Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004500.1 Hibiscus syriacus cultivar Beakdansim tig00009928_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: 63110
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:3409 original size:25 final size:26
Alignment explanation
Indices: 3380--3433 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3370 AAAAACAAAG
*
3380 CTTG-AAAATAAAAGAAAACTGAAAA
1 CTTGAAAAATAAAAGAAAACGGAAAA
* *
3405 CTTGAAAAATAAAATAAAAGGGAAAA
1 CTTGAAAAATAAAAGAAAACGGAAAA
3431 CTT
1 CTT
3434 TAATAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.19
Consensus pattern (26 bp):
CTTGAAAAATAAAAGAAAACGGAAAA
Found at i:4479 original size:22 final size:21
Alignment explanation
Indices: 4445--4485 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4435 AATGCATTTG
*
4445 ATTTTTTTCTTTTTTTTTCAT
1 ATTTTTTTCTTTTGTTTTCAT
*
4466 ATTTTTGTTGTTTTGTTTTC
1 ATTTTT-TTCTTTTGTTTTC
4486 CATTCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (21 bp):
ATTTTTTTCTTTTGTTTTCAT
Found at i:8851 original size:21 final size:21
Alignment explanation
Indices: 8825--8878 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
8815 TATTAATATA
*
8825 AATTTCAAGTTTCTTGTTATG
1 AATTTCAAGTTTCATGTTATG
*
8846 AATTTCAAGTTTGATGTTATG
1 AATTTCAAGTTTCATGTTATG
* *
8867 GATGTCAAGTTT
1 AATTTCAAGTTT
8879 ATTGAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (21 bp):
AATTTCAAGTTTCATGTTATG
Found at i:9062 original size:43 final size:42
Alignment explanation
Indices: 8975--9527 Score: 552
Period size: 43 Copynumber: 12.9 Consensus size: 42
8965 TATTTGTATA
* * *
8975 AAAAACGCCGCTATAGATATGACCTTTTACGACGTTTGTTCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC
* * *
9017 AAAAACGCCGCTATAGATATGGCTTTTTGCGGCGTTTGTATCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCC
*
9060 AAAAACGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC
* * * * **
9102 AAAAATGACGCTATCGATCTGACCTTTTGCGGCGTTTATTTT
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC
* * ** * *
9144 GAAAACGCCGCTATATATCTTGATATTTTGTGGCGTTTGTTCT
1 AAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCC
* * ** **
9187 GAAAACGCCGCTATAGATATTGACCTTTTGCGATGTTT-TTGGA
1 AAAAACGCCGCTATAGAT-CTGACCTTTTGCGGCGTTTGTT-CC
9230 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCC
1 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGT-TCC
* * ** *
9274 AAAAACGCCGCTATAGATCTGACCTTTTACGGTGTTTGAGAACA
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTT--GTTCC
*
9318 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCT
1 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGT-TCC
* * *
9362 AAAAACGCCGCTATAGATCTGACCTTTTGTGGCATTTGTTCA
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC
* ** * * * **
9404 AAAAATGATGCTATTGATATGACCTTTTGCGGCCTTT-TTGG
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC
* *
9445 AAAAACGCCGTTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCC
* *
9488 AAAAAAACGCCGCAATAGATCTTGACCTATTGCGGCGTTT
1 --AAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTT
9528 TTTGTTCTCA
Statistics
Matches: 419, Mismatches: 76, Indels: 29
0.80 0.15 0.06
Matches are distributed among these distances:
41 15 0.04
42 138 0.33
43 153 0.37
44 63 0.15
45 49 0.12
46 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC
Found at i:9076 original size:85 final size:84
Alignment explanation
Indices: 8974--9527 Score: 572
Period size: 85 Copynumber: 6.5 Consensus size: 84
8964 GTATTTGTAT
* * * * *
8974 AAAAAACGCCGCTATAGATATGACCTTTTACGACGTTTGTTCCAAAAACGCCGCTATAGATATGG
1 AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
*
9039 CTTTTTGCGGCGTTTGTATC
66 CCTTTTGCGGCGTTTGT-TC
* * * * *
9059 CAAAAACGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAATGACGCTATCGATCTGA
1 AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
* *
9124 CCTTTTGCGGCGTTTATTT
66 CCTTTTGCGGCGTTTGTTC
** * ** * ** *
9143 TGAAAACGCCGCTATATATCTTGATATTTTGTGGCGTTTGTTCTGAAAACGCCGCTATAGATATT
1 AAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-CT
** *
9208 GACCTTTTGCGATGTTT-TTGG
64 GACCTTTTGCGGCGTTTGTT-C
9229 AAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT
1 AAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCT
* * **
9294 GACCTTTTACGGTGTTTGAGAAC
64 GACCTTTTGCGGCGTTT--GTTC
*
9317 AAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATCT
1 AAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCT
* *
9382 GACCTTTTGTGGCATTTGTTC
64 GACCTTTTGCGGCGTTTGTTC
* ** * * * ** * *
9403 AAAAAATGATGCTATTGATATGACCTTTTGCGGCCTTT-TTGGAAAAACGCCGTTATAAATCTCG
1 AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-G
9467 ACCTTTTGCGGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTT-C
* *
9488 AAAAAAACGCCGCAATAGATCTTGACCTATTGCGGCGTTT
1 -AAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTT
9528 TTTGTTCTCA
Statistics
Matches: 389, Mismatches: 68, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
83 19 0.05
84 37 0.10
85 124 0.32
86 97 0.25
87 35 0.09
88 77 0.20
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (84 bp):
AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
CCTTTTGCGGCGTTTGTTC
Found at i:20125 original size:60 final size:60
Alignment explanation
Indices: 20086--20223 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 60
20076 GTTTATTTAT
* **
20086 TATTAAGAATTATAAAATAGTCATTTGATTATAAAATATTATTTTGTTGAGTCTTTCGAC
1 TATTAAGAATTATAAAATAGTCATTTGATTATAAAATATTATTTTATTGAGTCTTTTAAC
* **
20146 TATTAA-AAGTTATAAAATTGTTGTTTGATTATAAAA-AGTTATTTTATTGAGTCTTTTAAC
1 TATTAAGAA-TTATAAAATAGTCATTTGATTATAAAATA-TTATTTTATTGAGTCTTTTAAC
*
20206 TATTAAGAGTTATAAAAT
1 TATTAAGAATTATAAAAT
20224 GATCACTCGA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.04
60 64 0.94
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (60 bp):
TATTAAGAATTATAAAATAGTCATTTGATTATAAAATATTATTTTATTGAGTCTTTTAAC
Found at i:20194 original size:29 final size:30
Alignment explanation
Indices: 20104--20201 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
20094 ATTATAAAAT
*
20104 AGTCATTTGATTATAAAATA-TTATTTTGTTG
1 AGTC-TTTGATTATAAAA-AGTTATTTTATTG
* * ***
20135 AGTCTTTCGACTATTAAAAGTTATAAAATTG
1 AGTCTTT-GATTATAAAAAGTTATTTTATTG
* *
20166 -TTGTTTGATTATAAAAAGTTATTTTATTG
1 AGTCTTTGATTATAAAAAGTTATTTTATTG
20195 AGTCTTT
1 AGTCTTT
20202 TAACTATTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 18 0.37
30 12 0.24
31 19 0.39
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (30 bp):
AGTCTTTGATTATAAAAAGTTATTTTATTG
Found at i:24717 original size:30 final size:30
Alignment explanation
Indices: 24683--24804 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 30
24673 CTGCTGCTCC
*
24683 TGTAAATGTAGCTTGTGCGACTGCAGTTCA
1 TGTAAATGCAGCTTGTGCGACTGCAGTTCA
* * * *
24713 TGTAAATGCAGCACCTTCTGCAATTGCAGTTCG
1 TGTAAATGCAG---CTTGTGCGACTGCAGTTCA
* * *
24746 GGTAAATGCAACTTGTGTGACTGCAGTTCA
1 TGTAAATGCAGCTTGTGCGACTGCAGTTCA
* ** *
24776 TGTAAGTGCAGCTCATGCGACTGCTGTTC
1 TGTAAATGCAGCTTGTGCGACTGCAGTTC
24805 GTGCTCAAGC
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
30 46 0.66
33 24 0.34
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (30 bp):
TGTAAATGCAGCTTGTGCGACTGCAGTTCA
Found at i:24842 original size:63 final size:63
Alignment explanation
Indices: 24775--25022 Score: 354
Period size: 63 Copynumber: 3.9 Consensus size: 63
24765 ACTGCAGTTC
*
24775 ATGTAAGTGCAGCTCATGCGACTGCTGTTCGTGCTCAAGCTGCTGCACAATCCCGAAATCACG
1 ATGTAAGTGCAGCTCATGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAATCACG
* * *
24838 ATGTACGTGCAGCTCATGCGACTGCTGTTTGTGTTCAAGCTGCTGCACAATCCCAAAATCACG
1 ATGTAAGTGCAGCTCATGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAATCACG
* * ** *
24901 ATGTAAGTGCAGCTCATGCGACTTCTGTTCGTGTTCAAGCTGCTGCACAATCACGAAATGGCA
1 ATGTAAGTGCAGCTCATGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAATCACG
* * * * *
24964 ATGTAAGTGCTGCTCATGC-AGCTGCTGTTCATGTTCGAGCTGTTGCACGATCCCGAAAT
1 ATGTAAGTGCAGCTCATGCGA-CTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAAT
25023 GGCAATGCTT
Statistics
Matches: 165, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
62 1 0.01
63 164 0.99
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (63 bp):
ATGTAAGTGCAGCTCATGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAATCACG
Found at i:27024 original size:3 final size:3
Alignment explanation
Indices: 27016--27045 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
27006 TTTATGATTA
*
27016 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27046 TAAGAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28462 original size:3 final size:3
Alignment explanation
Indices: 28454--28553 Score: 128
Period size: 3 Copynumber: 32.7 Consensus size: 3
28444 TTATTTATTA
*
28454 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * ** *
28501 TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28549 AAT AA
1 AAT AA
28554 ATTTAAATGA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
3 77 0.93
4 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:28813 original size:76 final size:76
Alignment explanation
Indices: 28685--29043 Score: 571
Period size: 76 Copynumber: 4.7 Consensus size: 76
28675 TGGAAATGTT
*
28685 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCC
1 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAAACATCAAAAAGCTCCC
*
28750 GAAGGCTTTTTA
65 GAAGGCTTTTTG
* * * * *
28762 G-AAACATCATGCACTGTAGGACTTAAAGACGACCCTG-AGGCTTTGAGAACATCAAAAAGCTCC
1 GAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGCTTT-AAAACATCAAAAAGCTCC
28825 CGAAGGCTTTTTG
64 CGAAGGCTTTTTG
* *
28838 G-AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTAAAACATCAAAAAGCTCCCG
1 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTAAAACATCAAAAAGCTCCCG
28902 AAGGCTTTTTG
66 AAGGCTTTTTG
28913 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTAAAACATCAAAAAGCTCCCG
1 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTAAAACATCAAAAAGCTCCCG
28978 AAGGCTTTTTG
66 AAGGCTTTTTG
*
28989 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAAACATCA
29044 TGCACTGAAG
Statistics
Matches: 264, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
75 32 0.12
76 222 0.84
77 10 0.04
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
GAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:28995 original size:152 final size:152
Alignment explanation
Indices: 28687--29621 Score: 1174
Period size: 152 Copynumber: 6.1 Consensus size: 152
28677 GAAATGTTGA
* * *
28687 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * * * * *
28752 AGGCTTTTTAGAAACATCATGCACTGTAGGACTTAAAGACGACCCTG-AGGCTTTGAGAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGCTTTGAAAACATCA
28816 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
*
28839 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTT-AAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28903 AGGCTTTTTGGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAAACATCA
66 AGGCTTTTTGG-AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
28967 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
* *
28990 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGG
1 -AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAA-A-CAT---C--AA--
* * * * *** **
29055 ACTTACAGATAACCCGAAGGC--TTTGAAAACATCAAAAAGCTCCTGAA-GGCTTTTTG--GAAA
55 A---A-AGCT--CCCGAAGGCTTTTTGGAAACATC---ATGC-ACTGAAGGGCTTACAGATGACC
* ** ** * * * *
29115 C-ATCATGCACTGAAGGGC-TTACAGATG-ACCCGAAGGCTTTTTGG
110 CGA--AGGCTTTGAA-AACATCA-AAAAGCTCCCGAAGGCTTTTTGG
*
29159 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
29224 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
29289 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
* * *
29311 AAACATCATGCACTGAA-GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * *
29375 AGGCTTTTTGGAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
29440 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
29462 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * * *
29527 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCTAAGGTTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
29592 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
29614 AAACATCA
1 AAACATCA
29622 AAAAGCTCCC
Statistics
Matches: 681, Mismatches: 64, Indels: 76
0.83 0.08 0.09
Matches are distributed among these distances:
150 5 0.01
151 220 0.32
152 302 0.44
153 3 0.00
154 18 0.03
155 2 0.00
156 3 0.00
158 1 0.00
159 1 0.00
160 2 0.00
161 2 0.00
162 1 0.00
163 1 0.00
165 3 0.00
166 10 0.01
167 13 0.02
168 47 0.07
169 38 0.06
170 9 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:29041 original size:45 final size:45
Alignment explanation
Indices: 28974--29088 Score: 176
Period size: 45 Copynumber: 2.5 Consensus size: 45
28964 TCAAAAAGCT
* *
28974 CCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTT-GAAAACATCATGCACTGAAGGACTTACAGATAA
29022 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATAA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATAA
*
29067 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
29089 AAAAGCTCCT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
45 52 0.81
46 4 0.06
48 8 0.12
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATAA
Found at i:29168 original size:47 final size:47
Alignment explanation
Indices: 29099--29201 Score: 206
Period size: 47 Copynumber: 2.2 Consensus size: 47
29089 AAAAGCTCCT
29099 GAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC
29146 GAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC
29193 GAAGGCTTT
1 GAAGGCTTT
29202 GAAAACATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (47 bp):
GAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC
Found at i:29199 original size:123 final size:123
Alignment explanation
Indices: 28898--29277 Score: 685
Period size: 123 Copynumber: 3.1 Consensus size: 123
28888 TCAAAAAGCT
28898 CCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAAA
1 CCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
28962 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGGCTTACAGATGA
65 CATCAAAAAGCTCCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGGCTTACAGATGA
* * *
29022 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATAACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
*
29085 ATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
29143 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
29208 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
29266 CCCGAAGGCTTT
1 CCCGAAGGCTTT
29278 GAAAACATCA
Statistics
Matches: 245, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
121 80 0.33
122 36 0.15
123 121 0.49
124 8 0.03
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (123 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:29223 original size:76 final size:76
Alignment explanation
Indices: 29143--29621 Score: 845
Period size: 76 Copynumber: 6.3 Consensus size: 76
29133 TTACAGATGA
*
29143 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
29208 ATCAAAAAGCT
66 ATCAAAAAGCT
*
29219 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
29284 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
29295 CCCGAAGGCTTTTTGGAAACATCATGCACTGAA-GACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
29359 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
29370 CTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGA-TTAAAGATGACCCGAAGGTTTTGAAAA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAA-GGACTTACAGATGACCCGAAGGCTTTGAAAA
29434 CATCAAAAAGCT
65 CATCAAAAAGCT
29446 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
29511 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
29522 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
29587 ATCAAAAAGCT
66 ATCAAAAAGCT
29598 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
29622 AAAAGCTCCC
Statistics
Matches: 388, Mismatches: 12, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
75 74 0.19
76 312 0.80
77 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:29540 original size:227 final size:228
Alignment explanation
Indices: 29143--29621 Score: 897
Period size: 227 Copynumber: 2.1 Consensus size: 228
29133 TTACAGATGA
* *
29143 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGCTTTGAAAAC
*
29208 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
29273 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA-GACTTACAG
131 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
29337 ATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
196 ATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
* *
29370 CTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGCTTTGAAAAC
29435 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
29500 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
131 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
*
29565 ATGATCCTAAGGTTTTGAAAACATCAAAAAGCT
196 ATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
29598 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
29622 AAAAGCTCCC
Statistics
Matches: 244, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
227 180 0.74
228 64 0.26
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (228 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
ATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
Found at i:29612 original size:31 final size:31
Alignment explanation
Indices: 29577--29652 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
29567 GATCCTAAGG
* *
29577 TTTTGAAAACATCAAAAAGCTCCCGAAGGCT
1 TTTTGGAAACATCAAAAAGCTCCCAAAGGCT
29608 TTTTGGAAACATCAAAAAGCTCCCAAAGGCT
1 TTTTGGAAACATCAAAAAGCTCCCAAAGGCT
29639 TTTTGGAAACATCA
1 TTTTGGAAACATCA
29653 TGCACTGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (31 bp):
TTTTGGAAACATCAAAAAGCTCCCAAAGGCT
Found at i:29620 original size:107 final size:107
Alignment explanation
Indices: 29493--29728 Score: 422
Period size: 107 Copynumber: 2.2 Consensus size: 107
29483 TTACAGATGA
* *
29493 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
*
29556 GACTTACAGATGATCCTAAGGTTTTGAAAACATCAAAAAGCT
66 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
29598 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
29663 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
66 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
*
29705 TCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
29729 TGCACTGAAG
Statistics
Matches: 125, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
105 9 0.07
107 116 0.93
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (107 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
Found at i:29628 original size:183 final size:183
Alignment explanation
Indices: 29417--29804 Score: 708
Period size: 183 Copynumber: 2.1 Consensus size: 183
29407 TTAAAGATGA
* *
29417 CCCGAAGG--TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
29480 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
*
29545 ATGCACTGAAGGACTTACAGATGATCCTAAGGTTTTGAAAACATCAAAAAGCT
131 ATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
29598 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
* * *
29663 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATC
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
29728 ATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
131 ATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
29781 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
29805 TGCACTGAAG
Statistics
Matches: 199, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
181 8 0.04
183 191 0.96
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (183 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
ATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
Found at i:29656 original size:259 final size:259
Alignment explanation
Indices: 29349--29880 Score: 967
Period size: 259 Copynumber: 2.1 Consensus size: 259
29339 GACCCTAAGG
* * *
29349 TTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGA-TTAAAG
1 TTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAA-GGACTTAAAG
29413 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
65 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
29478 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
130 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
*
29543 TCATGCACTGAAGGACTTACAGATGATCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
195 TCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
*
29608 TTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTAAAGA
* *
29673 TGACCCTAAGGTTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAA
66 TGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
* *
29738 GGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
131 GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
29803 CATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
196 CATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
29867 TTTTGGAAACATCA
1 TTTTGGAAACATCA
29881 TGCACTGAAG
Statistics
Matches: 263, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
258 3 0.01
259 260 0.99
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (259 bp):
TTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTAAAGA
TGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
CATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
Found at i:29813 original size:335 final size:334
Alignment explanation
Indices: 29266--29956 Score: 1237
Period size: 335 Copynumber: 2.1 Consensus size: 334
29256 TTACAGATGA
* *
29266 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
29329 ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCA
66 ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCA
29394 TGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
131 TGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
29459 TGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCC
196 TGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCC
* * *
29524 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCTAAGGTTTTGAAAACAT
261 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
29589 CAAAAAGCT
326 CAAAAAGCT
29598 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAA-
29663 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT-TCCGAAGGCTTTTTGGAAACAT
65 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCT-CGAAGGCTTTTTGGAAACAT
* *
29727 CATGCACTGAA-GGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
129 CATGCACTGAAGGGA-TTAAAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* *
29791 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGC
193 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
29856 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
258 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
29921 CATCAAAAAGCT
323 CATCAAAAAGCT
*
29933 CCCAAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
29957 TGCACTGAAG
Statistics
Matches: 344, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
332 9 0.03
334 55 0.16
335 280 0.81
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (334 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAG
ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCA
TGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
TGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCC
CGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCT
Found at i:30081 original size:76 final size:76
Alignment explanation
Indices: 29608--30055 Score: 833
Period size: 76 Copynumber: 5.9 Consensus size: 76
29598 CCCGAAGGCT
*
29608 TTTTGGAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
29673 TGACCCTAAGG
66 TGACCCTAAGG
* *
29684 TTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
29749 TGACCCTAAGG
66 TGACCCTAAGG
*
29760 TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
29825 TGACCCTAAGG
66 TGACCCTAAGG
*
29836 TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
*
29901 TGACCCGAAGG
66 TGACCCTAAGG
*
29912 CTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
29977 TGACCCTAAGG
66 TGACCCTAAGG
29988 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
30053 TGA
66 TGA
30056 GGGAAATAGT
Statistics
Matches: 363, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 363 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (76 bp):
TTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
TGACCCTAAGG
Found at i:32231 original size:74 final size:76
Alignment explanation
Indices: 32094--32263 Score: 220
Period size: 74 Copynumber: 2.3 Consensus size: 76
32084 GTTGTGGGCC
* *
32094 TTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAACAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTGGCTAATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
* * *
32158 TTAAATGGGTT
66 TGAAAAGAGTT
* * * ** *
32169 TTCAGCATGCCCCAACATTTTGCTGATA-AA-TATTCAGAATATTTCAACATTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTGGCTAATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
32232 TGAAAAGAGTT
66 TGAAAAGAGTT
32243 TTCAGCATGCCCCAACATTTG
1 TTCAGCATGCCCCAACATTTG
32264 CTTCTTGTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 55 0.67
75 19 0.23
76 8 0.10
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (76 bp):
TTCAGCATGCCCCAACATTTGGCTAATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
TGAAAAGAGTT
Found at i:33617 original size:114 final size:114
Alignment explanation
Indices: 33406--33631 Score: 398
Period size: 114 Copynumber: 2.0 Consensus size: 114
33396 GATCATGCAG
* *
33406 TTCACCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCACCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
33471 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
33520 TTCATCTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCACCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
33585 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
33632 CATGACACTT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCACCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:35640 original size:14 final size:15
Alignment explanation
Indices: 35623--35676 Score: 62
Period size: 14 Copynumber: 3.7 Consensus size: 15
35613 CTTGATTCAA
35623 TTTTTTCTT-T-TTCT
1 TTTTTTCTTCTGTT-T
35637 TTTTTTCTTCTGTTT
1 TTTTTTCTTCTGTTT
35652 TTTGTTT-TT-TGTTT
1 TTT-TTTCTTCTGTTT
35666 TTTTTTCTTCT
1 TTTTTTCTTCT
35677 TTCTTTGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.09
14 19 0.54
15 8 0.23
16 5 0.14
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTCTGTTT
Found at i:35659 original size:26 final size:26
Alignment explanation
Indices: 35623--35673 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35613 CTTGATTCAA
35623 TTTTTTCTTTTTCT-TTTTTTCTTCTG
1 TTTTTTCTTTTT-TGTTTTTTCTTCTG
* *
35649 TTTTTTGTTTTTTGTTTTTTTTTCT
1 TTTTTTCTTTTTTGTTTTTTCTTCT
35674 TCTTTCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (26 bp):
TTTTTTCTTTTTTGTTTTTTCTTCTG
Found at i:35884 original size:2 final size:2
Alignment explanation
Indices: 35877--35902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35867 ACAACAAATG
35877 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
35903 TAAAGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41105 original size:3 final size:3
Alignment explanation
Indices: 41097--41127 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41087 TATTTATGAC
*
41097 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
41128 TAAGAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42522 original size:3 final size:3
Alignment explanation
Indices: 42514--42628 Score: 160
Period size: 3 Copynumber: 37.7 Consensus size: 3
42504 TTATTTATTA
*
42514 AAT AAT AAT AAT -AT ATAT AAT ATT AAT AAT AAT AAT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT
*
42561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
42609 AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
42629 ATTTAAATGA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.02
3 89 0.88
4 10 0.10
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:46275 original size:13 final size:13
Alignment explanation
Indices: 46230--46278 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
46220 AAAGTTGAGT
46230 TATTATATTCAAA
1 TATTATATTCAAA
* * *
46243 TATTTTTTTGAAA
1 TATTATATTCAAA
46256 TAAATTATATTCAAA
1 T--ATTATATTCAAA
46271 TATTATAT
1 TATTATAT
46279 AAAAAATAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 18 0.64
15 10 0.36
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (13 bp):
TATTATATTCAAA
Found at i:47228 original size:17 final size:17
Alignment explanation
Indices: 47200--47235 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
47190 TTAAATTATA
47200 TAAAAGCCCCAAAATACC
1 TAAAAGCCCCAAAAT-CC
47218 TAAAA-CCCCAAAATCC
1 TAAAAGCCCCAAAATCC
47234 TA
1 TA
47236 TCCTTAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.50, C:0.33, G:0.03, T:0.14
Consensus pattern (17 bp):
TAAAAGCCCCAAAATCC
Found at i:47332 original size:34 final size:34
Alignment explanation
Indices: 47287--47358 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
47277 GCAACTGTCC
*
47287 TAGTCCCTGACATCCTCCTAATCATATGTCATCG
1 TAGTCCCTGACATCCTCCTAATCATATGCCATCG
*
47321 TAGTCCTTGACATCCTCCTAATCATATGCCATCG
1 TAGTCCCTGACATCCTCCTAATCATATGCCATCG
47355 TAGT
1 TAGT
47359 TGTCGTCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (34 bp):
TAGTCCCTGACATCCTCCTAATCATATGCCATCG
Found at i:48379 original size:21 final size:21
Alignment explanation
Indices: 48355--48417 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
48345 TCAATGAAAG
48355 GACTTAACATTTTGATTAAAA
1 GACTTAACATTTTGATTAAAA
** * * *
48376 GACTTCTCCTTTTGATGAAAG
1 GACTTAACATTTTGATTAAAA
* *
48397 GGCTTAACATTTTCA-TAAAA
1 GACTTAACATTTTGATTAAAA
48417 G
1 G
48418 GATTTAATCT
Statistics
Matches: 30, Mismatches: 12, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (21 bp):
GACTTAACATTTTGATTAAAA
Found at i:50313 original size:23 final size:24
Alignment explanation
Indices: 50258--50313 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
50248 AGTTGAGGGT
* ** *
50258 TCTATGCGGTCCTTCGGGACAAAT
1 TCTATGTGGTCCTTCAAGACAAAA
*
50282 TCTACGTGGTCCTTCAAGA-AAAA
1 TCTATGTGGTCCTTCAAGACAAAA
50305 TCTATGTGG
1 TCTATGTGG
50314 CACTTTGGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
TCTATGTGGTCCTTCAAGACAAAA
Done.