Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000297.1 Hibiscus syriacus cultivar Beakdansim tig00000546_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: 83983
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3627 original size:20 final size:20
Alignment explanation
Indices: 3604--3646 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3594 GTAAAAAGAC
*
3604 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
* *
3624 CATTTAGAAGCATTTAGTTG
1 CATTTAGAAGCATATAGATG
3644 CAT
1 CAT
3647 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:16852 original size:36 final size:35
Alignment explanation
Indices: 16812--16925 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 35
16802 CACTCAAATT
*
16812 TGTTTTTCTTAAAACATATTGTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACAGATT-TGTCTCACTTGAGAC
* * * ** *
16848 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACAGATTTGTCTCACTTGAGAC
*
16884 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-AGATTTGTCTCACTTGAGAC
*
16920 CGTTTT
1 TGTTTT
16926 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 47 0.80
37 7 0.12
38 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (35 bp):
TGTTTTTCTTAAAACAGATTTGTCTCACTTGAGAC
Found at i:16889 original size:72 final size:75
Alignment explanation
Indices: 16796--16970 Score: 218
Period size: 72 Copynumber: 2.4 Consensus size: 75
16786 ATGCAGATGA
* * * *
16796 TTATCTCACTCAA-ATTTGTTTTTCTTAAAAC-ATATTGTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATT-TGTCTCACTTGAGACCGTTTTCACTC
16858 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
16868 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
16933 AAGAAGGCAT
66 AAGAAGGCAT
**
16943 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
16971 GAAGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
72 47 0.52
73 15 0.17
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:17005 original size:73 final size:72
Alignment explanation
Indices: 16812--17007 Score: 177
Period size: 73 Copynumber: 2.7 Consensus size: 72
16802 CACTCAAATT
* * * * *
16812 TGTTTTTCTTAAA-ACATATTGTGTCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTTAAACA-AGATT-TATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
16875 ACTCAAGAT
64 ACTCAAGAC
* *
16884 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
16949 TCACTCAAGGC
62 TCACTCAAGAC
* * * *
16960 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
17008 CAGAAAATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
72 29 0.28
73 34 0.32
74 17 0.16
75 6 0.06
76 19 0.18
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:17111 original size:36 final size:36
Alignment explanation
Indices: 17064--17139 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
17054 ATTGAAAACA
* * *
17064 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
17100 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
17136 TTTC
1 TTTC
17140 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:17153 original size:101 final size:103
Alignment explanation
Indices: 16975--17164 Score: 294
Period size: 101 Copynumber: 1.9 Consensus size: 103
16965 TTTTAAGAAG
* * *
16975 ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCTTTGAGATAGTTTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG-AAATTTTGTCTCCCTTGAGACAGTTTCT
**
17040 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 CTCCAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
17079 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G-AATTTTGTCTCCCTTGAGACAGTTTCTC
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAATTTTGTCTCCCTTGAGACAGTTTCTC
*
17142 TCCAAACATAAACTTTGAAAACA
66 TCCAAACATAAACATTGAAAACA
17165 ATTTAACGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 46 0.58
103 1 0.01
104 32 0.41
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (103 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAATTTTGTCTCCCTTGAGACAGTTTCTC
TCCAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:17543 original size:105 final size:105
Alignment explanation
Indices: 17339--17864 Score: 742
Period size: 105 Copynumber: 5.0 Consensus size: 105
17329 ATATCGTGAC
* * * *
17339 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
17403 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
17445 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
17510 ATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
17550 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
17615 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
17655 ACTCCAGACAACGCAAGTTCAACTCCACGACAAAGGGACCGATGCTTGTCAATAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
17716 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
17755 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
** * * *
17819 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
17861 ACTC
1 ACTC
17865 GGAACAATGC
Statistics
Matches: 379, Mismatches: 33, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
99 2 0.01
100 77 0.20
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 202 0.53
106 83 0.22
107 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:18464 original size:37 final size:37
Alignment explanation
Indices: 18408--18511 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
18398 ATTTTCGTCT
* *
18408 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAAGATTCAAACTCCTAAAAATAGGATAAAATTC
* * * *
18445 TGCTATGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAAGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
18482 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAAGATTCAAACTCCTAAAAATAGGAT
18512 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAAGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:18907 original size:18 final size:17
Alignment explanation
Indices: 18868--18910 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
18858 ATTATATGGA
18868 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
18884 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
18902 TATTATTAT
1 TATTATTAT
18911 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:19426 original size:2 final size:2
Alignment explanation
Indices: 19419--19448 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19409 TAATACTTTG
*
19419 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19449 TTTTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:25535 original size:94 final size:94
Alignment explanation
Indices: 25402--25644 Score: 296
Period size: 94 Copynumber: 2.7 Consensus size: 94
25392 TATAATATTA
* * *
25402 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACTCCCC-GCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
* *
25466 TAATATTCAGCTAGCCTGATAAAGGTAAT
66 TAAGATTCAGCTAACCTGATAAAGGTAAT
25495 TATACTATACAATAAAGCTTGAGCTATCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTATG
*
25559 GATAAGATTCAGCTAACCTGATAAAGGT-GT
64 GATAAGATTCAGCTAACCTGATAAAGGTAAT
* * *
25589 T-TATAT---ATTAAG-TT--G---TCCCTCTAGAGCAATTGGTTAAACACCCTGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
25644 T
66 T
25645 CCAGCTAGCC
Statistics
Matches: 137, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
83 37 0.27
84 1 0.01
86 1 0.01
88 2 0.01
89 5 0.04
92 3 0.02
93 7 0.05
94 47 0.34
95 34 0.25
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:27238 original size:165 final size:161
Alignment explanation
Indices: 26764--27953 Score: 1163
Period size: 165 Copynumber: 7.2 Consensus size: 161
26754 TAAAGAAACT
* * * * *
26764 ATTTACAGCATAGCTTAA-GTTGAGAAGGGCTATCTG-CCAAAGACCTTCGAGTTCGAATACACT
1 ATTTACAGCATAACTCAAGGCT-AGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGACTACACT
* * * *
26827 CAGCTTTGAGGGCACATCATTTGCAACATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAGAC
65 CAGCTCT-AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C--CAAAGAC
26892 CTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
126 CTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
* * * * * * * * *
26928 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTCAAGTTCGATTACACTC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGACTACACTC
* * * * * * *
26992 AGCTTCGAGGGCACATCATTTACAGCATAAC-TCAGGCTAGAAGGGTTAT-TAGTCACCAAAAAA
66 AGC-TCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-G---CC-AAAGA
*
27055 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
125 CCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
* * * * * *
27092 ATTTGCAGCATAGCTTAA-GTTGAGAAGGGCTATCTGTTAAAAGACCTTCGAGTTCGACTACGCT
1 ATTTACAGCATAACTCAAGGCT-AGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGACTACACT
*
27156 CAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTCTCTGCCAACTAAAGAC
65 CAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C--C-AAAGAC
* * * *
27221 CTTCGAGTTTGACTACGCTCAGCTCTAAGACATATC
126 CTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
* * * *
27257 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCAAGTTCGACTTCG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGT---CAAAAGACCTTCGAGTTCGACTACA
* * *
27322 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
63 CTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCT
* * *
27387 TCGGGTTCGATTACACTCAGCTCCGATGGCATATC
128 TCGAGTTCGACTACACTCAGCTCC-AAGGCATATC
* * * *
27422 ATTTAAAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTTCA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGT---CAAAAGACCTTCGAGTTCGACTACA
* * *
27487 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGATGGGCTATCTGCCAAAGACCC
63 CTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGA-CC
* *
27552 TT-GGGTTCGATTACACTCAGCTCCAAGGGCATATC
127 TTCGAGTTCGACTACACTCAGCTCCAA-GGCATATC
* * * * *
27587 ATTTACATCATAACTCAAGGATAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTTCG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTC-A--AAAGACCTTCGAGTTCGACTACA
* ** *
27652 CTCAGCTCTAAGGCACATCATTTGTAGCATAGGTTAAGTCGAGAAGGGCTATCTGCCAAAGACCT
63 CTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCT
* * * * *
27717 TTGAGTTCGACTACACTCAGCTTCGAGGGAACATC
128 TCGAGTTCGACTACACTCAGC-TCCAAGGCATATC
* * * * * **
27752 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACATTTGAGTTCGGTTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTC-A-AAAGACCTTCGAGTTCGACTACAC
* * * * * * *
27817 TCAGCTC-AACGACATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAGAAG
64 TCAGCTCTAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC--T-GCCA-AAG
* * * * * *
27881 ACCTTTGAGTTTGACTACGCTCAACTTCAAGGCACATC
124 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
* * *
27919 ATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCT
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCT
27954 ATGAACAAAA
Statistics
Matches: 882, Mismatches: 115, Indels: 55
0.84 0.11 0.05
Matches are distributed among these distances:
162 2 0.00
163 21 0.02
164 266 0.30
165 441 0.50
166 10 0.01
167 43 0.05
168 99 0.11
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (161 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGACTACACTC
AGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCG
AGTTCGACTACACTCAGCTCCAAGGCATATC
Found at i:27863 original size:578 final size:577
Alignment explanation
Indices: 26764--27953 Score: 1672
Period size: 578 Copynumber: 2.1 Consensus size: 577
26754 TAAAGAAACT
* *
26764 ATTTACAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGAATACACTCA
1 ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGAATACACTCA
** * * * *
26829 GCTTTGAGGGCACATCATTTGCAACATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAGACCT
66 GCTCCGAGGGCACATCATTTGAAACATAACTCAAGGCAAGAAGGGTTATATGCCAACAAAGACCT
* *
26894 TCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
131 TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCT
* *
26959 ATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
196 ATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTCCAAGGGCACATCATTTACAGCATAACT
* *
27024 CAGGCTAGAAGGGTTATTAGTCACCAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
261 CAGGATAGAAGGGTTATTAGTCACCAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * *
27089 ATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGTTAAAAGACCTTCGAGTTCGACTACG
326 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGACTACA
* * * * * * *
27154 CTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTCTCTGCCAACTAAAG
391 CTCAGCTCGAAGGAACATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCAACTAAAG
* * *
27219 ACCTTCGAGTTTGACTACGCTCAGCTCTAAGACATATCATTTACAGCATAACTCAAGGCTAGAAG
456 ACATTCGAGTTCGACTACACTCAGCTCTAAGACATATCATTTACAGCATAACTCAAGGCTAGAAG
* * *
27284 GGTTATCTGTCACCAAAAGACCTTCAAGTTCGACTTCGCTCAGCTCCAAGGCACATC
521 GGTTATCTATCACCAAAAGACCTTCAAGTTCGACTACGCTCAACTCCAAGGCACATC
* * * *
27341 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGGGTTCGATTACACTCA
1 ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGAATACACTCA
* * * * *
27406 GCTCCGATGGCATATCATTT-AAAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGAC
66 GCTCCGAGGGCACATCATTTGAAA-CATAACTCAAGGCAAGAAGGGTTATATGCCAAC-AAAGAC
* *
27470 CTTCGAGTTCGACTTCACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGATGGG
129 CTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
*** * *
27535 CTATCTGCCAAAGACCCTTGGGTTCGATTACACTCAGCTCCAAGGGCATATCATTTACATCATAA
194 CTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTCCAAGGGCACATCATTTACAGCATAA
* * *
27600 CTCAAGGATAGAAGGGTTATCT-GTCAACC-AAAGACCTTCGAGTTCGACTTCGCTCAGCTCTAA
259 CTC-AGGATAGAAGGGTTAT-TAGTC-ACCAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAA
* * * *
27663 GGCACATCATTTGTAGCATAGGTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCTTTGAGTTCGA
321 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGA
* *
27727 CTACACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAA
386 CTACACTCAGC-TCGAAGGAACATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCAA
* **
27792 C-AAAGACATTTGAGTTCGGTTACACTCAGCTC-AACGACATATCATTTACAGCATAACTCAAGG
450 CTAAAGACATTCGAGTTCGACTACACTCAGCTCTAA-GACATATCATTTACAGCATAACTCAAGG
* ** * *
27855 CTAGAAGGGTTATCTATCACCAGAAGACCTTTGAGTTTGACTACGCTCAACTTCAAGGCACATC
514 CTAGAAGGGTTATCTATCACCAAAAGACCTTCAAGTTCGACTACGCTCAACTCCAAGGCACATC
* * * *
27919 ATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCT
1 ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCT
27954 ATGAACAAAA
Statistics
Matches: 537, Mismatches: 69, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
576 2 0.00
577 104 0.19
578 293 0.55
579 134 0.25
580 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (577 bp):
ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGAATACACTCA
GCTCCGAGGGCACATCATTTGAAACATAACTCAAGGCAAGAAGGGTTATATGCCAACAAAGACCT
TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCT
ATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTCCAAGGGCACATCATTTACAGCATAACT
CAGGATAGAAGGGTTATTAGTCACCAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCAAAAGACCTTCGAGTTCGACTACA
CTCAGCTCGAAGGAACATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCAACTAAAG
ACATTCGAGTTCGACTACACTCAGCTCTAAGACATATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTATCACCAAAAGACCTTCAAGTTCGACTACGCTCAACTCCAAGGCACATC
Found at i:27955 original size:84 final size:83
Alignment explanation
Indices: 26764--27953 Score: 1042
Period size: 84 Copynumber: 14.4 Consensus size: 83
26754 TAAAGAAACT
* * ** * *
26764 ATTTACAGCATAGCTTAAGTTGAGAAGGGCTATCTG---CCAAAGACCTTCGAGTTCGAATACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
* *
26826 TCAGCTTTGAGGGCACATC
66 TCAGC-TTCAAGGCACATC
* * * * * * *
26845 ATTTGCAACATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
* *
26910 TCAGCTCCAAGGCATATC
66 TCAGCTTCAAGGCACATC
* * * * * * * *
26928 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCAAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
*
26990 TCAGCTTCGAGGGCACATC
66 TCAGCTTC-AAGGCACATC
* *
27009 ATTTACAGCATAACTC-AGGCTAGAAGGGTTAT-TAGTCACCAAAAAACCTTCGAGTTCGACTAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCT-GTCACC-AAAGACCTTCGAGTTCGACTAC
* * *
27072 GCTCAGCTCCAAGGCATATC
64 ACTCAGCTTCAAGGCACATC
* * * ** * * *
27092 ATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGTTA--AAAGACCTTCGAGTTCGACTACGC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
27155 TCAGC-TCTAAGGCACATC
66 TCAGCTTC-AAGGCACATC
* * * * * * * *
27173 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTCTCTGCCAACTAAAGACCTTCGAGTTTGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACA
* *
27238 CTCAGC-TCTAAGACATATC
65 CTCAGCTTC-AAGGCACATC
* * * *
27257 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCAAGTTCGACTTCG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACA
*
27322 CTCAGCTCCAAGGCACATC
65 CTCAGCTTCAAGGCACATC
* * * * * * *
27341 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCTCGGGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
* * *
27403 TCAGCTCCGATGGCATATC
66 TCAGCTTC-AAGGCACATC
* * * *
27422 ATTTAAAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTTCA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACA
*
27487 CTCAGCTCCAAGGCACATC
65 CTCAGCTTCAAGGCACATC
* * * * * * *
27506 ATTTGCAGCATAACTTAAGTCGAGATGGGCTATCTG---CCAAAGACCCTT-GGGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGA-CCTTCGAGTTCGACTACA
* *
27567 CTCAGCTCCAAGGGCATATC
65 CTCAGCTTCAA-GGCACATC
* ** * *
27587 ATTTACATCATAACTCAAGGATAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTTCG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACA
27652 CTCAGC-TCTAAGGCACATC
65 CTCAGCTTC-AAGGCACATC
** ** * * * *
27671 ATTTGTAGCATAGGTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCTTTGAGTTCGACTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
* *
27733 TCAGCTTCGAGGGAACATC
66 TCAGCTTC-AAGGCACATC
* * * * * * **
27752 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACATTTGAGTTCGGTTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
* *
27817 TCAGC-TCAACGACATATC
66 TCAGCTTCAA-GGCACATC
* * * * *
27835 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAGAAGACCTTTGAGTTTGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCA-AAGACCTTCGAGTTCGACTACA
*
27900 CTCAACTTCAAGGCACATC
65 CTCAGCTTCAAGGCACATC
* * * *
27919 ATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCT
27954 ATGAACAAAA
Statistics
Matches: 901, Mismatches: 171, Indels: 71
0.79 0.15 0.06
Matches are distributed among these distances:
79 1 0.00
80 124 0.14
81 237 0.26
82 2 0.00
83 111 0.12
84 368 0.41
85 58 0.06
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
TCAGCTTCAAGGCACATC
Found at i:28319 original size:2 final size:2
Alignment explanation
Indices: 28314--28362 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
28304 TTTTTTACAC
* * *
28314 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AC AC AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
28355 AT GT AT AT
1 AT AT AT AT
28363 TATTTTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30544 original size:15 final size:16
Alignment explanation
Indices: 30519--30548 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30509 GATGATTATG
30519 AGAGTTGACCAAAAGT
1 AGAGTTGACCAAAAGT
30535 AGAG-TGACCAAAAG
1 AGAGTTGACCAAAAG
30549 GGTAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (16 bp):
AGAGTTGACCAAAAGT
Found at i:31582 original size:20 final size:20
Alignment explanation
Indices: 31546--31583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31536 CTAAAAATGG
*
31546 TATCGATACCCAGGGGTCGA
1 TATCGATACCCAAGGGTCGA
*
31566 TATCGATACTCAAGGGTC
1 TATCGATACCCAAGGGTC
31584 AGTACCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (20 bp):
TATCGATACCCAAGGGTCGA
Found at i:33122 original size:21 final size:21
Alignment explanation
Indices: 33098--33226 Score: 113
Period size: 21 Copynumber: 6.1 Consensus size: 21
33088 CATATTCGTA
*
33098 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCGCG
* *
33119 TTGCGATAGTCGAAGTTCGCA
1 TTGCGATAGTCCAAGTTCGCG
* *
33140 TTGTGATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* *
33161 TTGCGATATTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
33182 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
33203 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
33224 TTG
1 TTG
33227 GTATTGCATT
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
19 19 0.22
21 50 0.57
23 18 0.21
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:33223 original size:42 final size:42
Alignment explanation
Indices: 33118--33226 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
33108 CCAAGTTCGT
* * *
33118 GTTGCGATAGTCGAAGTTCGCATTGTGATTTATTCCAAGTTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
*
33160 GTTGCGATATTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
*
33202 GTTGCGATAGTCCAAGTTCGCGTTG
1 GTTGCGATAGTCGAAGTTCGCGTTG
33227 GTATTGCATT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (42 bp):
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
Found at i:33815 original size:5 final size:5
Alignment explanation
Indices: 33799--33846 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
33789 GCCGCCGCCG
33799 TCGTC T-GTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGT
1 TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGT
33847 GGTCGTGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 38 0.90
ACGTcount: A:0.00, C:0.38, G:0.21, T:0.42
Consensus pattern (5 bp):
TCGTC
Found at i:33854 original size:6 final size:6
Alignment explanation
Indices: 33843--33891 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
33833 TCGTCTCGTC
33843 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
33891 T
1 T
33892 AATACGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:33996 original size:19 final size:19
Alignment explanation
Indices: 33969--34039 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
33959 AATACCAATG
33969 CGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAA
* *
33988 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGACT--ATCGCAA
*
34009 CGCAAACTTGGACTATCACAA
1 CG--AACTTGGACTATCGCAA
*
34030 CGAATTTGGA
1 CGAACTTGGA
34040 ATAAATCGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 17 0.40
21 17 0.40
23 8 0.19
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:34007 original size:21 final size:21
Alignment explanation
Indices: 33981--34050 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
33971 AACTTGGACT
33981 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
34002 ATCGCAACGCAAACTTGGACT--
1 ATCGCAACG--AATTTGGAATAA
*
34023 ATCACAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
34044 ATCGCAA
1 ATCGCAA
34051 TGCGATAGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 8 0.21
21 23 0.59
23 8 0.21
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:34031 original size:42 final size:42
Alignment explanation
Indices: 33971--34050 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
33961 TACCAATGCG
*
33971 AACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCA
1 AACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCA
34013 AACTTGGACTATCACAACGAATTTGGAATAAATCGCAA
1 AACTTGGACTATCACAACGAATTTGGAATAAATCGCAA
34051 TGCGATAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (42 bp):
AACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCA
Found at i:54547 original size:27 final size:27
Alignment explanation
Indices: 54517--54579 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
54507 AAATACTTGA
54517 TCTATTTTCTTTCTTCTTTTCC-TTTT-T
1 TCTATTTTCTTT-TTC-TTTCCTTTTTCT
54544 TCTATTTTTCTTTTTCTTTCCTTTTTCT
1 TCTA-TTTTCTTTTTCTTTCCTTTTTCT
54572 TCTATTTT
1 TCTATTTT
54580 TTGTTGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.15
27 15 0.45
28 13 0.39
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.75
Consensus pattern (27 bp):
TCTATTTTCTTTTTCTTTCCTTTTTCT
Found at i:54556 original size:21 final size:20
Alignment explanation
Indices: 54521--54562 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
54511 ACTTGATCTA
54521 TTTTCTTTCTTCTTTTCCTT
1 TTTTCTTTCTTCTTTTCCTT
* *
54541 TTTTCTATTTTTCTTTTTCTT
1 TTTTCT-TTCTTCTTTTCCTT
54562 T
1 T
54563 CCTTTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTTCTTCTTTTCCTT
Found at i:54556 original size:28 final size:28
Alignment explanation
Indices: 54517--54580 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
54507 AAATACTTGA
54517 TCTA-TTTTCTTTCTTCTTTTCC-TTTT-T
1 TCTATTTTTCTTT-TTC-TTTCCTTTTTCT
54544 TCTATTTTTCTTTTTCTTTCCTTTTTCT
1 TCTATTTTTCTTTTTCTTTCCTTTTTCT
54572 TCTATTTTT
1 TCTATTTTT
54581 TGTTGTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 5 0.15
27 11 0.32
28 18 0.53
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (28 bp):
TCTATTTTTCTTTTTCTTTCCTTTTTCT
Found at i:54602 original size:28 final size:28
Alignment explanation
Indices: 54517--54602 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
54507 AAATACTTGA
* *
54517 TCTA-TTTTCTTTCTTCTTTTC-CTTTTT
1 TCTATTTTTCTTT-GTCTTTCCTCTTTTT
*
54544 TCTATTTTTCTTTTTCTTTCCT-TTTTCT
1 TCTATTTTTCTTTGTCTTTCCTCTTTT-T
54572 TCTATTTTT-TGTTGT-TTTCTCTCTTTTT
1 TCTATTTTTCT-TTGTCTTTC-CTCTTTTT
54600 TCT
1 TCT
54603 CTTCTCTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
27 20 0.39
28 27 0.53
29 4 0.08
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.74
Consensus pattern (28 bp):
TCTATTTTTCTTTGTCTTTCCTCTTTTT
Found at i:54617 original size:44 final size:41
Alignment explanation
Indices: 54539--54643 Score: 110
Period size: 44 Copynumber: 2.6 Consensus size: 41
54529 CTTCTTTTCC
* *
54539 TTTTTTCTATTTT-TC-TTTT-TCTTTCCTTTTTCTTCTAT
1 TTTTTTCTGTTTTCTCTTTTTTTCTTTCCTGTTTCTTCTAT
*
54577 TTTTTGT-TGTTTTCTCTCTTTTTTCTCTTCTCTGTTTCTTCTGT
1 TTTTT-TCTGTTTTCTCT-TTTTTTCT-TTC-CTGTTTCTTCTAT
*
54621 TTTTTTCTTTTTTCTCTTTTTTT
1 TTTTTTCTGTTTTCTCTTTTTTT
54644 GAATATAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
38 10 0.18
39 3 0.05
41 4 0.07
42 3 0.05
43 10 0.18
44 25 0.45
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (41 bp):
TTTTTTCTGTTTTCTCTTTTTTTCTTTCCTGTTTCTTCTAT
Found at i:54632 original size:9 final size:9
Alignment explanation
Indices: 54539--54643 Score: 54
Period size: 9 Copynumber: 11.6 Consensus size: 9
54529 CTTCTTTTCC
54539 TTTTTTC-T
1 TTTTTTCTT
*
54547 ATTTTTCTT
1 TTTTTTCTT
54556 TTTCTTTCCTT
1 TTT-TTT-CTT
* *
54567 TTTCTTCTA
1 TTTTTTCTT
*
54576 TTTTTTGTT
1 TTTTTTCTT
* *
54585 GTTTTCTCTC
1 -TTTTTTCTT
54595 TTTTTTC--
1 TTTTTTCTT
* * *
54602 TCTTCTCTG
1 TTTTTTCTT
*
54611 TTTCTTCTGT
1 TTTTTTCT-T
54621 TTTTTTCTT
1 TTTTTTCTT
*
54630 TTTTCTCTT
1 TTTTTTCTT
54639 TTTTT
1 TTTTT
54644 GAATATAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
7 5 0.07
8 6 0.09
9 35 0.50
10 18 0.26
11 6 0.09
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:59696 original size:15 final size:16
Alignment explanation
Indices: 59665--59698 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
59655 TTTATAACAG
59665 TTCTACCCCGACATGTT
1 TTCTACCCC-ACATGTT
59682 TTCTACCCC-CATGTT
1 TTCTACCCCACATGTT
59697 TT
1 TT
59699 GTTCAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.15, C:0.35, G:0.09, T:0.41
Consensus pattern (16 bp):
TTCTACCCCACATGTT
Found at i:61733 original size:14 final size:14
Alignment explanation
Indices: 61710--61750 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
61700 TGTAAAAATC
61710 AAATGACTGAAATGT
1 AAATG-CTGAAATGT
*
61725 AAATGCTGAAATTT
1 AAATGCTGAAATGT
*
61739 AAAGGCTGAAAT
1 AAATGCTGAAAT
61751 TAGAATAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (14 bp):
AAATGCTGAAATGT
Found at i:61779 original size:29 final size:29
Alignment explanation
Indices: 61754--61843 Score: 153
Period size: 29 Copynumber: 3.1 Consensus size: 29
61744 CTGAAATTAG
61754 AATAACATAAATTAAAGGGCAAAAATGTA
1 AATAACATAAATTAAAGGGCAAAAATGTA
61783 AATAACATAAATTAAAGGGCAAAAATGTA
1 AATAACATAAATTAAAGGGCAAAAATGTA
* * *
61812 AATAACAGAAATTAAAAGACAAAAATGTA
1 AATAACATAAATTAAAGGGCAAAAATGTA
61841 AAT
1 AAT
61844 GGTAGAAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (29 bp):
AATAACATAAATTAAAGGGCAAAAATGTA
Found at i:61784 original size:15 final size:14
Alignment explanation
Indices: 61762--61813 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
61752 AGAATAACAT
61762 AAATTAAAGGGCAA
1 AAATTAAAGGGCAA
*** *
61776 AAATGTAAATAACAT
1 AAAT-TAAAGGGCAA
61791 AAATTAAAGGGCAA
1 AAATTAAAGGGCAA
61805 AAATGTAAA
1 AAAT-TAAA
61814 TAACAGAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (14 bp):
AAATTAAAGGGCAA
Found at i:61823 original size:15 final size:15
Alignment explanation
Indices: 61773--61843 Score: 67
Period size: 14 Copynumber: 4.9 Consensus size: 15
61763 AATTAAAGGG
61773 CAAAAATGTAAATAA
1 CAAAAATGTAAATAA
* ***
61788 CATAAAT-TAAAGGG
1 CAAAAATGTAAATAA
61802 CAAAAATGTAAATAA
1 CAAAAATGTAAATAA
*
61817 CAGAAAT-TAAA-AGA
1 CAAAAATGTAAATA-A
61831 CAAAAATGTAAAT
1 CAAAAATGTAAAT
61844 GGTAGAAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
13 1 0.02
14 21 0.50
15 20 0.48
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (15 bp):
CAAAAATGTAAATAA
Found at i:61850 original size:29 final size:29
Alignment explanation
Indices: 61754--61859 Score: 131
Period size: 29 Copynumber: 3.7 Consensus size: 29
61744 CTGAAATTAG
* * *
61754 AATAACATAAATTAAAGGGCAAAAATGTA
1 AATAACAGAAATTAAAAGACAAAAATGTA
* * *
61783 AATAACATAAATTAAAGGGCAAAAATGTA
1 AATAACAGAAATTAAAAGACAAAAATGTA
61812 AATAACAGAAATTAAAAGACAAAAATGTA
1 AATAACAGAAATTAAAAGACAAAAATGTA
***
61841 AATGGTAGAAATTAAAAGA
1 AATAACAGAAATTAAAAGA
61860 AATCAAATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (29 bp):
AATAACAGAAATTAAAAGACAAAAATGTA
Found at i:61853 original size:58 final size:57
Alignment explanation
Indices: 61719--61856 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 57
61709 CAAATGACTG
* ** * * *
61719 AAATGTAAATGCT-GAAATTTAAAGGCTGAAATTAGAATAACATAAATTAAAGGGCAA
1 AAATGTAAATGATAGAAA-TTAAAGGCAAAAATTAGAATAACAGAAATTAAAAGACAA
* * *
61776 AAATGTAAATAACATAAATTAAAGGGCAAAAATGTA-AATAACAGAAATTAAAAGACAA
1 AAATGTAAATGATAGAAATTAAA-GGCAAAAAT-TAGAATAACAGAAATTAAAAGACAA
*
61834 AAATGTAAATGGTAGAAATTAAA
1 AAATGTAAATGATAGAAATTAAA
61857 AGAAATCAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
57 15 0.23
58 48 0.74
59 2 0.03
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (57 bp):
AAATGTAAATGATAGAAATTAAAGGCAAAAATTAGAATAACAGAAATTAAAAGACAA
Found at i:71127 original size:2 final size:2
Alignment explanation
Indices: 71120--71231 Score: 117
Period size: 2 Copynumber: 57.5 Consensus size: 2
71110 AGTTTTTAGA
71120 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
* * * * * *
71162 AT -T AT AT GT GT -T AT AGT AT AT AC AT AT AT TT AA AA AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
71203 AT AGT AT AT AT AT -T AT AT -T AT AT AT -T AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
71232 ATAGGATGTA
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
1 5 0.05
2 87 0.91
3 4 0.04
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73171 original size:20 final size:20
Alignment explanation
Indices: 73148--73185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
73138 TTTTTTAGCA
73148 TTTAATT-ACTTATTTTTAAT
1 TTTAATTGA-TTATTTTTAAT
*
73168 TTTATTTGATTATTTTTA
1 TTTAATTGATTATTTTTA
73186 TATCAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTAATTGATTATTTTTAAT
Found at i:78982 original size:29 final size:29
Alignment explanation
Indices: 78950--79075 Score: 78
Period size: 29 Copynumber: 4.3 Consensus size: 29
78940 CATTTTACAC
78950 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
** *** * *
78979 AAATATTATTTTTTTTTCGAA--AATTACTA
1 AAATAGCA--CCATTTTCGAATTAATTCCCA
79008 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
* ****
79037 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
* *
79066 GAATAACACC
1 AAATAGCACC
79076 GGTCAACGGT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
27 7 0.10
28 3 0.04
29 54 0.75
31 8 0.11
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATAGCACCATTTTCGAATTAATTCCCA
Found at i:79122 original size:13 final size:13
Alignment explanation
Indices: 79104--79145 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
79094 AACGGTCAAC
79104 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
79117 GGTCAAC-GGTCT
1 GGTCAACGGGTCG
*
79129 GGTAAACGGGTCG
1 GGTCAACGGGTCG
79142 GGTC
1 GGTC
79146 GGGTAAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:79127 original size:7 final size:7
Alignment explanation
Indices: 79075--79112 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
79065 AGAATAACAC
79075 CGGTCAA
1 CGGTCAA
79082 CGGTCAA
1 CGGTCAA
79089 CGGTCAA
1 CGGTCAA
79096 CGGTCAA
1 CGGTCAA
79103 CGGTCAA
1 CGGTCAA
79110 CGG
1 CGG
79113 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:79150 original size:18 final size:18
Alignment explanation
Indices: 79124--79175 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
79114 TCGGGTCAAC
*
79124 GGTCTGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
79142 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
79160 GGTCGGGTAAACGGGT
1 GGTCGGGTAAACGGGT
79176 AAACGGGTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.46, T:0.21
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:79202 original size:9 final size:9
Alignment explanation
Indices: 79188--79255 Score: 82
Period size: 9 Copynumber: 7.1 Consensus size: 9
79178 ACGGGTCGTG
79188 ACCGGTCAA
1 ACCGGTCAA
79197 ACCGGTCAAA
1 ACCGGTC-AA
79207 ACCGGTTCAAA
1 ACCGG-TC-AA
*
79218 ACCGGTTAA
1 ACCGGTCAA
79227 ACCGGTCAAA
1 ACCGGTC-AA
*
79237 ACCGGTTAA
1 ACCGGTCAA
79246 ACCGGTCAA
1 ACCGGTCAA
79255 A
1 A
79256 ACCAGTTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
9 26 0.50
10 16 0.31
11 10 0.19
ACGTcount: A:0.37, C:0.28, G:0.21, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:79210 original size:19 final size:19
Alignment explanation
Indices: 79188--79258 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
79178 ACGGGTCGTG
*
79188 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
79207 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
79227 ACCGGTCAAAACCGGTTAA
1 ACCGGTCAAAACCGGTTAA
79246 ACCGGTCAAAACC
1 ACCGGTCAAAACC
79259 AGTTTCCAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 32 0.65
20 9 0.18
21 8 0.16
ACGTcount: A:0.37, C:0.30, G:0.20, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:79222 original size:30 final size:28
Alignment explanation
Indices: 79188--79255 Score: 109
Period size: 30 Copynumber: 2.4 Consensus size: 28
79178 ACGGGTCGTG
79188 ACCGGTCAAACCGGTCAAAACCGGTTCAAA
1 ACCGGTCAAACCGGTCAAAACCGGTT--AA
*
79218 ACCGGTTAAACCGGTCAAAACCGGTTAA
1 ACCGGTCAAACCGGTCAAAACCGGTTAA
79246 ACCGGTCAAA
1 ACCGGTCAAA
79256 ACCAGTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 11 0.31
30 25 0.69
ACGTcount: A:0.37, C:0.28, G:0.21, T:0.15
Consensus pattern (28 bp):
ACCGGTCAAACCGGTCAAAACCGGTTAA
Done.