Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3640817 original size:33 final size:33
Alignment explanation
Indices: 3640780--3640856 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
3640770 TTCATATCAG
*
3640780 GATGTTGAA-T-CCTTAAAGATGCCCCTATCATTC
1 GATGTTGAATTGCCTTAAAGAT-CCCCAAT-ATTC
* *
3640813 GATGTT-AATTGCTTTAAAGATTCCCAATATTC
1 GATGTTGAATTGCCTTAAAGATCCCCAATATTC
3640845 GATGTTG-ATTGC
1 GATGTTGAATTGC
3640857 TTCAACACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
32 17 0.45
33 12 0.32
34 9 0.24
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (33 bp):
GATGTTGAATTGCCTTAAAGATCCCCAATATTC
Found at i:3640831 original size:34 final size:32
Alignment explanation
Indices: 3640792--3640858 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
3640782 TGTTGAATCC
*
3640792 TTAAAGATGCCCCTATCATTCGATGTTAATTGCT
1 TTAAAGAT-CCCCAAT-ATTCGATGTTAATTGCT
* *
3640826 TTAAAGATTCCCAATATTCGATGTTGATTGCT
1 TTAAAGATCCCCAATATTCGATGTTAATTGCT
3640858 T
1 T
3640859 CAACACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 17 0.57
33 5 0.17
34 8 0.27
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (32 bp):
TTAAAGATCCCCAATATTCGATGTTAATTGCT
Found at i:3641898 original size:13 final size:13
Alignment explanation
Indices: 3641878--3641914 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
3641868 GCCTCTATGA
3641878 TCTTTGTTTTTGC
1 TCTTTGTTTTTGC
3641891 GT-TTTGTTTTTGC
1 -TCTTTGTTTTTGC
3641904 TCTTTGTTTTT
1 TCTTTGTTTTT
3641915 TTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.00, C:0.11, G:0.16, T:0.73
Consensus pattern (13 bp):
TCTTTGTTTTTGC
Found at i:3641925 original size:18 final size:20
Alignment explanation
Indices: 3641904--3641940 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3641894 TTGTTTTTGC
3641904 TCTTTG-TT-TTTTTCTTTT
1 TCTTTGTTTCTTTTTCTTTT
3641922 TCTTTGTTTCTTTTTCTTT
1 TCTTTGTTTCTTTTTCTTT
3641941 GCTTTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (20 bp):
TCTTTGTTTCTTTTTCTTTT
Found at i:3641931 original size:14 final size:14
Alignment explanation
Indices: 3641914--3641962 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
3641904 TCTTTGTTTT
3641914 TTTCTTTTTCTTTG
1 TTTCTTTTTCTTTG
3641928 TTTCTTTTTCTTTG
1 TTTCTTTTTCTTTG
3641942 ---CTTTTCTCTTTG
1 TTTCTTTT-TCTTTG
3641954 TTTCTTTTT
1 TTTCTTTTT
3641963 ATTCTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
14 15 0.48
15 5 0.16
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTCTTTTTCTTTG
Found at i:3641933 original size:26 final size:25
Alignment explanation
Indices: 3641904--3641976 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 25
3641894 TTGTTTTTGC
*
3641904 TCTTTGTTTTTTTCTTTTTCTTTGTT
1 TCTTT-TTATTTTCTTTTTCTTTGTT
* *
3641930 TCTTTTTCTTTGCTTTTCTCTTTGTT
1 TCTTTTTATTTTCTTTT-TCTTTGTT
*
3641956 TCTTTTTATTCTC-TTTTCTTT
1 TCTTTTTATTTTCTTTTTCTTT
3641977 CTGCTTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.12
25 13 0.32
26 23 0.56
ACGTcount: A:0.01, C:0.16, G:0.05, T:0.77
Consensus pattern (25 bp):
TCTTTTTATTTTCTTTTTCTTTGTT
Found at i:3645840 original size:29 final size:29
Alignment explanation
Indices: 3645805--3645867 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3645795 AAATAGAAGT
* *
3645805 TTAAAGGACTAAACTAGTAAAAACATAAAC
1 TTAAGGGACTAAA-TAGCAAAAACATAAAC
* * *
3645835 TTAAGGGTCTAAATAGCAAATATATAAAC
1 TTAAGGGACTAAATAGCAAAAACATAAAC
3645864 TTAA
1 TTAA
3645868 ATGACCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (29 bp):
TTAAGGGACTAAATAGCAAAAACATAAAC
Found at i:3656560 original size:60 final size:60
Alignment explanation
Indices: 3656483--3656642 Score: 250
Period size: 60 Copynumber: 2.7 Consensus size: 60
3656473 AAATAGTTAG
* * *
3656483 GTGACTATTTTGTAAC-TTTAATAGTCGAGAGATTCAACAAAAGCAACTCCCTATAAAGGA
1 GTGATTATTTTGTAACTTTTAATAGTCGAGAGACTCAA-AAAAGCAACTCCCTATAAACGA
*
3656543 GTGATTATTTTGTAACTTTTAATAGTCGGGAGACTCAAAAAAGCAACTCCCTATAAACGA
1 GTGATTATTTTGTAACTTTTAATAGTCGAGAGACTCAAAAAAGCAACTCCCTATAAACGA
* *
3656603 GTGATTATTTTGTAACTTTTAATAGTTGGGAGACTCAAAA
1 GTGATTATTTTGTAACTTTTAATAGTCGAGAGACTCAAAA
3656643 TAATATCTTA
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 75 0.80
61 19 0.20
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (60 bp):
GTGATTATTTTGTAACTTTTAATAGTCGAGAGACTCAAAAAAGCAACTCCCTATAAACGA
Found at i:3660764 original size:2 final size:2
Alignment explanation
Indices: 3660757--3660786 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3660747 AACGTTCGGT
3660757 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3660787 CCATCATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3663355 original size:3 final size:3
Alignment explanation
Indices: 3663349--3663432 Score: 87
Period size: 3 Copynumber: 27.3 Consensus size: 3
3663339 TTTTACTTAA
* ** * * *
3663349 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT GTT ATT ATT AAT ATAC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
3663398 ATT ATT ATT TTT ATT ATTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A
3663433 AATAAATACA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
3 60 0.92
4 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3664904 original size:15 final size:15
Alignment explanation
Indices: 3664884--3664954 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
3664874 ATCCTATAGT
3664884 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
3664899 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
3664913 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
*
3664929 TTTTAGTTTATTATTAC
1 TTTTA--ATATTATTAC
*
3664946 TTTTGATAT
1 TTTTAATAT
3664955 ATGTTTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 5 0.12
15 21 0.49
16 9 0.21
17 8 0.19
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:3665271 original size:117 final size:118
Alignment explanation
Indices: 3665120--3665337 Score: 323
Period size: 117 Copynumber: 1.9 Consensus size: 118
3665110 TTTTGATATG
* * *
3665120 TATTTATTTTTTAATATCTAAGAAAAGAGCTGTCTTAAAACACCTGGAAGTCATTTTCTAATATT
1 TATTTATTTTATAATATCGAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCATTTTCTAATATT
*
3665185 TTTAAATAAATAAATATCCTATTTTATAAAT-TATATTAATTGTTTTAATTATT
66 TCTAAATAAATAAATATCCTA-TTTATAAATATATATTAATTGTTTTAATTATT
* ** *
3665238 TATTTA-TTTATAATATCGAAGAAAAGAGTTGTCTTAAGGCACCTAGAAGTCATTTTCTGATATT
1 TATTTATTTTATAATATCGAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCATTTTCTAATATT
**
3665302 TCTAAATAAATAAATATTTTATTTATAAATATATAT
66 TCTAAATAAATAAATATCCTATTTATAAATATATAT
3665338 AAGTTAATAT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 9 0.10
117 74 0.83
118 6 0.07
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (118 bp):
TATTTATTTTATAATATCGAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCATTTTCTAATATT
TCTAAATAAATAAATATCCTATTTATAAATATATATTAATTGTTTTAATTATT
Found at i:3676145 original size:184 final size:185
Alignment explanation
Indices: 3675830--3676199 Score: 643
Period size: 184 Copynumber: 2.0 Consensus size: 185
3675820 CCAATCAACA
3675830 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
3675895 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
66 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
* * * *
3675960 TGTATGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGT
131 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGT
* **
3676015 TGTTATTTTGAAAAATAATGAGAAAACTATTTCCATAGTTTCTCATTTTATCTTTTCT-AAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
* *
3676079 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCTACATC
66 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
*
3676144 TGTAAGTCTTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGT
131 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGT
3676199 T
1 T
3676200 TTCAAAGCCT
Statistics
Matches: 175, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
184 120 0.69
185 55 0.31
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (185 bp):
TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGT
Found at i:3676239 original size:76 final size:76
Alignment explanation
Indices: 3676140--3676321 Score: 301
Period size: 76 Copynumber: 2.4 Consensus size: 76
3676130 CTATTTCCTA
* *
3676140 CATCTGTAAGTCTTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACATTCGGGAGCTTTTTGATGTTTTCAA
*
3676205 AGCCTTAGGGT
66 AGCCTTAGGGC
*
3676216 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACATTCGGGAGCTTTTTGATGTTTTCAA
*
3676281 AGCCTTCGGGC
66 AGCCTTAGGGC
* *
3676292 CATCTGTAAGTCCTTCAGTGCTTGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
3676322 TTAAAACCTT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 99 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACATTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGC
Found at i:3676322 original size:45 final size:45
Alignment explanation
Indices: 3676268--3676686 Score: 642
Period size: 45 Copynumber: 9.3 Consensus size: 45
3676258 CGGGAGCTTT
* * *
3676268 TTGATGTTTTCAAAGCCTTCGGGCCATCTGTAAGTCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* * *
3676313 TTGATGTTTTTAAAACCTTTGGGTCATCTGTAAGTCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
3676358 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* *
3676403 ATGATGTCTTT-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGC
1 TTGATGT-TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* * *
3676448 TTGATGTCTTCAAAACCTTCGGATCATCTGTAAGTCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* *
3676493 TTGATTTTTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
3676538 TTGATGTTTTCAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
3676583 TAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* * *
3676628 ATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
* *
3676673 ATGGTGTTTTCAAA
1 TTGATGTTTTCAAA
3676687 CATTTCCATC
Statistics
Matches: 345, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
44 2 0.01
45 340 0.99
46 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (45 bp):
TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
Found at i:3676811 original size:3 final size:3
Alignment explanation
Indices: 3676803--3676878 Score: 77
Period size: 3 Copynumber: 26.3 Consensus size: 3
3676793 TTTTACTTAA
* ** * *
3676803 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT GTT ATT ATT AAT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3676850 ACT -TT ATT ATT -TT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3676879 AATAAATACA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 5 0.08
3 55 0.92
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3677150 original size:15 final size:15
Alignment explanation
Indices: 3677126--3677171 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
3677116 TAGGGACCAA
3677126 GCGG-CGCCGCTGTT
1 GCGGCCGCCGCTGTT
3677140 GCGGCCGCCGCTGTT
1 GCGGCCGCCGCTGTT
3677155 GCGGCCGCCGCTGTT
1 GCGGCCGCCGCTGTT
3677170 GC
1 GC
3677172 TGCCATCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 4 0.13
15 27 0.87
ACGTcount: A:0.00, C:0.39, G:0.41, T:0.20
Consensus pattern (15 bp):
GCGGCCGCCGCTGTT
Found at i:3680836 original size:104 final size:99
Alignment explanation
Indices: 3680714--3680901 Score: 286
Period size: 104 Copynumber: 1.8 Consensus size: 99
3680704 TATCATTGTA
*
3680714 ACTAATTATGTGCTAAGTGGCTTTACATTTAATATTATATATAAAATCTTATTATATATATGTTT
1 ACTAATTATGTGCTAAGTGACTTTACATTTAATATTATATATAAAATCTTA-T-TATATATGTTT
* *
3680779 TGTATGGAATCATTAAGTGTTCTCCACATGTAATAT
64 TGTATGGAAGCATTAAATGTTCTCCACATGTAATAT
* *
3680815 ACTAATTATGTGTGCTAAAGTGACTTTGCATTTAATATTATATATACAATCTTATTATATATGTT
1 ACTAATTA--TGTGCT-AAGTGACTTTACATTTAATATTATATATAAAATCTTATTATATATGTT
3680880 TTGTATGGAAGCATTAAATGTT
63 TTGTATGGAAGCATTAAATGTT
3680902 TTGATATATG
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
101 8 0.10
102 30 0.38
103 7 0.09
104 34 0.43
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.45
Consensus pattern (99 bp):
ACTAATTATGTGCTAAGTGACTTTACATTTAATATTATATATAAAATCTTATTATATATGTTTTG
TATGGAAGCATTAAATGTTCTCCACATGTAATAT
Found at i:3682801 original size:167 final size:171
Alignment explanation
Indices: 3682525--3682863 Score: 650
Period size: 167 Copynumber: 2.0 Consensus size: 171
3682515 TGCAGTTAGG
3682525 TTTAATTTTTCGAATAAGCATGCGAACTAGATGACATGAGGTTAGGATAAACAAAGAATGTGGGT
1 TTTAATTTTTCGAATAAGCATGCGAACTAGATGACATGAGGTTAGGATAAACAAAGAATGTGGGT
3682590 AGAAATCCTGTTTGGGGTAGGATCTACTAAAGCATGATTGGGTAGCCAGCATGTGAAGGTAGG-T
66 AGAAATCCTGTTTGGGGTAGGATCTACTAAAGCATGATTGGGTAGCCAGCATGTGAAGGTAGGTT
3682654 TTA-TTG-TGTTTACAATATTTATTATCTTGGTG-TTATCT
131 TTATTTGATGTTTACAATATTTATTATCTTGGTGTTTATCT
3682692 TTTAATTTTTCGAATAAGCATGCGAACTAGATGACATGAGGTTAGGATAAACAAAGAATGTGGGT
1 TTTAATTTTTCGAATAAGCATGCGAACTAGATGACATGAGGTTAGGATAAACAAAGAATGTGGGT
3682757 AGAAATCCTGTTTGGGGTAGGATCTACTAAAGCATGATTGGGTAGCCAGCATGTGAAGGTAGGTT
66 AGAAATCCTGTTTGGGGTAGGATCTACTAAAGCATGATTGGGTAGCCAGCATGTGAAGGTAGGTT
3682822 TTATTTGATGTTTACAATATTTATTATCTTGGTGTTTATCT
131 TTATTTGATGTTTACAATATTTATTATCTTGGTGTTTATCT
3682863 T
1 T
3682864 ATGTGGACTA
Statistics
Matches: 168, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
167 128 0.76
168 4 0.02
169 3 0.02
170 26 0.15
171 7 0.04
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (171 bp):
TTTAATTTTTCGAATAAGCATGCGAACTAGATGACATGAGGTTAGGATAAACAAAGAATGTGGGT
AGAAATCCTGTTTGGGGTAGGATCTACTAAAGCATGATTGGGTAGCCAGCATGTGAAGGTAGGTT
TTATTTGATGTTTACAATATTTATTATCTTGGTGTTTATCT
Found at i:3683128 original size:55 final size:55
Alignment explanation
Indices: 3683043--3683192 Score: 201
Period size: 55 Copynumber: 2.7 Consensus size: 55
3683033 CATTTAAATG
*
3683043 ATTCATGAAGAAGAACATCCAATGAATGAAGAAATTTGAAACTGATTGAAGAACA
1 ATTCATGAAGAAGAACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGAACA
* * * * * *
3683098 ATTCATGAAGAGGGACATCCGATGACTGAAGAAATCTGAAACTGATTGAAGACCG
1 ATTCATGAAGAAGAACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGAACA
* * * *
3683153 ATCCATAAAGAAAAACATCCGATGAATGAAGAAGTTTGAA
1 ATTCATGAAGAAGAACATCCGATGAATGAAGAAATTTGAA
3683193 GTTGATCAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 80 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (55 bp):
ATTCATGAAGAAGAACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGAACA
Found at i:3686228 original size:22 final size:22
Alignment explanation
Indices: 3686200--3686256 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
3686190 TTTCCAATCA
3686200 AGGGAGAAAGAGCTGAAAAGGT
1 AGGGAGAAAGAGCTGAAAAGGT
* *
3686222 AGGGAGAAAGAGTTGAAAGGGT
1 AGGGAGAAAGAGCTGAAAAGGT
*
3686244 AGAGAGAATAGAG
1 AGGGAGAA-AGAG
3686257 AAATGCCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.42, T:0.11
Consensus pattern (22 bp):
AGGGAGAAAGAGCTGAAAAGGT
Found at i:3688278 original size:59 final size:59
Alignment explanation
Indices: 3688215--3688572 Score: 263
Period size: 59 Copynumber: 6.1 Consensus size: 59
3688205 TAGCACTATC
* * *
3688215 AGTGCTCTATCTGGAAAACCATACACTTAGTATG-CTTCTCTTTTCATTTTAGCACACAA
1 AGTGCCCTATCTGGAAAACCATACACTTAGTATGATTTC-CTTATCATTTTAGCACACAA
* ** * *
3688274 AGTGCCCTAT-TCGAAAATCCATAC-CATTAGTATGATTTTGTTACCATTTTAGCACATAA
1 AGTGCCCTATCTGGAAAA-CCATACAC-TTAGTATGATTTCCTTATCATTTTAGCACACAA
** * * **
3688333 TA-TGCCCTATCT-GAAAATCCATA-TTTTCAATATGATTTCCTTATCA-TTTAGCACCCTT
1 -AGTGCCCTATCTGGAAAA-CCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACAA
** * * * *
3688391 AGTGCTTTATCTGG-AAACTCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAA
1 AGTGCCCTATCTGGAAAAC-CATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
* * * * **
3688450 TA-TTCCCTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCA-TTTAGCACACTT
1 -AGTGCCCTATCTGGAAAACCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACAA
* * * * *
3688508 AGTGCTCC-ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTCTAGCACATAA
1 AGTGC-CCTATCTGGAAAACCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
3688567 AGTGCC
1 AGTGCC
3688573 ATTCGGTAAT
Statistics
Matches: 230, Mismatches: 50, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
57 3 0.01
58 92 0.40
59 127 0.55
60 8 0.03
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (59 bp):
AGTGCCCTATCTGGAAAACCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
Found at i:3688423 original size:117 final size:117
Alignment explanation
Indices: 3688288--3688566 Score: 409
Period size: 117 Copynumber: 2.4 Consensus size: 117
3688278 CCCTATTCGA
* **
3688288 AAATCCATAC-CATTAGTATGATTTTGTTACCATTTTAGCACATAATATGCCCTATCTGAAAATC
1 AAATCCATACAC-TCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATC
* * ** *
3688352 CATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCTTTATCTGG
65 CATAATTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGG
* * *
3688405 AAA-CTCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATTCCCTATCTGGAAATC
1 AAATC-CATACACTCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATC
3688469 CATAATTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGG
65 CATAATTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGG
* *
3688522 AAATCCATACACTCAGTATGATTTCCTTATCATTCTAGCACATAA
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAA
3688567 AGTGCCATTC
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
116 1 0.01
117 142 0.98
118 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (117 bp):
AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATCC
ATAATTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGG
Found at i:3689057 original size:19 final size:19
Alignment explanation
Indices: 3689033--3689084 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
3689023 TATTTAGGTG
*
3689033 TGCATCGATGCACTACTTA
1 TGCATCGATGCACCACTTA
3689052 TGCATCGATGCACCACTTA
1 TGCATCGATGCACCACTTA
3689071 TGCATCGATGCACC
1 TGCATCGATGCACC
3689085 TTGCCCAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCACCACTTA
Found at i:3695510 original size:59 final size:59
Alignment explanation
Indices: 3695447--3695706 Score: 183
Period size: 58 Copynumber: 4.4 Consensus size: 59
3695437 ATACCATTAG
** * *
3695447 TATGATTTTGTTACCATTTTAACACATAATATGCCCTATCTGAAAATCCATATTTTCAA
1 TATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
* * ** * * *** *
3695506 TATGATTTCCTTATCA-TTTAGCACCCT--TAGTGCTTTATTTGGAAACCCATACACTCAG
1 TATGATTTCCTTACCATTTTAGCA-CATAATA-TGCCCTATCTGGAAATCCATATTTTCAA
*
3695564 TATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTT-AA
1 TATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCAT-ATTTTCAA
* * * * * * *** *
3695623 TATGATTTACTTATCA-TTTAGAACACTCA-GTGCTCC-ATATGGAAATCCATACACTCAG
1 TATGATTTCCTTACCATTTTAGCACA-TAATATGC-CCTATCTGGAAATCCATATTTTCAA
* *
3695681 TATGATTTCCTTATCATTCTAGCACA
1 TATGATTTCCTTACCATTTTAGCACA
3695707 CAAAGTGCCA
Statistics
Matches: 152, Mismatches: 39, Indels: 20
0.72 0.18 0.09
Matches are distributed among these distances:
57 4 0.03
58 81 0.53
59 63 0.41
60 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Consensus pattern (59 bp):
TATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
Found at i:3695576 original size:58 final size:58
Alignment explanation
Indices: 3695506--3695705 Score: 190
Period size: 58 Copynumber: 3.4 Consensus size: 58
3695496 ATATTTTCAA
* * *
3695506 TATGATTTCCTTATCATTTAGCACCCTTAGTGCTTTATTTGGAAACCCATACACTCAG
1 TATGATTTCCTTATCATTTAGCACCCTTAGTGCTCTATATGGAAATCCATACACTCAG
* * * * * * * *
3695564 TATGATTCCCTTACCATTTTAGCA-CATAATA-TGCCCTATCTGGAAATCCATA-ATTTTAA
1 TATGATTTCCTTATCA-TTTAGCACCCT--TAGTGCTCTATATGGAAATCCATACA-CTCAG
* * * * *
3695623 TATGATTTACTTATCATTTAGAACACTCAGTGCTCCATATGGAAATCCATACACTCAG
1 TATGATTTCCTTATCATTTAGCACCCTTAGTGCTCTATATGGAAATCCATACACTCAG
3695681 TATGATTTCCTTATCATTCTAGCAC
1 TATGATTTCCTTATCATT-TAGCAC
3695706 ACAAAGTGCC
Statistics
Matches: 109, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
57 1 0.01
58 60 0.55
59 46 0.42
60 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (58 bp):
TATGATTTCCTTATCATTTAGCACCCTTAGTGCTCTATATGGAAATCCATACACTCAG
Found at i:3695704 original size:117 final size:117
Alignment explanation
Indices: 3695431--3695706 Score: 376
Period size: 117 Copynumber: 2.4 Consensus size: 117
3695421 CCTTATTCGA
* ** *
3695431 AAATCCATAC-CATTAGTATGATTTTGTTACCATTTTAACACATAATATGCCCTATCTGAAAATC
1 AAATCCATACAC-TCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATC
* * * * ** *
3695495 CATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCTTTATTTGG
65 CATATTTTCAATATGATTTACTTATCATTTAGAACACTCAGTGCTCCATATGG
* * *
3695548 AAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCC
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATCC
3695613 ATAATTTT-AATATGATTTACTTATCATTTAGAACACTCAGTGCTCCATATGG
66 AT-ATTTTCAATATGATTTACTTATCATTTAGAACACTCAGTGCTCCATATGG
* *
3695665 AAATCCATACACTCAGTATGATTTCCTTATCATTCTAGCACA
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACA
3695707 CAAAGTGCCA
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
117 133 0.96
118 6 0.04
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (117 bp):
AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATCC
ATATTTTCAATATGATTTACTTATCATTTAGAACACTCAGTGCTCCATATGG
Found at i:3696154 original size:17 final size:18
Alignment explanation
Indices: 3696112--3696159 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
3696102 ATCTTAAGGG
3696112 AGTGCATCGATACACTACC
1 AGTGCATCGATACACTA-C
*
3696131 TGTGCATCGATACACT-C
1 AGTGCATCGATACACTAC
3696148 AGTGCATTCGAT
1 AGTGCA-TCGAT
3696160 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 15 0.58
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (18 bp):
AGTGCATCGATACACTAC
Found at i:3697619 original size:1 final size:1
Alignment explanation
Indices: 3697615--3697762 Score: 125
Period size: 1 Copynumber: 148.0 Consensus size: 1
3697605 AAAAAGTAAG
* * ** ** ** ** **
3697615 AAAAAAAAGAGAAAAAAAAGGAAAAAAGGAAAAAAAAAAAAAAAAGGAAAAAAGGAAAAAAAGGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
3697680 AAAAAGAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
3697745 AAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAA
3697763 GAAAGAATAA
Statistics
Matches: 119, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 119 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:3697624 original size:9 final size:9
Alignment explanation
Indices: 3697616--3697785 Score: 174
Period size: 9 Copynumber: 19.2 Consensus size: 9
3697606 AAAAGTAAGA
3697616 AAAAAAAGAG
1 AAAAAAA-AG
3697626 AAAAAAAAG
1 AAAAAAAAG
* *
3697635 GAAAAAAGG
1 AAAAAAAAG
3697644 AAAAAAAA-
1 AAAAAAAAG
3697652 AAAAAAAAG
1 AAAAAAAAG
*
3697661 -GAAAAAAG
1 AAAAAAAAG
*
3697669 GAAAAAAAG
1 AAAAAAAAG
*
3697678 -GAAAAAAG
1 AAAAAAAAG
3697686 --AAAAAAG
1 AAAAAAAAG
3697693 AAAAAAAAG
1 AAAAAAAAG
3697702 AAAAAAAA-
1 AAAAAAAAG
*
3697710 AAAAAAAAA
1 AAAAAAAAG
3697719 AAAAAAAAG
1 AAAAAAAAG
3697728 -AAAAAAAG
1 AAAAAAAAG
3697736 AAAAAAAAG
1 AAAAAAAAG
*
3697745 AAAAAAAAA
1 AAAAAAAAG
3697754 AGAAAAAAAG
1 A-AAAAAAAG
*
3697764 AAAGAATAAG
1 AAA-AAAAAG
*
3697774 TAATAAAAAG
1 -AAAAAAAAG
3697784 AA
1 AA
3697786 TGAGGAAGAT
Statistics
Matches: 138, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
7 7 0.05
8 38 0.28
9 66 0.48
10 25 0.18
11 2 0.01
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3697647 original size:26 final size:26
Alignment explanation
Indices: 3697617--3697766 Score: 162
Period size: 26 Copynumber: 5.8 Consensus size: 26
3697607 AAAGTAAGAA
3697617 AAAAAAGAGAAAAAAAAGGAAAAAAGG
1 AAAAAA-AGAAAAAAAAGGAAAAAAGG
*
3697644 AAAAAAAAAAAAAAAAGGAAAAAAGG
1 AAAAAAAGAAAAAAAAGGAAAAAAGG
* *
3697670 AAAAAAAG-GAAAAAA-GAAAAAAGA
1 AAAAAAAGAAAAAAAAGGAAAAAAGG
** **
3697694 AAAAAAAGAAAAAAAAAAAAAAAAAA
1 AAAAAAAGAAAAAAAAGGAAAAAAGG
* *
3697720 AAAAAAAG-AAAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAGGAAAAAAGG
* *
3697745 AAAAAAAAAAGAAAAAAAGAAA
1 AAAAAAAGAA-AAAAAAGGAAA
3697767 GAATAAGTAA
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
24 16 0.15
25 34 0.32
26 42 0.39
27 15 0.14
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAAAAAAAGGAAAAAAGG
Found at i:3697751 original size:8 final size:8
Alignment explanation
Indices: 3697604--3697785 Score: 135
Period size: 8 Copynumber: 22.1 Consensus size: 8
3697594 ATATTACACT
*
3697604 AAAAAAGT
1 AAAAAAGA
*
3697612 AAGAAA-A
1 AAAAAAGA
*
3697619 AAAAGAGAA
1 AAAAAAG-A
3697628 AAAAAAGGA
1 AAAAAA-GA
*
3697637 AAAAAGGAA
1 AAAAAAG-A
*
3697646 AAAAAAAA
1 AAAAAAGA
3697654 AAAAAAGGA
1 AAAAAA-GA
*
3697663 AAAAAGGA
1 AAAAAAGA
*
3697671 AAAAAAGG
1 AAAAAAGA
3697679 AAAAAAG-
1 AAAAAAGA
3697686 AAAAAAGAA
1 AAAAAAG-A
3697695 AAAAAAGA
1 AAAAAAGA
3697703 AAAAAA-A
1 AAAAAAGA
3697710 AAAAAA-A
1 AAAAAAGA
3697717 AAAAAA-A
1 AAAAAAGA
3697724 AAAGAAA-A
1 AAA-AAAGA
3697732 AAAGAAA-A
1 AAA-AAAGA
*
3697740 AAAAGAAAA
1 AAAA-AAGA
3697749 AAAAAAGA
1 AAAAAAGA
3697757 AAAAAAGA
1 AAAAAAGA
3697765 AAGAATAAGTA
1 AA-AA-AAG-A
3697776 ATAAAAAGA
1 A-AAAAAGA
3697785 A
1 A
3697786 TGAGGAAGAT
Statistics
Matches: 147, Mismatches: 13, Indels: 27
0.79 0.07 0.14
Matches are distributed among these distances:
7 30 0.20
8 65 0.44
9 40 0.27
10 7 0.05
11 4 0.03
12 1 0.01
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:3697752 original size:43 final size:43
Alignment explanation
Indices: 3697616--3697766 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 43
3697606 AAAAGTAAGA
* * *
3697616 AAAAAAAGAGAAAAAAAAGGAAAAAAGGAAAAAAAAAAAAAAAA
1 AAAAAAAAAG-AAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAA
** * * *
3697660 GGAAAAAAGGAAAAAAAG-GAAAAAAGAAAAAAGAAAAAAAAGA
1 AAAAAAAAAGAAAAAAAGAAAAAAAAGAAAAAA-AAAAAAAAAA
3697703 AAAAAAAAA-AAAAAAA-AAAAAAAAGAAAAAAAGAAAAAAAAGA
1 AAAAAAAAAGAAAAAAAGAAAAAAAAGAAAAAAA-AAAAAAAA-A
3697746 AAAAAAAAAGAAAAAAAGAAA
1 AAAAAAAAAGAAAAAAAGAAA
3697767 GAATAAGTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 39 0.44
43 33 0.37
44 13 0.15
45 3 0.03
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (43 bp):
AAAAAAAAAGAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAA
Found at i:3699126 original size:51 final size:51
Alignment explanation
Indices: 3698938--3699133 Score: 268
Period size: 52 Copynumber: 3.8 Consensus size: 51
3698928 GGTCCATATT
* *
3698938 ATCCATGT-GGGTATCTTGAAGGCTCGCATCAGCATGAAAAGATAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
*
3698988 ATCCACGTGGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGATAGAAGTA
1 ATCCATGT-GGGGCATCTTGAAGGCTCACATCAGCATG-AAAAGATAGAAGTA
* * * *
3699041 ATCCATGTGGGGCATCTTGAAGGGTCACATCAGCATGAAGAGACAAAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* * * *
3699092 ATTCATGTGGGGCATCTTAAAGGCTCAGACCAGCATGAAAAG
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAG
3699134 GTTGGGATAT
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
50 7 0.05
51 47 0.36
52 54 0.42
53 21 0.16
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (51 bp):
ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
Found at i:3700698 original size:43 final size:43
Alignment explanation
Indices: 3700635--3700851 Score: 312
Period size: 43 Copynumber: 5.1 Consensus size: 43
3700625 ATAAGAAACT
* *
3700635 AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCTTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
3700678 AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
3700721 AAGCTTGAGAGACCAACGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* * *
3700764 AAGCTTAAGGGATCATCGTGATATGTAGGGGTTCCTTGATGA-
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* * * *
3700806 ACA-CTTAAGGGGCCAACGTGATATATAGGGGTTCCTTGGTGAC
1 A-AGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
3700849 AAG
1 AAG
3700852 TAAGAAACTG
Statistics
Matches: 157, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
42 36 0.23
43 121 0.77
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
Found at i:3701212 original size:91 final size:90
Alignment explanation
Indices: 3700932--3701221 Score: 472
Period size: 90 Copynumber: 3.2 Consensus size: 90
3700922 AGCATGATGC
* *
3700932 GTAAGTCCTTCGGGCTATCCATAAGACCTTCAGTGCAGGATGTTTTCTAATGAGATTTAAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
3700997 TAAGCCTTCGGGGGTTTCTTGATTT
66 TAAGCCTTCGGGGGTTTCTTGATTT
* * * *
3701022 GTAAGTCCTTCGGGCCATCTATAAGACCATCAGTGCATGATGTTTTCAAATGAAATTTAAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
3701087 TAAGCCTTCGGGGGTTTCTTGATTT
66 TAAGCCTTCGGGGGTTTCTTGATTT
*
3701112 GTAAGTCCTTTGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAA
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGA-TTTAAGAAA
3701177 CTAAGCCTTCGGGGGTTTCTTGATTT
65 CTAAGCCTTCGGGGGTTTCTTGATTT
* * * *
3701203 TTAAATCCTTTGGGTCATC
1 GTAAGTCCTTCGGGCCATC
3701222 AGTAAGTCTT
Statistics
Matches: 185, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
90 134 0.72
91 51 0.28
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (90 bp):
GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAAC
TAAGCCTTCGGGGGTTTCTTGATTT
Found at i:3701262 original size:42 final size:41
Alignment explanation
Indices: 3701203--3701299 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
3701193 TTCTTGATTT
* * * * *
3701203 TTAAATCCTTTGGGTCATCAGTAAGTCTTTTGAGCATGATG
1 TTAAATCCTTCGGGTCATCAGAAAGCCTTTCGAGCAAGATG
*
3701244 CTTAAATCCTTCGGGTCATCTGAAAGCCTTTCGAGCAAGATG
1 -TTAAATCCTTCGGGTCATCAGAAAGCCTTTCGAGCAAGATG
* *
3701286 ATAAGTCCTTCGGG
1 TTAAATCCTTCGGG
3701300 CCATTCATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 12 0.26
42 35 0.74
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
TTAAATCCTTCGGGTCATCAGAAAGCCTTTCGAGCAAGATG
Found at i:3701715 original size:3 final size:3
Alignment explanation
Indices: 3701709--3701743 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3701699 AAAAAATTGA
3701709 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3701744 ATTTTGGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3702178 original size:22 final size:22
Alignment explanation
Indices: 3702153--3702204 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3702143 TAAACACCCG
*
3702153 AAATGCCACTAAAATCCTACTA
1 AAATACCACTAAAATCCTACTA
* *
3702175 AAATATCACTAAAATCCTACTC
1 AAATACCACTAAAATCCTACTA
*
3702197 AAACACCA
1 AAATACCA
3702205 TTATTCGGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (22 bp):
AAATACCACTAAAATCCTACTA
Found at i:3703700 original size:103 final size:102
Alignment explanation
Indices: 3703588--3703789 Score: 316
Period size: 104 Copynumber: 2.0 Consensus size: 102
3703578 TGTCTTATAT
*
3703588 CACGTGTAATACACTAATTAT-TGTGCTAAAGTGGCTTTACATTTAATATTATATATAAAATCTT
1 CACGTGTAATACACTAATTATGTGTGCTAAAGTGACTTTACATTTAATATTATATATAAAATCTT
* *
3703652 ATTATATATATGTTTTGTATGGAATCATTAAGTGTTCTC
66 ATTATATATA--TTTTGTATGGAAGCATTAAATGTTCTC
* * * *
3703691 CACGTGTAATATACTAATTATGTGTGCTAAAGTGACTTTGCATTTAATATTATGTATACAATCTT
1 CACGTGTAATACACTAATTATGTGTGCTAAAGTGACTTTACATTTAATATTATATATAAAATCTT
3703756 ATTATATATATTTTGTATGGAAGCATTAAATGTT
66 ATTATATATATTTTGTATGGAAGCATTAAATGTT
3703790 TTGATATATG
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
102 22 0.24
103 20 0.22
104 49 0.54
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (102 bp):
CACGTGTAATACACTAATTATGTGTGCTAAAGTGACTTTACATTTAATATTATATATAAAATCTT
ATTATATATATTTTGTATGGAAGCATTAAATGTTCTC
Found at i:3704964 original size:12 final size:12
Alignment explanation
Indices: 3704941--3704981 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
3704931 CCGTCCCGGC
3704941 GGAAAGAAGAAAA
1 GGAAA-AAGAAAA
3704954 GGAAAAAGAAAA
1 GGAAAAAGAAAA
3704966 GGAAAAAGAAAA
1 GGAAAAAGAAAA
3704978 GGAA
1 GGAA
3704982 TAATGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
GGAAAAAGAAAA
Found at i:3705649 original size:3 final size:3
Alignment explanation
Indices: 3705604--3705630 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3705594 TGATGAATGG
3705604 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3705631 TTTCACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3708073 original size:21 final size:21
Alignment explanation
Indices: 3708034--3708073 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3708024 ATGAAATTGA
*
3708034 TAAATATTCATGTATGTTTCG
1 TAAATATTCATGTAGGTTTCG
*
3708055 TAAATATTCATTTAGGTTT
1 TAAATATTCATGTAGGTTT
3708074 TATATTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
TAAATATTCATGTAGGTTTCG
Found at i:3708655 original size:2 final size:2
Alignment explanation
Indices: 3708643--3708679 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3708633 TTCTCTAATC
3708643 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3708680 TCTTTAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3709337 original size:31 final size:31
Alignment explanation
Indices: 3709283--3709377 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 31
3709273 TTATTTAGAT
* *
3709283 CCCCAACTTTTAAAAC--TTGCAATATAGTC
1 CCCCAACATTTAATACGTTTGCAATATAGTC
* *
3709312 CCCCAACATTTAATACGTTTGCAATACAATCC
1 CCCCAACATTTAATACGTTTGCAATATAGT-C
* * *
3709344 CCCCAACATTTAGT-CTGTTTGTAATATGGTC
1 CCCCAACATTTAATAC-GTTTGCAATATAGTC
3709375 CCC
1 CCC
3709378 GATGTAACCG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 14 0.26
31 15 0.28
32 24 0.45
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (31 bp):
CCCCAACATTTAATACGTTTGCAATATAGTC
Found at i:3711442 original size:30 final size:31
Alignment explanation
Indices: 3711377--3711442 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3711367 TCGGGGACCA
*
3711377 TATTGCAAATGGACTAAATGTTGGGGGACTG
1 TATTGCAAACGGACTAAATGTTGGGGGACTG
* *
3711408 TATTGCAAACGGGCTAAATGTTGGGGG-TTG
1 TATTGCAAACGGACTAAATGTTGGGGGACTG
3711438 TATTG
1 TATTG
3711443 TAAGTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.32
Consensus pattern (31 bp):
TATTGCAAACGGACTAAATGTTGGGGGACTG
Found at i:3711590 original size:16 final size:16
Alignment explanation
Indices: 3711569--3711601 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3711559 CTAATAATTC
3711569 AATTTGAATAATTTAA
1 AATTTGAATAATTTAA
3711585 AATTTGAATAATTTAA
1 AATTTGAATAATTTAA
3711601 A
1 A
3711602 CCAACCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTTGAATAATTTAA
Found at i:3719388 original size:20 final size:21
Alignment explanation
Indices: 3719360--3719411 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
3719350 TTAATATGAT
* * *
3719360 AATTTTTAAATATTATAA-TA
1 AATTATTAAATATGACAATTA
*
3719380 AATTATTAATTATGACAATTA
1 AATTATTAAATATGACAATTA
*
3719401 AATTAATAAAT
1 AATTATTAAAT
3719412 TTACTTACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTATTAAATATGACAATTA
Found at i:3719535 original size:29 final size:28
Alignment explanation
Indices: 3719503--3719593 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
3719493 TTGAACATGA
3719503 TTAATTAAATTAATTATAATCATTACAAG
1 TTAATTAAATTAATTATAATCATTA-AAG
* * ** * * *
3719532 TTAA-AATAATTTATTGGAATTGAATAAAA
1 TTAATTA-AATTAATTATAA-TCATTAAAG
*
3719561 ATAATTAAATTAATTATAATCATTAAAAG
1 TTAATTAAATTAATTATAATCATT-AAAG
3719590 TTAA
1 TTAA
3719594 AACAATTTAT
Statistics
Matches: 42, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
28 4 0.10
29 33 0.79
30 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (28 bp):
TTAATTAAATTAATTATAATCATTAAAG
Found at i:3719776 original size:23 final size:23
Alignment explanation
Indices: 3719750--3719796 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3719740 TGAATTTCCT
3719750 TGATATTAAAAAATTGAATAACA
1 TGATATTAAAAAATTGAATAACA
* *
3719773 TGATATTGAAAATTTGAATAACA
1 TGATATTAAAAAATTGAATAACA
3719796 T
1 T
3719797 AAAACTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (23 bp):
TGATATTAAAAAATTGAATAACA
Found at i:3720986 original size:22 final size:22
Alignment explanation
Indices: 3720958--3721000 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3720948 AAAAAACAAA
*
3720958 GAAAACA-AAATAATTAAATTAT
1 GAAAACATAAA-AAATAAATTAT
3720980 GAAAACATAAAAAATAAATTA
1 GAAAACATAAAAAATAAATTA
3721001 AAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (22 bp):
GAAAACATAAAAAATAAATTAT
Found at i:3724123 original size:23 final size:23
Alignment explanation
Indices: 3724069--3724126 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3724059 CATTCGGGAT
3724069 AATTCTATGTGGTCCTTTAGGAC
1 AATTCTATGTGGTCCTTTAGGAC
** * *
3724092 AATAATATGTGGTCCTTTGGGTC
1 AATTCTATGTGGTCCTTTAGGAC
*
3724115 ATTTCTATGTGG
1 AATTCTATGTGG
3724127 CACTTCGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (23 bp):
AATTCTATGTGGTCCTTTAGGAC
Found at i:3724171 original size:24 final size:24
Alignment explanation
Indices: 3724125--3724171 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3724115 ATTTCTATGT
* *
3724125 GGCACTTCGGTGAATATTCTACGC
1 GGCACTTCAGTGAATATTATACGC
* *
3724149 GGCACTTCAGTGCATTTTATACG
1 GGCACTTCAGTGAATATTATACG
3724172 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (24 bp):
GGCACTTCAGTGAATATTATACGC
Found at i:3725236 original size:23 final size:23
Alignment explanation
Indices: 3725202--3725277 Score: 136
Period size: 23 Copynumber: 3.3 Consensus size: 23
3725192 CACCACCGTT
3725202 CACATA-ATTTGTCCCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
*
3725224 CACATAGATTTGTCTCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
3725247 CACATAGATTTGTCCCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
3725270 CACATAGA
1 CACATAGA
3725278 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 6 0.12
23 45 0.88
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
CACATAGATTTGTCCCGAAGGAC
Found at i:3727699 original size:46 final size:46
Alignment explanation
Indices: 3727643--3727822 Score: 213
Period size: 46 Copynumber: 4.0 Consensus size: 46
3727633 AGACAGAATA
* * *
3727643 AGATGAAGAGTCTCGGTTAGATATAGGGCTAGAGAAGATGAACATG
1 AGATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATG
* *
3727689 AGATGAAGAGTCTCGATAAGATTTAGGGTTATAGAAGATGAACAAT-
1 AGATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAAC-ATG
* * *
3727735 AGATGAAGAGTCTCGATAAGATTTAGGGTTAAAG-ATATGAACATG
1 AGATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATG
* * * * *
3727780 ACATGAATAGTCTTGTTTAGATTTATGGTTAGAGAA-ATGAACA
1 AGATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACA
3727823 GAACATGAAC
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
44 2 0.02
45 41 0.35
46 72 0.62
47 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (46 bp):
AGATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATG
Found at i:3727802 original size:91 final size:91
Alignment explanation
Indices: 3727643--3727822 Score: 227
Period size: 91 Copynumber: 2.0 Consensus size: 91
3727633 AGACAGAATA
* * * *
3727643 AGATGAAGAGTCTCGGTTAGATATAGGGCTAGAGAAGATGAACATGAGATGAAGAGTCTCGATAA
1 AGATGAAGAGTCTCGATAAGATATAGGGCTAAAGAAGATGAACATGACATGAAGAGTCTCGATAA
*
3727708 GATTTAGGGTTATAGAAGATGAACAAT
66 GATTTAGGGTTAGAGAA-ATGAACAAT
* * * * * * *
3727735 AGATGAAGAGTCTCGATAAGATTTAGGGTTAAAG-ATATGAACATGACATGAATAGTCTTGTTTA
1 AGATGAAGAGTCTCGATAAGATATAGGGCTAAAGAAGATGAACATGACATGAAGAGTCTCGATAA
*
3727799 GATTTATGGTTAGAGAAATGAACA
66 GATTTAGGGTTAGAGAAATGAACA
3727823 GAACATGAAC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
90 7 0.09
91 39 0.52
92 29 0.39
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (91 bp):
AGATGAAGAGTCTCGATAAGATATAGGGCTAAAGAAGATGAACATGACATGAAGAGTCTCGATAA
GATTTAGGGTTAGAGAAATGAACAAT
Found at i:3727845 original size:45 final size:46
Alignment explanation
Indices: 3727645--3727846 Score: 207
Period size: 46 Copynumber: 4.4 Consensus size: 46
3727635 ACAGAATAAG
* * * *
3727645 ATGAAGAGTCTCGGTTAGATATAGGGCTAGAGAAGATGAACATGAG
1 ATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATGAC
* * *
3727691 ATGAAGAGTCTCGATAAGATTTAGGGTTATAGAAGATGAACAAT-AG
1 ATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAAC-ATGAC
* * *
3727737 ATGAAGAGTCTCGATAAGATTTAGGGTTAAAG-ATATGAACATGAC
1 ATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATGAC
* * * *
3727782 ATGAATAGTCTTGTTTAGATTTATGGTTAGAGAA-ATGAACA-GAAC
1 ATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATG-AC
*
3727827 ATGAACAGTCTC-AGTTAGAT
1 ATGAAGAGTCTCGA-TTAGAT
3727847 GAACAATTTA
Statistics
Matches: 134, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
44 3 0.02
45 59 0.44
46 70 0.52
47 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (46 bp):
ATGAAGAGTCTCGATTAGATTTAGGGTTAGAGAAGATGAACATGAC
Found at i:3728152 original size:102 final size:102
Alignment explanation
Indices: 3727985--3728220 Score: 271
Period size: 102 Copynumber: 2.3 Consensus size: 102
3727975 TGGGATTGGG
* *
3727985 TGTTTG-AAGAGATGGAATGAGGATTTTGGGGATGAACTCAAATGAACAGTGGTTGAGTTTAGGG
1 TGTTTGTAAG-GATCGAATGAGG-TTTTGGGGATGAACACAAATGAACAGTGGTTGAGTTTAGGG
* *
3728049 TGTTTGATTG-AAAAAATAGGTTTGATCTTGGGTTTAGA
64 TGTTTGATCGAAAAAAACAGGTTTGATCTTGGGTTTAGA
* *
3728087 TGTTTGTAAGGATCGAATGAGAGTTTTGGGGATGAACACAAATGAACAAG-GGTTGATTTTTGGG
1 TGTTTGTAAGGATCGAATGAG-GTTTTGGGGATGAACACAAATGAAC-AGTGGTTGAGTTTAGGG
* *
3728151 TGTTTGATCGAAAAAAAAAAACAGGTTTGATCTTGGGTTTTGG
64 TGTTTGATCG----AAAAAAACAGGTTTGATCTTGGGTTTAGA
** *
3728194 TGTTTGTAAAAATCAAATGAGGGTTTT
1 TGTTTGTAAGGATCGAATGA-GGTTTT
3728221 ATGATGAACA
Statistics
Matches: 114, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
102 60 0.53
103 6 0.05
107 47 0.41
108 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (102 bp):
TGTTTGTAAGGATCGAATGAGGTTTTGGGGATGAACACAAATGAACAGTGGTTGAGTTTAGGGTG
TTTGATCGAAAAAAACAGGTTTGATCTTGGGTTTAGA
Found at i:3728949 original size:295 final size:294
Alignment explanation
Indices: 3728401--3728931 Score: 920
Period size: 295 Copynumber: 1.8 Consensus size: 294
3728391 TAATTTTGAG
*
3728401 TTTATATATTAGTTTAAATTCAGGCAGGTTGGCCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
1 TTTATATATTAGTTTAAATTCAGGCAGGTTGACCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
* * *
3728466 GTGTCGCCCCTTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACATAATTTATTGAATTTA
66 GTATCACCCCTTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACACAATTTATTGAATTTA
* *
3728531 AGCATTATATTTTTAATTCTTCTAATTTGATCCCTATATATTTTTCATTTCTTTCAATTAATATT
131 AGCATTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATATT
* *
3728596 ATATGTACACTTATACATTAATGTATTCAACTATATTGTATATACTTTGAATTTATATAGTGTAA
196 ATATGTACACTTATACATTAATGTATTCAACTATATAGTATATACTAT-AATTTATATAGTGTAA
3728661 ATTATATAAATACAAACTATATACTAGTTTATAAC
260 ATTATATAAATACAAACTATATACTAGTTTATAAC
* * *
3728696 TTTATATATTAGTTTAAATTCGGGCCGGTTGACCCGTGTGTTTTTAAAGTTTAGTTGTCATTTTA
1 TTTATATATTAGTTTAAATTCAGGCAGGTTGACCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
*
3728761 GTATCACCCCATTG-TTTAAATTCGTTCAGTTTAGTCCAAATGTATAACACAATTTATTGAATTT
66 GTATCACCCC-TTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACACAATTTATTGAATTT
*
3728825 AAGCTTTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATAT
130 AAGCATTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATAT
3728890 TATATGTACACTTATACATTAATGTATTCAACTATATAGTAT
195 TATATGTACACTTATACATTAATGTATTCAACTATATAGTAT
3728932 TCATACATAT
Statistics
Matches: 223, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
295 220 0.99
296 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (294 bp):
TTTATATATTAGTTTAAATTCAGGCAGGTTGACCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
GTATCACCCCTTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACACAATTTATTGAATTTA
AGCATTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATATT
ATATGTACACTTATACATTAATGTATTCAACTATATAGTATATACTATAATTTATATAGTGTAAA
TTATATAAATACAAACTATATACTAGTTTATAAC
Found at i:3728977 original size:14 final size:14
Alignment explanation
Indices: 3728958--3728998 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
3728948 TACTTTGAAT
3728958 TTATATAATATAAA
1 TTATATAATATAAA
3728972 TTATATAAATATAAA
1 TTATAT-AATATAAA
* *
3728987 CTATATTATATA
1 TTATATAATATA
3728999 GTATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:3728998 original size:295 final size:293
Alignment explanation
Indices: 3728401--3728997 Score: 891
Period size: 295 Copynumber: 2.0 Consensus size: 293
3728391 TAATTTTGAG
*
3728401 TTTATATATTAGTTTAAATTCAGGCAGGTTGGCCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
1 TTTATATATTAGTTTAAATTCAGGCAGGTTGACCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
* * *
3728466 GTGTCGCCCCTTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACATAATTTATTGAATTTA
66 GTATCACCCCTTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACACAATTTATTGAATTTA
* *
3728531 AGCATTATATTTTTAATTCTTCTAATTTGATCCCTATATATTTTTCATTTCTTTCAATTAATATT
131 AGCATTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATATT
* * *
3728596 ATATGTACACTTATACATTAATGTATTCAACTATATTGTATATACTTTGAATTTATATAGTGTAA
196 ATATGTACACTTATACATTAATGTATTCAACTATATAGTATATACTAT-AATTTATATACTGTAA
* *
3728661 ATTATATAAATACAAACTATATACTAGTTTATAAC
260 ATTATATAAATACAAACTATATAC-AATATATAAC
* * *
3728696 TTTATATATTAGTTTAAATTCGGGCCGGTTGACCCGTGTGTTTTTAAAGTTTAGTTGTCATTTTA
1 TTTATATATTAGTTTAAATTCAGGCAGGTTGACCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
*
3728761 GTATCACCCCATTG-TTTAAATTCGTTCAGTTTAGTCCAAATGTATAACACAATTTATTGAATTT
66 GTATCACCCC-TTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACACAATTTATTGAATTT
*
3728825 AAGCTTTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATAT
130 AAGCATTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATAT
*
3728890 TATATGTACACTTATACATTAATGTATTCAACTATATAGTATTCATAC-AT-ATATTATATACTT
195 TATATGTACACTTATACATTAATGTATTCAACTATATAGTA-T-ATACTATAAT-TTATATACTG
* * *
3728953 TGAATT-TATATAATATAAATTATATA-AATATA-AAC
257 TAAATTATATA-AATACAAACTATATACAATATATAAC
*
3728988 TATATTATAT
1 TTTA-TATAT
3728998 AGTATATAAA
Statistics
Matches: 275, Mismatches: 21, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
292 6 0.02
293 9 0.03
294 6 0.02
295 245 0.89
296 5 0.02
297 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (293 bp):
TTTATATATTAGTTTAAATTCAGGCAGGTTGACCCGCGTGTTTTTAAAGTTTAGTTGTCATTTTA
GTATCACCCCTTGTTTTAAATTCGTTCAATTTAGTCCAAATGTATAACACAATTTATTGAATTTA
AGCATTATATTTTTAATTCTTCCAATTTGATACCTATATATTTTTCATTTCTTTCAATTAATATT
ATATGTACACTTATACATTAATGTATTCAACTATATAGTATATACTATAATTTATATACTGTAAA
TTATATAAATACAAACTATATACAATATATAAC
Found at i:3729024 original size:27 final size:27
Alignment explanation
Indices: 3728961--3729043 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
3728951 TTTGAATTTA
* *
3728961 TATAATATAAATTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
* * *
3728988 TATATTATATAGTATATAAATGTCAAC
1 TATAATATATAGTATATAAATATAAAC
**
3729015 TATAATATATAGT-T-TATTTATAAAC
1 TATAATATATAGTATATAAATATAAAC
3729040 TATA
1 TATA
3729044 GTTTATATAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
25 11 0.24
26 1 0.02
27 34 0.74
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (27 bp):
TATAATATATAGTATATAAATATAAAC
Found at i:3729079 original size:20 final size:20
Alignment explanation
Indices: 3729064--3729109 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3729054 TTCATATATA
3729064 ATATATGGTTTACATATAGT
1 ATATATGGTTTACATATAGT
*
3729084 ATATATGGTTTATATATAGT
1 ATATATGGTTTACATATAGT
*
3729104 TTATAT
1 ATATAT
3729110 ATATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (20 bp):
ATATATGGTTTACATATAGT
Found at i:3729080 original size:11 final size:11
Alignment explanation
Indices: 3729064--3729154 Score: 68
Period size: 11 Copynumber: 8.6 Consensus size: 11
3729054 TTCATATATA
*
3729064 ATATATGGTTT
1 ATATATAGTTT
*
3729075 ACATATAG--T
1 ATATATAGTTT
*
3729084 ATATATGGTTT
1 ATATATAGTTT
3729095 ATATATAGTTT
1 ATATATAGTTT
*
3729106 ATATATA-TAT
1 ATATATAGTTT
* *
3729116 ATTTATA-TAT
1 ATATATAGTTT
3729126 ATAT-TA-TATT
1 ATATATAGT-TT
3729136 ATTATATAGTTT
1 A-TATATAGTTT
3729148 ATATATA
1 ATATATA
3729155 TATTATAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
9 10 0.15
10 16 0.25
11 33 0.51
12 5 0.08
13 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:3729080 original size:18 final size:19
Alignment explanation
Indices: 3729059--3729102 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3729049 TATACTTCAT
3729059 ATATA-ATATATGGTTTAC
1 ATATAGATATATGGTTTAC
*
3729077 ATATAGTATATATGGTTTAT
1 ATATAG-ATATATGGTTTAC
3729097 ATATAG
1 ATATAG
3729103 TTTATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
20 18 0.78
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (19 bp):
ATATAGATATATGGTTTAC
Found at i:3729099 original size:2 final size:2
Alignment explanation
Indices: 3729094--3729161 Score: 63
Period size: 2 Copynumber: 35.0 Consensus size: 2
3729084 ATATATGGTT
* *
3729094 TA TA TA TA GTT TA TA TA TA TA TA TT TA TA TA TA TA T- TA TA T-
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3729135 TA T- TA TA TA GTT TA TA TA TA TA T- TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
3729162 ATTATTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
1 4 0.07
2 48 0.89
3 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3729116 original size:17 final size:15
Alignment explanation
Indices: 3729094--3729157 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
3729084 ATATATGGTT
3729094 TATATATAGT-TTATA
1 TATATATA-TATTATA
3729109 TATATATAT-TTATA
1 TATATATATATTATA
3729123 TATATATTATATTAT-
1 TATATA-TATATTATA
*
3729138 TATATA-GT-TTATA
1 TATATATATATTATA
3729151 TATATAT
1 TATATAT
3729158 TATAATTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 12 0.27
15 17 0.39
16 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATATATATATTATA
Found at i:3731199 original size:17 final size:17
Alignment explanation
Indices: 3731156--3731201 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
3731146 AGCCAAGAAT
3731156 ATATGCATACATAAATA
1 ATATGCATACATAAATA
* *
3731173 ATATGAATACATATATA
1 ATATGCATACATAAATA
*
3731190 ATATCCATACAT
1 ATATGCATACAT
3731202 GGTAAAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
ATATGCATACATAAATA
Found at i:3731627 original size:16 final size:16
Alignment explanation
Indices: 3731589--3731634 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
3731579 CAATTAGTAA
*
3731589 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
3731605 TTA---GTTAGAAAAG
1 TTAGCGGTTAGAAAAG
*
3731618 TTAGCGGTTAGCAAAG
1 TTAGCGGTTAGAAAAG
3731634 T
1 T
3731635 CCGAATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 12 0.48
16 13 0.52
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:3731830 original size:130 final size:132
Alignment explanation
Indices: 3731613--3731892 Score: 350
Period size: 130 Copynumber: 2.1 Consensus size: 132
3731603 GGTTAGTTAG
** * * *
3731613 AAAAGTTAGCGGTTAGCAAAGTCCGAATCATAATAATACAGATCATACCCCGGATCAGATTACCA
1 AAAAGTTAGTAGTTAGCAAAGTCCGAACCATAATAATACAGATCATACCCCAGATCAGATCACCA
** * *
3731678 CAAGGTCAAATCGAATGTTAGAAAC-GATAAATAAATAAAT-AACAATGGTTA-AAGTGCAATAA
66 CAAGGTCAAATCGAATAATAGAAACAAATAAATAAATAAATAAAAAATGGTTAGAA-TGCAATAA
3731740 AAT
130 AAT
* * * * * *
3731743 AAAAGTTAGTAGTTAGCAGAGTCTGAACCATAATAATGCAGATCATACCCCATATCTGGTCACCA
1 AAAAGTTAGTAGTTAGCAAAGTCCGAACCATAATAATACAGATCATACCCCAGATCAGATCACCA
*
3731808 CAAGGTCGAATCGAATAATAGAAACAATAAATAAATAAATAAATAAAAAATGGTTAGAATGCAAT
66 CAAGGTCAAATCGAATAATAGAAAC---AAATAAATAAATAAATAAAAAATGGTTAGAATGCAAT
3731873 AAAAT
128 AAAAT
*
3731878 AAAAGTCAGTAGTTA
1 AAAAGTTAGTAGTTA
3731893 ATATGCAATA
Statistics
Matches: 127, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
130 76 0.60
134 14 0.11
135 35 0.28
136 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (132 bp):
AAAAGTTAGTAGTTAGCAAAGTCCGAACCATAATAATACAGATCATACCCCAGATCAGATCACCA
CAAGGTCAAATCGAATAATAGAAACAAATAAATAAATAAATAAAAAATGGTTAGAATGCAATAAA
AT
Found at i:3731892 original size:29 final size:29
Alignment explanation
Indices: 3731860--3731924 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 29
3731850 ATAAAAAATG
3731860 GTTAGAATGCAATAAAATAAAAGTCAGTA
1 GTTAGAATGCAATAAAATAAAAGTCAGTA
*
3731889 GTTA-ATATGCAATAAAATAAAAGTTAGTA
1 GTTAGA-ATGCAATAAAATAAAAGTCAGTA
3731918 GTTAGAA
1 GTTAGAA
3731925 ATAAATAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 31 0.94
30 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.28
Consensus pattern (29 bp):
GTTAGAATGCAATAAAATAAAAGTCAGTA
Found at i:3731931 original size:29 final size:29
Alignment explanation
Indices: 3731860--3731932 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
3731850 ATAAAAAATG
* *
3731860 GTTAGAATGCAATAAAATAAAAGTCAGTA
1 GTTAAAATGAAATAAAATAAAAGTCAGTA
* * *
3731889 GTTAATATGCAATAAAATAAAAGTTAGTA
1 GTTAAAATGAAATAAAATAAAAGTCAGTA
3731918 GTTAGAAAT-AAATAA
1 GTTA-AAATGAAATAA
3731933 CATAGCATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 35 0.92
30 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.27
Consensus pattern (29 bp):
GTTAAAATGAAATAAAATAAAAGTCAGTA
Found at i:3732876 original size:55 final size:56
Alignment explanation
Indices: 3732816--3732920 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 56
3732806 CAATAGGTAT
* * * *
3732816 AATTATAGGTTTGGTCCTTACACTTT-TTTCCTCTTTAATTTTTGGACAATGGCAC
1 AATTATAAGTTTGGTCCTTACACTTTGTTCCCTCTTTAATTCTCGGACAATGGCAC
3732871 AATTATAAGTTTGGTCCTTACACTTTGTTCCCTCTTTAATTCTCGGACAA
1 AATTATAAGTTTGGTCCTTACACTTTGTTCCCTCTTTAATTCTCGGACAA
3732921 AATTAGGGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 25 0.56
56 20 0.44
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (56 bp):
AATTATAAGTTTGGTCCTTACACTTTGTTCCCTCTTTAATTCTCGGACAATGGCAC
Found at i:3733761 original size:131 final size:130
Alignment explanation
Indices: 3733283--3733767 Score: 551
Period size: 131 Copynumber: 3.7 Consensus size: 130
3733273 GTTCTAGTCG
* * * * * *
3733283 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGC
1 TCTAGGGGTGACACGTCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGT
* ** * * ** *
3733348 GATGAGTATGACTGCCATCTTTAGGAAGGGTGATAACACAGTTCCTACACGATGAGGACGACTAG
66 GATGAGGATGGTTGCCATCTTTA-G-A-GATGATAACACGGTTCCTACGTGATGAGGACGACTGG
3733413 TTA
128 TTA
* * * * * *
3733416 TCTAGGGGTGACACGGCTCATACGTGATGAAGAGGTCTAGTCGGGGGATGACACAGTTTCTATGT
1 TCTAGGGGTGACACGTCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGT
** * * *
3733481 GATGAGGATGACATACCATCTTTAGGGATGATAACACGGTTCCTATGTGATGAGGACGACTGGTT
66 GATGAGGATG-GTTGCCATCTTTAGAGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTT
3733546 A
130 A
* * ** * * *
3733547 TCTAGGGGTAACACGAT-TCCTACGTGATGAGGAGGTTTGGTCGGGAAATGAAACGGTTCTTACG
1 TCTAGGGGTGACACG-TCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACG
* *
3733611 TGATGAGGATGGTAAGCCATCTATAGAGATGATAACACGGTTCCTACGTGATGAGGACGACTGGT
65 TGATGAGGATGGT-TGCCATCTTTAGAGATGATAACACGGTTCCTACGTGATGAGGACGACTGGT
3733676 TA
129 TA
* *
3733678 TCTAGGGATGACACGTCTCCTACGTGATGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGT
1 TCTAGGGGTGACACGTCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGT
*
3733743 -AGTGAGGACGGTTGGCCATCTTTAG
66 GA-TGAGGATGGTT-GCCATCTTTAG
3733768 GGATTTATTT
Statistics
Matches: 293, Mismatches: 53, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
130 2 0.01
131 217 0.74
133 64 0.22
134 10 0.03
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (130 bp):
TCTAGGGGTGACACGTCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGT
GATGAGGATGGTTGCCATCTTTAGAGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTA
Found at i:3733890 original size:36 final size:35
Alignment explanation
Indices: 3733840--3734021 Score: 91
Period size: 36 Copynumber: 5.4 Consensus size: 35
3733830 CAAAGATTGG
3733840 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
* * ****
3733875 TCGTTTCAAGGGAAAC-GT-TCTAA---A-AGATGGG
1 T-GTTTCAAGAGAAACTGTCTC-AAGGGAGACAAAAT
* *
3733906 TGTTTTAAGAGAAAATGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-T
* * * * ***
3733942 TATTTCAAGGGAAA-TATTCTTAA---AGA-TGGA-
1 TGTTTCAAGAGAAACT-GTCTCAAGGGAGACAAAAT
3733972 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
*
3734007 TCGTTTCAAGGGAAA
1 T-GTTTCAAGAGAAA
3734022 TGTTCTCCAA
Statistics
Matches: 100, Mismatches: 30, Indels: 33
0.61 0.18 0.20
Matches are distributed among these distances:
30 28 0.28
31 8 0.08
32 4 0.04
33 6 0.06
34 4 0.04
35 9 0.09
36 41 0.41
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
Found at i:3733925 original size:66 final size:66
Alignment explanation
Indices: 3733775--3734049 Score: 397
Period size: 66 Copynumber: 4.2 Consensus size: 66
3733765 TAGGGATTTA
* * * *
3733775 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTTAAGGGAAACGATCTCAAAGATTGG
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTCGTTTCAAGGGAAACGTTCTCAAAGATGGG
3733840 TG
65 TG
*
3733842 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGTTCTAAAAGATGGGT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGATGGGT
3733907 G
66 G
* * ** ** * *
3733908 TTTTAAGAGAAAATGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAATATTCTTAAAGATGGAT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGATGGGT
3733973 G
66 G
* * *
3733974 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGTTCTCCAAGATTGGT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGATGGGT
3734039 G
66 G
3734040 TTTCAAGAGA
1 TTTCAAGAGA
3734050 GACAAAACTT
Statistics
Matches: 186, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
66 154 0.83
67 32 0.17
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (66 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGATGGGT
G
Found at i:3734142 original size:36 final size:36
Alignment explanation
Indices: 3734080--3734155 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
3734070 GAAACAATTT
*
3734080 CAAAGTTTGTCTTAAGGAAGACTGTCTCAAGTGAGA
1 CAAAGTTTGTCTTAAGGAAGACTGTCTCAAGCGAGA
* * *
3734116 CAAAGTTTGTTTTGA-GAGAGATTGTCTCAAGCGAGA
1 CAAAGTTTGTCTTAAGGA-AGACTGTCTCAAGCGAGA
3734152 CAAA
1 CAAA
3734156 ATTTTTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (36 bp):
CAAAGTTTGTCTTAAGGAAGACTGTCTCAAGCGAGA
Found at i:3738217 original size:21 final size:21
Alignment explanation
Indices: 3738188--3738227 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3738178 ATCATAACCA
*
3738188 TTTTTTTAAAAAACAATTAAG
1 TTTTATTAAAAAACAATTAAG
*
3738209 TTTTATTAAAAAATAATTA
1 TTTTATTAAAAAACAATTA
3738228 TGACTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTTATTAAAAAACAATTAAG
Found at i:3738235 original size:22 final size:21
Alignment explanation
Indices: 3738193--3738238 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3738183 AACCATTTTT
*
3738193 TTAAAAAACAATTAAGTTTTA
1 TTAAAAAACAATTAAGCTTTA
* *
3738214 TTAAAAAATAATTATGACTTTA
1 TTAAAAAACAATTAAG-CTTTA
3738236 TTA
1 TTA
3738239 TTTGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
TTAAAAAACAATTAAGCTTTA
Found at i:3739457 original size:16 final size:16
Alignment explanation
Indices: 3739416--3739457 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3739406 CAATTAGTAA
3739416 TTAGCGGTTAGAAAGT
1 TTAGCGGTTAGAAAGT
**
3739432 TTAGTTGTTAGAAAAG-
1 TTAGCGGTTAG-AAAGT
3739448 TTAGCGGTTA
1 TTAGCGGTTA
3739458 ACAAAGTCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (16 bp):
TTAGCGGTTAGAAAGT
Found at i:3740625 original size:95 final size:95
Alignment explanation
Indices: 3740452--3740625 Score: 253
Period size: 95 Copynumber: 1.8 Consensus size: 95
3740442 CCATTGAGGC
* *
3740452 AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCAAACCTAATTTTGGTATCGATA
* *
3740517 TCGTAAGGGGTATCAGTACATTAGTAAGGT
66 ACGTAAGGAGTATCAGTACATTAGTAAGGT
* **
3740547 AGTATCGATACCATGGTAAGGGTATTGATACC-ATTAAACATCAAACCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCAAACCTAATTTTGGTATCGATA
3740611 ACAGGT-AGGAGTATC
66 AC--GTAAGGAGTATC
3740626 GGTAACCTAG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 29 0.41
95 39 0.56
96 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCAAACCTAATTTTGGTATCGATA
ACGTAAGGAGTATCAGTACATTAGTAAGGT
Found at i:3740665 original size:20 final size:20
Alignment explanation
Indices: 3740614--3740673 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
3740604 ATCGATAACA
*
3740614 GGTAGGAGTATCGGTAACCTAG
1 GGTAGAAGTATCGGT-A-CTAG
* *
3740636 TGTAAAAGTATCGGTACTAG
1 GGTAGAAGTATCGGTACTAG
* *
3740656 GGTAGTAGTATCGATACT
1 GGTAGAAGTATCGGTACT
3740674 TCAGAACCAG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 18 0.58
21 1 0.03
22 12 0.39
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (20 bp):
GGTAGAAGTATCGGTACTAG
Found at i:3741170 original size:45 final size:45
Alignment explanation
Indices: 3741120--3741427 Score: 390
Period size: 45 Copynumber: 6.9 Consensus size: 45
3741110 AAAGGATGCC
* *
3741120 ATAGTTGAAATGTATATGGGTACATTATCAACATAATAA-CATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAA-AAGTATACT
* * * *
3741165 TTAGTTGAAATATATATGGGTACATTATCAATAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
3741210 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
3741255 AGAGTTGAAATGTATATGGGTGCAGTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
3741300 AGAGTTGAAATGTATATGGGTATC-TTATCAACA-AAAAGTATAAT
1 ATAGTTGAAATGTATATGGGTA-CATTATCAACAGAAAAGTATACT
* *
3741344 ATGGTTAAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
3741389 ATAGTTGAATTGCATATGGGTGA-ATTATCAACAGAAAAG
1 ATAGTTGAAATGTATATGGGT-ACATTATCAACAGAAAAG
3741428 ATGTTATAGT
Statistics
Matches: 230, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.00
44 39 0.17
45 188 0.82
46 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:3741406 original size:134 final size:135
Alignment explanation
Indices: 3741167--3741427 Score: 375
Period size: 134 Copynumber: 1.9 Consensus size: 135
3741157 AACATACTTT
* ** * *
3741167 AGTTGAAATATATATGGGTACATTATCAATAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTG
1 AGTTGAAATATATATGGGTACATTATCAACAGAAAAGTATAATAGAGTTAAAATGCATATGGGTA
* *
3741232 CATTATCAACAGAAAAGTATACTAGAGTTGAAATGTATATGGGTGCAGTATCAACAGAAAAGTAT
66 CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGAAGTATCAACAGAAAAGTAT
3741297 GCTAG
131 GCTAG
* *
3741302 AGTTGAAATGTATATGGGTATC-TTATCAACA-AAAAGTATAATATG-GTTAAAATGTATATGGG
1 AGTTGAAATATATATGGGTA-CATTATCAACAGAAAAGTATAATA-GAGTTAAAATGCATATGGG
* * *
3741364 TACATTATCAACAGAAAAGTATACTATAGTTGAATTGCATATGGGTGAATTATCAACAGAAAAG
64 TACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGAAGTATCAACAGAAAAG
3741428 ATGTTATAGT
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
134 83 0.74
135 28 0.25
136 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (135 bp):
AGTTGAAATATATATGGGTACATTATCAACAGAAAAGTATAATAGAGTTAAAATGCATATGGGTA
CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGAAGTATCAACAGAAAAGTAT
GCTAG
Found at i:3747645 original size:94 final size:96
Alignment explanation
Indices: 3747472--3747657 Score: 238
Period size: 94 Copynumber: 2.0 Consensus size: 96
3747462 TTGTTGAGGC
* *
3747472 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAAACAATGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGAAAGGGTATCGATACCAAGAAAACAATGAACCTAATTTTGGTATCGATA
* *
3747537 CCGTAAGGGGGTATCGATACCTTAGTAAGGT
66 CCGTAAGGGAGTATCGATACCCTAGTAAGGT
* * *
3747568 AGTATCTATACCAT-GAAAGGGTATCGGTACCATG-AAAC-ATCGAACCTAATTTTGGTATCGAT
1 AGTATCGATACCATGGAAAGGGTATCGATACCAAGAAAACAAT-GAACCTAATTTTGGTATCGAT
*
3747630 ATCAGGT-A-GGAGTATCGATACCCTAGTA
65 A-C-CGTAAGGGAGTATCGATACCCTAGTA
3747658 TAGAAGTATC
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
93 2 0.03
94 43 0.54
95 19 0.24
96 15 0.19
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (96 bp):
AGTATCGATACCATGGAAAGGGTATCGATACCAAGAAAACAATGAACCTAATTTTGGTATCGATA
CCGTAAGGGAGTATCGATACCCTAGTAAGGT
Found at i:3755207 original size:45 final size:45
Alignment explanation
Indices: 3755190--3755496 Score: 431
Period size: 45 Copynumber: 6.8 Consensus size: 45
3755180 ATGATGCCAT
* * * **
3755190 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGCATACTTT
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAG
3755235 AGTTGAAATGTATATGGGTAG-ATTATCAACAGAAAAGTATGCTAG
1 AGTTGAAATGTATATGGGT-GCATTATCAACAGAAAAGTATGCTAG
*
3755280 AGTTGAAATGCT-TATGGGTGCATTATCAACAGAAAAGTATACTAG
1 AGTTGAAATG-TATATGGGTGCATTATCAACAGAAAAGTATGCTAG
* *
3755325 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCAG
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAG
* *
3755370 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTA-G
* * * *
3755416 A-TTGAAATGTATATGGGTACATTATCAACAAAAAAGTATACTAT
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAG
*
3755460 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAG
3755497 ATATTATAGT
Statistics
Matches: 238, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
44 2 0.01
45 233 0.98
46 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAG
Found at i:3755517 original size:45 final size:45
Alignment explanation
Indices: 3755188--3755535 Score: 400
Period size: 45 Copynumber: 7.7 Consensus size: 45
3755178 AAATGATGCC
* * *
3755188 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGCATACTT
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATA-TT
* **
3755234 -TAGTTGAAATGTATATGGGTAG-ATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGCATATGGGT-GCATTATCAACAGAAAAGTATATT
* * *
3755278 AGAGTTGAAATGCTTATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
* ***
3755323 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCC
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
* * * *
3755368 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
* * * *
3755413 AT-GATTGAAATGTATATGGGTACATTATCAACAAAAAAGTATACT
1 ATAG-TTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
3755458 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATATT
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
* * *
3755502 ATAGTTTAAAGTGCATAAT-GGTGTATTATAAACA
1 ATAGTTGAAA-TGCAT-ATGGGTGCATTATCAACA
3755536 TAAATGGAGG
Statistics
Matches: 271, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
44 16 0.06
45 252 0.93
46 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
Found at i:3755530 original size:90 final size:89
Alignment explanation
Indices: 3755190--3755535 Score: 446
Period size: 90 Copynumber: 3.8 Consensus size: 89
3755180 ATGATGCCAT
* * * *
3755190 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGCATACTTTAGTTGAAATGTATATGGGTA
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTA
3755255 GATTATCAACAGAAAAGTATGCTAG
66 -ATTATCAACAGAAAAGTATGCTAG
* * *
3755280 AGTTGAAATGCTTATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGT-
* *
3755345 CATTATCAACAGAAAAGTATGCCAG
65 AATTATCAACAGAAAAGTATGCTAG
* *
3755370 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAT-GATTGAAATGTATATGGGT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAG-TTGAAATGCATATGGGT
* * *
3755434 ACATTATCAACAAAAAAGTATACTAT
65 A-ATTATCAACAGAAAAGTATGCTAG
* * *
3755460 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATATTATAGTTTAAAGTGCATAATGGT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAA-TGCAT-ATGG-
*
3755524 GT-ATTATAAACA
63 GTAATTATCAACA
3755536 TAAATGGAGG
Statistics
Matches: 224, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
89 12 0.05
90 206 0.92
91 4 0.02
92 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (89 bp):
AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTA
ATTATCAACAGAAAAGTATGCTAG
Found at i:3756034 original size:12 final size:12
Alignment explanation
Indices: 3756001--3756034 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3755991 TAATAGAAAC
* *
3756001 AATAAATAAATA
1 AATAAACAATTA
3756013 AATAAACAATTA
1 AATAAACAATTA
3756025 AATAAACAAT
1 AATAAACAAT
3756035 CGTTAGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAACAATTA
Found at i:3756106 original size:29 final size:29
Alignment explanation
Indices: 3756036--3756108 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
3756026 ATAAACAATC
3756036 GTTAG-AATACAATAAAATAAAAGTCAGTA
1 GTTAGAAATA-AATAAAATAAAAGTCAGTA
* *
3756065 GTTA-ATATGAAATAAAATAAAAGTTAGTA
1 GTTAGAAAT-AAATAAAATAAAAGTCAGTA
3756094 GTTAGAAATAAATAA
1 GTTAGAAATAAATAA
3756109 CATAGCAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (29 bp):
GTTAGAAATAAATAAAATAAAAGTCAGTA
Found at i:3757058 original size:56 final size:56
Alignment explanation
Indices: 3756950--3757058 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
3756940 TTATAATAGG
* * * * *
3756950 TACAATTACAGGTTTGCTCGTTACACTTTGTTCCCTCTTTAATTTTTAGACAATGA
1 TACAATTACAAGTTTGCTCCTTACACTTTGTTCCCTCATTAATTCTCAGACAATGA
* * *
3757006 TACAATTGCAAGTTTGGTCCTTACACTTTGTTCCCTCATTAATTCTCGGACAA
1 TACAATTACAAGTTTGCTCCTTACACTTTGTTCCCTCATTAATTCTCAGACAA
3757059 AATTAAGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (56 bp):
TACAATTACAAGTTTGCTCCTTACACTTTGTTCCCTCATTAATTCTCAGACAATGA
Found at i:3757780 original size:12 final size:12
Alignment explanation
Indices: 3757760--3757793 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3757750 GTTAAAGGGA
*
3757760 AATGATGCATTC
1 AATGGTGCATTC
3757772 AATGGTGCATTC
1 AATGGTGCATTC
3757784 AATGGTGCAT
1 AATGGTGCAT
3757794 CCAGATCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (12 bp):
AATGGTGCATTC
Found at i:3759674 original size:11 final size:11
Alignment explanation
Indices: 3759660--3759689 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3759650 ATAATATACA
3759660 TAGTTTATATG
1 TAGTTTATATG
*
3759671 TAGTTTACATG
1 TAGTTTATATG
3759682 TAGTTTAT
1 TAGTTTAT
3759690 TAATAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (11 bp):
TAGTTTATATG
Found at i:3759873 original size:9 final size:9
Alignment explanation
Indices: 3759859--3759891 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3759849 GTGTAAACAA
*
3759859 TATATAAAC
1 TATATAAAG
3759868 TATATAAAG
1 TATATAAAG
3759877 TAT-TAAAG
1 TATATAAAG
3759885 TATATAA
1 TATATAA
3759892 TTTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:3759899 original size:19 final size:20
Alignment explanation
Indices: 3759858--3759967 Score: 96
Period size: 18 Copynumber: 5.8 Consensus size: 20
3759848 TGTGTAAACA
3759858 ATATATAAACTATATAA---
1 ATATATAAACTATATAATTT
*
3759875 AGTAT-TAAAGTATATAATTT
1 A-TATATAAACTATATAATTT
3759895 ATAT-TAATA-TAATATAAGTTT
1 ATATATAA-ACT-ATATAA-TTT
3759916 ATATATAAACTATAT-ATTT
1 ATATATAAACTATATAATTT
3759935 AT-TATAAACTATATAA-TT
1 ATATATAAACTATATAATTT
*
3759953 AT-TATAAGCTATATA
1 ATATATAAACTATATA
3759968 TATATAAACT
Statistics
Matches: 81, Mismatches: 2, Indels: 19
0.79 0.02 0.19
Matches are distributed among these distances:
17 12 0.15
18 31 0.38
19 13 0.16
20 9 0.11
21 12 0.15
22 4 0.05
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATATAAACTATATAATTT
Found at i:3759942 original size:18 final size:18
Alignment explanation
Indices: 3759913--3759979 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
3759903 ATAATATAAG
3759913 TTTATATATAAACTATATA
1 TTTAT-TATAAACTATATA
3759932 TTTATTATAAACTATATA
1 TTTATTATAAACTATATA
* *
3759950 ATTATTATAAGCTATATA
1 TTTATTATAAACTATATA
3759968 --TA-TATAAACTAT
1 TTTATTATAAACTAT
3759980 GCTTATATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
15 9 0.20
16 2 0.04
18 29 0.64
19 5 0.11
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (18 bp):
TTTATTATAAACTATATA
Found at i:3759973 original size:15 final size:15
Alignment explanation
Indices: 3759915--3760539 Score: 174
Period size: 15 Copynumber: 42.4 Consensus size: 15
3759905 AATATAAGTT
3759915 TATATATAAACTATA
1 TATATATAAACTATA
3759930 TATTTATTATAAACTATA
1 TA--TA-TATAAACTATA
*
3759948 TAATTATTATAAGCTATA
1 T-A-TA-TATAAACTATA
*
3759966 TATATATAAACTATGC
1 TATATATAAACTAT-A
*
3759982 T-TATATGAAC--TA
1 TATATATAAACTATA
3759994 TATATATAAACTATA
1 TATATATAAACTATA
*
3760009 TATGTATAAAC----
1 TATATATAAACTATA
*
3760020 TATA-A-AAAGTATA
1 TATATATAAACTATA
*
3760033 TAGTTTATAAACTATAA
1 TA-TATATAAACTAT-A
* *
3760050 TTTATATTAA-TATA
1 TATATATAAACTATA
* *
3760064 -ATATATATA-TGTA
1 TATATATAAACTATA
* *
3760077 TGTATATAAACTGTA
1 TATATATAAACTATA
* *
3760092 TATGTATAAACTAAA
1 TATATATAAACTATA
* * *
3760107 TAAAGTATATAGT-T-
1 TATA-TATAAACTATA
*
3760121 TATA-A-AAAC-A-C
1 TATATATAAACTATA
**
3760132 TATGCATAAACTATATA
1 TATATATAAAC--TATA
*
3760149 TATAATATAAATTATA
1 TAT-ATATAAACTATA
*
3760165 TAGTTATTATAAAC--TC
1 TA--TA-TATAAACTATA
3760181 TATATATAAACTATA
1 TATATATAAACTATA
*
3760196 TGGTTATTATAAAC--TA
1 T--ATA-TATAAACTATA
3760212 TATATATAAACTATA
1 TATATATAAACTATA
*
3760227 TGGTTATTATAAAC--TA
1 T--ATA-TATAAACTATA
3760243 TATATATAAAC--TA
1 TATATATAAACTATA
* *
3760256 TATATGTAATCTATGTA
1 TATATATAAACTA--TA
* *
3760273 GTTTTTATAAACTAATGAA
1 -TATATATAAACT-AT--A
3760292 TTATATATAAA--A-A
1 -TATATATAAACTATA
* *
3760305 -A-A-ACTATAC-ATG
1 TATATA-TAAACTATA
*
3760317 TAAATATAAACTATA
1 TATATATAAACTATA
* *
3760332 TATGTATGAAC--TA
1 TATATATAAACTATA
3760345 TATATATAAACTATA
1 TATATATAAACTATA
*
3760360 TAGTTTATATAAACTACA
1 TA---TATATAAACTATA
* *
3760378 TATGTTTAAAC--TA
1 TATATATAAACTATA
*
3760391 TGTATATAAA-T-TA
1 TATATATAAACTATA
*
3760404 TATAAATAAACTATA
1 TATATATAAACTATA
*
3760419 TAGATAT--A-TATA
1 TATATATAAACTATA
*
3760431 TATATATATA-TATA
1 TATATATAAACTATA
*
3760445 TATATATATA-TATA
1 TATATATAAACTATA
*
3760459 TATATATATA-TATA
1 TATATATAAACTATA
* *
3760473 TATATATAAGCTACA
1 TATATATAAACTATA
*
3760488 TATGTATAAAC--TA
1 TATATATAAACTATA
* *
3760501 TATATGTAATCTATA
1 TATATATAAACTATA
3760516 TAGTTTATATAAACTATA
1 TA---TATATAAACTATA
3760534 TATATA
1 TATATA
3760540 AACAATATAA
Statistics
Matches: 453, Mismatches: 85, Indels: 144
0.66 0.12 0.21
Matches are distributed among these distances:
9 4 0.01
10 5 0.01
11 10 0.02
12 13 0.03
13 97 0.21
14 65 0.14
15 106 0.23
16 38 0.08
17 16 0.04
18 88 0.19
19 11 0.02
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:3760048 original size:83 final size:83
Alignment explanation
Indices: 3759954--3760126 Score: 217
Period size: 83 Copynumber: 2.1 Consensus size: 83
3759944 TATATAATTA
* **
3759954 TTATAAGCTAT-ATATATATAAACTATGCT-TATATGAACTATATATATAAACTATATATGTATA
1 TTATAAACTATAATATATATAAA-TATAATATATAT-AACTATATATATAAACTATATATGTATA
3760017 AACTATAA-AAAGTATATAGT
64 AACTA-AATAAAGTATATAGT
* * ** * *
3760037 TTATAAACTATAATTTATATTAATATAATATATATATGTATGTATATAAACTGTATATGTATAAA
1 TTATAAACTATAATATATATAAATATAATATATATAACTATATATATAAACTATATATGTATAAA
3760102 CTAAATAAAGTATATAGT
66 CTAAATAAAGTATATAGT
3760120 TTATAAA
1 TTATAAA
3760127 AACACTATGC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
82 2 0.03
83 62 0.79
84 14 0.18
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (83 bp):
TTATAAACTATAATATATATAAATATAATATATATAACTATATATATAAACTATATATGTATAAA
CTAAATAAAGTATATAGT
Found at i:3760083 original size:21 final size:21
Alignment explanation
Indices: 3760059--3760098 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3760049 ATTTATATTA
3760059 ATATAATA-TATATATGTATGT
1 ATATAA-ACTATATATGTATGT
*
3760080 ATATAAACTGTATATGTAT
1 ATATAAACTATATATGTAT
3760099 AAACTAAATA
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:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (21 bp):
ATATAAACTATATATGTATGT
Found at i:3760164 original size:18 final size:18
Alignment explanation
Indices: 3760137--3760189 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3760127 AACACTATGC
3760137 ATAAACTATATATATAAT
1 ATAAACTATATATATAAT
* *
3760155 ATAAATTATATAGT-TATT
1 ATAAACTATATA-TATAAT
*
3760173 ATAAACTCTATATATAA
1 ATAAACTATATATATAA
3760190 ACTATATGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAAACTATATATATAAT
Found at i:3760196 original size:31 final size:31
Alignment explanation
Indices: 3760147--3760259 Score: 181
Period size: 31 Copynumber: 3.6 Consensus size: 31
3760137 ATAAACTATA
*
3760147 TATATAATATAAATTATATAGTTATTATAAAC
1 TATAT-ATATAAACTATATAGTTATTATAAAC
* *
3760179 TCTATATATAAACTATATGGTTATTATAAAC
1 TATATATATAAACTATATAGTTATTATAAAC
*
3760210 TATATATATAAACTATATGGTTATTATAAAC
1 TATATATATAAACTATATAGTTATTATAAAC
3760241 TATATATATAAACTATATA
1 TATATATATAAACTATATA
3760260 TGTAATCTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 72 0.95
32 4 0.05
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (31 bp):
TATATATATAAACTATATAGTTATTATAAAC
Found at i:3760207 original size:49 final size:49
Alignment explanation
Indices: 3760106--3760215 Score: 116
Period size: 49 Copynumber: 2.2 Consensus size: 49
3760096 TATAAACTAA
* *
3760106 ATAAAGTATATAGTTTATAAAAACACTATGCATAAACTATATATATAAT
1 ATAAACTATATAGTTTATAAAAACACTATACATAAACTATATATATAAT
* * * * * *
3760155 ATAAATTATATAG-TTATTATAAACTCTATATATAAACTATATGGT-TATT
1 ATAAACTATATAGTTTA-TAAAAACACTATACATAAACTATAT-ATATAAT
3760204 ATAAACTATATA
1 ATAAACTATATA
3760216 TATAAACTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.06
49 47 0.92
50 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (49 bp):
ATAAACTATATAGTTTATAAAAACACTATACATAAACTATATATATAAT
Found at i:3760208 original size:18 final size:18
Alignment explanation
Indices: 3760185--3760245 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
3760175 AAACTCTATA
3760185 TATAAACTATATGGTTAT
1 TATAAACTATATGGTTAT
3760203 TATAAACTATA----TA-
1 TATAAACTATATGGTTAT
3760216 TATAAACTATATGGTTAT
1 TATAAACTATATGGTTAT
3760234 TATAAACTATAT
1 TATAAACTATAT
3760246 ATATAAACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.29
14 2 0.05
17 2 0.05
18 23 0.61
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (18 bp):
TATAAACTATATGGTTAT
Found at i:3760370 original size:18 final size:19
Alignment explanation
Indices: 3760347--3760385 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3760337 ATGAACTATA
*
3760347 TATATAAACTATATA-GTT
1 TATATAAACTACATATGTT
3760365 TATATAAACTACATATGTT
1 TATATAAACTACATATGTT
3760384 TA
1 TA
3760386 AACTATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (19 bp):
TATATAAACTACATATGTT
Found at i:3760381 original size:46 final size:46
Alignment explanation
Indices: 3760203--3760407 Score: 167
Period size: 46 Copynumber: 4.6 Consensus size: 46
3760193 ATATGGTTAT
* *
3760203 TATAAACTATATATATAAACTATAT-GGTTATTATAAACT--ATATA
1 TATAAACTATATATATAAACTATATAGTTTA-TATAAACTACATATG
* * * *
3760247 TATAAACTATATATGTAATCTATGTAGTTTTTATAAACTA-ATGAAT-
1 TATAAACTATATATATAAACTATATAGTTTATATAAACTACAT--ATG
* * * ** *
3760293 TAT--A-TATA-AAAAAAACTATACATGTAAATATAAACTATATATG
1 TATAAACTATATATATAAACTATATA-GTTTATATAAACTACATATG
*
3760336 TATGAACTATATATATAAACTATATAGTTTATATAAACTACATATG
1 TATAAACTATATATATAAACTATATAGTTTATATAAACTACATATG
* * *
3760382 TTTAAACTATGTATATAAATTATATA
1 TATAAACTATATATATAAACTATATA
3760408 AATAAACTAT
Statistics
Matches: 126, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
42 10 0.08
43 18 0.14
44 33 0.26
45 6 0.05
46 46 0.37
47 13 0.10
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (46 bp):
TATAAACTATATATATAAACTATATAGTTTATATAAACTACATATG
Found at i:3760407 original size:2 final size:2
Alignment explanation
Indices: 3760393--3760480 Score: 124
Period size: 2 Copynumber: 44.0 Consensus size: 2
3760383 TTAAACTATG
* * * *
3760393 TA TA TA AA T- TA TA TA AA TA AA CTA TA TA GA 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 TA TA
3760435 TA TA 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 TA TA
3760477 TA TA
1 TA TA
3760481 AGCTACATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.01
2 74 0.97
3 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3760547 original size:11 final size:13
Alignment explanation
Indices: 3759964--3760548 Score: 135
Period size: 13 Copynumber: 43.5 Consensus size: 13
3759954 TTATAAGCTA
3759964 TATATATATAAAC
1 TATATATATAAAC
* *
3759977 TATGCTTATATGAAC
1 TAT--ATATATAAAC
3759992 TATATATATAAAC
1 TATATATATAAAC
3760005 TATATATGTATAAAC
1 TATATA--TATAAAC
3760020 TATA-A-A-AAGTA-
1 TATATATATAA--AC
*
3760031 TATAGTTTATAAAC
1 TATA-TATATAAAC
*
3760045 TATAATTTATATTAA-
1 TAT-A--TATATAAAC
**
3760060 TATAATATATATATG
1 TAT-ATATATA-AAC
*
3760075 TATGTATATAAAC
1 TATATATATAAAC
*
3760088 TGTATATGTATAAAC
1 --TATATATATAAAC
* * *
3760103 TAAATAAAGTATA-
1 TATATATA-TAAAC
* *
3760116 TAGTTTATAAAAAC
1 TA-TATATATAAAC
**
3760130 -ACTATGCATAAAC
1 TA-TATATATAAAC
3760143 TATATATAT-AA-
1 TATATATATAAAC
* * *
3760154 TATAAATTATATAG
1 TATATA-TATAAAC
3760168 T-TAT-TATAAAC
1 TATATATATAAAC
*
3760179 TCTATATATAAAC
1 TATATATATAAAC
3760192 TATATGGTTATTATAAAC
1 TATA----TA-TATAAAC
3760210 TATATATATAAAC
1 TATATATATAAAC
3760223 TATATGGTTATTATAAAC
1 TATA----TA-TATAAAC
3760241 TATATATATAAAC
1 TATATATATAAAC
* *
3760254 TATATATGTAATC
1 TATATATATAAAC
* * **
3760267 TATGTAGTTTTTA-
1 TATATA-TATAAAC
* *
3760280 TAAACTA-ATGAA-
1 TATA-TATATAAAC
3760292 T-TATATATAAA-
1 TATATATATAAAC
* * *
3760303 -AAAAACTATACA-
1 TATATA-TATAAAC
* *
3760315 TGTAAATATAAAC
1 TATATATATAAAC
*
3760328 TATATATGTATGAAC
1 TATATA--TATAAAC
3760343 TATATATATAAAC
1 TATATATATAAAC
3760356 TATATAGTTTATATAAAC
1 --TATA---TATATAAAC
* *
3760374 TACATATGTTTAAAC
1 T--ATATATATAAAC
* *
3760389 TATGTATATAAAT
1 TATATATATAAAC
*
3760402 TATATAAATAAAC
1 TATATATATAAAC
*
3760415 TATATAGAT--A-
1 TATATATATAAAC
3760425 TATATATAT--A-
1 TATATATATAAAC
*
3760435 TATATATATATA-
1 TATATATATAAAC
*
3760447 TATATATATATA-
1 TATATATATAAAC
*
3760459 TATATATATATA-
1 TATATATATAAAC
*
3760471 TATATATATAAGC
1 TATATATATAAAC
*
3760484 TACATATGTATAAAC
1 T--ATATATATAAAC
* *
3760499 TATATATGTAATC
1 TATATATATAAAC
3760512 TATATAGTTTATATAAAC
1 --TATA---TATATAAAC
3760530 TATATATATAAAC
1 TATATATATAAAC
*
3760543 AATATA
1 TATATA
3760549 AAGTATATAG
Statistics
Matches: 428, Mismatches: 82, Indels: 124
0.68 0.13 0.20
Matches are distributed among these distances:
10 22 0.05
11 24 0.06
12 57 0.13
13 158 0.37
14 28 0.07
15 83 0.19
16 11 0.03
17 4 0.01
18 41 0.10
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:3760556 original size:31 final size:31
Alignment explanation
Indices: 3760492--3760557 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3760482 GCTACATATG
* * * ***
3760492 TATAAACTATATATGTAATCTATATAGTTTA
1 TATAAACTATATATATAAACAATATAAAGTA
3760523 TATAAACTATATATATAAACAATATAAAGTA
1 TATAAACTATATATATAAACAATATAAAGTA
3760554 TATA
1 TATA
3760558 GTTTATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (31 bp):
TATAAACTATATATATAAACAATATAAAGTA
Found at i:3760678 original size:56 final size:56
Alignment explanation
Indices: 3760605--3760744 Score: 191
Period size: 54 Copynumber: 2.6 Consensus size: 56
3760595 ATGTATAAAC
* * **
3760605 TATATAT-AGTTATTATAAACTATATATATGTAACCTATAGTTTATAAGGAATAGTT
1 TATATATAATTTA-TATAAACTATATATATGTAACCTATAGTCTATAAACAATAGTT
3760661 TATATATAATTTATATAAACTATATATA--TAACCTATAGTCTATAAACAATAGTT
1 TATATATAATTTATATAAACTATATATATGTAACCTATAGTCTATAAACAATAGTT
*
3760715 GATATATAATTTATATAAA-T-TATATATGTA
1 TATATATAATTTATATAAACTATATATATGTA
3760745 TAGACACAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
52 6 0.08
53 1 0.01
54 43 0.57
56 22 0.29
57 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (56 bp):
TATATATAATTTATATAAACTATATATATGTAACCTATAGTCTATAAACAATAGTT
Found at i:3760688 original size:13 final size:14
Alignment explanation
Indices: 3760672--3760713 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
3760662 ATATATAATT
3760672 TATATAAACTATA-
1 TATATAAACTATAG
*
3760685 TATATAACCTATAG
1 TATATAAACTATAG
* *
3760699 TCTATAAACAATAG
1 TATATAAACTATAG
3760713 T
1 T
3760714 TGATATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (14 bp):
TATATAAACTATAG
Found at i:3760883 original size:21 final size:21
Alignment explanation
Indices: 3760857--3760906 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
3760847 TAATCTATAG
3760857 TATATGTATACATGTAAACTA
1 TATATGTATACATGTAAACTA
3760878 TATATGTATACATGTAAACTA
1 TATATGTATACATGTAAACTA
3760899 TATATGTA
1 TATATGTA
3760907 ACTTATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATGTATACATGTAAACTA
Found at i:3761095 original size:21 final size:21
Alignment explanation
Indices: 3761069--3761111 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3761059 ATTATTGTAC
* *
3761069 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
3761090 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
3761111 T
1 T
3761112 TTGTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:3761172 original size:36 final size:36
Alignment explanation
Indices: 3761126--3761218 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
3761116 TAATTATCTT
*
3761126 AACTATAATTTATATTAATATAGTATATAGTTTATA
1 AACTATAATTTATATTAATATAGTAGATAGTTTATA
* *
3761162 AACTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATATAGTAGATAGTTTATA
* *
3761198 AACTATAGTTTACATTAATAT
1 AACTATAATTTATATTAATAT
3761219 TAACATATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGTAGATAGTTTATA
Found at i:3761280 original size:25 final size:25
Alignment explanation
Indices: 3761239--3761287 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3761229 ACAATAGTTA
*
3761239 TATTAATATAGTATATAGTATATAG
1 TATTAATATAATATATAGTATATAG
*
3761264 TATTAATATTAAT-TATAGTCTATA
1 TATTAATA-TAATATATAGTATATA
3761288 AACCATATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TATTAATATAATATATAGTATATAG
Found at i:3761309 original size:36 final size:34
Alignment explanation
Indices: 3761264--3761336 Score: 110
Period size: 36 Copynumber: 2.1 Consensus size: 34
3761254 TAGTATATAG
*
3761264 TATTAATATTAATTATAGTCTATAAACCATATACTA
1 TATTAATATTAACTATAGTCTATAAA-C-TATACTA
*
3761300 TATTAATATTAACTATAGTTTATAAACTATACTA
1 TATTAATATTAACTATAGTCTATAAACTATACTA
3761334 TAT
1 TAT
3761337 AATTTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 10 0.29
35 1 0.03
36 24 0.69
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (34 bp):
TATTAATATTAACTATAGTCTATAAACTATACTA
Found at i:3761446 original size:22 final size:21
Alignment explanation
Indices: 3761406--3761475 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
3761396 AACTACAAAT
*
3761406 TATAAACTATATT-ATATTAA
1 TATAATCTATATTAATATTAA
*
3761426 TATGAGT-TAATATTAATATTAA
1 TAT-AATCT-ATATTAATATTAA
3761448 TTATAATCTATATTAATATTAA
1 -TATAATCTATATTAATATTAA
3761470 TTATAA
1 -TATAA
3761476 ATGATAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.10
21 6 0.14
22 28 0.67
23 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (21 bp):
TATAATCTATATTAATATTAA
Found at i:3762008 original size:112 final size:109
Alignment explanation
Indices: 3761834--3762129 Score: 242
Period size: 112 Copynumber: 2.6 Consensus size: 109
3761824 TGTTCTTTGA
* * * *
3761834 AAAACCCTACATTTGATCTTCAAAACCACCAAATCCCAAACATTTTTCTATTTTTTCGATCAAGC
1 AAAACCCTTC-TTTGATCTTCAAAA-CACCAAAACCC--ATATTTTTCTATTTTTTCGATCAAAC
* * *
3761899 A-CATGAAA-TTTCT-TAACTTGTTCATCCGAGTTCATCCAAGTTCATAC-C
62 ACCA-AAAATTTTCTCT--CATGTTCATCCCAGTTCATCCAAGTTC-TACAC
* **
3761947 AAAACCCTTCTTTGATCTTCATAAACACCAAAACCCATATGTTTTCTTGTTTTTTTTATCAAACA
1 AAAACCCTTCTTTGATCTTCA-AAACACCAAAACCCATAT-TTTTC-TATTTTTTCGATCAAACA
** *
3762012 CCAAAAATTTTCTCTCATGTTCATCCCAGTTCATCCTTGTTCTTCAC
63 CCAAAAATTTTCTCTCATGTTCATCCCAGTTCATCCAAGTTCTACAC
* * * * *
3762059 AAAAACCTTCCATTGATCTTCACAAACATCAAAACACATATCATTTACTATTTTTT-GTATCAAA
1 AAAACCCTT-CTTTGATCTTCA-AAACACCAAAACCCATAT--TTTTCTATTTTTTCG-ATCAAA
*
3762123 CCCCAAA
61 CACCAAA
3762130 CCCAAGCAGT
Statistics
Matches: 150, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
110 3 0.02
111 7 0.05
112 70 0.47
113 65 0.43
114 5 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (109 bp):
AAAACCCTTCTTTGATCTTCAAAACACCAAAACCCATATTTTTCTATTTTTTCGATCAAACACCA
AAAATTTTCTCTCATGTTCATCCCAGTTCATCCAAGTTCTACAC
Found at i:3762113 original size:113 final size:112
Alignment explanation
Indices: 3761917--3762129 Score: 259
Period size: 113 Copynumber: 1.9 Consensus size: 112
3761907 TTTCTTAACT
* * * * *
3761917 TGTTCATCCGAGTTCATCCAAGTTCATACCAAAACCCTTCTTTGATCTTCATAAACACCAAAACC
1 TGTTCATCCCAGTTCATCCAAGTTCATACCAAAAACCTTCATTGATCTTCACAAACACCAAAACA
* * * *
3761982 CATATGTTTTCTTGTTTTTTTTATCAAACACCAAAAATTTTCTCTCA
66 CATATATTTACTTATTTTTTGTATCAAACACCAAAAATTTTCTCTCA
** * *
3762029 TGTTCATCCCAGTTCATCCTTGTTC-TTCACAAAAACCTTCCATTGATCTTCACAAACATCAAAA
1 TGTTCATCCCAGTTCATCCAAGTTCATAC-CAAAAACCTT-CATTGATCTTCACAAACACCAAAA
*
3762093 CACATATCATTTAC-TATTTTTTGTATCAAACCCCAAA
64 CACATAT-ATTTACTTATTTTTTGTATCAAACACCAAA
3762130 CCCAAGCAGT
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
111 2 0.02
112 31 0.37
113 47 0.56
114 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (112 bp):
TGTTCATCCCAGTTCATCCAAGTTCATACCAAAAACCTTCATTGATCTTCACAAACACCAAAACA
CATATATTTACTTATTTTTTGTATCAAACACCAAAAATTTTCTCTCA
Found at i:3762281 original size:6 final size:6
Alignment explanation
Indices: 3762272--3762371 Score: 83
Period size: 6 Copynumber: 16.7 Consensus size: 6
3762262 TCCAAACCTG
* * * **
3762272 AACCCT AACCCA AACCCA AACCCG AACCCG AACCCA AACCCA AAATCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
*** * * * * *
3762320 AACCCA AACATG AACCCG AACCCA AATCCA AACCAA AATCCA AACTCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
3762368 AACC
1 AACC
3762372 TAAAAAACCC
Statistics
Matches: 73, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.48, C:0.42, G:0.04, T:0.06
Consensus pattern (6 bp):
AACCCA
Found at i:3762281 original size:24 final size:24
Alignment explanation
Indices: 3762253--3762315 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3762243 TCATCTTCTA
* * *
3762253 TAACCTAAATCCAAACCTGAACCC
1 TAACCCAAACCCAAACCCGAACCC
3762277 TAACCCAAACCCAAACCCGAACCC
1 TAACCCAAACCCAAACCCGAACCC
*
3762301 GAACCCAAACCCAAA
1 TAACCCAAACCCAAA
3762316 ATCAAACCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.44, C:0.43, G:0.05, T:0.08
Consensus pattern (24 bp):
TAACCCAAACCCAAACCCGAACCC
Done.