Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008187.1 Hibiscus syriacus cultivar Beakdansim tig00110794_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: 1300289
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 4 of 5
Found at i:940938 original size:18 final size:17
Alignment explanation
Indices: 940919--940955 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
940909 TATGTGATTA
940919 TATAATGTATATATA-T
1 TATAATGTATATATATT
940935 TATAATGTATATATATGT
1 TATAATGTATATATAT-T
940953 TAT
1 TAT
940956 TTACACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
18 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TATAATGTATATATATT
Found at i:940940 original size:16 final size:16
Alignment explanation
Indices: 940919--940950 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
940909 TATGTGATTA
940919 TATAATGTATATATAT
1 TATAATGTATATATAT
940935 TATAATGTATATATAT
1 TATAATGTATATATAT
940951 GTTATTTACA
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:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TATAATGTATATATAT
Found at i:945421 original size:18 final size:18
Alignment explanation
Indices: 945398--945432 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
945388 AGAAAAAGGT
*
945398 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
945416 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
945433 CAACCGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:945742 original size:140 final size:140
Alignment explanation
Indices: 945490--945772 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
945480 GAAAACGTTG
*
945490 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
945555 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAATG
66 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
945620 CGAATTTGAC
131 CGAATTTGAC
945630 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
945695 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
945760 CGAATTTGGC
131 CGAATTTGAC
945770 TAT
1 TAT
945773 CGCAACGCGA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:945773 original size:20 final size:20
Alignment explanation
Indices: 945743--945833 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
945733 TTACACATTC
*
945743 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
945763 ATTTGGCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
945783 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
945802 A----A-AATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
945817 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
945834 AGAAAATTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
14 9 0.15
15 3 0.05
19 3 0.05
20 44 0.75
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:945819 original size:34 final size:35
Alignment explanation
Indices: 945771--945868 Score: 137
Period size: 34 Copynumber: 2.9 Consensus size: 35
945761 GAATTTGGCT
945771 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
*
945805 ATCGCAACGTGAATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
* * * *
945839 ATTGCAAAGCGTATTAGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGC
945869 GAATTGACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 1 0.02
34 55 0.98
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (35 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
Found at i:945901 original size:20 final size:20
Alignment explanation
Indices: 945876--945913 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
945866 CGCGAATTGA
* *
945876 CTTTCGCGTTGGGATTTTGG
1 CTTTCGCATTGCGATTTTGG
945896 CTTTCGCATTGCGATTTT
1 CTTTCGCATTGCGATTTT
945914 TAGTGGCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.18, G:0.26, T:0.47
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:945946 original size:16 final size:16
Alignment explanation
Indices: 945925--945964 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
945915 AGTGGCAAGC
945925 TCAGCCTCCGTGGGTG
1 TCAGCCTCCGTGGGTG
945941 TCAGCCTCCGTGGGTG
1 TCAGCCTCCGTGGGTG
945957 TCAGCCTC
1 TCAGCCTC
945965 TGTAATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.35, G:0.33, T:0.25
Consensus pattern (16 bp):
TCAGCCTCCGTGGGTG
Found at i:947596 original size:22 final size:22
Alignment explanation
Indices: 947569--947615 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
947559 GAGATAGACA
947569 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
* *
947591 GATTTCGTCGGAGATGGGGATG
1 GATTTCGCCGGAGATGGGGACG
947613 GAT
1 GAT
947616 GTCGTCGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.13, G:0.45, T:0.23
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:947620 original size:22 final size:22
Alignment explanation
Indices: 947577--947622 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
947567 CAGATTTCGC
*
947577 CGGAGATGGGGACGGATTTCGT
1 CGGAGATGGGGACGGATGTCGT
*
947599 CGGAGATGGGGATGGATGTCGT
1 CGGAGATGGGGACGGATGTCGT
947621 CG
1 CG
947623 TAGAGAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.48, T:0.22
Consensus pattern (22 bp):
CGGAGATGGGGACGGATGTCGT
Found at i:947812 original size:20 final size:20
Alignment explanation
Indices: 947789--947844 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
947779 TTATCGCAAC
947789 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
947809 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAGAATCGCGTT
*
947830 ACGATAGTCAGAATC
1 GCGATAGTCAGAATC
947845 ACATTTCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.36
21 14 0.50
22 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:947931 original size:20 final size:19
Alignment explanation
Indices: 947908--947950 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
947898 GGAAACTGAT
*
947908 TTGCGATACTAGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
947928 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
947947 TTGC
1 TTGC
947951 AATTTTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:947941 original size:19 final size:19
Alignment explanation
Indices: 947917--947955 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
947907 TTTGCGATAC
* *
947917 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCAATT
947936 TAGAGATCGCATTGCAATT
1 TAGAGATCGCATTGCAATT
947955 T
1 T
947956 TGTTAGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCAATT
Found at i:948917 original size:2 final size:2
Alignment explanation
Indices: 948897--948964 Score: 54
Period size: 2 Copynumber: 35.5 Consensus size: 2
948887 ATTAATCAGT
* * * *
948897 TA TA -A TA TT TA TT TA TA TA TA TA TA TA T- TA TA TT TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
948937 T- TA T- TCA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
948965 TATTTTTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
1 4 0.08
2 48 0.91
3 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:948926 original size:36 final size:36
Alignment explanation
Indices: 948886--948964 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
948876 CATATTCATT
*
948886 TATTA-ATCAGTTATAATATTTATTTATATATATATA
1 TATTATAT-AGTTATAATATTCATTTATATATATATA
** *
948922 TATTATATTTTTATATTATTCATTTATATATATATA
1 TATTATATAGTTATAATATTCATTTATATATATATA
948958 TA-TATAT
1 TATTATAT
948965 TATTTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 5 0.13
36 31 0.82
37 2 0.05
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (36 bp):
TATTATATAGTTATAATATTCATTTATATATATATA
Found at i:948958 original size:40 final size:38
Alignment explanation
Indices: 948896--948981 Score: 140
Period size: 36 Copynumber: 2.3 Consensus size: 38
948886 TATTAATCAG
* *
948896 TTATAATATTTATTTATATATATATATAT-TA-TATTT
1 TTATATTATTCATTTATATATATATATATATATTATTT
948932 TTATATTATTCATTTATATATATATATATATATTATTT
1 TTATATTATTCATTTATATATATATATATATATTATTT
948970 TTATATTATTCA
1 TTATATTATTCA
948982 ACTATTTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 27 0.59
37 2 0.04
38 17 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (38 bp):
TTATATTATTCATTTATATATATATATATATATTATTT
Found at i:949620 original size:15 final size:15
Alignment explanation
Indices: 949600--949635 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
949590 TAATTATACG
949600 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
949615 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
949630 ATTAAT
1 TTTAAT
949636 TTAACGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATACTTTATAA
Found at i:950770 original size:2 final size:2
Alignment explanation
Indices: 950763--950791 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
950753 TAAAATTGTA
950763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
950792 ATTTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:961462 original size:3 final size:3
Alignment explanation
Indices: 961454--961503 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
961444 GATTGCTCAA
961454 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
961502 AA
1 AA
961504 AAACCATCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:968990 original size:16 final size:16
Alignment explanation
Indices: 968969--969000 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
968959 ATAGGCCAAA
968969 ATGGCATCTCAGCAAT
1 ATGGCATCTCAGCAAT
968985 ATGGCATCTCAGCAAT
1 ATGGCATCTCAGCAAT
969001 TCTAAGTCCT
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:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGGCATCTCAGCAAT
Found at i:991467 original size:16 final size:17
Alignment explanation
Indices: 991435--991469 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
991425 TCTACTTGGT
991435 ACATTTTACTCTTTAAC
1 ACATTTTACTCTTTAAC
*
991452 ACATTTT-CTTTTTAAC
1 ACATTTTACTCTTTAAC
991468 AC
1 AC
991470 CTTCAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (17 bp):
ACATTTTACTCTTTAAC
Found at i:995233 original size:32 final size:32
Alignment explanation
Indices: 995186--995246 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
995176 ATATATAATC
995186 AATGTATGAAATTTTAGATGAAATTTGGTATA
1 AATGTATGAAATTTTAGATGAAATTTGGTATA
* *
995218 AATGTGTGAACTTTTAGATGAAATTTGGT
1 AATGTATGAAATTTTAGATGAAATTTGGT
995247 GTAATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (32 bp):
AATGTATGAAATTTTAGATGAAATTTGGTATA
Found at i:999884 original size:17 final size:17
Alignment explanation
Indices: 999858--999891 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
999848 CCAGAAAAGG
*
999858 ATTTCTTTCAAACTTTC
1 ATTTCCTTCAAACTTTC
*
999875 ATTTCCTTCAAATTTTC
1 ATTTCCTTCAAACTTTC
999892 CAAGAGATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTCCTTCAAACTTTC
Found at i:1009352 original size:2 final size:2
Alignment explanation
Indices: 1009347--1009373 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1009337 GTACAGAAAC
1009347 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 T
1009374 TGCTGAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1011239 original size:21 final size:21
Alignment explanation
Indices: 1011210--1011249 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1011200 TTTATTAATT
*
1011210 TAAATTTTGAAAACAATTTTC
1 TAAAGTTTGAAAACAATTTTC
1011231 TAAAGTTTGAAAACAATTT
1 TAAAGTTTGAAAACAATTT
1011250 ATAAGAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
TAAAGTTTGAAAACAATTTTC
Found at i:1013304 original size:52 final size:52
Alignment explanation
Indices: 1013242--1013344 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
1013232 AAATTGGACA
1013242 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
1013294 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1013345 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:1019337 original size:32 final size:32
Alignment explanation
Indices: 1019247--1019341 Score: 120
Period size: 31 Copynumber: 3.0 Consensus size: 32
1019237 TTAAGTTTGA
1019247 ATATTATTATATAAATTTAAAATAATCAACTT
1 ATATTATTATATAAATTTAAAATAATCAACTT
* * ** * * *
1019279 AT-TCATTAGATATGTGTCAAATAATCAATTT
1 ATATTATTATATAAATTTAAAATAATCAACTT
1019310 ATATTATTATATAAATTTAAAATAATCAACTT
1 ATATTATTATATAAATTTAAAATAATCAACTT
1019342 CGTCGTAGAG
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (32 bp):
ATATTATTATATAAATTTAAAATAATCAACTT
Found at i:1027981 original size:13 final size:13
Alignment explanation
Indices: 1027963--1027988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1027953 AACCAAAGGA
1027963 AAGTTAATATTTG
1 AAGTTAATATTTG
1027976 AAGTTAATATTTG
1 AAGTTAATATTTG
1027989 GTCAGATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AAGTTAATATTTG
Found at i:1035047 original size:6 final size:6
Alignment explanation
Indices: 1035038--1035087 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
1035028 AGGTTTTATA
* * *
1035038 TTTAAT TTT-AT ATT-AT ATTTGAT TTTAAT TTTAAT TTTAAT ATTAAT
1 TTTAAT TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
1035085 TTT
1 TTT
1035088 TTAAATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 6 0.16
6 29 0.78
7 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (6 bp):
TTTAAT
Found at i:1035074 original size:17 final size:17
Alignment explanation
Indices: 1035031--1035074 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1035021 TTCAAAGAGG
1035031 TTTTATATTTAATTTTA
1 TTTTATATTTAATTTTA
* *
1035048 TATTATATTTGATTTTAA
1 TTTTATATTTAATTTT-A
1035066 TTTTA-ATTT
1 TTTTATATTT
1035075 TAATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTATATTTAATTTTA
Found at i:1035140 original size:63 final size:64
Alignment explanation
Indices: 1035067--1035203 Score: 233
Period size: 63 Copynumber: 2.2 Consensus size: 64
1035057 TGATTTTAAT
* *
1035067 TTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTGA-TTTTTAATATTATATTATATATA
1 TTTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1035131 -TTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1 TTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1035194 TTTAATTTTA
1 TTTAATTTTA
1035204 TATCATATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
62 22 0.32
63 38 0.55
64 9 0.13
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (64 bp):
TTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
Found at i:1035143 original size:12 final size:12
Alignment explanation
Indices: 1035059--1035203 Score: 91
Period size: 13 Copynumber: 11.5 Consensus size: 12
1035049 ATTATATTTG
*
1035059 ATTTTAATTTTA
1 ATTTTAATATTA
1035071 ATTTTAATATTA
1 ATTTTAATATTA
1035083 ATTTTTTAA-A-TA
1 A--TTTTAATATTA
* *
1035095 AATTAAATATTGA
1 ATTTTAATATT-A
*
1035108 TTTTTAATATTA
1 ATTTTAATATTA
*
1035120 TATTATATATATTA
1 -ATTTTA-ATATTA
1035134 ATTTTAATATTA
1 ATTTTAATATTA
1035146 ATTTTTAA-A-TA
1 A-TTTTAATATTA
* *
1035157 AATTAAATATTA
1 ATTTTAATATTA
1035169 ATTTTTTAATATTA
1 A--TTTTAATATTA
*
1035183 TATTATAGATATTTA
1 -ATTTTA-ATA-TTA
1035198 ATTTTA
1 ATTTTA
1035204 TATCATATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
10 8 0.08
11 5 0.05
12 28 0.27
13 29 0.28
14 29 0.28
15 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:1035253 original size:17 final size:18
Alignment explanation
Indices: 1035197--1035247 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1035187 ATAGATATTT
1035197 AATTTTATATCA-TA-TAA
1 AATTTTATAT-ATTATTAA
*
1035214 ATTCTTTATATATTATTAA
1 AAT-TTTATATATTATTAA
1035233 AATTTTATAT-TTATT
1 AATTTTATATATTATT
1035248 TTAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 8 0.28
18 16 0.55
19 5 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTATATATTATTAA
Found at i:1035759 original size:31 final size:31
Alignment explanation
Indices: 1035723--1035782 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1035713 TAGTTGTATG
* *
1035723 AATTATTTAAATTTCAGCATTGTAAAACTAA
1 AATTATTTAAATCTCAGCATTGCAAAACTAA
*
1035754 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGCATTGCAAAACT
1035783 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (31 bp):
AATTATTTAAATCTCAGCATTGCAAAACTAA
Found at i:1037586 original size:20 final size:20
Alignment explanation
Indices: 1037563--1037602 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1037553 TTCGCAATGC
*
1037563 GAATATGTAAATCGCAACAT
1 GAATATGTAAATCACAACAT
*
1037583 GAATTTGTAAATCACAACAT
1 GAATATGTAAATCACAACAT
1037603 AGAAGTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
GAATATGTAAATCACAACAT
Found at i:1037631 original size:20 final size:19
Alignment explanation
Indices: 1037605--1037655 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1037595 CACAACATAG
1037605 AAGTCAAATTCGAAACGCGA
1 AAGTCAAATTCGAAACGC-A
* *
1037625 TAGTCAAATTCGCAACGCA
1 AAGTCAAATTCGAAACGCA
*
1037644 AAGTTAAATTCG
1 AAGTCAAATTCG
1037656 CAACTGAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (19 bp):
AAGTCAAATTCGAAACGCA
Found at i:1037654 original size:19 final size:20
Alignment explanation
Indices: 1037605--1037716 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 20
1037595 CACAACATAG
*
1037605 AAGTCAAATTCGAAACGCGA
1 AAGTCAAATTCGCAACGCGA
*
1037625 TAGTCAAATTCGCAACGC-A
1 AAGTCAAATTCGCAACGCGA
* *
1037644 AAGTTAAATTCGCAAC-TGA
1 AAGTCAAATTCGCAACGCGA
** *
1037663 ATTTCAAATTCGCAAC-TGA
1 AAGTCAAATTCGCAACGCGA
** *
1037682 ATTTCAAATTCGCAAC-TGA
1 AAGTCAAATTCGCAACGCGA
**
1037701 ATTTCAAATTCGCAAC
1 AAGTCAAATTCGCAAC
1037717 AGGTTTTAGT
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 67 0.81
20 16 0.19
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:1037672 original size:38 final size:38
Alignment explanation
Indices: 1037628--1037716 Score: 137
Period size: 38 Copynumber: 2.3 Consensus size: 38
1037618 AACGCGATAG
1037628 TCAAATTCGCAAC-GCAAAGTT-AAATTCGCAACTGAATT
1 TCAAATTCGCAACTG--AAGTTCAAATTCGCAACTGAATT
*
1037666 TCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAAGTTCAAATTCGCAACTGAATT
1037704 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1037717 AGGTTTTAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
37 4 0.08
38 43 0.90
39 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (38 bp):
TCAAATTCGCAACTGAAGTTCAAATTCGCAACTGAATT
Found at i:1037868 original size:22 final size:22
Alignment explanation
Indices: 1037843--1037888 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1037833 GACATCCGTT
1037843 CCTATATCCAACGATATCCTTC
1 CCTATATCCAACGATATCCTTC
1037865 CCTATATCCAACGATATCCTTC
1 CCTATATCCAACGATATCCTTC
1037887 CC
1 CC
1037889 CATCTCTAAT
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:0.39, G:0.04, T:0.30
Consensus pattern (22 bp):
CCTATATCCAACGATATCCTTC
Found at i:1037914 original size:14 final size:15
Alignment explanation
Indices: 1037895--1037932 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1037885 TCCCCATCTC
1037895 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1037909 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1037925 TAATTTTT
1 TAATTTTT
1037933 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1041724 original size:18 final size:18
Alignment explanation
Indices: 1041703--1041746 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1041693 TTGGAGTTTG
1041703 AATTTAAATTTCAATTTC
1 AATTTAAATTTCAATTTC
* * *
1041721 AATTTGAGTTTGAATTTC
1 AATTTAAATTTCAATTTC
*
1041739 AATATAAA
1 AATTTAAA
1041747 ATTCGGCTCC
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
AATTTAAATTTCAATTTC
Found at i:1042061 original size:35 final size:35
Alignment explanation
Indices: 1041986--1042061 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
1041976 AATAATAACA
* * *
1041986 AAAATAATAAGTCCGAAATGCTTCCGAGTGCCACC
1 AAAATCATAAGTCCGAAATGCATCCGAGTACCACC
* * *
1042021 CAAATCATAAGTTCGAAATGCATCCGA-TACTCATC
1 AAAATCATAAGTCCGAAATGCATCCGAGTAC-CACC
1042056 AAAATC
1 AAAATC
1042062 CAAAGCTCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.22
Consensus pattern (35 bp):
AAAATCATAAGTCCGAAATGCATCCGAGTACCACC
Found at i:1042096 original size:39 final size:39
Alignment explanation
Indices: 1042053--1042139 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1042043 TCCGATACTC
1042053 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
1042092 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1042131 ATCAAAATC
1 ATCAAAATC
1042140 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:1042376 original size:20 final size:20
Alignment explanation
Indices: 1042353--1042391 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1042343 AATAAGCGTT
*
1042353 GCGATAGCCAAATTCGCAAC
1 GCGAAAGCCAAATTCGCAAC
*
1042373 GCGAAAGTCAAATTCGCAA
1 GCGAAAGCCAAATTCGCAA
1042392 ACCGAAAATC
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:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
GCGAAAGCCAAATTCGCAAC
Found at i:1042580 original size:66 final size:60
Alignment explanation
Indices: 1042494--1042633 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 60
1042484 TTTTAGAAAC
*
1042494 AACAAATCAATTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAAC-A--AAAAAAA-AATT-TTATTTACACATC-AATT
1042559 A
60 A
* * * * *
1042560 AATAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATTTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAAAAAAAAATTTTATTTACACATCAATTA
1042620 AACAAATCAACTTT
1 AACAAATCAACTTT
1042634 CAATGTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
60 18 0.27
61 11 0.16
62 4 0.06
63 6 0.09
65 1 0.01
66 27 0.40
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.33
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAAAAAAAAATTTTATTTACACATCAATTA
Found at i:1044030 original size:21 final size:21
Alignment explanation
Indices: 1044006--1044104 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
1043996 GCAGACAGGA
*
1044006 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
1044027 CCTCTTGAACGGTGGGATGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
1044048 CTTCTTCG-ATGATGAGAGTGG
1 CCTCTT-GAACGATGAGAGGGG
* **
1044069 CCTCTTGAACGATAAGAGGCA
1 CCTCTTGAACGATGAGAGGGG
*
1044090 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1044105 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1046316 original size:19 final size:20
Alignment explanation
Indices: 1046256--1046318 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
1046246 AAACTTAAAT
* *
1046256 TCGCAACGCAAAAATAAAAA
1 TCGCAACGCGAAAATGAAAA
*
1046276 TCACAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
1046296 TCGCAACGTGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1046315 TCGC
1 TCGC
1046319 GTTGTGATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1046835 original size:20 final size:20
Alignment explanation
Indices: 1046810--1046934 Score: 114
Period size: 20 Copynumber: 6.2 Consensus size: 20
1046800 GCGTAAAAAC
*
1046810 ATTTGACTTTCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1046830 ATTTGACTATCGCGTTTCGA
1 ATTTGACTTTCGCGTTGCGA
1046850 ATTTGACTATT-GCGTTGCGA
1 ATTTGACT-TTCGCGTTGCGA
* * *
1046870 ATTTGACTATCACATTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1046890 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
1046909 ATTT-ACAGATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
1046930 ATTTG
1 ATTTG
1046935 GAAACTGGGT
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
18 2 0.02
19 7 0.08
20 67 0.80
21 8 0.10
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1046855 original size:40 final size:40
Alignment explanation
Indices: 1046810--1046934 Score: 141
Period size: 40 Copynumber: 3.1 Consensus size: 40
1046800 GCGTAAAAAC
*
1046810 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTTCGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
* * *
1046850 ATTTGACTATT-GCGTTGCGAATTTGACTATCACATTGCGA
1 ATTTGACT-TTCGTGTTGCGAATTTGACTATCGCGTTGCGA
*
1046890 ATTTGAC-TTCTGTGTTGCG-ATTT-ACAGATTCGCGTTGCGA
1 ATTTGACTTTC-GTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
1046930 ATTTG
1 ATTTG
1046935 GAAACTGGGT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
38 4 0.06
39 5 0.07
40 61 0.85
41 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (40 bp):
ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:1048731 original size:24 final size:23
Alignment explanation
Indices: 1048698--1048745 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1048688 ACCTTTTAGA
*
1048698 AAAATAAAAAATTATTTAA-ATAT
1 AAAATAAAAAAATA-TTAATATAT
1048721 AAAATATAAAAAATATTAATATAT
1 AAAATA-AAAAAATATTAATATAT
1048745 A
1 A
1048746 CAATGCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAAAAAAATATTAATATAT
Found at i:1050127 original size:28 final size:28
Alignment explanation
Indices: 1050095--1050149 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1050085 AGTTATTTAC
*
1050095 ATTATGCTATCGAGTCAGTGCTTGAAAT
1 ATTATGCTATCGAGTCAGTGATTGAAAT
* *
1050123 ATTATGTTGTCGAGTCAGTGATTGAAA
1 ATTATGCTATCGAGTCAGTGATTGAAA
1050150 GCAATGACGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (28 bp):
ATTATGCTATCGAGTCAGTGATTGAAAT
Found at i:1061918 original size:66 final size:64
Alignment explanation
Indices: 1061771--1061892 Score: 201
Period size: 66 Copynumber: 1.9 Consensus size: 64
1061761 TCCCGGAGGG
*
1061771 GGACCTGGCGGCTTTGGGCCTGGGGGTCCCGGAGGTCCTTGGGGCCCTGGATTTGGAGGGTCAGG
1 GGACCTGGAGGCTTTGGGCCTGGGGGTCCC-G-GGTCCTTGGGGCCCTGGATTTGGAGGGTCAGG
1061836 A
64 A
*
1061837 GGACCTGGAGGCTTTGGTCCTGGGGGTCCC-GGTCCTTGGGGCCCTGGATTTGGAGG
1 GGACCTGGAGGCTTTGGGCCTGGGGGTCCCGGGTCCTTGGGGCCCTGGATTTGGAGG
1061893 TCCTGTTGGT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 26 0.48
66 28 0.52
ACGTcount: A:0.08, C:0.23, G:0.46, T:0.23
Consensus pattern (64 bp):
GGACCTGGAGGCTTTGGGCCTGGGGGTCCCGGGTCCTTGGGGCCCTGGATTTGGAGGGTCAGGA
Found at i:1073019 original size:19 final size:19
Alignment explanation
Indices: 1072995--1073031 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1072985 ATGACCAACA
*
1072995 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1073014 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1073032 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1073122 original size:21 final size:21
Alignment explanation
Indices: 1073096--1073150 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1073086 TAATATGTAT
1073096 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
1073117 ATCGCAACGCGATAATACGAA
1 ATCGCAACGCGATAATACAAA
*
1073138 ATCGCAATGCGAT
1 ATCGCAACGCGAT
1073151 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:1073578 original size:19 final size:20
Alignment explanation
Indices: 1073546--1073588 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1073536 ACAACACATT
*
1073546 TTTTAAACTCTCGCAACACA
1 TTTTAAACTATCGCAACACA
1073566 TTTT-AACTATCGCAACACA
1 TTTTAAACTATCGCAACACA
1073585 TTTT
1 TTTT
1073589 TCAAAATCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTTAAACTATCGCAACACA
Found at i:1073597 original size:20 final size:19
Alignment explanation
Indices: 1073537--1073598 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
1073527 ACTATCACAA
*
1073537 CAACACATTTTTTAAACTCTCG
1 CAACACA-TTTTTAAA--ATCG
*
1073559 CAACACA-TTTTAACTATCG
1 CAACACATTTTTAA-AATCG
1073578 CAACACATTTTTCAAAATCG
1 CAACACATTTTT-AAAATCG
1073598 C
1 C
1073599 GTTGCGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 10 0.29
20 15 0.44
21 2 0.06
22 7 0.21
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (19 bp):
CAACACATTTTTAAAATCG
Found at i:1076609 original size:24 final size:24
Alignment explanation
Indices: 1076582--1076681 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1076572 AGATATCAAA
*
1076582 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1076606 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1076630 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1076654 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1076678 ATCA
1 ATCA
1076682 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1076681 original size:48 final size:48
Alignment explanation
Indices: 1076576--1076683 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1076566 AAACAGAGAT
* * * *
1076576 ATCA-AAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1076623 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1076671 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1076684 TAAAATATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1079182 original size:7 final size:7
Alignment explanation
Indices: 1079170--1079201 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1079160 TGGTCAACTC
1079170 CGGTCAA
1 CGGTCAA
1079177 CGGTCAA
1 CGGTCAA
1079184 CGGGTCAA
1 C-GGTCAA
1079192 CGGTCAA
1 CGGTCAA
1079199 CGG
1 CGG
1079202 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1079191 original size:15 final size:15
Alignment explanation
Indices: 1079171--1079217 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1079161 GGTCAACTCC
1079171 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1079186 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1079201 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1079214 GGTC
1 GGTC
1079218 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1079211 original size:13 final size:13
Alignment explanation
Indices: 1079178--1079253 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
1079168 TCCGGTCAAC
*
1079178 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1079193 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1079206 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
1079224 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1079237 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1079250 GGTC
1 GGTC
1079254 GGGTAAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1079222 original size:18 final size:18
Alignment explanation
Indices: 1079199--1079275 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
1079189 CAACGGTCAA
*
1079199 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
1079217 CGGGTCGGGTCAA-----
1 CGGGTCGGGTAAACGGGT
1079230 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1079248 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1079266 CGGGTCGGGT
1 CGGGTCGGGT
1079276 TGTGACCGGT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
13 12 0.23
18 41 0.77
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1079231 original size:31 final size:31
Alignment explanation
Indices: 1079193--1079271 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1079183 ACGGGTCAAC
1079193 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1079224 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1079255 GGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1079272 GGGTTGTGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1079235 original size:8 final size:8
Alignment explanation
Indices: 1079171--1079217 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1079161 GGTCAACTCC
1079171 GGTCAAC-
1 GGTCAACG
1079178 GGTCAACG
1 GGTCAACG
1079186 GGTCAAC-
1 GGTCAACG
1079193 GGTCAACG
1 GGTCAACG
1079201 GGT---CG
1 GGTCAACG
1079206 GGTCAACG
1 GGTCAACG
1079214 GGTC
1 GGTC
1079218 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1081426 original size:24 final size:24
Alignment explanation
Indices: 1081399--1081498 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1081389 GATATCAAAA
*
1081399 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1081423 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1081447 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1081471 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1081495 ATCA
1 ATCA
1081499 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1081498 original size:48 final size:48
Alignment explanation
Indices: 1081392--1081500 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1081382 AAACAGAGAT
* * * * *
1081392 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1081440 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1081488 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1081501 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1083999 original size:7 final size:7
Alignment explanation
Indices: 1083987--1084018 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1083977 TGGTCAACTC
1083987 CGGTCAA
1 CGGTCAA
1083994 CGGTCAA
1 CGGTCAA
1084001 CGGGTCAA
1 C-GGTCAA
1084009 CGGTCAA
1 CGGTCAA
1084016 CGG
1 CGG
1084019 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1084008 original size:15 final size:15
Alignment explanation
Indices: 1083988--1084034 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1083978 GGTCAACTCC
1083988 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1084003 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1084018 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1084031 GGTC
1 GGTC
1084035 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1084028 original size:13 final size:13
Alignment explanation
Indices: 1083995--1084070 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
1083985 TCCGGTCAAC
*
1083995 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1084010 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1084023 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
1084041 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1084054 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1084067 GGTC
1 GGTC
1084071 GGGTAAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1084039 original size:18 final size:18
Alignment explanation
Indices: 1084016--1084092 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
1084006 CAACGGTCAA
*
1084016 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
1084034 CGGGTCGGGTCAA-----
1 CGGGTCGGGTAAACGGGT
1084047 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1084065 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1084083 CGGGTCGGGT
1 CGGGTCGGGT
1084093 TGTGACCGGT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
13 12 0.23
18 41 0.77
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1084048 original size:31 final size:31
Alignment explanation
Indices: 1084010--1084088 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1084000 ACGGGTCAAC
1084010 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1084041 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1084072 GGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1084089 GGGTTGTGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1084052 original size:8 final size:8
Alignment explanation
Indices: 1083988--1084034 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1083978 GGTCAACTCC
1083988 GGTCAAC-
1 GGTCAACG
1083995 GGTCAACG
1 GGTCAACG
1084003 GGTCAAC-
1 GGTCAACG
1084010 GGTCAACG
1 GGTCAACG
1084018 GGT---CG
1 GGTCAACG
1084023 GGTCAACG
1 GGTCAACG
1084031 GGTC
1 GGTC
1084035 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1085058 original size:6 final size:6
Alignment explanation
Indices: 1085020--1085054 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1085010 TATTAAATGC
*
1085020 TTTCTA TTTCTA TTTCTA TTTCTA TTTCTT TTTCT
1 TTTCTA TTTCTA TTTCTA TTTCTA TTTCTA TTTCT
1085055 TTTTGTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTCTA
Found at i:1085190 original size:8 final size:8
Alignment explanation
Indices: 1085172--1085205 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1085162 GGGTGATGGT
1085172 ATTTTTAAA
1 ATTTTT-AA
1085181 ATTTTTAA
1 ATTTTTAA
1085189 ATTTTTAA
1 ATTTTTAA
*
1085197 ACTTTTAA
1 ATTTTTAA
1085205 A
1 A
1085206 ATATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (8 bp):
ATTTTTAA
Found at i:1085194 original size:17 final size:17
Alignment explanation
Indices: 1085172--1085207 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1085162 GGGTGATGGT
*
1085172 ATTTTTAAAATTTTTAA
1 ATTTTTAAAATTTTAAA
*
1085189 ATTTTTAAACTTTTAAA
1 ATTTTTAAAATTTTAAA
1085206 AT
1 AT
1085208 ATAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTAAAATTTTAAA
Found at i:1093785 original size:20 final size:20
Alignment explanation
Indices: 1093762--1093813 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1093752 AACGCGATCC
1093762 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1093782 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1093802 CCAAAATCGCAA
1 CCAGAATCGCAA
1093814 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1093830 original size:21 final size:20
Alignment explanation
Indices: 1093803--1093901 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1093793 AATCAGTTTC
1093803 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1093824 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1093845 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1093865 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1093886 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1093902 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1093930 original size:20 final size:20
Alignment explanation
Indices: 1093868--1094061 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1093858 CGATTTTCCA
* ** *
1093868 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1093888 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1093908 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1093928 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1093948 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1093968 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1093988 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1094008 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1094028 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1094049 AAATCGCAACGCG
1 AAATCGCAACGCG
1094062 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1093952 original size:60 final size:60
Alignment explanation
Indices: 1093868--1094061 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1093858 CGATTTTCCA
* ** * *
1093868 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1093928 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1093988 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1094049 AAATCGCAACGCG
1 AAATCGCAACGCG
1094062 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1094478 original size:33 final size:33
Alignment explanation
Indices: 1094439--1094509 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1094429 TTCACTTAGA
*
1094439 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1094472 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1094505 TTTCA
1 TTTCA
1094510 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1094649 original size:14 final size:14
Alignment explanation
Indices: 1094630--1094684 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1094620 AGAATGACTG
1094630 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1094644 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1094663 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1094677 TCGCAACG
1 TCGCAACG
1094685 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1094667 original size:33 final size:33
Alignment explanation
Indices: 1094630--1094700 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1094620 AGAATGACTG
**
1094630 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1094663 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1094696 TCGCA
1 TCGCA
1094701 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1094718 original size:19 final size:19
Alignment explanation
Indices: 1094696--1094793 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1094686 GAAACCAAAA
*
1094696 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1094715 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1094729 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1094748 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1094762 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1094781 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1094794 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1094737 original size:14 final size:14
Alignment explanation
Indices: 1094718--1094807 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1094708 TTTCATTTCG
1094718 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1094732 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1094751 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1094765 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1094782 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1094798 CGTTGCGATT
1 CGTTGCGATT
1094808 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1094743 original size:33 final size:33
Alignment explanation
Indices: 1094701--1094815 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1094691 CAAAATCGCA
1094701 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1094734 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1094767 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1094800 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1094816 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1096741 original size:185 final size:186
Alignment explanation
Indices: 1096512--1096891 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
1096502 TAGATTGCTT
1096512 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1096577 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1096642 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1096697 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1096762 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1096827 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1096883 AGTAAATTT
1 AGTAAATTT
1096892 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1096826 original size:93 final size:93
Alignment explanation
Indices: 1096512--1096891 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
1096502 TAGATTGCTT
1096512 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1096577 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1096605 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1096669 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1096697 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1096762 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1096790 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1096855 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1096883 AGTAAATTT
1 AGTAAATTT
1096892 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1096975 original size:19 final size:19
Alignment explanation
Indices: 1096935--1097063 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1096925 TAGTTTACTT
* *
1096935 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1096955 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1096974 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1096993 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1097007 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1097026 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1097040 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1097059 TCGCA
1 TCGCA
1097064 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1097014 original size:33 final size:32
Alignment explanation
Indices: 1096971--1097063 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1096961 CGCGAAACCA
**
1096971 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1097003 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1097036 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1097064 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1097061 original size:52 final size:52
Alignment explanation
Indices: 1096935--1097063 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1096925 TAGTTTACTT
**
1096935 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1096987 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1097040 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1097064 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1097081 original size:19 final size:19
Alignment explanation
Indices: 1097059--1097193 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1097049 GAAACCAAAA
*
1097059 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1097078 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1097094 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1097111 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1097127 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1097144 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1097163 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1097183 TCGTGTTGCGA
1 TCGCGTTGCGA
1097194 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1097100 original size:14 final size:14
Alignment explanation
Indices: 1097081--1097137 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1097071 TTTCATTTCG
1097081 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1097095 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1097112 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1097128 CGTTGCGATT
1 CGTTGCGATT
1097138 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1097106 original size:33 final size:33
Alignment explanation
Indices: 1097064--1097156 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1097054 CAAAATCGCA
*
1097064 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1097097 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1097130 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1097157 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1099052 original size:38 final size:38
Alignment explanation
Indices: 1099009--1099081 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1098999 AATTGATTGT
*
1099009 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1099047 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1099082 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:1099068 original size:19 final size:19
Alignment explanation
Indices: 1099004--1099068 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1098994 AGTTTAATTG
*
1099004 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1099023 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1099041 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1099061 ATTGATTT
1 ATTGATTT
1099069 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:1099082 original size:14 final size:14
Alignment explanation
Indices: 1099063--1099098 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1099053 ATTGTTTAAT
1099063 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1099077 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1099091 TGATTTGT
1 TGATTTGT
1099099 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1099221 original size:19 final size:19
Alignment explanation
Indices: 1099205--1099306 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1099195 AAAAATGACT
1099205 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1099224 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1099243 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1099257 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1099276 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1099296 ATCGCAATGCG
1 ATCGCAATGCG
1099307 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1099359 original size:19 final size:19
Alignment explanation
Indices: 1099335--1099660 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
1099325 GATTATCTCG
1099335 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1099354 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1099373 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1099387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1099406 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1099425 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1099444 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1099463 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1099482 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1099496 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1099515 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1099534 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1099548 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1099567 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1099586 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1099600 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1099620 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1099634 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1099653 TTGCGATT
1 TTGCGATT
1099661 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1099375 original size:52 final size:52
Alignment explanation
Indices: 1099313--1099632 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
1099303 TGCGTTTATA
*
1099313 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1099365 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1099417 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1099474 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1099526 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1099578 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1099631 AT
1 AT
1099633 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1099410 original size:71 final size:72
Alignment explanation
Indices: 1099335--1099660 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
1099325 GATTATCTCG
1099335 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1099399 TTTCGCA
66 TTTCGCA
* *
1099406 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
1099471 TTCATTTCGCA
62 TTCATTTCGCA
*
1099482 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
1099540 TTC-TCTCG--
62 TTCATTTCGCA
*
1099548 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1099612 TTTCCGCA
66 TTT-CGCA
* *
1099620 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1099661 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:1099578 original size:161 final size:157
Alignment explanation
Indices: 1099313--1099632 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
1099303 TGCGTTTATA
1099313 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
1099378 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1099443 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
1099474 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1099539 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
1099604 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
1099631 AT
1 AT
1099633 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:1099604 original size:33 final size:33
Alignment explanation
Indices: 1099354--1099660 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
1099344 TCATTTCGCA
*
1099354 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1099387 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1099423 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
1099461 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1099496 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1099532 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1099567 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1099600 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1099634 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1099661 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1101983 original size:12 final size:12
Alignment explanation
Indices: 1101966--1101990 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1101956 TCTTCGGGGA
1101966 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1101978 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1101990 C
1 C
1101991 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1102199 original size:24 final size:24
Alignment explanation
Indices: 1102165--1102211 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1102155 CTGAAACATC
1102165 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1102189 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1102212 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1102913 original size:20 final size:20
Alignment explanation
Indices: 1102885--1103253 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1102875 AAATTTCAGT
* * * *
1102885 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1102905 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1102925 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1102945 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1102965 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1102985 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1103005 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1103025 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1103045 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1103065 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1103085 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1103105 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1103125 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1103145 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1103165 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1103185 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1103205 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1103225 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1103245 GTTGCGATT
1 GTTGCGATT
1103254 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1110672 original size:89 final size:89
Alignment explanation
Indices: 1110570--1110750 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
1110560 AACTACATTT
*
1110570 AAATAATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAATTTGAAAATA
1 AAATAATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAATTTAAAAATA
1110635 ATCCCAAAATATGGAAAACCGAAA
66 ATCCCAAAATATGGAAAACCGAAA
*
1110659 AAATAATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAGTTTAAAAATA
1 AAATAATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAATTTAAAAATA
1110724 ATCCCAAAATATGGAAAACCGAAA
66 ATCCCAAAATATGGAAAACCGAAA
1110748 AAA
1 AAA
1110751 CCGTGTTAAC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (89 bp):
AAATAATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAATTTAAAAATA
ATCCCAAAATATGGAAAACCGAAA
Found at i:1110795 original size:89 final size:88
Alignment explanation
Indices: 1110574--1110786 Score: 221
Period size: 89 Copynumber: 2.4 Consensus size: 88
1110564 ACATTTAAAT
* ** * * *
1110574 AATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAATTTGAAAATAATCC
1 AATTAAATCTAATAAATCCAAATCGGTTTTT-AATGGATTTAATTTTTTAATTTAAAAATAATCC
*
1110639 CAAAATATGGAAAACCGAAAAAAT
65 CAAAATATGGAAAACCGAAAAAAC
* ** * * *
1110663 AATTAAATTTAATAAATGTAAGTTGGTTTTTCAATGGATTTAATTTTTTAGTTTAAAAATAATCC
1 AATTAAATCTAATAAATCCAAATCGGTTTTT-AATGGATTTAATTTTTTAATTTAAAAATAATCC
1110728 CAAAATATGGAAAACCGAAAAAAC
65 CAAAATATGGAAAACCGAAAAAAC
** *
1110752 CGTGTTAA-CTAATTAAATCCAACCATCGGTTTTTA
1 AAT-TAAATCTAA-TAAATCCAA--ATCGGTTTTTA
1110787 TGTTTTAATC
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
89 90 0.83
90 10 0.09
91 1 0.01
92 8 0.07
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (88 bp):
AATTAAATCTAATAAATCCAAATCGGTTTTTAATGGATTTAATTTTTTAATTTAAAAATAATCCC
AAAATATGGAAAACCGAAAAAAC
Found at i:1112132 original size:4 final size:4
Alignment explanation
Indices: 1112123--1112168 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
1112113 GTTATCGAAT
* *
1112123 AATA AATAA AATA ATATA AATA TATT AATA AATA AATA AATA AATA
1 AATA AAT-A AATA A-ATA AATA AATA AATA AATA AATA AATA AATA
1112169 CGAATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (4 bp):
AATA
Found at i:1112137 original size:12 final size:13
Alignment explanation
Indices: 1112123--1112179 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 13
1112113 GTTATCGAAT
1112123 AATAAATAAAATA
1 AATAAATAAAATA
1112136 ATATAAATATATTAATA
1 A-ATAAATA-A--AATA
1112153 AATAAAT-AAATA
1 AATAAATAAAATA
1112165 AATACGAATAAAATA
1 AATA--AATAAAATA
1112180 CAAACACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 8 0.22
13 1 0.03
14 11 0.30
15 6 0.16
16 6 0.16
17 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:1115879 original size:25 final size:25
Alignment explanation
Indices: 1115837--1115885 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1115827 AAATTCCATC
*
1115837 AATTCATTATTTTAATTAATTAATT
1 AATTCATTATTTAAATTAATTAATT
1115862 AATTCATT-TTTAAGATTAATTAAT
1 AATTCATTATTTAA-ATTAATTAAT
1115886 ATCGCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTCATTATTTAAATTAATTAATT
Found at i:1125165 original size:60 final size:59
Alignment explanation
Indices: 1125034--1125204 Score: 164
Period size: 60 Copynumber: 2.9 Consensus size: 59
1125024 AACGTACATC
* * * * * * * *
1125034 CCCAAACTATGACTCTTGTTCTAAATTTGTCTATAAACTTTTGAATATTTTAATTTCATT
1 CCCAAACTATGACTC-TATTCTAAATTAGTCTCTAAAATTTTGAACATTTCAAATTCATG
* * * *
1125094 CCTAAATTATGACTACCATTCTAAATTGGTCTCTAAAATTTTGAACATTTCAAATTCATG
1 CCCAAACTATGACT-CTATTCTAAATTAGTCTCTAAAATTTTGAACATTTCAAATTCATG
* * * *
1125154 CCCAAACTATGATCTTTATTCTAAATTAGTC-CCAAAATTCTGAACTTTTCA
1 CCCAAACTATGA-CTCTATTCTAAATTAGTCTCTAAAATTTTGAACATTTCA
1125205 TAATATCCCC
Statistics
Matches: 90, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
59 17 0.19
60 70 0.78
61 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (59 bp):
CCCAAACTATGACTCTATTCTAAATTAGTCTCTAAAATTTTGAACATTTCAAATTCATG
Found at i:1148400 original size:37 final size:37
Alignment explanation
Indices: 1148346--1148446 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
1148336 CCTTTTCGTC
*
1148346 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* ** *
1148383 TTGTTAGGATTCAAACTCCTAAAAATAAGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* *
1148420 CTACTATGATTTAAACTCCTAAAAATA
1 CTACTAGGATTCAAACTCCTAAAAATA
1148447 GGATCCACAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:1148779 original size:37 final size:37
Alignment explanation
Indices: 1148722--1148826 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1148712 TCTTTTCGTC
* *
1148722 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* ** *
1148759 TTGTTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
*
1148796 CTACTATGATTTAAACTCCTAAAAATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
1148827 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1148938 original size:376 final size:376
Alignment explanation
Indices: 1148245--1149004 Score: 1448
Period size: 376 Copynumber: 2.0 Consensus size: 376
1148235 TGTGTTAATT
1148245 TTTTTCTTCTTAAAATGCGGTATAAGGTTTTCATGTACTTAAGATTCAGGTTCAAGTTTGAGCTT
1 TTTTTCTTCTTAAAATGCGGTATAAGGTTTTCATGTACTTAAGATTCAGGTTCAAGTTTGAGCTT
*
1148310 CAACCGAGTTAAGTTTTGTCAACACACCTTTTCGTCCTACTAGGATTCAAACTCCTAAAAATATG
66 CAACCGAATTAAGTTTTGTCAACACACCTTTTCGTCCTACTAGGATTCAAACTCCTAAAAATATG
1148375 ATAGAATTTTGTTAGGATTCAAACTCCTAAAAATAAGATAGAGTTCTACTATGATTTAAACTCCT
131 ATAGAATTTTGTTAGGATTCAAACTCCTAAAAATAAGATAGAGTTCTACTATGATTTAAACTCCT
1148440 AAAAATAGGATCCACAAGCACTATAAATAGCCATTGTAACTCACTATTGTGACACACGATTTACA
196 AAAAATAGGATCCACAAGCACTATAAATAGCCATTGTAACTCACTATTGTGACACACGATTTACA
*
1148505 GACAAAATACAGAGGAACGCACGAAAAATACAAAGGCAAAACTATTGTAAACGATTCGAAAATGA
261 GACAAAATACAGAGGAACGCACGAAAAATACAAAGGCAAAACTATTGTAAACGATTCGAAAAGGA
*
1148570 AATAAAAGGTAGCATTTTTTTGATTCGTTCATTTCTCGCATGTGCACGTTA
326 AATAAAAGGTAACATTTTTTTGATTCGTTCATTTCTCGCATGTGCACGTTA
1148621 TTTTTCTTCTTAAAATGCGGTATAAGGTTTTCATGTACTTAAGATTCAGGTTCAAGTTTGAGCTT
1 TTTTTCTTCTTAAAATGCGGTATAAGGTTTTCATGTACTTAAGATTCAGGTTCAAGTTTGAGCTT
*
1148686 CAACCGAATTAAGTTTTGTCAACACATCTTTTCGTCCTACTAGGATTCAAACTCCTAAAAATATG
66 CAACCGAATTAAGTTTTGTCAACACACCTTTTCGTCCTACTAGGATTCAAACTCCTAAAAATATG
* *
1148751 ATAGAATTTTGTTATGATTCAAACTCCTAAAAATAGGATAGAGTTCTACTATGATTTAAACTCCT
131 ATAGAATTTTGTTAGGATTCAAACTCCTAAAAATAAGATAGAGTTCTACTATGATTTAAACTCCT
1148816 AAAAATAGGATCCACAAGCACTATAAATAGCCATTGTAACTCACTATTGTGACACACGATTTACA
196 AAAAATAGGATCCACAAGCACTATAAATAGCCATTGTAACTCACTATTGTGACACACGATTTACA
*
1148881 GACAAAATACAGAGGAACGCACGGAAAATACAAAGGCAAAACTATTGTAAACGATTCGAAAAGGA
261 GACAAAATACAGAGGAACGCACGAAAAATACAAAGGCAAAACTATTGTAAACGATTCGAAAAGGA
*
1148946 AATAAAAGGTAACATTTTTTTTATTCGTTCATTTCTCGCATGTGCACGTTA
326 AATAAAAGGTAACATTTTTTTGATTCGTTCATTTCTCGCATGTGCACGTTA
1148997 TTTTTCTT
1 TTTTTCTT
1149005 GAGATTTGGT
Statistics
Matches: 376, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
376 376 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (376 bp):
TTTTTCTTCTTAAAATGCGGTATAAGGTTTTCATGTACTTAAGATTCAGGTTCAAGTTTGAGCTT
CAACCGAATTAAGTTTTGTCAACACACCTTTTCGTCCTACTAGGATTCAAACTCCTAAAAATATG
ATAGAATTTTGTTAGGATTCAAACTCCTAAAAATAAGATAGAGTTCTACTATGATTTAAACTCCT
AAAAATAGGATCCACAAGCACTATAAATAGCCATTGTAACTCACTATTGTGACACACGATTTACA
GACAAAATACAGAGGAACGCACGAAAAATACAAAGGCAAAACTATTGTAAACGATTCGAAAAGGA
AATAAAAGGTAACATTTTTTTGATTCGTTCATTTCTCGCATGTGCACGTTA
Found at i:1149202 original size:21 final size:22
Alignment explanation
Indices: 1149176--1149224 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1149166 TTATTTTTCT
*
1149176 TTATATTAG-TCCTTTTATTTA
1 TTATATTAGATACTTTTATTTA
*
1149197 TTATA-TAGATATTTTTATTTA
1 TTATATTAGATACTTTTATTTA
1149218 TT-TATTA
1 TTATATTA
1149225 TTTACATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATATTAGATACTTTTATTTA
Found at i:1149388 original size:19 final size:19
Alignment explanation
Indices: 1149355--1149413 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1149345 CATTTGGTTA
*
1149355 TTTTTTAATACTATATTTA-
1 TTTTTTTATA-TATATTTAC
*
1149374 TTATTTTTATATATATATAC
1 TT-TTTTTATATATATTTAC
*
1149394 TTTTTTTAAATAT-TTTAC
1 TTTTTTTATATATATTTAC
1149412 TT
1 TT
1149414 ATAAGCGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.18
19 19 0.56
20 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTTATATATATTTAC
Found at i:1149595 original size:13 final size:13
Alignment explanation
Indices: 1149563--1149598 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1149553 GGTTTATATA
1149563 TTTATTTGTTTTT
1 TTTATTTGTTTTT
*
1149576 GTT-TTTGTTTTT
1 TTTATTTGTTTTT
1149588 TTTATTTGTTT
1 TTTATTTGTTT
1149599 ATATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (13 bp):
TTTATTTGTTTTT
Found at i:1149687 original size:4 final size:4
Alignment explanation
Indices: 1149673--1149761 Score: 56
Period size: 4 Copynumber: 21.5 Consensus size: 4
1149663 TATATATATA
1149673 TTAT TTCAT TTAT TTAT TTAT TTAT TTAT TT-T TCCT-T TTATT TTAT
1 TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT T--TAT TTA-T TTAT
* * * * * * *
1149719 TTTT TTAC TTAT TTTT ATTCT TCAT TTTT TTAT TTAT TCAT TT
1 TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TT
1149762 TTTCCCTCTA
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
3 3 0.05
4 49 0.74
5 14 0.21
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:1149745 original size:25 final size:23
Alignment explanation
Indices: 1149708--1149756 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
1149698 TTATTTTTCC
1149708 TTTTATTTTATTTTTTTACTTAT
1 TTTTATTTTATTTTTTTACTTAT
*
1149731 TTTTATTCTTCATTTTTTTATTTAT
1 TTTTATT-TT-ATTTTTTTACTTAT
1149756 T
1 T
1149757 CATTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 2 0.09
25 14 0.61
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTATTTTATTTTTTTACTTAT
Found at i:1149750 original size:15 final size:16
Alignment explanation
Indices: 1149681--1149764 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 16
1149671 TATTATTTCA
* *
1149681 TTTATTTATTTATTTA
1 TTTATTTATTCATTTT
*
1149697 TTTATTT-TTCCTTTTAT
1 TTTATTTATT-CATTT-T
* *
1149714 TTTATTTTTTTACTTATT
1 TTTATTTATTCA-TT-TT
*
1149732 TTTA-TTCTTCATTTT
1 TTTATTTATTCATTTT
1149747 TTTATTTATTCATTTT
1 TTTATTTATTCATTTT
1149763 TT
1 TT
1149765 CCCTCTAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.15
16 24 0.44
17 12 0.22
18 9 0.17
19 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTATTCATTTT
Done.