Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 89 of 173
Found at i:27933867 original size:3 final size:3
Alignment explanation
Indices: 27933859--27933885 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27933849 TTTAAAAATA
27933859 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
27933886 ATGTAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27935176 original size:17 final size:16
Alignment explanation
Indices: 27935136--27935185 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
27935126 TAAAAACTCA
27935136 TTAAAAT-TCAAAAAAT
1 TTAAAATAT-AAAAAAT
**
27935152 AAAAAATATAAAAGAAT
1 TTAAAATATAAAA-AAT
27935169 TTAAAATATAAAAAAT
1 TTAAAATATAAAAAAT
27935185 T
1 T
27935186 CCAAAATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
TTAAAATATAAAAAAT
Found at i:27935191 original size:17 final size:17
Alignment explanation
Indices: 27935154--27935192 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
27935144 CAAAAAATAA
*
27935154 AAAATATAAAAGAATTT
1 AAAATATAAAAGAATTC
27935171 AAAATATAAAA-AATTCC
1 AAAATATAAAAGAATT-C
27935188 AAAAT
1 AAAAT
27935193 CTAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAGAATTC
Found at i:27942224 original size:28 final size:28
Alignment explanation
Indices: 27942185--27942252 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
27942175 GAATTTTGGA
27942185 ATTTTTATATTTAAAAATATATTTTT-ATAT
1 ATTTTTA-ATTTAAAAAT-T-TTTTTCATAT
* *
27942215 -TTTTTAATTTTAAAGTTTTTTTCATAT
1 ATTTTTAATTTAAAAATTTTTTTCATAT
27942242 ATTTTTAATTT
1 ATTTTTAATTT
27942253 TTTTAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.15
27 5 0.15
28 18 0.53
29 6 0.18
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTTTTAATTTAAAAATTTTTTTCATAT
Found at i:27942248 original size:37 final size:38
Alignment explanation
Indices: 27942201--27942273 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
27942191 ATATTTAAAA
*
27942201 ATATATTTTT-ATATTTTTT-AATTTTAAAGTTTTTTTC
1 ATATATTTTTAAT-TTTTTTAAATTATAAAGTTTTTTTC
*
27942238 ATATATTTTTAATTTTTTTAAATTATAATGTTTTTT
1 ATATATTTTTAATTTTTTTAAATTATAAAGTTTTTT
27942274 CTTTAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 16 0.50
38 16 0.50
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (38 bp):
ATATATTTTTAATTTTTTTAAATTATAAAGTTTTTTTC
Found at i:27942972 original size:16 final size:17
Alignment explanation
Indices: 27942935--27942975 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
27942925 AAAAATTTTA
*
27942935 AAAAAATAACAAAAATT
1 AAAATATAACAAAAATT
*
27942952 -TAATATAAC-AAAATT
1 AAAATATAACAAAAATT
27942967 AAAATATAA
1 AAAATATAA
27942976 AAATTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATATAACAAAAATT
Found at i:27945248 original size:22 final size:22
Alignment explanation
Indices: 27945190--27945248 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
27945180 GAATGGTATC
27945190 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
27945212 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
27945235 TACATATCAAATCT
1 TACAAATCAAATCT
27945249 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:27950379 original size:22 final size:22
Alignment explanation
Indices: 27950322--27950379 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
27950312 GAATGGTATC
27950322 TACAAATC-AATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
27950343 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
27950366 TACATATCAAATCT
1 TACAAATCAAATCT
27950380 ACGATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 3 0.10
22 14 0.45
23 8 0.26
24 6 0.19
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:27952385 original size:15 final size:15
Alignment explanation
Indices: 27952365--27952395 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27952355 GACAGTTCTG
27952365 TGTGCTCTAATTCAT
1 TGTGCTCTAATTCAT
27952380 TGTGCTCTAATTCAT
1 TGTGCTCTAATTCAT
27952395 T
1 T
27952396 ACTGATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48
Consensus pattern (15 bp):
TGTGCTCTAATTCAT
Found at i:27963833 original size:16 final size:18
Alignment explanation
Indices: 27963797--27963834 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
27963787 ATTTAGTTTT
27963797 TTAACTTATATACTATAA
1 TTAACTTATATACTATAA
*
27963815 TTAACTTA-ATA-TTTAA
1 TTAACTTATATACTATAA
27963831 TTAA
1 TTAA
27963835 AAATAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAACTTATATACTATAA
Found at i:27966430 original size:50 final size:50
Alignment explanation
Indices: 27966305--27966550 Score: 242
Period size: 50 Copynumber: 4.8 Consensus size: 50
27966295 ATTTGGGTAA
* * *
27966305 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* * * *
27966361 TGAGGTCCCATGTAAGACCATGTCTGGGAGATGGCGTTGGCACCGAGATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** ** *
27966411 AGAGGTCCTATGTAAGACCACATCTGGGACATGGTGTTGGCACTGAGATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
27966461 AGAGGTCCTCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
27966511 AGAACT-CTCATGTAAGACCATATCTGGGATATGGCATTGG
1 AGAGGTCCT-ATGTAAGACCATGTCTGGGACATGGCATTGG
27966551 TAGTACATAA
Statistics
Matches: 161, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.01
50 117 0.73
53 3 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:27974152 original size:50 final size:51
Alignment explanation
Indices: 27974035--27974216 Score: 224
Period size: 50 Copynumber: 3.5 Consensus size: 51
27974025 TAAAGAGATG
* * * *
27974035 CCATGTAAGACCATGTTTGGGACATGGCATTAGCATCATTGAGATTATGTGAGGTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC--TGAG---ATGAGAGGTC
* * *
27974091 CTATGTAAGACCATGTTTGGGAGATTGCGTTGGCA-CTGAGATGAGAGGTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
27974141 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC-GAGATGAGAGGTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
**
27974191 CCCCGTAAGACCATGTTTGGGACATG
1 CCATGTAAGACCATGTTTGGGACATG
27974217 ACATGGGCAC
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
50 78 0.68
51 1 0.01
53 4 0.04
55 1 0.01
56 30 0.26
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (51 bp):
CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
Found at i:27974226 original size:100 final size:102
Alignment explanation
Indices: 27974035--27974254 Score: 239
Period size: 100 Copynumber: 2.1 Consensus size: 102
27974025 TAAAGAGATG
* * * *
27974035 CCATGTAAGACCATGTTTGGGACATGGCATTAGCATCATTGAGATTATGTGAGGTCCTATGTAAG
1 CCATGTAAGACCATGTTTGGGACATGGCATTAGCAGC--TGAG--TATGAGAGGTCCCACGTAAG
* * * * **
27974100 ACCATGTTTGGGAGATTGCGTTGGCACTGAGATGAGAGGTC
62 ACCATGTTTGGGACATTGCATGGGCACCGAGATGAGAACTC
* * *
27974141 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC-GAG-ATGAGAGGTCCCCCGTAAGACCA
1 CCATGTAAGACCATGTTTGGGACATGGCATTAGCAGCTGAGTATGAGAGGTCCCACGTAAGACCA
*
27974204 TGTTTGGGACA-TGACATGGGCACCGATATGAGAACTC
66 TGTTTGGGACATTG-CATGGGCACCGAGATGAGAACTC
*
27974241 TCATGTAAGACCAT
1 CCATGTAAGACCAT
27974255 ATCTGGGATA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
99 2 0.02
100 59 0.60
103 3 0.03
106 34 0.35
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (102 bp):
CCATGTAAGACCATGTTTGGGACATGGCATTAGCAGCTGAGTATGAGAGGTCCCACGTAAGACCA
TGTTTGGGACATTGCATGGGCACCGAGATGAGAACTC
Found at i:27974235 original size:50 final size:49
Alignment explanation
Indices: 27974085--27974254 Score: 187
Period size: 50 Copynumber: 3.4 Consensus size: 49
27974075 GAGATTATGT
* * * *
27974085 GAGGTCCTATGTAAGACCATGTTTGGGAGATTGCGTTGGCACTGAGATGA
1 GAGGTCCCACGTAAGACCATGTTTGGGACA-TGCGTTGGCACCGAGATGA
* *
27974135 GAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCGAGATGA
1 GAGGTCCCACGTAAGACCATGTTTGGGACAT-GCGTTGGCACCGAGATGA
* * * *
27974185 GAGGTCCCCCGTAAGACCATGTTTGGGACATGACATGGGCACCGATATGA
1 GAGGTCCCACGTAAGACCATGTTTGGGACATG-CGTTGGCACCGAGATGA
** * *
27974235 GAACTCTCATGTAAGACCAT
1 GAGGTCCCACGTAAGACCAT
27974255 ATCTGGGATA
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
49 2 0.02
50 101 0.98
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (49 bp):
GAGGTCCCACGTAAGACCATGTTTGGGACATGCGTTGGCACCGAGATGA
Found at i:27974262 original size:100 final size:100
Alignment explanation
Indices: 27974095--27974276 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 100
27974085 GAGGTCCTAT
* * * * ** * *
27974095 GTAAGACCATGTTTGGGAGATTGCGTTGGCACTGAGATGAGAGGTCCCATGTAAGACCATGTTTG
1 GTAAGACCATGTTTGGGACATTGCATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* *
27974160 GGACATGGCGTTGGCAGCGAGATGAGAGGTCCCCC
66 GGACATGACATTGGCAGCGAGATGAGAGGTCCCCC
* *
27974195 GTAAGACCATGTTTGGGACA-TGACATGGGCACCGATATGAGAACTCTCATGTAAGACCATATCT
1 GTAAGACCATGTTTGGGACATTG-CATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCT
*
27974259 GGGATATGACATTGGCAG
65 GGGACATGACATTGGCAG
27974277 TACAGAAAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
99 2 0.03
100 66 0.97
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (100 bp):
GTAAGACCATGTTTGGGACATTGCATGGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
GGACATGACATTGGCAGCGAGATGAGAGGTCCCCC
Found at i:27974541 original size:12 final size:12
Alignment explanation
Indices: 27974524--27974555 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27974514 ATGAGTTATT
*
27974524 TAAGTAAGCAAG
1 TAAGTAAACAAG
27974536 TAAGTAAACAAG
1 TAAGTAAACAAG
27974548 TAAGTAAA
1 TAAGTAAA
27974556 AAAACGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:27977453 original size:9 final size:9
Alignment explanation
Indices: 27977439--27977466 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
27977429 TTTTGTTACA
27977439 ACAATTAAT
1 ACAATTAAT
27977448 ACAATTAAT
1 ACAATTAAT
27977457 ACAATTAAT
1 ACAATTAAT
27977466 A
1 A
27977467 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:27977488 original size:68 final size:68
Alignment explanation
Indices: 27977409--27977609 Score: 298
Period size: 59 Copynumber: 3.1 Consensus size: 68
27977399 TCAAGTTTGT
*
27977409 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
27977474 AAA
66 AAA
27977477 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
27977533 AAA
66 AAA
*
27977536 TTTACTAATCAAATGTTAGATTTTATTACAATAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
27977599 AAT
66 AAA
27977602 TTTACTAA
1 TTTACTAA
27977610 CAATTAATTT
Statistics
Matches: 121, Mismatches: 3, Indels: 20
0.84 0.02 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 1 0.01
65 2 0.02
66 27 0.22
67 2 0.02
68 32 0.26
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:27977619 original size:16 final size:16
Alignment explanation
Indices: 27977598--27977639 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
27977588 AATAATTTGA
*
27977598 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
27977614 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
27977630 TAGTTTTAAT
1 TAATTTTAAT
27977640 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:27977623 original size:22 final size:22
Alignment explanation
Indices: 27977613--27977673 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
27977603 TTACTAACAA
* * *
27977613 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
27977635 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
27977657 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
27977674 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:27978841 original size:20 final size:21
Alignment explanation
Indices: 27978818--27978865 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
27978808 AATCAAGTAA
27978818 AATTAACATAA-TTAAACATT
1 AATTAACATAATTTAAACATT
**
27978838 AATTAATTTAATTTAAACA-T
1 AATTAACATAATTTAAACATT
*
27978858 GATTAACA
1 AATTAACA
27978866 AGGTGAACGG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTAACATAATTTAAACATT
Found at i:27985127 original size:45 final size:45
Alignment explanation
Indices: 27985063--27985154 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
27985053 TACAATTGAA
27985063 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
1 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
27985108 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
1 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
27985153 TT
1 TT
27985155 GAGCTCCGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (45 bp):
TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
Found at i:27989645 original size:59 final size:59
Alignment explanation
Indices: 27989553--27989670 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
27989543 GAGTTGATGC
27989553 TTCAAATATCAGACTTGAGCGAGAAAAAATCATTCTATTGGTTTAAAGATGGGTTAAAT
1 TTCAAATATCAGACTTGAGCGAGAAAAAATCATTCTATTGGTTTAAAGATGGGTTAAAT
27989612 TTCAAATATCAGACTTGAGCGAGAAAAAATCATTCTATTGGTTTAAAGATGGGTTAAAT
1 TTCAAATATCAGACTTGAGCGAGAAAAAATCATTCTATTGGTTTAAAGATGGGTTAAAT
27989671 CCTTAGGCGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (59 bp):
TTCAAATATCAGACTTGAGCGAGAAAAAATCATTCTATTGGTTTAAAGATGGGTTAAAT
Found at i:27993905 original size:25 final size:26
Alignment explanation
Indices: 27993874--27993929 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
27993864 AAATTAAAAG
27993874 AAAAGAAAAAG-AACGAAGAAGA-AGA
1 AAAAG-AAAAGTAACGAAGAAGAGAGA
*
27993899 AAAAGAAGAGTAACGAAGAAGATGAGA
1 AAAAGAAAAGTAACGAAGAAGA-GAGA
27993926 AAAA
1 AAAA
27993930 CTAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
27 7 0.26
ACGTcount: A:0.68, C:0.04, G:0.25, T:0.04
Consensus pattern (26 bp):
AAAAGAAAAGTAACGAAGAAGAGAGA
Found at i:27994414 original size:20 final size:21
Alignment explanation
Indices: 27994391--27994431 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27994381 TTCTATTTTC
27994391 AAAAAACT-TAGTTTT-TAGAA
1 AAAAAACTGT-GTTTTGTAGAA
27994411 AAAAAACTGTGTTTTGTAGAA
1 AAAAAACTGTGTTTTGTAGAA
27994432 TTGTAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (21 bp):
AAAAAACTGTGTTTTGTAGAA
Found at i:28011040 original size:20 final size:20
Alignment explanation
Indices: 28011008--28011054 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28010998 TGACCCATGC
*
28011008 TTTCAAAATTTTCAATTTT-
1 TTTCAAAACTTTCAATTTTA
*
28011027 TTTCTAAAACTTTCTATTTTA
1 TTTC-AAAACTTTCAATTTTA
28011048 TTTCAAA
1 TTTCAAA
28011055 TTAGTCCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTCAAAACTTTCAATTTTA
Found at i:28018190 original size:16 final size:17
Alignment explanation
Indices: 28018157--28018208 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
28018147 TTTAAAATTT
* *
28018157 ATATATGAATTGTAAAA
1 ATATATAAATTATAAAA
28018174 ATATATAAATT-TAAAA
1 ATATATAAATTATAAAA
*
28018190 A-ATCTAAAATTATAAAA
1 ATATAT-AAATTATAAAA
28018207 AT
1 AT
28018209 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.10
16 11 0.37
17 16 0.53
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATATATAAATTATAAAA
Found at i:28018213 original size:15 final size:15
Alignment explanation
Indices: 28018164--28018214 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
28018154 TTTATATATG
28018164 AATTGTAAAAATATATA
1 AATT-TAAAAATATA-A
*
28018181 AATTTAAAAAATCTAA
1 AATTT-AAAAATATAA
28018197 AATTATAAAAAT-TAA
1 AATT-TAAAAATATAA
28018212 AAT
1 AAT
28018215 AAAAAAACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 6 0.19
16 12 0.39
17 13 0.42
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATTTAAAAATATAA
Found at i:28018436 original size:16 final size:16
Alignment explanation
Indices: 28018398--28018436 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28018388 ATATGCATTT
**
28018398 TTAATTTTTTTAATTA
1 TTAATTTTTTTAAAAA
28018414 TTAATTTTTTTAAAAA
1 TTAATTTTTTTAAAAA
*
28018430 TTTATTT
1 TTAATTT
28018437 ACTTTCTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATTTTTTTAAAAA
Found at i:28020650 original size:20 final size:20
Alignment explanation
Indices: 28020627--28020673 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
28020617 GGGTTAAGAT
*
28020627 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTAAGCTC-AAG
* *
28020647 TGAGCCGACTTAAGCTCAAG
1 TGAGCTGAATTAAGCTCAAG
28020667 TGAGCTG
1 TGAGCTG
28020674 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCAAG
Found at i:28022574 original size:12 final size:12
Alignment explanation
Indices: 28022541--28022621 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
28022531 TTTCCACTCG
28022541 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
28022552 AGCTCTCTTTCA
1 ATTTCTTTTTCA
28022564 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
28022577 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
28022590 --TTCTCTTTCA
1 ATTTCTTTTTCA
28022600 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
28022612 ATCTCTTTTT
1 ATTTCTTTTT
28022622 TCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:28022582 original size:21 final size:20
Alignment explanation
Indices: 28022556--28022611 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
28022546 TTTTCAAGCT
28022556 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
28022577 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
28022592 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
28022612 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:28022629 original size:18 final size:19
Alignment explanation
Indices: 28022601--28022638 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28022591 TCTCTTTCAA
28022601 TTTCTTTTTCAATCTCTTT
1 TTTCTTTTTCAATCTCTTT
*
28022620 TTTC-TTTTCACTCTCTTT
1 TTTCTTTTTCAATCTCTTT
28022638 T
1 T
28022639 ATTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTCAATCTCTTT
Found at i:28022674 original size:15 final size:15
Alignment explanation
Indices: 28022651--28022697 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
28022641 TTTTGAAATA
28022651 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
28022666 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
28022681 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
28022697 T
1 T
28022698 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:28023754 original size:12 final size:12
Alignment explanation
Indices: 28023739--28023774 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
28023729 AGACTTTTCA
28023739 CTTCTTTTTTTT
1 CTTCTTTTTTTT
28023751 CTTCTTTTTTTT
1 CTTCTTTTTTTT
28023763 -TTACTTTTTTTT
1 CTT-CTTTTTTTT
28023775 TGTTTTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.09
12 21 0.91
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTCTTTTTTTT
Found at i:28025380 original size:20 final size:20
Alignment explanation
Indices: 28025357--28025403 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28025347 GGGTTAAGAT
*
28025357 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTAAGCTC-AAG
*
28025377 TGAGCTGACTTAAGCTCAAG
1 TGAGCTGAATTAAGCTCAAG
28025397 TGAGCTG
1 TGAGCTG
28025404 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCAAG
Found at i:28038487 original size:15 final size:15
Alignment explanation
Indices: 28038462--28038496 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28038452 GACTCTATTT
*
28038462 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
28038476 TAATTAATATTAAGA
1 TAATTAATATTAAGA
28038491 TAATTA
1 TAATTA
28038497 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:28040800 original size:13 final size:14
Alignment explanation
Indices: 28040764--28040848 Score: 52
Period size: 14 Copynumber: 5.9 Consensus size: 14
28040754 TCTCACATTT
28040764 CTTTTCTTTT-TCA
1 CTTTTCTTTTCTCA
28040777 TCTTATTCTTTTCTCA
1 -CTT-TTCTTTTCTCA
*
28040793 -TTTTCTTTTCACTTA
1 CTTTTCTTTT--CTCA
*
28040808 CTTTTACTATTTTTCA
1 CTTTT-CT-TTTCTCA
28040824 --TTTCTTTTTCTCA
1 CTTTTC-TTTTCTCA
*
28040837 TTTTTCTTTTCT
1 CTTTTCTTTTCT
28040849 TTTACATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
13 14 0.25
14 15 0.26
15 14 0.25
16 9 0.16
17 2 0.04
18 3 0.05
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (14 bp):
CTTTTCTTTTCTCA
Found at i:28040819 original size:24 final size:27
Alignment explanation
Indices: 28040765--28040820 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 27
28040755 CTCACATTTC
28040765 TTTTCTTTTTCATCTTATTCTTTTCTCA
1 TTTTCTTTTTCATCTTA-TCTTTTCTCA
28040793 TTTTC-TTTTCA-CTTA-CTTTTACT-A
1 TTTTCTTTTTCATCTTATCTTTT-CTCA
28040817 TTTT
1 TTTT
28040821 TCATTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 10 0.37
25 2 0.07
26 4 0.15
27 6 0.22
28 5 0.19
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTCTTTTTCATCTTATCTTTTCTCA
Found at i:28040830 original size:19 final size:19
Alignment explanation
Indices: 28040798--28040858 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
28040788 TCTCATTTTC
*
28040798 TTTTCACTTACTTTTACTAT
1 TTTTCA-TTTCTTTTACTAT
*
28040818 TTTTCATTTCTTTTTCTCAT
1 TTTTCATTTCTTTTACT-AT
*
28040838 TTTTCTTTTCTTTTAC-AT
1 TTTTCATTTCTTTTACTAT
28040856 TTT
1 TTT
28040859 CACTCTGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 9 0.25
20 22 0.61
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTCATTTCTTTTACTAT
Found at i:28040873 original size:45 final size:44
Alignment explanation
Indices: 28040785--28040873 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 44
28040775 CATCTTATTC
* *
28040785 TTTTCTCATTTTCTTTTCACTTACTTTTACTATTTTTCATTTCT
1 TTTTCTCATTTTCTTTTCACTTACTTTTACTACTGTTCATTTCT
**
28040829 TTTTCTCATTTTTCTTTTCTTTTACATTTTCACT-CTGTTC-TTTCT
1 TTTTCTCA-TTTTCTTTTCACTTAC-TTTT-ACTACTGTTCATTTCT
28040874 CTCTCATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
44 8 0.21
45 19 0.50
46 8 0.21
47 3 0.08
ACGTcount: A:0.11, C:0.21, G:0.01, T:0.66
Consensus pattern (44 bp):
TTTTCTCATTTTCTTTTCACTTACTTTTACTACTGTTCATTTCT
Found at i:28045831 original size:23 final size:22
Alignment explanation
Indices: 28045788--28045845 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
28045778 AAAGGGTATC
* *
28045788 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28045809 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
28045832 TACATATCATATCT
1 TACAAATCATATCT
28045846 AAGATTACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28045839 original size:17 final size:17
Alignment explanation
Indices: 28045817--28045869 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 17
28045807 ATTACAAAAT
28045817 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
28045834 CATATCATATCTAAGATTA
1 CATATC-T-TCTAAGATTA
* *
28045853 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
28045870 AGTTTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:28045848 original size:19 final size:20
Alignment explanation
Indices: 28045801--28045858 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 20
28045791 AAATTAAATC
*
28045801 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
28045824 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
28045843 TCTAAGATTACATATC
1 TCTAAGATTACATATC
28045859 CTCGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
22 7 0.21
23 11 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:28053547 original size:20 final size:20
Alignment explanation
Indices: 28053522--28053568 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28053512 AATAAGAAAG
28053522 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
28053542 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
28053562 ATATAAA
1 ATATAAA
28053569 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:28055087 original size:28 final size:28
Alignment explanation
Indices: 28055041--28055114 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
28055031 ATTCAAATAA
* *
28055041 CTTCGTTCCAGTCCACTGTGTCTTGTTG
1 CTTCGATCCACTCCACTGTGTCTTGTTG
*
28055069 CTTCGATCCACTCCTCTGTGTCTTGTTG
1 CTTCGATCCACTCCACTGTGTCTTGTTG
28055097 CTTCGATCCACTCCACTG
1 CTTCGATCCACTCCACTG
28055115 CACTTCAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.09, C:0.34, G:0.18, T:0.39
Consensus pattern (28 bp):
CTTCGATCCACTCCACTGTGTCTTGTTG
Found at i:28055337 original size:44 final size:43
Alignment explanation
Indices: 28055192--28055504 Score: 224
Period size: 44 Copynumber: 7.3 Consensus size: 43
28055182 GTTTTTTCTG
** * *
28055192 TCTGCTCTGCTACTGCTTAGGGAGATAAGACTTG--A--TGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* *** **
28055232 TCTGCTCCACTACTGCTTAGGGAGATAGGACTCG-TGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* * *
28055275 TCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* * ** *
28055319 TCTGCTCCACTACTGCTTAGGGAAATAGGATCTAACATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC-GCCATCTTCGA
* * **** **
28055363 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC-GCCATCTTCGA
* * * * *
28055406 TCTGCTTCACTACTGCTTAGGGAGATGAGATTTGCCATTTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
*
28055450 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC-GCCATCTTCGA
*
28055494 CCTGCTCCACT
1 TCTGCTCCACT
28055505 GTAACCTCAG
Statistics
Matches: 213, Mismatches: 52, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
40 30 0.14
43 67 0.31
44 116 0.54
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCGCCATCTTCGA
Found at i:28055409 original size:87 final size:86
Alignment explanation
Indices: 28055231--28055479 Score: 261
Period size: 87 Copynumber: 2.8 Consensus size: 86
28055221 ACTTGATGCG
* ** *
28055231 ATCTGCTCCACTACTGCTTAGGGAGATAGGA-CTCGTGGCTTAAATCTGCTTCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTCAT--CTTTGATCTGCTCCACTACTGCTTAG
* * * **
28055295 GAAGATAAGATTCGCCGTCTTCG
64 GGAGATAAGACTCGCCGGCTTAA
* *
28055318 ATCTGCTCCACTACTGCTTAGGGAAATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCT--CATCTTTGATCTGCTCCACTACTGCTTAG
* **
28055383 GGAGATAGGACT-GGTGGCTTAA
64 GGAGATAAGACTCGCCGGCTTAA
* * *
28055405 ATCTGCTTCACTACTGCTTAGGGAGAT-GAGATTTGCCATTTTTGATCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAG-GATCT--CATCTTTGATCTGCTCCACTACTGCTTA
28055469 GGGAGATAAGA
63 GGGAGATAAGA
28055480 TCTACCATCT
Statistics
Matches: 136, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
86 1 0.01
87 100 0.74
88 33 0.24
90 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (86 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTCATCTTTGATCTGCTCCACTACTGCTTAGGG
AGATAAGACTCGCCGGCTTAA
Found at i:28055422 original size:131 final size:131
Alignment explanation
Indices: 28055233--28055504 Score: 445
Period size: 131 Copynumber: 2.1 Consensus size: 131
28055223 TTGATGCGAT
28055233 CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
* * *
28055298 GATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAAATAGGATCTAACATCTTTGA
66 GATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTAACATCTTCGA
28055363 C
131 C
* *
28055364 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGGA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
* * * * * *
28055429 GATGAGATTTGCCATTTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
66 GATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTAACATCTTCGA
28055494 C
131 C
28055495 CTGCTCCACT
1 CTGCTCCACT
28055505 GTAACCTCAG
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
GATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTAACATCTTCGA
C
Found at i:28055552 original size:46 final size:46
Alignment explanation
Indices: 28055468--28055969 Score: 305
Period size: 44 Copynumber: 11.3 Consensus size: 46
28055458 ACTACTGCTT
* * *
28055468 AGGGAGATAAGATCT-ACCA-TCTTCGACCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTGA-AATTCTTCGATCTACTCCACTGTAACCTC
* * * *
28055513 AGGGAGATAAGATCTGAAATTCTTCGGTTTACTCCACTGTAACTTT
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * * *
28055559 AGGGAGATAAGATTTG----T-TGCAATCTACTCTACTGTAACTTC
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * ** * * *
28055600 AGAGAGATGAGATCCT-TTATT-TT-AATCCACTCCACTGTAACTTC
1 AGGGAGATAAGAT-CTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * *
28055644 AGGGAGATAGGAT-T-ACTAGTTC--CAATCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTGA--AATTCTTCGATCTACTCCACTGTAACCTC
* *
28055688 AGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAACCTC
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * * * * * *
28055734 AAGGAGATAAGA-CTTG-CA-TATTCAACCTGCCCCACTGTAACTTC
1 AGGGAGATAAGATC-TGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * * * *
28055778 AGGGAGATAAGGTTTG---TGGCTTCGATCTGCTCCTCTGTAATCTC
1 AGGGAGATAAGATCTGAAAT-TCTTCGATCTACTCCACTGTAACCTC
* * * * *
28055822 AGGGAGATAGGATCT---CTGGCTTCAATCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTGAAAT-TCTTCGATCTACTCCACTGTAACCTC
* *
28055866 AGGGAGATAAGAAT-TGAAATTCTTCGGTCTACTCCACTGTAATCTC
1 AGGGAGATAAG-ATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * *
28055912 AGGGAGATAAGACCTAAAATTCTTCGGTCTACTCCACTGTAACATC
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
*
28055958 AAGGAGATAAGA
1 AGGGAGATAAGA
28055970 CTTGCATATT
Statistics
Matches: 358, Mismatches: 74, Indels: 49
0.74 0.15 0.10
Matches are distributed among these distances:
41 29 0.08
42 3 0.01
44 161 0.45
45 24 0.07
46 140 0.39
47 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (46 bp):
AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
Found at i:28055701 original size:88 final size:88
Alignment explanation
Indices: 28055495--28055923 Score: 396
Period size: 88 Copynumber: 4.9 Consensus size: 88
28055485 CATCTTCGAC
* ** *
28055495 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTTTACTCCACTGTAACTTTA
1 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCCACTCCACTGTAACTTCA
28055560 GGGAGATAAGATT-T-GTTGCAAT
66 GGGAGATAAGATTCTAGTT-CAAT
* * * * * ** *
28055582 CTACTCTACTGTAACTTCAGAGAGATGAGATCCT-TTATT-TT-AATCCACTCCACTGTAACTTC
1 CTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGATCCACTCCACTGTAACTTC
*
28055644 AGGGAGATAGGATTACTAGTTCCAAT
65 AGGGAGATAAGATT-CTAGTT-CAAT
* *
28055670 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAACCTCA
1 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCCACTCCACTGTAACTTCA
* *
28055735 AGGAGATAAGACTTGCATA-TTCAAC
66 GGGAGATAAGA-TT-C-TAGTTCAAT
* * * * * ** *
28055760 CTGCCCCACTGTAACTTCAGGGAGATAAGGTTTG---TGGCTTCGATCTGCTCCTCTGTAA-TCT
1 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGATCCACTCCACTGTAACT-T
* *
28055821 CAGGGAGATAGGATCTCTGGCTTCAAT
64 CAGGGAGATAAGAT-TCTAG-TTCAAT
* *
28055848 CTGCTCCACTGTAACCTCAGGGAGATAAGAAT-TGAAATTCTTCGGTCTACTCCACTGTAA-TCT
1 CTGCTCCACTGTAACCTCAGGGAGATAAG-ATCTGAAATTCTTCGATCCACTCCACTGTAACT-T
28055911 CAGGGAGATAAGA
64 CAGGGAGATAAGA
28055924 CCTAAAATTC
Statistics
Matches: 274, Mismatches: 50, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
85 29 0.11
86 3 0.01
87 35 0.13
88 102 0.37
89 3 0.01
90 94 0.34
91 6 0.02
92 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (88 bp):
CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCCACTCCACTGTAACTTCA
GGGAGATAAGATTCTAGTTCAAT
Found at i:28055886 original size:178 final size:174
Alignment explanation
Indices: 28055495--28055924 Score: 528
Period size: 178 Copynumber: 2.4 Consensus size: 174
28055485 CATCTTCGAC
* * *
28055495 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTTTACTCCACTGTAACTTTA
1 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCA
* * * * * * *
28055560 GGGAGATAAGATTTGTTGCAATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAA
66 GGGAGATAAGACTTGTTGCAACCTACCCCACTGTAACTTCAGAGAGATAAGAT-CTTTACTTCAA
28055625 TCCACTCCACTGTAACTTCAGGGAGATAGGATTACTAGTTCCAAT
130 TCCACTCCACTGTAACTTCAGGGAGATAGGATTACTAGTTCCAAT
*
28055670 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAACCTCA
1 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCA
* * * * * *
28055735 AGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGT-TTGTGGCT
66 GGGAGATAAGACTTG--T-TGCAACCTACCCCACTGTAACTTCAGAGAGATAAGATCTT-T-ACT
* ** * *
28055799 TCGATCTGCTCCTCTGTAA-TCTCAGGGAGATAGGATCT-CTGGCTT-CAAT
126 TCAATCCACTCCACTGTAACT-TCAGGGAGATAGGAT-TACTAG-TTCCAAT
*
28055848 CTGCTCCACTGTAACCTCAGGGAGATAAGAAT-TGAAATTCTTCGGTCTACTCCACTGTAATCTC
1 CTGCTCCACTGTAACCTCAGGGAGATAAG-ATCTGAAATTCTTCGGTCTACTCCACTGTAACCTC
28055912 AGGGAGATAAGAC
65 AGGGAGATAAGAC
28055925 CTAAAATTCT
Statistics
Matches: 221, Mismatches: 25, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
175 74 0.33
176 2 0.01
177 3 0.01
178 137 0.62
179 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (174 bp):
CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCA
GGGAGATAAGACTTGTTGCAACCTACCCCACTGTAACTTCAGAGAGATAAGATCTTTACTTCAAT
CCACTCCACTGTAACTTCAGGGAGATAGGATTACTAGTTCCAAT
Found at i:28056008 original size:44 final size:44
Alignment explanation
Indices: 28055629--28056012 Score: 203
Period size: 44 Copynumber: 8.6 Consensus size: 44
28055619 TTTTAATCCA
* * * * *
28055629 CTCCACTGTAACTTCAGGGAGATAGGA-TTACTAGTTCCAATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGCAAATT-CAACCTG
* ** **
28055673 CTCCACTGTAACCTCAGGGAGATAAGA-TCTG-AAATTCTTCGGTCCA
1 CTCCACTGTAACTTCAGGGAGATAAGACT-TGCAAATTCAAC---CTG
* * *
28055719 CTCCACTGTAACCTCAAGGAGATAAGACTTGCATATTCAACCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGCAAATTCAACCTG
* ** **** * *
28055763 CCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGCAAATTCAACCTG
* * *
28055807 CTCCTCTGTAA-TCTCAGGGAGATAGGATCTCTGGC---TTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGA-CT-T-GCAAATTCAACCTG
* * ** *
28055851 CTCCACTGTAACCTCAGGGAGATAAGAATTG-AAATTCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGCAAATTCAAC---CTG
* * ** *
28055897 CTCCACTGTAA-TCTCAGGGAGATAAGACCT-AAAATTCTTCGGTCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGACTTGCAAATTCAAC---CTG
* * *
28055943 CTCCACTGTAACATCAAGGAGATAAGACTTGCATATTCAACCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGCAAATTCAACCTG
*
28055987 CCCCACTGTAACTTCAGGGAGATAAG
1 CTCCACTGTAACTTCAGGGAGATAAG
28056013 GTTTGTGGCT
Statistics
Matches: 263, Mismatches: 56, Indels: 42
0.73 0.16 0.12
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 6 0.02
44 140 0.53
45 2 0.01
46 99 0.38
47 14 0.05
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGACTTGCAAATTCAACCTG
Found at i:28056094 original size:224 final size:222
Alignment explanation
Indices: 28055546--28056098 Score: 744
Period size: 224 Copynumber: 2.5 Consensus size: 222
28055536 TCGGTTTACT
* * * * *
28055546 CCACTGTAACTTTAGGGAGATAAGATTTGT---TGCAATCTACTCTACTGTAACTTCAGAGAGAT
1 CCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTACTCTTCTGTAACTTCAGAGAGAT
* * *
28055608 -GAGATCCTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGAT-AGGATTACTAGTTCCAATC
66 AG-GATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGAATTAC-AATTCCAATC
* * * *
28055671 TGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAACCTCAA
129 TACTCCACTGTAACCTCAGGGAGATAAGACCTAAAATTCTTCGGTCCACTCCACTGTAACATCAA
28055736 GGAGATAAGACTTGCATATTCAACCTGCC
194 GGAGATAAGACTTGCATATTCAACCTGCC
* * *
28055765 CCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTGCTCCTCTGTAA-TCTCAGGGAGA
1 CCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTACTCTTCTGTAACT-TCAGAGAGA
*** * * * *
28055829 TAGGAT-CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGAATTGA-AATTCTTCG
65 TAGGATCCT-TTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGAATT-ACAATTC--CA
* * *
28055892 GTCTACTCCACTGTAATCTCAGGGAGATAAGACCTAAAATTCTTCGGTCTACTCCACTGTAACAT
126 ATCTACTCCACTGTAACCTCAGGGAGATAAGACCTAAAATTCTTCGGTCCACTCCACTGTAACAT
28055957 CAAGGAGATAAGACTTGCATATTCAACCTGCC
191 CAAGGAGATAAGACTTGCATATTCAACCTGCC
28055989 CCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTACTCTTCTGTAACTTCAGAGAGAT
1 CCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTACTCTTCTGTAACTTCAGAGAGAT
* *
28056054 AGGATCCTTTATTTTAATCCGCTCTACTATAACTTCAGGGAGATA
66 AGGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATA
28056099 GGATAGCGTC
Statistics
Matches: 286, Mismatches: 36, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
219 28 0.10
221 3 0.01
222 60 0.21
223 6 0.02
224 186 0.65
225 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (222 bp):
CCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTACTCTTCTGTAACTTCAGAGAGAT
AGGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGAATTACAATTCCAATCTA
CTCCACTGTAACCTCAGGGAGATAAGACCTAAAATTCTTCGGTCCACTCCACTGTAACATCAAGG
AGATAAGACTTGCATATTCAACCTGCC
Found at i:28057389 original size:7 final size:7
Alignment explanation
Indices: 28057377--28057428 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
28057367 GCCTCTCCAT
28057377 TTTTTCA
1 TTTTTCA
28057384 TTTTTCA
1 TTTTTCA
*
28057391 -TTTTCT
1 TTTTTCA
28057397 TTTTTCCA
1 TTTTT-CA
28057405 -TTTTCA
1 TTTTTCA
*
28057411 -TTCTCA
1 TTTTTCA
28057417 TTTTTCA
1 TTTTTCA
28057424 TTTTT
1 TTTTT
28057429 TCTGAGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 12 0.32
7 25 0.66
8 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCA
Found at i:28057400 original size:13 final size:14
Alignment explanation
Indices: 28057378--28057412 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
28057368 CCTCTCCATT
28057378 TTTTCATTTTT-CA
1 TTTTCATTTTTCCA
*
28057391 TTTTCTTTTTTCCA
1 TTTTCATTTTTCCA
28057405 TTTTCATT
1 TTTTCATT
28057413 CTCATTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCATTTTTCCA
Found at i:28057401 original size:20 final size:20
Alignment explanation
Indices: 28057376--28057428 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
28057366 AGCCTCTCCA
*
28057376 TTTTTTCATTTTTCATTTTC
1 TTTTTTCATTTTTCATTCTC
28057396 TTTTTTCCA-TTTTCATTCTC
1 TTTTTT-CATTTTTCATTCTC
*
28057416 ATTTTTCATTTTT
1 TTTTTTCATTTTT
28057429 TCTGAGTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTCATTTTTCATTCTC
Found at i:28063114 original size:20 final size:20
Alignment explanation
Indices: 28063089--28063135 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28063079 AATAAGAAAG
28063089 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
28063109 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
28063129 ATATAAA
1 ATATAAA
28063136 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:28083572 original size:17 final size:16
Alignment explanation
Indices: 28083550--28083592 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
28083540 AAGGTGGTCT
28083550 TTTTATTTTTCACTTCA
1 TTTTATTTTTCACTT-A
*
28083567 TTTTATTTATTTACTTA
1 TTTTATTT-TTCACTTA
28083584 -TTTATTTTT
1 TTTTATTTTT
28083593 TTAGAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 7 0.29
17 9 0.38
18 6 0.25
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTTTCACTTA
Found at i:28087872 original size:58 final size:59
Alignment explanation
Indices: 28087790--28087903 Score: 169
Period size: 58 Copynumber: 1.9 Consensus size: 59
28087780 TTTAAAAAGG
* *
28087790 AAAAGATAAAAACAACATATATTAAATACTTT-ATTTTATTTATTTTTCAAATAAAACCC
1 AAAAGATAAAAACAACATATATTAAATA-TTTGATTTTATTTATTTTTAAAACAAAACCC
* *
28087849 AAAAGAT-AAAACATCATATATTAATTATTTGATTTTATTTATTTTTAAAACAAAA
1 AAAAGATAAAAACAACATATATTAAATATTTGATTTTATTTATTTTTAAAACAAAA
28087904 TTCATTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 3 0.06
58 40 0.80
59 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (59 bp):
AAAAGATAAAAACAACATATATTAAATATTTGATTTTATTTATTTTTAAAACAAAACCC
Found at i:28088399 original size:18 final size:19
Alignment explanation
Indices: 28088376--28088413 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
28088366 TTTTAATATT
28088376 ATATATATTAAT-TTTTTA
1 ATATATATTAATATTTTTA
* *
28088394 ATATATTTTTATATTTTTA
1 ATATATATTAATATTTTTA
28088413 A
1 A
28088414 AAATTGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATATTAATATTTTTA
Found at i:28091497 original size:22 final size:22
Alignment explanation
Indices: 28091454--28091497 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28091444 TAATCTCATG
* ** *
28091454 TAATACTATATTCTTTTCATTA
1 TAATACTATATTATCATAATTA
28091476 TAATACTATATTATCATAATTA
1 TAATACTATATTATCATAATTA
28091498 CATATAATAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATACTATATTATCATAATTA
Found at i:28091997 original size:27 final size:29
Alignment explanation
Indices: 28091946--28092000 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
28091936 TATGTTATAA
28091946 TAATAGTTATATATGTAATAATATTTTAG
1 TAATAGTTATATATGTAATAATATTTTAG
*
28091975 TAATAGTTATATAT-T-ATATTATTTTA
1 TAATAGTTATATATGTAATAATATTTTA
28092001 TGTATTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 1 0.04
29 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (29 bp):
TAATAGTTATATATGTAATAATATTTTAG
Found at i:28093050 original size:161 final size:161
Alignment explanation
Indices: 28092781--28093111 Score: 637
Period size: 161 Copynumber: 2.1 Consensus size: 161
28092771 GTTCAAAACA
28092781 ATAT-AACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
1 ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
28092845 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
66 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
28092910 CAATCAAAACTATATAAAAAAACCATTGAAT
131 CAATCAAAACTATATAAAAAAACCATTGAAT
*
28092941 ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTTCCTATT
1 ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
*
28093006 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTTACTGTCT
66 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
28093071 CAATCAAAACTATATAAAAAAACCATTGAAT
131 CAATCAAAACTATATAAAAAAACCATTGAAT
28093102 ATATGAACTT
1 ATATGAACTT
28093112 TTACATTATA
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
160 4 0.02
161 164 0.98
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (161 bp):
ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
CAATCAAAACTATATAAAAAAACCATTGAAT
Found at i:28093548 original size:131 final size:131
Alignment explanation
Indices: 28093314--28093578 Score: 467
Period size: 131 Copynumber: 2.0 Consensus size: 131
28093304 GGAGGCTACA
* *
28093314 CATCCTCCTCTAGAAACACACCTGAATCACTATAAAGATAGCTCGGTAATCCGCAACAAATGCTA
1 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTA
* *
28093379 GATTCCAATAAGTTTAGTGAATAAATAGTACGTCATCATCTTGTCTTATATCAAACCCATACAAC
66 GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
28093444 G
131 G
*
28093445 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTG
1 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTA
* *
28093510 GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTGTTATATCAAACCCGTACAAC
66 GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
28093575 G
131 G
28093576 CAT
1 CAT
28093579 GAAATAACTC
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 127 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.26
Consensus pattern (131 bp):
CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTA
GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
G
Found at i:28095748 original size:15 final size:15
Alignment explanation
Indices: 28095730--28095800 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
28095720 TTTATTGTTG
28095730 TTGTTATTATTATTA
1 TTGTTATTATTATTA
28095745 TTGTTATTAGTGATATTA
1 TTGTTATTA-T--TATTA
* * *
28095763 TTGCTACTATT-TGA
1 TTGTTATTATTATTA
* *
28095777 TGTGTTATTAGTATTG
1 T-TGTTATTATTATTA
28095793 TTGTTATT
1 TTGTTATT
28095801 TTTCATTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
14 3 0.07
15 24 0.56
16 3 0.07
17 1 0.02
18 12 0.28
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (15 bp):
TTGTTATTATTATTA
Found at i:28095751 original size:9 final size:9
Alignment explanation
Indices: 28095688--28095765 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
28095678 AAATTCGCAA
28095688 ATTGTTATT
1 ATTGTTATT
*
28095697 GTTGTTATT
1 ATTGTTATT
28095706 ACTCATGTT-TT
1 A-T--TGTTATT
*
28095717 ATTTTTATT
1 ATTGTTATT
* *
28095726 GTTGTTGTT
1 ATTGTTATT
*
28095735 ATTATTATT
1 ATTGTTATT
28095744 ATTGTTATT
1 ATTGTTATT
* *
28095753 AGTGATATT
1 ATTGTTATT
28095762 ATTG
1 ATTG
28095766 CTACTATTTG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
8 3 0.06
9 40 0.77
10 2 0.04
11 3 0.06
12 4 0.08
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.63
Consensus pattern (9 bp):
ATTGTTATT
Found at i:28095876 original size:23 final size:21
Alignment explanation
Indices: 28095848--28095901 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
28095838 CTGTTTATGA
*
28095848 TTTATTTTCTAAATGTTTTATT
1 TTTATTTT-GAAATGTTTTATT
*
28095870 TTCTATTCCTTGATATGTTTTATT
1 TT-TATT--TTGAAATGTTTTATT
28095894 TTTATTTT
1 TTTATTTT
28095902 TATTTGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 8 0.30
24 13 0.48
25 2 0.07
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTATTTTGAAATGTTTTATT
Found at i:28104613 original size:19 final size:19
Alignment explanation
Indices: 28104591--28104655 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
28104581 AGTGTAACAT
28104591 AATTTAATAAAATCTAAAC
1 AATTTAATAAAATCTAAAC
* * *
28104610 AATTTAA-ATAAGTGTAACAT
1 AATTTAATA-AAATCTAA-AC
* *
28104630 AATCTAATAAAACCTAAAC
1 AATTTAATAAAATCTAAAC
28104649 AATTTAA
1 AATTTAA
28104656 ATTGATTAAG
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 12 0.35
21 1 0.03
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (19 bp):
AATTTAATAAAATCTAAAC
Found at i:28104621 original size:39 final size:39
Alignment explanation
Indices: 28104578--28104657 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
28104568 CATCCATATC
* *
28104578 ATAAGTGTAACATAATTTAATAAAATCTAAACAATTTAA
1 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
28104617 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
1 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
28104656 AT
1 AT
28104658 TGATTAAGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (39 bp):
ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
Found at i:28107506 original size:113 final size:114
Alignment explanation
Indices: 28107292--28107778 Score: 524
Period size: 113 Copynumber: 4.3 Consensus size: 114
28107282 TAAAGAAAGT
** * * *
28107292 ATTAGTGGCGCTTATTTAAAATCGCCGCTAAAGCATAGAATTAGCGGCGAGTCA--CAAAAAGCG
1 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGT-AGTGAAAAA-CG
* * *
28107355 CCGCAATACATCTTAACGAAAACGCAGAGTTTGGTCTTGAGGTACACTAGC
64 CCGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
* *
28107406 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGAATAGTATTGGCGGCGAGTAGTGAAAAACG-C
1 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAACGCC
* * *
28107470 GCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGG
66 GCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
* * ** * * *
28107519 ATTAGTGGCGCTTAT-CGGAAAACGCCACTAAAGCATAGTATTAGCGGCGCTTATTGTAAAGCGC
1 ATTAGTGGCGCTTATAC-AAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAACGC
* *
28107583 CGCAA-A-ATATTAACCAAAACGCA-ACGCTTTGGTCTTGATGTATACTAGC
65 CGCAATATATCTTAACCAAAACGCAGA-G-TTTGGTCTTGAGGTATACTAGC
* * * * **
28107632 AGTAGTGGCGCTTATATC-AAAATGCCGCTAAATCATAGTATTAGCGGTGAGTAGTGAAAAGTGC
1 ATTAGTGGCGCTTATA-CAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAACGC
* * * *
28107696 CGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGC
65 CGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTA-GC
*** *
28107747 -TTAGTGGCGCTTATTGGAAAACGCCGCAAAAG
1 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAG
28107779 ATTAACCAAA
Statistics
Matches: 312, Mismatches: 48, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
111 1 0.00
112 17 0.05
113 173 0.55
114 96 0.31
115 24 0.08
116 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (114 bp):
ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAACGCC
GCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
Found at i:28107714 original size:227 final size:226
Alignment explanation
Indices: 28107292--28107771 Score: 637
Period size: 227 Copynumber: 2.1 Consensus size: 226
28107282 TAAAGAAAGT
** * *
28107292 ATTAGTGGCGCTTATTTAAAATCGCCGCTAAAGCATAGAATTAGCGGCGAGTCACAAAAAGCGCC
1 ATTAGTGGCGCTTATGGAAAA-CGCCACTAAAGCATAGAATTAGCGGCGACTCACAAAAAGCGCC
* * *
28107357 GCAATACATCTTAACGAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGGCGCTTATA
65 GCAATACATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATA
* *
28107422 CAAAAACGCCGCTAAAGAATAGTATTGGCGGCGAGTAGTGAAAAACGCGCAATATTTCTTAACCA
130 CAAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCGCAAGATTTCTTAACCA
28107487 AAACGCAGAGTTTGGTCTTGAGGTATATTAGG
195 AAACGCAGAGTTTGGTCTTGAGGTATATTAGG
* * ***
28107519 ATTAGTGGCGCTTATCGGAAAACGCCACTAAAGCATAGTATTAGCGGCG-CTTATTGTAAAGCGC
1 ATTAGTGGCGCTTAT-GGAAAACGCCACTAAAGCATAGAATTAGCGGCGACTCA-CAAAAAGCGC
* *
28107583 CGCAA-A-ATATTAACCAAAACGCA-ACGCTTTGGTCTTGATGTATACTAGCAGTAGTGGCGCTT
64 CGCAATACATATTAACCAAAACGCAGA-G-TTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTT
* ** * **
28107645 ATATC-AAAATGCCGCTAAATCATAGTATTAGCGGTGAGTAGTGAAAAGTGCCGCAAGATTTCTT
127 ATA-CAAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACG-CGCAAGATTTCTT
*
28107709 AACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGG
190 AACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGG
*
28107746 CTTAGTGGCGCTTATTGGAAAACGCC
1 ATTAGTGGCGCTTA-TGGAAAACGCC
28107772 GCAAAAGATT
Statistics
Matches: 222, Mismatches: 24, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
224 1 0.00
225 16 0.07
226 76 0.34
227 124 0.56
228 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (226 bp):
ATTAGTGGCGCTTATGGAAAACGCCACTAAAGCATAGAATTAGCGGCGACTCACAAAAAGCGCCG
CAATACATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATAC
AAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCGCAAGATTTCTTAACCAA
AACGCAGAGTTTGGTCTTGAGGTATATTAGG
Found at i:28107842 original size:74 final size:73
Alignment explanation
Indices: 28107707--28107846 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 73
28107697 GCAAGATTTC
* * * **
28107707 TTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGCTTAGTGGCGCTTATTGGAAAACGCC
1 TTAACCAAAACGCAGAGTTTGATCTTGAGGTATAGTAGGCTTAGTGGCGCTTATACGAAAACGCC
28107772 GCAAAAGA
66 GCAAAAGA
* * * *
28107780 TTAACCAAAACGCAGCGCTTTGATCTTGATGTGTAGTA-GCATTAGTGGCGCTTATACTAAAACG
1 TTAACCAAAACGCAGAG-TTTGATCTTGAGGTATAGTAGGC-TTAGTGGCGCTTATACGAAAACG
28107844 CCG
64 CCG
28107847 TTAAAGTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
73 18 0.32
74 38 0.68
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (73 bp):
TTAACCAAAACGCAGAGTTTGATCTTGAGGTATAGTAGGCTTAGTGGCGCTTATACGAAAACGCC
GCAAAAGA
Found at i:28107888 original size:188 final size:186
Alignment explanation
Indices: 28107558--28108056 Score: 739
Period size: 188 Copynumber: 2.7 Consensus size: 186
28107548 AAAGCATAGT
* *
28107558 ATTAGCGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAACGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * * *
28107623 TATACTAGCAGTAGTGGCGCTTATATCAAAATGCCGCTAAATCATAGTATTAGCGGTGAGTAGTG
66 TATACTAGCATTAGTGGCGCTTATAT-AAAACGCCGCTAAAT-ATAGTATTAGCGGCGAGTACTG
* * *
28107688 AAAAGTGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGG
129 AAAAGCGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
* * * * *
28107746 CTTAGTGGCGCTTATTGGAAAACGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGATCTTGATG
1 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * *
28107811 TGTAGTAGCATTAGTGGCGCTTATACTAAAACGCCGTTAAAGTATAGTATTAGCGGCGAGTACTG
66 TATACTAGCATTAGTGGCGCTTATA-TAAAACGCCGCTAAA-TATAGTATTAGCGGCGAGTACTG
*
28107876 AAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
129 AAAAGCGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
28107934 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * *
28107999 TATACTAGCAGTT-GTGGCGCTTATGGTAAAACGCCGCTAAAACATATTATTAGCGGCG
66 TATACTAGCA-TTAGTGGCGCTTAT-ATAAAACGCCGCT-AAATATAGTATTAGCGGCG
28108057 CGTTGTAGGA
Statistics
Matches: 277, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
188 270 0.97
189 7 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (186 bp):
ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
TATACTAGCATTAGTGGCGCTTATATAAAACGCCGCTAAATATAGTATTAGCGGCGAGTACTGAA
AAGCGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
Found at i:28108016 original size:74 final size:73
Alignment explanation
Indices: 28107877--28108040 Score: 195
Period size: 74 Copynumber: 2.2 Consensus size: 73
28107867 CGAGTACTGA
* * * *
28107877 AAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGGATTAGTGG
1 AAAGCGCCGCAA-A-ATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGG
*
28107942 CGCTTATTGT
64 CGCTTATGGT
* * *
28107952 AAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAGTT-GTGG
1 AAAGCGCCGCAAAATATTAACCAAAACGCAGAG-TTTGGTCTTGAGGTACACTAGCA-TTAGTGG
28108016 CGCTTATGGT
64 CGCTTATGGT
*
28108026 AAAACGCCGCTAAAA
1 AAAGCGCCGC-AAAA
28108041 CATATTATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
73 17 0.22
74 42 0.55
75 18 0.23
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (73 bp):
AAAGCGCCGCAAAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGGCG
CTTATGGT
Found at i:28108869 original size:15 final size:16
Alignment explanation
Indices: 28108849--28108879 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
28108839 TATTTATGTT
28108849 TATTAAAAATA-AAAA
1 TATTAAAAATATAAAA
28108864 TATTAAAAATATAAAA
1 TATTAAAAATATAAAA
28108880 AAATATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATTAAAAATATAAAA
Found at i:28111703 original size:18 final size:18
Alignment explanation
Indices: 28111682--28112470 Score: 717
Period size: 18 Copynumber: 44.7 Consensus size: 18
28111672 CACAAATTAA
28111682 ATAACTTACATTAA-TTAC
1 ATAACTTACA-TAACTTAC
* * * *
28111700 ATAACTTATAAAAATTAA
1 ATAACTTACATAACTTAC
28111718 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
28111736 ATAAATTA-AGAACCTTAC
1 ATAACTTACATAA-CTTAC
28111754 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
28111772 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
*
28111790 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
28111808 ATTAA-TTACATAACTTAC
1 A-TAACTTACATAACTTAC
* * *
28111826 AAAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
28111844 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
28111862 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
* *
28111880 ATAACTTACATAAATTAA
1 ATAACTTACATAACTTAC
*
28111898 ATAACTTACGTAACTTAC
1 ATAACTTACATAACTTAC
*
28111916 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
*
28111934 ATAA---A-TTAACTTAC
1 ATAACTTACATAACTTAC
28111948 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
28111966 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
*
28111984 ATAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
28112001 AGTAACTTACATTAA-TTAC
1 A-TAACTTACA-TAACTTAC
* * *
28112020 ATAACTTACAAAAATTAA
1 ATAACTTACATAACTTAC
28112038 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
28112056 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
* *
28112074 ATAACTTACATAAATTAA
1 ATAACTTACATAACTTAC
**
28112092 ATAACTTATGTAACTTAC
1 ATAACTTACATAACTTAC
*
28112110 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
* *
28112128 ATAACTTACATAAATTAA
1 ATAACTTACATAACTTAC
28112146 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
28112164 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
*
28112182 ATTAA-TTACATAAATTA-
1 A-TAACTTACATAACTTAC
28112199 AGTAACTTACATAACTTAC
1 A-TAACTTACATAACTTAC
*
28112218 ATAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
28112235 AGTAACTTACATAACTTAC
1 A-TAACTTACATAACTTAC
* * *
28112254 ATAACTTACAAAAATTAA
1 ATAACTTACATAACTTAC
28112272 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
28112290 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
* * **
28112308 ATAAATTAAATAACTGGC
1 ATAACTTACATAACTTAC
*
28112326 ATAACTTACATTA--TAC
1 ATAACTTACATAACTTAC
* *
28112342 ATAACCTT-CTTAACTGAC
1 ATAA-CTTACATAACTTAC
* * *
28112360 ATTA--TACACAACTCAC
1 ATAACTTACATAACTTAC
*
28112376 ATAA-TTA-AT-ATTATAC
1 ATAACTTACATAACT-TAC
*
28112392 ACAACTTACATAA--TAC
1 ATAACTTACATAACTTAC
*
28112408 ATTACTTACATAACTTAC
1 ATAACTTACATAACTTAC
28112426 AGT-ACTTACATAA--TAC
1 A-TAACTTACATAACTTAC
28112442 ATAA--TACATAACTTAC
1 ATAACTTACATAACTTAC
28112458 ATAACTTACATAA
1 ATAACTTACATAA
28112471 TACATAAAAA
Statistics
Matches: 636, Mismatches: 89, Indels: 92
0.78 0.11 0.11
Matches are distributed among these distances:
14 19 0.03
15 5 0.01
16 50 0.08
17 28 0.04
18 512 0.81
19 22 0.03
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:28111726 original size:27 final size:27
Alignment explanation
Indices: 28111696--28112320 Score: 661
Period size: 27 Copynumber: 23.6 Consensus size: 27
28111686 CTTACATTAA
* *
28111696 TTACATAACTTATAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28111723 TTACATAACTTACATAAATTAAGA-ACC
1 TTACATAACTTACATAAATTAA-ATAAC
* * *
28111750 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* *
28111777 TTAAATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28111804 TTAC---A--T---T-AATTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
* * * * *
28111822 TTACAAAAATTAAATAACTTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28111849 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
28111876 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
28111903 TTACGTAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
* * *
28111930 TTACATAA---A-TTAACTTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
28111953 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28111980 TTACATAACTTACATAAATTAAGTAACTTACATTAA
1 TTACATAACTTACATAAATT-A--AA--T--A--AC
*
28112016 TTACATAACTTACAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28112043 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
28112070 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
** *
28112097 TTATGTAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
28112124 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28112151 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
*
28112178 TTACATTAA-TTACATAAATTAAGTAAC
1 TTACA-TAACTTACATAAATTAAATAAC
* * *
28112205 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
28112232 TTA-AGTAACTTAC---------ATAAC
1 TTACA-TAACTTACATAAATTAAATAAC
*
28112250 TTACATAACTTACAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
28112277 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
28112304 TTACATAAATTAAATAA
1 TTACATAACTTACATAA
28112321 CTGGCATAAC
Statistics
Matches: 507, Mismatches: 54, Indels: 74
0.80 0.09 0.12
Matches are distributed among these distances:
18 28 0.06
19 2 0.00
21 1 0.00
22 1 0.00
23 19 0.04
24 2 0.00
26 7 0.01
27 413 0.81
28 5 0.01
29 1 0.00
30 2 0.00
31 1 0.00
32 1 0.00
33 2 0.00
34 1 0.00
35 1 0.00
36 20 0.04
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (27 bp):
TTACATAACTTACATAAATTAAATAAC
Found at i:28112417 original size:25 final size:25
Alignment explanation
Indices: 28112362--28112426 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
28112352 TAACTGACAT
* *
28112362 TATACACAACTCACATAATTAATAT
1 TATACACAACTTACATAATTAATAC
28112387 TATACACAACTTACATAA-TACATTAC
1 TATACACAACTTACATAATTA-A-TAC
*
28112413 T-TACATAACTTACA
1 TATACACAACTTACA
28112427 GTACTTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.06
25 30 0.86
26 3 0.09
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (25 bp):
TATACACAACTTACATAATTAATAC
Found at i:28112444 original size:7 final size:7
Alignment explanation
Indices: 28112432--28112477 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
28112422 TTACAGTACT
28112432 TACATAA
1 TACATAA
28112439 TACATAA
1 TACATAA
28112446 TACATAA
1 TACATAA
28112453 CTTACATAA
1 --TACATAA
28112462 CTTACATAA
1 --TACATAA
28112471 TACATAA
1 TACATAA
28112478 AAATATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.57
9 16 0.43
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:28117843 original size:21 final size:21
Alignment explanation
Indices: 28117817--28117882 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
28117807 CAACTTAAAA
*
28117817 CAGAGGCTGCAGCGAGGGAAG
1 CAGAGGCTGCAGCGAGAGAAG
*
28117838 CAGAGGCTACAGCGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
* * *
28117859 CAAAGGCCGTAGCGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
28117880 CAG
1 CAG
28117883 CGAGAGAAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.41, T:0.05
Consensus pattern (21 bp):
CAGAGGCTGCAGCGAGAGAAG
Found at i:28117886 original size:12 final size:12
Alignment explanation
Indices: 28117869--28117894 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28117859 CAAAGGCCGT
28117869 AGCGAGAGAAGC
1 AGCGAGAGAAGC
28117881 AGCGAGAGAAGC
1 AGCGAGAGAAGC
28117893 AG
1 AG
28117895 AGGTTCAAAA
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:0.42, C:0.15, G:0.42, T:0.00
Consensus pattern (12 bp):
AGCGAGAGAAGC
Found at i:28118360 original size:43 final size:43
Alignment explanation
Indices: 28118313--28118451 Score: 122
Period size: 43 Copynumber: 3.3 Consensus size: 43
28118303 TCATATCATA
*
28118313 TAGTGGCGTTTGTGAAAT-AAGCGCCG-TGAAAGAACACTACTTT
1 TAGTGGCGTTTGT-AAATGAAGCACCGCT-AAAGAACACTACTTT
* *
28118356 TAGTGGCGTTTGTAGATGAAGCACCGCTAAAGAACATTACTTT
1 TAGTGGCGTTTGTAAATGAAGCACCGCTAAAGAACACTACTTT
* * ** ** * * *
28118399 TAGCGGTGTTT-TCTACCAAGCGCCGCTATAGAACATTACTTT
1 TAGTGGCGTTTGTAAATGAAGCACCGCTAAAGAACACTACTTT
*
28118441 TAGCGGCGTTT
1 TAGTGGCGTTT
28118452 TTTACCAACC
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 38 0.46
43 43 0.52
44 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
TAGTGGCGTTTGTAAATGAAGCACCGCTAAAGAACACTACTTT
Found at i:28118440 original size:85 final size:85
Alignment explanation
Indices: 28118330--28118622 Score: 234
Period size: 85 Copynumber: 3.4 Consensus size: 85
28118320 GTTTGTGAAA
* * ** * *
28118330 TAAGCGCCG-TGAAAGAACACTACTTTTAGTGGCGTTTGTAGATGAAGCACCGCTAAAGAACATT
1 TAAGCGCCGCT-AAAGAACATTACTTTTAGCGGCGTTT-TAGACCAACCACCACTAAAGAACATT
*
28118394 ACTTTTAGCGGTGTTTTCTACC
64 ACTTTTAGCGGCGTTTTCTACC
* ** * **
28118416 -AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTACCAACCGCCACTATTGAACATTAC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTAGACCAACCACCACTAAAGAACATTAC
* *
28118480 TTTTAGCGGCGTTTTTTTCC
66 TTTTAGCGGCGTTTTCTACC
* * *** * * ** *
28118500 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGTGTTTTTTCCCAAGCGCTGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTAGACCAACCACCACTAAAGAACATTA
* * * * *
28118564 -TCATTAACGGCGTTTTTTTCT
65 CT-TTTAGCGGCGTTTTCTACC
* *
28118585 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT
28118623 TTTCTGTAAG
Statistics
Matches: 172, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
84 38 0.22
85 133 0.77
86 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (85 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTAGACCAACCACCACTAAAGAACATTAC
TTTTAGCGGCGTTTTCTACC
Found at i:28118518 original size:43 final size:43
Alignment explanation
Indices: 28118330--28118643 Score: 282
Period size: 42 Copynumber: 7.3 Consensus size: 43
28118320 GTTTGTGAAA
* * * ***
28118330 TAAGCGCCG-TGAAAGAACACTACTTTTAGTGGCG-TTTGTAGA
1 TAAGCGCCGCT-AAAGAACATTACTTTTAGCGGCGTTTTTTTCC
* * * *
28118372 TGAAGCACCGCTAAAGAACATTACTTTTAGCGGTGTTTTCTACC
1 T-AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTCC
* *
28118416 -AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTACC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTCC
* * **
28118458 -AACCGCCACTATTGAACATTACTTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTCC
* *
28118500 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGTG-TTTTTTCC
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTTCC
* * * * * *
28118542 CAAGCGCTGCTAAAGAACATGA-TCATTAACGGCGTTTTTTTCT
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTTCC
* * *
28118585 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTG
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC-C
*
28118629 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
28118644 TTAGCGATGT
Statistics
Matches: 230, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
42 115 0.50
43 95 0.41
44 20 0.09
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTCC
Found at i:28118623 original size:85 final size:85
Alignment explanation
Indices: 28118382--28118624 Score: 274
Period size: 85 Copynumber: 2.9 Consensus size: 85
28118372 TGAAGCACCG
* * * * * * * * *
28118382 CTAAAGAACATTACTTTTAGCGGTGTTTTCTACC-AAGCGCCGCTATAGAACATTACTTTTAGCG
1 CTAAAGAACATGACTATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGCG
28118446 GCGTTTTTTACCAACCGCCA
66 GCGTTTTTTACCAACCGCCA
** * * * *
28118466 CTATTGAACATTACTTTTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCG
1 CTAAAGAACATGACTATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGCG
* * * **
28118531 GTGTTTTTTCCCAAGCGCTG
66 GCGTTTTTTACCAACCGCCA
*
28118551 CTAAAGAACATGA-TCATTAACGGCGTTTTTTTCTTAAGCGCCGCTAAAGAACATGACCTTTAGC
1 CTAAAGAACATGACT-ATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGC
28118615 GGCGTTTTTT
65 GGCGTTTTTT
28118625 TCTGTAAGCG
Statistics
Matches: 135, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
84 30 0.22
85 105 0.78
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (85 bp):
CTAAAGAACATGACTATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGCG
GCGTTTTTTACCAACCGCCA
Found at i:28119677 original size:436 final size:435
Alignment explanation
Indices: 28118772--28119789 Score: 1723
Period size: 436 Copynumber: 2.3 Consensus size: 435
28118762 TGGTGTAGTG
* * *
28118772 GTTCCAGATGTTGACAGTCTTTCCGTCGCCTATTCTTCAACCAACACCTGATTCTAATAAGTCCC
1 GTTCCAGATGTTAACAGTATTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
* *
28118837 TTGCACCCTATATACTTCTCCAAGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
66 TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
* *
28118902 CCATGTGGGTAGTAGACTTTCATTTCCCAGCAAATTTAAATCTTCAGTAATACACCACTTGTATC
131 CCATGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
* * *
28118967 CACTCTTCTACGTGTATTTGCTAGTATTGTCTTCTCGCCAGACCTAGTGTCTGGCTGCAAAGTTT
196 CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACCTAGTGTCTGGCTACAAAGTGT
*
28119032 TCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACCCATCT
261 TCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACACATCT
28119097 TCCTTCCAGGTATTTAAATTTGTTTAAATTAATTCTTCCACCATGGTATATCTCCTATCAATATT
326 TCCTTCCAGGTATTTAAATTTGTTTAAATTAATTCTTCCACCATGGTATATCTCCTATCAATATT
* *
28119162 CTAATTTTGTAGTTTTCCATTCCTAGGATATAGAAGCCATGTGTC
391 CTAATTTTGTAGTTTTCCATTCCCAGGATATAGAAGCCATGTGTA
* * *
28119207 GTTCCAGATGTTAACAGTATTTCTGTCGCCTATTCTTCAACCAACCCCTGGTTCTAATAAGTCCT
1 GTTCCAGATGTTAACAGTATTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
*
28119272 TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCGGCATTTAAAAAATCA
66 TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
* * *
28119337 CCACGTGGGTAGTAGATTTTCATTTCCTATCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
131 CCATGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
* *
28119402 CACTCTTCTCCGTGTATTTGGTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTACAAAGTG
196 CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACC-TAGTGTCTGGCTACAAAGTG
*
28119467 TTCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCATAAAAAAGATTTCTTAACACATC
260 TTCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACACATC
* * * *
28119532 TTCTTTCCAGGTATTTAAATTT-TTATTAATTAATTCTTCTACCATGGTATATCTCCTATCCATA
325 TTCCTTCCAGGTATTTAAATTTGTT-TAAATTAATTCTTCCACCATGGTATATCTCCTATCAATA
*
28119596 TTCTAATTTTGTAGTTTTCCATTCCCAGGATATTGAAGCCATGTGTA
389 TTCTAATTTTGTAGTTTTCCATTCCCAGGATATAGAAGCCATGTGTA
* * *
28119643 GTTCCAGATGTTAACAGTTTTTCCGTCACCTATTCTTCAATCAACCCCTGATTCTAATAAGTCCC
1 GTTCCAGATGTTAACAGTATTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
28119708 TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
66 TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
*
28119773 TCATGTGGGTAGTAGAT
131 CCATGTGGGTAGTAGAT
28119790 AGCTTTCATG
Statistics
Matches: 544, Mismatches: 37, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
435 224 0.41
436 320 0.59
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (435 bp):
GTTCCAGATGTTAACAGTATTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
CCATGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACCTAGTGTCTGGCTACAAAGTGT
TCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACACATCT
TCCTTCCAGGTATTTAAATTTGTTTAAATTAATTCTTCCACCATGGTATATCTCCTATCAATATT
CTAATTTTGTAGTTTTCCATTCCCAGGATATAGAAGCCATGTGTA
Found at i:28123635 original size:7 final size:6
Alignment explanation
Indices: 28123581--28123633 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
28123571 TTAGTTCATC
** * *
28123581 TTTATT TTTCCT TTTATT TCTATT TGTAGTGT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT TTTATT
28123631 TTT
1 TTT
28123634 TAATTTCAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 32 0.84
7 2 0.05
8 4 0.11
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:28123667 original size:3 final size:3
Alignment explanation
Indices: 28123659--28123692 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28123649 TTTTTAATCC
28123659 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28123693 TCTCCTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28128209 original size:41 final size:38
Alignment explanation
Indices: 28128161--28128276 Score: 106
Period size: 41 Copynumber: 2.9 Consensus size: 38
28128151 TATTTGCTTC
28128161 AATCTGCTCCACTGTAACCTTAGGGAGATAAGATTTGATGT
1 AATCTGCTCCACTGTAA-CTTAGGGAGATAAGATTT--TGT
* * * * *
28128202 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATATTTTT
1 AATCTGCTCCACTGTAACTT-AGGGAGATAAGAT-TTTGT
** *
28128242 AATCCACTCCACTGTAATCTTAGGGAGATAGGATT
1 AATCTGCTCCACTGTAA-CTTAGGGAGATAAGATT
28128277 AATTTCTTCT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
39 1 0.02
40 28 0.47
41 29 0.48
42 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (38 bp):
AATCTGCTCCACTGTAACTTAGGGAGATAAGATTTTGT
Found at i:28128618 original size:87 final size:87
Alignment explanation
Indices: 28128520--28129026 Score: 676
Period size: 87 Copynumber: 5.8 Consensus size: 87
28128510 CAATGTCGAC
* *
28128520 GCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATAGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
* *
28128585 TTCAATTTGCTTCGCTGTTAAT
66 TTCGATCTGCTTCGCTGTTAAT
* * * * *
28128607 GCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACTGATGGATGCAAGGCATTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
*
28128672 TTCGATCTGCTTCGCTGTTAAC
66 TTCGATCTGCTTCGCTGTTAAT
** * *
28128694 GCAGGAAGGCAAGATCTATTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
** *
28128759 TTCGATCTTATTCGCTATTAAT
66 TTCGATCTGCTTCGCTGTTAAT
*
28128781 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
* * *
28128846 TTTGATCTGCTTTGCTGTTAAC
66 TTCGATCTGCTTCGCTGTTAAT
* * * *
28128868 GCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCATTGA-AACCGATGAAGGCAAGGCTTTAT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT-ACAACCGATGGAGGCAAGGCTTTGT
* *
28128932 TTTTGATCTGCTTCGCTGTTATT
65 TTTCGATCTGCTTCGCTGTTAAT
* * * * * * * *
28128955 GTAGAAAGGCAAAATTTGCT-TCTTTAGCCAACTCCACTGCAACCGATGGAGGCAAGGTTTTGTT
1 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
28129019 TTCGATCT
66 TTCGATCT
28129027 TCACTGATCT
Statistics
Matches: 365, Mismatches: 53, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
86 43 0.12
87 322 0.88
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (87 bp):
GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
TTCGATCTGCTTCGCTGTTAAT
Found at i:28130728 original size:16 final size:17
Alignment explanation
Indices: 28130695--28130738 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
28130685 GATTTCTCTT
28130695 TTTTTCTTTTGACTTTTA
1 TTTTTCTTTT-ACTTTTA
28130713 TTTTTCTTTT-CTTTTA
1 TTTTTCTTTTACTTTTA
*
28130729 TTTTTGTTTT
1 TTTTTCTTTT
28130739 TGATTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
18 10 0.40
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTACTTTTA
Found at i:28136624 original size:17 final size:18
Alignment explanation
Indices: 28136602--28136635 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28136592 ATAATTGTAA
28136602 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
28136619 TTTAAATGTTTAATTAT
1 TTTAAATGTCTAATTAT
28136636 CACAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:28136643 original size:24 final size:24
Alignment explanation
Indices: 28136616--28136684 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 24
28136606 AATTCTAATT
28136616 ATTTTTAAATGTTTAATTATCACA
1 ATTTTTAAATGTTTAATTATCACA
* * * **
28136640 ATTTCT--A--TTAAATTATAATT
1 ATTTTTAAATGTTTAATTATCACA
*
28136660 ATTTTTAAATGTATAATTATCACA
1 ATTTTTAAATGTTTAATTATCACA
28136684 A
1 A
28136685 CTTTATTTTA
Statistics
Matches: 30, Mismatches: 11, Indels: 8
0.61 0.22 0.16
Matches are distributed among these distances:
20 14 0.47
22 2 0.07
24 14 0.47
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (24 bp):
ATTTTTAAATGTTTAATTATCACA
Found at i:28146903 original size:40 final size:39
Alignment explanation
Indices: 28146844--28147022 Score: 180
Period size: 40 Copynumber: 4.5 Consensus size: 39
28146834 GGTACCACTG
* *
28146844 TTTGTACTTCGGTATCCCTGATTGCACATATGTGCCCCTA
1 TTTGTACTT-GATACCCCTGATTGCACATATGTGCCCCTA
* *
28146884 TTTGTACCTTGATACCCCTGATTGCACATACT-TTCCCCTG
1 TTTGTA-CTTGATACCCCTGATTGCACATA-TGTGCCCCTA
* * * *
28146924 TTTGTACTTTAGTATCCCTGATTGCACATACGTGCCCCTG
1 TTTGTACTTGA-TACCCCTGATTGCACATATGTGCCCCTA
* * **
28146964 TTTGTACTTCGGTACCCCTGATTGCACATGTGTGCCTTTA
1 TTTGTACTT-GATACCCCTGATTGCACATATGTGCCCCTA
*
28147004 TTTGTACTTCAGTACCCCT
1 TTTGTACTTGA-TACCCCT
28147023 AAATGCAATT
Statistics
Matches: 115, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
39 4 0.03
40 107 0.93
41 4 0.03
ACGTcount: A:0.17, C:0.28, G:0.16, T:0.39
Consensus pattern (39 bp):
TTTGTACTTGATACCCCTGATTGCACATATGTGCCCCTA
Found at i:28146951 original size:80 final size:80
Alignment explanation
Indices: 28146841--28146992 Score: 243
Period size: 80 Copynumber: 1.9 Consensus size: 80
28146831 TTCGGTACCA
* *
28146841 CTGTTTGTACTTCGGTATCCCTGATTGCACATATGTGCCCCTATTTGTACCTT-GATACCCCTGA
1 CTGTTTGTACTTCAGTATCCCTGATTGCACATACGTGCCCCTATTTGTA-CTTCGATACCCCTGA
28146905 TTGCACATACTTTCCC
65 TTGCACATACTTTCCC
* * *
28146921 CTGTTTGTACTTTAGTATCCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
1 CTGTTTGTACTTCAGTATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTGAT
28146986 TGCACAT
66 TGCACAT
28146993 GTGTGCCTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 3 0.05
80 63 0.95
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.38
Consensus pattern (80 bp):
CTGTTTGTACTTCAGTATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTGAT
TGCACATACTTTCCC
Found at i:28146962 original size:20 final size:20
Alignment explanation
Indices: 28146896--28146992 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
28146886 TGTACCTTGA
*
28146896 TACCCCTGATTGCACATACT
1 TACCCCTGATTGCACATACG
* * * *
28146916 TTCCCCTGTTTGTACTTTA-G
1 TACCCCTGATTGCAC-ATACG
*
28146936 TATCCCTGATTGCACATACG
1 TACCCCTGATTGCACATACG
* * * *
28146956 TGCCCCTGTTTGTAC-TTCGG
1 TACCCCTGATTGCACATAC-G
28146976 TACCCCTGATTGCACAT
1 TACCCCTGATTGCACAT
28146993 GTGTGCCTTT
Statistics
Matches: 55, Mismatches: 18, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
19 4 0.07
20 48 0.87
21 3 0.05
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (20 bp):
TACCCCTGATTGCACATACG
Found at i:28147008 original size:80 final size:80
Alignment explanation
Indices: 28146844--28147022 Score: 227
Period size: 80 Copynumber: 2.2 Consensus size: 80
28146834 GGTACCACTG
* *
28146844 TTTGTACTTCGGTATCCCTGATTGCACATATGTGCCCCTATTTGTACCTTGATACCCCTGATTGC
1 TTTGTACTTCAGTATCCCTGATTGCACATACGTGCCCCTATTTGTACCTTGATACCCCTGATTGC
* *
28146909 ACATACTTTCCCCTG
66 ACATACTTGCCCCTA
* * *
28146924 TTTGTACTTTAGTATCCCTGATTGCACATACGTGCCCCTGTTTGTA-CTTCGGTACCCCTGATTG
1 TTTGTACTTCAGTATCCCTGATTGCACATACGTGCCCCTATTTGTACCTT-GATACCCCTGATTG
* **
28146988 CACAT-GTGTGCCTTTA
65 CACATACT-TGCCCCTA
*
28147004 TTTGTACTTCAGTACCCCT
1 TTTGTACTTCAGTATCCCT
28147023 AAATGCAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 4 0.05
80 81 0.95
ACGTcount: A:0.17, C:0.28, G:0.16, T:0.39
Consensus pattern (80 bp):
TTTGTACTTCAGTATCCCTGATTGCACATACGTGCCCCTATTTGTACCTTGATACCCCTGATTGC
ACATACTTGCCCCTA
Found at i:28147040 original size:120 final size:120
Alignment explanation
Indices: 28146841--28147064 Score: 301
Period size: 120 Copynumber: 1.9 Consensus size: 120
28146831 TTCGGTACCA
* * * *
28146841 CTGTTTGTACTTCGGTATCCCTGATTGCACATATGTGCCCCTATTTGTACCTTGATACCCCTGAT
1 CTGTTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTTGTACCTTCATACCCCTAAA
* * * *
28146906 TGCACATACTTTCCCCTGTTTGTACTTTAGTATCCCTGATTGCACATACGTGCCC
66 TGCACATACTTTCCCCTATTTATACTCTAGTAACCCTGATTGCACATACGTGCCC
* **
28146961 CTGTTTGTACTTCGGTACCCCTGATTGCACATGTGTGCCTTTATTTGTA-CTTCAGTACCCCTAA
1 CTGTTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTTGTACCTTCA-TACCCCTAA
28147025 ATGCA-ATTA-TATTCCCCTATTTATACTCTAGTAACCCTGA
65 ATGCACA-TACT-TTCCCCTATTTATACTCTAGTAACCCTGA
28147065 ATCAAACAGT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
119 6 0.07
120 84 0.93
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (120 bp):
CTGTTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTTGTACCTTCATACCCCTAAA
TGCACATACTTTCCCCTATTTATACTCTAGTAACCCTGATTGCACATACGTGCCC
Found at i:28158993 original size:25 final size:24
Alignment explanation
Indices: 28158938--28158994 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28158928 TTTAATTAGT
*
28158938 ATAAAATATTAATAATTCAATAAA
1 ATAAAATATTAATAATTAAATAAA
*
28158962 TTGAAAA-ATTAAATAATTAAATAAAA
1 AT-AAAATATT-AATAATTAAAT-AAA
28158988 ATAAAAT
1 ATAAAAT
28158995 TTAGGAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAAAATATTAATAATTAAATAAA
Found at i:28159699 original size:22 final size:19
Alignment explanation
Indices: 28159660--28159701 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
28159650 TGCAAAGTTG
28159660 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
28159679 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
28159701 A
1 A
28159702 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:28160555 original size:16 final size:16
Alignment explanation
Indices: 28160534--28160570 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28160524 TTGGTTCGCT
*
28160534 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
28160550 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
28160566 GTAAT
1 GTAAT
28160571 AGGTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:28160639 original size:44 final size:46
Alignment explanation
Indices: 28160552--28160644 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
28160542 ATAGATGCGT
* *
28160552 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGG
28160598 AATGGAATAGAGGCGTAAT-GGT-ATTCTTCTATTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGG
28160642 AAT
1 AAT
28160645 AGCGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGG
Found at i:28160640 original size:39 final size:44
Alignment explanation
Indices: 28160552--28160657 Score: 123
Period size: 46 Copynumber: 2.5 Consensus size: 44
28160542 ATAGATGCGT
* *
28160552 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTT--ATGG
28160598 AATGGAATAGAGGCGTAAT-GGT-ATTCTTCTATTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTATGG
* *
28160637 AATGGAATAGCGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
28160658 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 12 0.22
45 3 0.05
46 19 0.35
ACGTcount: A:0.29, C:0.06, G:0.30, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTATGG
Found at i:28160855 original size:18 final size:17
Alignment explanation
Indices: 28160803--28160855 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
28160793 TTATTATTAA
28160803 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
28160821 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
28160838 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
28160856 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28170563 original size:26 final size:24
Alignment explanation
Indices: 28170526--28170575 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
28170516 TGTCGAGCCG
* *
28170526 AATTAATTAAAATGTGATATAAAATT
1 AATTAATCAAAA-GTAAT-TAAAATT
28170552 AATTAATCAAAAGTAATTAAAATT
1 AATTAATCAAAAGTAATTAAAATT
28170576 CAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (24 bp):
AATTAATCAAAAGTAATTAAAATT
Found at i:28170568 original size:14 final size:14
Alignment explanation
Indices: 28170546--28170595 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
28170536 AATGTGATAT
28170546 AAAATTAATTAATC
1 AAAATTAATTAATC
*
28170560 AAAAGTAATTAAAATTC
1 AAAATTAATT--AA-TC
*
28170577 AAAATTAATTAACC
1 AAAATTAATTAATC
28170591 AAAAT
1 AAAAT
28170596 AATCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.50
15 2 0.07
16 2 0.07
17 11 0.37
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATTAATTAATC
Found at i:28170584 original size:31 final size:30
Alignment explanation
Indices: 28170546--28170643 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
28170536 AATGTGATAT
28170546 AAAATTAATTAATCAAAAGTAATTAAAATTC
1 AAAATTAATTAATCAAAA-TAATTAAAATTC
* *
28170577 AAAATTAATTAACCAAAATAATCAAAATTTATC
1 AAAATTAATTAATCAAAATAATTAAAA--T-TC
*
28170610 AAAATT--TGATAT-AAAATTAATTAAAATTC
1 AAAATTAATTA-ATCAAAA-TAATTAAAATTC
28170639 AAAAT
1 AAAAT
28170644 GTTAATAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
29 7 0.12
30 9 0.16
31 23 0.40
32 10 0.18
33 8 0.14
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAATTAATTAATCAAAATAATTAAAATTC
Found at i:28172585 original size:39 final size:39
Alignment explanation
Indices: 28172542--28172640 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
28172532 CATATTCACT
* * * *
28172542 TTTAAGCATGTATCACATTACACATATAATCACATAGCA
1 TTTAAGCATATATCACAATACACATATAACCACATAACA
* * * *
28172581 TTTAAGCATATATTACAATACTCATATTACCACATAACG
1 TTTAAGCATATATCACAATACACATATAACCACATAACA
* *
28172620 TTCAAGCATATATCATAATAC
1 TTTAAGCATATATCACAATAC
28172641 TCAAAAACAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAACCACATAACA
Found at i:28180987 original size:22 final size:22
Alignment explanation
Indices: 28180962--28181007 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28180952 TGCTAACATT
28180962 GTGAGTTGTATATTTTGATACA
1 GTGAGTTGTATATTTTGATACA
28180984 GTGAGTTGTATATTTTGATACA
1 GTGAGTTGTATATTTTGATACA
28181006 GT
1 GT
28181008 CAAAGGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (22 bp):
GTGAGTTGTATATTTTGATACA
Found at i:28182955 original size:12 final size:13
Alignment explanation
Indices: 28182931--28182959 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28182921 GGGCTATAAC
28182931 TATTGCATTTATT
1 TATTGCATTTATT
28182944 TATTGC-TTTATT
1 TATTGCATTTATT
28182956 TATT
1 TATT
28182960 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:28190349 original size:48 final size:48
Alignment explanation
Indices: 28190266--28190446 Score: 267
Period size: 48 Copynumber: 3.8 Consensus size: 48
28190256 CTTTGTGTAA
* *
28190266 TAACAG-ATTTTGGTAGCCTGCACATAGTCCGTGCCACCCTTGTATCT
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
* * * *
28190313 TAACAGAATATTGGTGGTCTGCACACAATCCATGCCACCCTTGTATCT
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
* *
28190361 TAACAGAAAATTGGTGGCCTGCACA-AGGTCCGTGCCACCCTTGTATCT
1 TAACAGAATATTGGTAGCCTGCACACA-GTCCGTGCCACCCTTGTATCT
28190409 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCAC
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCAC
28190447 ATACGCGACC
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
47 7 0.06
48 111 0.93
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (48 bp):
TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
Found at i:28193458 original size:18 final size:16
Alignment explanation
Indices: 28193433--28193509 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 16
28193423 ACCTCAAACC
28193433 CCTAAACCTAGTAAAAA
1 CCTAAACCTA-TAAAAA
28193450 CCATAAACC-ATAAAAA
1 CC-TAAACCTATAAAAA
*
28193466 TTCCTAAACCCATAAAAA
1 --CCTAAACCTATAAAAA
28193484 CCCTCAAACCTA-AATAAA
1 -CCT-AAACCTATAA-AAA
*
28193502 CATAAACC
1 CCTAAACC
28193510 CTCAAGCCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
16 11 0.22
17 16 0.31
18 24 0.47
ACGTcount: A:0.53, C:0.29, G:0.01, T:0.17
Consensus pattern (16 bp):
CCTAAACCTATAAAAA
Found at i:28195033 original size:23 final size:24
Alignment explanation
Indices: 28195007--28195055 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
28194997 AAAGAATGGC
* **
28195007 TAAAAT-ATTTAATTTTGAAAAAT
1 TAAAATGATTAAATTTAAAAAAAT
28195030 T-AAATGATTAAATTTAAAAAAAT
1 TAAAATGATTAAATTTAAAAAAAT
28195053 TAA
1 TAA
28195056 TAATTGAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.19
23 16 0.76
24 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAAATGATTAAATTTAAAAAAAT
Found at i:28196152 original size:3 final size:3
Alignment explanation
Indices: 28196144--28196176 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28196134 TCTATTTACA
28196144 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28196177 TCTTTAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28196719 original size:41 final size:41
Alignment explanation
Indices: 28196674--28196874 Score: 242
Period size: 41 Copynumber: 4.9 Consensus size: 41
28196664 TGTCGGTAAC
**
28196674 GCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCATCGCTAAT
1 GCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAAT
* * *
28196715 GCTCTGGGTTTTAGCGGCGTTTTTTAAAAAGTGTCGCTAAT
1 GCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAAT
* * * *
28196756 GCTCTAGGTTTTACCGGCGTTTTTTAAAAAGCGCCGGTAAT
1 GCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAAT
* * * * *
28196797 GGTCTGGGTTTTACCTGTGTTTTTTTTAAAGCGCCGCTAAT
1 GCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAAT
* *
28196838 GGTCTTGGTTTTAGCGGCGTTTTTGTT-AAAGCGCCGC
1 GCTCTGGGTTTTAGCGGCGTTTTT-TTAAAAGCGCCGC
28196875 AAAAAACATT
Statistics
Matches: 140, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 138 0.99
42 2 0.01
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (41 bp):
GCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAAT
Found at i:28196779 original size:82 final size:82
Alignment explanation
Indices: 28196642--28196867 Score: 245
Period size: 82 Copynumber: 2.7 Consensus size: 82
28196632 ATTTGGTGGC
* * * * * * *
28196642 TTTAGTGGCGTTTATGAGAAAGTGTCGGTAACGCTCTGGGTTTTAGCGGCGTTTTTTTAAAAGCA
1 TTTAGCGGCGTTTTTTAAAAAGTGTCGCTAATGCTCTAGGTTTTAGCGGCGTTTTTTTAAAAGCA
*
28196707 TCGCTAATGCTCTGGGT
66 CCGCTAATGCTCTGGGT
* * *
28196724 TTTAGCGGCGTTTTTTAAAAAGTGTCGCTAATGCTCTAGGTTTTACCGGCGTTTTTTAAAAAGCG
1 TTTAGCGGCGTTTTTTAAAAAGTGTCGCTAATGCTCTAGGTTTTAGCGGCGTTTTTTTAAAAGCA
* *
28196789 CCGGTAATGGTCTGGGT
66 CCGCTAATGCTCTGGGT
* * * ** * * * *
28196806 TTTACCTGTGTTTTTTTTAAAGCGCCGCTAATGGTCTTGGTTTTAGCGGCGTTTTTGTTAAA
1 TTTAGCGGCGTTTTTTAAAAAGTGTCGCTAATGCTCTAGGTTTTAGCGGCGTTTTT-TTAAA
28196868 GCGCCGCAAA
Statistics
Matches: 119, Mismatches: 24, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
82 115 0.97
83 4 0.03
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.39
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTTAAAAAGTGTCGCTAATGCTCTAGGTTTTAGCGGCGTTTTTTTAAAAGCA
CCGCTAATGCTCTGGGT
Found at i:28197270 original size:14 final size:14
Alignment explanation
Indices: 28197251--28197278 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28197241 ATATGGATTA
28197251 ATTAGGGATTATGG
1 ATTAGGGATTATGG
28197265 ATTAGGGATTATGG
1 ATTAGGGATTATGG
28197279 TTTAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (14 bp):
ATTAGGGATTATGG
Found at i:28197696 original size:332 final size:318
Alignment explanation
Indices: 28197168--28198090 Score: 1086
Period size: 327 Copynumber: 2.9 Consensus size: 318
28197158 GGGTTTTCAA
** * *
28197168 TTTAGGGTATATGATTTTATTTAAAGATTTAAGGTCAGTTTAAGAGTTCATATTTTAAGGTTTTA
1 TTTAGGGTATATGA-TAAATTT-AAGATTTAAGGCCAGTTTAGGAGTTCATATTTTAAGG-TTTA
28197233 TGGAGTATATATGGATTA-ATTAGGGATTATGGATTAGGGATTATGGTTTAATTAAGGGTTGGGA
63 -GGAGTATATATGGATTATA-TAGGGATTATGGATTAGGGATTATGGTTTAATTAAGGGTTGGGA
* * *
28197297 TTTAA--T--GT-TTAGGGG-CTATGGGTTTAGGGGTTAGACGTTAGGGGTTAATAGTTAGGGAT
126 TTTAATTTAGGTGTTAGGGGTTTA-GGGTTTAGAGGTTAGACGTTAGGGGTTAAGAGTTAGGGAT
* * *
28197356 TTGGGGTTTATGAATTTAGGGGTCGGGTTAGGGTTTTGGGATTAGATT-GTTTTTTATTTATATT
190 TTGGGGTTTACGAATTTAGGGGTCGGGTTAGGGTTTTGGGTTTAGATTAATTTTTTATTTATATT
* *
28197420 TTAAATATGTTATTATATATGTAATTGTAATTTAACATAATAATAAAATTGTTTAGGGTTTTTAG
255 TTAAATATGTT-TTAT-TATGTAATTGTAA---AACATAATAATAAAAATGTTTAGGGTTTTTAA
28197485 TTAG
315 TTAG
28197489 TTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTTCATATTTTAAGGTTTAGGT
1 TTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTTCATATTTTAAGGTTTAGG-
28197554 AGTATATATGGATTTAGCTATAGGGATTATGGATTAGGGATTATGGTTTAATATTTAAGGGTTGG
65 AGTATATATGGA-TTA--TATAGGGATTATGGATTAGGGATTATGGTTT-A-A-TTAAGGGTTGG
28197619 GATTTAAGGTTTAGGTGTTAGGGGTTTAGGGGTTTAGAGGTTAGACGTTAGGGGTTAAGAGTTAG
124 GATTTAA--TTTAGGTGTTAGGGGTTTA-GGGTTTAGAGGTTAGACGTTAGGGGTTAAGAGTTAG
* * * *
28197684 GGATTTGGGGTTTACAAATTTAGGGGTCGTGTTAGGGTTTTGGGTTTAGATTATTATTTTTCTTT
186 GGATTTGGGGTTTACGAATTTAGGGGTCGGGTTAGGGTTTTGGGTTTAGATTAAT-TTTTTATTT
* *
28197749 ATATTTTAAATATG--TTATTATGTAGTTGTAAAAGATAATAATAAAAATGTTTAGGGTTTTTAA
250 ATATTTTAAATATGTTTTATTATGTAATTGTAAAACATAATAATAAAAATGTTTAGGGTTTTTAA
28197812 TTAG
315 TTAG
* *
28197816 TTTAGGGTATATGATAAATTTAAGATTTAAGGCCGGTTTAGGAGTTTATATTTTAAGGTTTAGGG
1 TTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTTCATATTTTAAGGTTTA-GG
* * ** *
28197881 AGTACTATAT--A-TATATGGGGATTA---ATTAGGGATTATAG----ATT-AGGGATTATGTTT
65 AGTA-TATATGGATTATATAGGGATTATGGATTAGGGATTATGGTTTAATTAAGGG-TTGGGATT
* * * * *
28197935 TAATTAAGG-GTT-GGCCTGATTTAAGGTTTAGAGGTTAGACGTTAGCGGTTAAGAGTTAGAGAT
128 TAATTTAGGTGTTAGG---GGTTTAGGGTTTAGAGGTTAGACGTTAGGGGTTAAGAGTTAGGGAT
* * ** **
28197998 TTAGGGTTTAGGGTTTTAAAGGTCGGGTTAGGGTTTTGGGTTTAGATTAATTTTTTATTTATATT
190 TTGGGGTTTACGAATTTAGGGGTCGGGTTAGGGTTTTGGGTTTAGATTAATTTTTTATTTATATT
*
28198063 TTAAATATG--TTCTTATGTAATTGTAAAA
255 TTAAATATGTTTTATTATGTAATTGTAAAA
28198091 TATGTATAAT
Statistics
Matches: 536, Mismatches: 42, Indels: 60
0.84 0.07 0.09
Matches are distributed among these distances:
308 2 0.00
309 42 0.08
310 84 0.16
311 9 0.02
312 10 0.02
313 1 0.00
317 2 0.00
318 16 0.03
319 51 0.10
320 5 0.01
321 43 0.08
322 12 0.02
323 1 0.00
324 20 0.04
326 1 0.00
327 97 0.18
328 8 0.01
330 14 0.03
331 11 0.02
332 84 0.16
333 1 0.00
334 22 0.04
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (318 bp):
TTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTTCATATTTTAAGGTTTAGGA
GTATATATGGATTATATAGGGATTATGGATTAGGGATTATGGTTTAATTAAGGGTTGGGATTTAA
TTTAGGTGTTAGGGGTTTAGGGTTTAGAGGTTAGACGTTAGGGGTTAAGAGTTAGGGATTTGGGG
TTTACGAATTTAGGGGTCGGGTTAGGGTTTTGGGTTTAGATTAATTTTTTATTTATATTTTAAAT
ATGTTTTATTATGTAATTGTAAAACATAATAATAAAAATGTTTAGGGTTTTTAATTAG
Found at i:28198410 original size:19 final size:18
Alignment explanation
Indices: 28198386--28198434 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28198376 AAATTATACG
28198386 AAATAAAATTAAAATACAA
1 AAATAAAATTAAAATA-AA
* *
28198405 AAATAAAAATGAAATAAA
1 AAATAAAATTAAAATAAA
28198423 AACACTAAAATT
1 AA-A-TAAAATT
28198435 TTTAATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 6 0.24
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAAATTAAAATAAA
Done.