Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008595.1 Hibiscus syriacus cultivar Beakdansim tig00111544_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: 53556
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2636 original size:3 final size:3
Alignment explanation
Indices: 2630--2684 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
2620 ATATTATTAT
* * * *
2630 TAA TAA TAC TAA TAA TAC TAT TAC TAA TAA TAA TAA TAA TTAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
2675 TAA TAA TAA T
1 TAA TAA TAA T
2685 TGTAGACACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2838 original size:71 final size:68
Alignment explanation
Indices: 2756--2893 Score: 181
Period size: 68 Copynumber: 2.0 Consensus size: 68
2746 TTTAAACTAT
*
2756 ATAATATATAG-TTTTGAAAACA-GTTTGAAAATATTTATACATTATATAATTTTTAAACATTTT
1 ATAATATATAGTTTTTAAAAACATGTTTG--AATA--TATACATTATAT-ATTTTTAAACATTTT
2819 GAAAATAA
61 GAAAATAA
* * *
2827 ATAATATATAGTTTTTAAAAACATTTTTGAATATATATATTATATATTTTTAACCATTTTGAAAA
1 ATAATATATAGTTTTTAAAAACATGTTTGAATATATACATTATATATTTTTAAACATTTTGAAAA
2892 TA
66 TA
2894 TGTATAGTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
68 21 0.34
69 11 0.18
71 15 0.25
72 10 0.16
73 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (68 bp):
ATAATATATAGTTTTTAAAAACATGTTTGAATATATACATTATATATTTTTAAACATTTTGAAAA
TAA
Found at i:2871 original size:36 final size:35
Alignment explanation
Indices: 2718--2879 Score: 131
Period size: 36 Copynumber: 4.7 Consensus size: 35
2708 TTTATATATC
* * *
2718 TATATAT-ATATATGGTTTTAAAAAAC-TTTTTAA
1 TATATATAATATATAGTTTTTAAAAACATTTTGAA
* *
2751 -ACTATATAATATATAG-TTTTGAAAACAGTTTGAAAA
1 TA-TATATAATATATAGTTTTTAAAAACATTTTG--AA
* *
2787 TATTTATACATTATATAATTTTT--AAACATTTTGAA
1 TATATATA-A-TATATAGTTTTTAAAAACATTTTGAA
* *
2822 AATAAATAATATATAGTTTTTAAAAACATTTTTGAA
1 TATATATAATATATAGTTTTTAAAAACA-TTTTGAA
*
2858 TATATATATTATATA-TTTTTAA
1 TATATATAATATATAGTTTTTAA
2880 CCATTTTGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
32 1 0.01
33 24 0.24
34 11 0.11
35 19 0.19
36 26 0.25
37 11 0.11
38 6 0.06
39 4 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
TATATATAATATATAGTTTTTAAAAACATTTTGAA
Found at i:3075 original size:4 final size:4
Alignment explanation
Indices: 3066--3104 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
3056 TACATTATTA
* *
3066 TTAT TTAT TTAC TTAT TTAT TTAT TTAT ATTAT TAAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TT
3105 TATCTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:4469 original size:24 final size:26
Alignment explanation
Indices: 4416--4473 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
4406 TATTTAGTAC
**
4416 CATTTTTTTTATATTTTTTATCTTTT
1 CATTTTTTTTATATTTTTTATCTTAA
4442 CATTTTTTATT-TATTTTTT-TC-TAA
1 CATTTTTT-TTATATTTTTTATCTTAA
4466 CATTTTTT
1 CATTTTTT
4474 GCCTTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 2 0.07
26 16 0.55
27 2 0.07
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (26 bp):
CATTTTTTTTATATTTTTTATCTTAA
Found at i:5910 original size:43 final size:43
Alignment explanation
Indices: 5849--5932 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
5839 AAACAAGCTC
5849 GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTTTT
1 GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTTTT
*
5892 GGTAGAAAGTGAAAGTCGGAGATGCAGTCCTTCGAGATCTT
1 GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTT
5933 CTTTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (43 bp):
GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTTTT
Found at i:6229 original size:19 final size:19
Alignment explanation
Indices: 6191--6235 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
6181 ATTTAGACAT
6191 TTTGCA-TTTCTTATTCTC
1 TTTGCATTTTCTTATTCTC
* *
6209 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTCTC
6228 TTTGCATT
1 TTTGCATT
6236 CACATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.11, C:0.16, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTGCATTTTCTTATTCTC
Found at i:9803 original size:84 final size:82
Alignment explanation
Indices: 9595--10487 Score: 970
Period size: 84 Copynumber: 10.9 Consensus size: 82
9585 GCTCAAGGCC
* * *
9595 AGAAGGG-TACCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* *
9659 CAGAATAGCTTAAGTCG
66 CAGCATAACTTAAGTCG
* * * * * * *
9676 AGAAGGGCTATCTGC--CAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATT
1 AGAAGGGTTATCTGCAACAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
* * * *
9738 TACAGCATAACTCAAGGCT
64 TGCAGCATAACTTAAGTCG
* * *
9757 AGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
9822 GTAGAATAGCTTAAGTCG
65 GCAGCATAACTTAAGTCG
* * * * * * *
9840 AGAAGGGCTATCTGC--CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGAGCATAACATTT
1 AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTT
* * * *
9903 ACAGCATAACTCAAGGCT
65 GCAGCATAACTTAAGTCG
* * *
9921 AGAAGGGTTATCTGTCAACACA-ACCGTCGAGTTCGACTACGCTCAG-TTCAACGGCACATCATT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
9984 TGCAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * *
10003 AGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTG-CAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
10068 TGCAGCACAACTTAAGTCT
64 TGCAGCATAACTTAAGTCG
* *
10087 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCAT
1 AGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
*
10151 TTGCAGCATAGCTTAAGTCG
63 TTGCAGCATAACTTAAGTCG
* ** * * * *
10171 AGAAGGGCTATCTGC--C-AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
*
10233 GCAGCATAACTTAAGTCA
65 GCAGCATAACTTAAGTCG
* *
10251 AGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATA-CTATT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC-ATT
* *
10315 TGCAGCACAACTTAAGTCT
64 TGCAGCATAACTTAAGTCG
* *
10334 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
10399 TGCAGCATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * *
10418 AGAAGGGCTATCTGC--CAAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTA
1 AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
10481 CAGCATA
66 CAGCATA
10488 GCTCAAGGCA
Statistics
Matches: 680, Mismatches: 106, Indels: 53
0.81 0.13 0.06
Matches are distributed among these distances:
79 23 0.03
80 150 0.22
81 83 0.12
82 52 0.08
83 116 0.17
84 251 0.37
85 5 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (82 bp):
AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAACTTAAGTCG
Found at i:9855 original size:164 final size:164
Alignment explanation
Indices: 9613--10512 Score: 1073
Period size: 164 Copynumber: 5.5 Consensus size: 164
9603 ACCTGCCACC
*
9613 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * * * *
9678 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGGCATATCATTTGCAG
* * * *
9743 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTTAAGTCTAGAAGGGTTATCTGTCAACA
* * *
9777 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * * * * *
9842 AAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGAGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGGCATATCATTTGCAG
* *
9907 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
131 CATAACTTAAGTCTAGAAGGGTTATCTGTCAACA
* * * *
9941 CA-ACCGTCGAGTTCGACTACGCTCAG-TTCAACGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * * *
10004 GAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTATGCTCAGCTCCAA-GGCATATCATT
65 GAAGGGCTATCTGCCAA--AGA-CCCTT-GAGTTCGACTACGCTCAGCTTCAAGGGCATATCATT
* * *
10068 TGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
126 TGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCAAC-A
*
10108 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGA
** * * * *
10172 GAAGGGCTATCTGCC-AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
65 GAAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGGCATATCATTTGCA
* *
10236 GCATAACTTAAGTCAAGAAGGGTTATCTGTCAACC
130 GCATAACTTAAGTCTAGAAGGGTTATCTGTCAACA
* * * *
10271 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATA-CTATTTGCAGCACAACTTAAGTCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC-ATTTGCAGCATAGCTTAAGTCGA
* * * * *
10335 GAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
65 GAAGGGCTATCTG-C--C-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGGCATATCATT
* * *
10399 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CA
126 TGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTCAACA
* * * * * *
10435 AAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC-GA
10500 GAAGGGCTATCTG
65 GAAGGGCTATCTG
10513 TCAATAAAAT
Statistics
Matches: 634, Mismatches: 84, Indels: 35
0.84 0.11 0.05
Matches are distributed among these distances:
162 5 0.01
163 149 0.24
164 257 0.41
165 17 0.03
166 46 0.07
167 64 0.10
168 95 0.15
169 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGGCATATCATTTGCAG
CATAACTTAAGTCTAGAAGGGTTATCTGTCAACA
Found at i:10051 original size:247 final size:246
Alignment explanation
Indices: 9605--10512 Score: 1098
Period size: 247 Copynumber: 3.7 Consensus size: 246
9595 AGAAGGGTAC
* * * *
9605 CTGCCAC-CAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCT
1 CTGCCACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
* ** * * *
9669 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAA
66 TAAGTCGAGAAGGGCTATCTGCCAAACA-CCTCGAGTTCGACTACACTCAGCTTCAAGGGCACAT
* * * ** * *
9734 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACG
130 CATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * * * *
9799 CTCAGCTCCAAGGCACATCATTTGTAGAATAGCTTAAGTCGAGAAGGGCTAT
195 CTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGT
* * * * * * * *
9851 CTG-C-C-AAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGAGCATAACATTTACAGCATAAC
1 CTGCCACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAG-GCACATCATTTGCAGCATAGC
* * * * * * *
9913 TCAAGGCTAGAAGGGTTATCTGTCAACACAACCGTCGAGTTCGACTACGCTCAG-TTCAACGGCA
65 TTAAGTCGAGAAGGGCTATCTGCCAA-AC-ACC-TCGAGTTCGACTACACTCAGCTTCAAGGGCA
* * *
9977 CATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGAC
127 CATCATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGAC
*
10042 TATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGT
191 TACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGT
10098 CTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAATGGCACATCATTTGCAGCATAG
1 CTGCC-ACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCATTTGCAGCATAG
* * *
10162 CTTAAGTCGAGAAGGGCTATCTGCCAAGAC-CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
64 CTTAAGTCGAGAAGGGCTATCTGCCAA-ACACCTCGAGTTCGACTACACTCAGCTTCAAGGGCAC
*
10226 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGTCAACC-AAGACCTTCGAGTTCGACT
128 ATCATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
10290 ACGCTCAGCTCCAAGGCATA-CTATTTGCAGCACAACTTAAGTCTAGAAGGGTTGT
192 ACGCTCAGCTCCAAGGCATATC-ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGT
*
10345 CTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
1 CTGCC-ACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGC
* * * * *
10410 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCAACTCCAA-GGCACA
65 TTAAGTCGAGAAGGGCTATCTGCCAAACACC-TCGAGTTCGACTACACTCAGCTTCAAGGGCACA
* * * *
10474 TCATTTACAGCATAGCTCAAGGCAAAGAAGGGCTATCTG
129 TCATTTACAGCATAACTTAAGTC-AAGAAGGGTTATCTG
10513 TCAATAAAAT
Statistics
Matches: 568, Mismatches: 78, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
244 31 0.05
245 38 0.07
246 51 0.09
247 286 0.50
248 91 0.16
250 44 0.08
251 27 0.05
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (246 bp):
CTGCCACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
TAAGTCGAGAAGGGCTATCTGCCAAACACCTCGAGTTCGACTACACTCAGCTTCAAGGGCACATC
ATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGT
Found at i:11119 original size:38 final size:36
Alignment explanation
Indices: 11067--11382 Score: 238
Period size: 38 Copynumber: 8.7 Consensus size: 36
11057 ATATATCTAT
* * * *
11067 ATATATATATTATATGGTTTTAAAAAACTTTTTTAAA
1 ATATATATAATATATAGTTTT-AAAAACATTTTGAAA
*
11104 CATATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 -ATATATATAATATATAGTTTTAAAAACAT-TTTGAAA
* * *
11142 ATATTTATACATTATATAATTTTTAAAACATTTTGAAA
1 ATATATATA-A-TATATAGTTTTAAAAACATTTTGAAA
* *
11180 ATAAATATAATATATAGTTTTTAAAAACATTTTTGAAT
1 ATATATATAATATATAG-TTTTAAAAACA-TTTTGAAA
* * *
11218 ATATATATATTATATAGTTTT-TAACCATTTTGAAA
1 ATATATATAATATATAGTTTTAAAAACATTTTGAAA
* * **
11253 ATATGTATAGT-T-T--TTAAAAAAAACATTTTGAAAAA
1 ATATATATAATATATAGTT-TTAAAAACATTTTG--AAA
* *
11288 CATATATATATTATATAGTTTTAAAAATATTTTG-AA
1 -ATATATATAATATATAGTTTTAAAAACATTTTGAAA
* * *
11324 A-A-A-A-ACTATATAGCTTTAAAAACATTTTTAAGAA
1 ATATATATAATATATAGTTTTAAAAACA-TTTTGA-AA
*
11358 ATATATATAATATATAATTTTAAAA
1 ATATATATAATATATAGTTTTAAAA
11383 TGTTTTTTAA
Statistics
Matches: 221, Mismatches: 36, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
31 19 0.09
32 5 0.02
33 11 0.05
34 5 0.02
35 21 0.10
36 22 0.10
37 31 0.14
38 77 0.35
39 28 0.13
40 2 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTAAAAACATTTTGAAA
Found at i:11461 original size:7 final size:7
Alignment explanation
Indices: 11433--11473 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
11423 TTACATTACA
11433 TTATTA-
1 TTATTAT
11439 TTATTTAT
1 TTA-TTAT
11447 TTACTTAT
1 TTA-TTAT
11455 TTATTAT
1 TTATTAT
11462 TTATTA-
1 TTATTAT
11468 TTATTA
1 TTATTA
11474 ATTTTATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 9 0.28
7 13 0.41
8 10 0.31
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATTAT
Found at i:12561 original size:2 final size:2
Alignment explanation
Indices: 12554--12608 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
12544 GGTCCTTATT
12554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12596 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
12609 TTTGCAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12889 original size:24 final size:26
Alignment explanation
Indices: 12836--12894 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
12826 TATTTAGTAC
**
12836 CATTTTTTTTATATTTTTTATCTTTT
1 CATTTTTTTTATATTTTTTATCTTAA
12862 CATTTTTTATT-TATTTTTT-TC-TAA
1 CATTTTTT-TTATATTTTTTATCTTAA
12886 CATTTTTTT
1 CATTTTTTT
12895 GCCTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 2 0.07
26 16 0.53
27 2 0.07
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
CATTTTTTTTATATTTTTTATCTTAA
Found at i:14191 original size:34 final size:32
Alignment explanation
Indices: 14111--14199 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
14101 GTTAGTATTT
* * *
14111 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
14143 TTTATGTAAATATTATTTTATTAT-TAAAATAATA
1 TTTATATAATTATTATTTT-TTATAT-AAAT-ATA
14177 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
14200 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 16 0.35
33 7 0.15
34 22 0.48
35 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:15939 original size:21 final size:21
Alignment explanation
Indices: 15909--15956 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
15899 GCAGGGGTAC
* *
15909 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
15930 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
15951 ATGCCA
1 ATGCCA
15957 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:15986 original size:21 final size:21
Alignment explanation
Indices: 15960--16053 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
15950 TATGCCATCT
* *
15960 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
15981 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
16002 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
16023 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
16044 CCGCAGGGTT
1 CCGCAGGGTT
16054 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:16624 original size:33 final size:34
Alignment explanation
Indices: 16574--16669 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 34
16564 TAAATGTTTT
*
16574 TAAAATACAAATTATATTATTCGAAATTTAAA-A
1 TAAAATAAAAATTATATTATTCGAAATTTAAATA
* *
16607 TAAAATAAAAATAATATTATTC-AAA-TTAAATT
1 TAAAATAAAAATTATATTATTCGAAATTTAAATA
* *
16639 TAAAATATAAATTATAGTATTCGAAATTTAA
1 TAAAATAAAAATTATATTATTCGAAATTTAA
16670 CATTAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
31 5 0.09
32 22 0.41
33 23 0.43
34 4 0.07
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
TAAAATAAAAATTATATTATTCGAAATTTAAATA
Found at i:17375 original size:125 final size:125
Alignment explanation
Indices: 17056--17657 Score: 1116
Period size: 125 Copynumber: 4.8 Consensus size: 125
17046 TTTAAGTTAT
*
17056 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
17121 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
17182 ACCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
17247 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
17308 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
17372 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
17433 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
17498 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
17558 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
17623 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
17658 CCGATTATAG
Statistics
Matches: 466, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
125 279 0.60
126 187 0.40
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (125 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:17501 original size:251 final size:250
Alignment explanation
Indices: 17056--17657 Score: 1116
Period size: 251 Copynumber: 2.4 Consensus size: 250
17046 TTTAAGTTAT
*
17056 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
17121 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
17186 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
130 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCG-
* *
17251 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
194 CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
17308 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
17372 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTGTCCC
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCC
17437 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
130 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
*
17502 CCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
195 CCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
17558 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
17623 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
17658 CCGATTATAG
Statistics
Matches: 342, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
250 87 0.25
251 254 0.74
252 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (250 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCCC
GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCC
CCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:17738 original size:8 final size:8
Alignment explanation
Indices: 17725--17765 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
17715 TCACAATCTT
17725 TCAAATTC
1 TCAAATTC
17733 TCAAATTC
1 TCAAATTC
* *
17741 CCAAACTC
1 TCAAATTC
17749 T-AAATTC
1 TCAAATTC
17756 TCAAATTC
1 TCAAATTC
17764 TC
1 TC
17766 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:20788 original size:12 final size:13
Alignment explanation
Indices: 20755--20792 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
20745 AAATACATAA
20755 ATATATTTAATAT
1 ATATATTTAATAT
*
20768 ATTTATTTAATAT
1 ATATATTTAATAT
20781 A-ATATTTAATAT
1 ATATATTTAATAT
20793 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:20843 original size:20 final size:20
Alignment explanation
Indices: 20806--20859 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
20796 TAGTTATAAT
*
20806 TTTTACATTATAATCGAAACA
1 TTTTACATAAT-ATCGAAACA
20827 TTTTACATAATATCGAAACA
1 TTTTACATAATATCGAAACA
20847 TTTTACATAATAT
1 TTTTACATAATAT
20860 ATTATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.41
Consensus pattern (20 bp):
TTTTACATAATATCGAAACA
Found at i:24274 original size:12 final size:12
Alignment explanation
Indices: 24257--24287 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24247 GACTAGGACT
24257 TATTGTTATTAC
1 TATTGTTATTAC
*
24269 TATTGTTATTAT
1 TATTGTTATTAC
24281 TATTGTT
1 TATTGTT
24288 TATTTCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (12 bp):
TATTGTTATTAC
Found at i:28758 original size:2 final size:2
Alignment explanation
Indices: 28751--28805 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
28741 GTAATTTGTA
* *
28751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT AA AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28791 A- AT A- AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT
28806 TAATAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
1 5 0.11
2 39 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28798 original size:22 final size:22
Alignment explanation
Indices: 28749--28824 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
28739 ATGTAATTTG
*
28749 TAATATA-TATATATAT-ATATA
1 TAATATATTATATAAATAATA-A
28770 TATATATATT-TAATAAATAATAA
1 TA-ATATATTAT-ATAAATAATAA
*
28793 TAATATATTATATTAATAATAA
1 TAATATATTATATAAATAATAA
*
28815 TTATA-ATTAT
1 TAATATATTAT
28825 TATTATGAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 7 0.15
22 27 0.57
23 10 0.21
24 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATTATATAAATAATAA
Found at i:28823 original size:16 final size:17
Alignment explanation
Indices: 28786--28823 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28776 TATTTAATAA
28786 ATAA-TAATAATATATT
1 ATAATTAATAATATATT
28802 AT-ATTAATAATA-ATT
1 ATAATTAATAATATATT
28817 ATAATTA
1 ATAATTA
28824 TTATTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATTAATAATATATT
Found at i:28828 original size:22 final size:22
Alignment explanation
Indices: 28785--28829 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28775 ATATTTAATA
28785 AATAATAATAATATATTATATT
1 AATAATAATAATATATTATATT
*
28807 AATAATAATTATA-ATTATTATT
1 AATAATAATAATATATTA-TATT
28829 A
1 A
28830 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAATAATAATATATTATATT
Found at i:29445 original size:74 final size:73
Alignment explanation
Indices: 29205--29557 Score: 634
Period size: 73 Copynumber: 4.8 Consensus size: 73
29195 AACTCGAAAT
29205 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
*
29270 TTCAAGTGA
65 TTCGAGTGA
* * *
29279 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTT
29344 TCGAGTGA
66 TCGAGTGA
*
29352 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTTTCTGT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTT-TGT
29417 TTCGAGTGA
65 TTCGAGTGA
*
29426 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTT
29491 TCGAGTGA
66 TCGAGTGA
29499 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
29558 GCTATTTGAA
Statistics
Matches: 267, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
73 175 0.66
74 92 0.34
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTT
TCGAGTGA
Found at i:29472 original size:147 final size:146
Alignment explanation
Indices: 29205--29557 Score: 652
Period size: 147 Copynumber: 2.4 Consensus size: 146
29195 AACTCGAAAT
29205 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
29270 TTCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
65 TTCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
29335 AGTTCTGTTTCGAGTGA
130 AGTTCTGTTTCGAGTGA
*
29352 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTTTCTGT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTT-TGT
* *
29417 TTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
65 TTCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
*
29482 AGTTTTGTTTCGAGTGA
130 AGTTCTGTTTCGAGTGA
29499 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
29558 GCTATTTGAA
Statistics
Matches: 200, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
146 38 0.19
147 162 0.81
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (146 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTT
TCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
GTTCTGTTTCGAGTGA
Found at i:29846 original size:165 final size:165
Alignment explanation
Indices: 29599--29923 Score: 499
Period size: 165 Copynumber: 2.0 Consensus size: 165
29589 TATGGATGTG
* * * * *
29599 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTC
** *
29664 AAAAAAGATTGAATGAGAAACTATGAAAATTGTTTTCTCATTATTTTTCAAAATAACAAGTTAAT
66 AAAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACAAGTTAAT
**
29729 TGGGTAACATGCCCCAATCTCAAGATAATGTTGTT
131 TGGGTAACATAACCCAATCTCAAGATAATGTTGTT
29764 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
* * * * *
29829 C-GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATATCATGTTGA
65 CAAAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACAAGTTAA
29893 TTGGGTAACATAACCCAATCTCAAGATAATG
130 TTGGGTAACATAACCCAATCTCAAGATAATG
29924 CTCATTCTTG
Statistics
Matches: 144, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
165 102 0.71
166 42 0.29
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTC
AAAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACAAGTTAAT
TGGGTAACATAACCCAATCTCAAGATAATGTTGTT
Found at i:41438 original size:28 final size:26
Alignment explanation
Indices: 41380--41438 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
41370 CTCATTTCTC
*
41380 TTCTCTCTAGAGAAGAGAAATATTAT
1 TTCTCTCTAGAGAAGAGAAATATAAT
41406 TTCTCTCTAGAGAAGAGAAATATAAT
1 TTCTCTCTAGAGAAGAGAAATATAAT
41432 TTCTCTC
1 TTCTCTC
41439 GCTTCTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (26 bp):
TTCTCTCTAGAGAAGAGAAATATAAT
Found at i:42238 original size:2 final size:2
Alignment explanation
Indices: 42231--42284 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
42221 GTAATTTGTA
* *
42231 AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT AA AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42270 A- AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
42285 ATAATAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:42269 original size:3 final size:3
Alignment explanation
Indices: 42256--42298 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
42246 TATATATATT
*
42256 TAA TAAA TAA TAA TAA TAA TATA TATA TAA TAA TAA TTA TAA T
1 TAA T-AA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA T
42299 TATTATTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 26 0.72
4 10 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:45648 original size:24 final size:24
Alignment explanation
Indices: 45621--45712 Score: 68
Period size: 24 Copynumber: 4.0 Consensus size: 24
45611 TCTTATGTGG
45621 TTTTTATAAATAATATTAGTATAA
1 TTTTTATAAATAATATTAGTATAA
* **
45645 TTTTCATGGTATAA-ATATAG-AT--
1 TTTTTAT-AAATAATAT-TAGTATAA
* *
45667 TTTTTGTTAATAATA-TAGTATAA
1 TTTTTATAAATAATATTAGTATAA
* *
45690 TTTTTATAAATAAAACTAGTATA
1 TTTTTATAAATAATATTAGTATA
45713 TAGTTTTGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
20 3 0.06
21 6 0.12
22 6 0.12
23 12 0.24
24 17 0.33
25 7 0.14
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTTTATAAATAATATTAGTATAA
Found at i:46548 original size:24 final size:25
Alignment explanation
Indices: 46492--46566 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
46482 AAAACGAGCG
46492 AAAAGCTTTAGATCTAACAGATTCA
1 AAAAGCTTTAGATCTAACAGATTCA
46517 AAAAGCTTTAGATCTAACAGATT-A
1 AAAAGCTTTAGATCTAACAGATTCA
46541 AAAAGCTTTAGATCTAACAGATTCA
1 AAAAGCTTTAGATCTAACAGATTCA
46566 A
1 A
46567 GGTGCATGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
24 24 0.49
25 25 0.51
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (25 bp):
AAAAGCTTTAGATCTAACAGATTCA
Found at i:46859 original size:35 final size:35
Alignment explanation
Indices: 46813--46888 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
46803 AAAACAGTCC
* *
46813 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
46848 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
46883 TCAATT
1 TCAATT
46889 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:47884 original size:28 final size:26
Alignment explanation
Indices: 47853--47913 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
47843 AGTTGATACA
*
47853 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTT-AAA-AATAAATTTAAGAATT
* * *
47881 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAAGAATT
47907 ATATTTT
1 ATATTTT
47914 TCATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.69
27 2 0.07
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAAGAATT
Found at i:50992 original size:14 final size:13
Alignment explanation
Indices: 50971--51000 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
50961 TTTAATCGGA
50971 AATAAATAATAAT
1 AATAAATAATAAT
50984 AATATAATAATAAT
1 AATA-AATAATAAT
50998 AAT
1 AAT
51001 TTTCCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAATAATAAT
Done.