Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:837566 original size:13 final size:11
Alignment explanation
Indices: 837511--837609 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
837501 GATACTATTT
837511 TCATCACCATAA
1 TCATCACCAT-A
*
837523 TCCATCTCCATTA
1 T-CATCACCA-TA
*
837536 TCA-CGCCTATA
1 TCATCACC-ATA
837547 TCATCACCATA
1 TCATCACCATA
837558 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
837572 TCA-CGCCTATA
1 TCATCACC-ATA
837583 TCATCACCATA
1 TCATCACCATA
837594 TTCCATCACCATA
1 -T-CATCACCATA
837607 TCA
1 TCA
837610 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:837638 original size:33 final size:33
Alignment explanation
Indices: 837523--837662 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
837513 ATCACCATAA
* * *
837523 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
837557 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
837595 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
837628 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
837661 TC
1 TC
837663 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:838034 original size:26 final size:23
Alignment explanation
Indices: 838005--838052 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
837995 GTGCTACAAC
838005 AACAAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAAG-AA-AAGAAA-AAGAA
*
838031 AACAAAAGAGAAAAGAAAAAGA
1 AACAAAAAAGAAAAGAAAAAGA
838053 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAAAAGAA
Found at i:838286 original size:16 final size:15
Alignment explanation
Indices: 838253--838304 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
838243 GTAAGTTATC
838253 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
838268 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
838284 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
838299 TTCATT
1 TTCATT
838305 ACCATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:845587 original size:20 final size:21
Alignment explanation
Indices: 845550--845588 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
845540 GATGGTCTTG
*
845550 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
845571 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
845589 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:851437 original size:36 final size:36
Alignment explanation
Indices: 851385--851497 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
851375 GATACTATTT
*
851385 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
851421 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
851457 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
851492 ACATCA
1 TCATCA
851498 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:851440 original size:13 final size:11
Alignment explanation
Indices: 851385--851483 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
851375 GATACTATTT
851385 TCATCACCATAA
1 TCATCACCAT-A
*
851397 TCCATCTCCATTA
1 T-CATCACCA-TA
*
851410 TCA-CGCCTATA
1 TCATCACC-ATA
851421 TCATCACCATA
1 TCATCACCATA
851432 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
851446 TCA-CGCCTATA
1 TCATCACC-ATA
851457 TCATCACCATA
1 TCATCACCATA
851468 TTCCATCACCATA
1 -T-CATCACCATA
851481 TCA
1 TCA
851484 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:851512 original size:33 final size:33
Alignment explanation
Indices: 851397--851536 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
851387 ATCACCATAA
* * *
851397 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
851431 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
851469 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
851502 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
851535 TC
1 TC
851537 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:852160 original size:16 final size:15
Alignment explanation
Indices: 852127--852178 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
852117 GTAAGTTATC
852127 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
852142 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
852158 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
852173 TTCATT
1 TTCATT
852179 ACCATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:856881 original size:20 final size:21
Alignment explanation
Indices: 856844--856882 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
856834 GATGGTCTTG
*
856844 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
856865 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
856883 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:861079 original size:8 final size:8
Alignment explanation
Indices: 861068--861092 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
861058 TCTTTTTCTT
861068 TTCTTTTC
1 TTCTTTTC
861076 TTCTTTTC
1 TTCTTTTC
861084 TTCTTTTC
1 TTCTTTTC
861092 T
1 T
861093 GATTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:861098 original size:29 final size:29
Alignment explanation
Indices: 861066--861121 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
861056 TCTCTTTTTC
861066 TTTTCTTT-TCTTCTTTTCT-TCTTTTCTGA
1 TTTT-TTTCTCTTCTTTT-TATCTTTTCTGA
861095 TTTTTTTCTCTTCTTTTTATCTTTTCT
1 TTTTTTTCTCTTCTTTTTATCTTTTCT
861122 TTCTTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTTTTCTCTTCTTTTTATCTTTTCTGA
Found at i:861122 original size:16 final size:15
Alignment explanation
Indices: 861066--861129 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
861056 TCTCTTTTTC
861066 TTTTCTTTTCTTCTT
1 TTTTCTTTTCTTCTT
**
861081 TTCTTCTTTTC-TGAT
1 TT-TTCTTTTCTTCTT
*
861096 TTTT-TTCTCTTCTT
1 TTTTCTTTTCTTCTT
861110 TTTATCTTTTCTTTCTT
1 TTT-TCTTTTC-TTCTT
861127 TTT
1 TTT
861130 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
13 4 0.11
14 7 0.18
15 7 0.18
16 12 0.32
17 8 0.21
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTCTTCTT
Found at i:861128 original size:29 final size:29
Alignment explanation
Indices: 861054--861129 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
861044 TCTTTTTGAA
* *
861054 CTTCTCTT-TTTCTTTTCTTTTCTTCTTTT
1 CTTCTTTTCTTTCTTTT-TTCTCTTCTTTT
*
861083 CTTCTTTTCTGAT-TTTTTTCTCTTCTTTT
1 CTTCTTTTCT-TTCTTTTTTCTCTTCTTTT
861112 -TATCTTTTCTTTCTTTTT
1 CT-TCTTTTCTTTCTTTTT
861130 GCACTCCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 2 0.05
29 31 0.79
30 5 0.13
31 1 0.03
ACGTcount: A:0.03, C:0.21, G:0.01, T:0.75
Consensus pattern (29 bp):
CTTCTTTTCTTTCTTTTTTCTCTTCTTTT
Found at i:866977 original size:19 final size:20
Alignment explanation
Indices: 866936--866986 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
866926 GAAACCCCTT
*
866936 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
866956 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
866975 TGAAGATACATG
1 TGAAAATACATG
866987 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:871171 original size:19 final size:20
Alignment explanation
Indices: 871130--871180 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
871120 GAAACCCCTT
*
871130 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
871150 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
871169 TGAAGATACATG
1 TGAAAATACATG
871181 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:879898 original size:34 final size:34
Alignment explanation
Indices: 879854--879921 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
879844 AATTACCTTA
879854 CATCAAGAAGAATTTGAGAACATGGGAGGAGAGT
1 CATCAAGAAGAATTTGAGAACATGGGAGGAGAGT
* *
879888 CATCAGGAAGAATTTGGGAACATGGGAGGAGAGT
1 CATCAAGAAGAATTTGAGAACATGGGAGGAGAGT
879922 TTACCACATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.35, T:0.18
Consensus pattern (34 bp):
CATCAAGAAGAATTTGAGAACATGGGAGGAGAGT
Found at i:885784 original size:11 final size:11
Alignment explanation
Indices: 885768--885845 Score: 51
Period size: 11 Copynumber: 7.6 Consensus size: 11
885758 CAATTTTGGC
*
885768 TTTTTTGGCTT
1 TTTTTTGCCTT
**
885779 TTTTTTGTTTT
1 TTTTTTGCCTT
885790 TTTTTTGCC--
1 TTTTTTGCCTT
885799 TTTTTTG---T
1 TTTTTTGCCTT
885807 TTTTTTGCC-T
1 TTTTTTGCCTT
**
885817 TTTTTTGTTTT
1 TTTTTTGCCTT
**
885828 TTTTTTGTTTT
1 TTTTTTGCCTT
885839 TTTTTTG
1 TTTTTTG
885846 AAAAAAATAG
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
8 7 0.12
9 7 0.12
10 8 0.14
11 35 0.61
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (11 bp):
TTTTTTGCCTT
Found at i:885809 original size:17 final size:18
Alignment explanation
Indices: 885789--885830 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
885779 TTTTTTGTTT
885789 TTTTTTTGCC-TTTTTTG
1 TTTTTTTGCCTTTTTTTG
885806 TTTTTTTGCCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
885824 TTTTTTT
1 TTTTTTT
885831 TTTGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:890537 original size:13 final size:12
Alignment explanation
Indices: 890521--890577 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
890511 TTTGAATTTC
890521 TTTTTCTTTTCTT
1 TTTTTCTTTT-TT
*
890534 TTTTTCTAATTTT
1 TTTTTCT-TTTTT
*
890547 TTCTTCTTTTTGT
1 TTTTTCTTTTT-T
* *
890560 CTTTTCTTTTCT
1 TTTTTCTTTTTT
890572 TTTTTC
1 TTTTTC
890578 ACTCCAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
12 9 0.26
13 24 0.69
14 2 0.06
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:892208 original size:17 final size:17
Alignment explanation
Indices: 892188--892237 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
892178 TTTAGGGAAG
892188 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
892205 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
892222 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
892238 TTAACTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:901999 original size:24 final size:21
Alignment explanation
Indices: 901964--902006 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
901954 GGCTCATTCT
*
901964 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
901987 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
902007 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:905329 original size:20 final size:21
Alignment explanation
Indices: 905306--905345 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
905296 AGATATAAAA
905306 CATATTTGAGAGAT-TGCTTT
1 CATATTTGAGAGATCTGCTTT
905326 CATATTTGAGAGATCTGCTT
1 CATATTTGAGAGATCTGCTT
905346 CAAGATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (21 bp):
CATATTTGAGAGATCTGCTTT
Found at i:910527 original size:19 final size:18
Alignment explanation
Indices: 910492--910539 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
910482 CTTGGCTTTG
910492 CTTTCTTTTTGAA-TTTT
1 CTTTCTTTTTGAATTTTT
**
910509 CTTCTTCTTTTTGTCTTTTT
1 C-T-TTCTTTTTGAATTTTT
910529 CTTTCTTTTTG
1 CTTTCTTTTTG
910540 CACTCCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 10 0.38
19 10 0.38
20 5 0.19
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTCTTTTTGAATTTTT
Found at i:914861 original size:36 final size:35
Alignment explanation
Indices: 914768--914878 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
914758 TTGGTGGTTA
* * * * *
914768 TATAGGCGTGAAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTAATGGAAGATGGTGATGT
*
914803 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTAATGGAAGATGGTGATGT
914838 TATAGGCGTGAAAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTAATGGAAGATGGTGATGT
914874 T-TAGG
1 TATAGG
914879 TAGTATCTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 43 0.63
36 25 0.37
ACGTcount: A:0.32, C:0.04, G:0.37, T:0.27
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTAATGGAAGATGGTGATGT
Found at i:923563 original size:11 final size:13
Alignment explanation
Indices: 923531--923560 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
923521 TGGAAAAATA
923531 TGAAAAGGTATGT
1 TGAAAAGGTATGT
923544 TGAAAAGGTATG-
1 TGAAAAGGTATGT
923556 TGAAA
1 TGAAA
923561 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:926694 original size:14 final size:13
Alignment explanation
Indices: 926677--926726 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
926667 GTGCAAAAAG
926677 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
926691 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
926704 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
926715 AAAGAAAAAGAA
1 AAAGAAAAAGAA
926727 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:926723 original size:19 final size:18
Alignment explanation
Indices: 926671--926726 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
926661 ATTGGAGTGC
926671 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
926688 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
926707 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
926726 A
1 A
926727 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:926724 original size:11 final size:11
Alignment explanation
Indices: 926671--926726 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
926661 ATTGGAGTGC
926671 AAAAAG-AAAG
1 AAAAAGAAAAG
926681 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
926695 AAGAAGAAAAG
1 AAAAAGAAAAG
926706 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
926719 AAAAAGAA
1 AAAAAGAA
926727 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:928190 original size:16 final size:16
Alignment explanation
Indices: 928169--928200 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
928159 CCCTGAACGA
928169 ACAAGAGACATACGTT
1 ACAAGAGACATACGTT
928185 ACAAGAGACATACGTT
1 ACAAGAGACATACGTT
928201 GCTTTAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
ACAAGAGACATACGTT
Found at i:931292 original size:14 final size:13
Alignment explanation
Indices: 931275--931324 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
931265 GTGCAAAAAG
931275 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
931289 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
931302 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
931313 AAAGAAAAAGAA
1 AAAGAAAAAGAA
931325 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:931321 original size:19 final size:18
Alignment explanation
Indices: 931269--931324 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
931259 ATTAGAGTGC
931269 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
931286 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
931305 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
931324 A
1 A
931325 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:931322 original size:11 final size:11
Alignment explanation
Indices: 931269--931324 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
931259 ATTAGAGTGC
931269 AAAAAG-AAAG
1 AAAAAGAAAAG
931279 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
931293 AAGAAGAAAAG
1 AAAAAGAAAAG
931304 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
931317 AAAAAGAA
1 AAAAAGAA
931325 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:935877 original size:14 final size:13
Alignment explanation
Indices: 935860--935909 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
935850 GTGCAAAAAG
935860 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
935874 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
935887 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
935898 AAAGAAAAAGAA
1 AAAGAAAAAGAA
935910 TTCAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:935906 original size:19 final size:18
Alignment explanation
Indices: 935854--935909 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
935844 ATTGGAGTGC
935854 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
935871 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
935890 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
935909 A
1 A
935910 TTCAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:940462 original size:14 final size:13
Alignment explanation
Indices: 940445--940494 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
940435 GTGCAAAAAG
940445 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
940459 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
940472 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
940483 AAAGAAAAAGAA
1 AAAGAAAAAGAA
940495 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:940491 original size:19 final size:18
Alignment explanation
Indices: 940439--940494 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
940429 ATTGGAGTGC
940439 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
940456 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
940475 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
940494 A
1 A
940495 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:940492 original size:11 final size:11
Alignment explanation
Indices: 940439--940494 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
940429 ATTGGAGTGC
940439 AAAAAG-AAAG
1 AAAAAGAAAAG
940449 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
940463 AAGAAGAAAAG
1 AAAAAGAAAAG
940474 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
940487 AAAAAGAA
1 AAAAAGAA
940495 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:947010 original size:18 final size:18
Alignment explanation
Indices: 946987--947025 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
946977 TTCAGGTTCC
946987 TCGTCAAAAATAGGCTCA
1 TCGTCAAAAATAGGCTCA
947005 TCGTCAAAAATAGGCTCA
1 TCGTCAAAAATAGGCTCA
947023 TCG
1 TCG
947026 GAATCTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (18 bp):
TCGTCAAAAATAGGCTCA
Found at i:948527 original size:28 final size:26
Alignment explanation
Indices: 948495--948574 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 26
948485 ATTCTTGATG
*
948495 AGTGCTTCAACTTTCTTTATTTTTTTTA
1 AGTGCTTCAA-TTTCTTT-TTTTTTTGA
** *
948523 AGTGCTGGAATTTCTTTCTTTCTTTTGG
1 AGTGCTTCAATTTCTTT-TTT-TTTTGA
948551 AGTGCTTCAATTTCTTTTTTTTTT
1 AGTGCTTCAATTTCTTTTTTTTTT
948575 CTAATTTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.09
27 13 0.30
28 27 0.61
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (26 bp):
AGTGCTTCAATTTCTTTTTTTTTTGA
Found at i:950403 original size:11 final size:11
Alignment explanation
Indices: 950387--950411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
950377 TTTTGATTCT
950387 TTCACTTGCAC
1 TTCACTTGCAC
950398 TTCACTTGCAC
1 TTCACTTGCAC
950409 TTC
1 TTC
950412 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:952580 original size:45 final size:45
Alignment explanation
Indices: 952530--952630 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 45
952520 TTCTTCCAAA
* *
952530 GACACATTCTTTGAATGAAAAATGGTGTCCTTTTGTTGTTCGATG
1 GACACATTCTTTGAATGAAAAATGGTGTCCTTTTGTTGCTCAATG
* *
952575 GACACATCCTTTGAATGAAAAATTGTGTCCTTTTGTTGCTCAATG
1 GACACATTCTTTGAATGAAAAATGGTGTCCTTTTGTTGCTCAATG
*
952620 GATACA-TCTTT
1 GACACATTCTTT
952631 TGGATTTGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 4 0.08
45 46 0.92
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (45 bp):
GACACATTCTTTGAATGAAAAATGGTGTCCTTTTGTTGCTCAATG
Found at i:982334 original size:13 final size:12
Alignment explanation
Indices: 982313--982364 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
982303 TTTTTTTTTC
982313 AAAAAA-ACAAA
1 AAAAAAGACAAA
982324 AAAAAAGAACAAA
1 AAAAAAG-ACAAA
*
982337 AAAAAAGGCAAA
1 AAAAAAGACAAA
* *
982349 AGAAAAGGCAAA
1 AAAAAAGACAAA
982361 AAAA
1 AAAA
982365 CAAAAAAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 6 0.17
12 18 0.50
13 12 0.33
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAGACAAA
Found at i:982348 original size:12 final size:12
Alignment explanation
Indices: 982320--982364 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
982310 TTCAAAAAAA
*
982320 CAAAAAAAAAGAA
1 CAAAAAAAAAG-G
982333 CAAAAAAAAAGG
1 CAAAAAAAAAGG
*
982345 CAAAAGAAAAGG
1 CAAAAAAAAAGG
982357 CAAAAAAA
1 CAAAAAAA
982365 CAAAAAAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:988574 original size:13 final size:13
Alignment explanation
Indices: 988556--988598 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
988546 TGGATAAAGA
988556 TGAAAAGGTATGT
1 TGAAAAGGTATGT
988569 TGAAAAGGTATGT
1 TGAAAAGGTATGT
988582 TGAAAAGGTATG-
1 TGAAAAGGTATGT
988594 TGAAA
1 TGAAA
988599 GGTGTTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 5 0.17
13 25 0.83
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:994744 original size:207 final size:207
Alignment explanation
Indices: 994389--994816 Score: 856
Period size: 207 Copynumber: 2.1 Consensus size: 207
994379 AATGAGAGGG
994389 CTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCTTTAGGAAAATACATAATGCTTG
1 CTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCTTTAGGAAAATACATAATGCTTG
994454 AGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAACTCTTCATGAAAGGCCTTAATG
66 AGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAACTCTTCATGAAAGGCCTTAATG
994519 ATTCGGTCAAAGGGTGGAGAGACATCTCCCTTGGTCGAATGGTGCATGCTTGTTCATCTTGGCGC
131 ATTCGGTCAAAGGGTGGAGAGACATCTCCCTTGGTCGAATGGTGCATGCTTGTTCATCTTGGCGC
994584 CAATTTCCTCTC
196 CAATTTCCTCTC
994596 CTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCTTTAGGAAAATACATAATGCTTG
1 CTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCTTTAGGAAAATACATAATGCTTG
994661 AGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAACTCTTCATGAAAGGCCTTAATG
66 AGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAACTCTTCATGAAAGGCCTTAATG
994726 ATTCGGTCAAAGGGTGGAGAGACATCTCCCTTGGTCGAATGGTGCATGCTTGTTCATCTTGGCGC
131 ATTCGGTCAAAGGGTGGAGAGACATCTCCCTTGGTCGAATGGTGCATGCTTGTTCATCTTGGCGC
994791 CAATTTCCTCTC
196 CAATTTCCTCTC
994803 CTTGGCCGAATAGT
1 CTTGGCCGAATAGT
994817 CATGTGCCTT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 221 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (207 bp):
CTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCTTTAGGAAAATACATAATGCTTG
AGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAACTCTTCATGAAAGGCCTTAATG
ATTCGGTCAAAGGGTGGAGAGACATCTCCCTTGGTCGAATGGTGCATGCTTGTTCATCTTGGCGC
CAATTTCCTCTC
Found at i:995558 original size:2 final size:2
Alignment explanation
Indices: 995547--995576 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
995537 TAACTATAGG
995547 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
995577 GAAAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:997854 original size:11 final size:11
Alignment explanation
Indices: 997840--997898 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 11
997830 CTTTTTTTGA
997840 TTTTCTTTTTC
1 TTTTCTTTTTC
997851 TTTTCTTTTT-
1 TTTTCTTTTTC
997861 TTTTCTGATTCTTC
1 TTTTCT--TT-TTC
997875 TTTTTGTCTTTTTC
1 --TTT-TCTTTTTC
997889 TTTTCTTTTT
1 TTTTCTTTTT
997899 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
10 6 0.15
11 17 0.41
12 5 0.12
13 2 0.05
14 3 0.07
15 2 0.05
16 3 0.07
17 3 0.07
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1004385 original size:13 final size:13
Alignment explanation
Indices: 1004350--1004391 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
1004340 CAATGAGTTT
*
1004350 AAAAG-AAAAGAG
1 AAAAGCAAAAAAG
1004362 AAAAGCAAAAAAAG
1 AAAAGC-AAAAAAG
1004376 AAAAGCAAAAAAG
1 AAAAGCAAAAAAG
1004389 AAA
1 AAA
1004392 GAAATTCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 10 0.37
14 12 0.44
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGCAAAAAAG
Found at i:1011186 original size:19 final size:20
Alignment explanation
Indices: 1011151--1011195 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1011141 AATCATTTTG
*
1011151 AAAATACATGATTTTTAATA
1 AAAATACATGATCTTTAATA
*
1011171 AAAATACATGA-CTTTAATG
1 AAAATACATGATCTTTAATA
1011190 AAAATA
1 AAAATA
1011196 ACTGCTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAATACATGATCTTTAATA
Found at i:1012070 original size:20 final size:21
Alignment explanation
Indices: 1012029--1012077 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1012019 ATAAAGCTAG
*
1012029 TGAGCTAATATAAACATAACA
1 TGAGCTAAAATAAACATAACA
*
1012050 TGAGCTAAAAT-AACATGACA
1 TGAGCTAAAATAAACATAACA
1012070 TGAGCTAA
1 TGAGCTAA
1012078 TGAATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAATAAACATAACA
Found at i:1017744 original size:8 final size:8
Alignment explanation
Indices: 1017733--1017765 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
1017723 TCTTTTTCTT
1017733 TTCTTTTC
1 TTCTTTTC
1017741 TTCTTTTC
1 TTCTTTTC
1017749 TTCTTTTC
1 TTCTTTTC
1017757 TTCTTTTC
1 TTCTTTTC
1017765 T
1 T
1017766 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:1017771 original size:16 final size:16
Alignment explanation
Indices: 1017736--1017771 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1017726 TTTTCTTTTC
**
1017736 TTTTCTTCTTTTCTTC
1 TTTTCTTCTTTTCTGA
1017752 TTTTCTTCTTTTCTGA
1 TTTTCTTCTTTTCTGA
1017768 TTTT
1 TTTT
1017772 TCTCTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTCTTCTTTTCTGA
Found at i:1021042 original size:60 final size:60
Alignment explanation
Indices: 1020949--1021063 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
1020939 CATGCTGTTG
* *
1020949 TGAAGTATTCGAGTAATATGAGCTATGAATGATCGTCTAGAAGCTAAGATAACATTACTA
1 TGAAGTATTCCAGTAATATGAGCTATGAATGATCGTCTAAAAGCTAAGATAACATTACTA
*
1021009 TGAAGTGTTCCAGTAATATGAGCTATGAATGATCGTCTAAAAGCTAAGATAACAT
1 TGAAGTATTCCAGTAATATGAGCTATGAATGATCGTCTAAAAGCTAAGATAACAT
1021064 GTATATAAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (60 bp):
TGAAGTATTCCAGTAATATGAGCTATGAATGATCGTCTAAAAGCTAAGATAACATTACTA
Found at i:1023951 original size:21 final size:21
Alignment explanation
Indices: 1023908--1023951 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1023898 GTTTTCAAGC
*
1023908 TTGAATAATGATTAAAATCAA
1 TTGAATAATGATTAAAATAAA
*
1023929 TTGAA-AATGTTTAAAGATAAA
1 TTGAATAATGATTAAA-ATAAA
1023950 TT
1 TT
1023952 TGGTTAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGAATAATGATTAAAATAAA
Found at i:1024742 original size:811 final size:815
Alignment explanation
Indices: 1022536--1025623 Score: 3916
Period size: 811 Copynumber: 3.8 Consensus size: 815
1022526 CATAGAATCT
* * * *
1022536 AAGAATGGTTAGAAGATAATTTTTATACCGTTGGATTTGTAAATCAGTCAATTTTTGTTTAAAAC
1 AAGAATGATTAGAAGATGATTTTTATACCGTTAGATTTGTAAATCAGTCTATTTTTGTTTAAAAC
* *
1022601 AAATGGCTATTTATTTAAAAGTGTATA-AAAAATATATGAATTTTTAACTGATGATATGTCCGAA
66 AAAT-GCTACTTATTTAAAAGTGTATACAAAAATATATGAATTTTTAACTGATGATAGGTCCGAA
** * * * *
1022665 ATTTGGGCAGCAGATTCTGTTCAAAACAAATTATGTAAGTTGGATTATAAAATTCGCCATAAAAT
130 ATTTGGGCAGCAGATTCTACTCAAAACAAATTATATAAGTTGGATTAGAAAATTCTCCATAAAAG
* * * * *
1022730 GATGTCATGAATTCAGAATTCATTTTAGTTAGAAATTAAGCCAAGCGTACATACATAGTTTTGTA
195 GATGTCATGAATTCAAAATTCATTTTAATTAG-AATT-AGTCAAGTGTACATACATATTTTTGTA
* *
1022795 CAAAATTCAGGAAAACTTCTTCTTCCTATTTAAATTGTTGTGA-CTT-ATTGAAATAGGAACAAG
258 CAAAATTCAAGAAAACTTCTTCTTCCTCTTTAAATTGTTGTGAGCTTCATTGAAATAGGAACAAG
* * * *
1022858 GTAAGTTTTTCCTATTTTCCTCATATTAGTCCATTTTCCATTGAATTTTGTATTAATTCATGAAA
323 GTAAGTTTTTCTTATTTTCTTCATATTAGTCCATTTTCCATTGAATTTTGGATTAAGTCATGAAA
* * * * *
1022923 TAGGAAAATGATTCATCTCAAATTTTCTATTATTTGGTAATAATTTTTCATTGTTTCCATTCTTG
388 TAGGAAAATGATTCATCTCAAATTCTCTATCATTTGGTGATAATATTTCATTGTTTCCATGCTTG
* *
1022988 AATCACTAGTTTGATTGCTAGAGTGGATGATGACTAACTTGGATTTTAATGATTTAGGGATAGAA
453 AATCACTAGTTTGATTGCTAGAGTGGATGATGAGTAAGTTGGATTTTAATGATTTAGGGATAGAA
* *
1023053 TTTTGTGTTAATGATGTTATAAAGTTGTTGTCAAGCTTGAATAATGATTAAAATCAATTTAAAAT
518 TTTTGTGTTAATGATGTTATAAAGTTGTTTTCAAGCTTGAATAATGATTAAAATCAATTGAAAAT
* *
1023118 CTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATTGAAAAGATTGAATTTTGATTTTCTTTATA
583 GTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATGGAAAAGATTGAATTTTGATTTT-TTTATA
* *
1023183 TGGAATTGGTTGAGATTGCATGAAAATGATGATAGGAACTTGAATTCATGTATATGTGTTCATTT
647 TGGAATTGGTTGAGATTGCATGAAAATGATTATAGGAACTTGAATTCATGCATATGTGTTCATTT
* * *
1023248 GATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGTAAATTACTGAAATCTGCCTAAATTGGTA
712 GATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCTGCCTAAATTGATA
* * * * *
1023313 ATTTGAATAATAGGTTTATAAAATTATCATAAATTCTAA
777 ATATGAATAGTAAGTTTATAAAATCATCATGAATTCTAA
* * *
1023352 AACAATGATTAGAAGATGATTTTTATACCATT-GTATTTGTAACTC-GATCTATTTTTGTTTAAA
1 AAGAATGATTAGAAGATGATTTTTATACCGTTAG-ATTTGTAAATCAG-TCTATTTTTGTTTAAA
* * * * * *
1023415 ACAAA--CAACTAATTTAGAAGTGTATACAAAAATATATAAAATTTTAA-TCGATGATAGGAT-T
64 ACAAATGCTACTTATTTAAAAGTGTATACAAAAATATATGAATTTTTAACT-GATGATAGG-TCC
* * * * *
1023476 GAAATTTGGGCAGCAGATTCAACTCAAAGCAGATTCTATAAGTTGGATTAGAAAATTCTCCATAG
127 GAAATTTGGGCAGCAGATTCTACTCAAAACAAATTATATAAGTTGGATTAGAAAATTCTCCATAA
* ** *
1023541 AAGGATGTCATAAATTTGAAATTCATTTTAATTAGAAATTAGGTCATGTGTACATACATATTTTT
192 AAGGATGTCATGAATTCAAAATTCATTTTAATTAG-AATTA-GTCAAGTGTACATACATATTTTT
* * * *
1023606 GTATAAAATTCAATAAAACTT-TGTCTTCCTCTTTAAATTGTTTTGAGCTTCATTAAAATAGGAA
255 GTACAAAATTCAAGAAAACTTCT-TCTTCCTCTTTAAATTGTTGTGAGCTTCATTGAAATAGGAA
* * * ** * *
1023670 CAAGGTAAGTTTTTTCTTTTTTGTTCTTTATTTTAGTCCATTTTCCATTGGTTTTTTGATTGAGT
319 CAAGGTAAG-TTTTTC-TTATT-TTCTTCATATTAGTCCATTTTCCATTGAATTTTGGATTAAGT
* *
1023735 CACGAAATAGGAAAATGATTCATCTTAAATTCTCTATCATTTGGTGATAATATTTCATTGTTTCC
381 CATGAAATAGGAAAATGATTCATCTCAAATTCTCTATCATTTGGTGATAATATTTCATTGTTTCC
* * * *
1023800 ATGCTTGAATCACTATTTTGATTGTTAGAGTGGATTATGAGTAAGTTGCATTTTAATGATTTAGG
446 ATGCTTGAATCACTAGTTTGATTGCTAGAGTGGATGATGAGTAAGTTGGATTTTAATGATTTAGG
* *
1023865 GATAGAATTTTGTGTTAAAGATGTTA-AAGATTTGTTTTCAAGCTTGAATAATGATTAAAATCAA
511 GATAGAATTTTGTGTTAATGATGTTATAA-AGTTGTTTTCAAGCTTGAATAATGATTAAAATCAA
* ** * *
1023929 TTGAAAATGTTTAAAGATAAATTTGGTTAAGGTTAGATTTTATGGAAAAGATTAAATTTGGATTT
575 TTGAAAATGTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATGGAAAAGATTGAATTTTGATTT
* * * * *
1023994 TTTT-TATGAAAATGGTTGAGATTGCATGAAAATAATTACAGGAACTTGAATTCATGCATGTGTG
640 TTTTATATGGAATTGGTTGAGATTGCATGAAAATGATTATAGGAACTTGAATTCATGCATATGTG
* * * * *
1024058 TTCATTTCATAAGCTAATAGAATTAGCGAATAAGTTAAGGACGCAAATTAGTGAAATCTTCCTAA
705 TTCATTTGATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCTGCCTAA
** *
1024123 ATTGATAATATGAACCGTAAGTTTATAAAATCATTATGAATTCTAA
770 ATTGATAATATGAATAGTAAGTTTATAAAATCATCATGAATTCTAA
* * * * *
1024169 AAGAATGATTAGAAGACGATTTTTATATCGTTATATTTGTAAATTAGTCTA-TTTTGGTTAAAAC
1 AAGAATGATTAGAAGATGATTTTTATACCGTTAGATTTGTAAATCAGTCTATTTTTGTTTAAAAC
*
1024233 AAAATGCTACTTATTTAAAAGTGTATACAAAAATATATGAATTTTTAA-TCAATGATAGGTCCGA
66 -AAATGCTACTTATTTAAAAGTGTATACAAAAATATATGAATTTTTAACT-GATGATAGGTCCGA
* * * *
1024297 AATTT-AGCAGTAGATTCTACTCAAAACAAATTCTATAAGTTTGATTAGAAAATTCTCCATAAAA
129 AATTTGGGCAGCAGATTCTACTCAAAACAAATTATATAAGTTGGATTAGAAAATTCTCCATAAAA
* * * * * *
1024361 GGATGGT-GTGAATTTAAAATTCGTTTTAATTAG-A-T-GTCAAATGTACACATATATTTTTGTA
194 GGAT-GTCATGAATTCAAAATTCATTTTAATTAGAATTAGTCAAGTGTACATACATATTTTTGTA
* * *
1024422 -AAAGGTTCAAGAAAACTTCTTCTTCCTCTTTAAATTGCTGTCAGCTTCATTGAAATAGGAACAA
258 CAAA-ATTCAAGAAAACTTCTTCTTCCTCTTTAAATTGTTGTGAGCTTCATTGAAATAGGAACAA
** ** * * * *
1024486 CATATTTTTTTTCTTATTTTCTTTATTTTAGT-CATTTTTCCTTTGAATTTTGGATTAAGTCCTG
322 GGTA-AGTTTTTCTTATTTTCTTCATATTAGTCCA-TTTTCCATTGAATTTTGGATTAAGTCATG
* * *
1024550 AAATAGAAAAATGATTCATCTCAAATTCTCTATAATTTAGTGATAATATTTCATTGTTTCCATG-
385 AAATAGGAAAATGATTCATCTCAAATTCTCTATCATTTGGTGATAATATTTCATTGTTTCCATGC
* * * * * * *
1024614 TCTGAATAATTGGTTTGAATGTTAGAGTGGATGATGAGTAAGTTGGATTTTAATGATCTAGGGTT
450 T-TGAATCACTAGTTTGATTGCTAGAGTGGATGATGAGTAAGTTGGATTTTAATGATTTAGGGAT
** * * *
1024679 AGGCTTTTGTGTTCATGATATTATAAAGTTGTTTTCAAGCTTGAATAATGAGTAAAATCAATTGA
514 AGAATTTTGTGTTAATGATGTTATAAAGTTGTTTTCAAGCTTGAATAATGATTAAAATCAATTGA
* *
1024744 AAATGTTTAAAAATGAATCTGGTTAAGGTTAGGGTTTAT-GAAAAGATTGAA-TTTGATTGTTTT
579 AAATGTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATGGAAAAGATTGAATTTTGATT-TTTT
* * * * *
1024807 TATATGGAATTGGTTGGGATTGCATGAAAATGTTTATATGAACTTGAATTCATGCGTATGGGTTC
643 TATATGGAATTGGTTGAGATTGCATGAAAATGATTATAGGAACTTGAATTCATGCATATGTGTTC
*
1024872 ATTTGATAAGATAATAGAACTT-GTGAATAAGCTAAGGATGCAAATTAGTGAAATCTGCCTAAAT
708 ATTTGATAAGCTAATAGAA-TTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCTGCCTAAAT
* *
1024936 TGATAATCTGAATAGTAAGTTTATATAATCATCATGAATTC-AA
772 TGATAATATGAATAGTAAGTTTATAAAATCATCATGAATTCTAA
* * *
1024979 CTAGAATGATTAGAATATGATTTTTATTCCGTTAGATTTGTAAATCAGTCTATTTTTGTTTAAAA
1 -AAGAATGATTAGAAGATGATTTTTATACCGTTAGATTTGTAAATCAGTCTATTTTTGTTTAAAA
* * * * * *
1025044 TAAACGACTACTTATTTAGAAGTGTATACGAAAATATATGAATTTTTAACTGATGATAAGTCGGA
65 CAAATG-CTACTTATTTAAAAGTGTATACAAAAATATATGAATTTTTAACTGATGATAGGTCCGA
* * * ** * * * *
1025109 AATTTGGGTAGAAGATTATGTTAAAAATAGATTATGTAAGTTGGATTAGAAAATT-TGCCATAAA
129 AATTTGGGCAGCAGATTCTACTCAAAACAAATTATATAAGTTGGATTAGAAAATTCT-CCATAAA
* * * *
1025173 AGGAAGGCATGAAATCAAAATTCATTTTAATTAGAAATAAAGTCAAGCT-TACATACATATTTTT
193 AGGATGTCATGAATTCAAAATTCATTTTAATTAG-AAT-TAGTCAAG-TGTACATACATATTTTT
* * *
1025237 GTACAAAATTCAATAAAACTTCTTCTTCCTTTTTAAATAGTTGTGAGCTTCATTGAAATAGGAAC
255 GTACAAAATTCAAGAAAACTTCTTCTTCCTCTTTAAATTGTTGTGAGCTTCATTGAAATAGGAAC
* ** * * *
1025302 AATGTAAGTTTTTCTTATTTTCTTCATATTAGTTTATTTTCCTTTTAATTTTGGATTAAGTTATG
320 AAGGTAAGTTTTTCTTATTTTCTTCATATTAGTCCATTTTCCATTGAATTTTGGATTAAGTCATG
* * *
1025367 AAATAGGAAAATGATTCATATCAAATTCTCTATCATTTGGTGATTATATTTCATTATTTCCATGC
385 AAATAGGAAAATGATTCATCTCAAATTCTCTATCATTTGGTGATAATATTTCATTGTTTCCATGC
** * *
1025432 TTGAATTGCTGGATTGATTGCTAGAGTGGATGATG-GCTAAGTTGGATTTTAATGATTTAGGGAT
450 TTGAATCACTAGTTTGATTGCTAGAGTGGATGATGAG-TAAGTTGGATTTTAATGATTTAGGGAT
* * * *
1025496 AGACTTTTGTATTAATAATGTTATAAA-TGTATTTTCAAGCTTGAATAATGATTAAAATCAATTG
514 AGAATTTTGTGTTAATGATGTTATAAAGT-TGTTTTCAAGCTTGAATAATGATTAAAATCAATTG
* *
1025560 -AAATGTTTAAAGATGAATTTGGTTAGGGTTAGGGTTTATGCAAAAGATTGAATTTTGATTTTTT
578 AAAATGTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATGGAAAAGATTGAATTTTGATTTTTT
1025624 AAGTTGGATT
Statistics
Matches: 1951, Mismatches: 272, Indels: 97
0.84 0.12 0.04
Matches are distributed among these distances:
809 6 0.00
810 21 0.01
811 431 0.22
812 80 0.04
813 173 0.09
814 174 0.09
815 8 0.00
816 130 0.07
817 428 0.22
818 174 0.09
819 326 0.17
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (815 bp):
AAGAATGATTAGAAGATGATTTTTATACCGTTAGATTTGTAAATCAGTCTATTTTTGTTTAAAAC
AAATGCTACTTATTTAAAAGTGTATACAAAAATATATGAATTTTTAACTGATGATAGGTCCGAAA
TTTGGGCAGCAGATTCTACTCAAAACAAATTATATAAGTTGGATTAGAAAATTCTCCATAAAAGG
ATGTCATGAATTCAAAATTCATTTTAATTAGAATTAGTCAAGTGTACATACATATTTTTGTACAA
AATTCAAGAAAACTTCTTCTTCCTCTTTAAATTGTTGTGAGCTTCATTGAAATAGGAACAAGGTA
AGTTTTTCTTATTTTCTTCATATTAGTCCATTTTCCATTGAATTTTGGATTAAGTCATGAAATAG
GAAAATGATTCATCTCAAATTCTCTATCATTTGGTGATAATATTTCATTGTTTCCATGCTTGAAT
CACTAGTTTGATTGCTAGAGTGGATGATGAGTAAGTTGGATTTTAATGATTTAGGGATAGAATTT
TGTGTTAATGATGTTATAAAGTTGTTTTCAAGCTTGAATAATGATTAAAATCAATTGAAAATGTT
TAAAGATGAATTTGGTTAAGGTTAGGGTTTATGGAAAAGATTGAATTTTGATTTTTTTATATGGA
ATTGGTTGAGATTGCATGAAAATGATTATAGGAACTTGAATTCATGCATATGTGTTCATTTGATA
AGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCTGCCTAAATTGATAATAT
GAATAGTAAGTTTATAAAATCATCATGAATTCTAA
Found at i:1026070 original size:478 final size:478
Alignment explanation
Indices: 1025145--1026097 Score: 1367
Period size: 478 Copynumber: 2.0 Consensus size: 478
1025135 ATAGATTATG
* *
1025145 TAAGTTGGATTAGAAAATTTGCCATAAAAGGAAGGCATGAAATCAAAATTCATTTTAATTAGAAA
1 TAAGTTGGATTAGAAAATTCGCCATAAAAAGAAGGCATGAAATCAAAATTCATTTTAATTAGAAA
* *
1025210 TAAAGTCAAGCTTACATACATATTTTTGTACAAAATTCAATAAAACTTCTTCTTCCTTTTTAAAT
66 TAAAGTCAAGCTTACATACATATTTTTGTACAAAATTCAAGAAAACTTCTTCTTCCTCTTTAAAT
* * *
1025275 AGTTGTGAGCTTCATTGAAATAGGAACAATGTAAGTTTTTCTTATTTTCTTCATATTAGTTTATT
131 AGTTGTGAGCTTCATTGAAATAGGAACAAGGTAAGGTTTTCTTATTTTCTTCATATTAGTTCATT
* * * *
1025340 TTCCTTTTAATTTTGGATTAAGTTATGAAATAGGAAAATGATTCATATCAAATTCTCTATCATTT
196 TTCCTTTGAATTTTGCATTAAGTCATGAAATAGGAAAATGATTCATATCAAATTCTATATCATTT
** *
1025405 GGTGATTATATTTCATTATTTCCATGCTTGAATTGCTGGATTGATTGCTAGAGTGGATGATGGCT
261 GGTGATTATATTTCATTATTTCCATGCTTGAATCACTGGATTGATTGCTAGAGTGGATGATAGCT
*
1025470 AAGTTGGATTTTAATGATTTAGGGATAGACTTTTGTATTAATAATGTTATAAATGTATTTTCAAG
326 AAGTTCGATTTTAATGATTTAGGGATAGACTTTTGTATTAATAATGTTATAAATGTATTTTCAAG
*
1025535 CTTGAATAATGATTAAAATCAATTGAAATGTTTAAAGATGAATTTGGTTAGGGTTAGGGTTTATG
391 CTTGAATAATGATTAAAATCAATTGAAATGTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATG
1025600 CAAAAGATTGAATTTTGATTTTT
456 CAAAAGATTGAATTTTGATTTTT
* ** * *
1025623 TAAGTTGGATTAGAAAATTCGCCATAAAAATATTGCATGAATTTAAAATTCATTTTAATTAGAAA
1 TAAGTTGGATTAGAAAATTCGCCATAAAAAGAAGGCATGAAATCAAAATTCATTTTAATTAGAAA
* * * * * *
1025688 TTAATTCAAGTTTACATACATATTTTTGTAGAAAATTCAAGAAAACTTTTTCTTTCTCTTTAAAT
66 TAAAGTCAAGCTTACATACATATTTTTGTACAAAATTCAAGAAAACTTCTTCTTCCTCTTTAAAT
** * * *
1025753 CTTTGTGAGCTTCATTTAAATAGGAACAAGGTAAGGTTTTCTTATTTTCTTTATTTTAGTTCATT
131 AGTTGTGAGCTTCATTGAAATAGGAACAAGGTAAGGTTTTCTTATTTTCTTCATATTAGTTCATT
* * * *
1025818 TTCCTTTGATTTTTGCATTAAGTCGTGAAAT-GGGAAATGATTCATCTCAAATTCTATATCATTT
196 TTCCTTTGAATTTTGCATTAAGTCATGAAATAGGAAAATGATTCATATCAAATTCTATATCATTT
* * * * * * *
1025882 TGTG-TTAATATGTTTATTGTTTTCATGCTTGAATCATTGGTTTGATTGTTAGAGTGGATGATTA
261 GGTGATT-ATAT-TTCATTATTTCCATGCTTGAATCACTGGATTGATTGCTAGAGTGGATGA-TA
* * * *
1025946 G-TAAGTTCGATTTTAATGATTTAGGGATAGACTTTTGTGTTAATGATGTTATTAA-GTTGTTTT
323 GCTAAGTTCGATTTTAATGATTTAGGGATAGACTTTTGTATTAATAATGTTATAAATG-TATTTT
* *
1026009 CGAGCTTGATTAATGATTAAAATCAATTGAAAATGTTTAAAGATGAATTTGG-TAAGGTTAGGGT
387 CAAGCTTGAATAATGATTAAAATCAATTG-AAATGTTTAAAGATGAATTTGGTTAAGGTTAGGGT
* *
1026073 TTATGGAAAAGATTTAATTTTGATT
451 TTATGCAAAAGATTGAATTTTGATT
1026098 GTTCTTTTAT
Statistics
Matches: 419, Mismatches: 51, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
476 2 0.00
477 38 0.09
478 355 0.85
479 24 0.06
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (478 bp):
TAAGTTGGATTAGAAAATTCGCCATAAAAAGAAGGCATGAAATCAAAATTCATTTTAATTAGAAA
TAAAGTCAAGCTTACATACATATTTTTGTACAAAATTCAAGAAAACTTCTTCTTCCTCTTTAAAT
AGTTGTGAGCTTCATTGAAATAGGAACAAGGTAAGGTTTTCTTATTTTCTTCATATTAGTTCATT
TTCCTTTGAATTTTGCATTAAGTCATGAAATAGGAAAATGATTCATATCAAATTCTATATCATTT
GGTGATTATATTTCATTATTTCCATGCTTGAATCACTGGATTGATTGCTAGAGTGGATGATAGCT
AAGTTCGATTTTAATGATTTAGGGATAGACTTTTGTATTAATAATGTTATAAATGTATTTTCAAG
CTTGAATAATGATTAAAATCAATTGAAATGTTTAAAGATGAATTTGGTTAAGGTTAGGGTTTATG
CAAAAGATTGAATTTTGATTTTT
Found at i:1027233 original size:23 final size:24
Alignment explanation
Indices: 1027196--1027240 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1027186 AGAAGGTGCC
1027196 TGACCCAATCAGACCCG-CCTGTT
1 TGACCCAATCAGACCCGACCTGTT
* *
1027219 TGACCCGATCTGACCCGACCTG
1 TGACCCAATCAGACCCGACCTG
1027241 GTTCAACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (24 bp):
TGACCCAATCAGACCCGACCTGTT
Found at i:1030890 original size:5 final size:5
Alignment explanation
Indices: 1030880--1030953 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
1030870 GAACTTCTCT
**
1030880 TTTTC TTTTC TTTTC TTTTC TTCTTC TTTTC --TTC TTTTC TGAT- TTTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
* *
1030928 TCTTC -TTT- TTGTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1030954 TGCACTCCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:1030893 original size:11 final size:11
Alignment explanation
Indices: 1030877--1030948 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
1030867 TTTGAACTTC
1030877 TCTTTTTCTTT
1 TCTTTTTCTTT
1030888 TC-TTTTCTTT
1 TCTTTTTCTTT
*
1030898 TCTTCTTCTTT
1 TCTTTTTCTTT
*
1030909 TCTTCTTT-TCT
1 TCTT-TTTCTTT
** *
1030920 GATTTTTCTCT
1 TCTTTTTCTTT
1030931 TCTTTTTGTCTTT
1 TC-TTTT-TCTTT
1030944 TCTTT
1 TCTTT
1030949 CTTTTTGCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
10 13 0.27
11 20 0.42
12 9 0.19
13 6 0.12
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:1030898 original size:16 final size:17
Alignment explanation
Indices: 1030877--1030912 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1030867 TTTGAACTTC
1030877 TCTTTTTCTT-TTCTTT
1 TCTTTTTCTTCTTCTTT
1030893 TC-TTTTCTTCTTCTTT
1 TCTTTTTCTTCTTCTTT
1030909 TCTT
1 TCTT
1030913 CTTTTCTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.39
16 10 0.56
17 1 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TCTTTTTCTTCTTCTTT
Found at i:1030903 original size:8 final size:8
Alignment explanation
Indices: 1030887--1030953 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
1030877 TCTTTTTCTT
1030887 TTCTTTTC
1 TTCTTTTC
1030895 TT-TTCTTC
1 TTCTT-TTC
1030903 TTCTTTTC
1 TTCTTTTC
1030911 TTCTTTTC
1 TTCTTTTC
*
1030919 TGATTTTTCTC
1 T--TCTTT-TC
1030930 TTCTTTT-
1 TTCTTTTC
1030937 TGTCTTTTC
1 T-TCTTTTC
1030946 TTTCTTTT
1 -TTCTTTT
1030954 TGCACTCCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 26 0.53
9 12 0.24
10 5 0.10
11 3 0.06
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (8 bp):
TTCTTTTC
Found at i:1030919 original size:16 final size:17
Alignment explanation
Indices: 1030888--1030953 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
1030878 CTTTTTCTTT
1030888 TCTTTTCTT-TTCTTCT-
1 TCTTTTCTTCTT-TTCTG
1030904 TCTTTTCTTCTTTTCTG
1 TCTTTTCTTCTTTTCTG
*
1030921 ATTTTTCTCTTCTTTT-TG
1 -TCTTT-TCTTCTTTTCTG
1030939 TCTTTTCTTTCTTTT
1 TCTTTTC-TTCTTTT
1030954 TGCACTCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 15 0.35
17 13 0.30
18 6 0.14
19 9 0.21
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTCTTCTTTTCTG
Found at i:1030925 original size:27 final size:27
Alignment explanation
Indices: 1030873--1030946 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
1030863 TCTTTTTGAA
**
1030873 CTTCTCTTTT-TCTTTTCTTTTCTTTTCTT
1 CTTCT-TTTTGTCTTTTCTGAT-TTTTC-T
1030902 CTTCTTTTCT-TCTTTTCTGATTTTTCT
1 CTTCTTTT-TGTCTTTTCTGATTTTTCT
1030929 CTTCTTTTTGTCTTTTCT
1 CTTCTTTTTGTCTTTTCT
1030947 TTCTTTTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 1 0.02
27 17 0.41
28 8 0.20
29 15 0.37
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.73
Consensus pattern (27 bp):
CTTCTTTTTGTCTTTTCTGATTTTTCT
Found at i:1030952 original size:17 final size:18
Alignment explanation
Indices: 1030904--1030955 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
1030894 CTTTTCTTCT
1030904 TCTTTTC-TTCTTTTCTGA
1 TCTTTTCTTTCTTTT-TGA
1030922 T-TTTTCTCTTCTTTTTG-
1 TCTTTTCT-TTCTTTTTGA
1030939 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCTTTTTG
1030956 CACTCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 15 0.48
18 9 0.29
19 7 0.23
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (18 bp):
TCTTTTCTTTCTTTTTGA
Found at i:1033570 original size:22 final size:22
Alignment explanation
Indices: 1033544--1033587 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1033534 GCTCATTCTG
1033544 TAAATTTTAACCTTTTCATATA
1 TAAATTTTAACCTTTTCATATA
1033566 TAAATTTTAACCTTTTCATATA
1 TAAATTTTAACCTTTTCATATA
1033588 GTACCAGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATTTTAACCTTTTCATATA
Found at i:1034432 original size:15 final size:15
Alignment explanation
Indices: 1034398--1034435 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1034388 GAAATGGAAG
1034398 AAGAAATGAAATGAT
1 AAGAAATGAAATGAT
*
1034413 AAGAATTGAAATGGAT
1 AAGAAATGAAAT-GAT
1034429 -AGAAATG
1 AAGAAATG
1034436 TTATCAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (15 bp):
AAGAAATGAAATGAT
Found at i:1035000 original size:19 final size:20
Alignment explanation
Indices: 1034962--1035004 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1034952 GAAACCCCTT
*
1034962 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
1034982 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
1035001 TGAA
1 TGAA
1035005 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:1041728 original size:18 final size:18
Alignment explanation
Indices: 1041707--1041753 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
1041697 AAAGTTAAAG
1041707 GGTCAGGTCAAGTCAACA
1 GGTCAGGTCAAGTCAACA
1041725 GGTCAGGTCAAGTCAACA
1 GGTCAGGTCAAGTCAACA
1041743 GGTCAGGTCAA
1 GGTCAGGTCAA
1041754 AGAGGTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.17
Consensus pattern (18 bp):
GGTCAGGTCAAGTCAACA
Found at i:1043511 original size:51 final size:51
Alignment explanation
Indices: 1043456--1043621 Score: 280
Period size: 51 Copynumber: 3.3 Consensus size: 51
1043446 GTAACTAATG
* * * *
1043456 AATAAAATAATAATCAAC-AAATGATAATGTTTTGATTCTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAA-GATAATATTTTAACTCTATCCTAATTCCT
1043507 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
1043558 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
1043609 AATAAAATAATAA
1 AATAAAATAATAA
1043622 ATCTAATCCT
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
51 107 0.97
52 3 0.03
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
Found at i:1045257 original size:48 final size:47
Alignment explanation
Indices: 1045189--1045283 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 47
1045179 ATCATATTTG
*
1045189 GCTATATACAATCAGTAGGTTACTATCTAGTTTAAATGGGCATCGAT
1 GCTATATACAATCAGTAGGTTACTATCTAGTTTAAATGAGCATCGAT
* *
1045236 GCTATATCCCAATCAGTAGGTTACTATCTAGTTTAAGTGAGCATCGAT
1 GCTATAT-ACAATCAGTAGGTTACTATCTAGTTTAAATGAGCATCGAT
1045284 TTCTTAACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 7 0.16
48 37 0.84
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (47 bp):
GCTATATACAATCAGTAGGTTACTATCTAGTTTAAATGAGCATCGAT
Found at i:1048699 original size:143 final size:141
Alignment explanation
Indices: 1048454--1048967 Score: 600
Period size: 143 Copynumber: 3.6 Consensus size: 141
1048444 AAAACTATTC
* * * *
1048454 TGTTGCTCAAACTATTTTCCTTTTATTTCCCCTAAAGGACCTAACTC-TATCGAAAACATATCAA
1 TGTTGCTCTAACTATTTTCCTTTTATTTCCCCTAAA-TACCT-ACCCATATCGAAAACATATCTA
* *
1048518 ACAC-TCAAATGTTATGAACTGTAACCTTGTTAGGTTCTCAAGTTAAGGTTTATTCAATTATTAG
64 ACACTTC-AATGTTATGAACTGTAACCTTGTTAGATTCTCAA-TTAAGGTTTATTCAATGATTAG
*
1048582 CGAGTGGATACTCTT
127 CGAGTGAATACTCTT
* *
1048597 GTGTTGGTCTAACTATTTTCCTTTTATTTCCCCCT-AATACCTACCCATATCGAAAACATACCTA
1 -TGTTGCTCTAACTATTTTCCTTTTATTT-CCCCTAAATACCTACCCATATCGAAAACATATCTA
* * *
1048661 ACACTTCAATGTTATGAACTGTAACCTCGTTAGATTCTCACATTAAGGTTTATTGAATGATTAGT
64 ACACTTCAATGTTATGAACTGTAACCTTGTTAGATTCTCA-ATTAAGGTTTATTCAATGATTAGC
1048726 GAGTGAATACTCTT
128 GAGTGAATACTCTT
** *
1048740 AAATTGCTCTAACTATTTTCCTTTT-TTTACACCCTAAAATACCTACCTATATCG--AA-A-A-C
1 -TGTTGCTCTAACTATTTTCCTTTTATTT-C-CCCT-AAATACCTACCCATATCGAAAACATATC
* * *
1048799 TAACACTTCAATGTTATGAACTGTAACCTTGCTACATTCTCAAATCTTA-GTTTATTCAATGATT
62 TAACACTTCAATGTTATGAACTGTAACCTTGTTAGATTCTC-AAT-TAAGGTTTATTCAATGATT
1048863 AGCGAGTGAATACTCTT
125 AGCGAGTGAATACTCTT
* * * * **
1048880 TGTTGCTCTAACTATTTTCCTTTTATTTCCCAT-AATACCAACCTATATTGAAATTATATCTAAC
1 TGTTGCTCTAACTATTTTCCTTTTATTTCCCCTAAATACCTACCCATATCGAAAACATATCTAAC
* *
1048944 ACATCTATGTTATGAACTGTAACC
66 ACTTCAATGTTATGAACTGTAACC
1048968 CTGTGAGTGA
Statistics
Matches: 323, Mismatches: 32, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
136 15 0.05
138 4 0.01
139 24 0.07
140 75 0.23
141 31 0.10
142 8 0.02
143 114 0.35
144 31 0.10
145 21 0.07
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (141 bp):
TGTTGCTCTAACTATTTTCCTTTTATTTCCCCTAAATACCTACCCATATCGAAAACATATCTAAC
ACTTCAATGTTATGAACTGTAACCTTGTTAGATTCTCAATTAAGGTTTATTCAATGATTAGCGAG
TGAATACTCTT
Found at i:1050942 original size:30 final size:30
Alignment explanation
Indices: 1050899--1050977 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
1050889 TTACTTTTGA
* * * *
1050899 CACTAATTTTTTAATT-TTGTTAATCAAAC
1 CACTAACTATTTAATTATTGTCAATAAAAC
*
1050928 CACTTAACTATTTAATTATTGTCAATAAAAT
1 CAC-TAACTATTTAATTATTGTCAATAAAAC
*
1050959 CACTAACTA-TTAATAATTG
1 CACTAACTATTTAATTATTG
1050978 ACCGAAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 12 0.29
30 17 0.40
31 13 0.31
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (30 bp):
CACTAACTATTTAATTATTGTCAATAAAAC
Found at i:1051438 original size:17 final size:16
Alignment explanation
Indices: 1051413--1051446 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1051403 GTTTGTTAAT
1051413 AGTAAAAGAAAATAGA
1 AGTAAAAGAAAATAGA
*
1051429 AGTAAGAAGAAATTAGA
1 AGTAA-AAGAAAATAGA
1051446 A
1 A
1051447 TTAGAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (16 bp):
AGTAAAAGAAAATAGA
Found at i:1051530 original size:2 final size:2
Alignment explanation
Indices: 1051523--1051557 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1051513 CTAAATGCAT
1051523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1051558 TAAATAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1060062 original size:20 final size:19
Alignment explanation
Indices: 1060007--1060067 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
1059997 GGTGCAGAGT
*
1060007 GAATCGATACCCCCATGAGG
1 GAATCGATACCCCCAAG-GG
* *
1060027 GAACCGATTCCCCCCACAGGG
1 GAATCGA-TACCCCCA-AGGG
1060048 GAATCGATACCCCCATAGGG
1 GAATCGATACCCCCA-AGGG
1060068 TTCTGGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 17 0.52
21 15 0.45
22 1 0.03
ACGTcount: A:0.28, C:0.34, G:0.25, T:0.13
Consensus pattern (19 bp):
GAATCGATACCCCCAAGGG
Found at i:1062540 original size:22 final size:23
Alignment explanation
Indices: 1062515--1062558 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1062505 AATTAAGTTT
1062515 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
1062537 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
1062559 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:1068508 original size:23 final size:23
Alignment explanation
Indices: 1068479--1068540 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1068469 ACCCCCATGA
1068479 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCCTTTAAAG
*
1068502 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTAAAG
*
1068525 GGGAATCGATTCCCCC
1 GGGAACCGATTCCCCC
1068541 CATAGGGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTAAAG
Found at i:1068549 original size:21 final size:21
Alignment explanation
Indices: 1068459--1068561 Score: 75
Period size: 23 Copynumber: 4.8 Consensus size: 21
1068449 TTTGGTAAGA
*
1068459 GGGAATCGA-TACCCCCAT-G
1 GGGAATCGATTCCCCCCATAG
* * *
1068478 AGGGAACCGATTCCCCCTTTAAAG
1 -GGGAATCGATTCCCCC--CATAG
* **
1068502 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCAT--AG
1068525 GGGAATCGATTCCCCCCATAG
1 GGGAATCGATTCCCCCCATAG
*
1068546 GGGAATCGATACCCCC
1 GGGAATCGATTCCCCC
1068562 TGGGGTTCTG
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
20 8 0.12
21 23 0.34
23 35 0.52
24 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.18
Consensus pattern (21 bp):
GGGAATCGATTCCCCCCATAG
Found at i:1069278 original size:21 final size:21
Alignment explanation
Indices: 1069245--1069284 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1069235 ACCGTCAACC
* *
1069245 AAATCCACCTCCTATTCCTGA
1 AAATCCAACTCCTAATCCTGA
*
1069266 AAATCCAATTCCTAATCCT
1 AAATCCAACTCCTAATCCT
1069285 AATCCCATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATCCAACTCCTAATCCTGA
Found at i:1070542 original size:17 final size:17
Alignment explanation
Indices: 1070506--1070550 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1070496 GTTTTAACAT
*
1070506 TTTGAATATTTTGGAATG
1 TTTGAAT-TTGTGGAATG
*
1070524 TTTGAATTTGTGGATTG
1 TTTGAATTTGTGGAATG
*
1070541 TTTGATTTTG
1 TTTGAATTTG
1070551 AATTTGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (17 bp):
TTTGAATTTGTGGAATG
Found at i:1077803 original size:370 final size:369
Alignment explanation
Indices: 1077097--1077842 Score: 1388
Period size: 370 Copynumber: 2.0 Consensus size: 369
1077087 TAGTCCATCT
1077097 ATTGTTTCTTGATATCTAGAGTAGACTATAATTAACGAATATGATATCACATATCAACTTATTCG
1 ATTGTTTCTTGATATCTAGAGTAGACTATAATTAACGAATATGATATCACATATCAACTTATTCG
*
1077162 AGCATGGTCATGCATTTATAGTCTCACTCAATCAAGTGGCCTGTAATATATTTCCTATTATGTAG
66 AGCATGGTCATGCATTTATAGTCTCACTCAATCAAGTGGCCAGTAATATATTTCCTATTATGTAG
*
1077227 GAAGGACAAATCCTATCTTAACCATATACACCCGACTATATATATCAAAATATATTCAATAACAG
131 GAAGGACAAATCCTATCTTAACCATATACACCCCAC-ATATATATCAAAATATATTCAATAACAG
1077292 TCTTTATAGTGTAATCAGATACGGAGCATGTTTAACTGTATCAAAACATACAACAATATATTTTG
195 TCTTTATAGTGTAATCAGATACGGAGCATGTTTAACTGTATCAAAACATACAACAATATATTTTG
1077357 GGATGACATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGAGCAATGTTATGACC
260 GGATGACATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGAGCAATGTTATGACC
1077422 GTTATATAATCCAAGACATATGCTCATGATGGTTCAATCCAATAC
325 GTTATATAATCCAAGACATATGCTCATGATGGTTCAATCCAATAC
*
1077467 ATTGTTTCTTGATATCTAGAGTAGACTATGATTAACGAATATGATATCACATATCAACTTATTCG
1 ATTGTTTCTTGATATCTAGAGTAGACTATAATTAACGAATATGATATCACATATCAACTTATTCG
*
1077532 AGCATGGTTATGCATTTATAGTCTCACTCAATCAAGTGGCCAGTAATATATTTCCTATTATGTAG
66 AGCATGGTCATGCATTTATAGTCTCACTCAATCAAGTGGCCAGTAATATATTTCCTATTATGTAG
1077597 GAAGGACAAATCCTATCTTAACCATATACACCCCAC-TATATATCAAAATATATTCAATAACAGT
131 GAAGGACAAATCCTATCTTAACCATATACACCCCACATATATATCAAAATATATTCAATAACAGT
1077661 CTTTATAGTGTAATCAGATACGGAGCATGTTTAACTGTATCAAAACATACAACAATATA-TTTGG
196 CTTTATAGTGTAATCAGATACGGAGCATGTTTAACTGTATCAAAACATACAACAATATATTTTGG
* *
1077725 GATGATATTTATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGAGCAATGTTATGACCG
261 GATGACATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGAGCAATGTTATGACCG
1077790 TTACATAATAATCCAAGACATATGCTCATGATGGTTCAATCCAATAC
326 TT--AT-ATAATCCAAGACATATGCTCATGATGGTTCAATCCAATAC
1077837 ATTGTT
1 ATTGTT
1077843 CTCTAACAAT
Statistics
Matches: 367, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
367 70 0.19
368 87 0.24
369 2 0.01
370 208 0.57
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (369 bp):
ATTGTTTCTTGATATCTAGAGTAGACTATAATTAACGAATATGATATCACATATCAACTTATTCG
AGCATGGTCATGCATTTATAGTCTCACTCAATCAAGTGGCCAGTAATATATTTCCTATTATGTAG
GAAGGACAAATCCTATCTTAACCATATACACCCCACATATATATCAAAATATATTCAATAACAGT
CTTTATAGTGTAATCAGATACGGAGCATGTTTAACTGTATCAAAACATACAACAATATATTTTGG
GATGACATTGATCTCAAGTCTGAGGATCATACATATAGTCATCACCATGAGCAATGTTATGACCG
TTATATAATCCAAGACATATGCTCATGATGGTTCAATCCAATAC
Found at i:1093793 original size:42 final size:42
Alignment explanation
Indices: 1093716--1093807 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1093706 TTATTAAGGA
* *
1093716 GTGGTCCTCCGGGATATATATGTGGTTCTTCGGGACATCTAT
1 GTGGTCCTCCGGGATATATATGTGATTCTTCGGGACATATAT
* * *
1093758 GTGGTCTTCTGGGATATATATGTGA-TCTTTTGGGACATATAT
1 GTGGTCCTCCGGGATATATATGTGATTC-TTCGGGACATATAT
*
1093800 GTAGTCCT
1 GTGGTCCT
1093808 TTGGGACAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (42 bp):
GTGGTCCTCCGGGATATATATGTGATTCTTCGGGACATATAT
Found at i:1093810 original size:21 final size:21
Alignment explanation
Indices: 1093716--1093815 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
1093706 TTATTAAGGA
** *
1093716 GTGGTCCTCCGGGATATATAT
1 GTGGTCCTTTGGGACATATAT
* * *
1093737 GTGGTTCTTCGGGACATCTAT
1 GTGGTCCTTTGGGACATATAT
*
1093758 GTGGT-CTTCTGGGATATATAT
1 GTGGTCCTT-TGGGACATATAT
* *
1093779 GTGATCTTTTGGGACATATAT
1 GTGGTCCTTTGGGACATATAT
*
1093800 GTAGTCCTTTGGGACA
1 GTGGTCCTTTGGGACA
1093816 AATTCTATGT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 3 0.05
21 59 0.92
22 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
GTGGTCCTTTGGGACATATAT
Found at i:1094757 original size:20 final size:20
Alignment explanation
Indices: 1094720--1094758 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1094710 AAGAGACACG
* *
1094720 TAGGATCATATAGATGCATT
1 TAGGAGCATATACATGCATT
*
1094740 TAGGAGCATATACTTGCAT
1 TAGGAGCATATACATGCAT
1094759 ATGGTGGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATACATGCATT
Found at i:1097406 original size:13 final size:13
Alignment explanation
Indices: 1097388--1097412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1097378 AGAGGTATTT
1097388 GACATTTTGGATG
1 GACATTTTGGATG
1097401 GACATTTTGGAT
1 GACATTTTGGAT
1097413 AGGATTGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
GACATTTTGGATG
Found at i:1101089 original size:12 final size:12
Alignment explanation
Indices: 1101074--1101130 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
1101064 GAATCCAGAT
1101074 CAGAAATCAAAA
1 CAGAAATCAAAA
* * *
1101086 CAGAATTCATAT
1 CAGAAATCAAAA
*
1101098 CAGAAATCATAA
1 CAGAAATCAAAA
* *
1101110 CAGAATTCAAAT
1 CAGAAATCAAAA
*
1101122 CAAAAATCA
1 CAGAAATCA
1101131 GATAAACATT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.56, C:0.18, G:0.07, T:0.19
Consensus pattern (12 bp):
CAGAAATCAAAA
Found at i:1101090 original size:24 final size:24
Alignment explanation
Indices: 1101063--1101130 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
1101053 ATATCGGAAT
* *
1101063 AGAATCCAGATCAGAAATCAAAAC
1 AGAATTCAAATCAGAAATCAAAAC
* *
1101087 AGAATTCATATCAGAAATCATAAC
1 AGAATTCAAATCAGAAATCAAAAC
*
1101111 AGAATTCAAATCAAAAATCA
1 AGAATTCAAATCAGAAATCA
1101131 GATAAACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (24 bp):
AGAATTCAAATCAGAAATCAAAAC
Found at i:1105447 original size:55 final size:55
Alignment explanation
Indices: 1105363--1105472 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
1105353 CAGAACCATA
* * *
1105363 CACCCCCTATACAATAGTAAGGCCCTGAGCACAAAGCCGAGGAACCTGCAGATAT
1 CACCCCCTACACAACAGTAAGGCCCTGAGCACAAAGCCGAGAAACCTGCAGATAT
* * *
1105418 CACCCCCTGCACAACAGTAAGGCCCTGAGCATAAAGTCGAGAAACCTGCAGATAT
1 CACCCCCTACACAACAGTAAGGCCCTGAGCACAAAGCCGAGAAACCTGCAGATAT
1105473 AAACCCTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.15
Consensus pattern (55 bp):
CACCCCCTACACAACAGTAAGGCCCTGAGCACAAAGCCGAGAAACCTGCAGATAT
Found at i:1105587 original size:24 final size:24
Alignment explanation
Indices: 1105525--1105587 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1105515 AAATTGAGAT
* * *
1105525 ATCAGAAA-CAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATCCAA
* **
1105548 ATCAGATATCCGAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATCCAA
1105572 ATCAGAAATCAAAACA
1 ATCAGAAATCAAAACA
1105588 AAATAAAATA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.16
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAA
Found at i:1113323 original size:20 final size:20
Alignment explanation
Indices: 1113294--1113332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1113284 AGAGCCCATG
*
1113294 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1113314 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1113333 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1118474 original size:21 final size:22
Alignment explanation
Indices: 1118404--1118500 Score: 87
Period size: 21 Copynumber: 4.6 Consensus size: 22
1118394 ATCCTTTGAA
* *
1118404 ATATATGTGATCCTC-CGAGAT
1 ATATATGTGGTCCTCTAGAGAT
* * *
1118425 ATATATGTGGT-CT-TCGTGAC
1 ATATATGTGGTCCTCTAGAGAT
*
1118445 ATCTATGTGGTCCTCTAG-GAT
1 ATATATGTGGTCCTCTAGAGAT
* *
1118466 ATATATGTGGT-CTTTAGGGAT
1 ATATATGTGGTCCTCTAGAGAT
1118487 ATATATGTGGTCCT
1 ATATATGTGGTCCT
1118501 TCGAGACAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
20 21 0.33
21 38 0.60
22 4 0.06
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (22 bp):
ATATATGTGGTCCTCTAGAGAT
Found at i:1119675 original size:77 final size:79
Alignment explanation
Indices: 1119531--1119681 Score: 191
Period size: 77 Copynumber: 1.9 Consensus size: 79
1119521 CCGAATATAG
* * *
1119531 TAAATAAACATTAGAAGAATGTAATTCTGATTACAACTCTTTCAATGGATATTTAATTCGGAATA
1 TAAATAAACATTAGAAGAATGCAATTCGGATTACAACTCTTTCAATGGATATTTAATTCGAAATA
1119596 ATTAAATAAGAGTT
66 ATTAAATAAGAGTT
* * * * * *
1119610 TAAATAAATATTA-AAGAGTGCAATTCGGATTATAAGTCTTT-AATGGATATTTAGTT-TAAATT
1 TAAATAAACATTAGAAGAATGCAATTCGGATTACAACTCTTTCAATGGATATTTAATTCGAAA-T
1119672 AATTAAATAA
65 AATTAAATAA
1119682 AAATTTAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
76 2 0.03
77 25 0.40
78 23 0.37
79 12 0.19
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (79 bp):
TAAATAAACATTAGAAGAATGCAATTCGGATTACAACTCTTTCAATGGATATTTAATTCGAAATA
ATTAAATAAGAGTT
Found at i:1120794 original size:14 final size:15
Alignment explanation
Indices: 1120768--1120799 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1120758 TTTTCACCAT
1120768 TTCCTTATCTTCTTC
1 TTCCTTATCTTCTTC
1120783 TTCCTT-TCTTCTTC
1 TTCCTTATCTTCTTC
1120797 TTC
1 TTC
1120800 TTCTCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCCTTATCTTCTTC
Found at i:1132515 original size:21 final size:21
Alignment explanation
Indices: 1132466--1132522 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1132456 TATTCGAGTG
*
1132466 GTATCGATACTCAGGTGTCTG
1 GTATCGATACTCAGGTGTCTA
** *
1132487 GTGCCGATACTCAGGTGTGTA
1 GTATCGATACTCAGGTGTCTA
*
1132508 GTATCGATATTCAGG
1 GTATCGATACTCAGG
1132523 GTCCATTTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (21 bp):
GTATCGATACTCAGGTGTCTA
Found at i:1132903 original size:29 final size:30
Alignment explanation
Indices: 1132869--1132934 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
1132859 GATTTATTTA
* *
1132869 TGACCAATTATAAA-TTTGGTAAAGTTT-GG
1 TGACCAAGTATAAACTTT-GAAAAGTTTAGG
1132898 TGACCAAAGTATAAACTTTGAAAAGTTTAGG
1 TGACC-AAGTATAAACTTTGAAAAGTTTAGG
1132929 -GACCAA
1 TGACCAA
1132935 AATGTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 7 0.22
30 20 0.62
31 5 0.16
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (30 bp):
TGACCAAGTATAAACTTTGAAAAGTTTAGG
Found at i:1135115 original size:45 final size:45
Alignment explanation
Indices: 1135051--1135186 Score: 238
Period size: 45 Copynumber: 3.0 Consensus size: 45
1135041 GTAACCATGC
1135051 AAATAAGCTTACGAGCTTATGTGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGTGATAAATGGTAAGTATATTGGTA
1135096 AAATAAGCTTACGAGCTTAT-TGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGT-GATAAATGGTAAGTATATTGGTA
* *
1135141 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGTGATAAATGGTAAGTATATTGGTA
1135186 A
1 A
1135187 GAAATTTTAT
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
44 1 0.01
45 86 0.99
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGTGATAAATGGTAAGTATATTGGTA
Found at i:1135116 original size:25 final size:25
Alignment explanation
Indices: 1135088--1135160 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
1135078 ATGGTAAGTA
1135088 TATTGGTAAAATAAGCTTACGAGCT
1 TATTGGTAAAATAAGCTTACGAGCT
* **
1135113 TATTGG-ATAAAT--G-GTA--AGTA
1 TATTGGTA-AAATAAGCTTACGAGCT
1135133 TATTGGTAAAATAAGCTTACGAGCT
1 TATTGGTAAAATAAGCTTACGAGCT
1135158 TAT
1 TAT
1135161 GGGATAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 12 0.34
21 1 0.03
22 3 0.09
23 3 0.09
24 1 0.03
25 15 0.43
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (25 bp):
TATTGGTAAAATAAGCTTACGAGCT
Found at i:1135144 original size:20 final size:20
Alignment explanation
Indices: 1135076--1135144 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 20
1135066 CTTATGTGAT
1135076 AAATGGTAAGTATATTGGTA
1 AAATGGTAAGTATATTGGTA
*
1135096 AAATAAGCTTACGAGCT-TATTGG-A
1 AAAT--G-GTA--AG-TATATTGGTA
1135120 TAAATGGTAAGTATATTGGTA
1 -AAATGGTAAGTATATTGGTA
1135141 AAAT
1 AAAT
1135145 AAGCTTACGA
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 1 0.03
20 16 0.42
21 1 0.03
22 3 0.08
23 3 0.08
24 1 0.03
25 12 0.32
26 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (20 bp):
AAATGGTAAGTATATTGGTA
Found at i:1135734 original size:22 final size:22
Alignment explanation
Indices: 1135694--1135737 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1135684 TGCATCGGTA
*
1135694 CACTGTTCACGATATTATTCAT
1 CACTGTTCACGATACTATTCAT
1135716 CACTGTTCAC-AGTACTATTCAT
1 CACTGTTCACGA-TACTATTCAT
1135738 AAAAAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (22 bp):
CACTGTTCACGATACTATTCAT
Found at i:1136553 original size:75 final size:76
Alignment explanation
Indices: 1136405--1136544 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 76
1136395 AACATTATAT
* *
1136405 TTTATCTTTGTATTTTACTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATATT
1 TTTATCTTTATATTTTACTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATATTATATT
1136470 TATATTTTATC
66 TATATTTTATC
* *
1136481 TTTATCTTTATATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTA-GAGTATTATAT
1 TTTATCTTTATATTTTACTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGA-TATTATAT
1136544 T
65 T
1136545 ATTTTTTTAG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
74 2 0.03
75 31 0.53
76 26 0.44
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.58
Consensus pattern (76 bp):
TTTATCTTTATATTTTACTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATATTATATT
TATATTTTATC
Found at i:1136578 original size:75 final size:76
Alignment explanation
Indices: 1136407--1136562 Score: 178
Period size: 75 Copynumber: 2.1 Consensus size: 76
1136397 CATTATATTT
* * * *
1136407 TATCTTTGTATTTTACTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATATTTA
1 TATCTTTATATTATAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATATTATATTTA
***
1136472 TATTTTATCTT
66 TATTTTATAGG
* *
1136483 TATCTTTATATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTA-GAGTATTATA-TT
1 TATCTTTATATTATAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGA-TATTATATTT
*
1136545 AT-TTTTTTAGG
65 ATATTTTATAGG
1136556 TAT-TTTA
1 TATCTTTA
1136563 GTTTAAATAG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
72 4 0.06
73 8 0.11
74 6 0.08
75 29 0.41
76 24 0.34
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (76 bp):
TATCTTTATATTATAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATATTATATTTA
TATTTTATAGG
Found at i:1137213 original size:21 final size:22
Alignment explanation
Indices: 1137188--1137228 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1137178 CTTTAATTTG
1137188 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
1137209 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
1137229 TATTTTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:1142870 original size:8 final size:8
Alignment explanation
Indices: 1142857--1142894 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
1142847 TATAATTTTG
1142857 TTTTTATT
1 TTTTTATT
1142865 TTTTTATT
1 TTTTTATT
1142873 TTTTT-TT
1 TTTTTATT
1142880 ATTTTTATT
1 -TTTTTATT
1142889 TTTTTA
1 TTTTTA
1142895 GCGAACTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.07
8 24 0.86
9 2 0.07
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:1142880 original size:18 final size:16
Alignment explanation
Indices: 1142851--1142893 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 16
1142841 TTTCGTTATA
1142851 ATTTTGTTTTTATTTTTTT
1 ATTTT-TTTTTA--TTTTT
1142870 ATTTTTTTTTATTTTT
1 ATTTTTTTTTATTTTT
1142886 ATTTTTTT
1 ATTTTTTT
1142894 AGCGAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.54
18 6 0.25
19 5 0.21
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.86
Consensus pattern (16 bp):
ATTTTTTTTTATTTTT
Found at i:1144733 original size:72 final size:74
Alignment explanation
Indices: 1144645--1144802 Score: 223
Period size: 72 Copynumber: 2.2 Consensus size: 74
1144635 TTAAACTCAA
*
1144645 ATTTAGGATAATATTTTAAACATTATATTTATC-TTGTA-TTTAGTTTAAATAGGTTTTTAGTAT
1 ATTTAGGATATTATTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTAT
1144708 TTTAATTAAG
65 TTTAATTAAG
* ** *
1144718 -TTTAGGATATTATTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 ATTTAGGATATTATTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
1144782 TTAATTAGG
66 TTAATTAAG
*
1144791 ATTTAGAATATT
1 ATTTAGGATATT
1144803 TAATATTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
72 27 0.36
73 23 0.31
74 25 0.33
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (74 bp):
ATTTAGGATATTATTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAG
Found at i:1144790 original size:19 final size:20
Alignment explanation
Indices: 1144762--1144806 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1144752 TGTATTTTAG
* * *
1144762 TTTAAATAGGTTTTAGTAT-
1 TTTAATTAGGATTTAGAATA
1144781 TTTAATTAGGATTTAGAATA
1 TTTAATTAGGATTTAGAATA
1144801 TTTAAT
1 TTTAAT
1144807 ATTTTTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTAATTAGGATTTAGAATA
Found at i:1144802 original size:74 final size:72
Alignment explanation
Indices: 1144667--1144802 Score: 211
Period size: 74 Copynumber: 1.9 Consensus size: 72
1144657 ATTTTAAACA
*
1144667 TTATATTTATCTTGTATTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTAGGATATTATT
1 TTATATTTATCTTGTATTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTAGAATATTATT
1144732 TTATATT
66 TTATATT
* *
1144739 TTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATATTTATC-TTGTA-TTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAG-TTTAGAATATT
1144803 TAATATTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
72 10 0.17
73 23 0.40
74 25 0.43
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (72 bp):
TTATATTTATCTTGTATTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTAGAATATTATT
TTATATT
Found at i:1144814 original size:73 final size:72
Alignment explanation
Indices: 1144667--1144814 Score: 201
Period size: 73 Copynumber: 2.0 Consensus size: 72
1144657 ATTTTAAACA
* *
1144667 TTATATTTATCTTGTATTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTAGGATATTATT
1 TTATATTTATCTTGTATTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTAGAATATTATA
*
1144732 TTATATT
66 ATATATT
* *
1144739 TTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATATTTATC-TTGTA-TTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAG-TTTAGAATATT
*
1144803 -TAATATTTT
63 ATAATATATT
1144812 TTA
1 TTA
1144815 GGTATTTTAG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
72 10 0.15
73 32 0.48
74 25 0.37
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (72 bp):
TTATATTTATCTTGTATTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTAGAATATTATA
ATATATT
Found at i:1145470 original size:23 final size:23
Alignment explanation
Indices: 1145444--1145491 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1145434 TCTTTAATTG
*
1145444 TTATTTAATTATTATTTTTTCTT
1 TTATTTAATTATTATTTTTTATT
*
1145467 TTATTTAATTCTTATTTTTTATT
1 TTATTTAATTATTATTTTTTATT
1145490 TT
1 TT
1145492 GACCACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTAATTATTATTTTTTATT
Found at i:1146891 original size:31 final size:30
Alignment explanation
Indices: 1146852--1146916 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1146842 TTTATTACTA
* *
1146852 TTAATATTTATTATTATATT-ATTTTTCTTT
1 TTAATATTTATT-TTATATTAATATATCTTT
*
1146882 TTAATTATTTATTTTATTTTAATATATCTTT
1 TTAA-TATTTATTTTATATTAATATATCTTT
1146913 TTAA
1 TTAA
1146917 CTTCATCTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (30 bp):
TTAATATTTATTTTATATTAATATATCTTT
Found at i:1172549 original size:14 final size:14
Alignment explanation
Indices: 1172530--1172561 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1172520 AAATTCAAGT
1172530 AATTTCTGACTTGA
1 AATTTCTGACTTGA
1172544 AATTTCTGACTTGA
1 AATTTCTGACTTGA
1172558 AATT
1 AATT
1172562 GTTGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (14 bp):
AATTTCTGACTTGA
Found at i:1172719 original size:21 final size:21
Alignment explanation
Indices: 1172693--1172771 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
1172683 CATTCAAAGG
1172693 GGGGTATCGATACCTATTGAA
1 GGGGTATCGATACCTATTGAA
1172714 GGGGTATCGATACCTATTGAA
1 GGGGTATCGATACCTATTGAA
* ** **
1172735 AGGGTATTAATACCTAATCAAA
1 GGGGTATCGATACCT-ATTGAA
1172757 GGGGGTATCGATACC
1 -GGGGTATCGATACC
1172772 AGTCTTAGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 33 0.69
22 4 0.08
23 11 0.23
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (21 bp):
GGGGTATCGATACCTATTGAA
Found at i:1193082 original size:37 final size:37
Alignment explanation
Indices: 1193017--1193144 Score: 213
Period size: 37 Copynumber: 3.5 Consensus size: 37
1193007 ATTTAATAAT
* * **
1193017 ATATATAATTTTT-TAAACATTTCAAAAATATATATA
1 ATATATAGTTTTTGAAAACATTTTGAAAATATATATA
1193053 ATATATAGTTTTTGAAAACATTTTGAAAATATATATA
1 ATATATAGTTTTTGAAAACATTTTGAAAATATATATA
1193090 ATATATAGTTTTTGAAAACATTTTGAAAATATATATA
1 ATATATAGTTTTTGAAAACATTTTGAAAATATATATA
1193127 ATATATAGTTTTTGAAAA
1 ATATATAGTTTTTGAAAA
1193145 TGTTTTTCGA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.14
37 75 0.86
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATATAGTTTTTGAAAACATTTTGAAAATATATATA
Found at i:1193212 original size:4 final size:4
Alignment explanation
Indices: 1193172--1193205 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1193162 TTTATATGCT
1193172 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1193206 TTATTTAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1198118 original size:22 final size:22
Alignment explanation
Indices: 1198076--1198118 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1198066 TTAATGCTTT
* *
1198076 TAATGTAACGTATTAGTTAATG
1 TAATGTAACGTATAAGATAATG
*
1198098 TAATGTAATGTATAAGATAAT
1 TAATGTAACGTATAAGATAAT
1198119 ACTTCTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (22 bp):
TAATGTAACGTATAAGATAATG
Found at i:1198298 original size:2 final size:2
Alignment explanation
Indices: 1198291--1198317 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1198281 ACGATCTTCT
1198291 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1198318 TTTATAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1199473 original size:18 final size:18
Alignment explanation
Indices: 1199450--1199484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1199440 TAAAATATAT
1199450 AATTAAACTGTAAACATC
1 AATTAAACTGTAAACATC
*
1199468 AATTAAATTGTAAACAT
1 AATTAAACTGTAAACAT
1199485 TAGTATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (18 bp):
AATTAAACTGTAAACATC
Found at i:1199694 original size:24 final size:24
Alignment explanation
Indices: 1199651--1199718 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
1199641 ATATAATTAG
1199651 TATAAATTTTAAAAAATTACTAAAA
1 TATAAA-TTTAAAAAATTACTAAAA
* *
1199676 TATAAATTTAAAAATTTACTAACA
1 TATAAATTTAAAAAATTACTAAAA
*
1199700 TATAAAATTAAAAAATTAC
1 TATAAATTTAAAAAATTAC
1199719 CTTACAGGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 33 0.85
25 6 0.15
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
TATAAATTTAAAAAATTACTAAAA
Found at i:1209089 original size:94 final size:96
Alignment explanation
Indices: 1208958--1209138 Score: 262
Period size: 94 Copynumber: 1.9 Consensus size: 96
1208948 TGTATCGATA
1208958 GAGAAAAGGTATCAATACATTGGAATCCAGAAGGTAGAAA-TGATATCGATACTGAAAGGGAGTA
1 GAGAAAAGGTATCAATACATTGGAATCCAGAAGGTAGAAATTG-TATCGATACTGAAAGGGAGTA
** *
1209022 TTGGTACCATAGTATGGAAGTATTGGTACTAG
65 TCAGTACCATAGTATAGAAGTATTGGTACTAG
* *
1209054 GAGAAAA-GTATCGATACCA-TGG-ATCCAGAATGTAGAAATTGTATCGATACTGAAAGGGAGTA
1 GAGAAAAGGTATCAATA-CATTGGAATCCAGAAGGTAGAAATTGTATCGATACTGAAAGGGAGTA
*
1209116 TCAGTACCGTAGTATAGAAGTAT
65 TCAGTACCATAGTATAGAAGTAT
1209139 CAATACCATG
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 55 0.71
95 13 0.17
96 9 0.12
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (96 bp):
GAGAAAAGGTATCAATACATTGGAATCCAGAAGGTAGAAATTGTATCGATACTGAAAGGGAGTAT
CAGTACCATAGTATAGAAGTATTGGTACTAG
Done.