Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3086932 original size:21 final size:21
Alignment explanation
Indices: 3086899--3086956 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3086889 ATATAATTTA
*
3086899 TAGTTTATATTATTTTATTAT
1 TAGTTTATTTTATTTTATTAT
* *
3086920 TAGTATATTTTATTTTTTTAT
1 TAGTTTATTTTATTTTATTAT
3086941 TCA-TTTATTTTATTTT
1 T-AGTTTATTTTATTTT
3086957 GTTTTGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (21 bp):
TAGTTTATTTTATTTTATTAT
Found at i:3087966 original size:18 final size:17
Alignment explanation
Indices: 3087926--3087970 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3087916 ATTTTTCAGT
*
3087926 ATTTAATTTTTTATTTCA
1 ATTT-ATTTTTTATTCCA
*
3087944 TTTTATTTTTTATTCCAA
1 ATTTATTTTTTATTCC-A
3087962 ATTTATTTT
1 ATTTATTTT
3087971 GGTTTGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTATTTTTTATTCCA
Found at i:3088041 original size:18 final size:18
Alignment explanation
Indices: 3087992--3088047 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
3087982 TCATATTTTC
3087992 ATTATTATTTTTTATCTA-T
1 ATTA-TATTTTTTAT-TATT
3088011 ATT-TATTTATTTTATTATT
1 ATTATA-TT-TTTTATTATT
*
3088030 ATTATATTTTTTAATATT
1 ATTATATTTTTTATTATT
3088048 GTTTTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 2 0.06
18 13 0.41
19 15 0.47
20 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTATATTTTTTATTATT
Found at i:3090721 original size:28 final size:28
Alignment explanation
Indices: 3090689--3090755 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
3090679 TTTTAAGAGT
*
3090689 GATGCACCGATGCACCAATCCATGCATC
1 GATGCACCGATACACCAATCCATGCATC
3090717 GATGCACCGATACACCAATCCATGCATC
1 GATGCACCGATACACCAATCCATGCATC
3090745 GATGCACCGAT
1 GATGCACCGAT
3090756 TAATTTTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (28 bp):
GATGCACCGATACACCAATCCATGCATC
Found at i:3090824 original size:45 final size:46
Alignment explanation
Indices: 3090775--3090862 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
3090765 AAATATCGAA
* * *
3090775 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
*
3090820 TGCATTTGATGCATCGATGCACAAGATCATGAATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACT
3090863 AGCCTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
Found at i:3096411 original size:23 final size:23
Alignment explanation
Indices: 3096336--3096416 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
3096326 ACACTTAACA
*
3096336 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
3096358 GTGCATCGATTCAC-CAC--GAAG
1 GTGCATCGATGCACAC-CTTGAAT
* *
3096379 GTGTACCGATGCACACCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
3096402 GTGCATCGATGCACA
1 GTGCATCGATGCACA
3096417 AGGCCATGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
21 15 0.33
22 14 0.30
23 17 0.37
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:3098176 original size:20 final size:20
Alignment explanation
Indices: 3098147--3098184 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3098137 TTTAAGAGAG
3098147 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
3098167 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
3098185 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:3098287 original size:46 final size:43
Alignment explanation
Indices: 3098204--3098299 Score: 131
Period size: 46 Copynumber: 2.2 Consensus size: 43
3098194 AAACATCGAA
*
3098204 TGCATTTTGCATCGATGCACATACCATGCATCGATGCACTCAG
1 TGCATTTTGCATCGATGCACAGACCATGCATCGATGCACTCAG
*
3098247 TGCATTTGATGCATCGATGCACAAGATCATGCATCGATGCACTCA-
1 TGCATTT--TGCATCGATGCAC-AGACCATGCATCGATGCACTCAG
*
3098292 TGCTTTTT
1 TGCATTTT
3098300 CAAAACATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 8 0.17
45 19 0.40
46 20 0.43
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
TGCATTTTGCATCGATGCACAGACCATGCATCGATGCACTCAG
Found at i:3100269 original size:95 final size:95
Alignment explanation
Indices: 3100158--3100350 Score: 305
Period size: 95 Copynumber: 2.0 Consensus size: 95
3100148 ATATTATATG
3100158 TATACAATAAAACTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
1 TATACAATAAAACTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
3100223 ATTCAGCTAGCCTGATAAAGGCGATTATAA
66 ATTCAGCTAGCCTGATAAAGGCGATTATAA
* ** * * *
3100253 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAACTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
* * *
3100318 ATTCAGCTAGCCTGATAAATGTGCTTATAA
66 ATTCAGCTAGCCTGATAAAGGCGATTATAA
3100348 TAT
1 TAT
3100351 TAAGTTGTCC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (95 bp):
TATACAATAAAACTTGAACTGACCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
ATTCAGCTAGCCTGATAAAGGCGATTATAA
Found at i:3101664 original size:84 final size:84
Alignment explanation
Indices: 3101521--3103057 Score: 1635
Period size: 84 Copynumber: 18.5 Consensus size: 84
3101511 AAAAAAACTA
* * * * *
3101521 TTGCAGCATAACTCAAGGCGAAAAGGG-TATCTGTCAA-CAAAGTCCTTCGAGTTCGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
3101584 CAGCTCAAAGGCACATCAT
66 CAGCTCAAAGGCACATCAT
* * * * * * *
3101603 TTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
*
3101668 CAGCTCAAGGGCACATCAT
66 CAGCTCAAAGGCACATCAT
* * * * *
3101687 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ATCAAAGACCTTCGAGTTCGATTCCACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* *
3101751 CAACTCAAAGGTACATCAT
66 CAGCTCAAAGGCACATCAT
* * ** * *
3101770 TTGCAGCATAGCTTAATTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* *
3101835 CAG-TGCAAGGGCACAACAT
66 CAGCT-CAAAGGCACATCAT
* * * * * * **
3101854 TTGCATCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGATTTTGACTATGCT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
** *
3101919 CAGCTCTGAGGCATATCAT
66 CAGCTCAAAGGCACATCAT
* * * * *
3101938 TTACAGCATAACTCAAGGCTATAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTTGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
**
3102002 CAGCTCAAACACACATCAT
66 CAGCTCAAAGGCACATCAT
* **
3102021 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACGTT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* *
3102086 CAGCTCAAAGACATATCAT
66 CAGCTCAAAGGCACATCAT
* * *
3102105 TTCCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
*
3102170 CAGCTCCAAGGCACATCAT
66 CAGCTCAAAGGCACATCAT
* * * * * * *
3102189 TTGTAGCATAGCTCAAGGCTAGAAGGGCTATCTGCC-ACTAAAAAACCTTCGAGATCGACTACGC
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-CAAAGACCTTCGAGTTCGACTACAC
*
3102253 TCAGCTCAAAGGCATATCAT
65 TCAGCTCAAAGGCACATCAT
**
3102273 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* *
3102338 CAGCTCCAAGGTACATCAT
66 CAGCTCAAAGGCACATCAT
* * * *
3102357 TTGCAGCATAACTCGAGGCTAGAAGGGCTATTTGCC-ACCAAAAGACCTTCGAGTTCGACTACGC
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACAC
* * *
3102421 TCAACTCCAAGGCATATCAT
65 TCAGCTCAAAGGCACATCAT
* ** **
3102441 TTGAAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGACTATGCT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* *
3102506 CAGCTCCAAGGCACATTAT
66 CAGCTCAAAGGCACATCAT
* * * * * * *
3102525 TTGTAGCATAGCTCAAGGCTATAAGGGTTATCTACC-ACCAAAAGACCTTTGAGTTCGGCTACGC
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACAC
*
3102589 TCAGCTCCAAGGCACATCAT
65 TCAGCTCAAAGGCACATCAT
* * * * * * * * *
3102609 TTGCAACATAGCTCAAAGCAAAAAGGGTTATTTGCTAACAAAAGACCTTCGAGTTCGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* * *
3102674 CAGCTTCGAGGGCACACCAT
66 CAGC-TCAAAGGCACATCAT
* * * * * * *
3102694 TTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAA-CAAAAACCTTTGAGTTCGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
*
3102758 CAGCTCAACGGCACATCAT
66 CAGCTCAAAGGCACATCAT
* * * * * * *
3102777 TTGTAGTATAGCTCAAGGCTAGAAGGGCTATCTG-C-A--AAAGACCCTCAAGTTCGATTACACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* *
3102838 CAGCTACGAGGGCACATCAT
66 CAGCT-CAAAGGCACATCAT
* * * * *
3102858 TTACAGCATAACCCAAGGCTAGAAGGGTTATAT----ATCAAAGACCTTCGAGTTCGACTCCACT
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
3102919 CAGCTCAAAGGCACCATCAT
66 CAGCTCAAAGGCA-CATCAT
* * *
3102939 TTGCAGCATAGA-TCAAGG-TAAGAATGGTTATCTG----CCAAAGACCTTCGAGTTCGATTCCA
1 TTGCAGCATA-ACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
* *
3102998 CTCAGCTTAAAGGCACCATAAT
64 CTCAGCTCAAAGGCA-CATCAT
* * * *
3103020 TTACAGCATAGCTCAAGGCAATAAGGGTTATCTGCCAA
1 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
3103058 AAAAGTTATC
Statistics
Matches: 1228, Mismatches: 201, Indels: 49
0.83 0.14 0.03
Matches are distributed among these distances:
79 1 0.00
80 33 0.03
81 166 0.14
82 24 0.02
83 196 0.16
84 761 0.62
85 47 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
CAGCTCAAAGGCACATCAT
Found at i:3103736 original size:36 final size:34
Alignment explanation
Indices: 3103647--3104065 Score: 366
Period size: 36 Copynumber: 11.7 Consensus size: 34
3103637 AGTTAGAAGT
3103647 CATTTTG-AAATTATATAATATATAGTCTTTTAAAAATA
1 CATTTTGAAAATTATATAATATATA-T-TTTT--AAA-A
*
3103685 CATTTTG-AAAGTATATAATATATGATTTTTAAAA
1 CATTTTGAAAATTATATAATATAT-ATTTTTAAAA
* * *
3103719 CATTTTGAAAACTTATATAATGTATAGTTTTGAAAT
1 CATTTTGAAAA-TTATATAATATATA-TTTTTAAAA
3103755 CATTTTGAAAATATATATAATATATAATTTTTAAAA
1 CATTTTGAAAAT-TATATAATATAT-ATTTTTAAAA
* *
3103791 CATTTTTGAAAACTTATATAATATATAGTTTTGAAAT
1 CA-TTTTGAAAA-TTATATAATATATA-TTTTTAAAA
*
3103828 CATTTTGAAAACTTATATAATATA-GTTTTTAAAA
1 CATTTTGAAAA-TTATATAATATATATTTTTAAAA
**
3103862 CATTTTTGAAAACTTATATAATATAGT-TTTAAAAAA
1 CA-TTTTGAAAA-TTATATAATATA-TATTTTTAAAA
* *
3103898 CATTTTTGAAAAATTATAT-ATATATAGTTTAAAAA
1 CA-TTTTG-AAAATTATATAATATATATTTTTAAAA
* *
3103933 CATTTTTGAAAAATTATATAGTATATAGTTTTAAAA
1 CA-TTTTG-AAAATTATATAATATATATTTTTAAAA
*
3103969 TCATTTTGAAAACTTATATAATATATAGTTTTGAAAA
1 -CATTTTGAAAA-TTATATAATATATA-TTTTTAAAA
* * *
3104006 CTTTTTTTAAAA--ATATAATATATAGTTTTAAAAA
1 C-ATTTTGAAAATTATATAATATATA-TTTTTAAAA
* * *
3104040 TATTTTTAAAATATATATAATTTATA
1 CATTTTGAAAAT-TATATAATATATA
3104066 GTTTATTTTA
Statistics
Matches: 331, Mismatches: 28, Indels: 46
0.82 0.07 0.11
Matches are distributed among these distances:
33 9 0.03
34 39 0.12
35 65 0.20
36 137 0.41
37 56 0.17
38 24 0.07
39 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
CATTTTGAAAATTATATAATATATATTTTTAAAA
Found at i:3103885 original size:71 final size:72
Alignment explanation
Indices: 3103649--3104069 Score: 478
Period size: 71 Copynumber: 5.9 Consensus size: 72
3103639 TTAGAAGTCA
*
3103649 TTTTG-AAA-TTATATAATATATAGTCTTTTAAAAATACATTTTG-AAAGTATATA-ATATATGA
1 TTTTGAAAACTTATATAATATATAG--TTTTAAAAAT-CATTTTGAAAATTATATATATATA-G-
3103710 TTTTTAAAACA-
61 TTTTTAAAACAT
* * *
3103721 TTTTGAAAACTTATATAATGTATAGTTTT-GAAATCATTTTGAAAATATATATAATATATAATTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAAT-TATAT-ATATATAGTTT
3103785 TTAAAACAT
64 TTAAAACAT
*
3103794 TTTTGAAAACTTATATAATATATAGTTTT-GAAATCATTTTGAAAACTTATATA-ATATAGTTTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAA-TTATATATATATAGTTTT
3103857 TAAAACAT
65 TAAAACAT
*
3103865 TTTTGAAAACTTATAT-A-ATATAGTTTTAAAAAACATTTTTGAAAAATTATATATATATAG-TT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCA-TTTTG-AAAATTATATATATATAGTTT
*
3103927 TAAAAACAT
64 TTAAAACAT
* *
3103936 TTTTGAAAAATTATATAGTATATAGTTTT-AAAATCATTTTGAAAACTTATATAATATATAGTTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAA-TTATAT-ATATATAGTTT
* *
3104000 TGAAAACTT
64 TTAAAACAT
* * *
3104009 TTTTTAAAA---ATATAATATATAGTTTTAAAAAT-ATTTTTAAAATATATATAATTTATAGTTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAAT-TATAT-ATATATAGTTT
3104070 ATTTTATTTT
Statistics
Matches: 312, Mismatches: 18, Indels: 40
0.84 0.05 0.11
Matches are distributed among these distances:
69 11 0.04
70 58 0.19
71 93 0.30
72 50 0.16
73 80 0.26
74 20 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (72 bp):
TTTTGAAAACTTATATAATATATAGTTTTAAAAATCATTTTGAAAATTATATATATATAGTTTTT
AAAACAT
Found at i:3104011 original size:107 final size:109
Alignment explanation
Indices: 3103625--3104069 Score: 462
Period size: 107 Copynumber: 4.2 Consensus size: 109
3103615 TTTATATATA
* *
3103625 TATATATTATATAG--TTAGAAGTCATTTTG-AAATTATATAATATATAGTCTTTTAAAAATACA
1 TATATAATATATAGTTTTA-AAATCATTTTGAAAATTATATAATATATAG--TTTTAAAAA-ACA
* * *
3103687 -TTTTG--AAAGTATATAATATAT-GATTTTTAAAACATTTTGAAAACT
62 TTTTTGAAAAATTATATAATATATAG-TTTTAAAAACATTTTGAAAAAT
* * * *
3103732 TATATAATGTATAGTTTTGAAATCATTTTGAAAATATATATAATATATAATTTT-TAAAACATTT
1 TATATAATATATAGTTTTAAAATCATTTTGAAAAT-TATATAATATATAGTTTTAAAAAACATTT
* * * *
3103796 TTGAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAACT
65 TTGAAAAATTATATAATATATAGTTTTAAAAACATTTTGAAAAAT
3103841 TATAT-A-ATATAGTTTTTAAAA-CATTTTTGAAAACTTATAT-A-ATATAGTTTTAAAAAACAT
1 TATATAATATATAG-TTTTAAAATCA-TTTTGAAAA-TTATATAATATATAGTTTTAAAAAACAT
3103901 TTTTGAAAAATTATAT-ATATATAG-TTTAAAAACATTTTTGAAAAAT
63 TTTTGAAAAATTATATAATATATAGTTTTAAAAACA-TTTTGAAAAAT
* *
3103947 TATATAGTATATAGTTTTAAAATCATTTTGAAAACTTATATAATATATAGTTTT-GAAAAC-TTT
1 TATATAATATATAGTTTTAAAATCATTTTGAAAA-TTATATAATATATAGTTTTAAAAAACATTT
** * *
3104010 TTTTAAAA--ATATAATATATAGTTTTAAAAATATTTT-TAAAAT
65 TTGAAAAATTATATAATATATAGTTTTAAAAACATTTTGAAAAAT
*
3104052 ATATATAATTTATAGTTT
1 -TATATAATATATAGTTT
3104070 ATTTTATTTT
Statistics
Matches: 291, Mismatches: 26, Indels: 43
0.81 0.07 0.12
Matches are distributed among these distances:
105 17 0.06
106 62 0.21
107 92 0.32
108 50 0.17
109 56 0.19
110 14 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (109 bp):
TATATAATATATAGTTTTAAAATCATTTTGAAAATTATATAATATATAGTTTTAAAAAACATTTT
TGAAAAATTATATAATATATAGTTTTAAAAACATTTTGAAAAAT
Found at i:3105236 original size:17 final size:17
Alignment explanation
Indices: 3105210--3105252 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3105200 ATTTTTCAGT
* *
3105210 ATTTAATTTTTATTTCA
1 ATTTATTTTTTATTCCA
*
3105227 TTTTATTTTTTATTCCA
1 ATTTATTTTTTATTCCA
3105244 ATTTATTTT
1 ATTTATTTT
3105253 GGTTTGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTATTTTTTATTCCA
Found at i:3105303 original size:25 final size:24
Alignment explanation
Indices: 3105229--3105320 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 24
3105219 TTATTTCATT
* *
3105229 TTATTTTTTATTCCAATTTATTTTGG
1 TTATTTTTTATT-CTATTTATTTT-A
* *
3105255 TT-TGTTTTATTGTATTT-TTATTA
1 TTATTTTTTATTCTATTTATT-TTA
3105278 TTATTTTTTATCTCTATTTATTTTA
1 TTATTTTTTAT-TCTATTTATTTTA
3105303 TTATTTTATTATT-TATTT
1 TTATTTT-TTATTCTATTT
3105321 TATATTTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
23 4 0.07
24 18 0.33
25 25 0.45
26 8 0.15
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (24 bp):
TTATTTTTTATTCTATTTATTTTA
Found at i:3105329 original size:20 final size:20
Alignment explanation
Indices: 3105261--3105328 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
3105251 TTGGTTTGTT
*
3105261 TTATTGTATT-TTTATTATTA
1 TTATTTTATTATTTATT-TTA
3105281 TT-TTTTATCTCTATTTATTTTA
1 TTATTTTA--T-TATTTATTTTA
3105303 TTATTTTATTATTTATTTTA
1 TTATTTTATTATTTATTTTA
3105323 -TATTTT
1 TTATTTT
3105329 TCCTTTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
19 10 0.24
20 13 0.31
21 2 0.05
22 6 0.14
23 11 0.26
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (20 bp):
TTATTTTATTATTTATTTTA
Found at i:3107437 original size:15 final size:15
Alignment explanation
Indices: 3107417--3107446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3107407 ACTTTTTGAT
*
3107417 AATTTAGGGTTCATC
1 AATTTAAGGTTCATC
3107432 AATTTAAGGTTCATC
1 AATTTAAGGTTCATC
3107447 GATTGTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (15 bp):
AATTTAAGGTTCATC
Found at i:3107657 original size:24 final size:25
Alignment explanation
Indices: 3107605--3107657 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
3107595 AATTATGGTG
* *
3107605 TTTTCTTAAAAAAAGAATTTTTAAG
1 TTTTCTTAAAAAAAGAATTTTGAAA
* *
3107630 TTTTTTTAAATAAA-AATTTTGAAA
1 TTTTCTTAAAAAAAGAATTTTGAAA
3107654 TTTT
1 TTTT
3107658 ATAAATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTCTTAAAAAAAGAATTTTGAAA
Found at i:3119051 original size:29 final size:29
Alignment explanation
Indices: 3119009--3119076 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
3118999 TTAATACAAC
*
3119009 CATTCAACGCTGAATGTTGAACTGTTTAT
1 CATTCAGCGCTGAATGTTGAACTGTTTAT
*
3119038 CATTCAGCGTTGAATGTTGAACTGTTTAT
1 CATTCAGCGCTGAATGTTGAACTGTTTAT
3119067 CATTCAGCGC
1 CATTCAGCGC
3119077 CTTTGTTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (29 bp):
CATTCAGCGCTGAATGTTGAACTGTTTAT
Found at i:3119277 original size:2 final size:2
Alignment explanation
Indices: 3119270--3119298 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3119260 GGGTCAGCTA
3119270 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
3119299 ATTTTGAAAT
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:3127048 original size:22 final size:22
Alignment explanation
Indices: 3127022--3127082 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
3127012 ATAGGGCAGA
3127022 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
3127044 GGGAACCGATTCCCACTTTGAAG
1 GGGAATCGATACCC-CCTTGAAG
3127067 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
3127083 CACGGGTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:3129241 original size:2 final size:2
Alignment explanation
Indices: 3129234--3129260 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3129224 CCAACTTAAG
3129234 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 A
3129261 ATCAATTGGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3136353 original size:10 final size:10
Alignment explanation
Indices: 3136337--3136372 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3136327 ATGTTAAGAT
*
3136337 AAAATATATT
1 AAAATATATA
*
3136347 TAAATATATA
1 AAAATATATA
3136357 AAAATATATA
1 AAAATATATA
3136367 AAAATA
1 AAAATA
3136373 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATATA
Found at i:3136362 original size:20 final size:20
Alignment explanation
Indices: 3136337--3136393 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
3136327 ATGTTAAGAT
3136337 AAAATATATTTAAATATATA
1 AAAATATATTTAAATATATA
*
3136357 AAAATATA--TAAAAATA-A
1 AAAATATATTTAAATATATA
3136374 AAAATATATTTTAAATATAT
1 AAAATATA-TTTAAATATAT
3136394 GGATTTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
20 15 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATATTTAAATATATA
Found at i:3136389 original size:18 final size:19
Alignment explanation
Indices: 3136337--3136392 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 19
3136327 ATGTTAAGAT
3136337 AAAATATATTTAAATATATA
1 AAAATATATTTAAA-ATATA
*
3136357 AAAATATA-TAAAAATA-A
1 AAAATATATTTAAAATATA
*
3136374 AAAATATATTTTAAATATA
1 AAAATATATTTAAAATATA
3136393 TGGATTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 9 0.29
19 5 0.16
20 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATATTTAAAATATA
Found at i:3136727 original size:19 final size:19
Alignment explanation
Indices: 3136703--3136749 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3136693 TAATTGATAG
*
3136703 AAAATAAAT-ATATTAAATT
1 AAAATAAATCA-ATTAAAAT
3136722 AAAATAAATCAATTAAAAT
1 AAAATAAATCAATTAAAAT
*
3136741 AGAATAAAT
1 AAAATAAAT
3136750 TTAATCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAAATCAATTAAAAT
Found at i:3144465 original size:20 final size:20
Alignment explanation
Indices: 3144440--3144477 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3144430 TTTGGTTCAC
*
3144440 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
3144460 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
3144478 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:3144480 original size:18 final size:19
Alignment explanation
Indices: 3144440--3144483 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3144430 TTTGGTTCAC
*
3144440 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
3144460 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
3144478 GGAATA
1 GGAATA
3144484 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:3147527 original size:2 final size:2
Alignment explanation
Indices: 3147520--3147559 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3147510 TAGATTAGGA
3147520 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
3147560 TAAATCACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3150439 original size:3 final size:3
Alignment explanation
Indices: 3150431--3150470 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
3150421 ATTGGAAATA
*
3150431 AAT AAT AAT AAT AAT AAT AAT AAT AATT ACT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT A
3150471 TTATCTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3150478 original size:15 final size:16
Alignment explanation
Indices: 3150431--3150484 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
3150421 ATTGGAAATA
*
3150431 AATAATAATAA-TAAT
1 AATAATAATAATTACT
3150446 AATAATAATAATTACT
1 AATAATAATAATTACT
3150462 AATAA-AAT-ATTATCT
1 AATAATAATAATTA-CT
*
3150477 AAAAATAA
1 AATAATAA
3150485 AAATAGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 4 0.12
15 20 0.59
16 10 0.29
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAATAATTACT
Found at i:3150543 original size:3 final size:3
Alignment explanation
Indices: 3150535--3150561 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3150525 AGACCAAATA
3150535 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3150562 TACTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3157262 original size:13 final size:13
Alignment explanation
Indices: 3157244--3157268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3157234 TCGAATATAC
3157244 TTAGAAAATCTTT
1 TTAGAAAATCTTT
3157257 TTAGAAAATCTT
1 TTAGAAAATCTT
3157269 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:3159524 original size:21 final size:22
Alignment explanation
Indices: 3159499--3159577 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 22
3159489 CAGAACCCCA
3159499 GGGGGTATCGATTCCCCT-ATG
1 GGGGGTATCGATTCCCCTCATG
* *
3159520 GGGGG-AGTCGGTTCCCCTTCAAAG
1 GGGGGTA-TCGATTCCCC-TC-ATG
* *
3159544 GGGGGAATCGGTT-CCCTCAT-
1 GGGGGTATCGATTCCCCTCATG
3159564 GGGGGTATCGATTC
1 GGGGGTATCGATTC
3159578 TCTCTGCACC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 12 0.26
21 15 0.32
22 3 0.06
23 3 0.06
24 13 0.28
25 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTCATG
Found at i:3163418 original size:22 final size:21
Alignment explanation
Indices: 3163375--3163415 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3163365 TGAGTTTATT
*
3163375 ATCATTTTTCAATTTTGAAAC
1 ATCATTTTTCAATTTTAAAAC
3163396 ATCATTTTT-ATATTTTAAAA
1 ATCATTTTTCA-ATTTTAAAA
3163416 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (21 bp):
ATCATTTTTCAATTTTAAAAC
Found at i:3194812 original size:16 final size:17
Alignment explanation
Indices: 3194791--3194823 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3194781 ACAAGTACCT
3194791 ACAAAAGC-AAATAAAA
1 ACAAAAGCAAAATAAAA
3194807 ACAAAAGCAAAATAAAA
1 ACAAAAGCAAAATAAAA
3194824 TTAAACTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (17 bp):
ACAAAAGCAAAATAAAA
Found at i:3196108 original size:23 final size:23
Alignment explanation
Indices: 3196062--3196145 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
3196052 AGGATAAAAA
* *
3196062 TAAAATAGATATATTT-TTTTAT
1 TAAAAGAGATTTATTTCTTTTAT
3196084 TAAAAGAGATTTATTTCTTTTAT
1 TAAAAGAGATTTATTTCTTTTAT
3196107 TAAAAGAGATTTATTATCTTTTTAAT
1 TAAAAGAGATTTATT-TC-TTTT-AT
*
3196133 TAAAAGATATTTA
1 TAAAAGAGATTTA
3196146 ATAGCTCTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
22 14 0.25
23 21 0.38
24 2 0.04
25 4 0.07
26 14 0.25
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (23 bp):
TAAAAGAGATTTATTTCTTTTAT
Found at i:3201440 original size:102 final size:102
Alignment explanation
Indices: 3201232--3201433 Score: 300
Period size: 102 Copynumber: 2.0 Consensus size: 102
3201222 CTTAAGAATT
* * *
3201232 TCTTTCTATTCTTCTTCTTTCTTGGACTTAGTGAATCTAGAGGGAAAAGGAAGATCTATGAAATA
1 TCTTTCTATTCTGCTTCCTTCTTGGACTTAGCGAATCTAGAGGGAAAAGGAAGATCTATGAAATA
*
3201297 TTCCTTCGGTTTTTTGCTTTTGAGTCCTTTAGGTTGA
66 TTCCTTCGGTTTTTCGCTTTTGAGTCCTTTAGGTTGA
* * *
3201334 TCTTTCTCTTCTGCTTCCTTCTTGGACTTAGCGAATCTAGCGGGAAAAGGAGGA-CTTATGACAA
1 TCTTTCTATTCTGCTTCCTTCTTGGACTTAGCGAATCTAGAGGGAAAAGGAAGATC-TATGA-AA
*
3201398 -ATTCCTTCGGTTTTTCGCTTTTGATTCCTTTAGGTT
64 TATTCCTTCGGTTTTTCGCTTTTGAGTCCTTTAGGTT
3201434 TGTCTTTATG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 1 0.01
102 87 0.97
103 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (102 bp):
TCTTTCTATTCTGCTTCCTTCTTGGACTTAGCGAATCTAGAGGGAAAAGGAAGATCTATGAAATA
TTCCTTCGGTTTTTCGCTTTTGAGTCCTTTAGGTTGA
Found at i:3203753 original size:11 final size:11
Alignment explanation
Indices: 3203734--3203767 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3203724 AAGAACACCA
3203734 AAAGAAAAACTT
1 AAAG-AAAACTT
3203746 AAAGAAAACTT
1 AAAGAAAACTT
*
3203757 AATGAAAACTT
1 AAAGAAAACTT
3203768 GATGTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (11 bp):
AAAGAAAACTT
Found at i:3206269 original size:26 final size:29
Alignment explanation
Indices: 3206224--3206285 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
3206214 CATAAATATA
*
3206224 TAAAAGTAACATATAATTAAATAAT-GT-T
1 TAAAA-TAACATAAAATTAAATAATAGTAT
*
3206252 TAAAATAA-ATAAAATTAAATCATAGTAT
1 TAAAATAACATAAAATTAAATAATAGTAT
3206280 TAAAAT
1 TAAAAT
3206286 GTAAAGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 13 0.43
27 5 0.17
28 12 0.40
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAAATAACATAAAATTAAATAATAGTAT
Found at i:3207731 original size:3 final size:3
Alignment explanation
Indices: 3207723--3207766 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
3207713 ATTATTTATT
*
3207723 TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3207767 ATAAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3207744 original size:16 final size:15
Alignment explanation
Indices: 3207723--3207769 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
3207713 ATTATTTATT
3207723 TAATAATAATATAATA
1 TAATAATAATA-AATA
* *
3207739 TAATAATAAAACAAAA
1 TAATAATAATA-AATA
3207755 TAATAATAATAAATA
1 TAATAATAATAAATA
3207770 AAACAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAATAATAAATA
Found at i:3207756 original size:23 final size:23
Alignment explanation
Indices: 3207733--3207776 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3207723 TAATAATAAT
3207733 ATAAT-ATAAT-AATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
3207754 ATAATAATAATAAATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
3207777 TGAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
ATAATAATAATAAATAAAACAAA
Found at i:3208239 original size:122 final size:122
Alignment explanation
Indices: 3208022--3208246 Score: 328
Period size: 122 Copynumber: 1.8 Consensus size: 122
3208012 TGCTCCTTAT
* * * * * *
3208022 TCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGAAAATGTTAATGTTGGTTTATCTCCTTTT
1 TCTTCAGATAAGTTCTTCTCATTATGAACACTTCTGAAAATATTAATGTTGATCTATCTCATTCT
3208087 GTGATAGAGTCATGCAAAAGGTTGAACAAGCACTTCTCATTATGAACTTCTTATTCC
66 GTGATAGAGTCATGCAAAAGGTTGAACAAGCACTTCTCATTATGAACTTCTTATTCC
* *
3208144 TCTTCAGATAAGTTCTTCTCATTATGAAC-TTCTCTGAAACA-ATTGATGTTGATCTATCTCATT
1 TCTTCAGATAAGTTCTTCTCATTATGAACACT-TCTGAAA-ATATTAATGTTGATCTATCTCATT
* *
3208207 CTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTC
64 CTGTGATAGAGTCATGCAAAAGGTTGAACAAGCACTTCTC
3208247 TCTTCAGATG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
121 1 0.01
122 89 0.98
123 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (122 bp):
TCTTCAGATAAGTTCTTCTCATTATGAACACTTCTGAAAATATTAATGTTGATCTATCTCATTCT
GTGATAGAGTCATGCAAAAGGTTGAACAAGCACTTCTCATTATGAACTTCTTATTCC
Found at i:3208373 original size:113 final size:113
Alignment explanation
Indices: 3208247--3208650 Score: 497
Period size: 113 Copynumber: 3.5 Consensus size: 113
3208237 AGCTCTTCTC
3208247 TCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGCAATGATGATCCATCGAATGATGAATT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGCAATGATGATCCATCGAATGATGAATT
*
3208312 CAAGCGAAAAGTTGAACAATTTCTTCTCATTATGAACTTCTTCTTCCT
66 CAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
* * *
3208360 TCTTCAGATGAGTTCTTCTTAGTATGAACTCGACCTGGCAATGATGATCCATCGAATGATGAATT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGCAATGATGATCCATCGAATGATGAATT
3208425 CAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
66 CAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
** ** * * *
3208473 TCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGA-AAATGTTGATGCTGATCTATCTCCTTT
1 TCTTCAGATGAGTTCTTCTCATTATG-A-AC-TC-GACCTA-G-CAATGATGATCCA--T-C--G
** * * * *
3208537 TGTGATAGAA-TCAAGCAAAAAGTTGAATAAGTTATTCTCATTATGAACTTCTTCTTCCT
55 AATGAT-GAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
* * * *
3208596 TCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCTATCGA
1 TCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGCAATGATGATCCATCGA
3208651 TCAAACTAAA
Statistics
Matches: 249, Mismatches: 29, Indels: 26
0.82 0.10 0.09
Matches are distributed among these distances:
113 133 0.53
114 1 0.00
115 3 0.01
116 3 0.01
117 3 0.01
118 19 0.08
119 2 0.01
120 3 0.01
121 3 0.01
122 1 0.00
123 75 0.30
124 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGCAATGATGATCCATCGAATGATGAATT
CAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
Found at i:3208866 original size:112 final size:113
Alignment explanation
Indices: 3208669--3208949 Score: 469
Period size: 112 Copynumber: 2.5 Consensus size: 113
3208659 AAGTCAAACA
* * *
3208669 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
*
3208734 GTTGAACAAGTTCTTCTCATTATGAAC-TATTCTTCCTTCTTCAGATG
66 GTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
*
3208781 AGTTCTTCTCATTATGAACTTTCTCTGGAAATATTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
*
3208846 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
* *
3208894 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATTCAT--TGTGATGGATTTGA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGA
3208950 ATCTTTGCTA
Statistics
Matches: 159, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 13 0.08
112 87 0.55
113 59 0.37
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
GTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
Found at i:3208913 original size:288 final size:294
Alignment explanation
Indices: 3208394--3208931 Score: 727
Period size: 288 Copynumber: 1.8 Consensus size: 294
3208384 TGAACTCGAC
*
3208394 CTGGCAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATG
1 CTGGAAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATG
*
3208459 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGAAAATGTTGATGCTG
66 AACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGAAAA--TTGAT-CTG
* ** * *
3208524 ATCTATCTCCTTTTGTGATAGAATCAAGCAAAAAGTTGAATAAGTTATTCTCATTATGAACTTCT
128 ATCCA-CTCC-TAAGTGATAGAATCAAGCAAAAAGTTGAACAAGCTATTCTCATTATGAACTTCT
*
3208589 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCTATCGATC
191 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGTTGATCTATCGATC
3208653 AAACTAAAGTCAAACAAGTTCTTCTCATTATGAACTTCCT
255 AAACTAAAGTCAAACAAGTTCTTCTCATTATGAACTTCCT
* ** *
3208693 CTGGAAATGCTGATCCATC-AAGTGATGAATTTGAGC-AAAAGGTTGAACAAGTTCTTCTCATTA
1 CTGGAAATGATGATCCATCGAA-TGATGAATTCAAGCGAAAA-GTTGAACAAATTCTTCTCATTA
** *
3208756 TGAAC-TATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-T-AT-TG
64 TGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGAAAATTGATCTG
* * ** * *
3208817 ATCCA-T-C-AAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
128 ATCCACTCCTAAGTGATAGAATCAAGCAAAAAGTTGAACAAGCTATTCTCATTATGAACTTCTTC
*
3208879 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGAT
193 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGTTGAT
3208932 TCATTGTGAT
Statistics
Matches: 213, Mismatches: 22, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
287 2 0.01
288 93 0.44
290 1 0.00
291 1 0.00
293 6 0.03
295 2 0.01
296 1 0.00
298 45 0.21
299 62 0.29
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (294 bp):
CTGGAAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATG
AACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGAAAATTGATCTGATC
CACTCCTAAGTGATAGAATCAAGCAAAAAGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGTTGATCTATCGATCAAACTA
AAGTCAAACAAGTTCTTCTCATTATGAACTTCCT
Found at i:3209811 original size:53 final size:54
Alignment explanation
Indices: 3209709--3209811 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 54
3209699 TAACTGGTTC
** * *
3209709 GTAAAATATTTGACAACACATTCATCATCTCATGTGGTTTTTGCTCAGATGTTT
1 GTAAAATATTTGACAACACATTCATCATCTCATGTGACTTCTGCACAGATGTTT
* * *
3209763 GTAAAGTATTTGACAA-ACATTCATCATTTCTTGTGACTTCTGCACAGAT
1 GTAAAATATTTGACAACACATTCATCATCTCATGTGACTTCTGCACAGAT
3209812 TTCTGGTCAG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 27 0.64
54 15 0.36
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (54 bp):
GTAAAATATTTGACAACACATTCATCATCTCATGTGACTTCTGCACAGATGTTT
Found at i:3210779 original size:75 final size:75
Alignment explanation
Indices: 3210675--3211004 Score: 365
Period size: 76 Copynumber: 4.4 Consensus size: 75
3210665 AGGATGATAT
* ** * * * *
3210675 AGGCCTTCAGCACACCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTGATTC
1 AGGCTTTCAGCATGCCCCAACATTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATTC
*
3210740 TGATTGAAAT
66 TGATTGAAAG
* * * * *
3210750 AGGCTTTCAGCATGCCCCATCAATTGCTGATACGAACGTTCAAAATACATCAAAATTCTTCATTC
1 AGGCTTTCAGCATGCCCCAACATTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATTC
*
3210815 TGATTAAAAG
66 TGATTGAAAG
* * * ** *
3210825 GGGCTTTCAGCATGCCCCATCATTTTGCTGATATGAACATTCAGGATATATCAACATTCCTCATT
1 AGGCTTTCAGCATGCCCCAACA-TTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATT
3210890 CTGATTGAAAG
65 CTGATTGAAAG
* * ** ** *
3210901 GGGTTTTCAGCATGCCCCAACATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTGATT
1 AGGCTTTCAGCATGCCCCAACA-TTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATT
3210966 CTGATTGAAA-
65 CTGATTGAAAG
* *
3210976 AGGGTTTTTAGCATGCCCCAACATTTGCT
1 A-GGCTTTCAGCATGCCCCAACATTTGCT
3211005 TCTTGTTAAT
Statistics
Matches: 228, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
75 94 0.41
76 134 0.59
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (75 bp):
AGGCTTTCAGCATGCCCCAACATTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATTC
TGATTGAAAG
Found at i:3211003 original size:151 final size:150
Alignment explanation
Indices: 3210680--3211004 Score: 382
Period size: 151 Copynumber: 2.2 Consensus size: 150
3210670 GATATAGGCC
** * * * *
3210680 TTCAGCACACCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTGATTCTGATT
1 TTCAGCATGCCCCAACATTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATTCTGATT
* * * * *
3210745 GAAATAGGCTTTCAGCATGCCCCATCAATTGCTGATACGAACGTTCAAAATACATCAAAATTCTT
66 GAAAGAGGCTTTCAGCATGCCCCAACAATTGCTGATACAAACATTCAAAATACATCAAAATTCCT
3210810 CATTCTGATTAAAAGGGGCT
131 CATTCTGATTAAAAGGGGCT
* * ** *
3210830 TTCAGCATGCCCCATCATTTTGCTGATATGAACATTCAGGATATATCAACATTCCTCATTCTGAT
1 TTCAGCATGCCCCAACA-TTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATTCTGAT
* * * * ** *
3210895 TGAAAGGGGTTTTCAGCATGCCCCAACATTTTGCTGATATAAACATTCAGGATACATCAACATTC
65 TGAAAGAGGCTTTCAGCATGCCCCAACA-ATTGCTGATACAAACATTCAAAATACATCAAAATTC
* *
3210960 CTGATTCTGATTGAAAA-GGGTT
129 CTCATTCTGATT-AAAAGGGGCT
*
3210982 TTTAGCATGCCCCAACATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
3211005 TCTTGTTAAT
Statistics
Matches: 145, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
150 14 0.10
151 69 0.48
152 58 0.40
153 4 0.03
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (150 bp):
TTCAGCATGCCCCAACATTTGCTGATACGAACATTCAAAATACATCAACATTCCTCATTCTGATT
GAAAGAGGCTTTCAGCATGCCCCAACAATTGCTGATACAAACATTCAAAATACATCAAAATTCCT
CATTCTGATTAAAAGGGGCT
Found at i:3214646 original size:2 final size:2
Alignment explanation
Indices: 3214639--3214680 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3214629 ACAACAAAGG
3214639 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
3214681 TTAAAAGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3216317 original size:14 final size:14
Alignment explanation
Indices: 3216298--3216369 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
3216288 AAATGTAATT
3216298 ATGTAAAAATGAAA
1 ATGTAAAAATGAAA
3216312 ATGT--AAAT-ACAA
1 ATGTAAAAATGA-AA
*
3216324 ATGTAAAAAATGCAA
1 ATGT-AAAAATGAAA
* **
3216339 ATGTAAATATGTGA
1 ATGTAAAAATGAAA
* *
3216353 ATGTAACAATAAAA
1 ATGTAAAAATGAAA
3216367 ATG
1 ATG
3216370 CAAATTGTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.02
12 10 0.23
14 23 0.52
15 10 0.23
ACGTcount: A:0.57, C:0.04, G:0.14, T:0.25
Consensus pattern (14 bp):
ATGTAAAAATGAAA
Found at i:3216339 original size:15 final size:15
Alignment explanation
Indices: 3216316--3216345 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3216306 ATGAAAATGT
3216316 AAATACAAATGTAAA
1 AAATACAAATGTAAA
*
3216331 AAATGCAAATGTAAA
1 AAATACAAATGTAAA
3216346 TATGTGAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (15 bp):
AAATACAAATGTAAA
Found at i:3216439 original size:7 final size:7
Alignment explanation
Indices: 3216405--3216446 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3216395 ATAAAAGTAT
3216405 AAATGCA
1 AAATGCA
* *
3216412 CAATGAA
1 AAATGCA
3216419 AAATGCA
1 AAATGCA
3216426 AAGATGCA
1 AA-ATGCA
3216434 AAATGC-
1 AAATGCA
3216440 AAATGCA
1 AAATGCA
3216447 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:3218923 original size:16 final size:15
Alignment explanation
Indices: 3218902--3218945 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
3218892 TAATGATAAT
3218902 TAAATATATATAAACG
1 TAAATATATATAAA-G
3218918 TAAATATATA-AAAG
1 TAAATATATATAAAG
3218932 TAACATATA-ATAAA
1 TAA-ATATATATAAA
3218946 ATAATGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 11 0.42
16 10 0.38
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (15 bp):
TAAATATATATAAAG
Found at i:3218924 original size:14 final size:15
Alignment explanation
Indices: 3218907--3218946 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3218897 ATAATTAAAT
*
3218907 ATATATAAACGTAA-
1 ATATATAAAAGTAAC
3218921 ATATATAAAAGTAAC
1 ATATATAAAAGTAAC
3218936 ATATAATAAAA
1 ATAT-ATAAAA
3218947 TAATGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
ATATATAAAAGTAAC
Found at i:3218946 original size:16 final size:15
Alignment explanation
Indices: 3218902--3218946 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
3218892 TAATGATAAT
*
3218902 TAAATATATATAAACG
1 TAAATATA-ATAAAAG
3218918 TAAATAT-ATAAAAG
1 TAAATATAATAAAAG
3218932 TAACATATAATAAAA
1 TAA-ATATAATAAAA
3218947 TAATGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 13 0.50
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (15 bp):
TAAATATAATAAAAG
Found at i:3220403 original size:3 final size:3
Alignment explanation
Indices: 3220395--3220438 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
3220385 ATTAATTATT
*
3220395 TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3220439 ATAAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3220416 original size:16 final size:15
Alignment explanation
Indices: 3220395--3220441 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
3220385 ATTAATTATT
3220395 TAATAATAATATAATA
1 TAATAATAATA-AATA
* *
3220411 TAATAATAAAACAAAA
1 TAATAATAATA-AATA
3220427 TAATAATAATAAATA
1 TAATAATAATAAATA
3220442 AAACAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAATAATAAATA
Found at i:3220428 original size:23 final size:23
Alignment explanation
Indices: 3220405--3220448 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3220395 TAATAATAAT
3220405 ATAAT-ATAAT-AATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
3220426 ATAATAATAATAAATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
3220449 TGAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
ATAATAATAATAAATAAAACAAA
Found at i:3222083 original size:28 final size:28
Alignment explanation
Indices: 3222043--3222101 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
3222033 TAGGCAGACT
*
3222043 TTCTAACAGTGACATGTTTAATAAAATG
1 TTCTAACAGTGACATGTTTAATAAAAGG
3222071 TTCTAACAGTGACATGTTTAATAAAAGG
1 TTCTAACAGTGACATGTTTAATAAAAGG
3222099 TTC
1 TTC
3222102 ATTGTACTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (28 bp):
TTCTAACAGTGACATGTTTAATAAAAGG
Found at i:3224371 original size:15 final size:15
Alignment explanation
Indices: 3224353--3224387 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3224343 ATTTAGTTTT
3224353 AATTTCAGTAATCTA
1 AATTTCAGTAATCTA
* *
3224368 AATTTCTGTAATTTA
1 AATTTCAGTAATCTA
3224383 AATTT
1 AATTT
3224388 TACATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (15 bp):
AATTTCAGTAATCTA
Found at i:3227061 original size:14 final size:14
Alignment explanation
Indices: 3227039--3227068 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3227029 TTTTTGTATA
*
3227039 TAATTAATTTTATT
1 TAATAAATTTTATT
3227053 TAATAAATTTTATT
1 TAATAAATTTTATT
3227067 TA
1 TA
3227069 TTCAGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATAAATTTTATT
Found at i:3227484 original size:9 final size:11
Alignment explanation
Indices: 3227462--3227548 Score: 65
Period size: 9 Copynumber: 9.0 Consensus size: 11
3227452 CACAAATTTA
3227462 AATATATATAT
1 AATATATATAT
3227473 AATAT-TAT-T
1 AATATATATAT
3227482 AATA-AT-TA-
1 AATATATATAT
3227490 AATATATA-AT
1 AATATATATAT
3227500 AATATA-ATAT
1 AATATATATAT
*
3227510 --CATATATAT
1 AATATATATAT
3227519 AATATATA-AT
1 AATATATATAT
3227529 AATA-AT-TA-
1 AATATATATAT
3227537 AATATATCATAT
1 AATATAT-ATAT
3227549 TATTTTATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 27
0.67 0.02 0.30
Matches are distributed among these distances:
8 12 0.20
9 19 0.32
10 17 0.28
11 12 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AATATATATAT
Found at i:3227523 original size:7 final size:7
Alignment explanation
Indices: 3227463--3227548 Score: 73
Period size: 7 Copynumber: 13.3 Consensus size: 7
3227453 ACAAATTTAA
3227463 ATAT-AT
1 ATATAAT
3227469 ATATAAT
1 ATATAAT
*
3227476 AT-TATT
1 ATATAAT
3227482 A-ATAAT
1 ATATAAT
3227488 -TA-AAT
1 ATATAAT
3227493 ATATAAT
1 ATATAAT
3227500 AATATAAT
1 -ATATAAT
3227508 ATCAT-AT
1 AT-ATAAT
3227515 ATATAAT
1 ATATAAT
3227522 ATATAAT
1 ATATAAT
3227529 A-ATAAT
1 ATATAAT
3227535 -TA-AAT
1 ATATAAT
*
3227540 ATATCAT
1 ATATAAT
3227547 AT
1 AT
3227549 TATTTTATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
5 6 0.09
6 24 0.36
7 27 0.41
8 9 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:3227531 original size:32 final size:33
Alignment explanation
Indices: 3227469--3227548 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 33
3227459 TTAAATATAT
*
3227469 ATATAATATTAT-TAATAATTAAATATATAATA
1 ATATAATATCATATAATAATTAAATATATAATA
3227501 ATATAATATCATATATATAATATATAATA-ATAATTA
1 ATATAATATCATATA-ATAAT-TA-AATATATAA-TA
3227537 A-AT-ATATCATAT
1 ATATAATATCATAT
3227549 TATTTTATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
34 14 0.33
35 8 0.19
36 7 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAATATCATATAATAATTAAATATATAATA
Found at i:3227542 original size:37 final size:32
Alignment explanation
Indices: 3227469--3227534 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
3227459 TTAAATATAT
*
3227469 ATATAATATTATTAATAATTAAATATATAATA
1 ATATAATATCATTAATAATTAAATATATAATA
*
3227501 ATATAATATCATATATATAA-TATATA-ATAATA
1 ATATAATATCAT-TA-ATAATTAAATATATAATA
3227533 AT
1 AT
3227535 TAAATATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 19 0.63
33 7 0.23
34 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAATATCATTAATAATTAAATATATAATA
Found at i:3234040 original size:31 final size:31
Alignment explanation
Indices: 3234005--3234069 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
3233995 AGAACTCGCA
*
3234005 TGAATAATTGTCAATTATTAAGAAAATGAAG
1 TGAATAATTGTCAAATATTAAGAAAATGAAG
3234036 TGAATAATTGTCAAATATTAAGAAAATGAAG
1 TGAATAATTGTCAAATATTAAGAAAATGAAG
3234067 TGA
1 TGA
3234070 TTGAGAGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (31 bp):
TGAATAATTGTCAAATATTAAGAAAATGAAG
Found at i:3243338 original size:20 final size:23
Alignment explanation
Indices: 3243296--3243338 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3243286 TCAATGTATG
*
3243296 CTTCTAAAGTCAAATTTCTCTTT
1 CTTCTAAAGTCAAAATTCTCTTT
3243319 CTTCTAAA-T-AAAATTC-CTTT
1 CTTCTAAAGTCAAAATTCTCTTT
3243339 GCCTAGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 1 0.05
23 8 0.42
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.47
Consensus pattern (23 bp):
CTTCTAAAGTCAAAATTCTCTTT
Found at i:3249202 original size:49 final size:49
Alignment explanation
Indices: 3249096--3249195 Score: 130
Period size: 49 Copynumber: 2.1 Consensus size: 49
3249086 CATATGTGTT
* * *
3249096 ATTAAATTATTGATTTTATTGAAACTCGTCACATCGAGGTGACAAGTTC
1 ATTAAATTATTGATTTTATTGAAACTCGCCACATCAAGGTGACAAGTCC
* ** *
3249145 ATTAAATTATTGGTTTTATTGGGACTCGCCACATCAAGGTGA-GAGTCC
1 ATTAAATTATTGATTTTATTGAAACTCGCCACATCAAGGTGACAAGTCC
3249193 ATT
1 ATT
3249196 TCAATTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 7 0.16
49 37 0.84
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (49 bp):
ATTAAATTATTGATTTTATTGAAACTCGCCACATCAAGGTGACAAGTCC
Found at i:3250987 original size:21 final size:21
Alignment explanation
Indices: 3250958--3251007 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3250948 CTTGGGTTGG
* *
3250958 ACATTCATGGGATGTAATCCA
1 ACATACATGGAATGTAATCCA
3250979 ACATACATGGAATGTAATCCA
1 ACATACATGGAATGTAATCCA
3251000 ACATACAT
1 ACATACAT
3251008 ATATGGTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (21 bp):
ACATACATGGAATGTAATCCA
Found at i:3252463 original size:22 final size:22
Alignment explanation
Indices: 3252435--3252480 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3252425 AATCGGATCG
*
3252435 AATCGGTCGGTTCAATTTGTTC
1 AATCGGTCGGTTCAACTTGTTC
*
3252457 AATCGGTCGGTTTAACTTGTTC
1 AATCGGTCGGTTCAACTTGTTC
3252479 AA
1 AA
3252481 CCGAGAATCG
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:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (22 bp):
AATCGGTCGGTTCAACTTGTTC
Found at i:3269803 original size:21 final size:21
Alignment explanation
Indices: 3269777--3269816 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3269767 TTTTTCATGC
3269777 GTAGGATTCATATAAAGAAGT
1 GTAGGATTCATATAAAGAAGT
3269798 GTAGGATTCATATAAAGAA
1 GTAGGATTCATATAAAGAA
3269817 TCATACGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (21 bp):
GTAGGATTCATATAAAGAAGT
Found at i:3284597 original size:21 final size:19
Alignment explanation
Indices: 3284572--3284639 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 19
3284562 AAAGAAGAAG
3284572 AAAAATAAGTGAAAAAATAA
1 AAAAATAA-TGAAAAAATAA
*
3284592 TAAAAATAATAAAAAAAATAA
1 -AAAAATAAT-GAAAAAATAA
*
3284613 AAAAATGAATGAAAAAAATGA
1 AAAAAT-AATG-AAAAAATAA
3284634 AAAAAT
1 AAAAAT
3284640 GAGGGTTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.17
21 34 0.83
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAAATAATGAAAAAATAA
Found at i:3284605 original size:8 final size:9
Alignment explanation
Indices: 3284584--3284615 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3284574 AAATAAGTGA
3284584 AAAAATAAT
1 AAAAATAAT
3284593 AAAAATAAT
1 AAAAATAAT
*
3284602 AAAAAAAAT
1 AAAAATAAT
3284611 AAAAA
1 AAAAA
3284616 AATGAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAATAAT
Found at i:3284632 original size:9 final size:10
Alignment explanation
Indices: 3284572--3284639 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 10
3284562 AAAGAAGAAG
3284572 AAAAATAAGTGA
1 AAAAATAA-T-A
3284584 AAAAATAAT-
1 AAAAATAATA
3284593 AAAAATAATA
1 AAAAATAATA
3284603 AAAAA-AATAA
1 AAAAATAAT-A
*
3284613 AAAAATGAATG
1 AAAAAT-AATA
3284624 AAAAA-AATGA
1 AAAAATAAT-A
3284634 AAAAAT
1 AAAAAT
3284640 GAGGGTTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
9 15 0.31
10 16 0.33
11 6 0.12
12 11 0.23
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (10 bp):
AAAAATAATA
Found at i:3284640 original size:21 final size:21
Alignment explanation
Indices: 3284583--3284641 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
3284573 AAAATAAGTG
3284583 AAAAAATAATAAAAAT-AATAA
1 AAAAAATAA-AAAAATGAATAA
*
3284604 AAAAAATAAAAAAATGAATGA
1 AAAAAATAAAAAAATGAATAA
*
3284625 AAAAAATGAAAAAATGA
1 AAAAAATAAAAAAATGA
3284642 GGGTTCAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.17
21 29 0.83
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAAATAAAAAAATGAATAA
Found at i:3285708 original size:55 final size:55
Alignment explanation
Indices: 3285623--3286371 Score: 1015
Period size: 55 Copynumber: 13.7 Consensus size: 55
3285613 AGGTTCCCCA
* * * * *
3285623 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGGAATAGGGGGCGGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
3285678 CGATCGTTGAAGATTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGGG-AGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
3285732 CGATAGTTGAAGATTGTTCGAGTCTTATACTCTCT-AAGGAAATAGGGGGCGGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGGGCAGACG
* * *
3285787 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
3285842 CGATCGTTGAAGATTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGGGGAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * *
3285897 CGATAGTTGAAGATTGTTCAAGTCTTATACTCTCTGAGGAAATAGGGGGTAGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
3285952 CGATTGCTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
3286007 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
3286062 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGAAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * * *
3286117 CGATTGATGAAAATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCATACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
3286170 CCATCGTTGAAGATTGTTCAAGTCTTATACTCTCTGACGAAATAGGGGGCATACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
3286225 CAATTGATGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATGGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
3286278 TGATCATTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
3286333 CGATTGCTAAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
3286372 GACTATGGAG
Statistics
Matches: 616, Mismatches: 71, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
53 89 0.14
54 51 0.08
55 474 0.77
56 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:3300513 original size:20 final size:20
Alignment explanation
Indices: 3300488--3300559 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
3300478 TTGAAAATCA
* *
3300488 CGTTGCGATTTTTCATTTCG
1 CGTTGCGATTTTCCAGTTCG
3300508 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAGTTCG
3300528 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAGTTCG
3300548 CGTTGCGATTTT
1 CGTTGCGATTTT
3300560 ATTTTAAGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCCAGTTCG
Found at i:3308611 original size:2 final size:2
Alignment explanation
Indices: 3308604--3308647 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3308594 TATAACAATC
3308604 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
3308646 AT
1 AT
3308648 TCTTTCATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3313548 original size:75 final size:75
Alignment explanation
Indices: 3313420--3313613 Score: 223
Period size: 75 Copynumber: 2.6 Consensus size: 75
3313410 TGTTGTTTAA
* * * * *
3313420 TATTTTTCTAGACTTAATATTATGGTTTCAGTCTTAAGATTTAACACTTTAATATTAT-AGTTTG
1 TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAGATTTGACACTTTAATATTATGA-TTT-
3313484 A-TTATGGATTT
64 ATTTATGGATTT
* * * *
3313495 TATTATTCTAGAGTTAATATTGTGGTTTGAATCTTGAGATTTGACATTTTAATATTGTGATTTAT
1 TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAGATTTGACACTTTAATATTATGATTTAT
3313560 TTATGGATTT
66 TTATGGATTT
* * * * *
3313570 TA-TGTTATAAATTTAATATTGTGGTTTGAGTCTTGATATTTGAC
1 TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAGATTTGAC
3313614 TTTATTTATA
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
74 37 0.36
75 64 0.63
76 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (75 bp):
TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAGATTTGACACTTTAATATTATGATTTAT
TTATGGATTT
Found at i:3314879 original size:4 final size:4
Alignment explanation
Indices: 3314870--3314896 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3314860 TTCTTCAATT
3314870 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3314897 TGCTTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3318076 original size:90 final size:90
Alignment explanation
Indices: 3317917--3318090 Score: 208
Period size: 90 Copynumber: 1.9 Consensus size: 90
3317907 TAAATCAAGA
* ** * *
3317917 AACTAAAGCTAAACACATGCAAAATAGATATAACTAACTTTGGCCAGAATAAACCTTCCTTGTTC
1 AACTAAAGCTAAAAACAAACAAAACAAATATAACTAACTTTGGCCAGAATAAACCTTCCTTGTTC
*
3317982 AGTATATTGTATTGATCAAGAAGTT
66 AGTATATTGGATTGATCAAGAAGTT
* * * **
3318007 AACTAAAGCTAAAAACAAACAAAACAAATTTAGCTAACTTTGTCCAGAATGTACCTT-CTTCGCT
1 AACTAAAGCTAAAAACAAACAAAACAAATATAACTAACTTTGGCCAGAATAAACCTTCCTT-G-T
*
3318071 T-AGTATATTGGGTTGATCAA
64 TCAGTATATTGGATTGATCAA
3318091 CCAAAAGTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 3 0.04
90 65 0.93
91 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (90 bp):
AACTAAAGCTAAAAACAAACAAAACAAATATAACTAACTTTGGCCAGAATAAACCTTCCTTGTTC
AGTATATTGGATTGATCAAGAAGTT
Found at i:3318717 original size:15 final size:15
Alignment explanation
Indices: 3318697--3318727 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3318687 AAAAAAATAG
3318697 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
3318712 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
3318727 A
1 A
3318728 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:3318904 original size:18 final size:19
Alignment explanation
Indices: 3318881--3318925 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3318871 CCCAGTAACC
3318881 TTATTCC-CTGGTAATCTT
1 TTATTCCACTGGTAATCTT
*
3318899 TTATTCCTATTGGTAATCTT
1 TTATTCC-ACTGGTAATCTT
*
3318919 TCATTCC
1 TTATTCC
3318926 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (19 bp):
TTATTCCACTGGTAATCTT
Found at i:3325690 original size:28 final size:28
Alignment explanation
Indices: 3325650--3325712 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
3325640 TGGAAGAAAA
3325650 CTAGAATGCTTTTGGGATGGTTTTAAAG
1 CTAGAATGCTTTTGGGATGGTTTTAAAG
*
3325678 CTAGAATGCTTTTGGGATGGTTTTGAAG
1 CTAGAATGCTTTTGGGATGGTTTTAAAG
3325706 CTA-AATG
1 CTAGAATG
3325713 AGCTAGGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 4 0.12
28 30 0.88
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (28 bp):
CTAGAATGCTTTTGGGATGGTTTTAAAG
Found at i:3328539 original size:30 final size:30
Alignment explanation
Indices: 3328505--3328577 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
3328495 CCCGAAGGAC
3328505 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3328535 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3328565 CTGTCCATAGGTC
1 CTATCCAGAGGTC
3328578 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3328601 original size:31 final size:31
Alignment explanation
Indices: 3328563--3328690 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
3328553 GATCCTCGGT
* *
3328563 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** *
3328594 AACTGTCCATATGTTCCTTATAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
3328625 TACTGTCCATATGTCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
3328657 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
3328688 AAC
1 AAC
3328691 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
30 1 0.01
31 52 0.66
32 25 0.32
33 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:3328673 original size:63 final size:61
Alignment explanation
Indices: 3328560--3328688 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 61
3328550 AAAGATCCTC
* * *
3328560 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTATAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
3328621 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
3328684 GGTAA
1 GGTAA
3328689 ACCCTCGACT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.42
63 30 0.50
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:3330037 original size:21 final size:21
Alignment explanation
Indices: 3330013--3330053 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3330003 TTTTGTTCGT
* *
3330013 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3330034 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
3330054 TTGCCCATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3343165 original size:18 final size:18
Alignment explanation
Indices: 3343142--3343178 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3343132 ATGACACCTT
*
3343142 TTGCATTTGCATTTGGCA
1 TTGCATTTACATTTGGCA
*
3343160 TTGCATTTACATTTTGCA
1 TTGCATTTACATTTGGCA
3343178 T
1 T
3343179 AACATTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (18 bp):
TTGCATTTACATTTGGCA
Found at i:3344426 original size:20 final size:21
Alignment explanation
Indices: 3344396--3344435 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3344386 CAAGGATAAT
3344396 AAAGAAAAAAAACAAAGAAAG
1 AAAGAAAAAAAACAAAGAAAG
*
3344417 AAAG-AAAAAAATAAAGAAA
1 AAAGAAAAAAAACAAAGAAA
3344436 AAGGGAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAAAACAAAGAAAG
Found at i:3345310 original size:25 final size:25
Alignment explanation
Indices: 3345264--3345311 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3345254 AAGGGACAAT
*
3345264 ATTTTCTCAAAATCTTTGATTAAAC
1 ATTTTCTCAAAATCTTTAATTAAAC
3345289 ATTTT-TCAAAATCTTCTAATTAA
1 ATTTTCTCAAAATCTT-TAATTAA
3345312 TATTTTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTTCTCAAAATCTTTAATTAAAC
Found at i:3345316 original size:24 final size:25
Alignment explanation
Indices: 3345261--3345318 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
3345251 AGAAAGGGAC
*
3345261 AATATTTTCTCAAAATCTTTGATTA
1 AATATTTTCTCAAAATCTTTAATTA
*
3345286 AACATTTT-TCAAAATCTTCTAATT-
1 AATATTTTCTCAAAATCTT-TAATTA
3345310 AATATTTTC
1 AATATTTTC
3345319 AGATGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (25 bp):
AATATTTTCTCAAAATCTTTAATTA
Found at i:3345586 original size:33 final size:32
Alignment explanation
Indices: 3345449--3345615 Score: 237
Period size: 32 Copynumber: 5.2 Consensus size: 32
3345439 AAGCAATAGA
* *
3345449 GGGCATCTTTGAAGATTCAACATCACATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
3345481 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
3345513 GGGCATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
3345545 GGGCATCTTTGGAGATTCAACATCAAAATGTTA
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * * *
3345578 GGGTATCTTTGGTA-ATTCAATATCGAATATTG
1 GGGCATCTTTGG-AGATTCAACATCAAATGTTG
3345610 GGGCAT
1 GGGCAT
3345616 TCAATATCCT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
32 94 0.77
33 27 0.22
34 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:3345766 original size:34 final size:34
Alignment explanation
Indices: 3345723--3345808 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 34
3345713 AATTTTTTTC
* *
3345723 TCTCACTTGAGATAATTTCTCAAAACAAAATT-CG
1 TCTCACTTGAGACAATTTCTCAAAAC-AAATTCCA
*
3345757 TCTCGCTTGAGACAATTTCTCAAAACAAATTCCA
1 TCTCACTTGAGACAATTTCTCAAAACAAATTCCA
3345791 TCTCACTTGAGACAATTT
1 TCTCACTTGAGACAATTT
3345809 TTCTCTGAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 5 0.11
34 42 0.89
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (34 bp):
TCTCACTTGAGACAATTTCTCAAAACAAATTCCA
Found at i:3346098 original size:36 final size:36
Alignment explanation
Indices: 3346051--3346196 Score: 229
Period size: 36 Copynumber: 4.1 Consensus size: 36
3346041 TTTTTAAAGA
* * *
3346051 AAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
**
3346087 AAATTTTGTCTCCCTTGAGATGGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
3346123 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
3346159 AAATTTTGTCTCCCTTGAGACAGTCTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
3346195 AA
1 AA
3346197 TTTCACTTGA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:3346138 original size:21 final size:21
Alignment explanation
Indices: 3346112--3346176 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
3346102 TGAGATGGTT
3346112 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
3346133 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
3346148 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
3346169 TCCCTTGA
1 TCCCTTGA
3346177 GACAGTCTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 12 0.35
17 1 0.03
19 1 0.03
21 20 0.59
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:3346230 original size:39 final size:39
Alignment explanation
Indices: 3346182--3346258 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
3346172 CTTGAGACAG
*
3346182 TCTCCCTTGAGACAATTTCACTTGAAACAAAAGATTTTA
1 TCTCCCTTGAGACAATTTCACTCGAAACAAAAGATTTTA
* * * * *
3346221 TCTCGCTTGAGATAGTTTCACTCGAAACACAATATTTT
1 TCTCCCTTGAGACAATTTCACTCGAAACAAAAGATTTT
3346259 TAGAAACTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (39 bp):
TCTCCCTTGAGACAATTTCACTCGAAACAAAAGATTTTA
Found at i:3346328 original size:43 final size:43
Alignment explanation
Indices: 3346280--3346479 Score: 177
Period size: 43 Copynumber: 4.4 Consensus size: 43
3346270 CCTGATTTTC
3346280 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
* * **
3346323 AGGGGTTTCTTGATGAAAAACTCT-AGGGACCATCGTGATATGT
1 AGGGGTTTCTTGAAGAAAAGCT-TGAGAAACCATCGTGATATGT
* *
3346366 AGGGGTTCCTTGATGACAAATTTGATGACAAGCTTGAGAAACCATCGTAATATGT
1 AGGGGTTTC-T--TG---AA---GA--A-AAGCTTGAGAAACCATCGTGATATGT
* ** *
3346421 AGGGGTTTCTTGATGAAAAGCTTGAGGGACTATCGTGATATGT
1 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
*
3346464 AGGGGTTCCTTGAAGA
1 AGGGGTTTCTTGAAGA
3346480 CAAATTTGAT
Statistics
Matches: 125, Mismatches: 18, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
43 81 0.65
44 3 0.02
46 4 0.03
49 2 0.02
52 4 0.03
54 3 0.02
55 28 0.22
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.29
Consensus pattern (43 bp):
AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
Found at i:3346466 original size:98 final size:97
Alignment explanation
Indices: 3346296--3346521 Score: 348
Period size: 98 Copynumber: 2.3 Consensus size: 97
3346286 TTCTTGAAGA
3346296 AAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAACTCTAGGGACCATCGTGA
1 AAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAACTCTAGGGACCATCGTGA
*
3346361 TATGTAGGGGTTCCTTGATGACAAATTTGATG
66 TATGTAGGGGTTCCTTGAAGACAAATTTGATG
* * *
3346393 ACAAGCTTGAGAAACCATCGTAATATGTAGGGGTTTCTTGATGAAAAGCT-TGAGGGACTATCGT
1 A-AAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAACTCT-AGGGACCATCGT
3346457 GATATGTAGGGGTTCCTTGAAGACAAATTTGATG
64 GATATGTAGGGGTTCCTTGAAGACAAATTTGATG
** *
3346491 AACA-CTTGAGGGACCAACGTGATATGTAGGG
1 AA-AGCTTGAGAAACCATCGTGATATGTAGGG
3346522 TTCCTTGGTG
Statistics
Matches: 118, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
97 26 0.22
98 92 0.78
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (97 bp):
AAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAACTCTAGGGACCATCGTGA
TATGTAGGGGTTCCTTGAAGACAAATTTGATG
Found at i:3346810 original size:91 final size:89
Alignment explanation
Indices: 3346563--3346965 Score: 592
Period size: 90 Copynumber: 4.5 Consensus size: 89
3346553 ATTTTCAAGA
* * * *
3346563 GTTTCTTGACTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGAAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATGA
3346628 GATCTAAGAAACTGAGCCTTCGAGG
66 GATCTAAGAAACTGAGCCTTCG-GG
* *
3346653 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATGA
*
3346718 GATTTAAGAAACTGAGCCTTCGGTG
66 GATCTAAGAAACTGAGCCTTCGG-G
* *
3346743 GTTTCTTGATTTTTTAAGTCCTTCCGGTCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATG
1 GTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATG
*
3346808 AGATCTAAGAAACTGAGCCTTTAGGG
65 AGATCTAAGAAACTGAGCC-TTCGGG
*
3346834 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCACGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATGA
* * * * *
3346899 GATTTAAGAAATTAATCCTTCAGG
66 GATCTAAGAAACTGAGCCTTCGGG
* *
3346923 GTTTCTTGATTTTTTAAGTCCTTCAGG-CAACCATAAGACCTTC
1 GTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
3346966 GGGCAAAATA
Statistics
Matches: 286, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
89 28 0.10
90 175 0.61
91 79 0.28
92 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (89 bp):
GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATGA
GATCTAAGAAACTGAGCCTTCGGG
Found at i:3346877 original size:181 final size:180
Alignment explanation
Indices: 3346563--3346965 Score: 659
Period size: 181 Copynumber: 2.2 Consensus size: 180
3346553 ATTTTCAAGA
* * *
3346563 GTTTCTTGA-CTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGAAGGATGTTTTCAAATG
1 GTTTCTTGATTTTTTAAGTCCTTCAGGTCATCCATAAGACCTTCAGTGAACGATGTTTTCAAATG
*
3346627 AGATCTAAGAAACTGAGCCTTCGAGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGAC
66 AGATCTAAGAAACTGAGCCTTAGAGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGAC
* * *
3346692 CTTCAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGTG
131 CTTCAGTGCACGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAG-G
* *
3346743 GTTTCTTGATTTTTTAAGTCCTTCCGGTCATCCATAAGACCTTCAGTGCACGATGTTTTCAAATG
1 GTTTCTTGATTTTTTAAGTCCTTCAGGTCATCCATAAGACCTTCAGTGAACGATGTTTTCAAATG
3346808 AGATCTAAGAAACTGAGCCTTTAG-GGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGA
66 AGATCTAAGAAACTGAGCC-TTAGAGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGA
* *
3346872 CCTTCAGTGCACGATGTTTTCAAATGAGATTTAAGAAATTAATCCTTCAGG
130 CCTTCAGTGCACGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAGG
*
3346923 GTTTCTTGATTTTTTAAGTCCTTCAGG-CAACCATAAGACCTTC
1 GTTTCTTGATTTTTTAAGTCCTTCAGGTCATCCATAAGACCTTC
3346966 GGGCAAAATA
Statistics
Matches: 209, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
179 15 0.07
180 36 0.17
181 155 0.74
182 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (180 bp):
GTTTCTTGATTTTTTAAGTCCTTCAGGTCATCCATAAGACCTTCAGTGAACGATGTTTTCAAATG
AGATCTAAGAAACTGAGCCTTAGAGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGAC
CTTCAGTGCACGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAGG
Found at i:3347154 original size:3 final size:3
Alignment explanation
Indices: 3347146--3347184 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
3347136 GGGTTAAAAA
*
3347146 ATT ATT ATT A-A ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3347185 AGTGTGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3352173 original size:21 final size:21
Alignment explanation
Indices: 3352133--3352222 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
3352123 TACCAAGAGT
*
3352133 GAAAGAA-AGAAAAGGA-GAA
1 GAAAGAAGAGAAAAAGAGGAA
3352152 GAAAGAAGAGAAAAAGAGGAA
1 GAAAGAAGAGAAAAAGAGGAA
3352173 GAAAGAAGAGAAAAAGAGGAA
1 GAAAGAAGAGAAAAAGAGGAA
3352194 GAAAGAAGAG-AAAAGAGGAA
1 GAAAGAAGAGAAAAAGAGGAA
3352214 GAAAGAAGA
1 GAAAGAAGA
3352223 AGAAGAAAAG
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
19 7 0.10
20 27 0.40
21 34 0.50
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
GAAAGAAGAGAAAAAGAGGAA
Found at i:3352208 original size:10 final size:10
Alignment explanation
Indices: 3352134--3352234 Score: 57
Period size: 10 Copynumber: 9.6 Consensus size: 10
3352124 ACCAAGAGTG
3352134 AAAGAA-AGA
1 AAAGAAGAGA
*
3352143 AAAGGAGA-A
1 AAAGAAGAGA
3352152 GAAAGAAGAGAA
1 -AAAGAAGAG-A
*
3352164 AAAGAGGA-A
1 AAAGAAGAGA
3352173 GAAAGAAGAGAA
1 -AAAGAAGAG-A
*
3352185 AAAGAGGA-A
1 AAAGAAGAGA
3352194 GAAAGAAGAGA
1 -AAAGAAGAGA
*
3352205 AAAGAGGAAGAA
1 AAAGAAG-AG-A
3352217 AGAAGAAGAAGA
1 A-AAGAAG-AGA
3352229 AAAGAA
1 AAAGAA
3352235 AGTTAAAGTC
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
9 8 0.11
10 28 0.39
11 22 0.31
12 6 0.08
13 8 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAAGAAGAGA
Found at i:3352208 original size:41 final size:41
Alignment explanation
Indices: 3352133--3352222 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
3352123 TACCAAGAGT
*
3352133 GAAAGAA-AGAAAAGGAGAAGAAAGAAGAGAAAAAGAGGAA
1 GAAAGAAGAGAAAAAGAGAAGAAAGAAGAGAAAAAGAGGAA
3352173 GAAAGAAGAGAAAAAGAGGAAGAAAGAAGAG-AAAAGAGGAA
1 GAAAGAAGAGAAAAAGA-GAAGAAAGAAGAGAAAAAGAGGAA
3352214 GAAAGAAGA
1 GAAAGAAGA
3352223 AGAAGAAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 7 0.15
41 27 0.57
42 13 0.28
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (41 bp):
GAAAGAAGAGAAAAAGAGAAGAAAGAAGAGAAAAAGAGGAA
Found at i:3355556 original size:20 final size:19
Alignment explanation
Indices: 3355531--3355669 Score: 81
Period size: 19 Copynumber: 7.7 Consensus size: 19
3355521 TATTTGAATT
3355531 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAA-TTGA
*
3355551 TTTTATAATAATTTA-TGTA
1 TTTTATAATAATTAATTG-A
3355570 TATTTAT-AT-A-T--TTGA
1 T-TTTATAATAATTAATTGA
3355585 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAA-TTGA
* *
3355605 -TTTAAAATAATTTA-TGTA
1 TTTTATAATAATTAATTG-A
*
3355623 TATGTAT-AT-A-T--TTGA
1 T-TTTATAATAATTAATTGA
3355638 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAA-TTGA
3355658 -TTTATAATAATT
1 TTTTATAATAATT
3355670 TATGTATAGT
Statistics
Matches: 94, Mismatches: 6, Indels: 39
0.68 0.04 0.28
Matches are distributed among these distances:
14 9 0.10
15 8 0.09
16 6 0.06
17 6 0.06
18 5 0.05
19 30 0.32
20 30 0.32
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTATAATAATTAATTGA
Found at i:3355633 original size:53 final size:53
Alignment explanation
Indices: 3355516--3355703 Score: 274
Period size: 53 Copynumber: 3.5 Consensus size: 53
3355506 TTTCATGTAC
3355516 GTATATATTTGAATTTTTTATAATAATTAACTTGATTTTATAATAATTTATGTATAT
1 GTATATATTTG-A--TTTTATAATAATTAACTTGA-TTTATAATAATTTATGTATAT
* *
3355573 TTATATATTTGATTTTATAATAATTAACTTGATTTAAAATAATTTATGTATAT
1 GTATATATTTGATTTTATAATAATTAACTTGATTTATAATAATTTATGTATAT
3355626 GTATATATTTGATTTTATAATAATTAACTTGATTTATAATAATTTATGTATA-
1 GTATATATTTGATTTTATAATAATTAACTTGATTTATAATAATTTATGTATAT
3355678 GTA-ATTAACTTT-ATTTTATAATAATT
1 GTATA-T-A-TTTGATTTTATAATAATT
3355704 TATTTATTTT
Statistics
Matches: 124, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
51 1 0.01
52 4 0.03
53 85 0.69
54 23 0.19
56 1 0.01
57 10 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (53 bp):
GTATATATTTGATTTTATAATAATTAACTTGATTTATAATAATTTATGTATAT
Found at i:3355684 original size:33 final size:34
Alignment explanation
Indices: 3355534--3355706 Score: 131
Period size: 34 Copynumber: 5.0 Consensus size: 34
3355524 TTGAATTTTT
3355534 TATAATAATTAACTTGATTTTATAATAATTTATG
1 TATAATAATTAACTTGATTTTATAATAATTTATG
* * * *
3355568 TATATTTA-TATATTTGATTTTATAATAATTAACTTG
1 TATAATAATTA-ACTTGATTTTATAATAATTTA--TG
* * * * *
3355604 ATTTAA-AA-TAA-TTTATGTATATGTATATATTTGATTT
1 -TATAATAATTAACTTGAT-TTTAT-AATA-ATTT-A-TG
3355641 TATAATAATTAACTTGA-TTTATAATAATTTATG
1 TATAATAATTAACTTGATTTTATAATAATTTATG
* *
3355674 TATAGTAATTAACTTTATTTTATAATAATTTAT
1 TATAATAATTAACTTGATTTTATAATAATTTAT
3355707 TTATTTTTTA
Statistics
Matches: 108, Mismatches: 19, Indels: 24
0.72 0.13 0.16
Matches are distributed among these distances:
33 18 0.17
34 45 0.42
35 9 0.08
36 15 0.14
37 14 0.13
38 4 0.04
39 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (34 bp):
TATAATAATTAACTTGATTTTATAATAATTTATG
Found at i:3359120 original size:20 final size:22
Alignment explanation
Indices: 3359075--3359132 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
3359065 GCATGGGTAG
3359075 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
3359099 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
3359119 TGTATCGATGCACT
1 TGCATCGATGCACT
3359133 TCAAGGAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:3361327 original size:17 final size:17
Alignment explanation
Indices: 3361295--3361342 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3361285 GAATTCAATT
*
3361295 TAAAGATTATATTTAATA
1 TAAAAATTA-ATTTAATA
* *
3361313 TAAACATTAATTTAATC
1 TAAAAATTAATTTAATA
3361330 TAAAAATT-ATTTA
1 TAAAAATTAATTTA
3361343 CTAATTAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 14 0.52
18 8 0.30
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAAATTAATTTAATA
Found at i:3361684 original size:4 final size:4
Alignment explanation
Indices: 3361677--3361746 Score: 56
Period size: 4 Copynumber: 16.8 Consensus size: 4
3361667 TTTCTTCTTC
*
3361677 TTCT TTCT TTCT TTCT CT-T TTCTT TTCT TTCT TCCTCT TT-T TTC- TTCT
1 TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT T--TCT TTCT TTCT TTCT
3361725 TTCT TCTCCT CTTCT TTCT TTC
1 TTCT T-T-CT -TTCT TTCT TTC
3361747 ACTCTGGGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
3 8 0.15
4 32 0.58
5 7 0.13
6 7 0.13
7 1 0.02
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:3361695 original size:10 final size:10
Alignment explanation
Indices: 3361682--3361743 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
3361672 TCTTCTTCTT
3361682 TCTTTCTTTC
1 TCTTTCTTTC
3361692 TCTTTTCTTT-
1 TC-TTTCTTTC
*
3361702 TCTTTCTTCC
1 TCTTTCTTTC
3361712 TCTTT-TTTC
1 TCTTTCTTTC
3361721 TTCTTTC-TTC
1 -TCTTTCTTTC
3361731 TCCTCTTCTTTC
1 T-CT-TTCTTTC
3361743 T
1 T
3361744 TTCACTCTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 10 0.23
10 19 0.44
11 10 0.23
12 4 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TCTTTCTTTC
Found at i:3361703 original size:20 final size:19
Alignment explanation
Indices: 3361667--3361746 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 19
3361657 TAACTTTTTT
3361667 TTTCTTCTTCTTCTTTCTTTC
1 TTTC-TCTT-TTCTTTCTTTC
3361688 TTTCTCTTTTCTTTTCTTTC
1 TTTCTCTTTTC-TTTCTTTC
* *
3361708 TTCCTCTTTTTTCTTCTTTC
1 TTTCTCTTTTCT-TTCTTTC
*
3361728 -TTCTCCTCTTCTTTCTTTC
1 TTTCT-CTTTTCTTTCTTTC
3361747 ACTCTGGGTG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 14 0.27
20 33 0.65
21 4 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCTCTTTTCTTTCTTTC
Found at i:3368961 original size:16 final size:16
Alignment explanation
Indices: 3368940--3368971 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3368930 ATGTTCCAAT
3368940 TAATGAAATATGTTGA
1 TAATGAAATATGTTGA
*
3368956 TAATGAAGTATGTTGA
1 TAATGAAATATGTTGA
3368972 GTCAATCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (16 bp):
TAATGAAATATGTTGA
Found at i:3377433 original size:32 final size:29
Alignment explanation
Indices: 3377397--3377455 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 29
3377387 GAAGAGGGGA
3377397 GTATCGATACTCCATATAGAGTATCGATACCC
1 GTATCGATACT-CATA-A-AGTATCGATACCC
3377429 GTATCGATACTCATAAAGTATCGATAC
1 GTATCGATACTCATAAAGTATCGATAC
3377456 GAAAATAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 1 0.04
31 4 0.15
32 11 0.41
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (29 bp):
GTATCGATACTCATAAAGTATCGATACCC
Found at i:3380080 original size:13 final size:13
Alignment explanation
Indices: 3380062--3380087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3380052 TTTTTTATTG
3380062 TAATTGTATTGAA
1 TAATTGTATTGAA
3380075 TAATTGTATTGAA
1 TAATTGTATTGAA
3380088 ACAAAAATAT
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):
TAATTGTATTGAA
Found at i:3382257 original size:18 final size:19
Alignment explanation
Indices: 3382211--3382260 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
3382201 TAAAATTTTC
3382211 ATATATTTTCTATATAAATA
1 ATATATTTT-TATATAAATA
*
3382231 ATATATTTTTA-ATTAATA
1 ATATATTTTTATATAAATA
3382249 ATATATTTTTAT
1 ATATATTTTTAT
3382261 TTTATAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 17 0.61
19 2 0.07
20 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATTTTTATATAAATA
Found at i:3382830 original size:29 final size:31
Alignment explanation
Indices: 3382797--3382879 Score: 134
Period size: 29 Copynumber: 2.7 Consensus size: 31
3382787 GTGAAGTCGT
*
3382797 AGGTCGCCATGCACTCCGGGTGACCAA-G-G
1 AGGTCGCCATGCACTCCGGGCGACCAAGGAG
3382826 AGGTCGCCATGCACTCCGGGCGACCAAGGAG
1 AGGTCGCCATGCACTCCGGGCGACCAAGGAG
*
3382857 AGGTCGCCATGCACTCAGGGCGA
1 AGGTCGCCATGCACTCCGGGCGA
3382880 GCTATGCATG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 26 0.52
30 1 0.02
31 23 0.46
ACGTcount: A:0.22, C:0.31, G:0.35, T:0.12
Consensus pattern (31 bp):
AGGTCGCCATGCACTCCGGGCGACCAAGGAG
Done.