTGAAAC
18190063 TTGTTCTTGAATGGAAGAGATT
128 TTGTTCTTGAATGGAAGAGATT
* * * * * * *
18190085 TGGATTTCATTTTAAGGATCGTTGAGACTTGTTCTTGAATTGAAAAAATGTGAACTTCGATTCAA
1 TGGACTTCATTTCAAGGATCATTAAGACTTGTTATTGAATTCAAAAAATATGAACTTCGATTCAA
* * * *
18190150 AGGTCATTAAAACTTGTTCTTGAATTGAAGAAGTATGAACTTTGTTTAAAGGGTTGTTGAGACTT
66 AGGTCATTAAAACTTGTTCTTGAATTGAAAAAATATGAACTTCGTTTAAA-GGTTGTTGAAACTT
*
18190215 GTTCTTGAATTGAAGA
130 GTTCTTGAATGGAAGA
18190231 AACATGGTGT
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
148 1 0.01
149 5 0.04
150 111 0.92
151 4 0.03
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (149 bp):
TGGACTTCATTTCAAGGATCATTAAGACTTGTTATTGAATTCAAAAAATATGAACTTCGATTCAA
AGGTCATTAAAACTTGTTCTTGAATTGAAAAAATATGAACTTCGTTTAAAGGTTGTTGAAACTTG
TTCTTGAATGGAAGAGATT
Found at i:18191142 original size:22 final size:21
Alignment explanation
Indices: 18191117--18191270 Score: 120
Period size: 22 Copynumber: 7.3 Consensus size: 21
18191107 CCATATATAT
18191117 TATGTACATATCCTAAAAGCAC
1 TATGTACATAT-CTAAAAGCAC
*
18191139 TATGT--ATA--TAAAAACAC
1 TATGTACATATCTAAAAGCAC
* *
18191156 TATGTACATATC-ACAAATCAT
1 TATGTACATATCTA-AAAGCAC
*
18191177 TATATACATATCTAAAAAGCAC
1 TATGTACATATCT-AAAAGCAC
* * *
18191199 TATGTATATATCTTAAAAGAAT
1 TATGTACATATC-TAAAAGCAC
* * *
18191221 TATGTACTTATACCAAAAGCAT
1 TATGTACATAT-CTAAAAGCAC
*
18191243 TATATACATATCTCAAAAGCAC
1 TATGTACATATCT-AAAAGCAC
18191265 TATGTA
1 TATGTA
18191271 GTATATACAT
Statistics
Matches: 103, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
17 13 0.13
19 3 0.03
20 4 0.04
21 17 0.17
22 63 0.61
23 3 0.03
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (21 bp):
TATGTACATATCTAAAAGCAC
Found at i:18191195 original size:60 final size:62
Alignment explanation
Indices: 18191115--18191277 Score: 181
Period size: 66 Copynumber: 2.6 Consensus size: 62
18191105 TCCCATATAT
* * *
18191115 ATTATGTACATATCCTAAAAGCACTATGTATATA-AAAA-CACTATGTACATAT--CACAAATC
1 ATTATATACATAT-CTAAAAGCACTATGTATATATAAAAGAACTATGTACATATACCA-AAAGC
* *
18191175 ATTATATACATATCTAAAAAGCACTATGTATATATCTTAAAAGAATTATGTACTTATACCAAAAG
1 ATTATATACATATCT-AAAAGCACTATGTATATA---TAAAAGAACTATGTACATATACCAAAAG
18191240 C
62 C
18191241 ATTATATACATATCTCAAAAGCACTATGTAGTATATA
1 ATTATATACATATCT-AAAAGCACTATGTA-TATATA
18191278 CATACCTCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
59 2 0.02
60 30 0.34
64 6 0.07
65 11 0.12
66 33 0.38
67 6 0.07
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (62 bp):
ATTATATACATATCTAAAAGCACTATGTATATATAAAAGAACTATGTACATATACCAAAAGC
Found at i:18191652 original size:20 final size:21
Alignment explanation
Indices: 18191627--18191671 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
18191617 ATTTTATAAT
* *
18191627 AATAGCAA-CCAATAACATTA
1 AATAGCAATCAAATAACATCA
18191647 AATAGCAATCAAATAACATCA
1 AATAGCAATCAAATAACATCA
18191668 AATA
1 AATA
18191672 CAAAATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.58, C:0.18, G:0.04, T:0.20
Consensus pattern (21 bp):
AATAGCAATCAAATAACATCA
Found at i:18197009 original size:14 final size:14
Alignment explanation
Indices: 18196990--18197030 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
18196980 GAAGTTTATG
18196990 AATTTAAAAAAAAT
1 AATTTAAAAAAAAT
*
18197004 AATTTAATAAAAAT
1 AATTTAAAAAAAAT
18197018 --TTTAATAAAAAAT
1 AATTTAA-AAAAAAT
18197031 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 6 0.25
14 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTAAAAAAAAT
Found at i:18197027 original size:11 final size:12
Alignment explanation
Indices: 18196992--18197034 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
18196982 AGTTTATGAA
*
18196992 TTTAAAAAAAAT
1 TTTAATAAAAAT
18197004 AATTTAATAAAAAT
1 --TTTAATAAAAAT
*
18197018 TTTAATAAAAAA
1 TTTAATAAAAAT
18197030 TTTAA
1 TTTAA
18197035 ATTAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTTAATAAAAAT
Found at i:18198279 original size:1 final size:1
Alignment explanation
Indices: 18198241--18198265 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
18198231 GCATTGGTTC
18198241 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
18198266 TCGAGGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:18199355 original size:65 final size:63
Alignment explanation
Indices: 18199276--18199411 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 63
18199266 AAACACTTTA
* *
18199276 AATAATCCTCTTCAATTTTTAATTGAAA-AGGATTATTCAAGGCATTTT-TAGTTAGAAACGCCT
1 AATAATCCTCTTCAA-TTTT--TTGAAAGA-GATTATTCAAGGCATTTTATAGCTAAAAACGCCT
18199339 TG
62 TG
* **
18199341 AATAA-CCTCATTCAATTTTTTGTAAGAGATTATTCAAGGTGTTTTATAGCTAAAAACGCCTTG
1 AATAATCCTC-TTCAATTTTTTGAAAGAGATTATTCAAGGCATTTTATAGCTAAAAACGCCTTG
18199404 AATAATCC
1 AATAATCC
18199412 AAACAAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
62 21 0.34
63 21 0.34
64 10 0.16
65 10 0.16
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (63 bp):
AATAATCCTCTTCAATTTTTTGAAAGAGATTATTCAAGGCATTTTATAGCTAAAAACGCCTTG
Found at i:18199428 original size:62 final size:59
Alignment explanation
Indices: 18199362--18199602 Score: 227
Period size: 62 Copynumber: 4.0 Consensus size: 59
18199352 TCAATTTTTT
* * *
18199362 GTAAGAGATTATTCAAGGTGTTTTATAGCTAAAAACGCCTTGAATAATCCAAACAAAAAATG
1 GTAAGGGATTATTCAAGGCGTTTT-TAGC-AAAAACACCTTGAATAATCCAAA-AAAAAATG
* * **
18199424 GTAAGGGATTATTGAATGCGTTTTT-GACAGAAAACACCTTGAATAAT-CTTAAAAAAATG
1 GTAAGGGATTATTCAAGGCGTTTTTAG-CA-AAAACACCTTGAATAATCCAAAAAAAAATG
* **
18199483 G-AAGGGGATTATTTAAGGCGTTTTCTAGCAAAAAACACCTTGAATAATCTTTAAAAAAAATG
1 GTAA-GGGATTATTCAAGGCGTTTT-TAGC-AAAAACACCTTGAATAATC-CAAAAAAAAATG
* * * * * *
18199545 GAAAGGGATTATTCAAGGCATTTTTGGCCAGAAATACCTTGAATGATCCAAAAAAAAA
1 GTAAGGGATTATTCAAGGCGTTTTTAG-CAAAAACACCTTGAATAATCCAAAAAAAAA
18199603 AAGGGAAGAG
Statistics
Matches: 150, Mismatches: 19, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
58 2 0.01
59 27 0.18
60 31 0.21
61 38 0.25
62 50 0.33
63 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (59 bp):
GTAAGGGATTATTCAAGGCGTTTTTAGCAAAAACACCTTGAATAATCCAAAAAAAAATG
Found at i:18199471 original size:61 final size:59
Alignment explanation
Indices: 18199393--18199631 Score: 214
Period size: 61 Copynumber: 3.9 Consensus size: 59
18199383 TTTATAGCTA
* *
18199393 AAAACGCCTTGAATAATCCAAACAAAAAATGGTAAGGGATTATTGAATGCGTTTTTGACAG
1 AAAACACCTTGAATAATCCAAA-AAAAAATGG-AAGGGATTATTGAAGGCGTTTTTGACAG
** * *
18199454 AAAACACCTTGAATAAT-CTTAAAAAAATGGAAGGGGATTATTTAAGGCGTTTTCT-AGCAA
1 AAAACACCTTGAATAATCCAAAAAAAAATGGAA-GGGATTATTGAAGGCGTTTT-TGA-CAG
** * * *
18199514 AAAACACCTTGAATAATCTTTAAAAAAAATGGAAAGGGATTATTCAAGGCATTTTTGGCCAG
1 AAAACACCTTGAATAATC-CAAAAAAAAATGG-AAGGGATTATTGAAGGCGTTTTT-GACAG
* * * * * *
18199576 -AAATACCTTGAATGATCCAAAAAAAAAAAGGGAAGAGATTATTGAAGTCATTTTTG
1 AAAACACCTTGAATAATCC--AAAAAAAAATGGAAGGGATTATTGAAGGCGTTTTTG
18199632 GCTAGAAATG
Statistics
Matches: 148, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.01
59 28 0.19
60 23 0.16
61 52 0.35
62 41 0.28
63 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (59 bp):
AAAACACCTTGAATAATCCAAAAAAAAATGGAAGGGATTATTGAAGGCGTTTTTGACAG
Found at i:18199524 original size:121 final size:121
Alignment explanation
Indices: 18199368--18199588 Score: 293
Period size: 121 Copynumber: 1.8 Consensus size: 121
18199358 TTTTGTAAGA
* * * *
18199368 GATTATTCAAGGTGTTTTATAGCTAAAAACGCCTTGAATAATC-CAAACAAAAAATGGTAAGGGA
1 GATTATTCAAGGCGTTTTATAGCAAAAAACACCTTGAATAATCTCAAA-AAAAAATGGAAAGGGA
* * *
18199432 TTATTGAATGCGTTTTT-GACAGAAAACACCTTGAATAATCTTAAAAAAATGGAAGGG
65 TTATTCAAGGCATTTTTGGACAG-AAACACCTTGAATAATCTTAAAAAAATGGAAGGG
* * **
18199489 GATTATTTAAGGCGTTTTCTAGCAAAAAACACCTTGAATAATCTTTAAAAAAAATGGAAAGGGAT
1 GATTATTCAAGGCGTTTTATAGCAAAAAACACCTTGAATAATCTCAAAAAAAAATGGAAAGGGAT
* *
18199554 TATTCAAGGCATTTTTGGCCAGAAATACCTTGAAT
66 TATTCAAGGCATTTTTGGACAGAAACACCTTGAAT
18199589 GATCCAAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
121 79 0.93
122 6 0.07
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (121 bp):
GATTATTCAAGGCGTTTTATAGCAAAAAACACCTTGAATAATCTCAAAAAAAAATGGAAAGGGAT
TATTCAAGGCATTTTTGGACAGAAACACCTTGAATAATCTTAAAAAAATGGAAGGG
Found at i:18199632 original size:61 final size:61
Alignment explanation
Indices: 18199535--18199649 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
18199525 AATAATCTTT
* *
18199535 AAAAAAAATGGAAAGGGATTATTCAAGGCATTTTTGGCCAGAAATACCTTGAATGATCCAA
1 AAAAAAAAAGGAAAGAGATTATTCAAGGCATTTTTGGCCAGAAATACCTTGAATGATCCAA
* * * * *
18199596 AAAAAAAAAGGGAAGAGATTATTGAAGTCATTTTTGGCTAGAAATGCCTTGAAT
1 AAAAAAAAAGGAAAGAGATTATTCAAGGCATTTTTGGCCAGAAATACCTTGAAT
18199650 AACCCCATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (61 bp):
AAAAAAAAAGGAAAGAGATTATTCAAGGCATTTTTGGCCAGAAATACCTTGAATGATCCAA
Found at i:18215193 original size:3 final size:3
Alignment explanation
Indices: 18215187--18215224 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
18215177 AATAATAATA
*
18215187 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
18215225 AATAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:18215229 original size:3 final size:3
Alignment explanation
Indices: 18215217--18215388 Score: 141
Period size: 3 Copynumber: 56.3 Consensus size: 3
18215207 GATGATGATG
* *
18215217 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
18215265 ATA ATA ATA ATA ATA ATA ATA ATA ACA AT- ATA CCATA CT- ATA CCATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA --ATA
* * * * * *
18215312 CTA GTA ATA ATA ACA ATA ATA ATA ACAA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * ** * *
18215358 ACA AAA ATA ATA CCA GTA ATA GTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18215389 AAATTGACCC
Statistics
Matches: 133, Mismatches: 29, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.02
3 122 0.92
4 2 0.02
5 6 0.05
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:18218847 original size:50 final size:48
Alignment explanation
Indices: 18218734--18218859 Score: 123
Period size: 50 Copynumber: 2.5 Consensus size: 48
18218724 AAATTGATTA
* * *
18218734 CTAA-TAAACCTAACAACATGTAACTTAAACAAATTAAACTTAATTAAT
1 CTAATTAAACCTAACAACATGCAA-TTAAACAAATCAAACTTAATGAAT
*
18218782 CCTAATTAATCCCTAA-AACATGCCAATTAAACAAATCAAACTTTAACTGAAT
1 -CTAATTAA-ACCTAACAACATG-CAATTAAACAAATCAAAC-TTAA-TGAAT
*
18218834 -TAAATTAAACCTAAGAACATGCAATT
1 CT-AATTAAACCTAACAACATGCAATT
18218860 GAATCAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
49 4 0.06
50 34 0.52
51 23 0.35
52 4 0.06
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (48 bp):
CTAATTAAACCTAACAACATGCAATTAAACAAATCAAACTTAATGAAT
Found at i:18220629 original size:42 final size:42
Alignment explanation
Indices: 18220529--18220699 Score: 157
Period size: 42 Copynumber: 4.0 Consensus size: 42
18220519 GTTATCAAAT
* *
18220529 GGCAATGTGACTTTAAAATTTGAAAAAAA-TTCCTCTAACCA-A
1 GGCAATGTAACTTTAAAA-TT-AAAAAAAGTTCATCTAACCAGA
* * * *
18220571 GTGCAATGTAATTTTAAAATTAAAAAAAGCTCCTCTAACTAGA
1 G-GCAATGTAACTTTAAAATTAAAAAAAGTTCATCTAACCAGA
* * * * ** *
18220614 GACAGTGTGACTTTAAATTTTGAAAAAGTTCATCTAACCCGA
1 GGCAATGTAACTTTAAAATTAAAAAAAGTTCATCTAACCAGA
* * *
18220656 GGCAATGTAACTTTAAAATTCAAAAAGGTTCATCTAACTAGA
1 GGCAATGTAACTTTAAAATTAAAAAAAGTTCATCTAACCAGA
18220698 GG
1 GG
18220700 TAACAGAAAA
Statistics
Matches: 102, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 7 0.07
42 78 0.76
43 17 0.17
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (42 bp):
GGCAATGTAACTTTAAAATTAAAAAAAGTTCATCTAACCAGA
Found at i:18220681 original size:84 final size:85
Alignment explanation
Indices: 18220534--18220698 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 85
18220524 CAAATGGCAA
* *
18220534 TGTGACTTTAAAATTTGAAAAAAATTCCTCTAACCAAGTGCAATGTAATTTTAAAATTAAAAAAA
1 TGTGACTTTAAAATTTGAAAAAAATTCATCTAACCAAGTGCAATGTAACTTTAAAATTAAAAAAA
*
18220599 GCTCCTCTAACTAGAGACAG
66 GCTCATCTAACTAGAGACAG
* * * *
18220619 TGTGACTTTAAATTTTG-AAAAAGTTCATCTAACCCGAG-GCAATGTAACTTTAAAATTCAAAAA
1 TGTGACTTTAAAATTTGAAAAAAATTCATCTAA-CCAAGTGCAATGTAACTTTAAAATTAAAAAA
* *
18220682 GGTTCATCTAACTAGAG
65 AGCTCATCTAACTAGAG
18220699 GTAACAGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 50 0.71
85 20 0.29
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (85 bp):
TGTGACTTTAAAATTTGAAAAAAATTCATCTAACCAAGTGCAATGTAACTTTAAAATTAAAAAAA
GCTCATCTAACTAGAGACAG
Found at i:18220793 original size:41 final size:40
Alignment explanation
Indices: 18220748--18220894 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 40
18220738 AAAGTTGCGA
*
18220748 AACTTTGAAAATTTTAAAAGGCTTTTTAATTAGGGGCAATG
1 AACTTTGAAAA-TTTAAAAGGCTTTTTAATTAGAGGCAATG
* * **
18220789 AACTTTGGAAATTTAAAAAG-TTCCTTTAACCA-ATGGCAATG
1 AACTTTGAAAATTTAAAAGGCTT--TTTAATTAGA-GGCAATG
* * * *
18220830 AATTTTGGAAATTTAAAAGGCTCTTTCAATGTTAGAGGCAACG
1 AACTTTGAAAATTTAAAAGGCT-TTTTAA--TTAGAGGCAATG
*
18220873 AA-TTTAAAAATTTAAAAGGCTT
1 AACTTTGAAAATTTAAAAGGCTT
18220895 CTATAACCAA
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 46 0.54
42 18 0.21
43 10 0.12
44 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (40 bp):
AACTTTGAAAATTTAAAAGGCTTTTTAATTAGAGGCAATG
Found at i:18221131 original size:42 final size:42
Alignment explanation
Indices: 18221085--18221180 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
18221075 CAAACTTTTA
* * *
18221085 AAAATTTAAAATGCTCCCCAAAATAGAGGCTTTATAACTTTG
1 AAAATTTAAAATGCTCCCCAAAATAAAGGCTTAACAACTTTG
* * *
18221127 AAAATTTAAAATGCTCCTCTATATAAAGGCTTAACAACTTTG
1 AAAATTTAAAATGCTCCCCAAAATAAAGGCTTAACAACTTTG
18221169 -AAATCTTAAAAT
1 AAAAT-TTAAAAT
18221181 TTTCCTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (42 bp):
AAAATTTAAAATGCTCCCCAAAATAAAGGCTTAACAACTTTG
Found at i:18221440 original size:19 final size:19
Alignment explanation
Indices: 18221416--18221453 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18221406 CCAAGGAATG
18221416 AAAATCTTATCTTTGAAAA
1 AAAATCTTATCTTTGAAAA
*
18221435 AAAATCTTTTCTTTGAAAA
1 AAAATCTTATCTTTGAAAA
18221454 TTTTTCCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATCTTATCTTTGAAAA
Found at i:18223867 original size:22 final size:21
Alignment explanation
Indices: 18223828--18223869 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18223818 AAAATTGACA
*
18223828 ATTATTTAAAATTGTTTTGAG
1 ATTATTTAAAATTATTTTGAG
*
18223849 ATTATTTAAATTTTATTTTGA
1 ATTATTTAAA-ATTATTTTGA
18223870 TGACTTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
ATTATTTAAAATTATTTTGAG
Found at i:18230166 original size:129 final size:129
Alignment explanation
Indices: 18229928--18230189 Score: 400
Period size: 129 Copynumber: 2.0 Consensus size: 129
18229918 CATTGAGCTA
* * *
18229928 AGACTATAAACATCTAAACCTTTGCAAATGTCATTATGATTCTCAAGCTAATTTATATCTCAGAA
1 AGACTATAAACATCTAAAACTTTGCAAATATCATTATAATTCTCAAGCTAATTTATATCTCAGAA
* * *
18229993 ACTAATTATGTTTAAATGTAAAAACTAGTGGTAGAAATCAAAAGCCAATACAAATATTCACCAT
66 ACTAATTATGTTTAAATGTAAAAACTAGTAGTAGAAAGCAAAAGCCAATACAAACATTCACCAT
* * * * *
18230057 AGACTATAAACGTCTAAAACTTTGCCAATATCATTATAATTCTCATGCTAATTTCTATCTCATAA
1 AGACTATAAACATCTAAAACTTTGCAAATATCATTATAATTCTCAAGCTAATTTATATCTCAGAA
*
18230122 ACTAATTATGTTTAAATGTAAAAACTAGTAGTA-AGAAGCCAAAGCCAATACAAACATTCACCAT
66 ACTAATTATGTTTAAATGTAAAAACTAGTAGTAGA-AAGCAAAAGCCAATACAAACATTCACCAT
18230186 AGAC
1 AGAC
18230190 AAGGCTTATA
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
128 1 0.01
129 119 0.99
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.31
Consensus pattern (129 bp):
AGACTATAAACATCTAAAACTTTGCAAATATCATTATAATTCTCAAGCTAATTTATATCTCAGAA
ACTAATTATGTTTAAATGTAAAAACTAGTAGTAGAAAGCAAAAGCCAATACAAACATTCACCAT
Found at i:18245426 original size:25 final size:25
Alignment explanation
Indices: 18245366--18245417 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
18245356 AATTCATGTA
* *
18245366 TCTACAACATATTAAAGGTTCAGCC
1 TCTACAACACATTAAAGGCTCAGCC
18245391 TCTACAACACATTAAAGGCTCAGCC
1 TCTACAACACATTAAAGGCTCAGCC
18245416 TC
1 TC
18245418 AAACTCACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (25 bp):
TCTACAACACATTAAAGGCTCAGCC
Found at i:18253839 original size:25 final size:25
Alignment explanation
Indices: 18253811--18253942 Score: 101
Period size: 25 Copynumber: 5.2 Consensus size: 25
18253801 AATATATAAT
18253811 AAATGACACAATTTA-AATATGCATG
1 AAATGACA-AATTTACAATATGCATG
* * * *
18253836 AAATGACATACTTAAAATATACATG
1 AAATGACAAATTTACAATATGCATG
* * *
18253861 AAATTATATATTTACAATATGCAAT-
1 AAATGACAAATTTACAATATGC-ATG
*
18253886 AGAATGACATA-TTACAATATGCAATG
1 A-AATGACAAATTTACAATATGC-ATG
* *
18253912 GAATGATATAA-TTACAATATGCATG
1 AAATGACA-AATTTACAATATGCATG
18253937 AAATGA
1 AAATGA
18253943 AAAACACACA
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
24 4 0.05
25 63 0.72
26 21 0.24
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.30
Consensus pattern (25 bp):
AAATGACAAATTTACAATATGCATG
Found at i:18253921 original size:51 final size:51
Alignment explanation
Indices: 18253821--18253942 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 51
18253811 AAATGACACA
*
18253821 ATTTA-AATATGC-ATGAAATGACATACTTAAAATATACATGAAATTATAT
1 ATTTACAATATGCAATGAAATGACATACTTAAAATATACATGAAATGATAT
* * *
18253870 ATTTACAATATGCAAT-AGAATGACATA-TTACAATATGCAATGGAATGATAT
1 ATTTACAATATGCAATGA-AATGACATACTTAAAATATAC-ATGAAATGATAT
*
18253921 AATTACAATATGC-ATGAAATGA
1 ATTTACAATATGCAATGAAATGA
18253943 AAAACACACA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
49 5 0.08
50 24 0.38
51 34 0.54
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (51 bp):
ATTTACAATATGCAATGAAATGACATACTTAAAATATACATGAAATGATAT
Found at i:18254648 original size:15 final size:13
Alignment explanation
Indices: 18254612--18254662 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
18254602 TCCTTTTTCG
18254612 TTTTCTTTTT-TC
1 TTTTCTTTTTGTC
18254624 TTTTCGTTTTTGGTC
1 TTTTC-TTTTT-GTC
*
18254639 TTTCTCTTTTTTTC
1 TTT-TCTTTTTGTC
18254653 TTTTCTTTTT
1 TTTTCTTTTT
18254663 TTTTTTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
12 5 0.15
13 12 0.35
14 5 0.15
15 10 0.29
16 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTGTC
Found at i:18254663 original size:15 final size:15
Alignment explanation
Indices: 18254617--18254666 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
18254607 TTTCGTTTTC
*
18254617 TTTTTTCTTTTCGTT
1 TTTTTTCTTTTCTTT
** *
18254632 TTTGGTC-TTTCTCT
1 TTTTTTCTTTTCTTT
18254646 TTTTTTCTTTTCTTT
1 TTTTTTCTTTTCTTT
18254661 TTTTTT
1 TTTTTT
18254667 TTAGAAACAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTCTTT
Found at i:18255471 original size:32 final size:33
Alignment explanation
Indices: 18255405--18255475 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
18255395 AAGCTTATAG
* *
18255405 TATGAT-TTTGAGGATTTTCTAAGAACTACGAT
1 TATGATATTTGAAGATTTTCTAAGAACTACAAT
*
18255437 TATGATATTTGAAGA-TTTCTAAGAAGTTA-AAT
1 TATGATATTTGAAGATTTTCTAAGAA-CTACAAT
18255469 TATGATA
1 TATGATA
18255476 ATTAGATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 25 0.74
33 9 0.26
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (33 bp):
TATGATATTTGAAGATTTTCTAAGAACTACAAT
Found at i:18260354 original size:21 final size:20
Alignment explanation
Indices: 18260312--18260358 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
18260302 GTTATGGTGT
* *
18260312 AAGTTTAGGGTTTTAGGGTA
1 AAGTTTAGGGTATAAGGGTA
*
18260332 AAGTATTAGGGTATAAGGTTA
1 AAGT-TTAGGGTATAAGGGTA
18260353 AAGTTT
1 AAGTTT
18260359 CGGTTTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.32, C:0.00, G:0.30, T:0.38
Consensus pattern (20 bp):
AAGTTTAGGGTATAAGGGTA
Found at i:18260369 original size:6 final size:6
Alignment explanation
Indices: 18260355--18260507 Score: 51
Period size: 7 Copynumber: 23.7 Consensus size: 6
18260345 TAAGGTTAAA
* * * * * *
18260355 GTTTCG GTTTAG GTTTAG GGTTAG TGTTTAA GTTAAG G-TTAGG GATAAG
1 GTTTAG GTTTAG GTTTAG GTTTAG -GTTTAG GTTTAG GTTTA-G GTTTAG
* * *
18260404 G-TTAGG GTTTTGG GTTTAAG G-TTAGG GTTTAG GTTTTGG GATTTAT
1 GTTTA-G G-TTTAG GTTT-AG GTTTA-G GTTTAG G-TTTAG G-TTTAG
* *
18260450 GTTTGGG GTTTAGG GTTTAGG GTTTAAG GTTTAGG GTTTAG AGTTTGG
1 GTTT-AG GTTTA-G GTTTA-G GTTT-AG GTTTA-G GTTTAG -GTTTAG
*
18260498 GGTTAG GTTT
1 GTTTAG GTTT
18260508 TAAGGTTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 30
0.68 0.14 0.19
Matches are distributed among these distances:
5 5 0.05
6 48 0.44
7 54 0.49
8 3 0.03
ACGTcount: A:0.17, C:0.01, G:0.38, T:0.44
Consensus pattern (6 bp):
GTTTAG
Found at i:18260420 original size:7 final size:7
Alignment explanation
Indices: 18260405--18260515 Score: 95
Period size: 7 Copynumber: 16.3 Consensus size: 7
18260395 AGGGATAAGG
18260405 TTAGGGT
1 TTAGGGT
*
18260412 TTTGGGT
1 TTAGGGT
*
18260419 TTAAGG-
1 TTAGGGT
18260425 TTAGGGT
1 TTAGGGT
18260432 TTA-GGT
1 TTAGGGT
*
18260438 TTTGGGAT
1 TTAGGG-T
*
18260446 TTA-TGT
1 TTAGGGT
*
18260452 TTGGGGT
1 TTAGGGT
18260459 TTAGGGT
1 TTAGGGT
18260466 TTAGGGT
1 TTAGGGT
*
18260473 TTAAGGT
1 TTAGGGT
18260480 TTAGGGT
1 TTAGGGT
*
18260487 TTAGAGT
1 TTAGGGT
*
18260494 TT-GGGG
1 TTAGGGT
*
18260500 TTAGGTT
1 TTAGGGT
*
18260507 TTAAGGT
1 TTAGGGT
18260514 TT
1 TT
18260516 GGGAATTAAG
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
6 17 0.21
7 60 0.75
8 3 0.04
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:18264108 original size:17 final size:17
Alignment explanation
Indices: 18264086--18264118 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18264076 TTAATATTGA
*
18264086 AACTTTTAAAACTTTGG
1 AACTTTCAAAACTTTGG
18264103 AACTTTCAAAACTTTG
1 AACTTTCAAAACTTTG
18264119 AGGCATCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (17 bp):
AACTTTCAAAACTTTGG
Found at i:18270014 original size:14 final size:15
Alignment explanation
Indices: 18269989--18270017 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18269979 TTTAGGGACT
18269989 TGTTGAAAGGTAATA
1 TGTTGAAAGGTAATA
18270004 TGTTG-AAGGTAATA
1 TGTTGAAAGGTAATA
18270018 AGAAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (15 bp):
TGTTGAAAGGTAATA
Found at i:18274633 original size:22 final size:22
Alignment explanation
Indices: 18274605--18274648 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18274595 CTAAATCTTC
*
18274605 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
18274627 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
18274649 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:18278117 original size:18 final size:18
Alignment explanation
Indices: 18278091--18278125 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18278081 TAATCCATGA
*
18278091 GAACCAGAAGCTTTACCT
1 GAACCAGAAACTTTACCT
*
18278109 GAACTAGAAACTTTACC
1 GAACCAGAAACTTTACC
18278126 CAAAGAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (18 bp):
GAACCAGAAACTTTACCT
Found at i:18278352 original size:23 final size:23
Alignment explanation
Indices: 18278297--18278381 Score: 125
Period size: 23 Copynumber: 3.6 Consensus size: 23
18278287 TTAAAAGGGT
* *
18278297 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAA-A-AAG
18278322 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
18278345 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
*
18278368 TCAGCAATGAAGGC
1 TCGGCAATGAAGGC
18278382 TGAAAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 37 0.65
24 1 0.02
25 19 0.33
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (23 bp):
TCGGCAATGAAGGCCTAAAAAAG
Found at i:18278557 original size:22 final size:22
Alignment explanation
Indices: 18278529--18278572 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18278519 CTAAATCTTC
*
18278529 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
18278551 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
18278573 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:18278747 original size:22 final size:22
Alignment explanation
Indices: 18278722--18278766 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
18278712 TTTTTTTATC
18278722 TTTAATTCTA-AGGATACAAATA
1 TTTAATTCTAGA-GATACAAATA
18278744 TTTAATTCTAGAGATACAAATA
1 TTTAATTCTAGAGATACAAATA
18278766 T
1 T
18278767 AAATATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAATTCTAGAGATACAAATA
Found at i:18287689 original size:146 final size:144
Alignment explanation
Indices: 18287298--18287708 Score: 454
Period size: 145 Copynumber: 2.8 Consensus size: 144
18287288 TCAATTTTGA
* * ** *
18287298 GATTTTAAA-GCACCAAAAATTATGAAATATTATGAAATTGAGATCTAAAAAGTTTCGTGAAAAT
1 GATTTCAAATGCACCAAAAATTATGAAATATTATGAAATTGAGATC-GAAAAGTTTC-ACAAAAA
* * * * * *
18287362 TTGAA-TTTGGAAAAGTCAAATTATGAAAATACCCTTATATGGGTATTTTAGTAAATTCACATTT
64 TTCAAGCTTGGAAAAGTCAAATTATGAAAATACCCTTATAAGGGTATTTTAGTAATTTCACACTC
*
18287426 CTCGGGATACTACTAT
129 CTAGGGATACTACTAT
* * * *
18287442 GATTTCAAATGCACCAAAAATCATGAAATATTATAAAATCGAGATTTGAAAAGTTTCACAAAAA-
1 GATTTCAAATGCACCAAAAATTATGAAATATTATGAAATTGAGA-TCGAAAAGTTTCACAAAAAT
* * * * * * *
18287506 TCTGAGCTCGAAAAAGCCAAATTATGAAAATAACCTTATAAGGGTCTTTTAATAATTTCACACTC
65 TC-AAGCTTGGAAAAGTCAAATTATGAAAATACCCTTATAAGGGTATTTTAGTAATTTCACACTC
* *
18287571 CTTAGGGGTACTGCTAT
129 C-TAGGGATACTACTAT
* *
18287588 GATTTCAAATGGACCAAAATTTATGAAATATTATGAAATTGAGATCGAAACAGTTTCACAAAAAT
1 GATTTCAAATGCACCAAAAATTATGAAATATTATGAAATTGAGATCGAAA-AGTTTCACAAAAAT
* * *
18287653 TCAAGCTTGGAATA-TCAAATTACGAAAATACCCCTTA-AAGGATATTTTAGTAATTT
65 TCAAGCTTGGAAAAGTCAAATTATGAAAATA-CCCTTATAAGGGTATTTTAGTAATTT
18287709 TGTACTTCTC
Statistics
Matches: 218, Mismatches: 41, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
143 1 0.00
144 13 0.06
145 124 0.57
146 78 0.36
147 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (144 bp):
GATTTCAAATGCACCAAAAATTATGAAATATTATGAAATTGAGATCGAAAAGTTTCACAAAAATT
CAAGCTTGGAAAAGTCAAATTATGAAAATACCCTTATAAGGGTATTTTAGTAATTTCACACTCCT
AGGGATACTACTAT
Found at i:18291168 original size:39 final size:39
Alignment explanation
Indices: 18291090--18291167 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
18291080 CTTGATGTTG
* * *
18291090 ATGATTTTGAGTTGATTTCTTCCATTGGGTTTGATTTTT
1 ATGATTTTGAATTGATTTCTTCCATTGAGTATGATTTTT
*
18291129 ATGATTTTGAATTGATTTCTTCCTTTGAGTATGCATTTT
1 ATGATTTTGAATTGATTTCTTCCATTGAGTATG-ATTTT
18291168 ACTTACAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (39 bp):
ATGATTTTGAATTGATTTCTTCCATTGAGTATGATTTTT
Found at i:18302620 original size:2 final size:2
Alignment explanation
Indices: 18302613--18302650 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18302603 TATATGCTTT
18302613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18302651 AACTGCAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18303195 original size:255 final size:250
Alignment explanation
Indices: 18302744--18303245 Score: 844
Period size: 255 Copynumber: 2.0 Consensus size: 250
18302734 TACATAAACT
* *
18302744 AATTTAATTAAACTCTAAATCCATATTTTTTCTTGTCTTTTAATGAACAATATCGTCAGATCCAA
1 AATTAAATTAAACTCTAAATCCATATTTTTTCTTGTCTTTTAATGAACAATATCGTCAAATCCAA
18302809 TATTAACGGTGGAAACTGAAAAAAAACAAATTGACTGGTATGATAAGGTTAGACAAAAAAAAAAA
66 TATTAACGGTGGAAACTGAAAAAAAACAAATTGACTGGTATGATAAGGTTAGACAAAAAAAAAAA
* *
18302874 TCCAAATCTAAACTAGTTGCAAGAATAAAAAGCAAAGTTACTCATTATGCCTCACTTTTATCTTT
131 TCCAAATCTAAACTAGTTGCAAGAATAAAAAACAAAGTTACTCATCATGCCTCACTTTTATCTTT
*
18302939 CCTTTGTCTCCATGAAGAATCATTCCCTTCGCCTTCCAATATTGAAAAGCTTCTA
196 CCTTTGTCTCCATGAACAATCATTCCCTTCGCCTTCCAATATTGAAAAGCTTCTA
*
18302994 AATTAAATTAAACTCTAAATCCATATGTTTTTCTTTTCTTTTAATGAACAATATCGTCAAATCCA
1 AATTAAATTAAACTCTAAATCCATAT-TTTTTCTTGTCTTTTAATGAACAATATCGTCAAATCCA
*
18303059 ATATTAACGGTGGAAACTG-AAAAAAACAAATTGATTGGTATGATAAGGTTAGACAAAAAGAAAA
65 ATATTAACGGTGGAAACTGAAAAAAAACAAATTGACTGGTATGATAAGGTTAGAC----A-AAAA
* *
18303123 AAAAAATCCAAATCTAAACTAGTTGCATGAATAAAAAACAAAGTTCCTCATCATGCCTCACTTTT
125 AAAAAATCCAAATCTAAACTAGTTGCAAGAATAAAAAACAAAGTTACTCATCATGCCTCACTTTT
* *
18303188 ATCTTTCCTTTGTTTCCATGAACAATCATTCCCTTCGCCTTCCAATGTTGAAAAGCTT
190 ATCTTTCCTTTGTCTCCATGAACAATCATTCCCTTCGCCTTCCAATATTGAAAAGCTT
18303246 GTAATTTTCA
Statistics
Matches: 235, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
250 59 0.25
251 55 0.23
254 1 0.00
255 120 0.51
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (250 bp):
AATTAAATTAAACTCTAAATCCATATTTTTTCTTGTCTTTTAATGAACAATATCGTCAAATCCAA
TATTAACGGTGGAAACTGAAAAAAAACAAATTGACTGGTATGATAAGGTTAGACAAAAAAAAAAA
TCCAAATCTAAACTAGTTGCAAGAATAAAAAACAAAGTTACTCATCATGCCTCACTTTTATCTTT
CCTTTGTCTCCATGAACAATCATTCCCTTCGCCTTCCAATATTGAAAAGCTTCTA
Found at i:18311520 original size:29 final size:30
Alignment explanation
Indices: 18311474--18311531 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
18311464 GAAGCATTAT
18311474 TTTCAAGTTCTTTCTTTTCTTGTT-TTTAAG
1 TTTCAAGTTCTTTCTTTTCTT-TTCTTTAAG
18311504 TTTCAA-TTCTTAT-TTTTCTTTTCTTTAA
1 TTTCAAGTTCTT-TCTTTTCTTTTCTTTAA
18311532 ATTTGGCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 2 0.08
29 17 0.65
30 7 0.27
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTCAAGTTCTTTCTTTTCTTTTCTTTAAG
Found at i:18313218 original size:12 final size:12
Alignment explanation
Indices: 18313203--18313233 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18313193 ACCAACCCAC
18313203 CAACAACCAAAA
1 CAACAACCAAAA
*
18313215 CAACAACGAAAA
1 CAACAACCAAAA
18313227 CAACAAC
1 CAACAAC
18313234 TACCACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (12 bp):
CAACAACCAAAA
Found at i:18314471 original size:16 final size:16
Alignment explanation
Indices: 18314432--18314463 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18314422 AATCCTGTGC
18314432 TATTATTTTTATTATT
1 TATTATTTTTATTATT
18314448 TATTATTTTTA-TATT
1 TATTATTTTTATTATT
18314463 T
1 T
18314464 GTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTATTTTTATTATT
Found at i:18315439 original size:28 final size:28
Alignment explanation
Indices: 18315367--18315425 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
18315357 CTTTCCTCCC
*
18315367 ATAA-ATGGCCCACACTTGGAAAAGGCA
1 ATAACATGGCCCACATTTGGAAAAGGCA
*
18315394 ATGACATGGCCCACATTTGGAAAAGGCA
1 ATAACATGGCCCACATTTGGAAAAGGCA
18315422 ATAA
1 ATAA
18315426 TATAGTCCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (28 bp):
ATAACATGGCCCACATTTGGAAAAGGCA
Found at i:18316847 original size:144 final size:143
Alignment explanation
Indices: 18316554--18316944 Score: 434
Period size: 144 Copynumber: 2.7 Consensus size: 143
18316544 TGCTCATTTT
* * * **
18316554 TGTGATTTTAAA-GCTCCAAAAATCATGAAATATTATAAAATTGAGATCTGAAAAGTTTTGTGAA
1 TGTGATTTTAAATGCACCAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAA
** * * * * * * *
18316618 AATCCAAGCTCAAAAAGGTCAAATTATGAAAATACCCTTAAAGGGTATTCTAGTAATTTCATACT
66 AATTTAAGCTC-AAAAGATCAAATTACGAAAATACCCTTAAAAGATATTCGAGTAATTTCACACC
* *
18316683 TTTGGGGGTACTGC
130 TTTCGAGGTACTGC
* *
18316697 TATGATTTTAAATGCACCAAAAATCATAAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAA
1 TGTGATTTTAAATGCACCAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAA
*
18316762 AATTTAAGCTCAGAAAGATCAAATTACGAAAATA-TCTCTAAAAGATATTTCGA-TAATTTCACA
66 AATTTAAGCTCA-AAAGATCAAATTACGAAAATACCCT-TAAAAGATA-TTCGAGTAATTTCACA
* *
18316825 CCTTTCGATGTATTGC
128 CCTTTCGAGGTACTGC
* * * * *
18316841 TGTGATTTCAAATGCATCAAAAAT-ATGAAATATTATGAAATTAAGATATG-AAAGTTTCCTAAA
1 TGTGATTTTAAATGCACCAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAA
* * *
18316904 AATTTGAGCTCAAAAAAGTTAAATTACGAAAA-ACCCTTAAA
66 AATTTAAGCTCAAAAGA-TCAAATTACGAAAATACCCTTAAA
18316945 GGTATTTTAG
Statistics
Matches: 210, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
141 9 0.04
142 37 0.18
143 38 0.18
144 122 0.58
145 4 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (143 bp):
TGTGATTTTAAATGCACCAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAA
AATTTAAGCTCAAAAGATCAAATTACGAAAATACCCTTAAAAGATATTCGAGTAATTTCACACCT
TTCGAGGTACTGC
Found at i:18326747 original size:20 final size:20
Alignment explanation
Indices: 18326722--18326760 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18326712 GTAATAATTA
* *
18326722 ACAATAATAATAATTAAATG
1 ACAATAACAATAATAAAATG
18326742 ACAATAACAATAATAAAAT
1 ACAATAACAATAATAAAAT
18326761 TCAAATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAATAACAATAATAAAATG
Found at i:18326854 original size:3 final size:3
Alignment explanation
Indices: 18326832--18326885 Score: 83
Period size: 3 Copynumber: 17.7 Consensus size: 3
18326822 AATAAAAAAC
18326832 AAT AA- AAT AAGT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18326878 AAT AAT AA
1 AAT AAT AA
18326886 ACTTTTCCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 41 0.85
4 4 0.08
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18326990 original size:19 final size:21
Alignment explanation
Indices: 18326960--18327011 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
18326950 GATGTCGGGG
*
18326960 AATTATTATTAAAAAT-AATA
1 AATTAATATTAAAAATAAATA
*
18326980 AA-TAATATTAAAACTAAATA
1 AATTAATATTAAAAATAAATA
18327000 AATTAATATTAA
1 AATTAATATTAA
18327012 CTCTTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 8 0.29
21 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTAATATTAAAAATAAATA
Found at i:18331790 original size:21 final size:21
Alignment explanation
Indices: 18331760--18331841 Score: 119
Period size: 21 Copynumber: 3.9 Consensus size: 21
18331750 AGCAAAGATA
18331760 GCAGCAGACTGCTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
* * *
18331781 ACAGTAGACTGCTAGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
*
18331802 GCAGCAGACTGTTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
*
18331823 GCAGCAGACTACTGGTTTC
1 GCAGCAGACTGCTGGTTTC
18331842 TTTCAACAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
GCAGCAGACTGCTGGTTTCCT
Found at i:18332691 original size:33 final size:31
Alignment explanation
Indices: 18332606--18332695 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 31
18332596 TATTACTTTA
*
18332606 TTATTTTTTCATTATTTGAATATAATTTTATTT
1 TTATTTTTT-ATT-TTTGAATATAATTTAATTT
*
18332639 TTATTTATT-TTTTT-AATATAATTTAATTAT
1 TTATTTTTTATTTTTGAATATAATTTAATT-T
*
18332669 TTATTTTTTATTGTTTGGATATAATTT
1 TTATTTTTTATT-TTTGAATATAATTT
18332696 GATCACTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 13 0.27
30 12 0.24
31 4 0.08
32 3 0.06
33 17 0.35
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (31 bp):
TTATTTTTTATTTTTGAATATAATTTAATTT
Found at i:18345047 original size:108 final size:108
Alignment explanation
Indices: 18344851--18345049 Score: 274
Period size: 108 Copynumber: 1.8 Consensus size: 108
18344841 GTCATCTTTA
* * * * * *
18344851 TCCTCTTGACTTACGATTCAATCCTAGTCCTTGTGATTCTTTGACTCATGGTTTAATCTCGATCG
1 TCCTCTAGACTCACGATTCAACCCCAGTCCTTATGATTCCTTGACTCATGGTTTAATCTCGATCG
*
18344916 TCATTATTTTTTTAACTTGTGGTTCAATCCCAATCCTCGTTAT
66 TCATTATTTTTTTAACTTATGGTTCAATCCCAATCCTCGTTAT
* * * *
18344959 TCCTCTAGACTCACGGTTCAACCCCAGTCCTTATTATTCCTTGACTCGTGGTTTAATCTCGATTG
1 TCCTCTAGACTCACGATTCAACCCCAGTCCTTATGATTCCTTGACTCATGGTTTAATCTCGATCG
*
18345024 TCATTATTTTTTTGA-TTCATGGTTCA
66 TCATTATTTTTTTAACTT-ATGGTTCA
18345050 GTCTCAGTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 2 0.03
108 76 0.97
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.44
Consensus pattern (108 bp):
TCCTCTAGACTCACGATTCAACCCCAGTCCTTATGATTCCTTGACTCATGGTTTAATCTCGATCG
TCATTATTTTTTTAACTTATGGTTCAATCCCAATCCTCGTTAT
Found at i:18345114 original size:36 final size:36
Alignment explanation
Indices: 18345043--18345114 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
18345033 TTTTGATTCA
* *
18345043 TGGTTCAGTCTCAGTCATCTTTATCTTCTTGACTTG
1 TGGTTCAGTCCCAGTCATCTTTATCTTCTTAACTTG
*
18345079 TGGTTTAGTCCCAGTCATCTTTAT-TCTCTTAACTTG
1 TGGTTCAGTCCCAGTCATCTTTATCT-TCTTAACTTG
18345115 AGATTCAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.47
Consensus pattern (36 bp):
TGGTTCAGTCCCAGTCATCTTTATCTTCTTAACTTG
Found at i:18345127 original size:36 final size:36
Alignment explanation
Indices: 18345054--18345127 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
18345044 GGTTCAGTCT
* * * * *
18345054 CAGTCATCTTTATCTTCTTGACTTGTGGTTTAGTCC
1 CAGTCATCTTTATCTTCTTAACTTGAGATTCAATCC
18345090 CAGTCATCTTTAT-TCTCTTAACTTGAGATTCAATCC
1 CAGTCATCTTTATCT-TCTTAACTTGAGATTCAATCC
18345126 CA
1 CA
18345128 ATCCTTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.43
Consensus pattern (36 bp):
CAGTCATCTTTATCTTCTTAACTTGAGATTCAATCC
Found at i:18345209 original size:251 final size:249
Alignment explanation
Indices: 18344740--18345228 Score: 572
Period size: 251 Copynumber: 2.0 Consensus size: 249
18344730 TTGGTCACAT
* *
18344740 TTATTCTCTCGACTCGTGGTTTATTCCTGATTGTCATTAATTTCTTGACATGTGGTTTAGTCCCA
1 TTATTCTCTCGACTCGTGGTTTAATCCTGATTGTCATTAATTTCTTGACA-GTGGTTCAGTCCCA
* * * *
18344805 GTCGTCTTTATCCTCTTGACCCATGGATCCGTCCCGGTCATCTTTATCCTCTTGACTTACGATTC
65 GTCATCTTTATCCTCTTGACCCATGGATCAGTCCCAGTCATCTTTATCCTCTTAACTTACGATTC
* * * * * * *
18344870 AATCCTAGTCCTTGTGATTCTTTGACTCATGGTTTAATCTCGATCGTCATTATTTTTTTAACTTG
130 AATCCCAATCCTTGTAATTCCTTGACTCACGGTTTAATCCCGATCGTCATTATTTTTTTAACTCG
*
18344935 TGGTTCAATCCCAATCCTCGTTATTCCTCTAGACTCACGGTTCAACCCCAGTCCTTA
195 TGGTTCAATCCCAATCATCGTTATT--TCTAGACTCACGGTTCAACCCCAGTCCTTA
* * * *
18344992 TTATTC-CTTGACTCGTGGTTTAAT-CTCGATTGTCATTATTTTTTTGATTCA-TGGTTCAGTCT
1 TTATTCTCTCGACTCGTGGTTTAATCCT-GATTGTCATTAATTTCTTGA--CAGTGGTTCAGTCC
* *** * * *
18345054 CAGTCATCTTTATCTTCTTGACTTGTGGTTTAGTCCCAGTCATCTTTATTCTCTTAACTTGA-GA
63 CAGTCATCTTTATCCTCTTGACCCATGGATCAGTCCCAGTCATCTTTATCCTCTTAACTT-ACGA
* * * *
18345118 TTCAATCCCAATCCTTGTAATTCCTTGGCTCGCGGTTTAATCCCGGTCGTCATTATTTTTTTGAC
127 TTCAATCCCAATCCTTGTAATTCCTTGACTCACGGTTTAATCCCGATCGTCATTATTTTTTTAAC
* ** * * *
18345183 TCGTGGTTTAATCTTAGTCATCGTTATTTCTTGACTCGCGGTTCAA
192 TCGTGGTTCAATCCCAATCATCGTTATTTCTAGACTCACGGTTCAA
18345229 TCTCGATCTC
Statistics
Matches: 198, Mismatches: 35, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
249 16 0.08
250 2 0.01
251 171 0.86
252 7 0.04
253 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (249 bp):
TTATTCTCTCGACTCGTGGTTTAATCCTGATTGTCATTAATTTCTTGACAGTGGTTCAGTCCCAG
TCATCTTTATCCTCTTGACCCATGGATCAGTCCCAGTCATCTTTATCCTCTTAACTTACGATTCA
ATCCCAATCCTTGTAATTCCTTGACTCACGGTTTAATCCCGATCGTCATTATTTTTTTAACTCGT
GGTTCAATCCCAATCATCGTTATTTCTAGACTCACGGTTCAACCCCAGTCCTTA
Found at i:18345224 original size:71 final size:71
Alignment explanation
Indices: 18344992--18345230 Score: 190
Period size: 71 Copynumber: 3.4 Consensus size: 71
18344982 CCAGTCCTTA
* * * * * * *
18344992 TTATTCCTTGACTCGTGGTTTAATCTCGATTGTCATTATTTTTTTGATTCATGGTTCAGTCTCAG
1 TTATTCCTTGACTCGCGGTTTAATCCCGGTCGTCATTATTTTTTTGACTCGTGGTTCAATCTCAG
*
18345057 TCATCT
66 TCATCG
* * * * * * * * * * * * * *
18345063 TTATCTTCTTGACTTGTGGTTTAGTCCCAGTCATCTTTATTCTCTTAACTTGAGATTCAATCCCA
1 TTAT-TCCTTGACTCGCGGTTTAATCCCGGTCGTCATTATTTTTTTGACTCGTGGTTCAATCTCA
* * *
18345128 ATCCTTG
65 GTCATCG
* * * *
18345135 TAATTCCTTGGCTCGCGGTTTAATCCCGGTCGTCATTATTTTTTTGACTCGTGGTTTAATCTTAG
1 TTATTCCTTGACTCGCGGTTTAATCCCGGTCGTCATTATTTTTTTGACTCGTGGTTCAATCTCAG
18345200 TCATCG
66 TCATCG
* *
18345206 TTATTTCTTGACTCGCGGTTCAATC
1 TTATTCCTTGACTCGCGGTTTAATC
18345231 TCGATCTCTT
Statistics
Matches: 119, Mismatches: 48, Indels: 2
0.70 0.28 0.01
Matches are distributed among these distances:
71 72 0.61
72 47 0.39
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (71 bp):
TTATTCCTTGACTCGCGGTTTAATCCCGGTCGTCATTATTTTTTTGACTCGTGGTTCAATCTCAG
TCATCG
Found at i:18345401 original size:104 final size:104
Alignment explanation
Indices: 18345209--18345445 Score: 255
Period size: 104 Copynumber: 2.3 Consensus size: 104
18345199 GTCATCGTTA
* ** * *
18345209 TTTCTTGACTCGCGGTTCAATCTCGATCTCTTTACTTCTAAGTTGTGGTTTAATCCCGATCTTCA
1 TTTCTTGACTCGCGGTTCAATCTCGATCTCTTTACCTCTAAGTTGCAGTTTAATCCCAATCCTCA
* *
18345274 TTATTTCTCTAAGGTGCAGTTTAATCCCGATTTCTTTAT
66 TTATTTCTCTAAGATGCAGTTTAATCCCGATCTCTTTAT
* * * *
18345313 TTTCTTGATTCGTGGTTCAATTTTGATCTCTTTACCTCTAAGTTGCAGTTTAATCCCAATCCTCA
1 TTTCTTGACTCGCGGTTCAATCTCGATCTCTTTACCTCTAAGTTGCAGTTTAATCCCAATCCTCA
* ** * *
18345378 TTATTTCT-T-TGATTTATGATTTAATCTCGGTCTCTTTAT
66 TTATTTCTCTAAGATGCA-G-TTTAATCCCGATCTCTTTAT
* * * *
18345417 TTT-TTGACTTGCAGTTAAATCCCGATCTC
1 TTTCTTGACTCGCGGTTCAATCTCGATCTC
18345446 ATAATCCACC
Statistics
Matches: 107, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
102 3 0.03
103 20 0.19
104 84 0.79
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (104 bp):
TTTCTTGACTCGCGGTTCAATCTCGATCTCTTTACCTCTAAGTTGCAGTTTAATCCCAATCCTCA
TTATTTCTCTAAGATGCAGTTTAATCCCGATCTCTTTAT
Found at i:18345519 original size:6 final size:6
Alignment explanation
Indices: 18345501--18345536 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
18345491 GACTCATGGT
*
18345501 AACAAA AAAAAA AACAAA AACAAA AA-AAA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA A
18345537 TTTTTTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:18345525 original size:11 final size:11
Alignment explanation
Indices: 18345504--18345536 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18345494 TCATGGTAAC
18345504 AAAAAAA-AAA
1 AAAAAAACAAA
*
18345514 ACAAAAACAAA
1 AAAAAAACAAA
18345525 AAAAAAACAAA
1 AAAAAAACAAA
18345536 A
1 A
18345537 TTTTTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:18345757 original size:28 final size:28
Alignment explanation
Indices: 18345709--18345771 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
18345699 TTTTGATTTG
* * *
18345709 ACTGGGC-CCTAGTCTTGATTTTGGCTCA
1 ACTGGGCTCCTAGGCTTAATTTT-ACTCA
18345737 ACTGGGCTCC-AGGCTTAATTTTACTCA
1 ACTGGGCTCCTAGGCTTAATTTTACTCA
*
18345764 ATTGGGCT
1 ACTGGGCT
18345772 TCAAGCCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 11 0.37
28 17 0.57
29 2 0.07
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (28 bp):
ACTGGGCTCCTAGGCTTAATTTTACTCA
Found at i:18347834 original size:71 final size:71
Alignment explanation
Indices: 18347718--18347860 Score: 205
Period size: 71 Copynumber: 2.0 Consensus size: 71
18347708 AGTAATTTTC
* *
18347718 CTATTTGGTTGCTAGAAAAACTCAAAAAAGTGTAGTTTTGATTGATCATCTACTTTTAGCAAAAT
1 CTATTTGGTTGCTAGAAAAACTCAAAAAAGTATAATTTTGATTGATCATCTACTTTTAGCAAAAT
18347783 GTGAGT
66 GTGAGT
* * ** ** *
18347789 CTATTTGGTTGTTGGAAAAACTCAGGAAAGTATAATTTTGATTGATTGTCTATTTTTAGCAAAAT
1 CTATTTGGTTGCTAGAAAAACTCAAAAAAGTATAATTTTGATTGATCATCTACTTTTAGCAAAAT
18347854 GTGAGT
66 GTGAGT
18347860 C
1 C
18347861 AATGATAGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (71 bp):
CTATTTGGTTGCTAGAAAAACTCAAAAAAGTATAATTTTGATTGATCATCTACTTTTAGCAAAAT
GTGAGT
Found at i:18348501 original size:26 final size:25
Alignment explanation
Indices: 18348438--18348505 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
18348428 TTCTGCTTTT
*
18348438 ATGTGAAATGTCTTGTTATGTAAAT
1 ATGTGAAATGTCTTGTTATGTAAAA
* *
18348463 ATG-GATAT-ACTTGTT-TGTAAAGCA
1 ATGTGAAATGTCTTGTTATGTAAA--A
18348487 ATGTGAAATGTCTTGTTAT
1 ATGTGAAATGTCTTGTTAT
18348506 TCATTATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
22 6 0.18
23 6 0.18
24 7 0.21
25 7 0.21
26 6 0.18
27 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.43
Consensus pattern (25 bp):
ATGTGAAATGTCTTGTTATGTAAAA
Found at i:18354021 original size:14 final size:14
Alignment explanation
Indices: 18354004--18354031 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18353994 ACCATTTTCA
18354004 GCTTTTTTTTTCTT
1 GCTTTTTTTTTCTT
18354018 GCTTTTTTTTTCTT
1 GCTTTTTTTTTCTT
18354032 TTCCTTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
GCTTTTTTTTTCTT
Found at i:18368937 original size:11 final size:12
Alignment explanation
Indices: 18368902--18368948 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
18368892 GCTAGCTTGC
*
18368902 AAAAGAAAAAGAA
1 AAAAGCAAAAG-A
* *
18368915 AAAACCACAAGA
1 AAAAGCAAAAGA
18368927 AAAAG-AAAAGA
1 AAAAGCAAAAGA
18368938 AAAAGCAAAAG
1 AAAAGCAAAAG
18368949 CAATAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 10 0.36
12 10 0.36
13 8 0.29
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGCAAAAGA
Found at i:18375287 original size:30 final size:30
Alignment explanation
Indices: 18375243--18375300 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
18375233 AAATTTAAAA
18375243 TTTTATTGATTTTTAGTGCTTTAATGCTTTT
1 TTTTATTGATTTTTAGTGCTTTAA-GCTTTT
*
18375274 TTTTATT-ATTTTTAGTGTTTTAAGCTT
1 TTTTATTGATTTTTAGTGCTTTAAGCTT
18375301 ATGGATGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 15 0.58
31 7 0.27
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (30 bp):
TTTTATTGATTTTTAGTGCTTTAAGCTTTT
Found at i:18378018 original size:13 final size:13
Alignment explanation
Indices: 18378000--18378025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18377990 TGTTTGAAAC
18378000 GTCAAACATAATT
1 GTCAAACATAATT
18378013 GTCAAACATAATT
1 GTCAAACATAATT
18378026 ATAAATACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
GTCAAACATAATT
Found at i:18390663 original size:27 final size:30
Alignment explanation
Indices: 18390604--18390678 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 30
18390594 TATTCTTTAT
*
18390604 TTTTAATTTTGTTAATATTATATATAATATAA
1 TTTT-ATTTTG-TAATTTTATATATAATATAA
18390636 TCTTT-TTTTGTAATTTTA-ATA-AAT-TAA
1 T-TTTATTTTGTAATTTTATATATAATATAA
*
18390663 TTTTATTTTCTAATTT
1 TTTTATTTTGTAATTT
18390679 AATTATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 3 0.08
27 14 0.36
28 3 0.08
29 3 0.08
30 7 0.18
31 5 0.13
32 1 0.03
33 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTTATTTTGTAATTTTATATATAATATAA
Found at i:18390686 original size:21 final size:22
Alignment explanation
Indices: 18390657--18390700 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
18390647 AATTTTAATA
*
18390657 AATTAATTTTATTTTC-TAATTT
1 AATTAATTTT-TTTACATAATTT
18390679 AATT-ATTTTTTTACATAATTT
1 AATTAATTTTTTTACATAATTT
18390700 A
1 A
18390701 TACTGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTAATTTTTTTACATAATTT
Found at i:18391471 original size:16 final size:17
Alignment explanation
Indices: 18391452--18391508 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 17
18391442 TCAAAAAATT
18391452 AATTTAAAAT-AATTTA
1 AATTTAAAATAAATTTA
18391468 AATTT-AAATAAATTTA
1 AATTTAAAATAAATTTA
*
18391484 ATTTTAAAAATAAA---A
1 AATTT-AAAATAAATTTA
18391499 AATTTAAAAT
1 AATTTAAAAT
18391509 CAAAATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 5 0.14
15 9 0.25
16 15 0.42
18 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:18393647 original size:6 final size:6
Alignment explanation
Indices: 18393636--18393663 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18393626 TGGATTAATT
18393636 AAATCA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAAT
18393664 AGAAAGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:18393893 original size:32 final size:32
Alignment explanation
Indices: 18393857--18393953 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 32
18393847 TTTTTTTTGA
18393857 AACTTTGATTTCCAAAGAAAATTGATACTTTC
1 AACTTTGATTTCCAAAGAAAATTGATACTTTC
** ** ** *
18393889 AAC--T--TTTCCTCA-AAAA-TCCTTTTTTGA
1 AACTTTGATTTCCAAAGAAAATTGATACTTT-C
18393916 AACTTTGATTTCCAAAGAAAATTGATACTTTC
1 AACTTTGATTTCCAAAGAAAATTGATACTTTC
18393948 AACTTT
1 AACTTT
18393954 TCCTCAAAAA
Statistics
Matches: 44, Mismatches: 14, Indels: 14
0.61 0.19 0.19
Matches are distributed among these distances:
26 5 0.11
27 7 0.16
28 6 0.14
29 1 0.02
30 1 0.02
31 6 0.14
32 13 0.30
33 5 0.11
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (32 bp):
AACTTTGATTTCCAAAGAAAATTGATACTTTC
Found at i:18393971 original size:117 final size:114
Alignment explanation
Indices: 18393698--18394086 Score: 482
Period size: 117 Copynumber: 3.4 Consensus size: 114
18393688 TCTCGTGTAG
* *
18393698 GGAAAATTGATACTTTCAACTTTTCC-CCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTT-GAAATTTATTTCTAAGGAAAAT
* *
18393762 TGATACTTTCAATTTTTTCC-CAAAAAT-ATTTTTTGGAAATTTATTTTCAA
65 TGATACTTTCAA-CTTTTCCTCAAAAATCCTTTTTT-GAAATTTATTTTCAA
* * * * * *
18393812 GGAAATTTGATATTTTCAACTTTTCTTCAAAAATATTTTTTTTGAAACTTTGATTTCCAAAGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-ATATTTTTTGAAA-TTT-ATTTCTAAGGAAA
*
18393877 ATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAACTTTGATTTCCAA
63 ATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAA-TTT-ATTTTCAA
* *
18393931 AGAAAATTGATACTTTCAACTTTTCCTC-AAAAATCCTTTTTTGAAAATTTATTTCTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAT-ATTTTTTG-AAATTTATTTCTAAGGAAAA
* * *
18393995 TTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTAAAAATTTATTTTTAA
64 TTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTT-GAAATTTATTTTCAA
*
18394048 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTT
18394087 GAATTTCAAA
Statistics
Matches: 238, Mismatches: 24, Indels: 24
0.83 0.08 0.08
Matches are distributed among these distances:
114 23 0.10
115 9 0.04
116 22 0.09
117 115 0.48
118 32 0.13
119 37 0.16
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (114 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTGAAATTTATTTCTAAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAATTTATTTTCAA
Found at i:18393999 original size:58 final size:58
Alignment explanation
Indices: 18393698--18394081 Score: 481
Period size: 59 Copynumber: 6.6 Consensus size: 58
18393688 TCTCGTGTAG
* * * *
18393698 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTGGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAA
* * *
18393755 GGAAAATTGATACTTTCAATTTTTTCC-CAAAAAT-ATTTTTTGGAAATTTATTT-TCAA
1 GGAAAATTGATACTTTCAA-CTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCT-AA
* * * ** * *
18393812 GGAAATTTGATATTTTCAACTTTTCTTCAAAAATATTTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CCTTTTTTGAAAATTT-ATTTCTAA
* * *
18393872 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTT-ATTTCTAA
*
18393931 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAA
* * *
18393989 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTAAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTTGAAAATTTATTTCTAA
18394048 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAAT
18394082 ATTTTGAATT
Statistics
Matches: 296, Mismatches: 22, Indels: 16
0.89 0.07 0.05
Matches are distributed among these distances:
56 6 0.02
57 71 0.24
58 48 0.16
59 135 0.46
60 36 0.12
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAA
Found at i:18394136 original size:86 final size:89
Alignment explanation
Indices: 18394009--18394172 Score: 289
Period size: 86 Copynumber: 1.9 Consensus size: 89
18393999 TACTTTCAAC
18394009 TTTTCCTCAAAAACCCTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCC
1 TTTTCCTCAAAAACCCTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCC
18394074 CTAAAAATATTTTGAATTTCAAAT
66 CTAAAAATATTTTGAATTTCAAAT
* *
18394098 TTTTCCTCAAAAA-CC-TTTTTT-GAAATTTATTTTTAAGGAAAATTGATGCTTTCAACTTTTCC
1 TTTTCCTCAAAAACCCTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCC
18394160 CTAAAAATATTTT
66 CTAAAAATATTTT
18394173 TTCGAAAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
86 52 0.71
87 6 0.08
88 2 0.03
89 13 0.18
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (89 bp):
TTTTCCTCAAAAACCCTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCC
CTAAAAATATTTTGAATTTCAAAT
Found at i:18394152 original size:57 final size:60
Alignment explanation
Indices: 18394090--18394251 Score: 197
Period size: 60 Copynumber: 2.7 Consensus size: 60
18394080 ATATTTTGAA
* * * * *
18394090 TTTCAAATTTTTCCTCAAAAACCTTTTTT-G-AAA-TTT-ATTTTTAAGGAAAATTGATGC
1 TTTCAACTTTTCCCT-AAAAACATTTTTTCGAAAATTTTGATTTTCAAGGAAAATTGATAC
*
18394147 TTTCAACTTTTCCCTAAAAATATTTTTTCGAAAATTTTGATTTTCAAGGAAAATTGATAC
1 TTTCAACTTTTCCCTAAAAACATTTTTTCGAAAATTTTGATTTTCAAGGAAAATTGATAC
* * *
18394207 TTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTT
1 TTTCAACTTTTCCCTAAAAACA-TTTTTTCGAAAATTTTGATTTT
18394252 TATTTAAAGA
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
56 11 0.12
57 14 0.15
58 3 0.03
59 3 0.03
60 41 0.45
61 20 0.22
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (60 bp):
TTTCAACTTTTCCCTAAAAACATTTTTTCGAAAATTTTGATTTTCAAGGAAAATTGATAC
Found at i:18394203 original size:60 final size:61
Alignment explanation
Indices: 18394126--18394251 Score: 209
Period size: 60 Copynumber: 2.1 Consensus size: 61
18394116 TTTGAAATTT
* *
18394126 ATTTTTAAGGAAAATTGATGCTTTCAACTTTTCCCTAAAAATA-TTTTTTCGAAAATTTTG
1 ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTCGAAAATTTTG
* *
18394186 ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTG
1 ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTCGAAAATTTTG
18394247 ATTTT
1 ATTTT
18394252 TATTTAAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 41 0.67
61 20 0.33
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.47
Consensus pattern (61 bp):
ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTCGAAAATTTTG
Found at i:18394221 original size:146 final size:147
Alignment explanation
Indices: 18393951--18394232 Score: 446
Period size: 146 Copynumber: 1.9 Consensus size: 147
18393941 TACTTTCAAC
18393951 TTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCT
1 TTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCT
* * *
18394016 CAAAAACCCTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAA
66 CAAAAACCATTTTTTGAAAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAA
18394081 TATTTTGAATTTCAAAT
131 TATTTTGAATTTCAAAT
* *
18394098 TTTTCCTCAAAAA-CCTTTTTTG-AAATTTATTTTTAAGGAAAATTGATGCTTTCAACTTTTCC-
1 TTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCT
* *
18394160 CTAAAAA-TATTTTTTCGAAAATTTTGATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAA
66 C-AAAAACCATTTTTT-GAAAAATTT-ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAA
18394224 AAATATTTT
128 AAATATTTT
18394233 TTTTGGAAAT
Statistics
Matches: 125, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
144 7 0.06
145 50 0.40
146 55 0.44
147 13 0.10
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (147 bp):
TTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCT
CAAAAACCATTTTTTGAAAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAA
TATTTTGAATTTCAAAT
Found at i:18394295 original size:17 final size:17
Alignment explanation
Indices: 18394275--18394328 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
18394265 TAGAATAATA
18394275 AAAAAATAAATGAAAAT
1 AAAAAATAAATGAAAAT
18394292 AAAAAATAAA-GAAAAGT
1 AAAAAATAAATGAAAA-T
18394309 AAAACAA-AAAT-AAAAT
1 AAAA-AATAAATGAAAAT
18394325 AAAA
1 AAAA
18394329 TAAAGATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.29
17 22 0.65
18 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.13
Consensus pattern (17 bp):
AAAAAATAAATGAAAAT
Found at i:18394332 original size:21 final size:21
Alignment explanation
Indices: 18394293--18394332 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18394283 AATGAAAATA
*
18394293 AAAAATAAAGAAAAGTAAAAC
1 AAAAATAAAGAAAAATAAAAC
18394314 AAAAATAAA-ATAAAATAAA
1 AAAAATAAAGA-AAAATAAA
18394333 GATAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAATAAAGAAAAATAAAAC
Found at i:18394337 original size:16 final size:16
Alignment explanation
Indices: 18394294--18394339 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
18394284 ATGAAAATAA
*
18394294 AAAATAAAGA-AAAGT
1 AAAATAAAGATAAAAT
* *
18394309 AAAACAAAAATAAAAT
1 AAAATAAAGATAAAAT
18394325 AAAATAAAGATAAAA
1 AAAATAAAGATAAAA
18394340 AGAATATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAT
Found at i:18395374 original size:27 final size:26
Alignment explanation
Indices: 18395344--18395430 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 26
18395334 TAAACCCAAA
18395344 AAATATTACAAGATAAAAAATAATAAT
1 AAATATTA-AAGATAAAAAATAATAAT
**
18395371 AAATATATAACTATATAAAAATACAT-AT
1 AAATAT-TAAAGATA-AAAAATA-ATAAT
18395399 AAATATTAACAG--AAAAAATAAATAAAT
1 AAATATTAA-AGATAAAAAAT-AAT-AAT
18395426 AAATA
1 AAATA
18395431 AGTAAAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 20 0.41
28 17 0.35
29 2 0.04
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (26 bp):
AAATATTAAAGATAAAAAATAATAAT
Found at i:18401338 original size:21 final size:21
Alignment explanation
Indices: 18401313--18401356 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
18401303 TCGGCCTTAT
*
18401313 AAGAGAATTGTATTGTAATAC
1 AAGAGAATTGTATTGCAATAC
18401334 AAGAGAATTGTATTGCAATAC
1 AAGAGAATTGTATTGCAATAC
18401355 AA
1 AA
18401357 TTGTGAGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (21 bp):
AAGAGAATTGTATTGCAATAC
Found at i:18415438 original size:3 final size:3
Alignment explanation
Indices: 18415430--18415514 Score: 111
Period size: 3 Copynumber: 28.3 Consensus size: 3
18415420 TTTTTGTTTT
*
18415430 ATA ATA ATA ATTA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
18415476 ATA ATA ATA ATA ATA ATTA A-A A-A ACA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA A
18415515 AAATTCAAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
2 4 0.05
3 64 0.86
4 6 0.08
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:18415725 original size:19 final size:21
Alignment explanation
Indices: 18415695--18415746 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
18415685 AATATTGAGG
*
18415695 AATTATTATTAAAAAT-AATA
1 AATTAATATTAAAAATAAATA
*
18415715 AA-TAATATTAAAACTAAATA
1 AATTAATATTAAAAATAAATA
18415735 AATTAATATTAA
1 AATTAATATTAA
18415747 CTCTTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 8 0.29
21 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTAATATTAAAAATAAATA
Found at i:18419594 original size:28 final size:28
Alignment explanation
Indices: 18419500--18419596 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 28
18419490 TGCAAACTTA
* * *
18419500 ATTAGTCTTAAACCTTTATGCCAATTAG
1 ATTAGGCTTAAAACTCTATGCCAATTAG
*
18419528 ATTAGGCTTAAAACTCAAGTAATGCTAATTTA-
1 ATTAGGCTTAAAACTC---T-ATGCCAA-TTAG
* * *
18419560 ACTAGGCTTAAATCTCTATGCCAACTAG
1 ATTAGGCTTAAAACTCTATGCCAATTAG
18419588 ATTAGGCTT
1 ATTAGGCTT
18419597 GGAATTCAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.04
28 27 0.50
29 1 0.02
31 1 0.02
32 20 0.37
33 3 0.06
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (28 bp):
ATTAGGCTTAAAACTCTATGCCAATTAG
Found at i:18419611 original size:60 final size:60
Alignment explanation
Indices: 18419497--18419611 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
18419487 GGATGCAAAC
* * * * *
18419497 TTAATTAGTCTTAAACCTTTATGCCAATTAGATTAGGCTTAAAACTCAAGTAATGCTAAT
1 TTAACTAGGCTTAAACCTCTATGCCAACTAGATTAGGCTTAAAACTCAACTAATGCTAAT
* ** *
18419557 TTAACTAGGCTTAAATCTCTATGCCAACTAGATTAGGCTTGGAATTCAACTAATG
1 TTAACTAGGCTTAAACCTCTATGCCAACTAGATTAGGCTTAAAACTCAACTAATG
18419612 AAATCATCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (60 bp):
TTAACTAGGCTTAAACCTCTATGCCAACTAGATTAGGCTTAAAACTCAACTAATGCTAAT
Found at i:18419881 original size:13 final size:15
Alignment explanation
Indices: 18419865--18419897 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18419855 TCTTATAAAC
18419865 TTTTCT-TT-CTTTT
1 TTTTCTCTTCCTTTT
18419878 TTTTCTCTTCCTTTT
1 TTTTCTCTTCCTTTT
18419893 TTTTC
1 TTTTC
18419898 ATACTCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 2 0.11
15 10 0.56
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTCTTCCTTTT
Found at i:18421342 original size:12 final size:12
Alignment explanation
Indices: 18421322--18421355 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18421312 TTAGAATAGG
18421322 AAATACAAATCC
1 AAATACAAATCC
*
18421334 AAATCCAAATCC
1 AAATACAAATCC
18421346 AAATAGCAAA
1 AAATA-CAAA
18421356 AATCAAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.59, C:0.24, G:0.03, T:0.15
Consensus pattern (12 bp):
AAATACAAATCC
Found at i:18424849 original size:25 final size:28
Alignment explanation
Indices: 18424802--18424852 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
18424792 TACTTGAATC
18424802 AAATTGTTTATCATTTTCCTTAATACTT
1 AAATTGTTTATCATTTTCCTTAATACTT
*
18424830 AAATTG-TTAT-A-TTTCTTTAATAC
1 AAATTGTTTATCATTTTCCTTAATAC
18424853 ACTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 4 0.18
28 6 0.27
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (28 bp):
AAATTGTTTATCATTTTCCTTAATACTT
Found at i:18432873 original size:6 final size:6
Alignment explanation
Indices: 18432862--18432894 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
18432852 ATATATTTAA
18432862 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATA
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATA
18432895 AAATGATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATAGAT
Found at i:18444579 original size:32 final size:32
Alignment explanation
Indices: 18444538--18444599 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
18444528 AAAAAGGGAG
*
18444538 ATTTCCTACTAGTCATGCAAACCATACTTTTT
1 ATTTCCTACTAGTCATACAAACCATACTTTTT
18444570 ATTTCCTACTAGTCATACAAACCATACTTT
1 ATTTCCTACTAGTCATACAAACCATACTTT
18444600 CTCTTTAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.39
Consensus pattern (32 bp):
ATTTCCTACTAGTCATACAAACCATACTTTTT
Found at i:18446529 original size:17 final size:16
Alignment explanation
Indices: 18446487--18446530 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 16
18446477 TATTGTATTT
18446487 TTATTAAAT--TAA-G
1 TTATTAAATAATAATG
18446500 TTATTAAATAATAATG
1 TTATTAAATAATAATG
18446516 TTATTAATATAATAA
1 TTATTAA-ATAATAA
18446531 ATAAAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.33
15 3 0.11
16 8 0.30
17 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
TTATTAAATAATAATG
Found at i:18455193 original size:25 final size:25
Alignment explanation
Indices: 18455159--18455216 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
18455149 CGAAGGTGGA
18455159 TGTTTGTTTCATATGTTATTAAAAT
1 TGTTTGTTTCATATGTTATTAAAAT
* * *
18455184 TGTTTGTTTCATGTGTTTTTGAAAT
1 TGTTTGTTTCATATGTTATTAAAAT
18455209 TGTTTGTT
1 TGTTTGTT
18455217 GCAAAACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.03, G:0.17, T:0.60
Consensus pattern (25 bp):
TGTTTGTTTCATATGTTATTAAAAT
Found at i:18462906 original size:25 final size:25
Alignment explanation
Indices: 18462872--18462929 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
18462862 CGAAGGTGGA
18462872 TGTTTGTTTCATATGTTATTAAAAT
1 TGTTTGTTTCATATGTTATTAAAAT
* * *
18462897 TGTTTGTTTCATGTGTTTTTGAAAT
1 TGTTTGTTTCATATGTTATTAAAAT
18462922 TGTTTGTT
1 TGTTTGTT
18462930 GCAAAACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.03, G:0.17, T:0.60
Consensus pattern (25 bp):
TGTTTGTTTCATATGTTATTAAAAT
Found at i:18465649 original size:13 final size:12
Alignment explanation
Indices: 18465633--18465752 Score: 62
Period size: 13 Copynumber: 9.2 Consensus size: 12
18465623 CAAAGTCCTA
18465633 AACCTTAAACCCT
1 AACC-TAAACCCT
*
18465646 AACCCAAACCCT
1 AACCTAAACCCT
*
18465658 AAACCTAAACCTT
1 -AACCTAAACCCT
*
18465671 AAACCTAAAACCCAA
1 -AACCT-AAACCC-T
* *
18465686 AACCCAAAACCT
1 AACCTAAACCCT
*
18465698 AAACCCT-AACCCA
1 -AA-CCTAAACCCT
18465711 AGACCTAAACCCT
1 A-ACCTAAACCCT
*
18465724 AATCCAAAACCCT
1 AA-CCTAAACCCT
*
18465737 AAACATAAAGCCCT
1 -AACCTAAA-CCCT
18465751 AA
1 AA
18465753 AACTTAGACC
Statistics
Matches: 82, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
12 12 0.15
13 53 0.65
14 17 0.21
ACGTcount: A:0.47, C:0.38, G:0.02, T:0.13
Consensus pattern (12 bp):
AACCTAAACCCT
Found at i:18465660 original size:19 final size:19
Alignment explanation
Indices: 18465632--18465740 Score: 98
Period size: 19 Copynumber: 5.6 Consensus size: 19
18465622 CCAAAGTCCT
*
18465632 AAACCTTAAACCCTAACCC
1 AAACCCTAAACCCTAACCC
*
18465651 AAACCCTAAA-CCTAAACCTT
1 AAACCCTAAACCCT-AACC-C
*
18465671 AAA-CCTAAAACCCAAAACCC
1 AAACCCT-AAACCC-TAACCC
*
18465691 AAAACCTAAACCCTAACCC
1 AAACCCTAAACCCTAACCC
*
18465710 AAGA-CCTAAACCCTAATCCA
1 AA-ACCCTAAACCCTAA-CCC
18465730 AAACCCTAAAC
1 AAACCCTAAAC
18465741 ATAAAGCCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.04
19 36 0.48
20 27 0.36
21 9 0.12
ACGTcount: A:0.48, C:0.39, G:0.01, T:0.13
Consensus pattern (19 bp):
AAACCCTAAACCCTAACCC
Found at i:18465705 original size:7 final size:7
Alignment explanation
Indices: 18465629--18465801 Score: 102
Period size: 7 Copynumber: 26.0 Consensus size: 7
18465619 AAACCAAAGT
18465629 CCTAAAC
1 CCTAAAC
*
18465636 CTTAAAC
1 CCTAAAC
18465643 CCT-AAC
1 CCTAAAC
18465649 CC-AAAC
1 CCTAAAC
18465655 CCTAAA-
1 CCTAAAC
18465661 CCTAAAC
1 CCTAAAC
*
18465668 CTTAAA-
1 CCTAAAC
18465674 CCTAAAAC
1 CCT-AAAC
*
18465682 CCAAAAC
1 CCTAAAC
*
18465689 CC-AAAA
1 CCTAAAC
18465695 CCTAAAC
1 CCTAAAC
18465702 CCT-AAC
1 CCTAAAC
18465708 CC-AAGA-
1 CCTAA-AC
18465714 CCTAAAC
1 CCTAAAC
*
18465721 CCT-AAT
1 CCTAAAC
*
18465727 CCAAAAC
1 CCTAAAC
18465734 CCTAAA-
1 CCTAAAC
*
18465740 CATAAAGC
1 CCTAAA-C
*
18465748 CCTAAAA
1 CCTAAAC
* *
18465755 CTTAGAC
1 CCTAAAC
18465762 CCTAAA-
1 CCTAAAC
*
18465768 -CTAAAA
1 CCTAAAC
18465774 CC-ATAAC
1 CCTA-AAC
*
18465781 CCTAGAC
1 CCTAAAC
*
18465788 CCTAGAC
1 CCTAAAC
18465795 CCTAAAC
1 CCTAAAC
18465802 TAAAACCCTA
Statistics
Matches: 127, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
5 5 0.04
6 42 0.33
7 72 0.57
8 8 0.06
ACGTcount: A:0.46, C:0.37, G:0.03, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:18465782 original size:19 final size:18
Alignment explanation
Indices: 18465640--18465839 Score: 59
Period size: 19 Copynumber: 10.5 Consensus size: 18
18465630 CTAAACCTTA
* * *
18465640 AACCCTAACCCAAACCCT
1 AACCCTAAACTAAAACCT
* *
18465658 AAACCTAAACCTTAAACCT
1 AACCCTAAA-CTAAAACCT
* *
18465677 AAAACCCAAAACCCAAAACCT
1 --AACCCTAAA-CTAAAACCT
* * *
18465698 AAACCCTAACCCAAGACCT
1 -AACCCTAAACTAAAACCT
* *
18465717 AAACCCTAATCCAAAACCCT
1 -AACCCTAAACTAAAA-CCT
* * *
18465737 AAACATAAAGCCCTAAAACTT
1 AACCCTAAA---CTAAAACCT
18465758 AGACCCTAAACTAAAACCAT
1 A-ACCCTAAACTAAAACC-T
*
18465778 AACCCTAGAC-----CCT
1 AACCCTAAACTAAAACCT
18465791 AGACCCTAAACTAAAACCCT
1 A-ACCCTAAACTAAAA-CCT
* *
18465811 AACTCTAAACTTAAAACCG
1 AACCCTAAAC-TAAAACCT
18465830 ACACCCTAAA
1 A-ACCCTAAA
18465840 TTTTAGACAC
Statistics
Matches: 137, Mismatches: 27, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
13 2 0.01
14 10 0.07
18 7 0.05
19 60 0.44
20 29 0.21
21 18 0.13
22 11 0.08
ACGTcount: A:0.47, C:0.36, G:0.03, T:0.14
Consensus pattern (18 bp):
AACCCTAAACTAAAACCT
Found at i:18465784 original size:33 final size:33
Alignment explanation
Indices: 18465747--18465823 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
18465737 AAACATAAAG
18465747 CCCTAAAACTTAGACCCTAAACTAAAACCATAA
1 CCCTAAAACTTAGACCCTAAACTAAAACCATAA
* * * *
18465780 CCCTAGACCCTAGACCCTAAACTAAAACCCTAA
1 CCCTAAAACTTAGACCCTAAACTAAAACCATAA
*
18465813 CTCT-AAACTTA
1 CCCTAAAACTTA
18465824 AAACCGACAC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.43, C:0.34, G:0.04, T:0.19
Consensus pattern (33 bp):
CCCTAAAACTTAGACCCTAAACTAAAACCATAA
Found at i:18465811 original size:20 final size:20
Alignment explanation
Indices: 18465786--18465828 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
18465776 ATAACCCTAG
18465786 ACCCTAGACCCTAAAC-TAAA
1 ACCCTA-ACCCTAAACTTAAA
*
18465806 ACCCTAACTCTAAACTTAAA
1 ACCCTAACCCTAAACTTAAA
18465826 ACC
1 ACC
18465829 GACACCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (20 bp):
ACCCTAACCCTAAACTTAAA
Found at i:18465838 original size:20 final size:19
Alignment explanation
Indices: 18465793--18465839 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
18465783 TAGACCCTAG
*
18465793 ACCCTAAACTAAAACCCTA
1 ACCCTAAACTAAAACCCGA
*
18465812 ACTCTAAACTTAAAA-CCGA
1 ACCCTAAAC-TAAAACCCGA
18465831 CACCCTAAA
1 -ACCCTAAA
18465840 TTTTAGACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.47, C:0.34, G:0.02, T:0.17
Consensus pattern (19 bp):
ACCCTAAACTAAAACCCGA
Found at i:18466304 original size:164 final size:164
Alignment explanation
Indices: 18466019--18466351 Score: 474
Period size: 164 Copynumber: 2.0 Consensus size: 164
18466009 AGCATGCAAT
* * * * *
18466019 CCATGCATGCAAAGGCATATTCAGCCATGCAAGATTAAAGATGGGTCGAGCCTCGTTGATACAAT
1 CCATGCATGCAAAGGCATATTCAGCCATCCAAGATTAAAGATGGCTCAAACCTCATTGATACAAT
* *
18466084 CCCTTCAACCATGCAACAAAAGAAAAGTTTTACTTGCAAATGGACTCTTCCTTGTATT-CGACCA
66 CCCTTCAACCATGCAACAAAAGAAAAGTTTTACTTGCAAATAGACTCTTCCTTGTATTAAG-CCA
* *
18466148 AAGAGATTTACTTCAAGAGTGATTCATTTACTTAG
130 AAAAGATTTACTTCAAGAATGATTCATTTACTTAG
* *
18466183 CCATGCATGCAAAGGCATATTCAGCCATCCAAGATTAAGGGTAGGCT-AAACCTCATTGATACAA
1 CCATGCATGCAAAGGCATATTCAGCCATCCAAGATTAAAGAT-GGCTCAAACCTCATTGATACAA
* * *
18466247 TCCCTTCAACCATGCAACAAAAGAAGAGTTTTTCTTTCAAATAGACTC-TCTCTTGTATTAAGCC
65 TCCCTTCAACCATGCAACAAAAGAAAAGTTTTACTTGCAAATAGACTCTTC-CTTGTATTAAGCC
* *
18466311 AAAAAGATTTACTTTAAGAATGATTCTTTTACTTAG
129 AAAAAGATTTACTTCAAGAATGATTCATTTACTTAG
18466347 CCATG
1 CCATG
18466352 AAGGTGCATA
Statistics
Matches: 150, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
163 2 0.01
164 144 0.96
165 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (164 bp):
CCATGCATGCAAAGGCATATTCAGCCATCCAAGATTAAAGATGGCTCAAACCTCATTGATACAAT
CCCTTCAACCATGCAACAAAAGAAAAGTTTTACTTGCAAATAGACTCTTCCTTGTATTAAGCCAA
AAAGATTTACTTCAAGAATGATTCATTTACTTAG
Found at i:18469995 original size:19 final size:19
Alignment explanation
Indices: 18469927--18469996 Score: 113
Period size: 19 Copynumber: 3.7 Consensus size: 19
18469917 CCTAAATTCT
*
18469927 AAACCCTAAACTACCCATG
1 AAACCCTAAACCACCCATG
* *
18469946 TAACCCTAAATCACCCATG
1 AAACCCTAAACCACCCATG
18469965 AAACCCTAAACCACCCATG
1 AAACCCTAAACCACCCATG
18469984 AAACCCTAAACCA
1 AAACCCTAAACCA
18469997 AACCCCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.43, C:0.39, G:0.04, T:0.14
Consensus pattern (19 bp):
AAACCCTAAACCACCCATG
Found at i:18470096 original size:19 final size:20
Alignment explanation
Indices: 18470072--18470109 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
18470062 TTAACCTAGA
18470072 CCCTAAAACCAA-CCTTAAG
1 CCCTAAAACCAACCCTTAAG
18470091 CCCTAAAACCAACCCTTAA
1 CCCTAAAACCAACCCTTAA
18470110 CCATTCATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.16
Consensus pattern (20 bp):
CCCTAAAACCAACCCTTAAG
Found at i:18472972 original size:19 final size:19
Alignment explanation
Indices: 18472944--18473042 Score: 105
Period size: 19 Copynumber: 5.3 Consensus size: 19
18472934 TTCCAAACTT
* *
18472944 TAAACTACCCATGAAATCC
1 TAAACCACCCATGAAACCC
18472963 TAAACCACCCAT-AAGACCC
1 TAAACCACCCATGAA-ACCC
* *
18472982 -AAACTACCTATGAAACCC
1 TAAACCACCCATGAAACCC
* *
18473000 TAAATCACCCATAAAACACC
1 TAAACCACCCATGAAAC-CC
18473020 -AAACCACCCATGAAACCC
1 TAAACCACCCATGAAACCC
18473038 TAAAC
1 TAAAC
18473043 TAACCCTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
18 17 0.26
19 46 0.71
20 2 0.03
ACGTcount: A:0.45, C:0.36, G:0.04, T:0.14
Consensus pattern (19 bp):
TAAACCACCCATGAAACCC
Found at i:18472995 original size:37 final size:38
Alignment explanation
Indices: 18472945--18473042 Score: 144
Period size: 37 Copynumber: 2.6 Consensus size: 38
18472935 TCCAAACTTT
* *
18472945 AAACTACCCATGAAATCCTAAACCACCCATAAGAC-CC
1 AAACTACCCATGAAACCCTAAACCACCCATAAAACACC
* *
18472982 AAACTACCTATGAAACCCTAAATCACCCATAAAACACC
1 AAACTACCCATGAAACCCTAAACCACCCATAAAACACC
*
18473020 AAACCACCCATGAAACCCTAAAC
1 AAACTACCCATGAAACCCTAAAC
18473043 TAACCCTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 31 0.58
38 22 0.42
ACGTcount: A:0.46, C:0.37, G:0.04, T:0.13
Consensus pattern (38 bp):
AAACTACCCATGAAACCCTAAACCACCCATAAAACACC
Found at i:18473054 original size:19 final size:19
Alignment explanation
Indices: 18473032--18473111 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
18473022 ACCACCCATG
18473032 AAACCCTAAACTA-ACCCTT
1 AAACCCTAAACTAGACCC-T
* * *
18473051 AAACCCTGAACCAAACCCT
1 AAACCCTAAACTAGACCCT
* * *
18473070 AAA-CCTAAACCATAGCCT
1 AAACCCTAAACTAGACCCT
* *
18473088 TAACCCTAACCTAGACCCT
1 AAACCCTAAACTAGACCCT
18473107 AAACC
1 AAACC
18473112 AACCTAAACC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
18 14 0.29
19 30 0.62
20 4 0.08
ACGTcount: A:0.41, C:0.39, G:0.04, T:0.16
Consensus pattern (19 bp):
AAACCCTAAACTAGACCCT
Found at i:18473063 original size:38 final size:37
Alignment explanation
Indices: 18472945--18473056 Score: 120
Period size: 37 Copynumber: 3.0 Consensus size: 37
18472935 TCCAAACTTT
* * *
18472945 AAACTACCCATGAAATCCTAAAC-CACCCATAAGACCC
1 AAACCACCCATGAAACCCTAAACTCACCCTTAA-ACCC
* * *
18472982 AAACTACCTATGAAACCCTAAA-TCACCCATAAAACACC
1 AAACCACCCATGAAACCCTAAACTCACCC-TTAAAC-CC
*
18473020 AAACCACCCATGAAACCCTAAACTAACCCTTAAACCC
1 AAACCACCCATGAAACCCTAAACTCACCCTTAAACCC
18473057 TGAACCAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
37 29 0.46
38 29 0.46
39 5 0.08
ACGTcount: A:0.45, C:0.38, G:0.04, T:0.14
Consensus pattern (37 bp):
AAACCACCCATGAAACCCTAAACTCACCCTTAAACCC
Found at i:18473066 original size:12 final size:13
Alignment explanation
Indices: 18473050--18473127 Score: 60
Period size: 12 Copynumber: 6.4 Consensus size: 13
18473040 AACTAACCCT
*
18473050 TAAACCCTGAACC
1 TAAACCCTAAACC
18473063 -AAACCCTAAACC
1 TAAACCCTAAACC
* *
18473075 TAAACCAT-AGCC
1 TAAACCCTAAACC
*
18473087 TTAACCCT-AACC
1 TAAACCCTAAACC
*
18473099 TAGACCCTAAACC
1 TAAACCCTAAACC
18473112 --AA-CCTAAACCC
1 TAAACCCTAAA-CC
18473123 TAAAC
1 TAAAC
18473128 AAACCCAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
10 6 0.12
11 3 0.06
12 29 0.58
13 12 0.24
ACGTcount: A:0.42, C:0.38, G:0.04, T:0.15
Consensus pattern (13 bp):
TAAACCCTAAACC
Done.