Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_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: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:3118512 original size:11 final size:11
Alignment explanation
Indices: 3118496--3118562 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
3118486 GAATTATAGA
3118496 ATTTTTAATAT
1 ATTTTTAATAT
3118507 ATTTTTAA-A-
1 ATTTTTAATAT
3118516 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
3118527 ATCAATAGTAT
1 ATTTTTAATAT
*
3118538 ATTTTTATTAT
1 ATTTTTAATAT
3118549 ATTTTTAATA-
1 ATTTTTAATAT
3118559 ATTT
1 ATTT
3118563 AATTTTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
9 5 0.12
10 11 0.26
11 27 0.63
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:3126358 original size:21 final size:20
Alignment explanation
Indices: 3126329--3126420 Score: 85
Period size: 20 Copynumber: 4.3 Consensus size: 20
3126319 AATATATAAC
*
3126329 AAAAAAATAGAGAGAAAAGA
1 AAAAAAATAGAGATAAAAGA
*
3126349 AAAAAGAATAGATATAAAAGAA
1 AAAAA-AATAGAGATAAAAG-A
* *
3126371 AGCAAAAAATACAAAGAAAAAAGA
1 A--AAAAAAT--AGAGATAAAAGA
*
3126395 AAAAAAAAAGAGATAAAAGA
1 AAAAAAATAGAGATAAAAGA
3126415 AAAAAA
1 AAAAAA
3126421 TAAAAAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
20 21 0.36
21 12 0.21
22 8 0.14
23 3 0.05
24 6 0.10
25 8 0.14
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAAAATAGAGATAAAAGA
Found at i:3126423 original size:13 final size:14
Alignment explanation
Indices: 3126369--3126425 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
3126359 GATATAAAAG
*
3126369 AAAGCAAAAA-ATA
1 AAAGAAAAAAGATA
3126382 CAAAGAAAAAAGA-A
1 -AAAGAAAAAAGATA
3126396 AAA-AAAAAGAGATA
1 AAAGAAAAA-AGATA
3126410 AAAGAAAAAA-ATA
1 AAAGAAAAAAGATA
3126423 AAA
1 AAA
3126426 AAATAAACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 5 0.13
13 12 0.32
14 15 0.39
15 6 0.16
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.05
Consensus pattern (14 bp):
AAAGAAAAAAGATA
Found at i:3126437 original size:29 final size:27
Alignment explanation
Indices: 3126383--3126437 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
3126373 CAAAAAATAC
*
3126383 AAAGAAAAAAGAAAAAAAAAAGAGATA
1 AAAGAAAAAAGAAAAAAAAAACAGATA
*
3126410 AAAGAAAAAAATAAAAAAATAAACAGAT
1 AAAG-AAAAAAGAAAAAAA-AAACAGAT
3126438 CAAGTACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 13 0.54
29 7 0.29
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (27 bp):
AAAGAAAAAAGAAAAAAAAAACAGATA
Found at i:3128595 original size:57 final size:54
Alignment explanation
Indices: 3128407--3128687 Score: 293
Period size: 52 Copynumber: 5.1 Consensus size: 54
3128397 CTCCTTGATA
3128407 TGATGTTTTCAAATGAATTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTT-AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * * *
3128462 TAATGTTTTCAAATGAGTTTTT--AGAAACTAAGCCTGATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* *
3128514 TGATGATGATTTCCAATGAATTTTTAAAAGAAGCTAATCCTAATTTTTTTAGGGGTTTCT
1 TGATG-T--TTTCAAATGAATTTTT-AAAGAAGCTAAGCCTAA--TTTTTAGGGGTTTCT
* ** **
3128574 TGATGTTTTCAAATGAGTTTTT--AGAAATTAAGCCTGTTTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * *
3128626 TGATGATTATTTCCAA-GTAATGTTTAAAGAAGCTAAGCCTAATTTTTAGGTGTTTCT
1 TGATG--T-TTTCAAATG-AATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
3128683 TGATG
1 TGATG
3128688 ATAACTGAAA
Statistics
Matches: 185, Mismatches: 27, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
52 51 0.28
53 1 0.01
54 12 0.06
55 45 0.24
57 44 0.24
58 12 0.06
59 1 0.01
60 19 0.10
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (54 bp):
TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
Found at i:3128700 original size:112 final size:110
Alignment explanation
Indices: 3128406--3128745 Score: 432
Period size: 112 Copynumber: 3.0 Consensus size: 110
3128396 GCTCCTTGAT
* * * *
3128406 ATGATGTTTTCAAATGAATTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATGTTTT
1 ATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
*
3128471 CAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTG
66 CAAATGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTG
* *
3128516 ATGATGATTTCCAATGAATTTTTAAAAGAAGCTAATCCTAATTTTTTTAGGGGTTTCTTGATGTT
1 ATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAA--TTTTTAGGGGTTTCTTGATGTT
* *
3128581 TTCAAATGAGTTTTTAGAAATTAAGCCTGTTTTTTAGGGGTTTCTTG
64 TTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTG
* *
3128628 ATGATTATTTCCAA-GTAATGTTT-AAAGAAGCTAAGCCTAATTTTTAGGTGTTTCTTGATGATA
1 ATGATGATTTCCAATG-AATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-T-
* ** * * *
3128691 ACTGAAAATGAAAGATTTTAAGAAACTAAGCTTGATTTTTAAGGGTTTCTTG
63 -TTTCAAATG--AG-TTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTG
3128743 ATG
1 ATG
3128746 GGTAAGTCTT
Statistics
Matches: 202, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
109 19 0.09
110 39 0.19
111 17 0.08
112 90 0.45
114 2 0.01
115 35 0.17
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (110 bp):
ATGATGATTTCCAATGAATGTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
CAAATGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTG
Found at i:3129225 original size:216 final size:216
Alignment explanation
Indices: 3128851--3129348 Score: 829
Period size: 216 Copynumber: 2.3 Consensus size: 216
3128841 AGGCCATCCA
* * * *
3128851 TAAGACCTTCGGGCAGGATGTTTTCAACATTTCATTTGCTTGATTCACAACACTTTGAATCAGCA
1 TAAGACCTTCGGGAAGGATGTTTTCAATATTTTATTTGCTCGATTCACAACACTTTGAATCAGCA
* *
3128916 ACACCCCACTTGAGGGATCAACATTTCCTATCGTTCGATTCACAACACTTCGAATCAGCAAAAGT
66 ACACCCCACTTGAGGGATCAACATTTCCTATCGCTCGATTCACAACACTTCGAATCAACAAAAGT
* * * *
3128981 CCTTCGGGCCATCAGTAAGTTTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTT
131 CCTTCGAGCCATCAGCAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGCCATCTATAAGTCTT
3129046 TCGAGCAAGATGATAAGTCCT
196 TCGAGCAAGATGATAAGTCCT
*
3129067 TAAGACCATCGGGAAGGATGTTTTCAATATTTTATTTGCTCGATTCACAACACTTTGAATCAGCA
1 TAAGACCTTCGGGAAGGATGTTTTCAATATTTTATTTGCTCGATTCACAACACTTTGAATCAGCA
3129132 ACACCCCACTTGAGGGATCAACATTTCCTATCGCTCGATTCACAACACTTCGAATCAACAAAAGT
66 ACACCCCACTTGAGGGATCAACATTTCCTATCGCTCGATTCACAACACTTCGAATCAACAAAAGT
*
3129197 CCTTCGAGCCATCAGCAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGCCATCTATAAGTCTT
131 CCTTCGAGCCATCAGCAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGCCATCTATAAGTCTT
*
3129262 TCGAGCAAGATGATAAGTCTT
196 TCGAGCAAGATGATAAGTCCT
* * *
3129283 TAAGACCTTCGGGTAGGATGTTTTCACAT-TTCT-TTTGCTCGATTCACAACACTTCGAATCAGC
1 TAAGACCTTCGGGAAGGATGTTTTCA-ATATTTTATTTGCTCGATTCACAACACTTTGAATCAGC
3129346 AAC
65 AAC
3129349 GCATCAGTCG
Statistics
Matches: 264, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
215 32 0.12
216 230 0.87
217 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (216 bp):
TAAGACCTTCGGGAAGGATGTTTTCAATATTTTATTTGCTCGATTCACAACACTTTGAATCAGCA
ACACCCCACTTGAGGGATCAACATTTCCTATCGCTCGATTCACAACACTTCGAATCAACAAAAGT
CCTTCGAGCCATCAGCAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGCCATCTATAAGTCTT
TCGAGCAAGATGATAAGTCCT
Found at i:3129956 original size:21 final size:21
Alignment explanation
Indices: 3129932--3129983 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
3129922 TGGGGCCCAA
3129932 AACCTAACCCAACCTGGGTCT
1 AACCTAACCCAACCTGGGTCT
3129953 AACCTAACCCAACCTGGGTCT
1 AACCTAACCCAACCTGGGTCT
3129974 AACCTAACCC
1 AACCTAACCC
3129984 TACTGTAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.40, G:0.12, T:0.17
Consensus pattern (21 bp):
AACCTAACCCAACCTGGGTCT
Found at i:3132189 original size:160 final size:160
Alignment explanation
Indices: 3131925--3132212 Score: 576
Period size: 160 Copynumber: 1.8 Consensus size: 160
3131915 TTTTTAAACC
3131925 TAAGGCAATGTTCACTTATTAGGGAGTTAATGATATATCTCTCGTAAGTATGATAAGGGGTGACT
1 TAAGGCAATGTTCACTTATTAGGGAGTTAATGATATATCTCTCGTAAGTATGATAAGGGGTGACT
3131990 ACTGGTGATTCCTGAAATAGGTCGACATCCTTTTCAAAAGTTGCATCATGATTTTCTAAAATTAA
66 ACTGGTGATTCCTGAAATAGGTCGACATCCTTTTCAAAAGTTGCATCATGATTTTCTAAAATTAA
3132055 GGCAATGTCCGGTTATTAGGCACAATAGCT
131 GGCAATGTCCGGTTATTAGGCACAATAGCT
3132085 TAAGGCAATGTTCACTTATTAGGGAGTTAATGATATATCTCTCGTAAGTATGATAAGGGGTGACT
1 TAAGGCAATGTTCACTTATTAGGGAGTTAATGATATATCTCTCGTAAGTATGATAAGGGGTGACT
3132150 ACTGGTGATTCCTGAAATAGGTCGACATCCTTTTCAAAAGTTGCATCATGATTTTCTAAAATT
66 ACTGGTGATTCCTGAAATAGGTCGACATCCTTTTCAAAAGTTGCATCATGATTTTCTAAAATT
3132213 TTCAACTTTG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 128 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (160 bp):
TAAGGCAATGTTCACTTATTAGGGAGTTAATGATATATCTCTCGTAAGTATGATAAGGGGTGACT
ACTGGTGATTCCTGAAATAGGTCGACATCCTTTTCAAAAGTTGCATCATGATTTTCTAAAATTAA
GGCAATGTCCGGTTATTAGGCACAATAGCT
Found at i:3144601 original size:27 final size:27
Alignment explanation
Indices: 3144566--3144619 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3144556 TGGGCTTGTT
* *
3144566 CCTATGTTTGTTTTTAATTGGGATTGG
1 CCTAAGTTTGTTTTCAATTGGGATTGG
*
3144593 CCTAAGTTTGTTTTCAATTGGGCTTGG
1 CCTAAGTTTGTTTTCAATTGGGATTGG
3144620 ATCATTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (27 bp):
CCTAAGTTTGTTTTCAATTGGGATTGG
Found at i:3145228 original size:29 final size:29
Alignment explanation
Indices: 3145167--3145232 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
3145157 TGCTCCATTG
* * *
3145167 GATAATAAAAATAAGTTGTGTAATAGTCC
1 GATAATAAAAACAAGTTGTATAATAATCC
* * *
3145196 GATAATTAAAACAAGTTGTATGATAATCT
1 GATAATAAAAACAAGTTGTATAATAATCC
3145225 GATAATAA
1 GATAATAA
3145233 CAATGACAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (29 bp):
GATAATAAAAACAAGTTGTATAATAATCC
Found at i:3148224 original size:19 final size:21
Alignment explanation
Indices: 3148181--3148232 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
3148171 GAAACCCCTT
3148181 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
3148202 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
3148221 TGAAGATACATG
1 TGAAAATACATG
3148233 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:3152433 original size:19 final size:21
Alignment explanation
Indices: 3152390--3152441 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
3152380 GAAACCCCTT
3152390 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
3152411 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
3152430 TGAAGATACATG
1 TGAAAATACATG
3152442 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:3155849 original size:8 final size:8
Alignment explanation
Indices: 3155819--3155862 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
3155809 TCTTTTTGAA
3155819 CTTCTCTTT
1 CTTCT-TTT
3155828 -TTCTTTT
1 CTTCTTTT
3155835 CTTTTCTTTT
1 C--TTCTTTT
3155845 CTTCTTTT
1 CTTCTTTT
3155853 CTTCTTTT
1 CTTCTTTT
3155861 CT
1 CT
3155863 GATTTTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
10 8 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
CTTCTTTT
Found at i:3156641 original size:19 final size:21
Alignment explanation
Indices: 3156598--3156649 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
3156588 GAAACCCCTT
3156598 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
3156619 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
3156638 TGAAGATACATG
1 TGAAAATACATG
3156650 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:3157489 original size:17 final size:18
Alignment explanation
Indices: 3157453--3157489 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3157443 AACTATATAA
3157453 TGCATATAATAAATGATG
1 TGCATATAATAAATGATG
*
3157471 TGCATATTATAAA-GATG
1 TGCATATAATAAATGATG
3157488 TG
1 TG
3157490 AACTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (18 bp):
TGCATATAATAAATGATG
Found at i:3160059 original size:16 final size:17
Alignment explanation
Indices: 3160025--3160081 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
3160015 TTTGAACTTC
*
3160025 TCTTTT-TCTTTTCTTT
1 TCTTTTCTCTTTTCTCT
3160041 TCTTTTCTCTTTTC-CT
1 TCTTTTCTCTTTTCTCT
*
3160057 TCTTTTCTGATTTTTCTCT
1 TCTTTTCT--CTTTTCTCT
3160076 TCTTTT
1 TCTTTT
3160082 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 15 0.43
17 7 0.20
18 5 0.14
19 8 0.23
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.74
Consensus pattern (17 bp):
TCTTTTCTCTTTTCTCT
Found at i:3169221 original size:27 final size:28
Alignment explanation
Indices: 3169166--3169317 Score: 112
Period size: 30 Copynumber: 5.2 Consensus size: 28
3169156 GTTTAAAAAT
* *
3169166 ATATATTTTATTTTTATTCAACTTATTAA
1 ATATATTTTATTTTTATTTAACTT-TAAA
3169195 ATATATTTTATTTTTATTTTAA-TTTAAA
1 ATATATTTTATTTTTA-TTTAACTTTAAA
* * *
3169223 AAATATTTT-TTCTTAACTTAACTTTAAAA
1 ATATATTTTATT-TTTATTTAACTTT-AAA
* *
3169252 ATATATTTTATTCTTT-TGTTAACATAAACA
1 ATATATTTTATT-TTTAT-TTAACTTTAA-A
* * *
3169282 ATATATTTTACTATTATCTTAACTTCAAA
1 ATATATTTTATTTTTAT-TTAACTTTAAA
3169311 TATATAT
1 -ATATAT
3169318 ATATATATAT
Statistics
Matches: 99, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.06
28 17 0.17
29 34 0.34
30 42 0.42
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATATTTTATTTTTATTTAACTTTAAA
Found at i:3169232 original size:29 final size:29
Alignment explanation
Indices: 3169157--3169263 Score: 96
Period size: 29 Copynumber: 3.7 Consensus size: 29
3169147 ATATCCTAAG
3169157 TTTAAAAATATATATTTTATTTTTATTCAA
1 TTTAAAAA-ATATATTTTATTTTTATTCAA
* ** *
3169187 CTTATTAAATATATTTTATTTTTATTTTAA
1 TTTAAAAAATATATTTTATTTTTA-TTCAA
* *
3169217 TTTAAAAAATAT-TTTT-TCTTAACTT-AA
1 TTTAAAAAATATATTTTATTTTTA-TTCAA
3169244 CTTT-AAAAATATATTTTATT
1 -TTTAAAAAATATATTTTATT
3169264 CTTTTGTTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.16
28 13 0.21
29 21 0.34
30 18 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTAAAAAATATATTTTATTTTTATTCAA
Found at i:3169285 original size:57 final size:59
Alignment explanation
Indices: 3169159--3169317 Score: 139
Period size: 57 Copynumber: 2.7 Consensus size: 59
3169149 ATCCTAAGTT
* * * * **
3169159 TAAAAATATATATTTTATTTTTA-TTCAACTT-ATTAAATATATTTTATTTTTATTTTAATT
1 TAAAAA-ATATATTTTATATTAACTT-AACTTCA-AAAATATATTTTATTTTTATGTTAACA
* *
3169219 TAAAAAATAT-TTTT-TCTTAACTTAACTTTAAAAATATATTTTATTCTTT-TGTTAACA
1 TAAAAAATATATTTTATATTAACTTAACTTCAAAAATATATTTTATT-TTTATGTTAACA
* * *
3169276 TAAACAATATATTTTACTATTATCTTAACTTCAAATATATAT
1 TAAAAAATATATTTTA-TATTAACTTAACTTCAAAAATATAT
3169318 ATATATATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
57 37 0.45
58 14 0.17
59 4 0.05
60 27 0.33
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.53
Consensus pattern (59 bp):
TAAAAAATATATTTTATATTAACTTAACTTCAAAAATATATTTTATTTTTATGTTAACA
Found at i:3169317 original size:2 final size:2
Alignment explanation
Indices: 3169310--3169345 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3169300 TTAACTTCAA
3169310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3169346 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3169421 original size:30 final size:28
Alignment explanation
Indices: 3169386--3169512 Score: 121
Period size: 30 Copynumber: 4.2 Consensus size: 28
3169376 TTATTATCTT
*
3169386 AAGTTAATAAAAGAATAAAATATATCTTTA
1 AAGTTAACAAAA-AATAAAATATAT-TTTA
* * *
3169416 AAGTTAACATAAGAATAAAATACATTTTT
1 AAGTTAACA-AAAAATAAAATATATTTTA
*
3169445 AAGTTAA-AGTAAAAATAAAATATATTTAA
1 AAGTTAACA--AAAAATAAAATATATTTTA
3169474 TAAGTTTAACAAAAAATAAAATATATATTTTA
1 -AAG-TTAACAAAAAAT-AAA-ATATATTTTA
3169506 AAGTTAA
1 AAGTTAA
3169513 GATATGAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.01
29 26 0.32
30 32 0.40
31 12 0.15
32 10 0.12
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (28 bp):
AAGTTAACAAAAAATAAAATATATTTTA
Found at i:3169479 original size:59 final size:61
Alignment explanation
Indices: 3169399--3169512 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 61
3169389 TTAATAAAAG
* *
3169399 AATAAAATATATCTTTAAAG-TTAACATAAGAATAAAATACAT-TTTT-AAGTTAAAGTAAA
1 AATAAAATATATCTTAAAAGTTTAACA-AAAAATAAAATACATATTTTAAAGTTAAAGTAAA
*
3169458 AATAAAATATAT-TTAATAAGTTTAACAAAAAATAAAATATATATTTTAAAGTTAA
1 AATAAAATATATCTTAA-AAGTTTAACAAAAAATAAAATACATATTTTAAAGTTAA
3169513 GATATGAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
58 3 0.06
59 28 0.58
60 10 0.21
61 7 0.15
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (61 bp):
AATAAAATATATCTTAAAAGTTTAACAAAAAATAAAATACATATTTTAAAGTTAAAGTAAA
Found at i:3171653 original size:21 final size:21
Alignment explanation
Indices: 3171629--3171688 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
3171619 AAATTAAATG
3171629 CACCAAATTCGGTGCCCAATC
1 CACCAAATTCGGTGCCCAATC
3171650 CACCAAATTCGGTGCCCAATC
1 CACCAAATTCGGTGCCCAATC
3171671 CACCAAATTCGGTGCCCA
1 CACCAAATTCGGTGCCCA
3171689 TCTTTGTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.18
Consensus pattern (21 bp):
CACCAAATTCGGTGCCCAATC
Found at i:3179263 original size:34 final size:34
Alignment explanation
Indices: 3179220--3179284 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
3179210 TCAAATGTTG
3179220 CATTATGTTACAGAGGATCAAACTTACTAATCAA
1 CATTATGTTACAGAGGATCAAACTTACTAATCAA
*
3179254 CATTATGTTACGGAGGATCAAACTTACTAAT
1 CATTATGTTACAGAGGATCAAACTTACTAAT
3179285 AAATGGGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (34 bp):
CATTATGTTACAGAGGATCAAACTTACTAATCAA
Found at i:3181575 original size:131 final size:131
Alignment explanation
Indices: 3181359--3181731 Score: 410
Period size: 131 Copynumber: 2.8 Consensus size: 131
3181349 TGAATCTACA
* ** * * * * * *
3181359 ATGAGAATAGTAATATC-CTTTCATTTCGGTCGGAGAAATAAATGATTGCTTTAAGGCA-TAAGA
1 ATGA-AATAGTAATATCTCTTT-ATCTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAA-A
* * * *
3181422 GGTCATTTATTCTCGATTGGAAATAATTTGATATT-TCCGTTTTCTCTCAAATTAATATTGATTT
63 GGTCATTTATTCTCGATTGGAAATAATTAGATATTAT-CGTTTTCACTCAAATCAATATTGAATT
*
3181486 TTTAG
127 TTAAG
* * *
3181491 ATGAAATATTAATATCTCTTTATCTCAATTGGGGTAATCAATGACTGTTTTAATGCACGAAAGGT
1 ATGAAATAGTAATATCTCTTTATCTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGT
* * * * *** ** *
3181556 CGTTTATTCTCGATAGGAAATCATTAGATGTTATTAATTTCACTTGAATCGATATTGAATTTTAA
66 CATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAA
3181621 G
131 G
* * *
3181622 ATGAAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGATTGTTTTAATGCACGAAAGAT
1 ATGAAATAGTAATATCTCTTTATCTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGT
*
3181687 CATTTATTCTTGATTGGAAATAATTAGATATTATCGTTTTCACTC
66 CATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
3181732 TTAAAATTAT
Statistics
Matches: 196, Mismatches: 42, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
131 185 0.94
132 11 0.06
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (131 bp):
ATGAAATAGTAATATCTCTTTATCTCAATTGGAGTAATAAATGACTGTTTTAATGCACGAAAGGT
CATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAA
G
Found at i:3187741 original size:14 final size:14
Alignment explanation
Indices: 3187717--3187749 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3187707 ATAATTTTAG
3187717 ATATT-TTAAAAAT
1 ATATTATTAAAAAT
3187730 ATATTATTAAAAAT
1 ATATTATTAAAAAT
3187744 ATATTA
1 ATATTA
3187750 AAAATACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTATTAAAAAT
Found at i:3187748 original size:11 final size:11
Alignment explanation
Indices: 3187734--3187796 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3187724 AAAAATATAT
3187734 TATTAAAAATA
1 TATTAAAAATA
3187745 TATTAAAAATA
1 TATTAAAAATA
* * ***
3187756 CAGTATTGATA
1 TATTAAAAATA
3187767 -ATTATAAAAT-
1 TATTA-AAAATA
3187777 T-TTAAAAATA
1 TATTAAAAATA
3187787 TATTAAAAAT
1 TATTAAAAAT
3187797 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3187856 original size:20 final size:20
Alignment explanation
Indices: 3187827--3187864 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3187817 ACCCAAACCT
*
3187827 TAAACTATAAATCCTAAAAC
1 TAAACCATAAATCCTAAAAC
*
3187847 TAAACCATAAATCTTAAA
1 TAAACCATAAATCCTAAA
3187865 TCCTAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACCATAAATCCTAAAAC
Found at i:3187857 original size:27 final size:27
Alignment explanation
Indices: 3187821--3187886 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
3187811 ACTCAAACCC
*
3187821 AAACCTTAAACTATAAATCCTAAA-ACT
1 AAACCATAAACT-TAAATCCTAAACACT
*
3187848 AAACCATAAATCTTAAATCCTAAACATT
1 AAACCATAAA-CTTAAATCCTAAACACT
*
3187876 AAACCCTAAAC
1 AAACCATAAAC
3187887 CTTACCCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (27 bp):
AAACCATAAACTTAAATCCTAAACACT
Found at i:3187871 original size:14 final size:13
Alignment explanation
Indices: 3187827--3187886 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
3187817 ACCCAAACCT
3187827 TAAACTATAAATCC
1 TAAACT-TAAATCC
3187841 TAAAAC-TAAA-CC
1 T-AAACTTAAATCC
3187853 ATAAATCTTAAATCC
1 -TAAA-CTTAAATCC
*
3187868 TAAACATTAAACCC
1 TAAAC-TTAAATCC
3187882 TAAAC
1 TAAAC
3187887 CTTACCCCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
12 5 0.13
13 7 0.18
14 21 0.54
15 6 0.15
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAACTTAAATCC
Found at i:3200466 original size:24 final size:24
Alignment explanation
Indices: 3200433--3200479 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3200423 ACGACCAAAT
*
3200433 GGAAGCAAGAGCCTAATCCTTTCC
1 GGAAGCAAGAGCCTAATACTTTCC
*
3200457 GGAAGTAAGAGCCTAATACTTTC
1 GGAAGCAAGAGCCTAATACTTTC
3200480 TGAAAGCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
GGAAGCAAGAGCCTAATACTTTCC
Found at i:3211791 original size:14 final size:14
Alignment explanation
Indices: 3211772--3211803 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3211762 CATACTTAAC
3211772 ATAATGAAAAGAAA
1 ATAATGAAAAGAAA
3211786 ATAATGAAAAGAAA
1 ATAATGAAAAGAAA
3211800 ATAA
1 ATAA
3211804 AGAGATGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (14 bp):
ATAATGAAAAGAAA
Found at i:3214086 original size:33 final size:32
Alignment explanation
Indices: 3213978--3214095 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
3213968 AAATATCTTA
* * *
3213978 GGGCCTGAGAGCCTACCCAAGAGAGTACCTTA
1 GGGCCTAAGAGCCTACCCAAGAAAGTACCTTG
* * *
3214010 GAGCCTAAGACCCTACCCAAGGAAGTACCTTG
1 GGGCCTAAGAGCCTACCCAAGAAAGTACCTTG
* * *
3214042 GGGCCTTAGAGCCTACCCAAGAAAATGCCTTGG
1 GGGCCTAAGAGCCTACCCAAGAAAGTACCTT-G
*
3214075 GGGCCTCAGAGCCTACCCAAG
1 GGGCCTAAGAGCCTACCCAAG
3214096 GTCACCTTAG
Statistics
Matches: 72, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
32 51 0.71
33 21 0.29
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (32 bp):
GGGCCTAAGAGCCTACCCAAGAAAGTACCTTG
Found at i:3222513 original size:22 final size:26
Alignment explanation
Indices: 3222475--3222557 Score: 86
Period size: 22 Copynumber: 3.3 Consensus size: 26
3222465 GGTGTGACAT
* *
3222475 TATTATATATGTATATATACTTTATA
1 TATTATATACGTGTATATACTTTATA
*
3222501 T-TTA-ATAC-T-TATACACTTTATA
1 TATTATATACGTGTATATACTTTATA
*
3222523 TATTATATACGTGTATATA-TATATA
1 TATTATATACGTGTATATACTTTATA
3222548 TATATATATA
1 TAT-TATATA
3222558 TATATATCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
22 13 0.27
23 4 0.08
24 7 0.15
25 12 0.25
26 12 0.25
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTATATACGTGTATATACTTTATA
Found at i:3222541 original size:2 final size:2
Alignment explanation
Indices: 3222536--3223237 Score: 166
Period size: 2 Copynumber: 353.5 Consensus size: 2
3222526 TATATACGTG
* * *
3222536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TA TA CTT TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
3222578 T- TA T- TA TA TA TG TA TA TA TA T- TT TA TA CTA -A AA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
3222617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
3222659 TA GTT TA TA CA TA CA TA CA TA CA TA TA TA TA TA TA TA CT- TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
3222702 TT TA TA TA CTA TA TA CTT TA TA T- TA TA TA TA TA CTT TA T- TC
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
3222743 TT TA TA -A T- TA TA CTT TT TA TA TA TA TA -A TA TA CT- TA TA CTT
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * * * *
3222784 TA TA T- TA T- TA TG TA TG TA CA TA TA CTT TA TA CTA -A AA CTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA
* *
3222824 TA TA TA TA TA -A GTA TA TA -A TA TA AA GTA TA TA -A TA TA TA AA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
3222865 GT- TT TA GTA TA AA GTA TA TA TA CT- TCA TA GTT TA TA TA TA TA
1 -TA TA TA -TA TA TA -TA TA TA TA -TA T-A TA -TA TA TA TA TA TA
* *
3222907 CT- TA TA -A TA TA CT- TA TA CTT TA TA GTT 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
* * * * *
3222948 TA TA TA TA TA TA TA CA CTT TA TA CTT TA AA GTA TA TA TA TC T-
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * * *
3222990 TG TA GTT TA TA TA TA TA TA T- TA TA TA TA CTT TA TA GTT TA CA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * *
3223032 CTT TA TA TA TA TA -A T- TA TA CT- TA TA CT- TT TC T- TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* *
3223070 TG TA TA T- TA -A AA TA -A GTA TA TA TA TA TA -A CTA TA TA CT-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA
* * * * * * *
3223108 TA TA -A TG TA T- TA -A TC TA TG CA TA TG TA TA -A TG TA CA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3223145 TA TA TA TA CA TG CA TCA TA T- TA TCA TA -A CA T- TCG T- TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA T-A TA TA TA
3223184 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
3223226 TA TA T- TA TA TA T
1 TA TA TA TA TA TA T
3223238 TGTTCTAATT
Statistics
Matches: 512, Mismatches: 99, Indels: 178
0.65 0.13 0.23
Matches are distributed among these distances:
1 47 0.09
2 422 0.82
3 43 0.08
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3222745 original size:25 final size:26
Alignment explanation
Indices: 3222681--3222754 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 26
3222671 ACATACATAC
3222681 ATATATATA-TATATAC-TTAT-A-T
1 ATATATATACTATATACTTTATAATT
3222703 -T-TATATACTATATACTTTAT-ATT
1 ATATATATACTATATACTTTATAATT
* *
3222726 ATATATATACTTTATTCTTTATAATT
1 ATATATATACTATATACTTTATAATT
3222752 ATA
1 ATA
3222755 CTTTTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 6 0.14
21 8 0.18
22 5 0.11
23 1 0.02
24 1 0.02
25 17 0.39
26 6 0.14
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATATATACTATATACTTTATAATT
Found at i:3222859 original size:29 final size:29
Alignment explanation
Indices: 3222825--3222884 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3222815 CTAAAACTTT
3222825 ATATATATAAGTATATAATATAAAGTATATA
1 ATATATA-AAGT-TATAATATAAAGTATATA
* *
3222856 ATATATAAAGTTTTAGTATAAAGTATATA
1 ATATATAAAGTTATAATATAAAGTATATA
3222885 TACTTCATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 4 0.15
31 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (29 bp):
ATATATAAAGTTATAATATAAAGTATATA
Found at i:3222904 original size:29 final size:28
Alignment explanation
Indices: 3222842--3222930 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 28
3222832 TAAGTATATA
*
3222842 ATATAAAGTATATAATA-TATAAAGTTT-T
1 ATATAAAGTATAT-ATACT-TATAGTTTAT
3222870 AGTATAAAGTATATATACTTCATAGTTTAT
1 A-TATAAAGTATATATACTT-ATAGTTTAT
** *
3222900 ATATATACTTATAATATACTTATACTTTAT
1 ATATA-AAGTAT-ATATACTTATAGTTTAT
3222930 A
1 A
3222931 GTTTATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
28 5 0.10
29 23 0.45
30 15 0.29
31 8 0.16
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (28 bp):
ATATAAAGTATATATACTTATAGTTTAT
Found at i:3222948 original size:47 final size:46
Alignment explanation
Indices: 3222897--3223059 Score: 131
Period size: 47 Copynumber: 3.5 Consensus size: 46
3222887 CTTCATAGTT
3222897 TATATATATACTTATAATATACTTATACTTTATAGTTTATATATATA
1 TATATATATA-TTATAATATACTTATACTTTATAGTTTATATATATA
* * * * *
3222944 TATATATATA-TATATATACACTTTATACTTTAAAGTATATATATCTTG
1 TATATATATATTATA-ATATAC-TTATACTTTATAGTTTATATAT-ATA
* * *
3222992 TAGTTTATATATATATATTATA--TATACTTTATAGTTTACACT-T-TA
1 TA-TATATATAT-TATAATATACTTATACTTTATAGTTTATA-TATATA
*
3223037 TATATATA-ATTATACTTATACTT
1 TATATATATATTATA-ATATACTT
3223060 TTCTTATATA
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
42 4 0.04
43 7 0.08
44 5 0.05
45 8 0.09
46 5 0.05
47 46 0.49
48 4 0.04
49 7 0.08
50 3 0.03
51 4 0.04
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (46 bp):
TATATATATATTATAATATACTTATACTTTATAGTTTATATATATA
Found at i:3223582 original size:24 final size:24
Alignment explanation
Indices: 3223537--3223582 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3223527 TTTAGTCCAT
*
3223537 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
3223561 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
3223583 TATCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Found at i:3223700 original size:6 final size:6
Alignment explanation
Indices: 3223689--3223722 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3223679 AGCATAAGTA
* *
3223689 TATATG TATATG TATATG TATATA TATATA TATA
1 TATATG TATATG TATATG TATATG TATATG TATA
3223723 AAGTATAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:3224145 original size:24 final size:24
Alignment explanation
Indices: 3224100--3224145 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3224090 TTTAGTCCAT
*
3224100 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
3224124 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
3224146 TCCCTAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Found at i:3224295 original size:22 final size:22
Alignment explanation
Indices: 3224266--3224457 Score: 168
Period size: 22 Copynumber: 8.8 Consensus size: 22
3224256 TGTACATATC
3224266 TAAAGTA-TAAAGTATATAATA
1 TAAAGTATTAAAGTATATAATA
*
3224287 TAAAAGTATTAAATTATATAATA
1 T-AAAGTATTAAAGTATATAATA
* * * *
3224310 TAAAGTAATAAAGTGTTTGGATA
1 TAAAGTATTAAAGTATAT-AATA
*
3224333 T-AAGTATTAAAGTTTATAA-A
1 TAAAGTATTAAAGTATATAATA
*
3224353 TATAAGTGTTAAA-TATA-AAGTA
1 TA-AAGTATTAAAGTATATAA-TA
*
3224375 TATAAGTACTAAAGTATATAATA
1 TA-AAGTATTAAAGTATATAATA
*
3224398 TAAAGTATTAAACTATATAATA
1 TAAAGTATTAAAGTATATAATA
3224420 T-AAGTATTAAA-TATA-AAGTA
1 TAAAGTATTAAAGTATATAA-TA
3224440 TTAAAGTATATAAA-TATA
1 -TAAAGTAT-TAAAGTATA
3224458 AGTATTAAAT
Statistics
Matches: 142, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.01
20 10 0.07
21 16 0.11
22 78 0.55
23 34 0.24
24 2 0.01
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAAGTATTAAAGTATATAATA
Found at i:3224338 original size:66 final size:65
Alignment explanation
Indices: 3224232--3224457 Score: 209
Period size: 66 Copynumber: 3.5 Consensus size: 65
3224222 TATACATATA
* * *
3224232 TAAACTATAAAGTAT-AAGT-ATATATGTACAT-ATCTAAAGTA-TAAAGTATATAATATAAAAG
1 TAAA-TATAAAGTATAAAGTAATA-AAGTATATAATATAAAGTATTAAAGTATATAATAT-AAAG
3224293 TAT
63 TAT
* * * *
3224296 TAAATTATATAA-TATAAAGTAATAAAGTGTTTGGATAT-AAGTATTAAAGTTTATAA-ATATAA
1 TAAA-TATA-AAGTATAAAGTAATAAAGTATAT-AATATAAAGTATTAAAGTATATAATATA-AA
*
3224358 GTGT
62 GTAT
* *
3224362 TAAATATAAAGTATATAAGTACTAAAGTATATAATATAAAGTATTAAACTATATAATAT-AAGTA
1 TAAATATAAAGTATA-AAGTAATAAAGTATATAATATAAAGTATTAAAGTATATAATATAAAGTA
3224426 T
65 T
3224427 TAAATATAAAGTATTAAAGTATATAAA-TATA
1 TAAATATAAAGTA-TAAAGTA-ATAAAGTATA
3224458 AGTATTAAAT
Statistics
Matches: 133, Mismatches: 16, Indels: 25
0.76 0.09 0.14
Matches are distributed among these distances:
64 13 0.10
65 50 0.38
66 54 0.41
67 16 0.12
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (65 bp):
TAAATATAAAGTATAAAGTAATAAAGTATATAATATAAAGTATTAAAGTATATAATATAAAGTAT
Found at i:3224373 original size:14 final size:14
Alignment explanation
Indices: 3224349--3224472 Score: 91
Period size: 14 Copynumber: 8.7 Consensus size: 14
3224339 TTAAAGTTTA
*
3224349 TAAATAT-AAGTGT
1 TAAATATAAAGTAT
3224362 TAAATATAAAGTAT
1 TAAATATAAAGTAT
*
3224376 ATAAGTACTAAAGTA-
1 -TAAATA-TAAAGTAT
3224391 TATAATATAAAGTAT
1 TA-AATATAAAGTAT
3224406 TAAACTATATAA-TA-
1 TAAA-TATA-AAGTAT
*
3224420 TAAGTATTAAA-TA-
1 TAAATA-TAAAGTAT
3224433 TAAAGTATTAAAGTAT
1 TAAA-TA-TAAAGTAT
3224449 ATAAATAT-AAGTAT
1 -TAAATATAAAGTAT
3224463 TAAATATAAA
1 TAAATATAAA
3224473 ATATATTAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 25
0.76 0.04 0.20
Matches are distributed among these distances:
13 23 0.25
14 36 0.39
15 19 0.20
16 11 0.12
17 4 0.04
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (14 bp):
TAAATATAAAGTAT
Found at i:3224389 original size:8 final size:7
Alignment explanation
Indices: 3224362--3224477 Score: 75
Period size: 8 Copynumber: 16.3 Consensus size: 7
3224352 ATATAAGTGT
3224362 TAAA-TA
1 TAAAGTA
3224368 TAAAGTA
1 TAAAGTA
3224375 TATAAGTA
1 TA-AAGTA
3224383 CTAAAGTA
1 -TAAAGTA
3224391 TATAA-TA
1 TA-AAGTA
3224398 TAAAGTA
1 TAAAGTA
*
3224405 TTAAACTA
1 -TAAAGTA
3224413 TATAA-TA
1 TA-AAGTA
3224420 T-AAGTA
1 TAAAGTA
3224426 TTAAA-TA
1 -TAAAGTA
3224433 TAAAGTA
1 TAAAGTA
3224440 TTAAAGTA
1 -TAAAGTA
*
3224448 TATAAATA
1 TA-AAGTA
3224456 T-AAGTA
1 TAAAGTA
3224462 TTAAA-TA
1 -TAAAGTA
*
3224469 TAAAATA
1 TAAAGTA
3224476 TA
1 TA
3224478 TTAATTATCA
Statistics
Matches: 91, Mismatches: 3, Indels: 31
0.73 0.02 0.25
Matches are distributed among these distances:
5 2 0.02
6 20 0.22
7 31 0.34
8 36 0.40
9 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (7 bp):
TAAAGTA
Found at i:3224475 original size:43 final size:41
Alignment explanation
Indices: 3224232--3224477 Score: 134
Period size: 44 Copynumber: 5.9 Consensus size: 41
3224222 TATACATATA
* * * *
3224232 TAAACTATA-AAGTATAAGTATATATGTACATATCTAAAGTA-
1 TAAACTATATAA-TATAAGTATAAATATA-AAATATAAAGTAT
* * *
3224273 TAAAGTATATAATATAAAAGTATTAAATTATATAATATAAAGTAA
1 TAAACTATATAATAT--AAGTA-TAAA-TATAAAATATAAAGTAT
* * * * * *
3224318 TAAAGTGTTTGGATATAAGTATTAAAGTTTATAAATAT-AAGTGT
1 TAAACTATAT-AATATAAGTA-TAAA-TATA-AAATATAAAGTAT
* *
3224362 TAAA-TATAAAGTATATAAGTACTAAAGTATATAATATAAAGTAT
1 TAAACTATATA--ATATAAGTA-TAAA-TATAAAATATAAAGTAT
3224406 TAAACTATATAATATAAG--T--AT-T-AAATATAAAGTAT
1 TAAACTATATAATATAAGTATAAATATAAAATATAAAGTAT
*
3224441 TAAAGTATATAAATATAAGTATTAAATATAAAATATA
1 TAAACTATAT-AATATAAGTA-TAAATATAAAATATA
3224478 TTAATTATCA
Statistics
Matches: 160, Mismatches: 25, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
35 21 0.13
36 9 0.06
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 13 0.08
42 3 0.02
43 26 0.16
44 59 0.37
45 21 0.13
46 4 0.03
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (41 bp):
TAAACTATATAATATAAGTATAAATATAAAATATAAAGTAT
Found at i:3224478 original size:22 final size:22
Alignment explanation
Indices: 3224389--3224458 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 22
3224379 AGTACTAAAG
*
3224389 TATATAATATA-AAGTATTAAA
1 TATAAAATATATAAGTATTAAA
*
3224410 CTAT-ATA-ATATAAGTATTAAA
1 -TATAAAATATATAAGTATTAAA
*
3224431 TATAAAGTAT-TAAAGTATATAAA
1 TATAAAATATAT-AAGTAT-TAAA
3224454 TATAA
1 TATAA
3224459 GTATTAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.15
21 13 0.33
22 11 0.28
23 9 0.23
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (22 bp):
TATAAAATATATAAGTATTAAA
Found at i:3224491 original size:73 final size:73
Alignment explanation
Indices: 3224368--3224507 Score: 171
Period size: 73 Copynumber: 1.9 Consensus size: 73
3224358 GTGTTAAATA
* * *
3224368 TAAAGTATATAAGTACTAAAGTATATAATATAAAGTATTAAACTATATAATATAA-GTATTAAAT
1 TAAAGTATATAAATACTAAAGTATATAATATAAAATATTAAACTATATAAT-TAATATATTAAAT
3224432 ATAAAGTAT
65 ATAAAGTAT
* *
3224441 TAAAGTATATAAATA-T-AAGTAT-TAAATATAAAATATATTAATTATCATAATTAATATATTAA
1 TAAAGTATATAAATACTAAAGTATAT-AATATAAAATAT-TAAACTAT-ATAATTAATATATTAA
3224503 ATATA
63 ATATA
3224508 TTTATTAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
70 1 0.02
71 17 0.29
72 10 0.17
73 30 0.52
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (73 bp):
TAAAGTATATAAATACTAAAGTATATAATATAAAATATTAAACTATATAATTAATATATTAAATA
TAAAGTAT
Found at i:3224498 original size:21 final size:21
Alignment explanation
Indices: 3224472--3224532 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3224462 TTAAATATAA
3224472 AATATATTAATTATCATAATT
1 AATATATTAATTATCATAATT
*
3224493 AATATATTAA--AT-ATATTT
1 AATATATTAATTATCATAATT
* *
3224511 ATTAAATTAATTATCATAATT
1 AATATATTAATTATCATAATT
3224532 A
1 A
3224533 CTATTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.39
19 2 0.06
20 2 0.06
21 16 0.48
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATATTAATTATCATAATT
Found at i:3224522 original size:30 final size:29
Alignment explanation
Indices: 3224461--3224523 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
3224451 AAATATAAGT
*
3224461 ATTAAATATAAAATATATTAATTATCATA
1 ATTAAATATAAAATATATTAATTATAATA
* *
3224490 ATTAATATATTAAATATATTTATTA-AATTA
1 ATTAA-ATATAAAATATATTAATTATAA-TA
3224520 ATTA
1 ATTA
3224524 TCATAATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTAAATATAAAATATATTAATTATAATA
Found at i:3225726 original size:51 final size:51
Alignment explanation
Indices: 3225621--3225735 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
3225611 ATGACTAATG
* * * *
3225621 AATAAGATAATAATAAACTAAAGATAATGTTTCGATTCAATACTAACTCTT
1 AATAAAATAATAATAAACTAAAGATAATGTTTCAACTCAATACTAACTCAT
* * * *
3225672 AATAAAATAATAATAAACTAATGATAATGTTTTAACTCGA-ACTTAATTCAT
1 AATAAAATAATAATAAACTAAAGATAATGTTTCAACTCAATAC-TAACTCAT
3225723 AATAAAATAATAA
1 AATAAAATAATAA
3225736 ATCTAATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 2 0.04
51 53 0.96
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATGTTTCAACTCAATACTAACTCAT
Found at i:3226406 original size:64 final size:64
Alignment explanation
Indices: 3226315--3226517 Score: 193
Period size: 65 Copynumber: 3.1 Consensus size: 64
3226305 AAGAGTGTAC
* *
3226315 CGATGCACCAATCCATGCATTCGATGCAC-CATTGAATAAATTGAACATTGAATGCATTTTATGC
1 CGATGCA-CAAGCCATGCA-TCGATGCACTCATTGAATAAATT-AACATCGAATGCATTTTATGC
3226379 AT
63 AT
** *
3226381 CGATGCACATA-CCATGCATCGATGCACTCAGGTTTTTATGAA--AACATCGAATGCATTTTATG
1 CGATGCACA-AGCCATGCATCGATGCACTCA---TTGAATAAATTAACATCGAATGCATTTTATG
3226443 CAT
62 CAT
* ** **
3226446 CGATGCACAAGTCATGCATCGATGCACTCA--GGCTATTTTAAAACATCGAATGCATTTTATGCA
1 CGATGCACAAGCCATGCATCGATGCACTCATTGAATAAATT--AACATCGAATGCATTTTATGCA
3226509 T
64 T
3226510 CGATGCAC
1 CGATGCAC
3226518 CCTTAGTGCA
Statistics
Matches: 116, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
60 1 0.01
64 41 0.35
65 60 0.52
66 8 0.07
68 6 0.05
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (64 bp):
CGATGCACAAGCCATGCATCGATGCACTCATTGAATAAATTAACATCGAATGCATTTTATGCAT
Found at i:3226533 original size:64 final size:64
Alignment explanation
Indices: 3226358--3226537 Score: 233
Period size: 65 Copynumber: 2.8 Consensus size: 64
3226348 GAATAAATTG
* *
3226358 AACATTGAATGCATTTTATGCATCGATGCACATACC-ATGCATCGATGCACTCAGGTTTTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCAC--ACCTATGCATCGATGCACTCAGGTATTTATGA
3226422 A
64 A
**
3226423 AACATCGAATGCATTTTATGCATCGATGCACAAGTCATGCATCGATGCACTCAGGCTATTT-T-A
1 AACATCGAATGCATTTTATGCATCGATGCACACCT-ATGCATCGATGCACTCAGG-TATTTATGA
3226486 A
64 A
*
3226487 AACATCGAATGCATTTTATGCATCGATGCAC-CCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACC-TA-TGCATCGATGCACT
3226538 AAGTGTTCCA
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
63 2 0.02
64 47 0.46
65 50 0.49
66 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACCTATGCATCGATGCACTCAGGTATTTATGAA
Found at i:3229375 original size:23 final size:23
Alignment explanation
Indices: 3229345--3229393 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
3229335 TTGGTTATGA
3229345 CATAGGACATTAGGACATGCTAG
1 CATAGGACATTAGGACATGCTAG
3229368 CATAGGACATTAGGACATGCTAG
1 CATAGGACATTAGGACATGCTAG
3229391 CAT
1 CAT
3229394 GAGTGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (23 bp):
CATAGGACATTAGGACATGCTAG
Found at i:3234423 original size:2 final size:2
Alignment explanation
Indices: 3234416--3234449 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3234406 TTAGATCTTA
3234416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3234450 GTTTGGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3235251 original size:64 final size:65
Alignment explanation
Indices: 3235092--3235251 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 65
3235082 GAATAAATTG
*
3235092 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCAATGATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCAATGATGCACTCAGGTATTTATGAA
* * *
3235157 AACGTCGAATGCATTTTATACATCAATGCACA-AGCCATGC-ATCGATGCACTCAGGCTATTT-T
1 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCAAT-GATGCACTCAGG-TATTTAT
3235219 -AA
63 GAA
3235221 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
3235252 CCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 33 0.39
65 48 0.56
66 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCAATGATGCACTCAGGTATTTATGAA
Found at i:3239479 original size:133 final size:133
Alignment explanation
Indices: 3239241--3239507 Score: 534
Period size: 133 Copynumber: 2.0 Consensus size: 133
3239231 TTTCAAAGGC
3239241 CTTCTTCTGAACAAAAAGTGGTGCTACGCCTTTAAACAAATCAAAAAGTCGAAACTTTGATTTAT
1 CTTCTTCTGAACAAAAAGTGGTGCTACGCCTTTAAACAAATCAAAAAGTCGAAACTTTGATTTAT
3239306 TTATTTTTCTGTGTATGACCGAATAAATGTGTAGGTTAATAGGTGTGTAATCGAGCCGTGAGATT
66 TTATTTTTCTGTGTATGACCGAATAAATGTGTAGGTTAATAGGTGTGTAATCGAGCCGTGAGATT
3239371 GAA
131 GAA
3239374 CTTCTTCTGAACAAAAAGTGGTGCTACGCCTTTAAACAAATCAAAAAGTCGAAACTTTGATTTAT
1 CTTCTTCTGAACAAAAAGTGGTGCTACGCCTTTAAACAAATCAAAAAGTCGAAACTTTGATTTAT
3239439 TTATTTTTCTGTGTATGACCGAATAAATGTGTAGGTTAATAGGTGTGTAATCGAGCCGTGAGATT
66 TTATTTTTCTGTGTATGACCGAATAAATGTGTAGGTTAATAGGTGTGTAATCGAGCCGTGAGATT
3239504 GAA
131 GAA
3239507 C
1 C
3239508 CTGAATATTG
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (133 bp):
CTTCTTCTGAACAAAAAGTGGTGCTACGCCTTTAAACAAATCAAAAAGTCGAAACTTTGATTTAT
TTATTTTTCTGTGTATGACCGAATAAATGTGTAGGTTAATAGGTGTGTAATCGAGCCGTGAGATT
GAA
Found at i:3256760 original size:12 final size:12
Alignment explanation
Indices: 3256745--3256780 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3256735 TGGTGGAATA
3256745 GGAGGTGGGTTT
1 GGAGGTGGGTTT
*
3256757 GGAGGTGAGTTT
1 GGAGGTGGGTTT
*
3256769 GGAGGTCGGTTT
1 GGAGGTGGGTTT
3256781 TATTGACTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.11, C:0.03, G:0.53, T:0.33
Consensus pattern (12 bp):
GGAGGTGGGTTT
Found at i:3257484 original size:42 final size:41
Alignment explanation
Indices: 3257433--3257514 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
3257423 TACATATTCA
*
3257433 AAGAGGGTATTGATACCTGTTGAAGCAGTATCGATACCTAGC
1 AAGAGGGTATCGATACCTGTTGAAG-AGTATCGATACCTAGC
* * *
3257475 AAGAGGGTATCGATACCTGTTTATGGGTATCGATACCTAG
1 AAGAGGGTATCGATACCTGTTGAAGAGTATCGATACCTAG
3257515 TGCACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 14 0.39
42 22 0.61
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (41 bp):
AAGAGGGTATCGATACCTGTTGAAGAGTATCGATACCTAGC
Found at i:3264995 original size:3 final size:3
Alignment explanation
Indices: 3264982--3265085 Score: 77
Period size: 3 Copynumber: 33.7 Consensus size: 3
3264972 ATATTTATTA
* *
3264982 AAT AAT AAAT AAT AAT AACT ATT AAT AA- AAGGT AATT AAT ACT AAT
1 AAT AAT -AAT AAT AAT AA-T AAT AAT AAT AA--T AA-T AAT AAT AAT
* * * * *
3265028 ATT AAT ATT ACT AAT AAT ATT ACT AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3265075 AAA AAT AAT AA
1 AAT AAT AAT AA
3265086 ATCCTATATA
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.05
3 66 0.82
4 8 0.10
5 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3265958 original size:39 final size:39
Alignment explanation
Indices: 3265915--3265990 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
3265905 AGAATAAAAT
3265915 GGTTTCTAGAGAAATAG-TCTTAAAGAAGATAAGGTTGAG
1 GGTTTCTAGAGAAA-AGATCTTAAAGAAGATAAGGTTGAG
* * * *
3265954 GGTTTCTAGGGAAACGATCTTAAGGAAGATTAGGTTG
1 GGTTTCTAGAGAAAAGATCTTAAAGAAGATAAGGTTG
3265991 TTTCTAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (39 bp):
GGTTTCTAGAGAAAAGATCTTAAAGAAGATAAGGTTGAG
Found at i:3266037 original size:36 final size:36
Alignment explanation
Indices: 3265914--3266246 Score: 257
Period size: 36 Copynumber: 9.2 Consensus size: 36
3265904 AAGAATAAAA
* * *
3265914 TGGTTTCTAGAGAAATAGTCTTAAAGAAGA-TAAGGT
1 TGGTTTCTAGAGAAACAATCTTAAGGAAGACT-AGGT
* * *
3265950 TGAGGGTTTCTAGGGAAACGATCTTAAGGAAGATTAGGT
1 T---GGTTTCTAGAGAAACAATCTTAAGGAAGACTAGGT
* **
3265989 T-GTTTCTAGAGAAACAACCTTAAATAAGACTAGGT
1 TGGTTTCTAGAGAAACAATCTTAAGGAAGACTAGGT
* * *
3266024 TGGTTTCTAGAGAAACAA-CTTTAAGGAATAATACGT
1 TGGTTTCTAGAGAAACAATC-TTAAGGAAGACTAGGT
* * * *
3266060 TGGTTTCTACG-GAGACTATCTTAAGGAAGATTGGGT
1 TGGTTTCTA-GAGAAACAATCTTAAGGAAGACTAGGT
* * * * *
3266096 TGGTTTATAGGGAAA-AACCTTAAGGAAGACTCGAT
1 TGGTTTCTAGAGAAACAATCTTAAGGAAGACTAGGT
* * * *
3266131 TGGTTTCTAGCGAAA-AAGTCTTAAGGAAGAGTCGAT
1 TGGTTTCTAGAGAAACAA-TCTTAAGGAAGACTAGGT
* * * *
3266167 TGGTTTATA-AGGAAACATTCTTAAGGAATACTAGAT
1 TGGTTTCTAGA-GAAACAATCTTAAGGAAGACTAGGT
* *
3266203 TGGTTTCTAGGGAAACAATCTTAAAGAAGACTAGGT
1 TGGTTTCTAGAGAAACAATCTTAAGGAAGACTAGGT
*
3266239 TTGTTTCT
1 TGGTTTCT
3266247 CAAAAGAGAA
Statistics
Matches: 238, Mismatches: 46, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
35 61 0.26
36 144 0.61
37 3 0.01
39 29 0.12
40 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (36 bp):
TGGTTTCTAGAGAAACAATCTTAAGGAAGACTAGGT
Found at i:3266083 original size:107 final size:107
Alignment explanation
Indices: 3265954--3266246 Score: 333
Period size: 107 Copynumber: 2.7 Consensus size: 107
3265944 TAAGGTTGAG
* * *
3265954 GGTTTCTAGGGAAACGATCTTAAGGAAGATTAGGTT-GTTTCTAGAGAAACAACCTTAAATAAGA
1 GGTTTCTAAGGAAAC-ATCTTAAGGAAGATTAGGTTGGTTTCTAGGGAAACAACCTTAAAGAAGA
*
3266018 CTAGGTTGGTTTCTAGAGAAACAACT-TTAAGGAATAATACG-TT
65 CTAGGTTGGTTTCTAGAGAAA-AACTCTTAAGGAAGAAT-CGATT
* * * * *
3266061 GGTTTCTACGGAGACTATCTTAAGGAAGATTGGGTTGGTTTATAGGGAAA-AACCTTAAGGAAGA
1 GGTTTCTAAGGAAAC-ATCTTAAGGAAGATTAGGTTGGTTTCTAGGGAAACAACCTTAAAGAAGA
* * * * *
3266125 CTCGATTGGTTTCTAGCGAAAAAGTCTTAAGGAAGAGTCGATT
65 CTAGGTTGGTTTCTAGAGAAAAACTCTTAAGGAAGAATCGATT
* * * * *
3266168 GGTTTATAAGGAAACATTCTTAAGGAATACTAGATTGGTTTCTAGGGAAACAATCTTAAAGAAGA
1 GGTTTCTAAGGAAACA-TCTTAAGGAAGATTAGGTTGGTTTCTAGGGAAACAACCTTAAAGAAGA
*
3266233 CTAGGTTTGTTTCT
65 CTAGGTTGGTTTCT
3266247 CAAAAGAGAA
Statistics
Matches: 154, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
106 6 0.04
107 114 0.74
108 34 0.22
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (107 bp):
GGTTTCTAAGGAAACATCTTAAGGAAGATTAGGTTGGTTTCTAGGGAAACAACCTTAAAGAAGAC
TAGGTTGGTTTCTAGAGAAAAACTCTTAAGGAAGAATCGATT
Found at i:3266154 original size:143 final size:143
Alignment explanation
Indices: 3265914--3266232 Score: 299
Period size: 143 Copynumber: 2.2 Consensus size: 143
3265904 AAGAATAAAA
* * ** * * *
3265914 TGGTTTCTA-GAGAAATAGTCTTAAAGAAGATAAGGTTGAGGGTTTCTAGGGAAACGATCTTAAG
1 TGGTTTCTACG-GAAACAATCTTAAAGAAGATTGGGTT---GGTTTATAGGGAAACAACCTTAAG
* * * * *
3265978 GAAGATTAGGTTGTTTCTAGAGAAACAACCTTAAATAAGACTAGGTTGGTTTCT-AGAGAAACAA
62 GAAGACTAGATTGTTTCTAGAGAAACAACCTTAAAGAAGACTAGATTGGTTTATAAG-GAAAC-A
3266042 CT-TTAAGGAATAATACG-T
125 CTCTTAAGGAATAATA-GAT
* * *
3266060 TGGTTTCTACGGAGACTATCTTAAGGAAGATTGGGTTGGTTTATAGGGAAA-AACCTTAAGGAAG
1 TGGTTTCTACGGAAACAATCTTAAAGAAGATTGGGTTGGTTTATAGGGAAACAACCTTAAGGAAG
* * * * * * *
3266124 ACTCGATTGGTTTCTAGCGAAA-AAGTCTTAAGGAAGAGTCGATTGGTTTATAAGGAAACATTCT
66 ACTAGATT-GTTTCTAGAGAAACAA-CCTTAAAGAAGACTAGATTGGTTTATAAGGAAACACTCT
*
3266188 TAAGGAATACTAGAT
129 TAAGGAATAATAGAT
*
3266203 TGGTTTCTAGGGAAACAATCTTAAAGAAGA
1 TGGTTTCTACGGAAACAATCTTAAAGAAGA
3266233 CTAGGTTTGT
Statistics
Matches: 140, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
142 21 0.15
143 88 0.63
144 2 0.01
146 28 0.20
147 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (143 bp):
TGGTTTCTACGGAAACAATCTTAAAGAAGATTGGGTTGGTTTATAGGGAAACAACCTTAAGGAAG
ACTAGATTGTTTCTAGAGAAACAACCTTAAAGAAGACTAGATTGGTTTATAAGGAAACACTCTTA
AGGAATAATAGAT
Found at i:3266495 original size:17 final size:17
Alignment explanation
Indices: 3266454--3266497 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
3266444 AGGGGTCTAG
*
3266454 AAATAATGAA-AATAAT
1 AAATAATGAATAAAAAT
3266470 -AA-AAT-AATAAAAAT
1 AAATAATGAATAAAAAT
3266484 AAATAATGAATAAA
1 AAATAATGAATAAA
3266498 TGATGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
13 2 0.09
14 8 0.35
15 4 0.17
16 3 0.13
17 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATAATGAATAAAAAT
Found at i:3269639 original size:16 final size:16
Alignment explanation
Indices: 3269601--3269641 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
3269591 AGGCTCTTGA
*
3269601 TATTACCTCTTTGGCC
1 TATTACTTCTTTGGCC
3269617 TATTACTTCTTTGGCC
1 TATTACTTCTTTGGCC
3269633 TATTACTTC
1 TATTACTTC
3269642 AGCGGAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.15, C:0.27, G:0.10, T:0.49
Consensus pattern (16 bp):
TATTACTTCTTTGGCC
Found at i:3270908 original size:21 final size:21
Alignment explanation
Indices: 3270878--3270923 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3270868 CATCCGCTTA
3270878 TTTC-TTTCCCTCTTTAATTT
1 TTTCTTTTCCCTCTTTAATTT
3270898 TTTCTTTTCCCTCTTTAATTT
1 TTTCTTTTCCCTCTTTAATTT
3270919 TTTCT
1 TTTCT
3270924 ATGTTTGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCTTTTCCCTCTTTAATTT
Found at i:3272773 original size:15 final size:15
Alignment explanation
Indices: 3272753--3272781 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3272743 ATCAAGGATA
3272753 AAATACGCATAAATT
1 AAATACGCATAAATT
3272768 AAATACGCATAAAT
1 AAATACGCATAAAT
3272782 CATAAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (15 bp):
AAATACGCATAAATT
Found at i:3274399 original size:2 final size:2
Alignment explanation
Indices: 3274390--3274445 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
3274380 ATATACTTAC
3274390 TA TA -A 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
3274431 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3274446 GGGCTAGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3275410 original size:19 final size:19
Alignment explanation
Indices: 3275386--3275422 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3275376 GTTTTCAATT
3275386 GATTTCCTTTTTCTCTTTC
1 GATTTCCTTTTTCTCTTTC
* *
3275405 GATTTCTTTTTTTTCTTT
1 GATTTCCTTTTTCTCTTT
3275423 TATTTTTTTC
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:0.05, C:0.19, G:0.05, T:0.70
Consensus pattern (19 bp):
GATTTCCTTTTTCTCTTTC
Found at i:3282391 original size:12 final size:12
Alignment explanation
Indices: 3282374--3282399 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3282364 AAGGCTATAG
3282374 TCAAGTAGGCCA
1 TCAAGTAGGCCA
3282386 TCAAGTAGGCCA
1 TCAAGTAGGCCA
3282398 TC
1 TC
3282400 CCAGATCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (12 bp):
TCAAGTAGGCCA
Found at i:3283409 original size:31 final size:30
Alignment explanation
Indices: 3283353--3283415 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
3283343 CCTAATTCCC
*
3283353 AAATTATTTCACTCAACATTTTAAATTCTT
1 AAATTATTTCACTCAACATTCTAAATTCTT
*
3283383 AAATTATTTCAC-CGTAACATTCTAAATTTTT
1 AAATTATTTCACTC--AACATTCTAAATTCTT
3283414 AA
1 AA
3283416 TTTTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.03
30 12 0.41
31 16 0.55
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (30 bp):
AAATTATTTCACTCAACATTCTAAATTCTT
Found at i:3283424 original size:39 final size:39
Alignment explanation
Indices: 3283371--3283458 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
3283361 TCACTCAACA
3283371 TTTTAAATTCTTAAATTATTTCACCGTAACATTCTAAAT
1 TTTTAAATTCTTAAATTATTTCACCGTAACATTCTAAAT
* * *
3283410 TTTTAATTTTTTAAATTATTTCACCTTAACATTCTTAATTAT
1 TTTTAAATTCTTAAATTATTTCACCGTAACATTC-TAA--AT
3283452 TTTTAAA
1 TTTTAAA
3283459 AATATTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 31 0.74
40 3 0.07
42 8 0.19
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.52
Consensus pattern (39 bp):
TTTTAAATTCTTAAATTATTTCACCGTAACATTCTAAAT
Found at i:3285099 original size:46 final size:48
Alignment explanation
Indices: 3284983--3285111 Score: 135
Period size: 46 Copynumber: 2.8 Consensus size: 48
3284973 ATTGGAGGGA
* *
3284983 AAGCTCACTTGGGA-ACGTCGATTCCTTTGGAGATTTTTTTGGAAGACG
1 AAGCTCACTTGGGAGA-GTCGAATCCTTTGGAGATTTTTTAGGAAGACG
** *
3285031 AA-CTTTCTTGCGAGCA-TCGAATCCTTTGGAGATTTTTTA-G-AGA-G
1 AAGCTCACTTGGGAG-AGTCGAATCCTTTGGAGATTTTTTAGGAAGACG
*
3285075 CAAGCTCGCTTGGGAGAGTCGAATCCTTTGGAGATTT
1 -AAGCTCACTTGGGAGAGTCGAATCCTTTGGAGATTT
3285112 ATTGAAGGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
44 1 0.01
45 6 0.09
46 29 0.43
47 29 0.43
48 2 0.03
49 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (48 bp):
AAGCTCACTTGGGAGAGTCGAATCCTTTGGAGATTTTTTAGGAAGACG
Found at i:3285126 original size:46 final size:45
Alignment explanation
Indices: 3285047--3285431 Score: 146
Period size: 46 Copynumber: 8.4 Consensus size: 45
3285037 CTTGCGAGCA
* *
3285047 TCGAATCCTTTGGAGATTT-TTTAGAGAGCAAGCTCGCTTGGGAGAG
1 TCGAACCCTTTGGAGATTTATTGA-AG-GCAAGCTCGCTTGGGAGAG
* * *
3285093 TCGAATCCTTTGGAGATTTATTGAAGGTAAAGCTAC-CTTGGGGGTA-
1 TCGAACCCTTTGGAGATTTATTGAAGG-CAAGCT-CGCTTGGGAG-AG
* * * * *
3285139 TCGAACCCTTTGGAGAATCATTGGAGGGCGAGCTCGCTTGGGAGCG
1 TCGAACCCTTTGGAGATTTATT-GAAGGCAAGCTCGCTTGGGAGAG
* * ** ** *
3285185 TCAAACCCTTTGGACATTTATT-ATAGGGTGAG-TTACTTGGGAGAT
1 TCGAACCCTTTGGAGATTTATTGA-A-GGCAAGCTCGCTTGGGAGAG
* * ** ** *
3285230 TCGAACCCTTTGGA-ATTTTTTTGGAGGGGGAGCTCTATTGGGAGCG
1 TCGAACCCTTTGGAGA-TTTATT-GAAGGCAAGCTCGCTTGGGAGAG
* * * *
3285276 TCGAACCCTTTGGAGATTCATATG-AGAGCAAACTAGCTTTGGAGCA-
1 TCGAACCCTTTGGAGATTTAT-TGAAG-GCAAGCTCGCTTGGGAG-AG
* * * * ** *
3285322 TGGAATCGTTTGTAGA-TTATTTGGTGGGCTAGCTCGCTTGGGAGCA-
1 TCGAACCCTTTGGAGATTTA-TT-GAAGGCAAGCTCGCTTGGGAG-AG
* * * * * *
3285368 TTGAACCCTTTGGAGATTAATT-ATAGGGAAAGCTCCCTTAGAAGCA-
1 TCGAACCCTTTGGAGATTTATTGA-A-GGCAAGCTCGCTTGGGAG-AG
3285414 TCGAACCCTTTGGAGATT
1 TCGAACCCTTTGGAGATT
3285432 CATTTGCTCG
Statistics
Matches: 252, Mismatches: 64, Indels: 46
0.70 0.18 0.13
Matches are distributed among these distances:
44 2 0.01
45 38 0.15
46 197 0.78
47 15 0.06
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (45 bp):
TCGAACCCTTTGGAGATTTATTGAAGGCAAGCTCGCTTGGGAGAG
Found at i:3285263 original size:91 final size:92
Alignment explanation
Indices: 3285077--3285289 Score: 238
Period size: 91 Copynumber: 2.3 Consensus size: 92
3285067 TTAGAGAGCA
* * * *
3285077 AGCTCGCTTGGGAGAGTCGAATCCTTTGGAGATTTATTGAAGGTAAAGCTACCTTGGGGGTATCG
1 AGCTCGCTTGGGAGCGTCGAACCCTTTGGACATTTATTGAAGGTAAAGCTACCTTGGGGATATCG
3285142 AACCCTTTGGAGAATCATTGGAGGGCG
66 AACCCTTTGGAGAATCATTGGAGGGCG
* * *
3285169 AGCTCGCTTGGGAGCGTCAAACCCTTTGGACATTTATT-ATAGGGT-GAGTTA-CTTGGGAGAT-
1 AGCTCGCTTGGGAGCGTCGAACCCTTTGGACATTTATTGA-A-GGTAAAGCTACCTTGGG-GATA
* ** *
3285230 TCGAACCCTTTGGA-ATTTTTTTGGAGGGGG
63 TCGAACCCTTTGGAGA-ATCATTGGAGGGCG
**
3285260 AGCTCTATTGGGAGCGTCGAACCCTTTGGA
1 AGCTCGCTTGGGAGCGTCGAACCCTTTGGA
3285290 GATTCATATG
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
90 1 0.01
91 58 0.56
92 41 0.40
93 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (92 bp):
AGCTCGCTTGGGAGCGTCGAACCCTTTGGACATTTATTGAAGGTAAAGCTACCTTGGGGATATCG
AACCCTTTGGAGAATCATTGGAGGGCG
Found at i:3292774 original size:21 final size:21
Alignment explanation
Indices: 3292750--3292789 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3292740 TTGGTTTTAA
3292750 AAGACCCTTCATTTTTCTTCC
1 AAGACCCTTCATTTTTCTTCC
* *
3292771 AAGACTCTTCCTTTTTCTT
1 AAGACCCTTCATTTTTCTT
3292790 ACATCCTTCC
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:0.17, C:0.30, G:0.05, T:0.47
Consensus pattern (21 bp):
AAGACCCTTCATTTTTCTTCC
Found at i:3294942 original size:3 final size:3
Alignment explanation
Indices: 3294929--3294972 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
3294919 TTTTTTATCG
*
3294929 TTA TT- TTA TTA TTA TTA TTA TTTA TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
3294973 CATTTTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3294954 original size:16 final size:15
Alignment explanation
Indices: 3294933--3294965 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3294923 TTATCGTTAT
3294933 TTTATTATTATTATTA
1 TTTATTATTA-TATTA
3294949 TTTATTATTATATTA
1 TTTATTATTATATTA
3294964 TT
1 TT
3294966 AATATTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTATTATATTA
Found at i:3295029 original size:11 final size:11
Alignment explanation
Indices: 3295009--3295040 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3294999 CCCAATACAA
*
3295009 CAAGGTCCAAC
1 CAAGGCCCAAC
3295020 CAAGGCCCAAC
1 CAAGGCCCAAC
3295031 CAAGGCCCAA
1 CAAGGCCCAA
3295041 ACACGAGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.41, G:0.19, T:0.03
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:3298834 original size:31 final size:32
Alignment explanation
Indices: 3298798--3298859 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3298788 ATTTTACATG
*
3298798 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTCGTGTA
3298829 TACTAACTTATTTCTTCTCTTTTGTTCGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTCGTGT
3298860 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.15, C:0.16, G:0.10, T:0.60
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTCGTGTA
Found at i:3300278 original size:26 final size:25
Alignment explanation
Indices: 3300247--3300323 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
3300237 CCAATTTTTG
3300247 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
3300272 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
3300293 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
3300319 ACATT
1 ACATT
3300324 TTTTCCACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
20 7 0.17
21 5 0.12
22 4 0.10
23 3 0.07
24 4 0.10
25 4 0.10
26 14 0.34
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:3300944 original size:12 final size:11
Alignment explanation
Indices: 3300927--3300999 Score: 62
Period size: 12 Copynumber: 6.5 Consensus size: 11
3300917 ATCCAATGAA
3300927 AAAGAAATAAGC
1 AAAGAAA-AAGC
*
3300939 AAAGAAAAAAAC
1 AAAG-AAAAAGC
3300951 AAAGAGAAAAG-
1 AAAGA-AAAAGC
*
3300962 --AGAAAAATC
1 AAAGAAAAAGC
*
3300971 AAAGCAAAAATC
1 AAAG-AAAAAGC
3300983 AAAGAAAAAGC
1 AAAGAAAAAGC
3300994 AAAGAA
1 AAAGAA
3301000 CAAAAGAGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
11 15 0.29
12 26 0.51
13 3 0.06
ACGTcount: A:0.73, C:0.08, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAGC
Found at i:3300974 original size:32 final size:33
Alignment explanation
Indices: 3300924--3300992 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
3300914 AAGATCCAAT
3300924 GAAAA-AGAAATAAGCAAAGAAAAAAACAAAGA
1 GAAAAGAGAAATAAGCAAAGAAAAAAACAAAGA
* * *
3300956 GAAAAGAGAAA-AATCAAAGCAAAAATCAAAGA
1 GAAAAGAGAAATAAGCAAAGAAAAAAACAAAGA
3300988 -AAAAG
1 GAAAAG
3300993 CAAAGAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 5 0.15
32 23 0.70
33 5 0.15
ACGTcount: A:0.72, C:0.07, G:0.16, T:0.04
Consensus pattern (33 bp):
GAAAAGAGAAATAAGCAAAGAAAAAAACAAAGA
Found at i:3300979 original size:11 final size:12
Alignment explanation
Indices: 3300958--3301004 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3300948 AACAAAGAGA
3300958 AAAGAGAAAAATC
1 AAAGA-AAAAATC
*
3300971 AAAGCAAAAATC
1 AAAGAAAAAATC
*
3300983 AAAG-AAAAAGC
1 AAAGAAAAAATC
3300994 AAAGAACAAAA
1 AAAGAA-AAAA
3301005 GAGGACAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 8 0.27
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (12 bp):
AAAGAAAAAATC
Found at i:3302786 original size:105 final size:102
Alignment explanation
Indices: 3302645--3302878 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 102
3302635 TGAGAATTTT
* * * *
3302645 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
3302709 TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * * *
3302750 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
3302815 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
3302852 AAAACAAACTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
3302879 ACTTCTCTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
101 2 0.02
102 25 0.22
103 4 0.04
104 4 0.04
105 76 0.68
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:3302874 original size:36 final size:36
Alignment explanation
Indices: 3302846--3302913 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
3302836 TGAGATCGTT
*
3302846 TTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAAC
1 TTCTCTAAAAACAAACTTTGTCTCACTTGAGACAAC
* *
3302881 TTCTCTAAAAACAAATTTTGTCTCATTTGAGAC
1 TTCTCTAAAAACAAACTTTGTCTCACTTGAGAC
3302914 TATATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (36 bp):
TTCTCTAAAAACAAACTTTGTCTCACTTGAGACAAC
Found at i:3303238 original size:29 final size:29
Alignment explanation
Indices: 3303196--3303267 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
3303186 TTTCTCTTGA
*
3303196 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTGGTTCCTTTTGAAT
*
3303225 AAAAATCTTGGAGTTGGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTGGTTCCTTTTGAAT
*
3303254 AAATATCTTTGAGT
1 AAAAATCTTTGAGT
3303268 CGTTTCTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (29 bp):
AAAAATCTTTGAGTTGGTTCCTTTTGAAT
Found at i:3303380 original size:52 final size:54
Alignment explanation
Indices: 3303302--3303406 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 54
3303292 CTATTTATTT
* **
3303302 TGAAACAAAGTTTTGTCTCTCTTGAGACAA-TTT-CGTGAAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGTC
3303354 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGT
1 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGT
3303407 TTGTTTCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 29 0.60
53 3 0.06
54 16 0.33
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (54 bp):
TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGTC
Found at i:3303538 original size:74 final size:74
Alignment explanation
Indices: 3303391--3303530 Score: 246
Period size: 74 Copynumber: 1.9 Consensus size: 74
3303381 CAATTTTGCG
*
3303391 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAGTTTCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAATTTCTTTTG
3303456 AAAAAAAAA
66 AAAAAAAAA
*
3303465 AAAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATT-TTGTCTCTCTTAAGATAATTTCTTTT
1 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTT-TCTCTCTTAAGATAATTTCTTTT
3303529 GA
65 GA
3303531 GACAAAAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
73 2 0.03
74 61 0.97
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (74 bp):
AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAATTTCTTTTG
AAAAAAAAA
Found at i:3303591 original size:66 final size:67
Alignment explanation
Indices: 3303467--3303596 Score: 145
Period size: 66 Copynumber: 2.0 Consensus size: 67
3303457 AAAAAAAAAA
* * * * * *
3303467 AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAG
1 AAAAATCTTTGAATCTGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGAG
3303532 AC
66 AC
*** * **
3303534 AAAAATCTTTGAATCTGTTTCTCTT-AAATTGAATTTTGTATCTCTTGAGACCGTTTCTCTTGA
1 AAAAATCTTTGAATCTGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGA
3303597 AGTAAATCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
66 29 0.57
67 22 0.43
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (67 bp):
AAAAATCTTTGAATCTGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGAG
AC
Found at i:3303914 original size:64 final size:66
Alignment explanation
Indices: 3303776--3303895 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 66
3303766 AAGATGGGAT
* *
3303776 CCATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGGAAAA
1 CCATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGGAAAA
3303841 A
66 A
* * **
3303842 --ATCTTTGAGTTTGTTTCCTTTGAAAC-AAATTTTGTCTC-TCGAGACAACTTCTTT
1 CCATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTT
3303896 GAAAATACCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 13 0.27
63 11 0.23
64 24 0.50
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.44
Consensus pattern (66 bp):
CCATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGGAAAA
A
Found at i:3303940 original size:39 final size:40
Alignment explanation
Indices: 3303883--3303961 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
3303873 TTGTCTCTCG
*
3303883 AGACAACTTCTTTGAAAA-TACCCATATTTGAGATCGTTT
1 AGACAACTTCTTTGAAAATTACCCACATTTGAGATCGTTT
* * * *
3303922 AGACAATTTCTTTTAAAATTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTGAAAATTACCCACATTTGAGATCGTTT
3303962 TTATTAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 16 0.47
40 18 0.53
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (40 bp):
AGACAACTTCTTTGAAAATTACCCACATTTGAGATCGTTT
Found at i:3304434 original size:35 final size:36
Alignment explanation
Indices: 3304368--3304442 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
3304358 TATTTCTTTG
* *
3304368 GAAACAAAATTCACCATCTTTGAATCGGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCGGTTTCCCTT
*
3304404 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCGGTTTCCCTT
3304439 GAAA
1 GAAA
3304443 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCGGTTTCCCTT
Found at i:3304511 original size:1 final size:1
Alignment explanation
Indices: 3304505--3304535 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
3304495 CGTTTCCCTT
3304505 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3304536 CAAATTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3304790 original size:28 final size:28
Alignment explanation
Indices: 3304740--3304793 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3304730 TCAAAATCCA
* *
3304740 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
3304768 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
3304794 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:3304956 original size:43 final size:44
Alignment explanation
Indices: 3304805--3305099 Score: 218
Period size: 46 Copynumber: 6.8 Consensus size: 44
3304795 ATTATCCTAG
* * * *
3304805 AGATAACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACC-AT
** * * * **
3304851 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT-CCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCAT
*
3304894 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCA-ACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCAT
* * *
3304934 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACC-AT
** * * * * **
3304980 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCAT
*
3305024 AGAT---CAGATCTCCTCATCACGTAGGAGCCGTGTCA-ACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCAT
*
3305064 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGT
3305100 TATCACCTTA
Statistics
Matches: 197, Mismatches: 38, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
40 39 0.20
41 28 0.14
42 2 0.01
43 55 0.28
44 6 0.03
45 5 0.03
46 60 0.30
47 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (44 bp):
AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCAT
Found at i:3305219 original size:130 final size:129
Alignment explanation
Indices: 3304805--3305188 Score: 635
Period size: 130 Copynumber: 3.0 Consensus size: 129
3304795 ATTATCCTAG
*
3304805 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
3304870 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
3304934 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
3304999 TCACGTATGAGCCGTGTCATTCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
3305064 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTC
* ** * * * * *
3305129 ATCATGTATGAGTAGTGTCATCCTTC-GACCAGATGTCTTCATCACGTAGGAACCATGTCA
65 ATCACGTATGAGCCGTGTCATCC-CCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
3305189 CCCTTAGACG
Statistics
Matches: 240, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
129 83 0.35
130 129 0.54
131 28 0.12
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:3305402 original size:3 final size:3
Alignment explanation
Indices: 3305389--3305432 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
3305379 TTTTTTATCG
*
3305389 TTA TT- TTA TTA TTA TTA TTA TTTA TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
3305433 CATTTTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3305414 original size:16 final size:15
Alignment explanation
Indices: 3305393--3305425 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3305383 TTATCGTTAT
3305393 TTTATTATTATTATTA
1 TTTATTATTA-TATTA
3305409 TTTATTATTATATTA
1 TTTATTATTATATTA
3305424 TT
1 TT
3305426 AATATTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTATTATATTA
Found at i:3305489 original size:11 final size:11
Alignment explanation
Indices: 3305469--3305500 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3305459 CCCAATACAA
*
3305469 CAAGGTCCAAC
1 CAAGGCCCAAC
3305480 CAAGGCCCAAC
1 CAAGGCCCAAC
3305491 CAAGGCCCAA
1 CAAGGCCCAA
3305501 ACACGAGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.41, G:0.19, T:0.03
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:3309541 original size:56 final size:56
Alignment explanation
Indices: 3309471--3309583 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
3309461 ATTACTGTAG
*
3309471 AAATGAACTAAAGGCTAAAAAATGAAGTTAAATGTTGAATTGATTTATTGGTTTTA
1 AAATGAACTAAAGGCTAAAAAATGAAGTTAAATGTTGAATTGAGTTATTGGTTTTA
* *
3309527 AAATGAACTGAAGGCTGAAAAATGAAGTTAAATGTTGAATTGAGTTATTGGTTTTA
1 AAATGAACTAAAGGCTAAAAAATGAAGTTAAATGTTGAATTGAGTTATTGGTTTTA
3309583 A
1 A
3309584 TATGTGGTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.35
Consensus pattern (56 bp):
AAATGAACTAAAGGCTAAAAAATGAAGTTAAATGTTGAATTGAGTTATTGGTTTTA
Found at i:3314776 original size:12 final size:11
Alignment explanation
Indices: 3314759--3314802 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
3314749 TCATATTCAC
*
3314759 TCTTCTTTGTAT
1 TCTTCTTT-TCT
3314771 TCTTCTTTCTCT
1 TCTTCTTT-TCT
3314783 TCTTCTTCTTCT
1 TCTTCTT-TTCT
3314795 TCTTCTTT
1 TCTTCTTT
3314803 AACTTGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.68
Consensus pattern (11 bp):
TCTTCTTTTCT
Found at i:3321463 original size:2 final size:2
Alignment explanation
Indices: 3321456--3321489 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3321446 TCATTTATCC
3321456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3321490 CTTGTTGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3321680 original size:16 final size:15
Alignment explanation
Indices: 3321657--3321690 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
3321647 ATCCAATCAG
3321657 AACAAAAAGAGAACAGA
1 AACAAAAA-AGAA-AGA
3321674 AACAAAAAAGAAAGA
1 AACAAAAAAGAAAGA
3321689 AA
1 AA
3321691 AGCAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAAGA
Found at i:3321687 original size:22 final size:23
Alignment explanation
Indices: 3321662--3321714 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
3321652 ATCAGAACAA
3321662 AAAGAGAACAG-AAACAAAAAAG-
1 AAAGAGAA-AGCAAACAAAAAAGC
*
3321684 AAAGA-AAAGCAAAGAAAAAAGC
1 AAAGAGAAAGCAAACAAAAAAGC
3321706 AAAGAGAAA
1 AAAGAGAAA
3321715 ATAAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 10 0.37
23 3 0.11
ACGTcount: A:0.74, C:0.08, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAGAGAAAGCAAACAAAAAAGC
Found at i:3321705 original size:12 final size:12
Alignment explanation
Indices: 3321677--3321751 Score: 50
Period size: 12 Copynumber: 6.5 Consensus size: 12
3321667 GAACAGAAAC
3321677 AAAAAAG-AAAG
1 AAAAAAGCAAAG
3321688 --AAAAGCAAAG
1 AAAAAAGCAAAG
3321698 AAAAAAGCAAAG
1 AAAAAAGCAAAG
* * *
3321710 AGAAAA-TAAAA
1 AAAAAAGCAAAG
*
3321721 AACAAAAACAAAG
1 AA-AAAAGCAAAG
* **
3321734 GAAAAAGTGAAG
1 AAAAAAGCAAAG
3321746 AAAAAA
1 AAAAAA
3321752 AGGACAAGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
9 5 0.10
10 4 0.08
11 4 0.08
12 31 0.65
13 4 0.08
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAAAGCAAAG
Found at i:3322833 original size:32 final size:32
Alignment explanation
Indices: 3322787--3322936 Score: 174
Period size: 32 Copynumber: 4.7 Consensus size: 32
3322777 TGAGGAACAA
*
3322787 GCATATTTGAAGATTCAACATCAAATGTTGGG
1 GCATCTTTGAAGATTCAACATCAAATGTTGGG
* *
3322819 GCATCTTTGTAGATTCAACATCAAATGTTGAG
1 GCATCTTTGAAGATTCAACATCAAATGTTGGG
* ** *
3322851 TCATCTTTGAAGATTCAATGTCAAATGTTGGA
1 GCATCTTTGAAGATTCAACATCAAATGTTGGG
* * * *
3322883 GCATTTTTGGAGATTCAACATCGAATATTGGG
1 GCATCTTTGAAGATTCAACATCAAATGTTGGG
* **
3322915 CCATCTTTGGGGATTCAACATC
1 GCATCTTTGAAGATTCAACATC
3322937 CTGATGCGAA
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (32 bp):
GCATCTTTGAAGATTCAACATCAAATGTTGGG
Found at i:3323411 original size:61 final size:61
Alignment explanation
Indices: 3323315--3324225 Score: 1134
Period size: 61 Copynumber: 14.8 Consensus size: 61
3323305 TTAAAGTTTT
* *
3323315 CAAGATTGGATTTCAA-TATCACAATGAAGGATATCCAAGTCAAAGCCAATTTGGTGAAGCA
1 CAAGATTGGATTTCAACT-TCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * *
3323376 GAAGATTGGATTTCAACTTCACAATGGAGGATATCCAACTCAAAGCCAATTTGGTGAAACA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
3323437 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * * *
3323498 GAAGATTGGATTTCAACTTCACAATGAATGATATCCAACTTAAAGCCGATTTGGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * * *
3323559 CAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTTAAAACCAATTTAGTGAAACTTA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGC--A
* *
3323622 CACAAACTTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCA
1 CA-AGA-TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * *
3323685 -ATA-CTTGGATTTTAACTTCACAACGAAGGATATCTAACTCAAAGCCAATTTGATGAA--A
1 CA-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * *
3323743 CAATACTTGGATTTCAACTTCACAACGAAGGATATCCAGCTCAAAGCCGATTTGGTGAAGAA
1 CAAGA-TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * *
3323805 CAAGATTGGATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCCGATTTGGTGAAACTTAA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGC---A
* * * *
3323869 CAAGCTTGGATTTCAACTTCACATCGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTTATA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGC----A
* * * * **
3323934 CAAGATTGGATTTCAACTTCATAACAAAGGATATCCAACTTAAAGTCAATTCAGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * * * *
3323995 -ATA-CTTGGATTTCAACTTCACAGCGAAGGATATCCAACTTAAAACCGATTTGGTGAAGCC
1 CA-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
** *
3324055 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTGATTTGGTGAAACA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * *
3324116 TAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTAAAAGCCAAATTGGTGAAGCTATA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGC---A
* *
3324180 CAAGATTGGATTTCAAGTTCACGACGAAGGATATCCAACTCAAAGC
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
3324226 TCAACTTCAT
Statistics
Matches: 742, Mismatches: 88, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
58 2 0.00
59 1 0.00
60 146 0.20
61 379 0.51
62 8 0.01
63 4 0.01
64 101 0.14
65 101 0.14
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (61 bp):
CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
Found at i:3324974 original size:17 final size:17
Alignment explanation
Indices: 3324952--3324987 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3324942 GAAACCAGGG
3324952 GGAGAAAAGGAAAA-GGA
1 GGAGAAAA-GAAAATGGA
3324969 GGAGAAAAGAAAATGGA
1 GGAGAAAAGAAAATGGA
3324986 GG
1 GG
3324988 GGTTCTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.03
Consensus pattern (17 bp):
GGAGAAAAGAAAATGGA
Found at i:3325725 original size:3 final size:3
Alignment explanation
Indices: 3325717--3325822 Score: 185
Period size: 3 Copynumber: 35.3 Consensus size: 3
3325707 TATGAAGTGG
* * *
3325717 TAA TAA TAA TAA TAG TAA TAG TGA 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
3325765 TAA TAA TAA TAA TAA TAA TAA 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
3325813 TAA TAA TAA T
1 TAA TAA TAA T
3325823 TGTTGTTGGT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3326945 original size:22 final size:21
Alignment explanation
Indices: 3326919--3326959 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3326909 TTAAAAATTA
*
3326919 TAAAGGTAGCATCGATACTCAT
1 TAAAGG-AGCACCGATACTCAT
*
3326941 TAAAGGAGTACCGATACTC
1 TAAAGGAGCACCGATACTC
3326960 TCTATTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
TAAAGGAGCACCGATACTCAT
Found at i:3328616 original size:19 final size:20
Alignment explanation
Indices: 3328576--3328619 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3328566 AATGATTTTC
*
3328576 TTTTG-AAAGAAAAATTAGA
1 TTTTGAAAAGAAAAATGAGA
*
3328595 TTTTGAAAAGCAAAATGA-A
1 TTTTGAAAAGAAAAATGAGA
3328614 TTTTGA
1 TTTTGA
3328620 GCTTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (20 bp):
TTTTGAAAAGAAAAATGAGA
Found at i:3332047 original size:2 final size:2
Alignment explanation
Indices: 3332042--3332107 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
3332032 ACACATATTC
3332042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3332084 AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
3332108 TGTAACTTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3332574 original size:2 final size:2
Alignment explanation
Indices: 3332567--3332597 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3332557 CACATACATG
3332567 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3332598 GCACAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3340593 original size:3 final size:3
Alignment explanation
Indices: 3340587--3340631 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3340577 ATTTTTTATT
* *
3340587 TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3340632 AACAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3340943 original size:76 final size:76
Alignment explanation
Indices: 3340760--3342839 Score: 3967
Period size: 76 Copynumber: 27.5 Consensus size: 76
3340750 GATGGAAATG
* * *
3340760 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3340824 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3340835 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3340900 CCCGAAGGCTT
66 CCCGAAGGCTT
3340911 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3340975 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
3340986 TTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341051 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3341062 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341127 CCCGAAGGC-T
66 CCCGAAGGCTT
3341137 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341202 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3341213 TTTGGAACCATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341278 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
3341289 TTTTGAAACATCATGCACTGAAGGACTTACAGATAACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341354 CCCGAAGGCTT
66 CCCGAAGGCTT
3341365 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341430 CCCGAAGGCTT
66 CCCGAAGGCTT
3341441 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341506 CCCGAAGGCTT
66 CCCGAAGGCTT
3341517 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
3341582 CCCGAAGGCGT
66 CCCGAAGGCTT
* *
3341593 TTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341658 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3341669 TTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341733 CCCGAAGGCTT
66 CCCGAAGGCTT
3341744 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341809 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3341820 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341885 CCCGAAGGCTT
66 CCCGAAGGCTT
3341896 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341961 CCCGAAGGC-T
66 CCCGAAGGCTT
3341971 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342036 CCCGAAGGCTT
66 CCCGAAGGCTT
3342047 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342112 CCCGAAGGCTT
66 CCCGAAGGCTT
3342123 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342188 CCCGAAGGCTT
66 CCCGAAGGCTT
3342199 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342263 CCCGAAGGCTT
66 CCCGAAGGCTT
3342274 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342339 CCCGAAGGCTT
66 CCCGAAGGCTT
3342350 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342415 CCCGAAGGCTT
66 CCCGAAGGCTT
3342426 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342491 CCCGAAGGCTT
66 CCCGAAGGCTT
3342502 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342567 CCCGAAGGCTT
66 CCCGAAGGCTT
3342578 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342642 CCCGAAGGCTT
66 CCCGAAGGCTT
3342653 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342718 CCCGAAGGCTT
66 CCCGAAGGCTT
3342729 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342794 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3342805 TTTGGAAACATCATGCACAGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
3342840 TGGGAAATAG
Statistics
Matches: 1972, Mismatches: 26, Indels: 13
0.98 0.01 0.01
Matches are distributed among these distances:
75 501 0.25
76 1471 0.75
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:3341201 original size:227 final size:228
Alignment explanation
Indices: 3340760--3342839 Score: 3967
Period size: 227 Copynumber: 9.2 Consensus size: 228
3340750 GATGGAAATG
* * *
3340760 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
3340824 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3340889 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3340954 GCTTTGAAAACATC-AAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* *
3340986 TTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
3341051 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3341116 ATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3341180 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
3341213 TTTGGAACCATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
3341278 CCCGAAGGCTTTTTTGAAACATCATGCACTGAAGGACTTACAGATAACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3341343 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3341408 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
3341441 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341506 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* *
3341571 ATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
3341636 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
3341669 TTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341733 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3341798 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
3341863 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
3341896 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3341961 CCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3342025 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3342090 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
3342123 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342188 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3342253 ATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3342317 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
3342350 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342415 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3342480 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3342545 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
3342578 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3342642 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
3342707 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
3342772 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
3342805 TTTGGAAACATCATGCACAGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
3342840 TGGGAAATAG
Statistics
Matches: 1827, Mismatches: 21, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
226 112 0.06
227 1156 0.63
228 559 0.31
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Done.