Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 50
Found at i:3965490 original size:42 final size:42
Alignment explanation
Indices: 3965435--3965808 Score: 526
Period size: 42 Copynumber: 8.9 Consensus size: 42
3965425 GAAGGAAGTA
*
3965435 TTACCAGGT-CCTTTGTTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
3965476 TTCCCAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
*
3965518 TTACCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
3965560 TTACCAGGTCTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
3965602 TTATCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * *
3965644 TTCCCAGGTCCTTTTGCTGTGTGCGAA-GGCAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
*
3965686 TTACTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * *
3965728 TTCCCAGGTCCCTTTGCTGTGTGCAA-GGAAAACCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * *
3965769 TTTCCTAGG-CTCCTCTGCT-TGTGCACAGGTTAAGCCTTAC
1 TTACC-AGGTC-CCTTTGCTGTGTGCA-AGGGTAAGCCTTAC
3965809 TGGTGTATAG
Statistics
Matches: 299, Mismatches: 25, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.12
42 250 0.84
43 13 0.04
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (42 bp):
TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
Found at i:3971840 original size:7 final size:7
Alignment explanation
Indices: 3971828--3971867 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
3971818 GACCCGACCC
3971828 GACCGTT
1 GACCGTT
3971835 GACCGTT
1 GACCGTT
*
3971842 AACCGTT
1 GACCGTT
3971849 GACCGTT
1 GACCGTT
3971856 GACCGTT
1 GACCGTT
3971863 GACCG
1 GACCG
3971868 GTGCTATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:3971928 original size:29 final size:29
Alignment explanation
Indices: 3971867--3971933 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3971857 ACCGTTGACC
* * * *
3971867 GGTGCTATTCTGGGAATTTATTCAATTTT
1 GGTGCTATTCTAGGAATTAATTCAATATG
3971896 GGTGCTATTCTAGGAATTAATTCGAA-ATG
1 GGTGCTATTCTAGGAATTAATTC-AATATG
3971925 GGTGCTATT
1 GGTGCTATT
3971934 TTGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTAGGAATTAATTCAATATG
Found at i:3972054 original size:30 final size:29
Alignment explanation
Indices: 3971986--3972054 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
3971976 TTTGATTTTT
* *
3971986 GGTGCTATTATGGGAATTAATTAAAAATA
1 GGTGCTATTTTGGGAATTAATTAAAAAGA
* * *
3972015 GGTGATATTTTGGTAATTAATTCAAAAAGG
1 GGTGCTATTTTGGGAATTAATT-AAAAAGA
3972045 GGTGCTATTT
1 GGTGCTATTT
3972055 CTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTAAAAAGA
Found at i:3973024 original size:42 final size:42
Alignment explanation
Indices: 3972974--3973479 Score: 766
Period size: 42 Copynumber: 12.0 Consensus size: 42
3972964 GAAGGAAGTA
*
3972974 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAAAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
3973016 TTCCCAGGTCCCTTTGTTGTGTGCGAA-GGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
* *
3973058 TTACCATGTCCCTTTACTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
3973100 TTACCAGGTCCCTTTGCTGTGTGCAAGAGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
3973142 TTATCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
3973184 TTCCCAGGTCCCTTTGATGTGTGCGAA-GGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
* *
3973226 TTACCAGGTCCCTTTGATGTGTGCAATGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
3973268 TTACTAGGTCCCTTTGCTGTGTGCAAGAGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
3973310 TTATCAGGTCCCTTTGCTGTTTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
3973352 TTCCCAGGTCCCTTTGATGTGTGCGAA-GGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
*
3973394 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * * *
3973436 TTCCCAAGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
3973478 TT
1 TT
3973480 TCCTAGGCTC
Statistics
Matches: 422, Mismatches: 36, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
41 6 0.01
42 410 0.97
43 6 0.01
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (42 bp):
TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
Found at i:3990261 original size:12 final size:12
Alignment explanation
Indices: 3990215--3990269 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
3990205 TAACTAATTT
3990215 AATAATTTTT-A
1 AATAATTTTTAA
3990226 AAT-ATTTTTAAA
1 AATAATTTTT-AA
*
3990238 ATAGTAAATTTTTTA
1 A-A-T-AATTTTTAA
3990253 AATAATTTTTAA
1 AATAATTTTTAA
3990265 AATAA
1 AATAA
3990270 AAGTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 6 0.17
11 3 0.08
12 15 0.42
13 2 0.06
14 2 0.06
15 2 0.06
16 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
AATAATTTTTAA
Found at i:3991444 original size:82 final size:82
Alignment explanation
Indices: 3991252--3991703 Score: 313
Period size: 82 Copynumber: 5.5 Consensus size: 82
3991242 TCCAAACGCC
* * * * * *
3991252 ACAAAATAGTAACTTTAGTGGCGTTTCTT-TAAAAACGCCTCAATAGTATTCATCCATAGTGGCG
1 ACAAATTAGT-ACTTTAGCGGCGTTT-TTATATAAACGCCGCAATAG-GTTCATCTATAGTGGCG
* *
3991316 TTTTTCTTGAA-AAACGCCACA
63 -TTTT-TTCAATAAACGCCGCA
* * *** *
3991337 ACAGAGTAGTACTTTAGCATAGTTTTTATATAAACGCCGCAATAGGTCCATCTATAGTGGCGTTT
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATAGGTTCATCTATAGTGGCGTTT
*
3991402 TTTCAATAAACACCGCA
66 TTTCAATAAACGCCGCA
* * * * * * *
3991419 ACAAATTAGTACTTTAGCGGTGTTTTTATATAAATGTCGTAATAGGGTTCACCTATAATGGTG-T
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATA-GGTTCATCTATAGTGGCGTT
*
3991483 TTTTCAATAAATGCCGCA
65 TTTTCAATAAACGCCGCA
* * * * * * * *
3991501 ATAAATTAGAACTTTAGCGGCATTTTTACATAAATGCTG---TAGGGTTCACCTATAGTGGTGTT
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATA-GGTTCATCTATAGTGGCGTT
****
3991563 TTTTCAATAAACAATACA
65 TTTTCAATAAACGCCGCA
* * * ** * * * * * * *
3991581 ACATATTAGAACTTTAGTGGTATTTTTATACAAACACCGTAATAGTATTTATCTATAATGGCCTT
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATAG-GTTCATCTATAGTGGCGTT
* *
3991646 TTTTCAATAAGCGTCGCA
65 TTTTCAATAAACGCCGCA
* * * *
3991664 ATATATTAGTACTTTAGCGGCGTTTATATACAAACGCCGC
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGC
3991704 TAAAGACACA
Statistics
Matches: 290, Mismatches: 69, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
79 20 0.07
80 44 0.15
81 4 0.01
82 98 0.34
83 90 0.31
84 26 0.09
85 8 0.03
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (82 bp):
ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATAGGTTCATCTATAGTGGCGTTT
TTTCAATAAACGCCGCA
Found at i:3991566 original size:162 final size:162
Alignment explanation
Indices: 3991388--3991684 Score: 380
Period size: 162 Copynumber: 1.8 Consensus size: 162
3991378 ATAGGTCCAT
* * * * *
3991388 CTATAGTGGCGTTTTTTCAATAAACACCGCAACAAATTAGTACTTTAGCGGTGTTTTTATATAAA
1 CTATAGTGGCGTTTTTTCAATAAACAACACAACAAATTAGAACTTTAGCGGTATTTTTATACAAA
*** * *
3991453 TGTCGTAATAGGGTTCACCTATAATGG-TGTTTTTCAATAAATGCCGCAATAAATTAGAACTTTA
66 CACCGTAATAGGATTCACCTATAATGGCT-TTTTTCAATAAACGCCGCAATAAATTAGAACTTTA
3991517 GCGGCATTTTTACATAAATGCTGTAGGGTTCAC
130 GCGGCATTTTTACATAAATGCTGTAGGGTTCAC
* * * *
3991550 CTATAGTGGTGTTTTTTCAATAAACAATACAACATATTAGAACTTTAGTGGTATTTTTATACAAA
1 CTATAGTGGCGTTTTTTCAATAAACAACACAACAAATTAGAACTTTAGCGGTATTTTTATACAAA
* * * * * * *
3991615 CACCGTAATAGTATTTATCTATAATGGCCTTTTTTCAATAAGCGTCGCAATATATTAGTACTTTA
66 CACCGTAATAGGATTCACCTATAATGG-CTTTTTTCAATAAACGCCGCAATAAATTAGAACTTTA
3991680 GCGGC
130 GCGGC
3991685 GTTTATATAC
Statistics
Matches: 112, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
162 76 0.68
163 35 0.31
164 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (162 bp):
CTATAGTGGCGTTTTTTCAATAAACAACACAACAAATTAGAACTTTAGCGGTATTTTTATACAAA
CACCGTAATAGGATTCACCTATAATGGCTTTTTTCAATAAACGCCGCAATAAATTAGAACTTTAG
CGGCATTTTTACATAAATGCTGTAGGGTTCAC
Found at i:4003723 original size:261 final size:259
Alignment explanation
Indices: 4003286--4003823 Score: 968
Period size: 261 Copynumber: 2.1 Consensus size: 259
4003276 GAATGATTCC
4003286 ATATGTAACGACAAATATCGATATAAGACAACGACACACACATAACTATCATAGAGATTGGGAAA
1 ATATGTAACGACAAATATCGATATAAGACAACGACACACACATAACTATCATAGAGATTGGGAAA
4003351 TGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGTGT
66 TGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGTGT
* *
4003416 TAAATTTAAGGAAATTTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTGATAAT
131 TAAATTTAAGGAAAATTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAATAAT
4003481 ATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATACA
196 ATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATACA
4003545 ATATGTAACGACAAATATCGATATAAGACAACGACAAACACACATAACTATCATAGAGATTGGGA
1 ATATGTAACGACAAATATCGATATAAGACAACGAC--ACACACATAACTATCATAGAGATTGGGA
*
4003610 AATGATCAACACATTCAGAGTCTGTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGT
64 AATGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGT
* *
4003675 GTTAAATTTATGGAAAATTTATAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAATA
129 GTTAAATTTAAGGAAAATTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAATA
* * * *
4003740 ATATAATTAACGACAAATATTATTTTATAATAACAACAAATACATATAACCATATCTGATGATGC
194 ATATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATAC
4003805 A
259 A
*
4003806 ATATGTAACGAAAAATAT
1 ATATGTAACGACAAATAT
4003824 TGTTATAAAA
Statistics
Matches: 267, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
259 35 0.13
261 232 0.87
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (259 bp):
ATATGTAACGACAAATATCGATATAAGACAACGACACACACATAACTATCATAGAGATTGGGAAA
TGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGTGT
TAAATTTAAGGAAAATTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAATAAT
ATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATACA
Found at i:4005782 original size:24 final size:25
Alignment explanation
Indices: 4005746--4005792 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
4005736 AAATTTTTAG
4005746 AAAAAAATAAAATAGAAAAATATTT
1 AAAAAAATAAAATAGAAAAATATTT
* *
4005771 AAAAAAGT-AAATATAAAAATAT
1 AAAAAAATAAAATAGAAAAATAT
4005793 GAAGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAAAAATAAAATAGAAAAATATTT
Found at i:4008739 original size:247 final size:248
Alignment explanation
Indices: 4008301--4008790 Score: 889
Period size: 247 Copynumber: 2.0 Consensus size: 248
4008291 AATCGATATT
4008301 CTTTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGT
1 CTTTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGT
4008366 AATAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTT
66 AATAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTT
4008431 TATAATTTTAATAATAATAATATTTTTTTTATTTTCAAACAATTTTAAAATGTCAAAAAAATAAA
131 TATAATTTTAATAATAATAATATTTTTTTTATTTTCAAACAATTTTAAAATGTCAAAAAAATAAA
4008496 ATACTTTAATATTCTTTAAATTTACTATTTTGTATAATTTTGAAAATAATAAA
196 ATACTTTAATATTCTTTAAATTTACTATTTTGTATAATTTTGAAAATAATAAA
* *
4008549 CTTTTTTAATTTGCATAAGTAACGAGTCATAATTTAAA-AAGAAA-TTGAACTCGAATAAGTGTG
1 CTTTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAA-AAATTTGAACTCGAATAAGTGTG
*
4008612 TAATAGTTTTATGATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTT
65 TAATAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTT
4008677 TTATAATTTTAATAATAATTAATA-TTTTTTTATTTTCAAACAATTTTAAAATGTTC-AAAAAAT
130 TTATAATTTTAATAATAA-TAATATTTTTTTTATTTTCAAACAATTTTAAAATG-TCAAAAAAAT
*
4008740 AAAATATTTTAATATTCTTTAAATTTACTATTTTGTATAATTTTGAAAATA
193 AAAATACTTTAATATTCTTTAAATTTACTATTTTGTATAATTTTGAAAATA
4008791 TTATTATTCT
Statistics
Matches: 235, Mismatches: 4, Indels: 7
0.96 0.02 0.03
Matches are distributed among these distances:
247 189 0.80
248 46 0.20
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (248 bp):
CTTTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGT
AATAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTT
TATAATTTTAATAATAATAATATTTTTTTTATTTTCAAACAATTTTAAAATGTCAAAAAAATAAA
ATACTTTAATATTCTTTAAATTTACTATTTTGTATAATTTTGAAAATAATAAA
Found at i:4008880 original size:16 final size:17
Alignment explanation
Indices: 4008861--4008894 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4008851 AAAAAATAAT
4008861 TAATTT-AATATTTTTA
1 TAATTTAAATATTTTTA
4008877 TAATTTAAAATATTTTTA
1 TAATTT-AAATATTTTTA
4008895 AAATAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTAAATATTTTTA
Found at i:4022192 original size:65 final size:65
Alignment explanation
Indices: 4022039--4022195 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 65
4022029 AATAGCAAGA
* * * *
4022039 GTGCATCGATGCATGACTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTTG
1 GTGCATCGATGCATGATTGGTGCATCGATGCATCAAATACATTCGATGTTTTAATAACATCCATG
* * * * * *
4022104 GTGTATCGGTGCATGGTAT-GTGCATCGATGCATGAAATACATTCGATG-TTTAATTTA-ATTCA
1 GTGCATCGATGCATGAT-TGGTGCATCGATGCATCAAATACATTCGATGTTTTAA-TAACATCCA
4022166 TG
64 TG
4022168 GTGCATCGATGCATGAATTGGTGCATCG
1 GTGCATCGATGCATG-ATTGGTGCATCG
4022196 CTCTGAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
64 23 0.31
65 51 0.68
66 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATGATTGGTGCATCGATGCATCAAATACATTCGATGTTTTAATAACATCCATG
Found at i:4025923 original size:20 final size:20
Alignment explanation
Indices: 4025898--4025939 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4025888 TAAAGATAAA
4025898 GAAGACACAAAATTTACGTG
1 GAAGACACAAAATTTACGTG
4025918 GAAGACACAAAATTTACGTG
1 GAAGACACAAAATTTACGTG
4025938 GA
1 GA
4025940 GAACCCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.19
Consensus pattern (20 bp):
GAAGACACAAAATTTACGTG
Found at i:4027451 original size:76 final size:75
Alignment explanation
Indices: 4027370--4027517 Score: 226
Period size: 76 Copynumber: 2.0 Consensus size: 75
4027360 TAAACTCAAA
4027370 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
4027434 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * * *
4027446 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTATATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
4027511 TTAATTA
66 TTAATTA
4027518 GGATTTAGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 24 0.36
76 42 0.64
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:4027543 original size:75 final size:76
Alignment explanation
Indices: 4027397--4027544 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 76
4027387 AACATTATAT
* * *
4027397 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTA
4027462 TATATTTTATC
66 TATATTTTATC
* *
4027473 TTTATCTTTGTATTTTAGTTTATATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATTATATT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTAT-TT
4027537 AT-TATTTT
65 ATATATTTT
4027545 TAGATATTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 36 0.55
76 30 0.45
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (76 bp):
TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTA
TATATTTTATC
Found at i:4027546 original size:76 final size:76
Alignment explanation
Indices: 4027397--4027546 Score: 232
Period size: 76 Copynumber: 2.0 Consensus size: 76
4027387 AACATTATAT
* *
4027397 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTT
4027462 TATATTTTATC
66 TATATTTTATC
* *
4027473 TTTATCTTTGTATTTTAGTTTATATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATTATATT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTAT-TT
4027537 ATTAT-TTTTA
65 -TTATATTTTA
4027547 GATATTTTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
75 30 0.44
76 34 0.50
77 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (76 bp):
TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTT
TATATTTTATC
Found at i:4028275 original size:16 final size:18
Alignment explanation
Indices: 4028254--4028296 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
4028244 ATCCCCTTTT
4028254 TATTTATTA-C-TATTAA
1 TATTTATTATCATATTAA
*
4028270 TATTTATTATCATATTAT
1 TATTTATTATCATATTAA
4028288 TATTT-TTAT
1 TATTTATTAT
4028297 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 10 0.42
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATTATCATATTAA
Found at i:4033760 original size:8 final size:9
Alignment explanation
Indices: 4033733--4033759 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4033723 CATTTCGTTA
4033733 TATTTTTTT
1 TATTTTTTT
4033742 TATTTTTTT
1 TATTTTTTT
4033751 TATTTTTTT
1 TATTTTTTT
4033760 AACGAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TATTTTTTT
Found at i:4033940 original size:53 final size:50
Alignment explanation
Indices: 4033846--4033947 Score: 125
Period size: 53 Copynumber: 2.0 Consensus size: 50
4033836 AAATATTTAA
*
4033846 CGAAAAAAAGTGCAGAAAAACAGACTTGGTTCAAACTGTGCAGAAAAATT
1 CGAAAAAAAGTGCAGAAAAACAGACTTGGTTCAAACAGTGCAGAAAAATT
* **
4033896 CGAACAAAACAGTGCAGAAAAAACTA-ATTTGGTTTGAACAGTGCAGAAAAAT
1 CGAA-AAAA-AGTGCAG-AAAAAC-AGACTTGGTTCAAACAGTGCAGAAAAAT
4033948 ACACAGCAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 4 0.09
51 4 0.09
52 7 0.16
53 28 0.64
54 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.19
Consensus pattern (50 bp):
CGAAAAAAAGTGCAGAAAAACAGACTTGGTTCAAACAGTGCAGAAAAATT
Found at i:4036411 original size:17 final size:18
Alignment explanation
Indices: 4036368--4036430 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 18
4036358 TAAGTTTATC
4036368 TTATCTTAATCTCTTAATTTGT
1 TTAT-TTAAT-TCTT-ATTT-T
4036390 TTATTTAATT-TT-TTTCT
1 TTATTTAATTCTTATTT-T
4036407 TTATTTAATTCTTATTTT
1 TTATTTAATTCTTATTTT
4036425 TTATTT
1 TTATTT
4036431 TAACCACAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 14 0.37
18 9 0.24
19 5 0.13
20 1 0.03
21 5 0.13
22 4 0.11
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.70
Consensus pattern (18 bp):
TTATTTAATTCTTATTTT
Found at i:4040585 original size:13 final size:13
Alignment explanation
Indices: 4040563--4040612 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
4040553 TGATTCCAGT
*
4040563 AACTGGTTTGACA
1 AACTGATTTGACA
**
4040576 AACTGATTTGATT
1 AACTGATTTGACA
* *
4040589 ATCTGATTTGAGA
1 AACTGATTTGACA
4040602 AACTGATTTGA
1 AACTGATTTGA
4040613 TTATTCTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (13 bp):
AACTGATTTGACA
Found at i:4043768 original size:3 final size:3
Alignment explanation
Indices: 4043760--4043851 Score: 134
Period size: 3 Copynumber: 30.7 Consensus size: 3
4043750 TTTAATATAT
4043760 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
4043805 TAG TAA TATA TAA TAA T-A TAA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4043850 TA
1 TA
4043852 TGGATAAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.05
3 71 0.88
4 6 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4044224 original size:40 final size:40
Alignment explanation
Indices: 4044180--4044282 Score: 206
Period size: 40 Copynumber: 2.6 Consensus size: 40
4044170 AAGTTGAACA
4044180 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
4044220 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
4044260 AGTTCTTCTTATTATGAACTTCT
1 AGTTCTTCTTATTATGAACTTCT
4044283 CTGGAAAAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.18, C:0.19, G:0.10, T:0.52
Consensus pattern (40 bp):
AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
Found at i:4044452 original size:113 final size:113
Alignment explanation
Indices: 4044222--4044731 Score: 806
Period size: 113 Copynumber: 4.5 Consensus size: 113
4044212 TTCAGATGAG
* * *
4044222 TTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
4044286 GAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
4044334 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * * *
4044399 GAAAGGCTGATCCATCAAATGATGGACTCAGGTAAAAGGTTGAAAAAA
66 GAAAAGATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
*
4044447 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
4044512 GAAAAGTTAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
*
4044560 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
4044625 GAAAAGATAATTCATCAAGTGATAGATTTAAGAAAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGAT-GAATTCAGATAAAAGGTTGAACAAA
4044674 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
4044732 CGAACTGGAA
Statistics
Matches: 366, Mismatches: 30, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
112 54 0.15
113 234 0.64
114 78 0.21
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
Found at i:4045559 original size:84 final size:84
Alignment explanation
Indices: 4045451--4045869 Score: 765
Period size: 84 Copynumber: 5.0 Consensus size: 84
4045441 GATCATGCAG
* * *
4045451 TTCATCTT-TTAATTCCAACGATTGGTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCC
1 TTCATCTTCTAAATT-CAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
4045515 AGAAGATGCTATTGAGCACA
65 AGAAGATGCTATTGAGCACA
*
4045535 TTCATCTTCTAAATTCAATGATTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
4045600 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
4045619 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTC-AAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
4045683 GAAGATGCTATTGAG--CA
66 GAAGATGCTATTGAGCACA
4045700 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
4045765 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
4045784 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
4045849 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
4045868 TT
1 TT
4045870 ATATTTGTTC
Statistics
Matches: 326, Mismatches: 5, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
81 53 0.16
82 28 0.09
83 28 0.09
84 212 0.65
85 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (84 bp):
TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGAGCACA
Found at i:4045738 original size:165 final size:166
Alignment explanation
Indices: 4045451--4045865 Score: 753
Period size: 165 Copynumber: 2.5 Consensus size: 166
4045441 GATCATGCAG
* * *
4045451 TTCATCTT-TTAATTCCAACGATTGGTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCC
1 TTCATCTTCTAAATT-CAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
*
4045515 AGAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTTCAACCAGATCAGA
65 AGAAGATGCTATTGAG--CATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGA
4045580 TAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
128 TAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
4045619 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTC-AAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
4045683 GAAGATGCTATTGAGCATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAA
66 GAAGATGCTATTGAGCATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAA
4045748 CTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
131 CTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
4045784 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
4045849 GAAGATGCTATTGAGCA
66 GAAGATGCTATTGAGCA
4045866 CATTATATTT
Statistics
Matches: 241, Mismatches: 4, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
165 136 0.56
166 30 0.12
167 28 0.12
168 42 0.17
169 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29
Consensus pattern (166 bp):
TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGAGCATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAA
CTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
Found at i:4047034 original size:13 final size:12
Alignment explanation
Indices: 4047011--4047072 Score: 63
Period size: 13 Copynumber: 4.9 Consensus size: 12
4047001 ACCCCCCCCC
4047011 CTTTATTTTTCTT
1 CTTT-TTTTTCTT
4047024 CTTCTTTTTTCTTT
1 CTT-TTTTTTC-TT
*
4047038 CTTTTTTTTTTT
1 CTTTTTTTTCTT
4047050 CCTTTTTTTTC-T
1 -CTTTTTTTTCTT
*
4047062 ATTTTTTTTCT
1 CTTTTTTTTCT
4047073 ATTTTCTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
11 9 0.21
12 3 0.07
13 24 0.57
14 6 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (12 bp):
CTTTTTTTTCTT
Found at i:4047039 original size:11 final size:11
Alignment explanation
Indices: 4047025--4047091 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 11
4047015 ATTTTTCTTC
4047025 TTCTTTTTTCT
1 TTCTTTTTTCT
*
4047036 TTCTTTTTTTTT
1 TTC-TTTTTTCT
*
4047048 TTCCTTTTT-T
1 TTCTTTTTTCT
4047058 TTCTATTTTT-T
1 TTCT-TTTTTCT
*
4047069 TTCTATTTTCT
1 TTCTTTTTTCT
*
4047080 TTCTTTTCTCT
1 TTCTTTTTTCT
4047091 T
1 T
4047092 AAGCCTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.17
11 29 0.62
12 10 0.21
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:4047042 original size:22 final size:22
Alignment explanation
Indices: 4047017--4047088 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 22
4047007 CCCCCTTTAT
*
4047017 TTTTCTTCTTCTTTTTTCTTTC
1 TTTTCTTTTTCTTTTTTCTTTC
* *
4047039 TTTTTTTTTTTCCTTTTT-TTTC
1 -TTTTCTTTTTCTTTTTTCTTTC
*
4047061 TATTT-TTTTTCTATTTTCTTTC
1 T-TTTCTTTTTCTTTTTTCTTTC
4047083 TTTTCT
1 TTTTCT
4047089 CTTAAGCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 14 0.34
22 13 0.32
23 14 0.34
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTCTTTTTTCTTTC
Found at i:4050613 original size:10 final size:10
Alignment explanation
Indices: 4050595--4050628 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4050585 ATTTATGAAA
*
4050595 TAAATAAATG
1 TAAAAAAATG
4050605 TAAAAAAATG
1 TAAAAAAATG
*
4050615 TAAGAAAATG
1 TAAAAAAATG
4050625 TAAA
1 TAAA
4050629 GAATGATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (10 bp):
TAAAAAAATG
Found at i:4054339 original size:14 final size:15
Alignment explanation
Indices: 4054320--4054351 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4054310 TTTTTTTTTA
4054320 AATTTTAA-TTAATG
1 AATTTTAACTTAATG
4054334 AATTTTAACTTAATG
1 AATTTTAACTTAATG
4054349 AAT
1 AAT
4054352 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTTTAACTTAATG
Found at i:4059771 original size:3 final size:3
Alignment explanation
Indices: 4059763--4059874 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
4059753 TTAATATATT
*
4059763 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4059811 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4059859 TAT TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TA
4059875 TGGATAAAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.02
3 100 0.98
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4072926 original size:84 final size:83
Alignment explanation
Indices: 4072837--4072994 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 83
4072827 AATAAATAAA
*
4072837 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAGA-TAAA
1 TAAATCCTAATTAAAACACTTAAAACTATTT-AACT-AAATACCTAAAAC-AAGATAAAATTAAA
4072901 AT-ATAATAAAAATAATAACC
63 ATAATAATAAAAATAATAACC
*
4072921 TAAATCCTAATTAAAATACTTAAAACTATTTAACTAAATACCTAAAACAAGATAAAATTAAAATA
1 TAAATCCTAATTAAAACACTTAAAACTATTTAACTAAATACCTAAAACAAGATAAAATTAAAATA
*
4072986 ATCATAAAA
66 ATAATAAAA
4072995 CATGAGTTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
81 8 0.12
82 19 0.28
83 12 0.17
84 30 0.43
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.27
Consensus pattern (83 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAACTAAATACCTAAAACAAGATAAAATTAAAATA
ATAATAAAAATAATAACC
Found at i:4074680 original size:23 final size:24
Alignment explanation
Indices: 4074644--4074688 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4074634 AAGATAAATT
* *
4074644 AAAATAAATAAATAATTATAAAAA
1 AAAAAAAATAAATAATAATAAAAA
4074668 AAAAAAAAT-AATAATAATAAA
1 AAAAAAAATAAATAATAATAAA
4074689 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAAAAATAAATAATAATAAAAA
Found at i:4077358 original size:19 final size:19
Alignment explanation
Indices: 4077334--4077370 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4077324 GTTATATTCG
4077334 AACTTTTCTGCACAGTTCA
1 AACTTTTCTGCACAGTTCA
* *
4077353 AACTTTTTTGCACTGTTC
1 AACTTTTCTGCACAGTTC
4077371 GAACCAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (19 bp):
AACTTTTCTGCACAGTTCA
Found at i:4077689 original size:19 final size:18
Alignment explanation
Indices: 4077664--4077717 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
4077654 ATATCAAAGA
*
4077664 AAAATAAAAACAAAAATG
1 AAAATAAAAATAAAAATG
* *
4077682 AATCATAAAAATAAAATTG
1 AA-AATAAAAATAAAAATG
4077701 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
4077718 TGAACAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (18 bp):
AAAATAAAAATAAAAATG
Found at i:4077695 original size:6 final size:6
Alignment explanation
Indices: 4077663--4077717 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
4077653 AATATCAAAG
* ** * *
4077663 AAAAAT AAAAAC AAAAAT GAATCAT AAAAAT AAAATT GAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
4077712 AAAAAT
1 AAAAAT
4077718 TGAACAAACG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 34 0.89
7 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:4077718 original size:19 final size:19
Alignment explanation
Indices: 4077664--4077721 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
4077654 ATATCAAAGA
*
4077664 AAAATAAAAACAAAAA-TG
1 AAAATAAAAATAAAAATTG
*
4077682 AATCATAAAAAT-AAAATTG
1 AA-AATAAAAATAAAAATTG
4077701 AAAATAAAAATAAAAATTG
1 AAAATAAAAATAAAAATTG
4077720 AA
1 AA
4077722 CAAACGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.41
19 20 0.59
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAAAAATAAAAATTG
Found at i:4081626 original size:19 final size:21
Alignment explanation
Indices: 4081604--4081647 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4081594 TGCAATTAGC
4081604 TTTCCT-GGACGTAACCA-CT
1 TTTCCTAGGACGTAACCATCT
*
4081623 TTTCCTAGGACGTGACCATCT
1 TTTCCTAGGACGTAACCATCT
4081644 TTTC
1 TTTC
4081648 TGTAATTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (21 bp):
TTTCCTAGGACGTAACCATCT
Found at i:4084593 original size:20 final size:20
Alignment explanation
Indices: 4084568--4084607 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4084558 TGTGTCGTTC
4084568 TAGCCG-TTGGGGATGATTTT
1 TAGCCGTTTGGGGATG-TTTT
4084588 TAGCCGTTTGGGGATGTTTT
1 TAGCCGTTTGGGGATGTTTT
4084608 CTCTACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.12, C:0.10, G:0.35, T:0.42
Consensus pattern (20 bp):
TAGCCGTTTGGGGATGTTTT
Found at i:4084883 original size:20 final size:20
Alignment explanation
Indices: 4084855--4084965 Score: 150
Period size: 20 Copynumber: 5.5 Consensus size: 20
4084845 TCCTAATTCA
4084855 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* ** *
4084875 CAATACGAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
4084896 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
4084916 CAATGCGAATATGTAAATCG
1 CAATGCGAATACGTAAATCG
*
4084936 CAATGTGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
4084956 CAATGTGAAT
1 CAATGCGAAT
4084966 CTAACTATCG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 63 0.80
21 16 0.20
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:4084946 original size:40 final size:41
Alignment explanation
Indices: 4084855--4084965 Score: 170
Period size: 40 Copynumber: 2.7 Consensus size: 41
4084845 TCCTAATTCA
* *
4084855 CAATGCGAATACGTAAATCGCAATACGAATTTGGAAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATATGGAAAATCG
*
4084896 CAATGCGAATACGTAAATCGCAATGCGAATAT-GTAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATATGGAAAATCG
* *
4084936 CAATGTGAATACGTAAATCGCAATGTGAAT
1 CAATGCGAATACGTAAATCGCAATGCGAAT
4084966 CTAACTATCG
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 35 0.54
41 30 0.46
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (41 bp):
CAATGCGAATACGTAAATCGCAATGCGAATATGGAAAATCG
Found at i:4084975 original size:20 final size:20
Alignment explanation
Indices: 4084952--4085039 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
4084942 GAATACGTAA
* *
4084952 ATCGCAATGTGAATCTAACT
1 ATCGCAATGAGAATCTGACT
4084972 ATCGCAATGCA-AATCTGACT
1 ATCGCAATG-AGAATCTGACT
* *
4084992 ATCACAATGAGATTCTGACT
1 ATCGCAATGAGAATCTGACT
* * *
4085012 ATTGCAACGAGATTCTGACT
1 ATCGCAATGAGAATCTGACT
4085032 ATCGCAAT
1 ATCGCAAT
4085040 ACTGAATTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 56 0.98
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (20 bp):
ATCGCAATGAGAATCTGACT
Found at i:4084976 original size:40 final size:38
Alignment explanation
Indices: 4084855--4084981 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 38
4084845 TCCTAATTCA
* *
4084855 CAATGCGAATACGTAAATCGCAATACGAATTTGGAAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATCT---AAATCG
*
4084896 CAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCG
1 CAATGCGAATACGTAAATCGCAATGCG-A-ATCTAAATCG
* *
4084936 CAATGTGAATACGTAAATCGCAATGTGAATCTAACTATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATCTAA--ATCG
4084976 CAATGC
1 CAATGC
4084982 AAATCTGACT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
38 5 0.07
39 1 0.01
40 40 0.53
41 26 0.34
42 1 0.01
43 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (38 bp):
CAATGCGAATACGTAAATCGCAATGCGAATCTAAATCG
Found at i:4088197 original size:31 final size:32
Alignment explanation
Indices: 4088162--4088228 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
4088152 GCAGAAATAC
4088162 ATCGCAACG-GAGAATCGCAATGCG-AATGAAA
1 ATCGCAACGAGAGAAT-GCAATGCGAAATGAAA
*
4088193 ATCGCAACGAGTGAATGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATGCAATGCG-AAATGAAA
4088226 ATC
1 ATC
4088229 AACGCAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 17 0.53
32 5 0.16
33 10 0.31
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (32 bp):
ATCGCAACGAGAGAATGCAATGCGAAATGAAA
Found at i:4088285 original size:34 final size:34
Alignment explanation
Indices: 4088247--4088342 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
4088237 TTTAGTTTCG
4088247 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
4088281 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
4088314 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
4088343 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:4088288 original size:14 final size:14
Alignment explanation
Indices: 4088269--4088322 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
4088259 CATTTTCGCA
4088269 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
4088283 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
4088300 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
4088316 TTGCGAT
1 TTGCGAT
4088323 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:4090431 original size:20 final size:20
Alignment explanation
Indices: 4090408--4090536 Score: 150
Period size: 20 Copynumber: 6.5 Consensus size: 20
4090398 GAAACTTAAA
4090408 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
4090428 ATCGCAAAGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
4090448 ATCGCAAAGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
4090468 ATCACAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
4090488 ATCGCAATGTGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
4090508 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
4090528 ATCGCAACG
1 ATCGCAACG
4090537 AGAGAATCGC
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 95 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4090624 original size:20 final size:20
Alignment explanation
Indices: 4090601--4090665 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
4090591 CAAATTCACT
4090601 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
4090621 TTGCGATAGTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
4090640 -TGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
4090659 TTGCGAT
1 TTGCGAT
4090666 TTTGTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.27
19 12 0.29
20 18 0.44
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:4090645 original size:18 final size:19
Alignment explanation
Indices: 4090601--4090653 Score: 90
Period size: 18 Copynumber: 2.8 Consensus size: 19
4090591 CAAATTCACT
4090601 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCA-TTTCGCA
4090621 TTGCGATAGTCATTTCGCA
1 TTGCGATAGTCATTTCGCA
4090640 -TGCGATAGTCATTT
1 TTGCGATAGTCATTT
4090654 TTGCGTTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 14 0.42
19 7 0.21
20 12 0.36
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
TTGCGATAGTCATTTCGCA
Found at i:4090697 original size:33 final size:34
Alignment explanation
Indices: 4090601--4090732 Score: 122
Period size: 33 Copynumber: 3.8 Consensus size: 34
4090591 CAAATTCACT
* *
4090601 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTCG
1 TTGCAATAGTCATTTTCGCATTGCGAT--TC-TCTCG
* * * * * * *
4090638 CATGCGATAGTCATTTTTGCGTTGCGATTTTGTTG
1 -TTGCAATAGTCATTTTCGCATTGCGATTCTCTCG
**
4090673 TTGCAATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCAATAGTCATTTTCGCATTGCGATTCTCTCG
4090706 TTGCAATAGTCATTTTCGCATTGCGAT
1 TTGCAATAGTCATTTTCGCATTGCGAT
4090733 AATAAACTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
33 26 0.34
34 22 0.29
35 3 0.04
36 1 0.01
38 24 0.32
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCAATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:4092607 original size:20 final size:20
Alignment explanation
Indices: 4092582--4092631 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
4092572 CTGAAACTTT
4092582 AAATCGCAACACAAAAATGA
1 AAATCGCAACACAAAAATGA
*
4092602 AAATCGCAACACGAAAATGA
1 AAATCGCAACACAAAAATGA
**
4092622 CTATCGCAAC
1 AAATCGCAAC
4092632 GGGAATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACAAAAATGA
Found at i:4093058 original size:22 final size:22
Alignment explanation
Indices: 4092996--4093061 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
4092986 TTTGACCGAA
* *
4092996 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
4093018 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
4093040 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
4093062 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:4093268 original size:20 final size:20
Alignment explanation
Indices: 4093240--4093370 Score: 226
Period size: 20 Copynumber: 6.5 Consensus size: 20
4093230 GCTATGTAAA
*
4093240 TCGCATTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
4093260 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
*
4093280 TCGCGTTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTAT
*
4093300 TCGCGTTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTAT
4093320 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
4093340 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
*
4093360 TCGCATTGCGA
1 TCGCGTTGCGA
4093371 ATTAGGAAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 107 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGTAT
Found at i:4095033 original size:18 final size:18
Alignment explanation
Indices: 4094996--4095046 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
4094986 TATGATTTGA
* *
4094996 AAAATAAAAATTAGATTTT
1 AAAATAAAAA-TAAACTTT
4095015 AAAATAAAAATAAACTTT
1 AAAATAAAAATAAACTTT
* *
4095033 ATAATAAATATAAA
1 AAAATAAAAATAAA
4095047 AAGTGTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATAAAAATAAACTTT
Found at i:4096752 original size:12 final size:13
Alignment explanation
Indices: 4096735--4096763 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4096725 AATTCCCTGC
4096735 TTTTAGTTTTAG-
1 TTTTAGTTTTAGA
4096747 TTTTAGTTTTAGA
1 TTTTAGTTTTAGA
4096760 TTTT
1 TTTT
4096764 CCCTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (13 bp):
TTTTAGTTTTAGA
Found at i:4100992 original size:29 final size:29
Alignment explanation
Indices: 4100955--4101010 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
4100945 TTTAATCGGT
4100955 TTTCAACCGGTTCTG-ACCGGTTTGACCAA
1 TTTCAACCGGTTC-GAACCGGTTTGACCAA
*
4100984 TTTCGACCGGTTCGAACCGGTTTGACC
1 TTTCAACCGGTTCGAACCGGTTTGACC
4101011 GGTCTGACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (29 bp):
TTTCAACCGGTTCGAACCGGTTTGACCAA
Found at i:4101010 original size:19 final size:19
Alignment explanation
Indices: 4100959--4101013 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
4100949 ATCGGTTTTC
*
4100959 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
**
4100979 -ACCAATTTCGACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
4100998 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
4101014 CTGACCCGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.04
19 21 0.75
20 6 0.21
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:4101053 original size:22 final size:22
Alignment explanation
Indices: 4101025--4101071 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4101015 TGACCCGACC
* *
4101025 GACCCGACCTGACCCTACCGTT
1 GACCCGACCCGACCCGACCGTT
*
4101047 GACCCGACCCGACTCGACCGTT
1 GACCCGACCCGACCCGACCGTT
4101069 GAC
1 GAC
4101072 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.45, G:0.21, T:0.15
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:4108312 original size:19 final size:19
Alignment explanation
Indices: 4108288--4108327 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
4108278 CGACCGGTTC
4108288 GAACCGGTTTG-ACTGGTCT
1 GAACCGGTTTGAAC-GGTCT
4108307 GAACCGGTTTGAACGGTCT
1 GAACCGGTTTGAACGGTCT
4108326 GA
1 GA
4108328 CCCGACCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (19 bp):
GAACCGGTTTGAACGGTCT
Found at i:4108312 original size:29 final size:30
Alignment explanation
Indices: 4108250--4108328 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
4108240 AAACCGGTTT
* *
4108250 AACCGGTTCTG-ACCCGTTTGACTGGTTTCG
1 AACCGGTTC-GAACCGGTTTGACTGGTCTCG
4108280 -ACCGGTTCGAACCGGTTTGACTGGTCT-G
1 AACCGGTTCGAACCGGTTTGACTGGTCTCG
* *
4108308 AACCGGTTTGAA-CGGTCTGAC
1 AACCGGTTCGAACCGGTTTGAC
4108329 CCGACCGACC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 10 0.23
29 33 0.77
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (30 bp):
AACCGGTTCGAACCGGTTTGACTGGTCTCG
Found at i:4108358 original size:22 final size:22
Alignment explanation
Indices: 4108333--4108377 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4108323 TCTGACCCGA
4108333 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
* *
4108355 CCGACCCGACTCGATCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
4108377 C
1 C
4108378 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:4113707 original size:22 final size:21
Alignment explanation
Indices: 4113680--4113722 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4113670 ATTAGGAATG
4113680 TGTTGATGGTC-TTGATGGTTGA
1 TGTTGATGG-CGTTGAT-GTTGA
4113702 TGTTGATGGCGTTGATGTTGA
1 TGTTGATGGCGTTGATGTTGA
4113723 AATGGAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.14, C:0.05, G:0.37, T:0.44
Consensus pattern (21 bp):
TGTTGATGGCGTTGATGTTGA
Found at i:4119123 original size:22 final size:22
Alignment explanation
Indices: 4119065--4119125 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
4119055 ATTAGGAAGG
* *
4119065 TGTTGATGTTCTAGATGGATGA
1 TGTTGATGGTCTTGATGGATGA
4119087 TGTTGATGGTCTTGATGGATGA
1 TGTTGATGGTCTTGATGGATGA
4119109 TGTTGATGG-CGTTGATG
1 TGTTGATGGTC-TTGATG
4119126 TTGAAATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.18, C:0.05, G:0.36, T:0.41
Consensus pattern (22 bp):
TGTTGATGGTCTTGATGGATGA
Found at i:4123420 original size:31 final size:30
Alignment explanation
Indices: 4123356--4123435 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 30
4123346 AAATAATTTA
*
4123356 TTTATT-ATTAAAATATT-ATTTTTATAAT
1 TTTATTAATAAAAATATTAATTTTTATAAT
4123384 TTTATTAATAAAAATATTAATATTTGTAT-AT
1 TTTATTAATAAAAATATTAAT-TTT-TATAAT
*
4123415 TTTATTGAAGTAAGAATATTA
1 TTTATT-AA-TAAAAATATTA
4123436 TAAATTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 6 0.14
29 10 0.23
30 2 0.05
31 11 0.25
32 5 0.11
33 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTATTAATAAAAATATTAATTTTTATAAT
Found at i:4123511 original size:21 final size:22
Alignment explanation
Indices: 4123476--4123517 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4123466 AGTGTTATAT
4123476 TATATTTTAAAATATTAATTAG
1 TATATTTTAAAATATTAATTAG
*
4123498 TATATTTT-AAATATTTATTA
1 TATATTTTAAAATATTAATTA
4123518 AAATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATATTTTAAAATATTAATTAG
Found at i:4123523 original size:21 final size:22
Alignment explanation
Indices: 4123477--4123524 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
4123467 GTGTTATATT
**
4123477 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
*
4123499 ATATTTT-AAATATTTATTAAA
1 ATATTTTAAAATATTAATTAAA
4123520 ATATT
1 ATATT
4123525 ATTAGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:4123551 original size:29 final size:33
Alignment explanation
Indices: 4123470--4123549 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 33
4123460 AGTAATAGTG
*
4123470 TTATATTATATTTTAAAATATTAATTAGTATATT
1 TTATATTA-ATATTAAAATATTAATTAGTATATT
4123504 TTAAATATT--TATTAAAATATT-ATTAG-AT-TT
1 TT--ATATTAATATTAAAATATTAATTAGTATATT
4123534 TTATATTAATATTAAA
1 TTATATTAATATTAAA
4123550 TAAATAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
28 5 0.12
30 11 0.27
31 2 0.05
32 5 0.12
33 11 0.27
34 2 0.05
36 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (33 bp):
TTATATTAATATTAAAATATTAATTAGTATATT
Found at i:4123690 original size:16 final size:18
Alignment explanation
Indices: 4123655--4123707 Score: 67
Period size: 16 Copynumber: 3.1 Consensus size: 18
4123645 AAAATAAAAA
*
4123655 TATAATATCGTATATTAT
1 TATAATATCATATATTAT
4123673 TATAATAT-ATAT-TTAT
1 TATAATATCATATATTAT
*
4123689 TATAATATTA-ATATTAT
1 TATAATATCATATATTAT
4123706 TA
1 TA
4123708 GAAATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 14 0.44
17 10 0.31
18 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TATAATATCATATATTAT
Found at i:4123726 original size:21 final size:18
Alignment explanation
Indices: 4123669--4123719 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
4123659 ATATCGTATA
*
4123669 TTATTATAATA-T-ATAT
1 TTATTAAAATATTAATAT
*
4123685 TTATTATAATATTAATA-
1 TTATTAAAATATTAATAT
4123702 TTATTAGAAATATTAATA
1 TTATTA-AAATATTAATA
4123720 AATTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 11 0.35
17 7 0.23
18 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTATTAAAATATTAATAT
Found at i:4124800 original size:19 final size:19
Alignment explanation
Indices: 4124773--4124815 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
4124763 GGTTAATGAC
*
4124773 GATCGATAATAGAGGTTTT
1 GATCAATAATAGAGGTTTT
*
4124792 GATCAATAATAGGGGTTTT
1 GATCAATAATAGAGGTTTT
4124811 GATCA
1 GATCA
4124816 TTGGTTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (19 bp):
GATCAATAATAGAGGTTTT
Found at i:4125511 original size:23 final size:23
Alignment explanation
Indices: 4125442--4125530 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
4125432 CAACTCGTAA
4125442 TTTGCACCGAAGTGCCACATAA-
1 TTTGCACCGAAGTGCCACATAAG
** * *
4125464 -TTGTTCTGAA-TGACCACATAGG
1 TTTGCACCGAAGTG-CCACATAAG
4125486 TTTGCACCGAAGTGCCACATAAG
1 TTTGCACCGAAGTGCCACATAAG
4125509 TTTGCACCGAAGTGCCACATAA
1 TTTGCACCGAAGTGCCACATAA
4125531 TTGTCCCAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
20 2 0.04
21 14 0.25
23 37 0.67
24 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAAG
Found at i:4125678 original size:14 final size:15
Alignment explanation
Indices: 4125659--4125692 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4125649 TCTCTTATTG
4125659 ACATAG-GTCCTTTC
1 ACATAGAGTCCTTTC
*
4125673 ACATAGAGTCTTTTC
1 ACATAGAGTCCTTTC
4125688 ACATA
1 ACATA
4125693 CACTTGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (15 bp):
ACATAGAGTCCTTTC
Found at i:4130970 original size:18 final size:18
Alignment explanation
Indices: 4130944--4130996 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
4130934 GCGTAGGGTT
*
4130944 TGTCCCGAATGACCACTA
1 TGTCTCGAATGACCACTA
4130962 TGTCTCGAATGACCACTA
1 TGTCTCGAATGACCACTA
4130980 TGTCTCGAATGACCACT
1 TGTCTCGAATGACCACT
4130997 CTTAAGAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (18 bp):
TGTCTCGAATGACCACTA
Found at i:4131065 original size:21 final size:21
Alignment explanation
Indices: 4131039--4131089 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4131029 AATAAGTGTA
* *
4131039 CCAAAGTACTGCATATATGTT
1 CCAAAGGACTACATATATGTT
* *
4131060 CCAAAGGATTACATATATGTC
1 CCAAAGGACTACATATATGTT
*
4131081 CCGAAGGAC
1 CCAAAGGAC
4131090 CACGTAGAAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
CCAAAGGACTACATATATGTT
Found at i:4131435 original size:18 final size:19
Alignment explanation
Indices: 4131412--4131454 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4131402 AGATCATCAT
*
4131412 CATATAACATAT-ATATAA
1 CATATAACATATCACATAA
*
4131430 CATAT-ACATATCACATCA
1 CATATAACATATCACATAA
4131448 CATATAA
1 CATATAA
4131455 TACATATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 14 0.67
19 1 0.05
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (19 bp):
CATATAACATATCACATAA
Found at i:4131445 original size:13 final size:12
Alignment explanation
Indices: 4131410--4131464 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 12
4131400 ATAGATCATC
4131410 ATCATATAACAT
1 ATCATATAACAT
4131422 AT-ATATAACAT
1 ATCATATAACAT
*
4131433 ATACATATCACAT
1 AT-CATATAACAT
4131446 CA-CATATAATACAT
1 -ATCATAT-A-ACAT
4131460 ATCAT
1 ATCAT
4131465 GCACATTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
11 11 0.31
12 7 0.20
13 9 0.26
14 8 0.23
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (12 bp):
ATCATATAACAT
Found at i:4131951 original size:21 final size:21
Alignment explanation
Indices: 4131927--4131979 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
4131917 CGGTACCCTT
4131927 GGTATCGATACTACCTTCCCA
1 GGTATCGATACTACCTTCCCA
4131948 GGTATCGATACTACCTTCCCA
1 GGTATCGATACTACCTTCCCA
4131969 GGTATCGATAC
1 GGTATCGATAC
4131980 CCCATGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (21 bp):
GGTATCGATACTACCTTCCCA
Found at i:4134107 original size:21 final size:21
Alignment explanation
Indices: 4134083--4134217 Score: 82
Period size: 21 Copynumber: 6.3 Consensus size: 21
4134073 CCGAAGTGCA
4134083 ACATAATTTTCCCGAAGGACC
1 ACATAATTTTCCCGAAGGACC
* * **
4134104 ACATAGGTTTGTACTTAAGTG-CC
1 ACATA-ATTT-TCCCGAAG-GACC
*
4134127 ACATAAGTTTGCACCGAAGTG-CC
1 ACATAA-TTTTC-CCGAAG-GACC
*
4134150 ACAT-GTTTGTCCCGAA-GACC
1 ACATAATTT-TCCCGAAGGACC
* *
4134170 ACATAATTATCCCGGAGGACC
1 ACATAATTTTCCCGAAGGACC
*
4134191 ACATAATTGTCCC-AGAGGACC
1 ACATAATTTTCCCGA-AGGACC
4134212 ACATAA
1 ACATAA
4134218 AACTCATGAC
Statistics
Matches: 88, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.01
20 12 0.14
21 43 0.49
22 4 0.05
23 27 0.31
24 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (21 bp):
ACATAATTTTCCCGAAGGACC
Found at i:4134136 original size:23 final size:23
Alignment explanation
Indices: 4134067--4134153 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
4134057 CATCTCGTAA
*
4134067 TTTGCACCGAAGTGCAACATAA-
1 TTTGCACCGAAGTGCCACATAAG
* *
4134089 TTTTC-CCGAAG-GACCACATAGG
1 TTTGCACCGAAGTG-CCACATAAG
* **
4134111 TTTGTACTTAAGTGCCACATAAG
1 TTTGCACCGAAGTGCCACATAAG
4134134 TTTGCACCGAAGTGCCACAT
1 TTTGCACCGAAGTGCCACAT
4134154 GTTTGTCCCG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
22 7 0.14
23 29 0.58
24 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAAG
Found at i:4134173 original size:20 final size:21
Alignment explanation
Indices: 4134156--4134217 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
4134146 TGCCACATGT
*
4134156 TTGTCCC-GAAGACCACATAA
1 TTGTCCCAGAGGACCACATAA
* *
4134176 TTATCCCGGAGGACCACATAA
1 TTGTCCCAGAGGACCACATAA
4134197 TTGTCCCAGAGGACCACATAA
1 TTGTCCCAGAGGACCACATAA
4134218 AACTCATGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (21 bp):
TTGTCCCAGAGGACCACATAA
Found at i:4134812 original size:19 final size:19
Alignment explanation
Indices: 4134784--4134828 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4134774 TCAGGGGTAT
4134784 CGATACCTCCTTACGATAC
1 CGATACCTCCTTACGATAC
* *
4134803 CGATATCTCCTTACGGTAC
1 CGATACCTCCTTACGATAC
4134822 CGATACC
1 CGATACC
4134829 ATTCCGAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.36, G:0.13, T:0.27
Consensus pattern (19 bp):
CGATACCTCCTTACGATAC
Found at i:4144949 original size:19 final size:19
Alignment explanation
Indices: 4144903--4144955 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
4144893 TTTATAAATG
* *
4144903 ATGTGATTTAAACATTTAA
1 ATGTAATTTAAAAATTTAA
* * *
4144922 CTTTTATTTAAAAATTTAA
1 ATGTAATTTAAAAATTTAA
4144941 ATGTAATTTAAAAAT
1 ATGTAATTTAAAAAT
4144956 CGTACAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (19 bp):
ATGTAATTTAAAAATTTAA
Found at i:4147353 original size:13 final size:13
Alignment explanation
Indices: 4147332--4147368 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4147322 TTACATTAGG
*
4147332 TTAATATTTATTA
1 TTAAGATTTATTA
4147345 TTAAGATTTATTA
1 TTAAGATTTATTA
*
4147358 TTAAGGTTTAT
1 TTAAGATTTAT
4147369 ACTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (13 bp):
TTAAGATTTATTA
Found at i:4153824 original size:32 final size:32
Alignment explanation
Indices: 4153750--4153825 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
4153740 TACATAATGT
*
4153750 TTACTTTTTATTTCATTTTAGTACCCGCCAT-
1 TTACTTTTTGTTTCATTTTAGTACCCGCCATG
*
4153781 ATACTTTTTGTTTCATTTTAGTA-CC-CCATTG
1 TTACTTTTTGTTTCATTTTAGTACCCGCCA-TG
4153812 TTAACTTTTTGTTT
1 TT-ACTTTTTGTTT
4153826 TAGTACCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.08
30 3 0.08
31 22 0.56
32 11 0.28
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (32 bp):
TTACTTTTTGTTTCATTTTAGTACCCGCCATG
Found at i:4154334 original size:30 final size:30
Alignment explanation
Indices: 4154300--4154356 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4154290 TAAAAGTATG
4154300 CCCCTAATAACAAAT-ATTGAAAAAATTGGA
1 CCCCTAATAACAAATAATT-AAAAAATTGGA
* *
4154330 CCCCTGATAATAAATAATTAAAAAATT
1 CCCCTAATAACAAATAATTAAAAAATT
4154357 AGGCCGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (30 bp):
CCCCTAATAACAAATAATTAAAAAATTGGA
Found at i:4154471 original size:28 final size:27
Alignment explanation
Indices: 4154431--4154491 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
4154421 GAAAAAATAA
* *
4154431 ATTATAAAATAAACCCATGATGATAAAT
1 ATTA-AAAATAAACCCATAATAATAAAT
*
4154459 ATTAAAACATAAAGCCATAATAATAAAT
1 ATTAAAA-ATAAACCCATAATAATAAAT
4154487 ATTAA
1 ATTAA
4154492 GAAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (27 bp):
ATTAAAAATAAACCCATAATAATAAAT
Found at i:4159890 original size:19 final size:19
Alignment explanation
Indices: 4159866--4159903 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4159856 TGATTAAAAT
4159866 AAAGGGAAGTTAAAAATAG
1 AAAGGGAAGTTAAAAATAG
*
4159885 AAAGGGATGTTAAAAATAG
1 AAAGGGAAGTTAAAAATAG
4159904 GAAGTGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.18
Consensus pattern (19 bp):
AAAGGGAAGTTAAAAATAG
Found at i:4177970 original size:81 final size:81
Alignment explanation
Indices: 4177863--4178193 Score: 484
Period size: 81 Copynumber: 4.1 Consensus size: 81
4177853 GTTCTTAAAA
*
4177863 TAAAAGATTAATGACCTAGCTGTGCATTTGACAGAAAGGTGTCAATATTGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATATTGCCAGTTAGATGAAAG
* *
4177928 GTTAAATGGCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * ** *
4177944 TAAAATATTAATGGCCTTGCTATGCATTTGGCAGAAAAATGTCAATATTTCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATATTGCCAGTTAGATGAAAG
4178009 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
4178025 TAAAATATTAATGGCCTAGCCGTGCATTTGGA-AGAAAGGTGTCAATATTGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTT-GACAGAAAGGTGTCAATATTGCCAGTTAGATGAAA
*
4178089 GGCTAAATTCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * * * *
4178106 TAAAAGATTAACGGCCTAGCTGTGCATTTGGCAGAAAGTTGCCAATATTACCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATATTGCCAGTTAGATGAAAG
4178171 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
4178187 TAAAAGA
1 TAAAAGA
4178194 CTGATTGCTT
Statistics
Matches: 222, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
80 1 0.00
81 220 0.99
82 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATATTGCCAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:4179752 original size:73 final size:73
Alignment explanation
Indices: 4179633--4179838 Score: 324
Period size: 73 Copynumber: 2.8 Consensus size: 73
4179623 GAAAGAAAAT
4179633 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTCTATTTCG
1 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTCTATTTCG
4179698 AGGGAAAC
66 AGGGAAAC
* * *
4179706 TGTCTCAAGCGAGACGAAGTTTGTTTTTAA-AAGAACTATCTCGAGTGAGATAAATTTCTCTTTT
1 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAAAAACTATCTCGAGTGAGATAAATTTCTATTTC
*
4179770 GAGTGAAAC
65 GAGGGAAAC
* * *
4179779 TGTCTCAAGTGAGATGAAGTTTGTTTTAAGAAAAACCATCTCGAGTGAGATAAAATTTCT
1 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACTATCTCGAGTGAGAT-AAATTTCT
4179839 TGTATCAAAT
Statistics
Matches: 122, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
72 6 0.05
73 102 0.84
74 14 0.11
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (73 bp):
TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTCTATTTCG
AGGGAAAC
Found at i:4179829 original size:36 final size:36
Alignment explanation
Indices: 4179643--4179829 Score: 144
Period size: 36 Copynumber: 5.1 Consensus size: 36
4179633 TGTCTCAAGC
*
4179643 GAGACGAAGTTTGTTTTAAGAAAAACTATCTCGAGT
1 GAGATGAAGTTTGTTTTAAGAAAAACTATCTCGAGT
* * * ** * * *
4179679 GAGAT-AAATTTCTATTTCGAGGGAAACTGTCTCAAGC
1 GAGATGAAGTTTGT-TTT-AAGAAAAACTATCTCGAGT
* *
4179716 GAGACGAAGTTTGTTTTTAA-AAGAACTATCTCGAGT
1 GAGATGAAGTTTG-TTTTAAGAAAAACTATCTCGAGT
* * * * ** * *
4179752 GAGATAAATTTCTCTTTTGAGTGAAACTGTCTCAAGT
1 GAGATGAAGTT-TGTTTTAAGAAAAACTATCTCGAGT
*
4179789 GAGATGAAGTTTGTTTTAAGAAAAACCATCTCGAGT
1 GAGATGAAGTTTGTTTTAAGAAAAACTATCTCGAGT
4179825 GAGAT
1 GAGAT
4179830 AAAATTTCTT
Statistics
Matches: 107, Mismatches: 38, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
35 6 0.06
36 53 0.50
37 39 0.36
38 8 0.07
39 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (36 bp):
GAGATGAAGTTTGTTTTAAGAAAAACTATCTCGAGT
Found at i:4186255 original size:12 final size:12
Alignment explanation
Indices: 4186238--4186267 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
4186228 AATAAAGGAA
4186238 CATTTATTTTTC
1 CATTTATTTTTC
4186250 CATTTATTTTTC
1 CATTTATTTTTC
4186262 CATTTA
1 CATTTA
4186268 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (12 bp):
CATTTATTTTTC
Found at i:4189295 original size:25 final size:27
Alignment explanation
Indices: 4189263--4189340 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
4189253 TGAAAATATC
4189263 AAGTGTTAATTTCACCGGTGTAAGTCT
1 AAGTGTTAATTTCACCGGTGTAAGTCT
* * *
4189290 -A-TGTTAACTTCCACCGTTG-AAAT-T
1 AAGTGTTAA-TTTCACCGGTGTAAGTCT
* *
4189314 AAGTGTTAACTTCACGGGTGTAAGTCT
1 AAGTGTTAATTTCACCGGTGTAAGTCT
4189341 GTTATAAGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
24 1 0.03
25 17 0.45
26 19 0.50
27 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (27 bp):
AAGTGTTAATTTCACCGGTGTAAGTCT
Found at i:4189558 original size:153 final size:151
Alignment explanation
Indices: 4189330--4189889 Score: 632
Period size: 153 Copynumber: 3.7 Consensus size: 151
4189320 TAACTTCACG
4189330 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACTGGTGTAAGTATGTT
1 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACTGGTGTAAGTATGTT
*
4189395 ATGAGTTCAAT-TATGAAATTATATGATATATTTTACTAGTGTAAGTCTATTAAAAGTTCAATAC
66 ATGAGTTCAATAT-TGAAATTATATGATATATTTTACTAGTGTAAGTCTGTTAAAAGTTCAAT--
4189459 AGGAACAATATACTATATTTGACT
128 AGGAACAATATACTATATTTGACT
* *
4189483 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACTGTTGTAAGT-TCTT
1 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACTGGTGTAAGTAT-GT
* * **
4189547 TATGAGTTCAATATTGAAATTATATGCTATATTTTACTGGTGTAAGTCTGTTATGAGTTCAATAT
65 TATGAGTTCAATATTGAAATTATATGATATATTTTACTAGTGTAAGTCTGTTAAAAGTTCAATA-
4189612 TGGAACAATATACTATATTTGACT
129 -GGAACAATATACTATATTTGACT
* * * * * * * * *
4189636 AGTGTAAGTCTATTATGAG-TCTAATACTAGAAC-TATTTCTTATATTTGACTGGTGTAAGTCTA
1 GGTGTAAGTCTGTTATAAGTTC-AATA-TTGGACTTATATGTTATATTTGACTGGTGTAAGTATG
* * * * * * * *
4189699 TTATGAGTTCAATATTGGAACTATATGTTATATTTGACTTGTGTAAGTTTGTTATGAA-TTTAAT
64 TTATGAGTTCAATATTGAAATTATATGATATATTTTACTAGTGTAAGTCTGTTA-AAAGTTCAAT
*** *
4189763 -GGAATTGTATGCTATATTTGA-T
128 AGGAACAATATACTATATTTGACT
* * * * * * *
4189785 TGTGTAAGTCTGTAATGAGATCAATATTTGAATTATATGCTATATTTGACTGGTGTAAGTATGTT
1 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACTGGTGTAAGTATGTT
* * *
4189850 ACGAGTTCAATAATTG-AATTGTATGATATATTTAACTAGT
66 ATGAGTTCAAT-ATTGAAATTATATGATATATTTTACTAGT
4189890 TCTAGTCTGT
Statistics
Matches: 349, Mismatches: 47, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
148 2 0.01
149 77 0.22
150 23 0.07
151 1 0.00
152 3 0.01
153 236 0.68
154 7 0.02
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (151 bp):
GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACTGGTGTAAGTATGTT
ATGAGTTCAATATTGAAATTATATGATATATTTTACTAGTGTAAGTCTGTTAAAAGTTCAATAGG
AACAATATACTATATTTGACT
Found at i:4189867 original size:51 final size:50
Alignment explanation
Indices: 4189330--4189882 Score: 535
Period size: 51 Copynumber: 10.9 Consensus size: 50
4189320 TAACTTCACG
* * *
4189330 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTCAATATT-GAATTATATGCTATATTTGACT
* * *
4189381 GGTGTAAGTATGTTATGAGTTCAAT-TATGAAATTATATGATATATTTTACT
1 GGTGTAAGTCTGTTATGAGTTCAATAT-TG-AATTATATGCTATATTTGACT
* * ** ** ** *
4189432 AGTGTAAGTCTATTAAAAGTTCAATACAGGAACAATATACTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTCAATA-TTGAATTATATGCTATATTTGACT
* * *
4189483 GGTGTAAGTCTGTTATAAGTTCAATATTGGACTTATATGTTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTCAATATT-GAATTATATGCTATATTTGACT
* *
4189534 GTTGTAAGTTCT-TTATGAGTTCAATATTGAAATTATATGCTATATTTTACT
1 GGTGTAAG-TCTGTTATGAGTTCAATATTG-AATTATATGCTATATTTGACT
** *
4189585 GGTGTAAGTCTGTTATGAGTTCAATATTGGAACAATATACTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTCAATATT-GAATTATATGCTATATTTGACT
* * * * *
4189636 AGTGTAAGTCTATTATGAG-TCTAATACTAGAACTAT-TTCTTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTC-AATA-TTGAATTATATGC-TATATTTGACT
* * *
4189687 GGTGTAAGTCTATTATGAGTTCAATATTGGAACTATATGTTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTCAATATT-GAATTATATGCTATATTTGACT
* * * * * *
4189738 TGTGTAAGTTTGTTATGAATT-TA-ATGGAATTGTATGCTATATTTGA-T
1 GGTGTAAGTCTGTTATGAGTTCAATATTGAATTATATGCTATATTTGACT
* * *
4189785 TGTGTAAGTCTGTAATGAGATCAATATTTGAATTATATGCTATATTTGACT
1 GGTGTAAGTCTGTTATGAGTTCAATA-TTGAATTATATGCTATATTTGACT
* * * *
4189836 GGTGTAAGTATGTTACGAGTTCAATAATTGAATTGTATGATATATTT
1 GGTGTAAGTCTGTTATGAGTTCAAT-ATTGAATTATATGCTATATTT
4189883 AACTAGTTCT
Statistics
Matches: 413, Mismatches: 69, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
47 18 0.04
48 18 0.04
49 3 0.01
50 32 0.08
51 332 0.80
52 10 0.02
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (50 bp):
GGTGTAAGTCTGTTATGAGTTCAATATTGAATTATATGCTATATTTGACT
Found at i:4195735 original size:56 final size:56
Alignment explanation
Indices: 4195654--4195861 Score: 335
Period size: 56 Copynumber: 3.7 Consensus size: 56
4195644 ATGTATGGTG
* * *
4195654 ATTTCTGTATGGGTACTTTGTGTGCAAAAACTAAGAAATTCTTAATGAGTTTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGA
* * *
4195710 ATTTTCGTACGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGA
* *
4195766 ATTTCCGTATGAGCACCTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGA
*
4195822 ATTTCCGTATGGGCACTTTGTGTGCAAAAACCAAGAAATT
1 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATT
4195862 ATATGAATTT
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 138 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (56 bp):
ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGA
Found at i:4199930 original size:12 final size:12
Alignment explanation
Indices: 4199889--4199933 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
4199879 TTTTCTTTTC
*
4199889 TTTTCTTTTCAAG
1 TTTTATTTT-AAG
*
4199902 TTTTATTTTTA-
1 TTTTATTTTAAG
4199913 TTTTATTTTAAG
1 TTTTATTTTAAG
4199925 TTTTATTTT
1 TTTTATTTT
4199934 TAAACATGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.36
12 10 0.36
13 8 0.29
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:4199934 original size:23 final size:24
Alignment explanation
Indices: 4199884--4199935 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
4199874 CTTTCTTTTC
* *
4199884 TTTTCTTTTCTTTTCAAGTTTTAT
1 TTTTATTTTATTTTCAAGTTTTAT
4199908 TTTTATTTTATTTT-AAGTTTTAT
1 TTTTATTTTATTTTCAAGTTTTAT
4199931 TTTTA
1 TTTTA
4199936 AACATGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTTCAAGTTTTAT
Found at i:4205835 original size:42 final size:42
Alignment explanation
Indices: 4205770--4205861 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
4205760 TGATGAACTA
*
4205770 TGCGTTGAGTTTTGCTCCAAGAAGATTACGGGGTAAGGTTGG
1 TGCGTTGAGGTTTGCTCCAAGAAGATTACGGGGTAAGGTTGG
**
4205812 TGCGTTGAGGTTTGCTCTGAGAAGATTACGGGGTAAGGTTGG
1 TGCGTTGAGGTTTGCTCCAAGAAGATTACGGGGTAAGGTTGG
*
4205854 TTCGTTGA
1 TGCGTTGA
4205862 TATTGCTCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.20, C:0.11, G:0.37, T:0.33
Consensus pattern (42 bp):
TGCGTTGAGGTTTGCTCCAAGAAGATTACGGGGTAAGGTTGG
Found at i:4209262 original size:15 final size:15
Alignment explanation
Indices: 4209242--4209271 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4209232 TTAAAGTTAT
*
4209242 GAAAAGTATATGAAA
1 GAAAAGAATATGAAA
4209257 GAAAAGAATATGAAA
1 GAAAAGAATATGAAA
4209272 ATGAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
GAAAAGAATATGAAA
Found at i:4216300 original size:17 final size:17
Alignment explanation
Indices: 4216278--4216313 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4216268 TCTTTTGAAT
*
4216278 TTCTTTTTTTCTAATTC
1 TTCTTTTTGTCTAATTC
*
4216295 TTCTTTTTGTCTTATTC
1 TTCTTTTTGTCTAATTC
4216312 TT
1 TT
4216314 TTCTTTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (17 bp):
TTCTTTTTGTCTAATTC
Found at i:4217878 original size:15 final size:16
Alignment explanation
Indices: 4217858--4217900 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4217848 AGTTATCTTC
4217858 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
4217873 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
4217889 AAAATAACTATA
1 ATAATAACTATA
4217901 TTAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:4220792 original size:19 final size:20
Alignment explanation
Indices: 4220756--4220793 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4220746 TAGGGTTTGA
4220756 GTATCGATACTGGGATGAAC
1 GTATCGATACTGGGATGAAC
4220776 GTATCGATACT-GGATGAA
1 GTATCGATACTGGGATGAA
4220794 TTGAGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (20 bp):
GTATCGATACTGGGATGAAC
Found at i:4222375 original size:14 final size:13
Alignment explanation
Indices: 4222358--4222411 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 13
4222348 AAAAAGAATT
4222358 AATAATAATGATAA
1 AATAATAAT-ATAA
4222372 AATAATAA-ATGAA
1 AATAATAATAT-AA
4222385 AATAAATAAATATAA
1 AAT-AAT-AATATAA
4222400 AACTAATAATAT
1 AA-TAATAATAT
4222412 GTTTTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 5 0.14
14 16 0.46
15 9 0.26
16 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (13 bp):
AATAATAATATAA
Found at i:4222540 original size:34 final size:34
Alignment explanation
Indices: 4222492--4222606 Score: 117
Period size: 34 Copynumber: 3.3 Consensus size: 34
4222482 AAACTATATA
4222492 ATAT-ATATATTTTCAAAAATTGTTTTTCAAATCT
1 ATATAATATATTTTCAAAAATTGTTTTTCAAAT-T
*
4222526 ATATAATATA-TTTCAAAAATTGTTTTTGAAATT
1 ATATAATATATTTTCAAAAATTGTTTTTCAAATT
* * *** *
4222559 ATATATTATACGTTTTTAAAAATAAATTTTCAACACT
1 ATATAATATA--TTTTCAAAAATTGTTTTTCAA-ATT
4222596 ATATAATATAT
1 ATATAATATAT
4222607 ATGTCTTCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
33 10 0.15
34 25 0.37
35 6 0.09
36 15 0.22
37 11 0.16
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (34 bp):
ATATAATATATTTTCAAAAATTGTTTTTCAAATT
Found at i:4222564 original size:35 final size:36
Alignment explanation
Indices: 4222468--4222650 Score: 121
Period size: 36 Copynumber: 5.1 Consensus size: 36
4222458 ACATGCTTTA
* *
4222468 AAAAAATGTTTTCGAAACTATATAATATATATATTTTC
1 AAAAATTGTTTTTGAAA-TATAT-ATATATATATTTTC
* *
4222506 AAAAATTGTTTTTCAAATCTATATA-ATATA-TTTC
1 AAAAATTGTTTTTGAAATATATATATATATATTTTC
*
4222540 AAAAATTGTTTTTGAAAT-TATATAT-TATACGTTTTT
1 AAAAATTGTTTTTGAAATATATATATATATA--TTTTC
*** *
4222576 AAAAATAAATTTTCAACACTATATA-ATATATATGTCTTC
1 AAAAATTGTTTTTGAA-A-TATATATATATATAT-T-TTC
* * *
4222615 AAAATTTG-TTTTCAAA-ACTATA-ATATATGTTTTC
1 AAAAATTGTTTTTGAAATA-TATATATATATATTTTC
4222649 AA
1 AA
4222651 TTTTTTTTAA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
33 10 0.08
34 26 0.22
35 7 0.06
36 29 0.24
37 7 0.06
38 25 0.21
39 15 0.13
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (36 bp):
AAAAATTGTTTTTGAAATATATATATATATATTTTC
Found at i:4222666 original size:31 final size:32
Alignment explanation
Indices: 4222603--4222680 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
4222593 ACTATATAAT
*
4222603 ATATATGTCTTCAAAATTTGTTTTCAAAACTATA
1 ATATATGTTTTC--AATTTGTTTTCAAAACTATA
*
4222637 ATATATGTTTTCAATTT-TTTTTAAAACTATA
1 ATATATGTTTTCAATTTGTTTTCAAAACTATA
* *
4222668 TTATACGTTTTCA
1 ATATATGTTTTCA
4222681 TAACATTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.60
32 5 0.12
34 11 0.28
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (32 bp):
ATATATGTTTTCAATTTGTTTTCAAAACTATA
Found at i:4235034 original size:41 final size:39
Alignment explanation
Indices: 4234948--4235043 Score: 117
Period size: 41 Copynumber: 2.5 Consensus size: 39
4234938 ATATAGGTTT
4234948 AAAACTATATAT-TATATATGCTTTCGAAAAATGTTTTC
1 AAAACTATATATATATATATGCTTTCGAAAAATGTTTTC
* * *
4234986 GAAACTATATAGTATATATATGTTTTC-AAAAATTATTTTTC
1 AAAACTATATA-TATATATATGCTTTCGAAAAA-T-GTTTTC
4235027 AAAACTATATA-ATATAT
1 AAAACTATATATATATAT
4235044 TTCAAATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
38 10 0.20
39 12 0.24
40 13 0.26
41 15 0.30
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (39 bp):
AAAACTATATATATATATATGCTTTCGAAAAATGTTTTC
Found at i:4235070 original size:33 final size:34
Alignment explanation
Indices: 4235009--4235075 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
4234999 ATATATATGT
4235009 TTTCAAAAATTATTTTTCAAAACTATATAATATA
1 TTTCAAAAATTATTTTTCAAAACTATATAATATA
* * *
4235043 TTTCAAATATTATTTTT-TAAACTATATATTATA
1 TTTCAAAAATTATTTTTCAAAACTATATAATATA
4235076 CGTTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.49
Consensus pattern (34 bp):
TTTCAAAAATTATTTTTCAAAACTATATAATATA
Found at i:4235124 original size:37 final size:36
Alignment explanation
Indices: 4234948--4235171 Score: 119
Period size: 37 Copynumber: 6.3 Consensus size: 36
4234938 ATATAGGTTT
* * *
4234948 AAAACTATATATTATATATGCTTTCGAAAAA-TGTTTTC
1 AAAACTATATA--ATATATGTTTTC-AAAAATTATTTTA
* *
4234986 GAAACTATATAGTATATATATGTTTTCAAAAATTATTTTTC
1 AAAAC--TATA-TA-ATATATGTTTTCAAAAATTA-TTTTA
* *
4235027 AAAACTATATAATATA---TTTCAAATATTATTTTT
1 AAAACTATATAATATATGTTTTCAAAAATTATTTTA
* * * * *
4235060 TAAACTATATATTATACGTTTTTAAAAACGTATTTTA
1 AAAACTATATAATATATGTTTTCAAAAA-TTATTTTA
* * **
4235097 AAAATTATATAATATATGTCTTCAAAAA--A---GC
1 AAAACTATATAATATATGTTTTCAAAAATTATTTTA
* * *
4235128 AAAAC--TATAATATATGTTTTCAAAATTTGTTTTT
1 AAAACTATATAATATATGTTTTCAAAAATTATTTTA
4235162 AAAACTATAT
1 AAAACTATAT
4235172 TATACGTTTT
Statistics
Matches: 144, Mismatches: 26, Indels: 34
0.71 0.13 0.17
Matches are distributed among these distances:
29 19 0.13
31 4 0.03
33 18 0.12
34 17 0.12
36 10 0.07
37 33 0.23
38 6 0.04
39 9 0.06
40 17 0.12
41 11 0.08
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (36 bp):
AAAACTATATAATATATGTTTTCAAAAATTATTTTA
Found at i:4235234 original size:35 final size:36
Alignment explanation
Indices: 4235190--4235296 Score: 135
Period size: 35 Copynumber: 3.0 Consensus size: 36
4235180 TTCGTTTTCA
* *
4235190 AAACCATATATTATATGTTTTTAAAATTATTTTTTT
1 AAACTATATATTATACGTTTTTAAAATTATTTTTTT
* * * *
4235226 -AACTATATATTATACGTTTATGAGACTATTTTTTT
1 AAACTATATATTATACGTTTTTAAAATTATTTTTTT
*
4235261 AAAACTATATATTATACGTTTTCAAAATTATTTTTT
1 -AAACTATATATTATACGTTTTTAAAATTATTTTTT
4235297 AAAAAAATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
35 29 0.50
37 29 0.50
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (36 bp):
AAACTATATATTATACGTTTTTAAAATTATTTTTTT
Found at i:4235269 original size:37 final size:37
Alignment explanation
Indices: 4235184--4235315 Score: 126
Period size: 37 Copynumber: 3.6 Consensus size: 37
4235174 TACGTTTTCG
* * * * *
4235184 TTTTCAAAACCATATATTATATGTTTTTAAAATTATT
1 TTTTTAAAACTATATATTATACGTTTATAAAACTATT
* *
4235221 TTTTT--AACTATATATTATACGTTTATGAGACTATT
1 TTTTTAAAACTATATATTATACGTTTATAAAACTATT
*
4235256 TTTTTAAAACTATATATTATACGTTT-TCAAAATTATT
1 TTTTTAAAACTATATATTATACGTTTAT-AAAACTATT
* *
4235293 TTTTAAAAAAATTATATATTATA
1 TTTT--TAAAACTATATATTATA
4235316 TATTTTCAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
35 29 0.37
36 1 0.01
37 33 0.42
39 15 0.19
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (37 bp):
TTTTTAAAACTATATATTATACGTTTATAAAACTATT
Found at i:4235350 original size:38 final size:39
Alignment explanation
Indices: 4235261--4235366 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 39
4235251 CTATTTTTTT
** * **
4235261 AAAACTATATATTATACGTTTTCAAAATTATTTTTTAAA
1 AAAACTATATATTATATATTTTCAAAAATATAGTTTAAA
* **
4235300 AAAATTATATATTATATATTTTCAAAAATA-AGTTTCCA
1 AAAACTATATATTATATATTTTCAAAAATATAGTTTAAA
*
4235338 AAAACTATATATTATATATTTTTAAAAAT
1 AAAACTATATATTATATATTTTCAAAAAT
4235367 TATTATGTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 31 0.54
39 26 0.46
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (39 bp):
AAAACTATATATTATATATTTTCAAAAATATAGTTTAAA
Found at i:4241343 original size:14 final size:14
Alignment explanation
Indices: 4241324--4241352 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4241314 TTGTTTTAAA
4241324 CCCAACCTTAATTC
1 CCCAACCTTAATTC
4241338 CCCAACCTTAATTC
1 CCCAACCTTAATTC
4241352 C
1 C
4241353 TAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28
Consensus pattern (14 bp):
CCCAACCTTAATTC
Found at i:4247008 original size:12 final size:12
Alignment explanation
Indices: 4246991--4247018 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4246981 CCTAAATACC
4246991 TTTGTTTGAAAT
1 TTTGTTTGAAAT
4247003 TTTGTTTGAAAT
1 TTTGTTTGAAAT
4247015 TTTG
1 TTTG
4247019 GCTTTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (12 bp):
TTTGTTTGAAAT
Found at i:4247044 original size:27 final size:28
Alignment explanation
Indices: 4247014--4247066 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
4247004 TTGTTTGAAA
4247014 TTTTGGCT-TTTTTGTTTTT-TTTTTTGG
1 TTTT-GCTGTTTTTGTTTTTATTTTTTGG
**
4247041 TTTTTTTGTTTTTGTTTTTATTTTTT
1 TTTTGCTGTTTTTGTTTTTATTTTTT
4247067 TAAAAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 1 0.05
27 15 0.68
28 6 0.27
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (28 bp):
TTTTGCTGTTTTTGTTTTTATTTTTTGG
Found at i:4247065 original size:21 final size:21
Alignment explanation
Indices: 4247014--4247067 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4247004 TTGTTTGAAA
*
4247014 TTTTGGCTTTTTTGTTTTTTT
1 TTTTGGTTTTTTTGTTTTTTT
*
4247035 TTTTGGTTTTTTTGTTTTTGT
1 TTTTGGTTTTTTTGTTTTTTT
*
4247056 TTTT-ATTTTTTT
1 TTTTGGTTTTTTT
4247068 AAAAAAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (21 bp):
TTTTGGTTTTTTTGTTTTTTT
Found at i:4250212 original size:6 final size:6
Alignment explanation
Indices: 4250194--4250233 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
4250184 ATAAAACATA
*
4250194 ATAATT ATGATT ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAA
4250234 GGAGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:4251704 original size:21 final size:21
Alignment explanation
Indices: 4251675--4251719 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4251665 ATTCTGACTA
4251675 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
4251696 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
4251717 TCG
1 TCG
4251720 TAAAGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Done.