Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 38
Found at i:919427 original size:108 final size:108
Alignment explanation
Indices: 919290--919646 Score: 493
Period size: 108 Copynumber: 3.3 Consensus size: 108
919280 ATCAACTCAT
** * * * * *
919290 GATGAATTCCGTGGATTTGCACACATAGTGCCTGTATGGTTATTCAACAAC-TCATGATGAATTC
1 GATGAATTCCGT-GAAATGCACACATAGTGCCTGAACGGTTATTCATCCACAT-AGGATGAATTC
* * * *
919354 CGTGAAATGTACACTTAGTGTCGAAACGGTTATTCTTCCACATAG
64 CGTGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAG
**
919399 GATGAATTCCGTGAAATGCACACATAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCG
1 GATGAATTCCGTGAAATGCACACATAGTGCCTGAACGGTTATTCATCCACATAGGATGAATTCCG
* * *
919464 TGAAATGCATACTTAGTGCCAAAATAGTTATTCATCCACATAG
66 TGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAG
*
919507 GATGAATTCCGTGAAATGCACACTTAGTG-CTGAAACGGTTATTCATCCACATAGGATGAATTCC
1 GATGAATTCCGTGAAATGCACACATAGTGCCTG-AACGGTTATTCATCCACATAGGATGAATTCC
*
919571 GTGAAATGCACACTTAGTGCCGAAACTGTTATTCATCCACATAG
65 GTGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAG
* *
919615 GATGAATTCCATGAAATGCACACTTAGTGCCT
1 GATGAATTCCGTGAAATGCACACATAGTGCCT
919647 ATTTGGTAAT
Statistics
Matches: 221, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
107 1 0.00
108 205 0.93
109 15 0.07
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (108 bp):
GATGAATTCCGTGAAATGCACACATAGTGCCTGAACGGTTATTCATCCACATAGGATGAATTCCG
TGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAG
Found at i:919582 original size:25 final size:25
Alignment explanation
Indices: 919500--919582 Score: 60
Period size: 27 Copynumber: 3.2 Consensus size: 25
919490 GTTATTCATC
919500 CACATAGGATGAATTCCGTGAAATG
1 CACATAGGATGAATTCCGTGAAATG
* * * * * *
919525 CACACTTAGTGCTGAA-ACGGTTATTCATC
1 CACA--TAG-GATGAATTCCGTGA--AATG
919554 CACATAGGATGAATTCCGTGAAATG
1 CACATAGGATGAATTCCGTGAAATG
919579 CACA
1 CACA
919583 CTTAGTGCCG
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
25 10 0.25
26 5 0.12
27 14 0.35
28 5 0.12
29 6 0.15
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
CACATAGGATGAATTCCGTGAAATG
Found at i:923583 original size:46 final size:46
Alignment explanation
Indices: 923533--923673 Score: 146
Period size: 45 Copynumber: 3.1 Consensus size: 46
923523 AGAGCATCCA
*
923533 TTCATACTTATAATGCA-CCATTATGTATTTTCATTTATGACATTC-T
1 TTCATACTAATAATGCACCCA-TATGTATTTTCATTTATGACA-TCAT
* * * ** *
923579 TTCATGCCAATAATGCACCCATATGTA-TTTCAATTATGGTATCTT
1 TTCATACTAATAATGCACCCATATGTATTTTCATTTATGACATCAT
* * *
923624 TTAATACTGATAATGCACCCATATGCATTTT-ATTTATGACATCAT
1 TTCATACTAATAATGCACCCATATGTATTTTCATTTATGACATCAT
923669 TTCAT
1 TTCAT
923674 GCCCTTTTAT
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
44 2 0.03
45 48 0.63
46 23 0.30
47 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (46 bp):
TTCATACTAATAATGCACCCATATGTATTTTCATTTATGACATCAT
Found at i:924276 original size:54 final size:54
Alignment explanation
Indices: 924166--924370 Score: 252
Period size: 54 Copynumber: 3.8 Consensus size: 54
924156 TATTAAGATG
* * * *
924166 CATCAAC-TCATGATGAATTCCGTGAATTTGCACACATAGTGCCTATACGGTTATT
1 CATCAACAT-ATGATGAATTCCGTGAA-ATGCACACTTAGTGCCAAAACGGTTATT
924221 CATCAAC-TCATGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACGGTTATT
1 CATCAACAT-ATGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACGGTTATT
* * * * *
924275 CATCCACATAGGATGAATTCCGTTAAATGCACACTTAGTGCCGAAATGGTTATT
1 CATCAACATATGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACGGTTATT
* ** *
924329 CATCCACATATGATGAATTATGTGAAATGCAAACTTAGTGCC
1 CATCAACATATGATGAATTCCGTGAAATGCACACTTAGTGCC
924371 TATTTGGTAA
Statistics
Matches: 135, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 108 0.80
55 27 0.20
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
CATCAACATATGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACGGTTATT
Found at i:925027 original size:21 final size:22
Alignment explanation
Indices: 924992--925034 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
924982 GTCAGAGGGG
* *
924992 AACCGATTCCCCTGCTACAGTA
1 AACCGATTACCCTGCTAAAGTA
925014 AACCGA-TACCCTGCTAAAGTA
1 AACCGATTACCCTGCTAAAGTA
925035 CTACCGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.21
Consensus pattern (22 bp):
AACCGATTACCCTGCTAAAGTA
Found at i:925824 original size:31 final size:31
Alignment explanation
Indices: 925789--925913 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 31
925779 GAACCTCAGC
* *
925789 AACTGTCCATAGGT-TCCGAATAACCTAGGTA
1 AACTGTCCATAGGTCT-CGAAGAACATAGGTA
** *
925820 AACTGTATATATGTCTCGAAGAACATAGGTA
1 AACTGTCCATAGGTCTCGAAGAACATAGGTA
* *
925851 AACTGTCCATATGTCTC-AAAAGACATAGGTA
1 AACTGTCCATAGGTCTCGAAGA-ACATAGGTA
* * * **
925882 AATTGTCCATATGTCCCGAAGTTCATAGGTA
1 AACTGTCCATAGGTCTCGAAGAACATAGGTA
925913 A
1 A
925914 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
30 3 0.04
31 72 0.92
32 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAGAACATAGGTA
Found at i:926177 original size:19 final size:19
Alignment explanation
Indices: 926153--926192 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
926143 TGTAATCATA
926153 TAGATCATGTCACATAGCT
1 TAGATCATGTCACATAGCT
926172 TAGATCATGTCACATAGCT
1 TAGATCATGTCACATAGCT
926191 TA
1 TA
926193 TGTCTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (19 bp):
TAGATCATGTCACATAGCT
Found at i:933900 original size:16 final size:16
Alignment explanation
Indices: 933879--933909 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
933869 TAATAAATTA
933879 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
933895 ACGAACATAAACGAA
1 ACGAACATAAACGAA
933910 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:934020 original size:15 final size:15
Alignment explanation
Indices: 933977--934025 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
933967 CATTTAATAA
933977 ATAAACGAACACGAAC
1 ATAAACGAAC-CGAAC
933993 ATAAACG-ACCGAAC
1 ATAAACGAACCGAAC
*
934007 ATAAATGAACCGAAC
1 ATAAACGAACCGAAC
934022 ATAA
1 ATAA
934026 CGTTGGAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 11 0.35
15 13 0.42
16 7 0.23
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.10
Consensus pattern (15 bp):
ATAAACGAACCGAAC
Found at i:934786 original size:24 final size:24
Alignment explanation
Indices: 934745--934807 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
934735 AGATTGGGTT
*
934745 AAACATAAAT-GAATGAACATAAAC
1 AAACAT-AATCGAACGAACATAAAC
*
934769 GAACATAATCGAACGAACATAAAC
1 AAACATAATCGAACGAACATAAAC
*
934793 AAACATAACCGAACG
1 AAACATAATCGAACG
934808 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 3 0.09
24 31 0.91
ACGTcount: A:0.57, C:0.19, G:0.11, T:0.13
Consensus pattern (24 bp):
AAACATAATCGAACGAACATAAAC
Found at i:935557 original size:60 final size:58
Alignment explanation
Indices: 935477--935620 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 58
935467 CTACACATTT
* * * * *
935477 GGATGAAATTGAAATGTTCAAAAGTTTAAGAACCAATTTAGGTAGTGTA-TCATAACTTAG
1 GGATGAAATTAAAATATTCAAAAGTTTAAGAACCAATGTA-G-AATG-AGTCATAACTAAG
* *
935537 GGATGACATTAAAATATTCAAACA-TTTAAGAACTAATGTAGAATGAGTCATAACTAAG
1 GGATGAAATTAAAATATTCAAA-AGTTTAAGAACCAATGTAGAATGAGTCATAACTAAG
* * *
935595 GGATGAAATCAGAATATACAAAAGTT
1 GGATGAAATTAAAATATTCAAAAGTT
935621 CAAAGACTGA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
57 2 0.03
58 33 0.47
59 1 0.01
60 33 0.47
61 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.28
Consensus pattern (58 bp):
GGATGAAATTAAAATATTCAAAAGTTTAAGAACCAATGTAGAATGAGTCATAACTAAG
Found at i:936420 original size:27 final size:27
Alignment explanation
Indices: 936387--936505 Score: 157
Period size: 27 Copynumber: 4.4 Consensus size: 27
936377 ACTCCCATTT
*
936387 GGACTCCTGCTAGCACTACGCCTTTTA
1 GGACTCCTGCTAGCACTACGTCTTTTA
* * *
936414 GGGCTCCTGCTAGGACTACGTCTCTTA
1 GGACTCCTGCTAGCACTACGTCTTTTA
* *
936441 GGACTCCTGCTAGCACTGCGTCTTTTG
1 GGACTCCTGCTAGCACTACGTCTTTTA
* * *
936468 GGACTCCCGCTAACACTAGGTCTTTTA
1 GGACTCCTGCTAGCACTACGTCTTTTA
936495 GGACTCCTGCT
1 GGACTCCTGCT
936506 CCTTCCTTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.16, C:0.31, G:0.23, T:0.30
Consensus pattern (27 bp):
GGACTCCTGCTAGCACTACGTCTTTTA
Found at i:942655 original size:29 final size:29
Alignment explanation
Indices: 942621--942679 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
942611 CCTAAATTAA
*
942621 TTTGATGTTATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
942650 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
942679 T
1 T
942680 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:947241 original size:29 final size:29
Alignment explanation
Indices: 947207--947265 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
947197 CCTAAATTAA
947207 TTTGATGCCATTGCTTACATCAATTTAGT
1 TTTGATGCCATTGCTTACATCAATTTAGT
* *
947236 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGCCATTGCTTACATCAATTTAGT
947265 T
1 T
947266 AAGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGCCATTGCTTACATCAATTTAGT
Found at i:956619 original size:2 final size:2
Alignment explanation
Indices: 956612--956656 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
956602 GTTTTCCAAC
* *
956612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT -T TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
956653 AT AT
1 AT AT
956657 TTATTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:956669 original size:17 final size:17
Alignment explanation
Indices: 956615--956666 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
956605 TTCCAACATA
* *
956615 TATATATATATATATATA
1 TATATATATATTTAT-TT
956633 TATATATATATTTATTT
1 TATATATATATTTATTT
*
956650 TATATATTTA-TTATTT
1 TATATATATATTTATTT
956666 T
1 T
956667 TATCATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 7 0.23
17 10 0.32
18 14 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATATATTTATTT
Found at i:956772 original size:6 final size:6
Alignment explanation
Indices: 956761--956901 Score: 58
Period size: 6 Copynumber: 22.3 Consensus size: 6
956751 ATTTTCTTCC
* *
956761 TTATTT TTATTT TTATTT CATTCTATT TTGTTT ATTCA-TT TTACTTGT
1 TTATTT TTATTT TTATTT --TTAT-TT TTATTT -TT-ATTT TTA-TT-T
* * *
956809 TTTAT-T TTA-TT TTATTT ATT-TAT TTATTA TTATTT GTTTTGTT TTA-TT
1 -TTATTT TTATTT TTATTT -TTATTT TTATTT TTATTT -TTAT-TT TTATTT
* * * *
956857 TTGTCT TTATTT TTATTT TTATTT TTATTT TGTCTTT TAATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT T-TATTT TTATTT TT
956902 TAAATTTGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 34
0.66 0.11 0.22
Matches are distributed among these distances:
5 14 0.14
6 55 0.54
7 20 0.20
8 7 0.07
9 5 0.05
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:956818 original size:5 final size:5
Alignment explanation
Indices: 956765--956887 Score: 62
Period size: 5 Copynumber: 24.8 Consensus size: 5
956755 TCTTCCTTAT
* * * * * *
956765 TTTTA TTTTTA TTTCA TTCTA TTTT- GTTTA -TTCA TTTTA -CTTG TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
956813 TTTTA TTTTA -TTTA -TTTA -TTTA TTATTA -TTTG TTTTG TTTTA TTTTG
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
956860 TCTTTA TTTTTA TTTTTA TTTTTA TTTT
1 T-TTTA -TTTTA -TTTTA -TTTTA TTTT
956888 GTCTTTTAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
4 22 0.23
5 44 0.47
6 27 0.29
7 1 0.01
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:956826 original size:14 final size:14
Alignment explanation
Indices: 956765--956858 Score: 61
Period size: 14 Copynumber: 6.6 Consensus size: 14
956755 TCTTCCTTAT
956765 TTTTATTTTTATTTCA
1 TTTTA-TTTTATTT-A
* *
956781 TTCTATTTTGTTTA
1 TTTTATTTTATTTA
* * *
956795 -TTCATTTTACTTG
1 TTTTATTTTATTTA
956808 TTTTATTTTATTT-
1 TTTTATTTTATTTA
956821 TATTTA-TTTATTTA
1 T-TTTATTTTATTTA
*
956835 TTATTATTTGT-TTTG
1 TT-TTATTT-TATTTA
956850 TTTTATTTT
1 TTTTATTTT
956859 GTCTTTATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
13 18 0.29
14 25 0.40
15 14 0.23
16 5 0.08
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:956873 original size:37 final size:37
Alignment explanation
Indices: 956771--956858 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
956761 TTATTTTTAT
* * * * *
956771 TTTTATTTCATTCTATTTTGTTTATTCATT-TTACTTG
1 TTTTATTTTATTTTA-TTTATTTATTTATTATTATTTG
956808 TTTTATTTTATTTTATTTATTTATTTATTATTATTTG
1 TTTTATTTTATTTTATTTATTTATTTATTATTATTTG
*
956845 TTTTGTTTTATTTT
1 TTTTATTTTATTTT
956859 GTCTTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (37 bp):
TTTTATTTTATTTTATTTATTTATTTATTATTATTTG
Found at i:956879 original size:37 final size:37
Alignment explanation
Indices: 956771--956880 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 37
956761 TTATTTTTAT
* * * * *
956771 TTTTATTTCATTCTATTTTGTTTATTCA-TTTTACTTG
1 TTTTATTTTATTTTA-TTTATTTATTTATTTTTATTTG
*
956808 TTTTATTTTATTTTATTTATTTATTTATTATTATTTG
1 TTTTATTTTATTTTATTTATTTATTTATTTTTATTTG
* *
956845 TTTTGTTTTATTTTGTCTT-TATT-TTTATTTTTATTT
1 TTTTATTTTATTTTAT-TTAT-TTATTTATTTTTATTT
956881 TTATTTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
36 10 0.16
37 47 0.77
38 4 0.07
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (37 bp):
TTTTATTTTATTTTATTTATTTATTTATTTTTATTTG
Found at i:957644 original size:20 final size:20
Alignment explanation
Indices: 957619--957656 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
957609 TTTAGTTTAC
957619 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
957639 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
957657 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:957886 original size:37 final size:37
Alignment explanation
Indices: 957813--957887 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
957803 GTTGGAAAAT
* *
957813 ATTTATATATATTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATATTCTTTAAAAAATTAAAAATCATAAA
* **
957850 ATTTATATATATTTTTTTTTAAAATTAAAAAT-ATAAA
1 ATTTATATATA-TTCTTTAAAAAATTAAAAATCATAAA
957887 A
1 A
957888 AGTTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATATATTCTTTAAAAAATTAAAAATCATAAA
Found at i:964042 original size:21 final size:20
Alignment explanation
Indices: 963997--964047 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
963987 ACTCGAAGTG
963997 ATCAATTCACAAGATAGGAT
1 ATCAATTCACAAGATAGGAT
* *
964017 TTCAACTTCACAACGA-ATGAT
1 ATCAA-TTCACAA-GATAGGAT
964038 ATCAAATTCA
1 ATC-AATTCA
964048 AAGCTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (20 bp):
ATCAATTCACAAGATAGGAT
Found at i:966107 original size:7 final size:7
Alignment explanation
Indices: 966095--966148 Score: 72
Period size: 7 Copynumber: 7.1 Consensus size: 7
966085 TATACATATT
966095 TATTTTA
1 TATTTTA
966102 TATTTTA
1 TATTTTA
966109 TATTTTA
1 TATTTTA
966116 TATTTTA
1 TATTTTA
966123 TTATTTTTA
1 -TA-TTTTA
966132 TCATTTTTA
1 T-A-TTTTA
966141 TATTTTA
1 TATTTTA
966148 T
1 T
966149 TAAATACTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
7 27 0.61
8 4 0.09
9 13 0.30
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:966286 original size:9 final size:9
Alignment explanation
Indices: 966228--966347 Score: 65
Period size: 9 Copynumber: 13.2 Consensus size: 9
966218 ATTTTCTTCC
966228 TTATTT-TT
1 TTATTTATT
966236 TTATTTCATT
1 TTATTT-ATT
*
966246 CTATTT-TGT
1 TTATTTAT-T
*
966255 TTATTCATT
1 TTATTTATT
* * *
966264 GTACTTGTT
1 TTATTTATT
966273 TTATTT-TAT
1 TTATTTAT-T
966282 TTATTTATT
1 TTATTTATT
966291 TTA-TTATT
1 TTATTTATT
966299 ATTA-TTATT
1 -TTATTTATT
966308 ATTA-TTATT
1 -TTATTTATT
966317 ATTATTATTATT
1 -TTA-T-TTATT
966329 TTA-TTATT
1 TTATTTATT
*
966337 TTGTTTATT
1 TTATTTATT
966346 TT
1 TT
966348 TTATGTGTCT
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
8 20 0.22
9 54 0.59
10 9 0.10
11 3 0.03
12 5 0.05
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (9 bp):
TTATTTATT
Found at i:966299 original size:3 final size:3
Alignment explanation
Indices: 966273--966336 Score: 89
Period size: 3 Copynumber: 21.7 Consensus size: 3
966263 TGTACTTGTT
966273 TTA TT- TTA TTTA TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
966318 TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
966337 TTGTTTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.11
3 44 0.77
4 7 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:966343 original size:12 final size:11
Alignment explanation
Indices: 966273--966351 Score: 81
Period size: 12 Copynumber: 6.8 Consensus size: 11
966263 TGTACTTGTT
966273 TTATTTTATTTA
1 TTATTTTA-TTA
966285 TTTATTTTATTA
1 -TTATTTTATTA
966297 TTATTATTATTA
1 TTATT-TTATTA
966309 TTATTATTATTA
1 TTATT-TTATTA
966321 TTATTATT-TTA
1 TTATT-TTATTA
*
966332 TTATTTTGTTTA
1 TTATTTT-ATTA
966344 TT-TTTTAT
1 TTATTTTAT
966352 GTGTCTATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
10 3 0.05
11 17 0.27
12 34 0.55
13 8 0.13
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.73
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:971706 original size:13 final size:13
Alignment explanation
Indices: 971688--971721 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
971678 TAAGATTTTC
*
971688 TTTGAAAATCATT
1 TTTGAAAATCAAT
971701 TTTG-AAATCAAT
1 TTTGAAAATCAAT
971713 TTTGAAAAT
1 TTTGAAAAT
971722 TACCCCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:972018 original size:22 final size:22
Alignment explanation
Indices: 971971--972018 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
971961 ACATGAAGTT
* * *
971971 CAAACTAAATTTTCAAACCATT
1 CAAACAAAATTTCCAAACCATC
971993 CAAACAAAATTATCCAAA-CATC
1 CAAACAAAATT-TCCAAACCATC
972015 CAAA
1 CAAA
972019 AACACACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (22 bp):
CAAACAAAATTTCCAAACCATC
Found at i:981172 original size:21 final size:21
Alignment explanation
Indices: 981132--981186 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
981122 GATTCTTGAC
981132 AATCGCAATGCGATGGTACA-
1 AATCGCAATGCGATGGTACAG
* **
981152 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATGGTACAG
*
981174 AATCGCAACGCGA
1 AATCGCAATGCGA
981187 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATGGTACAG
Found at i:981268 original size:20 final size:20
Alignment explanation
Indices: 981174--981402 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
981164 GATTTTACAG
* ** *
981174 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
981194 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
981214 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
981234 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
981254 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
981274 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
981294 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
981314 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
981334 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
981354 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
981374 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
981394 AATCACAAC
1 AATCGCAAC
981403 ACTGAAATTT
Statistics
Matches: 178, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 174 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:982126 original size:24 final size:24
Alignment explanation
Indices: 982082--982128 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
982072 GAATTTGGTC
*
982082 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
982106 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
982129 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:982317 original size:12 final size:12
Alignment explanation
Indices: 982300--982324 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
982290 ATATAATCCT
982300 GAAGAAGAAAAA
1 GAAGAAGAAAAA
982312 GAAGAAGAAAAA
1 GAAGAAGAAAAA
982324 G
1 G
982325 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:984642 original size:19 final size:19
Alignment explanation
Indices: 984621--984829 Score: 236
Period size: 19 Copynumber: 11.7 Consensus size: 19
984611 TCCCAACAAG
984621 AAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
984641 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
984660 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
984674 GAATCGCAATGCGGAAATG-
1 AAATCGCAATGC-GAAATGA
984693 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
984712 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
984726 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
984745 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
984764 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
984778 GAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
984798 AAATCGCAATGCGAAATG-
1 AAATCGCAATGCGAAATGA
*
984816 AAATCGCATTGCGA
1 AAATCGCAATGCGA
984830 TTCTCTCGTT
Statistics
Matches: 164, Mismatches: 7, Indels: 38
0.78 0.03 0.18
Matches are distributed among these distances:
14 30 0.18
15 3 0.02
16 4 0.02
17 8 0.05
18 20 0.12
19 73 0.45
20 26 0.16
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:984643 original size:33 final size:32
Alignment explanation
Indices: 984576--984753 Score: 162
Period size: 33 Copynumber: 5.2 Consensus size: 32
984566 TGGAAATTAC
*
984576 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGA-AATCGCAATGCGAAATGAA
*
984609 AATCCCAACAAGAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAATCGCAATGC-GAAATGAA
* * *
984642 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-G-AAATCGCAATGCGA-AAT-GAA
* *
984681 AATGCGGAA-ATGAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAATCGCAATGCGAAATGAA
*
984713 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGA-AATCGCAATGCGAAATGAA
984746 AATCGCAA
1 AATCGCAA
984754 TGCGAAATGA
Statistics
Matches: 118, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
31 5 0.04
32 19 0.16
33 65 0.55
34 1 0.01
35 2 0.02
37 2 0.02
38 3 0.03
39 16 0.14
40 5 0.04
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (32 bp):
AATCGCAACAAGAAATCGCAATGCGAAATGAA
Found at i:984647 original size:52 final size:53
Alignment explanation
Indices: 984590--984823 Score: 422
Period size: 52 Copynumber: 4.5 Consensus size: 53
984580 GCAACGAGAG
* *
984590 AATCGCAATGCGAAATGAAAATCCCAACAAGA-AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
984642 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
984694 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
984746 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
984799 AATCGCAATGCGAAATG-AAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
984824 TTGCGATTCT
Statistics
Matches: 177, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
51 6 0.03
52 128 0.72
53 43 0.24
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:984709 original size:85 final size:84
Alignment explanation
Indices: 984576--984753 Score: 227
Period size: 85 Copynumber: 2.1 Consensus size: 84
984566 TGGAAATTAC
* *
984576 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAATCG-CAATGCGGAA-AT
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAT-GAAAAT-CGCAACA-
984639 GAAAATCGCAATGCGAAATGAA
63 GAAAATCGCAATGCGAAATGAA
* ***
984661 AATCGCAACGAGAGAATCGCAATGCGGAAATG-AAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAACAAGAAATGAAAATCGCAAC-AG
*
984725 AGAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
984746 AATCGCAA
1 AATCGCAA
984754 TGCGAAATGA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
84 5 0.06
85 70 0.85
86 7 0.09
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAATGAAAATCGCAACAGAA
AATCGCAATGCGAAATGAA
Found at i:984783 original size:33 final size:33
Alignment explanation
Indices: 984642--984806 Score: 158
Period size: 33 Copynumber: 4.8 Consensus size: 33
984632 CGGAAATGAA
984642 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
984675 AATCGCAATGCGGAAATG-AAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
984707 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
984746 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
984779 AATCGCAATGCGGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
984807 TGCGAAATGA
Statistics
Matches: 107, Mismatches: 11, Indels: 27
0.74 0.08 0.19
Matches are distributed among these distances:
30 4 0.04
31 2 0.02
32 7 0.07
33 44 0.41
34 23 0.21
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:984878 original size:19 final size:19
Alignment explanation
Indices: 984838--984925 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
984828 GATTCTCTCG
984838 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
984858 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
984877 TTGCGATTCTC--TT-G--
1 TTGCGATTTTCATTTCGCA
984891 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
984910 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
984926 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
16 3 0.05
17 3 0.05
19 30 0.49
20 15 0.25
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:984886 original size:53 final size:52
Alignment explanation
Indices: 984819--984925 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 52
984809 CGAAATGAAA
984819 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
*
984872 TCGCATTGCGATTCTCTTGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
984924 TC
1 TC
984926 AACATAATGC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 20 0.38
53 33 0.62
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:985035 original size:14 final size:14
Alignment explanation
Indices: 985016--985052 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
985006 CATCAATTAC
985016 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
985030 ACAAATCATCTTTT
1 ACAAATCAACTTTT
985044 ACAAATCAA
1 ACAAATCAA
985053 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:986543 original size:45 final size:45
Alignment explanation
Indices: 986491--986577 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
986481 TGATGACAGT
* * *
986491 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGGGG
* * *
986536 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
986578 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.21
Consensus pattern (45 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGGGG
Found at i:987014 original size:19 final size:19
Alignment explanation
Indices: 986988--987125 Score: 125
Period size: 19 Copynumber: 7.8 Consensus size: 19
986978 CACGAAACTT
986988 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* * **
987007 AGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATG
987026 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* *
987045 AAAACCGCAA--CGACA-G
1 AAAATCGCAACGCGAAATG
*
987061 --AATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
987078 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
987092 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
987111 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
987126 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 15, Indels: 20
0.73 0.12 0.16
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 7 0.07
17 7 0.07
18 1 0.01
19 61 0.65
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:987074 original size:33 final size:33
Alignment explanation
Indices: 986990--987120 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
986980 CGAAACTTAA
* *
986990 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
*
987028 AATCGCAACGCGAAATGAAAACCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
987061 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
987094 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
987121 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 58 0.67
34 1 0.01
36 1 0.01
38 26 0.30
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:987117 original size:52 final size:51
Alignment explanation
Indices: 986989--987125 Score: 143
Period size: 52 Copynumber: 2.6 Consensus size: 51
986979 ACGAAACTTA
* * * *
986989 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* * * **
987040 AAAT-GAAAAC-CGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCG-CAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
987092 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
987126 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
50 7 0.10
51 7 0.10
52 40 0.59
53 7 0.10
54 7 0.10
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:987156 original size:14 final size:14
Alignment explanation
Indices: 987137--987195 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
987127 TTTGGTTTCG
987137 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
987151 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
987168 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
987184 CGTTGCGATTTT
1 CGTTGCGATTTT
987196 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:987163 original size:33 final size:33
Alignment explanation
Indices: 987121--987244 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
987111 AAAATCGCAA
*
987121 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
987154 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
987187 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
987220 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
987245 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:987175 original size:19 final size:18
Alignment explanation
Indices: 987121--987212 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
987111 AAAATCGCAA
987121 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
987140 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
987154 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
987173 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
987187 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
987206 TGCGATT
1 TGCGATT
987213 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:987222 original size:14 final size:14
Alignment explanation
Indices: 987170--987226 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
987160 TTTGGTTTCG
*
987170 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
987184 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
987203 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
987217 CGTTGCGATT
1 CGTTGCGATT
987227 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:987551 original size:93 final size:93
Alignment explanation
Indices: 987269--987570 Score: 561
Period size: 93 Copynumber: 3.3 Consensus size: 93
987259 ACCAAAAGAC
987269 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAG
1 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAG
987334 TGTTAAAGAATACACAGTTTAGCAGAAT
66 TGTTAAAGAATACACAGTTTAGCAGAAT
*
987362 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAATAAAGACAAATACTATTTCACAG
1 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAG
987426 TGTTAAAGAATACACAGTTTAGCAGAAT
66 TGTTAAAGAATACACAGTTTAGCAGAAT
* *
987454 TGGCAGAAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAGACTATTTCACAG
1 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAG
987519 TGTTAAAGAATACACAGTTTAGCAGAAT
66 TGTTAAAGAATACACAGTTTAGCAGAAT
*
987547 TGGCAGCAACCGAATAAATTTACT
1 TGGCAGCAACCGAACAAATTTACT
987571 AAGCAATCTA
Statistics
Matches: 202, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
92 90 0.45
93 112 0.55
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAG
TGTTAAAGAATACACAGTTTAGCAGAAT
Found at i:989288 original size:20 final size:20
Alignment explanation
Indices: 989257--989363 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
989247 TTTTGGTTGA
989257 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
989277 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
989297 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
989316 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
989331 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
989350 AATGAAAATCGCAA
1 AATGAAAATCGCAA
989364 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 30 0.41
20 17 0.23
21 12 0.16
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:989309 original size:21 final size:21
Alignment explanation
Indices: 989255--989319 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
989245 TCTTTTGGTT
989255 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
989276 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
989296 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
989317 GAA
1 GAA
989320 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:989399 original size:14 final size:14
Alignment explanation
Indices: 989380--989436 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
989370 TTTGGTTTCG
989380 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
989394 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
989413 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
989427 CGTTGCGATT
1 CGTTGCGATT
989437 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:989412 original size:33 final size:33
Alignment explanation
Indices: 989364--989443 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
989354 AAAATCGCAA
**
989364 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
989397 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
989430 TGCGATTTTCATTT
1 TGCGATTTTCATTT
989444 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:989449 original size:21 final size:21
Alignment explanation
Indices: 989424--989497 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
989414 GTTGCGATTC
989424 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
989445 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
989466 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
989487 TCTCGTTGCGA
1 TCTCGTTGCGA
989498 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:989619 original size:33 final size:33
Alignment explanation
Indices: 989577--989647 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
989567 AATACTAACT
989577 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
989610 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
989643 TGAAA
1 TGAAA
989648 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:990051 original size:20 final size:20
Alignment explanation
Indices: 990026--990217 Score: 253
Period size: 20 Copynumber: 9.6 Consensus size: 20
990016 CTTTAAAAAT
990026 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
990046 CGCGTTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
*
990067 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
990086 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
990106 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
990126 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
990146 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
990166 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
990186 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
990206 CGCGTTGCGATT
1 CGCGTTGCGATT
990218 CTTGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:991605 original size:2 final size:2
Alignment explanation
Indices: 991598--991632 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
991588 TGTACTTCTT
991598 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
991633 TTCTTTGAAT
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:993834 original size:24 final size:24
Alignment explanation
Indices: 993807--993884 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
993797 TTCATTTATA
*
993807 TTCGTTCATTTATGTCTGTGTACG
1 TTCGTTCATTTATGTCTGTGTATG
* * *
993831 TTCGTTTATGTT-CGT-TCGTTTATG
1 TTCGTTCAT-TTATGTCT-GTGTATG
*
993855 TTCGTTCATTTATGTCCGTGTATG
1 TTCGTTCATTTATGTCTGTGTATG
993879 TTCGTT
1 TTCGTT
993885 ATATCCGTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
23 3 0.07
24 37 0.88
25 2 0.05
ACGTcount: A:0.10, C:0.15, G:0.21, T:0.54
Consensus pattern (24 bp):
TTCGTTCATTTATGTCTGTGTATG
Found at i:993848 original size:14 final size:14
Alignment explanation
Indices: 993829--993869 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
993819 TGTCTGTGTA
993829 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
993843 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
993857 CGTTCATTTATGT
1 CGTTCGTTTATGT
993870 CCGTGTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:993864 original size:48 final size:46
Alignment explanation
Indices: 993759--993900 Score: 151
Period size: 48 Copynumber: 3.0 Consensus size: 46
993749 ACAAAAGTCT
* * * * * *
993759 TGTTCGTTCATTTACGTTTGTGAACGTTTGGTAATTT-GTTCATTTA
1 TGTTCGTTCATTTATGTCTGTGTACG-TTCGTTATTTCGTTCGTTTA
*
993805 TATTCGTTCATTTATGTCTGTGTACGTTCGTTTATGTTCGTTCGTTTA
1 TGTTCGTTCATTTATGTCTGTGTACGTTCG-TTAT-TTCGTTCGTTTA
* * *
993853 TGTTCGTTCATTTATGTCCGTGTATGTTCGTTATATCCGTTCGTTTA
1 TGTTCGTTCATTTATGTCTGTGTACGTTCGTTAT-TTCGTTCGTTTA
993900 T
1 T
993901 ATTCATTCTA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
45 3 0.04
46 25 0.31
47 18 0.22
48 35 0.43
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (46 bp):
TGTTCGTTCATTTATGTCTGTGTACGTTCGTTATTTCGTTCGTTTA
Found at i:993966 original size:16 final size:16
Alignment explanation
Indices: 993941--993971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
993931 TATCATTAAT
993941 ATTTTAAAACCCAAAA
1 ATTTTAAAACCCAAAA
*
993957 ATTTTTAAACCCAAA
1 ATTTTAAAACCCAAA
993972 TCAATTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTTTAAAACCCAAAA
Found at i:996368 original size:3 final size:3
Alignment explanation
Indices: 996362--996416 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
996352 ATTTGGGTTT
*
996362 TTA TTA TTTA TTA TTA TTA TTA ATA TTA TTA TTA TTTA TTAA TT- TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA
996409 TTA -TA TTA
1 TTA TTA TTA
996417 CAGGCCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 4 0.09
3 32 0.71
4 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:996399 original size:28 final size:27
Alignment explanation
Indices: 996362--996416 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
996352 ATTTGGGTTT
996362 TTATTATTTATT-ATTATTATTAATATTA
1 TTATTATTTATTAATT-TTATT-ATATTA
996390 TTATTATTTATTAATTTTATTATATTA
1 TTATTATTTATTAATTTTATTATATTA
996417 CAGGCCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTATTTATTAATTTTATTATATTA
Found at i:997702 original size:16 final size:16
Alignment explanation
Indices: 997681--997713 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
997671 TTGCTTTTAA
997681 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
997697 ATTTATTTATAATATT
1 ATTTATTTATAATATT
997713 A
1 A
997714 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:997741 original size:17 final size:17
Alignment explanation
Indices: 997719--997752 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
997709 TATTAATTTG
997719 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
997736 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
997753 GTCACACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:1000247 original size:8 final size:7
Alignment explanation
Indices: 1000223--1000264 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1000213 TTTTCATACA
1000223 TGCA-TT
1 TGCATTT
1000229 TGCATTT
1 TGCATTT
1000236 TGCATCTT
1 TGCAT-TT
1000244 TGCATTT
1 TGCATTT
* *
1000251 TTCATTG
1 TGCATTT
1000258 TGCATTT
1 TGCATTT
1000265 ATACTCTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1000247 original size:15 final size:14
Alignment explanation
Indices: 1000223--1000264 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1000213 TTTTCATACA
1000223 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1000236 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
1000251 TTCATTGTGCATTT
1 TGCATTTTGCATTT
1000265 ATACTCTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1004579 original size:114 final size:114
Alignment explanation
Indices: 1004379--1004598 Score: 361
Period size: 114 Copynumber: 1.9 Consensus size: 114
1004369 CACGTTCTCG
1004379 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* * *
1004444 GGTATGAACCCTAAAACCAATCATTGGATTTGAAATATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
* * *
1004493 TAGTATAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
1004558 GGTA-GAAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTATG-AACCCCAAAACCAATCATTGGAATTGAAAGATGAA
1004599 CTGCATAATC
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 97 0.99
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:1007281 original size:23 final size:22
Alignment explanation
Indices: 1007229--1007303 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
1007219 TACATTCTTC
* * *
1007229 AAAGATGATAGATTTTCTCTTC
1 AAAGATGATAGATTCTCTTTTT
1007251 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
1007273 AAAAGATGATAGATTCTCTTTTT
1 -AAAGATGATAGATTCTCTTTTT
1007296 AAAGATGA
1 AAAGATGA
1007304 AAGCTTTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 27 0.55
23 22 0.45
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:1008296 original size:113 final size:113
Alignment explanation
Indices: 1008098--1008511 Score: 740
Period size: 113 Copynumber: 3.7 Consensus size: 113
1008088 TTTTTCTTAA
* *
1008098 AACATTTCCA-AGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAA
1 AACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
*
1008162 TGAGAAGAACTTATTCAACCTTTTGCTCAAAACCATCACTTGATGGATC
65 TGAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
* *
1008211 AACATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTTATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
1008276 GAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
66 GAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
1008324 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1008389 GAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
66 GAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
*
1008437 AACATTTCCAGAGAAAGTTCAAAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1008502 GAGAAGAACT
66 GAGAAGAACT
1008512 CATCTGAAGA
Statistics
Matches: 288, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
113 286 0.99
114 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (113 bp):
AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
Found at i:1008536 original size:39 final size:40
Alignment explanation
Indices: 1008451--1008550 Score: 184
Period size: 39 Copynumber: 2.5 Consensus size: 40
1008441 TTTCCAGAGA
*
1008451 AAGTTCAAAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1008491 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1008530 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
1008551 TGTTCAACCT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
39 30 0.51
40 29 0.49
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.18
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:1008695 original size:84 final size:83
Alignment explanation
Indices: 1008533--1008717 Score: 237
Period size: 84 Copynumber: 2.2 Consensus size: 83
1008523 GAAGAAGAAG
* * *
1008533 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTACCACAGAAGGAGATAGATTAGCA
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCAAGACTCTACCACAGAAGAAGATAGATCAGCA
* *
1008598 TATACTTTTCCAGAGAAAA
66 TATACATTGCCAGA-AAAA
* * * *
1008617 TTCATAATAAGAAGAACTTGTTCAACCTTTTGCAAGATTCTATCACAGAAGAAGATATATCAGCA
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCAAGACTCTACCACAGAAGAAGATAGATCAGCA
***
1008682 TCA-ACATTGCCAGAAGTG
66 T-ATACATTGCCAGAAAAA
1008700 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
1008718 CATCTGAAAG
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
83 18 0.21
84 68 0.78
85 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (83 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCAAGACTCTACCACAGAAGAAGATAGATCAGCA
TATACATTGCCAGAAAAA
Found at i:1008975 original size:3 final size:3
Alignment explanation
Indices: 1008969--1009023 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
1008959 ATTTGGTTTT
*
1008969 TTA TTA TTTA TTA TTA TTA TTA ATA TTA TTA TTA TTTA TTAA TT- TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA
1009016 TTA -TA TTA
1 TTA TTA TTA
1009024 CATGCCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 4 0.09
3 32 0.71
4 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1009006 original size:28 final size:27
Alignment explanation
Indices: 1008969--1009023 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
1008959 ATTTGGTTTT
1008969 TTATTATTTATT-ATTATTATTAATATTA
1 TTATTATTTATTAATT-TTATT-ATATTA
1008997 TTATTATTTATTAATTTTATTATATTA
1 TTATTATTTATTAATTTTATTATATTA
1009024 CATGCCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTATTTATTAATTTTATTATATTA
Found at i:1010309 original size:16 final size:16
Alignment explanation
Indices: 1010288--1010320 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1010278 TTGCTTTTAA
1010288 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
1010304 ATTTATTTATAATATT
1 ATTTATTTATAATATT
1010320 A
1 A
1010321 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:1010348 original size:17 final size:17
Alignment explanation
Indices: 1010326--1010359 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1010316 TATTAATTTG
1010326 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
1010343 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
1010360 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:1010376 original size:2 final size:2
Alignment explanation
Indices: 1010369--1010401 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1010359 AGTCACATAA
1010369 AT AT 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 AT AT A
1010402 ATAATGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1010523 original size:31 final size:33
Alignment explanation
Indices: 1010488--1010550 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
1010478 ATAATTAAAC
1010488 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
1010519 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
1010551 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:1010766 original size:16 final size:17
Alignment explanation
Indices: 1010735--1010767 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1010725 TCATTTTCTG
1010735 ATATTTTTAAATAAATAA
1 ATATTTTT-AATAAATAA
1010753 ATATTTTT-ATAAATA
1 ATATTTTTAATAAATA
1010768 TATTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTTTTAATAAATAA
Found at i:1012781 original size:18 final size:18
Alignment explanation
Indices: 1012760--1012800 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1012750 ATGGTGGTTG
1012760 TGATGTTGCAG-CTTGTGA
1 TGATGTTGCAGCCTT-TGA
1012778 TGATGTTGCAGCCTTTGA
1 TGATGTTGCAGCCTTTGA
1012796 TGATG
1 TGATG
1012801 GTGTAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (18 bp):
TGATGTTGCAGCCTTTGA
Found at i:1013790 original size:16 final size:16
Alignment explanation
Indices: 1013741--1013784 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1013731 AAAAATGGCT
1013741 TAGAATCATATTATAA
1 TAGAATCATATTATAA
1013757 TAGAATCATATTATAA
1 TAGAATCATATTATAA
*
1013773 TATAATCATATT
1 TAGAATCATATT
1013785 TAAATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (16 bp):
TAGAATCATATTATAA
Found at i:1015230 original size:17 final size:18
Alignment explanation
Indices: 1015182--1015227 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1015172 CTGTCAAAAT
1015182 GCATTAAAAAATCAGTCA
1 GCATTAAAAAATCAGTCA
1015200 GCATTAAAAAATCAGTCA
1 GCATTAAAAAATCAGTCA
1015218 GCATTAAAAA
1 GCATTAAAAA
1015228 TCAACTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (18 bp):
GCATTAAAAAATCAGTCA
Found at i:1015840 original size:22 final size:21
Alignment explanation
Indices: 1015783--1015841 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
1015773 TGTTCTCATA
*
1015783 AAAAAACCCTAAAAGTATTTC
1 AAAAAATCCTAAAAGTATTTC
1015804 AGAAAAATCACTAAAAGTATTTC
1 A-AAAAATC-CTAAAAGTATTTC
*
1015827 GAAAAAATCTTAAAA
1 -AAAAAATCCTAAAA
1015842 AAACGTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 11 0.33
23 20 0.61
24 1 0.03
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAAATCCTAAAAGTATTTC
Found at i:1016422 original size:16 final size:16
Alignment explanation
Indices: 1016401--1016434 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1016391 TTCATTTCTC
1016401 TTATTTATTCATCGAT
1 TTATTTATTCATCGAT
*
1016417 TTATTTATTCATTGAT
1 TTATTTATTCATCGAT
1016433 TT
1 TT
1016435 TGAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (16 bp):
TTATTTATTCATCGAT
Found at i:1023516 original size:21 final size:20
Alignment explanation
Indices: 1023488--1023526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1023478 TATTGCAGGA
1023488 ATTTATGG-TCTCAACAAAGG
1 ATTTATGGCT-TCAACAAAGG
1023508 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
1023527 AACCTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAGG
Found at i:1036808 original size:54 final size:54
Alignment explanation
Indices: 1036771--1037197 Score: 361
Period size: 54 Copynumber: 7.9 Consensus size: 54
1036761 TGCCTATACG
* * * *
1036771 GTCATTCAAAAACATATTATAAATTCCGTGATTTGCACACTTAGTGTCAAAATA
1 GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
** *
1036825 GTCATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCAAAACA
1 GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
* * ** * * * *
1036879 ATTATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACT
1 GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
* ** * * * * *
1036933 GTTATTCATCAACTTATGATGAATTCTGTGAATTGCACACTTAGTGTCGAAAC-
1 GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
* ** * * * *
1036986 GTTTATTCATCAATATATGATGAATTCCGTGAATTGCACACTTAGTACCGAAACA
1 G-TCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
* * ** * * * *
1037041 TTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCCTAAACG
1 GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
* ** * ** * *
1037095 GTTATTCATCAACATATGATGAATTTTGTGAATTGCACACTTAGTGCTAAAATA
1 GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
* ** * * *
1037149 GTTATTCATCAACATATGATGAATTCCATGAATTTGCACATTTAGTGCC
1 GTCATTCAAAAACATATGATAAATTCCGTGAA-TTGCACACTTAGTGCC
1037198 TATTTGGTAA
Statistics
Matches: 329, Mismatches: 41, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.00
54 314 0.95
55 14 0.04
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (54 bp):
GTCATTCAAAAACATATGATAAATTCCGTGAATTGCACACTTAGTGCCAAAACA
Found at i:1036940 original size:108 final size:109
Alignment explanation
Indices: 1036781--1037197 Score: 574
Period size: 108 Copynumber: 3.9 Consensus size: 109
1036771 GTCATTCAAA
* * * * *
1036781 AACATATTATAAATTCCGTGATTTGCACACTTAGTGTC-AAAATAGTCATTCATCAACATATGAT
1 AACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAATAGTTATTCATCAACATATGAT
* *
1036845 GAATTCCGTGAATTGCACACTTAGTGCCAAAACAATTATTCATC
66 GAATTCCATGAATTGCACACTTAGTGCCAAAACGATTATTCATC
* * *
1036889 AACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACT-GTTATTCATCAACTTATGAT
1 AACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAATAGTTATTCATCAACATATGAT
** * * *
1036953 GAATTCTGTGAATTGCACACTTAGTGTCGAAACGTTTATTCATC
66 GAATTCCATGAATTGCACACTTAGTGCCAAAACGATTATTCATC
* *
1036997 AATATATGATGAATTCCGTGAATTGCACACTTAGTACCGAAACAT--TTATTCATCAACATATGA
1 AACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAA-ATAGTTATTCATCAACATATGA
* *
1037060 TGAATTCCATGAATTGCACACTTAGTGCCTAAACGGTTATTCATC
65 TGAATTCCATGAATTGCACACTTAGTGCCAAAACGATTATTCATC
** *
1037105 AACATATGATGAATTTTGTGAATTGCACACTTAGTG-CTAAAATAGTTATTCATCAACATATGAT
1 AACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAATAGTTATTCATCAACATATGAT
*
1037169 GAATTCCATGAATTTGCACATTTAGTGCC
66 GAATTCCATGAA-TTGCACACTTAGTGCC
1037198 TATTTGGTAA
Statistics
Matches: 275, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
106 2 0.01
107 4 0.01
108 249 0.91
109 20 0.07
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (109 bp):
AACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAATAGTTATTCATCAACATATGAT
GAATTCCATGAATTGCACACTTAGTGCCAAAACGATTATTCATC
Found at i:1036974 original size:27 final size:27
Alignment explanation
Indices: 1036893--1036975 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
1036883 TTCATCAACA
1036893 TATGATGAATT-TCGTGAATTGCACACT
1 TATGATGAATTCT-GTGAATTGCACACT
** * *
1036920 TAGTGCCGAA-ACTGT-TATT-CATCAACT
1 TA-TGATGAATTCTGTGAATTGCA-C-ACT
1036947 TATGATGAATTCTGTGAATTGCACACT
1 TATGATGAATTCTGTGAATTGCACACT
1036974 TA
1 TA
1036976 GTGTCGAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
25 2 0.05
26 9 0.22
27 18 0.44
28 10 0.24
29 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (27 bp):
TATGATGAATTCTGTGAATTGCACACT
Found at i:1037025 original size:162 final size:161
Alignment explanation
Indices: 1036758--1037197 Score: 596
Period size: 162 Copynumber: 2.7 Consensus size: 161
1036748 AATGCACCCG
* * * ** * * * *
1036758 TAGTGCCTATACGGTCATTCAAAAACATATTATAAATTCCGTGATTTGCACACTTAGTGTCAAAA
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGTCAAAA
*
1036823 -TAGTCATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCAAAACAATTATTCA
66 GT--TTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCAAAACAATTATTCA
* *
1036887 TCAACATATGATGAATTTCGTGAATTGCACACT
129 TCAACATATGATGAATTCCATGAATTGCACACT
* *
1036920 TAGTGCCGAAACTGTTATTCATCAACTTATGATGAATTCTGTGAATTGCACACTTAGTGTCGAAA
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGTC-AAA
* * * * *
1036985 CGTTTATTCATCAATATATGATGAATTCCGTGAATTGCACACTTAGTACCGAAACATTTATTCAT
65 AGTTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCAAAACAATTATTCAT
1037050 CAACATATGATGAATTCCATGAATTGCACACT
130 CAACATATGATGAATTCCATGAATTGCACACT
* * *
1037082 TAGTGCCTAAACGGTTATTCATCAACATATGATGAATTTTGTGAATTGCACACTTAGTGCTAAAA
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTG-TCAAA
* *
1037147 TAG-TTATTCATCAACATATGATGAATTCCATGAATTTGCACATTTAGTGCC
65 -AGTTTATTCATCAACATATGATGAATTCCGTGAA-TTGCACACTTAGTGCC
1037198 TATTTGGTAA
Statistics
Matches: 244, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
162 224 0.92
163 19 0.08
164 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (161 bp):
TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGTCAAAA
GTTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCAAAACAATTATTCATC
AACATATGATGAATTCCATGAATTGCACACT
Found at i:1043779 original size:54 final size:54
Alignment explanation
Indices: 1043697--1044050 Score: 501
Period size: 54 Copynumber: 6.5 Consensus size: 54
1043687 AATGCACTCG
*
1043697 TGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGA
1 TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
*
1043751 TGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGA
1 TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
* ** * * * *
1043805 TGAATTCCGTGAATAACACACTTAGTGTCGAAACTGTTATTCATTAACTTATGA
1 TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
* * * * *
1043859 TGAATTCCGTAAATTGCACACTTAGTGCCAAAACGATTATTCATCAACTTATGA
1 TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
* * *
1043913 TGAATTTCGTGAATTGCACAGTTAGTGTCGAAACAGTTATTCATCAACATATGA
1 TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
* * *
1043967 TAAATTTCGTGAATTACACACTTAGTGTCGAAACGGTTATTCATCAACATATGA
1 TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
* *
1044021 TGAATTTCGTGAATTTTCACATTTAGTGCC
1 TGAATTTCGTGAA-TTGCACACTTAGTGCC
1044051 TATTTGGTAA
Statistics
Matches: 267, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
54 254 0.95
55 13 0.05
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (54 bp):
TGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGA
Found at i:1052787 original size:27 final size:26
Alignment explanation
Indices: 1052741--1052793 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 26
1052731 TAACATATAT
1052741 AATATATATAAAATCA-TTTTGAAAA
1 AATATATATAAAATCATTTTTGAAAA
1052766 AATATATATAATATAT-AGTTTTTGAAAA
1 AATATATATAA-A-ATCA-TTTTTGAAAA
1052794 CATTTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 2 0.08
28 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
AATATATATAAAATCATTTTTGAAAA
Found at i:1052817 original size:40 final size:39
Alignment explanation
Indices: 1052750--1052873 Score: 193
Period size: 40 Copynumber: 3.2 Consensus size: 39
1052740 TAATATATAT
1052750 AAAATCATTTTGAAAAAATATATATAATATATAGTTTTTG
1 AAAA-CATTTTGAAAAAATATATATAATATATAGTTTTTG
1052790 AAAACATTTTGAAAAAAATATATATAATATATAGTTTTTG
1 AAAACATTTTG-AAAAAATATATATAATATATAGTTTTTG
1052830 AAAACATTTTG--AAAATATATAT--TATATAGTTTTTG
1 AAAACATTTTGAAAAAATATATATAATATATAGTTTTTG
*
1052865 AAAATATTT
1 AAAACATTT
1052874 ATATGTATAT
Statistics
Matches: 82, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
35 21 0.26
37 11 0.13
39 7 0.09
40 43 0.52
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (39 bp):
AAAACATTTTGAAAAAATATATATAATATATAGTTTTTG
Found at i:1052891 original size:7 final size:7
Alignment explanation
Indices: 1052879--1052931 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
1052869 TATTTATATG
1052879 TATATTA
1 TATATTA
1052886 TATATTA
1 TATATTA
1052893 TA-A-TA
1 TATATTA
1052898 TAGTATTA
1 TA-TATTA
1052906 TATTATATA
1 TA-TAT-TA
1052915 TATATTA
1 TATATTA
*
1052922 TTTATTA
1 TATATTA
1052929 TAT
1 TAT
1052932 TATTGTGGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.10
6 1 0.03
7 20 0.51
8 10 0.26
9 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:1052907 original size:18 final size:19
Alignment explanation
Indices: 1052872--1052931 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
1052862 TTGAAAATAT
* *
1052872 TTATATGTATATTA-TATA
1 TTATATATATAGTATTATA
1052890 TTATA-ATATAGTATTATA
1 TTATATATATAGTATTATA
*
1052908 TTATATATATATTATT-TA
1 TTATATATATAGTATTATA
1052926 TTATAT
1 TTATAT
1052932 TATTGTGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 6 0.16
18 22 0.59
19 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATATATATAGTATTATA
Found at i:1052912 original size:23 final size:23
Alignment explanation
Indices: 1052879--1052934 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
1052869 TATTTATATG
1052879 TATATTATATATTATAATATAGTAT
1 TATATTATATA-TATAATAT-GTAT
* *
1052904 TATATTATATATATATTATTTAT
1 TATATTATATATATAATATGTAT
1052927 TATATTAT
1 TATATTAT
1052935 TGTGGTCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 11 0.38
24 7 0.24
25 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATTATATATATAATATGTAT
Found at i:1058657 original size:2 final size:2
Alignment explanation
Indices: 1058646--1058722 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
1058636 TAAAGGTGAT
1058646 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1058687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1058723 AAGCTTGAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1058898 original size:99 final size:99
Alignment explanation
Indices: 1058703--1059096 Score: 599
Period size: 99 Copynumber: 4.0 Consensus size: 99
1058693 TATATATATA
* * *
1058703 TATATATATATATATATATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCTAACT
1 TATA-ATATATATACA-ATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACT
*
1058768 TTATGGATAAGATTCAGCTAGCCTGATAAAGGTTAT
64 TTATGGATAAGATTCAGCTAGCCTGATAAAGGTGAT
*
1058804 TATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTT
1 TATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACTTT
* * *
1058869 ATGGATAAGATTCAGCTAGCCTAAAAAAGGCGAT
66 ATGGATAAGATTCAGCTAGCCTGATAAAGGTGAT
* ** * *
1058903 TATAATATATATACATTAAAGCTTGAGTTGTCCCTCTTTATCAATTGGTTAAACGCCCCAGCTTT
1 TATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACTTT
* *
1058968 ATGGATAAGATTTAGCTAACCTGATAAAGGTGAT
66 ATGGATAAGATTCAGCTAGCCTGATAAAGGTGAT
**
1059002 TATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTAAACTTT
1 TATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACTTT
* *
1059067 ATGGATAAGATTCACCTAGCCTGATTAAGG
66 ATGGATAAGATTCAGCTAGCCTGATAAAGG
1059097 AAAATTATAA
Statistics
Matches: 263, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
99 249 0.95
100 10 0.04
101 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (99 bp):
TATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACTTT
ATGGATAAGATTCAGCTAGCCTGATAAAGGTGAT
Found at i:1061388 original size:201 final size:201
Alignment explanation
Indices: 1061043--1061623 Score: 661
Period size: 201 Copynumber: 2.9 Consensus size: 201
1061033 GAAATGTTTG
* * * *
1061043 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCCATAAAAACTTTTGAGTTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGC
** *
1061108 TCGATGACATATCAACCGCATGGTAGAAGCGAGGAACTACTTTCTGGTTGTAGTTTAAACTGAGG
66 TCGATGACATATCAACCGCATGGTAGAAGCGAGGAACTACTTTCTAATTGAAGTTTAAACTGAGG
* * *
1061173 CCTTTAAGTCAAGAATAAGA-GTCGGGTTGGCTACGATTTAGCAACAAGGAACTATATCCTAGTC
131 CCTTTAAGTCAAGAAGAAGACCT-GGGTTGGCTACGATTTAGCAACAAGGAACTATATCCCAGTC
1061237 AAATTTA
195 AAATTTA
* *
1061244 CAGCATAGCTCAAGGCGAGAAGGGTTATCTTTGAACAAAAACCTTCGAGTTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGC
* * * *
1061309 TCGATGACATATCAACTGCATGGTAGTAGCTATGAACTACTTTAC-AATTGAAGTTTAAACTGAG
66 TCGATGACATATCAACCGCATGGTAGAAGCGAGGAACTACTTT-CTAATTGAAGTTTAAACTGAG
* * **
1061373 GTCTTTAAGTCAAGAAGAAGACCTGGGTTGGTTGTGATTTAGCAACAAGGAACTATATCCCAGTC
130 GCCTTTAAGTCAAGAAGAAGACCTGGGTTGGCTACGATTTAGCAACAAGGAACTATATCCCAGTC
1061438 AAATTTA
195 AAATTTA
* * * * * * * *
1061445 CATCATAGCTCAAGGCTAGAAGAGCTATATGTCAACGAAAACCTTCAAGTTCGATTTCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGC
* * * * * *** * * *
1061510 TTGAGGGA-ATATCAACCACAAGGTA-ACATCGAGGAACTACTTTCCGGTTAAATTTTTAAACCG
66 TCGA-TGACATATCAACCGCATGGTAGA-AGCGAGGAACTACTTTCTAATTGAA-GTTTAAACTG
* ** * *
1061573 A-GCTCTTTAA-ACAAAGAAGAAGACCAAGGTTGACTACGATTTGGCAACAAG
128 AGGC-CTTTAAGTC-AAGAAGAAGACCTGGGTTGGCTACGATTTAGCAACAAG
1061624 AGCCACCTTT
Statistics
Matches: 319, Mismatches: 53, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
200 1 0.00
201 268 0.84
202 50 0.16
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (201 bp):
CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGC
TCGATGACATATCAACCGCATGGTAGAAGCGAGGAACTACTTTCTAATTGAAGTTTAAACTGAGG
CCTTTAAGTCAAGAAGAAGACCTGGGTTGGCTACGATTTAGCAACAAGGAACTATATCCCAGTCA
AATTTA
Found at i:1061964 original size:2 final size:2
Alignment explanation
Indices: 1061957--1062014 Score: 54
Period size: 2 Copynumber: 30.5 Consensus size: 2
1061947 GTTCTATTTA
*
1061957 AT AT AT AT A- AT AT AT AT AT AT A- AT CAT -T TT GA- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT
1061997 AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1062015 GTTTTTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
1 5 0.10
2 41 0.85
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1062083 original size:39 final size:39
Alignment explanation
Indices: 1061997--1062264 Score: 334
Period size: 39 Copynumber: 6.8 Consensus size: 39
1061987 GAATATATAT
*
1061997 ATATATATATAATATATAGTTTTTTAAAACATTTTGAAAAC
1 ATATATATAT-A-ATATAGTTTTTGAAAACATTTTGAAAAC
*
1062038 ATATATATATATAATATAGTTTTTGAAAATATTTTGAAAAC
1 --ATATATATATAATATAGTTTTTGAAAACATTTTGAAAAC
1062079 ATATATATA-ATATATAGTTTTTGAAAACATTTTGAAAAC
1 ATATATATATA-ATATAGTTTTTGAAAACATTTTGAAAAC
1062118 ATATATATAATAA-ATAGTTTTTGAAAACATTTTGAAAA-
1 ATATATAT-ATAATATAGTTTTTGAAAACATTTTGAAAAC
1062156 ATATATATATAAAATATAGTTTTTGAAAACATTTTGAAAAC
1 ATATATATAT--AATATAGTTTTTGAAAACATTTTGAAAAC
**
1062197 ATATATATA-ATATATAGTTTTTG-AAATTTTTTG-AAA-
1 ATATATATATA-ATATAGTTTTTGAAAACATTTTGAAAAC
* * * *
1062233 ATATATATATTATATTGTTTTGGAAAATATTT
1 ATATATATATAATATAGTTTTTGAAAACATTT
1062265 ATATTTATAT
Statistics
Matches: 206, Mismatches: 9, Indels: 26
0.85 0.04 0.11
Matches are distributed among these distances:
36 19 0.09
37 12 0.06
38 18 0.09
39 83 0.40
40 27 0.13
41 36 0.17
42 1 0.00
43 10 0.05
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (39 bp):
ATATATATATAATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:1062191 original size:79 final size:78
Alignment explanation
Indices: 1061997--1062264 Score: 407
Period size: 79 Copynumber: 3.4 Consensus size: 78
1061987 GAATATATAT
*
1061997 ATATATATATAATATATAGTTTTTTAAAACATTTTGAAAACATATATATATATAATATAGTTTTT
1 ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATA-ATAA-ATAGTTTTT
1062062 GAAAATATTTTGAAA
64 GAAAATATTTTGAAA
*
1062077 ACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATAAATAGTTTTTGA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATAAATAGTTTTTGA
*
1062142 AAACATTTTGAAAA
66 AAATATTTTG-AAA
* *
1062156 ATATATATATAAAATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATATAGTTTTTG-
1 ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATAAATAGTTTTTGA
*
1062220 AAATTTTTTGAAA
66 AAATATTTTGAAA
* * *
1062233 ATATATATAT--TATATTGTTTTGGAAAATATTT
1 ATATATATATAATATATAGTTTTTGAAAACATTT
1062265 ATATTTATAT
Statistics
Matches: 175, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
75 18 0.10
77 13 0.07
78 28 0.16
79 68 0.39
80 48 0.27
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (78 bp):
ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATAAATAGTTTTTGA
AAATATTTTGAAA
Found at i:1062260 original size:26 final size:27
Alignment explanation
Indices: 1062224--1062274 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1062214 TTTTTGAAAT
*
1062224 TTTTTGAAAATATATATA-TTATATTG
1 TTTTGGAAAATATATATATTTATATTG
*
1062250 TTTTGGAAAATATTTATATTTATAT
1 TTTTGGAAAATATATATATTTATAT
1062275 GTATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (27 bp):
TTTTGGAAAATATATATATTTATATTG
Found at i:1062279 original size:12 final size:12
Alignment explanation
Indices: 1062259--1062325 Score: 61
Period size: 11 Copynumber: 5.7 Consensus size: 12
1062249 GTTTTGGAAA
*
1062259 ATATTTATATTT
1 ATATATATATTT
*
1062271 ATATGTATA-TT
1 ATATATATATTT
1062282 ATATA-ATATATT
1 ATATATATAT-TT
1062294 ATAGTATTATATTT
1 ATA-TA-TATATTT
1062308 ATATAT-TATTT
1 ATATATATATTT
1062319 AT-TATAT
1 ATATATAT
1062326 TATTGTGGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 6 0.13
11 14 0.30
12 14 0.30
13 4 0.09
14 5 0.11
15 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
ATATATATATTT
Found at i:1062303 original size:8 final size:7
Alignment explanation
Indices: 1062259--1062325 Score: 65
Period size: 7 Copynumber: 10.3 Consensus size: 7
1062249 GTTTTGGAAA
1062259 ATATT-T
1 ATATTAT
1062265 ATATT-T
1 ATATTAT
*
1062271 ATA-TGT
1 ATATTAT
1062277 ATATTAT
1 ATATTAT
1062284 ATA--AT
1 ATATTAT
1062289 ATATTAT
1 ATATTAT
1062296 AGTATTAT
1 A-TATTAT
1062304 AT-TTAT
1 ATATTAT
1062310 ATATTAT
1 ATATTAT
*
1062317 TTATTAT
1 ATATTAT
1062324 AT
1 AT
1062326 TATTGTGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
5 6 0.12
6 19 0.37
7 20 0.38
8 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (7 bp):
ATATTAT
Found at i:1062303 original size:20 final size:19
Alignment explanation
Indices: 1062278--1062325 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1062268 TTTATATGTA
1062278 TATTATATAATATATTATAG
1 TATTATATAATATATTAT-G
* *
1062298 TATTATATTTATATATTATT
1 TATTATA-TAATATATTATG
1062318 TATTATAT
1 TATTATAT
1062326 TATTGTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 14 0.56
21 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATTATATAATATATTATG
Found at i:1062326 original size:12 final size:11
Alignment explanation
Indices: 1062260--1062329 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 11
1062250 TTTTGGAAAA
1062260 TATTTATAT-T
1 TATTTATATAT
* *
1062270 TATATGTATAT
1 TATTTATATAT
*
1062281 TATATAATATAT
1 TAT-TTATATAT
*
1062293 TATAGTAT-TA-
1 TAT-TTATATAT
1062303 TATTTATATAT
1 TATTTATATAT
1062314 TATTTATTATAT
1 TATTTA-TATAT
1062326 TATT
1 TATT
1062330 GTGGTTTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
9 3 0.06
10 12 0.26
11 12 0.26
12 20 0.43
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (11 bp):
TATTTATATAT
Found at i:1073935 original size:16 final size:16
Alignment explanation
Indices: 1073916--1073953 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1073906 ATATATGTCA
1073916 ATTTTACTTAGAAAAC
1 ATTTTACTTAGAAAAC
1073932 ATTTTACTTAGAAAAC
1 ATTTTACTTAGAAAAC
1073948 ATTTTA
1 ATTTTA
1073954 AAATCATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTTTACTTAGAAAAC
Found at i:1076488 original size:12 final size:12
Alignment explanation
Indices: 1076471--1076587 Score: 60
Period size: 11 Copynumber: 10.6 Consensus size: 12
1076461 TTTTTATTAC
1076471 ATTATTATTAAT
1 ATTATTATTAAT
1076483 ATTATT-TTAAT
1 ATTATTATTAAT
* *
1076494 -TATACTGTT-AT
1 AT-TATTATTAAT
**
1076505 -TT-TTATTTTT
1 ATTATTATTAAT
1076515 A-TATTATTAAT
1 ATTATTATTAAT
1076526 ATTATT-TTAAT
1 ATTATTATTAAT
* *
1076537 -TATACTGTT-AT
1 AT-TATTATTAAT
**
1076548 -TT-TTATTTTT
1 ATTATTATTAAT
1076558 A-TATTATTAAT
1 ATTATTATTAAT
1076569 ATTATTATTAAT
1 ATTATTATTAAT
1076581 ATTATTA
1 ATTATTA
1076588 ATACTATTAC
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
9 6 0.07
10 8 0.10
11 36 0.44
12 31 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:1076505 original size:20 final size:20
Alignment explanation
Indices: 1076482--1076548 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
1076472 TTATTATTAA
1076482 TATTATTTTAATTATACTGT
1 TATTATTTTAATTATACTGT
**
1076502 TATTTTTATTTTTATATTAT--TAA
1 TA---TTA-TTTTA-ATTATACTGT
1076525 TATTATTTTAATTATACTGT
1 TATTATTTTAATTATACTGT
1076545 TATT
1 TATT
1076549 TTTATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
18 5 0.14
19 5 0.14
20 10 0.28
23 6 0.17
24 5 0.14
25 5 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTATTTTAATTATACTGT
Found at i:1076508 original size:43 final size:43
Alignment explanation
Indices: 1076473--1076580 Score: 207
Period size: 43 Copynumber: 2.5 Consensus size: 43
1076463 TTTATTACAT
1076473 TATTATTAATATTATTTTAATTATACTGTTATTTTTATTTTTA
1 TATTATTAATATTATTTTAATTATACTGTTATTTTTATTTTTA
1076516 TATTATTAATATTATTTTAATTATACTGTTATTTTTATTTTTA
1 TATTATTAATATTATTTTAATTATACTGTTATTTTTATTTTTA
1076559 TATTATTAATATTATTATTAAT
1 TATTATTAATATTATT-TTAAT
1076581 ATTATTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 59 0.92
44 5 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (43 bp):
TATTATTAATATTATTTTAATTATACTGTTATTTTTATTTTTA
Found at i:1076559 original size:20 final size:20
Alignment explanation
Indices: 1076493--1076560 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
1076483 ATTATTTTAA
1076493 TTATACTGTTATTTTTATTT
1 TTATACTGTTATTTTTATTT
* * * *
1076513 TTATATTATTAATATTATTTT
1 TTATACTGTTATTTTTA-TTT
1076534 AATTATACTGTTATTTTTATTT
1 --TTATACTGTTATTTTTATTT
1076556 TTATA
1 TTATA
1076561 TTATTAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 3 0.08
23 13 0.35
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
TTATACTGTTATTTTTATTT
Found at i:1076595 original size:12 final size:11
Alignment explanation
Indices: 1076514--1076596 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
1076504 TTTTTATTTT
1076514 TATATTATTAA
1 TATATTATTAA
1076525 TATTATT-TTAA
1 TA-TATTATTAA
* *
1076536 TTATACTGTT-A
1 -TATATTATTAA
* **
1076547 T-TTTTATTTT
1 TATATTATTAA
1076557 TATATTATTAA
1 TATATTATTAA
1076568 TATTATTATT-A
1 TA-TATTATTAA
1076579 -ATATTATTAA
1 TATATTATTAA
1076589 TACTATTA
1 TA-TATTA
1076597 CAAGCCCAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
9 11 0.20
10 4 0.07
11 20 0.36
12 20 0.36
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (11 bp):
TATATTATTAA
Found at i:1077852 original size:20 final size:20
Alignment explanation
Indices: 1077827--1077915 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
1077817 CAATATTTTG
1077827 TTATTACTTTTATATTTTAA
1 TTATTACTTTTATATTTTAA
*
1077847 TTATTA-TTTTA-ATTATTAT
1 TTATTACTTTTATATT-TTAA
**
1077866 TTATTTAC-AATATTATTTT-A
1 TTA-TTACTTTTA-TATTTTAA
1077886 TTATTACTTTTATATTTTAA
1 TTATTACTTTTATATTTTAA
*
1077906 TTATTTCTTT
1 TTATTACTTT
1077916 AATTATTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
18 3 0.05
19 21 0.38
20 26 0.47
21 2 0.04
22 3 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTACTTTTATATTTTAA
Found at i:1077854 original size:12 final size:12
Alignment explanation
Indices: 1077839--1077936 Score: 84
Period size: 12 Copynumber: 8.3 Consensus size: 12
1077829 ATTACTTTTA
1077839 TATTTTAATTAT
1 TATTTTAATTAT
1077851 TATTTTAATTAT
1 TATTTTAATTAT
*
1077863 TATTTATTTACAATAT
1 TA--T-TTTA-ATTAT
1077879 TATTTT-ATTAT
1 TATTTTAATTAT
*
1077890 TA-CTT--TTA-
1 TATTTTAATTAT
1077898 TATTTTAATTAT
1 TATTTTAATTAT
1077910 T-TCTTTAATTAT
1 TAT-TTTAATTAT
1077922 TATTTT-ATTAT
1 TATTTTAATTAT
1077933 TATT
1 TATT
1077937 ATCTTAGTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.03
9 5 0.07
10 2 0.03
11 19 0.26
12 28 0.39
13 4 0.06
14 2 0.03
15 4 0.06
16 6 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:1077910 original size:40 final size:40
Alignment explanation
Indices: 1077839--1077936 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 40
1077829 ATTACTTTTA
*
1077839 TATTTTAATTATTATTTTAATTATTATTTATTTAC-AA-TAT
1 TATTTT-ATTATTATTTTAATTATTAATTATTT-CTAATTAT
1077879 TATTTTATTATTACTTTTATATT-TTAATTATTTCTTTAATTAT
1 TATTTTATTATTA-TTTTA-ATTATTAATTATTTC--TAATTAT
1077922 TATTTTATTATTATT
1 TATTTTATTATTATT
1077937 ATCTTAGTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
39 8 0.16
40 20 0.39
41 3 0.06
42 4 0.08
43 16 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (40 bp):
TATTTTATTATTATTTTAATTATTAATTATTTCTAATTAT
Found at i:1077959 original size:59 final size:58
Alignment explanation
Indices: 1077829--1077947 Score: 136
Period size: 59 Copynumber: 2.0 Consensus size: 58
1077819 ATATTTTGTT
* * *
1077829 ATTACTTTTATATTTTAATTATTATTTTAATTATTATTTATTTACAATATTATTTTATT
1 ATTACTTATATATTTTAATTATTATTTTAATTATTATTTATTTA-AATATTATCTTATC
* *
1077888 ATTACTTTTATATTTTAATTATT-TCTTTAATTATTATTT-TATT-ATTATTATCTTAGTC
1 ATTACTTATATATTTTAATTATTAT-TTTAATTATTATTTAT-TTAAATATTATCTTA-TC
1077946 AT
1 AT
1077948 ATATATATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
57 10 0.19
58 5 0.09
59 39 0.72
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (58 bp):
ATTACTTATATATTTTAATTATTATTTTAATTATTATTTATTTAAATATTATCTTATC
Found at i:1078373 original size:2 final size:2
Alignment explanation
Indices: 1078366--1078431 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
1078356 AAAAATAAAG
1078366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1078408 AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1078432 TTTTTATTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 60 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1083554 original size:72 final size:72
Alignment explanation
Indices: 1083465--1083599 Score: 234
Period size: 72 Copynumber: 1.9 Consensus size: 72
1083455 ATACAATAAA
1083465 GCTTGAATTATCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAGT
1 GCTTGAATTATCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAGT
1083530 TTGTTAT
66 TTGTTAT
* * * *
1083537 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCCGACTTTATGGATAATATTCAGCTA
1 GCTTGAATTATCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTA
1083600 ACCTATTATA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (72 bp):
GCTTGAATTATCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAGT
TTGTTAT
Done.