Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1265460 original size:69 final size:69
Alignment explanation
Indices: 1265251--1265482 Score: 200
Period size: 69 Copynumber: 3.3 Consensus size: 69
1265241 ATATATATAT
* ** *
1265251 ATATATATATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAATATATAGTTTTTAAAACA
1 ATATATA-ATATATAG-TTTTAAAACATATTTT-AAAA-AAATATAATATATAG-TTTTAAAATA
1265316 TTTTTGAAAA
61 TTTTTG-AAA
* ** * * *
1265326 ATTATATAATATATAGTTTTAAAAACATATTTTGAAAACTTAT-ATA-ATATTTTTAAATTAATT
1 A-TATATAATATATAGTTTT-AAAACATATTTTAAAAAAATATAATATATAGTTTTAAAATATTT
1265389 TTGAAA
64 TTGAAA
* ** * *
1265395 ACTATATAATATATAGTTTT-GAATTTTTTTTAAAAAAATATAATATATAGTTTAAAAATATTTT
1 A-TATATAATATATAGTTTTAAAACATATTTTAAAAAAATATAATATATAGTTTTAAAATATTTT
1265459 TGAAA
65 TGAAA
* *
1265464 TATATATATTACATAGTTT
1 -ATATATAATATATAGTTT
1265483 ATATTATATT
Statistics
Matches: 129, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
67 14 0.11
68 3 0.02
69 56 0.43
70 14 0.11
71 3 0.02
72 3 0.02
73 3 0.02
74 7 0.05
75 20 0.16
76 6 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (69 bp):
ATATATAATATATAGTTTTAAAACATATTTTAAAAAAATATAATATATAGTTTTAAAATATTTTT
GAAA
Found at i:1265553 original size:28 final size:28
Alignment explanation
Indices: 1265497--1265559 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 28
1265487 TATATTATAA
*
1265497 TTATTTTTTTAATTTATTTTCTTTCGTT
1 TTATTTTTTTAATTTATTTTCTATCGTT
*
1265525 TTATTGTTTATTAATTTCTTTT-TAT-GTT
1 TTATT-TTT-TTAATTTATTTTCTATCGTT
1265553 TT-TTTTT
1 TTATTTTT
1265560 CTAGGTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 3 0.10
27 2 0.06
28 10 0.32
29 5 0.16
30 11 0.35
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (28 bp):
TTATTTTTTTAATTTATTTTCTATCGTT
Found at i:1269754 original size:98 final size:95
Alignment explanation
Indices: 1269496--1269755 Score: 290
Period size: 96 Copynumber: 2.7 Consensus size: 95
1269486 AAATTATAAT
* * * * * *
1269496 ATTATATATATACAATAAAGCTTGAGATGTCCCTATAAAGCAATTGGTTAAACGTCCCAACTTTA
1 ATTATA-ATATACAATAAA-CTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
*
1269561 TGGATGAGATTCAGCTAGCCTGATAAAAGGTG
64 TGGATAAGATTCAGCTAGCCTGATAAAAGGTG
* * * *
1269593 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCTGTCTTTAT
1 ATTATAATATACAATAAA-CTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
*
1269658 GGATAATATTCAGCTAGCCTGAT-AAAGGTG
65 GGATAAGATTCAGCTAGCCTGATAAAAGGTG
* * * *
1269688 ATTATTATATCTATACAGTGATA-TTAAGTTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGGCT
1 ATTA-TA-A--TATACAAT-AAACTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACT
1269752 TTAT
61 TTAT
1269756 AGATTCAACT
Statistics
Matches: 141, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
95 11 0.08
96 74 0.52
97 7 0.05
98 40 0.28
99 7 0.05
100 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (95 bp):
ATTATAATATACAATAAACTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATG
GATAAGATTCAGCTAGCCTGATAAAAGGTG
Found at i:1270981 original size:240 final size:240
Alignment explanation
Indices: 1270552--1271027 Score: 794
Period size: 240 Copynumber: 2.0 Consensus size: 240
1270542 AACCAACTTT
* *
1270552 CTCTATATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGATCAACTTCACAGATAAG
1 CTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGACCAACTTCACAGATAAG
*
1270617 GGGCTTCCCAGTTTCATTCAGAGTCAAATTCAACTTCACGGCGAAGGATATTGGACTCTAAACAA
66 GGGCTTCCCAGTTTCATTCAGAGTCAAATTCAACTTCACGGCGAAGGATATTGGACTCGAAACAA
* *
1270682 TACAAGCTTGGATTTCAACTTCACGACGAATGATATTCAAGTCAAGGCTCAACTTCACAACGAAT
131 TACAAGCTTGGATTTCAACTTCAAGACGAATGATATTCAAGTCAAGGCTCAACTTCACAACGAAA
*
1270747 GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAA
196 GGGCCATCCACGATTTCAACTTCACGACGAAGCATATCGTGCCAA
* *
1270792 CTCTAGATTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAAGCCCAACTTCAC-GATGAA
1 CTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGACCAACTTCACAGAT-AA
* * *
1270856 GGGGCTTCCCAGTTTCATTCAGAGTCAATTTCAACTTCATGGCGAAGGATATTGGACTCGAAATA
65 GGGGCTTCCCAGTTTCATTCAGAGTCAAATTCAACTTCACGGCGAAGGATATTGGACTCGAAACA
* *
1270921 ATACAATCTTGGATTTCAACTTCAAGATGAA-GAATATTCAAGTCAAGGCTCAACTTCACAACGA
130 ATACAAGCTTGGATTTCAACTTCAAGACGAATG-ATATTCAAGTCAAGGCTCAACTTCACAACGA
*
1270985 AAGGGCCATCCACGGTTTCAACTTCACGACGAAGCATATCGTG
194 AAGGGCCATCCACGATTTCAACTTCACGACGAAGCATATCGTG
1271028 TTCATTTGCA
Statistics
Matches: 220, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
239 4 0.02
240 216 0.98
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (240 bp):
CTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGACCAACTTCACAGATAAG
GGGCTTCCCAGTTTCATTCAGAGTCAAATTCAACTTCACGGCGAAGGATATTGGACTCGAAACAA
TACAAGCTTGGATTTCAACTTCAAGACGAATGATATTCAAGTCAAGGCTCAACTTCACAACGAAA
GGGCCATCCACGATTTCAACTTCACGACGAAGCATATCGTGCCAA
Found at i:1271219 original size:27 final size:27
Alignment explanation
Indices: 1271181--1271266 Score: 172
Period size: 27 Copynumber: 3.2 Consensus size: 27
1271171 CGACTACGCT
1271181 TAGCTCCAAGGCACATCATTTGCAACA
1 TAGCTCCAAGGCACATCATTTGCAACA
1271208 TAGCTCCAAGGCACATCATTTGCAACA
1 TAGCTCCAAGGCACATCATTTGCAACA
1271235 TAGCTCCAAGGCACATCATTTGCAACA
1 TAGCTCCAAGGCACATCATTTGCAACA
1271262 TAGCT
1 TAGCT
1271267 TAAGGCAAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (27 bp):
TAGCTCCAAGGCACATCATTTGCAACA
Found at i:1271328 original size:84 final size:84
Alignment explanation
Indices: 1271236--1271892 Score: 561
Period size: 84 Copynumber: 7.9 Consensus size: 84
1271226 TTTGCAACAT
* * * * *
1271236 AGCTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGAAGGGTTATTTGCCAGCAAAAGACC
1 AGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACC
* *
1271301 TTCGAGTTTGACTATGCTC
66 TTCGAGTTCGACTACGCTC
* * * * * *
1271320 AGCTCCAAGGCATATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACC
1 AGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACC
1271385 TTCGAGTTCGACTACGCTC
66 TTCGAGTTCGACTACGCTC
* * * * *
1271404 AGCTTCAAGGTACATCATTTGTAGCATAGCTCAAGGCTAGAAGGGTTATCTGCC-ACGAAAAAGA
1 AGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC--AAAAGA
*
1271468 CCTTCGAGTTCGACTATGCTC
64 CCTTCGAGTTCGACTACGCTC
* * * * *
1271489 AGCTCCAAGGCATATCATTTGTAGCATAACTCAAGCCTAA-AAGGTTTATTTGCCAACAAAAGAC
1 AGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGAC
1271553 CTTCGAGTTCGACTACGCTC
65 CTTCGAGTTCGACTACGCTC
* * * * * * *
1271573 AGCTTCAAGGCATGTCATTTGCAACATAGCTCAAGGCTAGTAGGGCTATCT-TC--C-AAAGATC
1 AGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGA-C
* * *
1271634 C-TCAAGTTCGATTACACTC
65 CTTCGAGTTCGACTACGCTC
* * * * * ** *
1271653 AGCTTCAAGGGCACATCATTTGTAGTATAACTCAAGGTTAGAAGGGTTATCTGTCAAC-AAAGAC
1 AGCTCCAA-GGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGAC
* * *
1271717 CTTTGAGTTCGATTACACTC
65 CTTCGAGTTCGACTACGCTC
* * * * *
1271737 AGCT-CAACGGCACATCATTTACAGTATAGCTCAAGGCTAA-AAGGGCTATATG-C--C-AAAGA
1 AGCTCCAA-GGCATATCATTTGCAGCATAGCTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGA
* * **
1271796 CCCTCGAGTTCGATTATACTC
64 CCTTCGAGTTCGACTACGCTC
* * * * * * * * * *
1271817 AGCTTCGAGGGCACATCCTTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGTCATC-AAATAC
1 AGC-TCCAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGAC
1271881 CTTCGAGTTCGA
65 CTTCGAGTTCGA
1271893 TTCCATTCAG
Statistics
Matches: 474, Mismatches: 81, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
80 56 0.12
81 72 0.15
82 5 0.01
83 44 0.09
84 225 0.47
85 69 0.15
86 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
AGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACC
TTCGAGTTCGACTACGCTC
Found at i:1271553 original size:169 final size:164
Alignment explanation
Indices: 1271236--1271892 Score: 728
Period size: 164 Copynumber: 4.0 Consensus size: 164
1271226 TTTGCAACAT
* * * * *
1271236 AGCTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGAAGGGTTATTTGCCAGCAAAAGACC
1 AGCTTCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGGGCTATCTGCC--C-AAAGACC
* * * ** *
1271301 TTCGAGTTTGACTATGCTCAGCTCCAAGGCATATCATTTACAGTATAACTCAAGGCTAGAAGGGT
63 TTCGAGTTCGACTATACTCAGCTCCAAGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGT
*
1271366 TATCTACCAACCAAAGACCTTCGAGTTCGACTACGCTC
128 TATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTC
* * * *
1271404 AGCTTCAAGGTACATCATTTGTAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCACGAAAAAGAC
1 AGCTTCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGGGCTATCTGCC-C---AAAGAC
* * * * *
1271469 CTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTCAAGCCTAAAAGGT
62 CTTCGAGTTCGACTATACTCAGCTCCAAGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGG
*
1271534 TTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
127 TTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTC
** * *
1271573 AGCTTCAAGGCATGTCATTTGCAACATAGCTCAAGGCTAGTAGGGCTATCT-TCCAAAGATCC-T
1 AGCTTCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGGGCTATCTGCCCAAAGA-CCTT
* * * * * *
1271636 CAAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGTAGTATAACTCAAGGTTAGAAGGGTT
65 CGAGTTCGACTATACTCAGCTCCAA-GGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTT
* * * *
1271701 ATCTGTCAACAAAGACCTTTGAGTTCGATTACACTC
129 ATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTC
* ** * * *
1271737 AGC-TCAACGGCACATCATTTACAGTATAGCTCAAGGCTAAAAGGGCTATATG-CCAAAGACCCT
1 AGCTTCAA-GGCACATCATTTGCAACATAGCTCAAGGCTAGAAGGGCTATCTGCCCAAAGACCTT
* * * *
1271800 CGAGTTCGATTATACTCAGCTTCGAGGGCACATCCTTTGTAGCATAACTCAAGGCTAGAAGGGTT
65 CGAGTTCGACTATACTCAGC-TCCAAGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTT
* * *
1271865 ATCTGTCATCAAATACCTTCGAGTTCGA
129 ATCTGCCAACAAAGACCTTCGAGTTCGA
1271893 TTCCATTCAG
Statistics
Matches: 420, Mismatches: 60, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
163 6 0.01
164 174 0.41
165 45 0.11
167 2 0.00
168 49 0.12
169 144 0.34
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (164 bp):
AGCTTCAAGGCACATCATTTGCAACATAGCTCAAGGCTAGAAGGGCTATCTGCCCAAAGACCTTC
GAGTTCGACTATACTCAGCTCCAAGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTTAT
CTGCCAACAAAGACCTTCGAGTTCGACTACGCTC
Found at i:1272516 original size:36 final size:36
Alignment explanation
Indices: 1272463--1272687 Score: 260
Period size: 38 Copynumber: 6.1 Consensus size: 36
1272453 ACGGTTTTCT
* * *
1272463 AAAATATGTATACTATATAGTTTTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
*
1272499 AAAATATATATATTATATAGTTTTGAAAA-ATTTTG
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
* *
1272534 AAAACATATATAATGTATAGTTTTTGAAAATGC-TTTTG
1 AAAATATATATAATATATAG-TTTTGAAAA--CATTTTG
1272572 AAAATATATATAATATATAGTTTTGAAATA-ATTTTG
1 AAAATATATATAATATATAGTTTTGAAA-ACATTTTG
* *
1272608 AAAAAAATATATAATATATAGTTTTTAAAACATTTTTTG
1 -AAAATATATATAATATATAGTTTTGAAAACA--TTTTG
*
1272647 AAAACT-TATATAATATATAGTTTTTAAAACATTTTTG
1 AAAA-TATATATAATATATAGTTTTGAAAACA-TTTTG
1272684 AAAA
1 AAAA
1272688 AACATTTTTG
Statistics
Matches: 167, Mismatches: 11, Indels: 21
0.84 0.06 0.11
Matches are distributed among these distances:
35 22 0.13
36 42 0.25
37 45 0.27
38 53 0.32
39 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTGAAAACATTTTG
Found at i:1272633 original size:75 final size:73
Alignment explanation
Indices: 1272471--1272689 Score: 275
Period size: 75 Copynumber: 3.0 Consensus size: 73
1272461 CTAAAATATG
* * *
1272471 TATACTATATAG-TTTTGAAAA-CATTTCGAAAATATATATATTATATAGTTTTGAAAAATTTTG
1 TATAATATATAGTTTTTGAAAATC-TTTTGAAAATATATATAATATATAGTTTTGAAAAATTTTG
*
1272534 -AAAACATA
65 AAAAAAATA
*
1272542 TATAATGTATAGTTTTTGAAAATGCTTTTGAAAATATATATAATATATAGTTTTGAAATAATTTT
1 TATAATATATAGTTTTTGAAAAT-CTTTTGAAAATATATATAATATATAGTTTTGAAA-AATTTT
1272607 GAAAAAAATA
64 GAAAAAAATA
* * *
1272617 TATAATATATAGTTTTTAAAACATTTTTTGAAAACT-TATATAATATATAGTTTTTAAAACATTT
1 TATAATATATAGTTTTTGAAA-ATCTTTTGAAAA-TATATATAATATATAGTTTTGAAAA-A-TT
1272681 TTGAAAAAA
62 TTGAAAAAA
1272690 CATTTTTGAA
Statistics
Matches: 130, Mismatches: 9, Indels: 13
0.86 0.06 0.09
Matches are distributed among these distances:
71 10 0.08
72 9 0.07
73 31 0.24
74 9 0.07
75 57 0.44
76 14 0.11
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (73 bp):
TATAATATATAGTTTTTGAAAATCTTTTGAAAATATATATAATATATAGTTTTGAAAAATTTTGA
AAAAAATA
Found at i:1272695 original size:13 final size:14
Alignment explanation
Indices: 1272672--1272706 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1272662 TATAGTTTTT
1272672 AAAACATTTTTGAA
1 AAAACATTTTTGAA
1272686 AAAACATTTTTGAA
1 AAAACATTTTTGAA
1272700 AAAACAT
1 AAAACAT
1272707 ATATAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (14 bp):
AAAACATTTTTGAA
Found at i:1272715 original size:53 final size:52
Alignment explanation
Indices: 1272634--1272741 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 52
1272624 TATAGTTTTT
* *
1272634 AAAACATTTTTTGAAAACTTATATAATATATAGTTTTTAAAACATTTTTGAA
1 AAAACATTTTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTGAA
1272686 AAAACA-TTTTTGAAAAAACATATATAATATATAGTTTTAAAAACATTTTTGAA
1 AAAACATTTTTTG--AAAACATATATAATATATAGTTTTAAAAACATTTTTGAA
1272739 AAA
1 AAA
1272742 TTATATAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
51 6 0.12
52 6 0.12
53 40 0.77
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (52 bp):
AAAACATTTTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTGAA
Found at i:1272747 original size:90 final size:91
Alignment explanation
Indices: 1272603--1272778 Score: 302
Period size: 90 Copynumber: 1.9 Consensus size: 91
1272593 TTTGAAATAA
* *
1272603 TTTTGAAAAAAATATATAATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAATATATAGT
1 TTTTGAAAAAAATATATAATATATAGTTTTAAAAACATTTTTTGAAAAATTATATAATATATAGT
*
1272668 TTTTAAAACA-TTTTTGAAAAAACAT
66 TTTAAAAACATTTTTTGAAAAAACAT
1272693 TTTTGAAAAAACATATATAATATATAGTTTTAAAAACA-TTTTTGAAAAATTATATAATATATAG
1 TTTTGAAAAAA-ATATATAATATATAGTTTTAAAAACATTTTTTGAAAAATTATATAATATATAG
1272757 TTTTAAAAACATTTTTTGAAAA
65 TTTTAAAAACATTTTTTGAAAA
1272779 CTTATATAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
90 46 0.57
91 35 0.43
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (91 bp):
TTTTGAAAAAAATATATAATATATAGTTTTAAAAACATTTTTTGAAAAATTATATAATATATAGT
TTTAAAAACATTTTTTGAAAAAACAT
Found at i:1272874 original size:34 final size:36
Alignment explanation
Indices: 1272705--1272895 Score: 181
Period size: 37 Copynumber: 5.5 Consensus size: 36
1272695 TTGAAAAAAC
1272705 ATATATAATATATAGTTTTAAAAACA-TTTTTGAAAA
1 ATATATAATATATAGTTTTAAAAACATTTTTTG-AAA
1272741 ATTATATAATATATAGTTTTAAAAACATTTTTTGAAA
1 A-TATATAATATATAGTTTTAAAAACATTTTTTGAAA
* *
1272778 ACT-TAT-ATA-ATATTTTTAAATTA-A--TTTTGAAA
1 A-TATATAATATATAGTTTTAAA-AACATTTTTTGAAA
* *
1272810 ACTATATAATATATAGTTTTGAAAAC-TTTTTTTAAA
1 A-TATATAATATATAGTTTTAAAAACATTTTTTGAAA
* *
1272846 A-ATATAATATATAG-TGTAAAAATA-TTTTTG-AA
1 ATATATAATATATAGTTTTAAAAACATTTTTTGAAA
* *
1272878 ATATATATTGTATAGTTT
1 ATATATAATATATAGTTT
1272896 ATATTATATT
Statistics
Matches: 129, Mismatches: 14, Indels: 26
0.76 0.08 0.15
Matches are distributed among these distances:
32 14 0.11
33 25 0.19
34 29 0.22
35 13 0.10
36 12 0.09
37 30 0.23
38 6 0.05
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATAATATATAGTTTTAAAAACATTTTTTGAAA
Found at i:1272875 original size:69 final size:69
Alignment explanation
Indices: 1272707--1272895 Score: 206
Period size: 69 Copynumber: 2.7 Consensus size: 69
1272697 GAAAAAACAT
*
1272707 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTT
1 ATATAATATATAG-TTTAAAAATATTTTTG-AAAA-TATATAATATATAGTTTTAAAAACATTTT
1272772 TTGAAAA
63 TTGAAAA
* * * * * *
1272779 CT-T-ATATAATATTTTTAAATTAATTTTGAAAACTATATAATATATAGTTTTGAAAAC-TTTTT
1 ATATAATAT-ATAGTTTAAAAATATTTTTGAAAA-TATATAATATATAGTTTTAAAAACATTTTT
*
1272841 TTAAAA
64 TGAAAA
* * *
1272847 ATATAATATATAGTGTAAAAATATTTTTG-AAATATATATTGTATAGTTT
1 ATATAATATATAGTTTAAAAATATTTTTGAAAATATATAATATATAGTTT
1272896 ATATTATATT
Statistics
Matches: 97, Mismatches: 17, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
67 15 0.15
68 14 0.14
69 43 0.44
70 20 0.21
71 4 0.04
72 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (69 bp):
ATATAATATATAGTTTAAAAATATTTTTGAAAATATATAATATATAGTTTTAAAAACATTTTTTG
AAAA
Found at i:1274316 original size:20 final size:20
Alignment explanation
Indices: 1274293--1274331 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1274283 TTAAAAAATA
*
1274293 TTTTT-ATTTTTTTTTTATT
1 TTTTTCATTTTTATTTTATT
1274312 TTTTTCATTTTTATTTTATT
1 TTTTTCATTTTTATTTTATT
1274332 CCTTCTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCATTTTTATTTTATT
Found at i:1274397 original size:19 final size:19
Alignment explanation
Indices: 1274361--1274398 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1274351 TTAGTTAGTG
*
1274361 TTATTTTAGTTAATATTTT
1 TTATTTTAGTTAACATTTT
1274380 TTATTTTA-TCTAACATTTT
1 TTATTTTAGT-TAACATTTT
1274399 CCCCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (19 bp):
TTATTTTAGTTAACATTTT
Found at i:1278095 original size:21 final size:21
Alignment explanation
Indices: 1278069--1278114 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1278059 TAAATGTCAA
*
1278069 GTCAGGTAAATATCAGATTAG
1 GTCAGGTAAATATCAGATCAG
1278090 GTCAGGTAAATATCAGATCAG
1 GTCAGGTAAATATCAGATCAG
1278111 GTCA
1 GTCA
1278115 ATAACAAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (21 bp):
GTCAGGTAAATATCAGATCAG
Found at i:1278536 original size:17 final size:17
Alignment explanation
Indices: 1278492--1278541 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
1278482 AACAGATTTT
*
1278492 TAATATAAAGAATTTAAA
1 TAATATGAA-AATTTAAA
*
1278510 -AA-AAGAAAATTTAAA
1 TAATATGAAAATTTAAA
1278525 TAATATGAAAATTTAAA
1 TAATATGAAAATTTAAA
1278542 ATTTTAGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TAATATGAAAATTTAAA
Found at i:1281429 original size:29 final size:29
Alignment explanation
Indices: 1281395--1281453 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1281385 CCTAAATTAA
1281395 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1281424 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1281453 T
1 T
1281454 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1286113 original size:29 final size:29
Alignment explanation
Indices: 1286079--1286134 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1286069 CCTAAATTAA
1286079 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1286108 TTTGATGTCATTGCTTACATCAATTTA
1 TTTGATGTCATTGCTTACATCAATTTA
1286135 ATTAGGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1296063 original size:22 final size:22
Alignment explanation
Indices: 1296035--1296077 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1296025 GCAATAACAC
*
1296035 TCATGATAAATATCATATACAT
1 TCATGATAAACATCATATACAT
1296057 TCATGATAAACATCATATACA
1 TCATGATAAACATCATATACA
1296078 ATAACCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (22 bp):
TCATGATAAACATCATATACAT
Found at i:1321822 original size:20 final size:20
Alignment explanation
Indices: 1321797--1321836 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1321787 TGATCTTCAC
1321797 ATAACCTGGAGGGGGAGGTT
1 ATAACCTGGAGGGGGAGGTT
1321817 ATAACCTGGAGGGGGAGGTT
1 ATAACCTGGAGGGGGAGGTT
1321837 GCCACTTCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.45, T:0.20
Consensus pattern (20 bp):
ATAACCTGGAGGGGGAGGTT
Found at i:1326361 original size:2 final size:2
Alignment explanation
Indices: 1326349--1326408 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1326339 ATAATAACAT
1326349 TA TA TA T- 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
1326390 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1326409 GCCCACAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1329541 original size:76 final size:76
Alignment explanation
Indices: 1329447--1329599 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
1329437 GCGCCAGAAG
1329447 GAAAGGAGCCGCCATTGTATAATCTGATCTCAGGAACCTCTATGGCATGTCCCCATGTTTCCGGG
1 GAAAGGAGCCGCCATTGTATAATCTGATCTCAGGAACCTCTATGGCATGTCCCCATGTTTCCGGG
1329512 ATTGCTGCCAC
66 ATTGCTGCCAC
1329523 GAAAGGAGCCGCCATTGTATAATCTGATCTCAGGAACCTCTATGGCATGTCCCCATGTTTCCGGG
1 GAAAGGAGCCGCCATTGTATAATCTGATCTCAGGAACCTCTATGGCATGTCCCCATGTTTCCGGG
1329588 ATTGCTGCCAC
66 ATTGCTGCCAC
1329599 G
1 G
1329600 GTCAAATCAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (76 bp):
GAAAGGAGCCGCCATTGTATAATCTGATCTCAGGAACCTCTATGGCATGTCCCCATGTTTCCGGG
ATTGCTGCCAC
Found at i:1333240 original size:26 final size:26
Alignment explanation
Indices: 1333160--1333227 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
1333150 TTGTATAGTA
*
1333160 AAATTACAAAAATACCCCTATGGGGT
1 AAATTATAAAAATACCCCTATGGGGT
*
1333186 AAATTATAAAAATACCCCTACGGGGT
1 AAATTATAAAAATACCCCTATGGGGT
1333212 AAATTATAAAAATACC
1 AAATTATAAAAATACC
1333228 ATTATGATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (26 bp):
AAATTATAAAAATACCCCTATGGGGT
Found at i:1334805 original size:170 final size:172
Alignment explanation
Indices: 1334523--1334864 Score: 670
Period size: 170 Copynumber: 2.0 Consensus size: 172
1334513 TATGAATGTA
1334523 GTTTTGGGGAACTGCATGTGGAGTGTTTAGTTGGAGGGTATTACTGAGTGTTCAAAAAAAAATGT
1 GTTTTGGGGAACTGCATGTGGAGTGTTTAGTTGGAGGGTATTACTGAGTGTTCAAAAAAAAATGT
1334588 TTTGTTGAAATAAATCATTATTTCTGGTTTTGTTGGAACGCACTCAACTCCGAACTCCATCTTCT
66 TTTGTTGAAATAAATCATTATTTCTGGTTTTGTTGGAACGCACTCAACTCCGAACTCCATCTTCT
1334653 AAATATGTCTCTTTGAACA-TTCCTCT-GATGGTAAGCTTCC
131 AAATATGTCTCTTTGAACATTTCCTCTAGATGGTAAGCTTCC
1334693 GTTTTGGGGAACTGCATGTGGAGTGTTTAGTTGGAGGGTATTACTGAGTGTTCAAAAAAAAATGT
1 GTTTTGGGGAACTGCATGTGGAGTGTTTAGTTGGAGGGTATTACTGAGTGTTCAAAAAAAAATGT
1334758 TTTGTTGAAATAAATCATTATTTCTGGTTTTGTTGGAACGCACTCAACTCCGAACTCCATCTTCT
66 TTTGTTGAAATAAATCATTATTTCTGGTTTTGTTGGAACGCACTCAACTCCGAACTCCATCTTCT
1334823 AAATATGTCTCTTTGAACATTTCCTCTAGATGGTAAGCTTCC
131 AAATATGTCTCTTTGAACATTTCCTCTAGATGGTAAGCTTCC
1334865 TAACTGTTAC
Statistics
Matches: 170, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
170 149 0.88
171 7 0.04
172 14 0.08
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (172 bp):
GTTTTGGGGAACTGCATGTGGAGTGTTTAGTTGGAGGGTATTACTGAGTGTTCAAAAAAAAATGT
TTTGTTGAAATAAATCATTATTTCTGGTTTTGTTGGAACGCACTCAACTCCGAACTCCATCTTCT
AAATATGTCTCTTTGAACATTTCCTCTAGATGGTAAGCTTCC
Found at i:1336748 original size:10 final size:10
Alignment explanation
Indices: 1336733--1336759 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1336723 GGGTCTCCAA
1336733 CGTTTATGTT
1 CGTTTATGTT
1336743 CGTTTATGTT
1 CGTTTATGTT
1336753 CGTTTAT
1 CGTTTAT
1336760 TTATTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1337160 original size:31 final size:32
Alignment explanation
Indices: 1337122--1337190 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1337112 ATCATTGGAT
* *
1337122 TTAAAATT-GCAATGCTGTTGTGTTATGGTAA
1 TTAAAATTAGCAATACTGTTGTATTATGGTAA
*
1337153 TTAAAATTAAAGCAATATTGTTGTATTATGGTAA
1 TTAAAATT--AGCAATACTGTTGTATTATGGTAA
1337187 TTAA
1 TTAA
1337191 TAAGATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 8 0.25
34 24 0.75
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (32 bp):
TTAAAATTAGCAATACTGTTGTATTATGGTAA
Found at i:1341090 original size:16 final size:15
Alignment explanation
Indices: 1341069--1341098 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1341059 CCGTGCTTCC
1341069 CCCTTTTTCTCTTTTT
1 CCCTTTTTCT-TTTTT
1341085 CCCTTTTTCTTTTT
1 CCCTTTTTCTTTTT
1341099 GCATACGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
CCCTTTTTCTTTTTT
Found at i:1343083 original size:34 final size:34
Alignment explanation
Indices: 1343028--1343104 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
1343018 AATTATCACA
*
1343028 GAAAAAGGAACAGTACGGTGAAATGAATGA-TATAG
1 GAAAAA-GAACAGTACAGTGAAA-GAATGAGTATAG
* * *
1343063 GAAAAAGAATAGTACAGTGAAAGGATTAGTATAG
1 GAAAAAGAACAGTACAGTGAAAGAATGAGTATAG
1343097 GAAAAAGA
1 GAAAAAGA
1343105 GAAAGTATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 4 0.11
34 27 0.73
35 6 0.16
ACGTcount: A:0.52, C:0.04, G:0.27, T:0.17
Consensus pattern (34 bp):
GAAAAAGAACAGTACAGTGAAAGAATGAGTATAG
Found at i:1352552 original size:21 final size:23
Alignment explanation
Indices: 1352527--1352585 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1352517 CATAATTGTC
*
1352527 CCGAAGAGCCATATA-GG-TGCA
1 CCGAAGTGCCATATAGGGTTGCA
*
1352548 TCGAAGTGCCATATAGGGTTGCA
1 CCGAAGTGCCATATAGGGTTGCA
1352571 CCGAAGTGCCATATA
1 CCGAAGTGCCATATA
1352586 TTTATCCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 13 0.39
22 2 0.06
23 18 0.55
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (23 bp):
CCGAAGTGCCATATAGGGTTGCA
Found at i:1352597 original size:21 final size:21
Alignment explanation
Indices: 1352587--1352628 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1352577 TGCCATATAT
1352587 TTATCCCGAAGGACCACATAA
1 TTATCCCGAAGGACCACATAA
*
1352608 TTATCCCGAATGACCACATAA
1 TTATCCCGAAGGACCACATAA
1352629 AACCCTAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (21 bp):
TTATCCCGAAGGACCACATAA
Found at i:1353255 original size:54 final size:53
Alignment explanation
Indices: 1353191--1353335 Score: 157
Period size: 54 Copynumber: 2.7 Consensus size: 53
1353181 GATACTTCCC
* *
1353191 TTCAAGGGTATCTATACCTCCTCATGGTACCGATATCGATATAACATTCGATGT
1 TTCAAGGGTATCTATACCTCCTCA-GGTACCGATACCAATATAACATTCGATGT
* ** *
1353245 TTCAAGGGTAT-TGATACCTCCTCAAGGTACCGATACCAATCTGGCATTTGATGT
1 TTCAAGGGTATCT-ATACCTCCTC-AGGTACCGATACCAATATAACATTCGATGT
* * *
1353299 TTTAAGGGTATCGATACCATCCTTCAGGTATCGATAC
1 TTCAAGGGTATCTATACC-TCC-TCAGGTACCGATAC
1353336 TACCCTTACA
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
53 1 0.01
54 59 0.77
55 15 0.19
56 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (53 bp):
TTCAAGGGTATCTATACCTCCTCAGGTACCGATACCAATATAACATTCGATGT
Found at i:1353330 original size:20 final size:21
Alignment explanation
Indices: 1353305--1353383 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
1353295 ATGTTTTAAG
*
1353305 GGTATCGATACCATCCTT-CA
1 GGTATCGATACCACCCTTACA
*
1353325 GGTATCGATACTACCCTTACA
1 GGTATCGATACCACCCTTACA
*
1353346 -GTATCGATA-C-CTCTTCAACA
1 GGTATCGATACCACCCTT--ACA
*
1353366 GGTATCGATACTACCCTT
1 GGTATCGATACCACCCTT
1353384 TAATTTTCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
18 4 0.09
20 28 0.60
21 11 0.23
23 4 0.09
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCACCCTTACA
Found at i:1362065 original size:157 final size:155
Alignment explanation
Indices: 1361808--1362679 Score: 749
Period size: 157 Copynumber: 5.4 Consensus size: 155
1361798 TTAGTCCCTG
* * ** * *
1361808 ATTTTATTATTCCTTCAATTCATCCTTTATTTTAAGTCTACTTTTTCACCAAATTTAAACCACAT
1 ATTTTATTATTTCTTCAATTCATCATTTATTTTAAGT-TTGTTTTTTACCAAATTTGAACCACAT
* * * * * *
1361873 GCTCTTAAAACATCTTATAATACAAATGTACTTTCAATTACTCTTTTTGGTAACAATTTTTTTAT
65 GCTCCTAAACCATCTT-GAATACATATGTATTTTCAATTACTCTTTTTGATAACAA-TTTTTTAT
1361938 TTTTCAATTTAGTCCCTAAATTTCTTATA
128 TTTTCAATTTAGTCCCTAAATTT-TTATA
*
1361967 ATTTTATTATTTCTTCAATTCATCATTTA-TTTAAGTTTGTTTTTTACCAAATTTGAACCACATA
1 ATTTTATTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTTACCAAATTTGAACCACATG
** * *
1362031 CTCCTAAAAGATCGTTGAATATATATGTATTTTCAATTTCTCTTTTTGATAACGAATTTTTTATT
66 CTCCTAAACCATC-TTGAATACATATGTATTTTCAATTACTCTTTTTGATAAC-AATTTTTTATT
* * * *
1362096 TTTTAATTTAATCCATCAATTTTTTATA
129 TTTCAATTTAGTCCCT-AAATTTTTATA
* * *** *
1362124 ATTTTCTTATTTCTTCAATTAATCATTTATTTTAAG-TCAATTTTTACCAAATTTGAACCACGTG
1 ATTTTATTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTTACCAAATTTGAACCACATG
** * * * *
1362188 CTCCTAAACCATCATAAAATACAAATGCATTTTTAATTACTCTTTTTGATAACAAAATTTTTATT
66 CTCCTAAACCATC-TTGAATACATATGTATTTTCAATTACTCTTTTTGATAAC-AATTTTTTATT
1362253 TTTCAATTTAGTCCCTTAATATTTTTATA
129 TTTCAATTTAGTCCC-TAA-ATTTTTATA
** * *
1362282 ATTGTTTTGATAATTTTCTTATTTCTTCAGCTCATCCTTTATTTTAAGTCCCTT-TTTTATTATC
1 A----TTT--T-A-----TTATTTCTTCAATTCATCATTTATTTTAAGT---TTGTTTT-TTACC
* * * * *
1362346 AAATTTGAATCACATGCTCCTTAACCATAGTAGAATACATATGTAATTTT-AATT-CCCTTAATT
50 AAATTTGAACCACATGCTCCTAAACCAT-CTTGAATACATATGT-ATTTTCAATTACTCTT--TT
* * * *
1362409 T--TATCAAATTTCTATTTTTCAATTTAGTCCCTTAATTTCTTTTATA
111 TGATAACAATTTTTTATTTTTCAATTTAGTCCC-TAA-AT-TTTTATA
* * * ** *
1362455 ATCTTCTTATTTCTTCAGTTCATCATTTATTTTAAGTCCG-TTTTTATCAAATTTGAACCACATG
1 ATTTTATTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTTACCAAATTTGAACCACATG
* * * *
1362519 CTCCTAAACTATCTTATAATACATATGTATTTTCAATTTCTCTTTTTGATAATAGATTTTCTATA
66 CTCCTAAACCATCTT-GAATACATATGTATTTTCAATTACTCTTTTTGATAACA-ATTTT-T-TA
*
1362584 TTTTTTCAATTTAGTCCCTCAAATTTTCAT-
127 -TTTTTCAATTTAGTCCCT-AAATTTTTATA
* * * *
1362614 ATTTTCCTTATTTCTTCAATTCAT-ACTTATTTTAAGTCTG-TTTTTACCAAATTTGAACCACGT
1 ATTTT-ATTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTTACCAAATTTGAACCACAT
1362677 GCT
65 GCT
1362680 AGTATATCAC
Statistics
Matches: 587, Mismatches: 86, Indels: 80
0.78 0.11 0.11
Matches are distributed among these distances:
156 9 0.02
157 254 0.43
158 42 0.07
159 73 0.12
160 22 0.04
161 33 0.06
162 22 0.04
164 1 0.00
167 1 0.00
169 2 0.00
170 26 0.04
172 31 0.05
173 18 0.03
174 45 0.08
175 8 0.01
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (155 bp):
ATTTTATTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTTACCAAATTTGAACCACATG
CTCCTAAACCATCTTGAATACATATGTATTTTCAATTACTCTTTTTGATAACAATTTTTTATTTT
TCAATTTAGTCCCTAAATTTTTATA
Found at i:1362471 original size:331 final size:313
Alignment explanation
Indices: 1361814--1362674 Score: 903
Period size: 331 Copynumber: 2.7 Consensus size: 313
1361804 CCTGATTTTA
* * * * *
1361814 TTATTCCTTCAATTCATCCTTTATTTTAAGTCTACTTTTTCACCAAATTTAAACCACATGCTCTT
1 TTATTTCTTCAATTCATCATTTATTTTAAGTC-AATTTTT-ACCAAATTTGAACCACATGCTCCT
* * * *
1361879 AAAACATCTTATAATACAAATGTACTTTCAATTACTCTTTTTGGTAACAATTTTTTTATTTTTCA
64 AAACCATCTTATAATACAAATGTATTTTCAATTACTCTTTTTGATAACAAATTTTTTATTTTTCA
*
1361944 ATTTAGTCCC-TAAATTTCTTATAATTTTATTATTTCTTCAATTCATCATTTATTTAAGTTTGTT
129 ATTTAGTCCCTTAAATTT-TTATAATTTTATTATTTCTTCAACTCATCATTTATTTAAGTTTGTT
* * * * *
1362008 TTTTACCAAATTTGAACCACATACTCCTAAAAGATCGTTGAATATATATGTATTTTCAATTTCTC
193 TTTTACCAAATTTGAACCACATACTCCTAAAACATAGTAGAATACATATGTATTTTCAATTTCCC
* * * *
1362073 TTTTTGATAACGAATTTTTTATTTTTTAATTTAATCCATCAATTTTTTATAATTTTC
258 TTTTT-ATAACGAAATTTCTATTTTTCAATTTAATCCATCAATTTTTTATAATCTTC
* *
1362130 TTATTTCTTCAATTAATCATTTATTTTAAGTCAATTTTTACCAAATTTGAACCACGTGCTCCTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCAATTTTTACCAAATTTGAACCACATGCTCCTAA
* * * * *
1362195 ACCATCATAAAATACAAATGCATTTTTAATTACTCTTTTTGATAACAAAATTTTTATTTTTCAAT
66 ACCATCTTATAATACAAATGTATTTTCAATTACTCTTTTTGATAACAAATTTTTTATTTTTCAAT
* *
1362260 TTAGTCCCTTAATATTTTTATAATTGTTTTGATAATTTTCTTATTTCTTCAGCTCATCCTTTATT
131 TTAGTCCCTTAA-ATTTTTATAA----TTT--T-A-----TTATTTCTTCAACTCATCATTTA-T
* * * * *
1362325 TTAAGTCCCTT-TTTTATTATCAAATTTGAATCACATGCTCCTTAACCATAGTAGAATACATATG
182 TTAAGT---TTGTTTT-TTACCAAATTTGAACCACATACTCCTAAAACATAGTAGAATACATATG
* * * *
1362389 TAATTTT-AA-TTCCCTTAATTT-TATC-AAATTTCTATTTTTCAATTTAGTCCCTTAATTTCTT
243 T-ATTTTCAATTTCCCTT--TTTATAACGAAATTTCTATTTTTCAATTTAATCCATCAA-TT-TT
1362450 TTATAATCTTC
303 TTATAATCTTC
* ** *
1362461 TTATTTCTTCAGTTCATCATTTATTTTAAGTCCGTTTTTATCAAATTTGAACCACATGCTCCTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCAATTTTTACCAAATTTGAACCACATGCTCCTAA
* * * * *
1362526 ACTATCTTATAATACATATGTATTTTCAATTTCTCTTTTTGATAATAGATTTTCTATATTTTTTC
66 ACCATCTTATAATACAAATGTATTTTCAATTACTCTTTTTGATAACAAATTTT-T-TA-TTTTTC
* * * * * *
1362591 AATTTAGTCCCTCAAATTTTCAT-ATTTTCCTTATTTCTTCAATTCAT-ACTTATTTTAAGTCTG
128 AATTTAGTCCCTTAAATTTTTATAATTTT-ATTATTTCTTCAACTCATCATTTA-TTTAAGTTTG
1362654 -TTTTTACCAAATTTGAACCAC
191 TTTTTTACCAAATTTGAACCAC
1362675 GTGCTAGTAT
Statistics
Matches: 453, Mismatches: 64, Indels: 56
0.79 0.11 0.10
Matches are distributed among these distances:
314 87 0.19
315 15 0.03
316 49 0.11
317 4 0.01
319 3 0.01
320 11 0.02
321 16 0.04
322 1 0.00
326 1 0.00
327 20 0.04
328 10 0.02
329 24 0.05
330 15 0.03
331 158 0.35
332 10 0.02
333 9 0.02
334 20 0.04
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (313 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTCAATTTTTACCAAATTTGAACCACATGCTCCTAA
ACCATCTTATAATACAAATGTATTTTCAATTACTCTTTTTGATAACAAATTTTTTATTTTTCAAT
TTAGTCCCTTAAATTTTTATAATTTTATTATTTCTTCAACTCATCATTTATTTAAGTTTGTTTTT
TACCAAATTTGAACCACATACTCCTAAAACATAGTAGAATACATATGTATTTTCAATTTCCCTTT
TTATAACGAAATTTCTATTTTTCAATTTAATCCATCAATTTTTTATAATCTTC
Found at i:1366139 original size:21 final size:21
Alignment explanation
Indices: 1366115--1366154 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1366105 ACGGTTCACA
1366115 ATATTAACGTGA-TAATTGACG
1 ATATTAACGT-ATTAATTGACG
*
1366136 ATATTGACGTATTAATTGA
1 ATATTAACGTATTAATTGA
1366155 TTATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (21 bp):
ATATTAACGTATTAATTGACG
Found at i:1367483 original size:26 final size:25
Alignment explanation
Indices: 1367453--1367514 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
1367443 GATTTAATGT
1367453 AAAGAGATAAAATTT-TAAAATTTTAA
1 AAAGAGATAAAATTTATAAAA--TTAA
* *
1367479 AAAGAGA-GAAATTTATAAAATTCA
1 AAAGAGATAAAATTTATAAAATTAA
1367503 AAAGAGATAAAA
1 AAAGAGATAAAA
1367515 ATAAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (25 bp):
AAAGAGATAAAATTTATAAAATTAA
Found at i:1367516 original size:26 final size:26
Alignment explanation
Indices: 1367453--1367516 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
1367443 GATTTAATGT
*
1367453 AAAGAGAT-AAAATTTTAAAATTTTA
1 AAAGAGATAAAAATTTTAAAATTTCA
* *
1367478 AAA-AGAGAGAAATTTATAAAA-TTCA
1 AAAGAGATAAAAATTT-TAAAATTTCA
1367503 AAAGAGATAAAAAT
1 AAAGAGATAAAAAT
1367517 AAATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.10
25 15 0.48
26 13 0.42
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.27
Consensus pattern (26 bp):
AAAGAGATAAAAATTTTAAAATTTCA
Found at i:1367577 original size:17 final size:18
Alignment explanation
Indices: 1367545--1367579 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1367535 ATATAAAAAA
1367545 TTAAAATAAAAAATAATT
1 TTAAAATAAAAAATAATT
*
1367563 TTAAAAT-AGAAATAATT
1 TTAAAATAAAAAATAATT
1367580 CGATAGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TTAAAATAAAAAATAATT
Found at i:1375809 original size:23 final size:23
Alignment explanation
Indices: 1375777--1375828 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1375767 TACAAGGATT
*
1375777 AAATTCGGTAATTTTCCCTTGCC
1 AAATTTGGTAATTTTCCCTTGCC
1375800 AAATTTGGTAATTTTCCCTTGCC
1 AAATTTGGTAATTTTCCCTTGCC
1375823 AAATTT
1 AAATTT
1375829 TTAACAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (23 bp):
AAATTTGGTAATTTTCCCTTGCC
Found at i:1381634 original size:15 final size:15
Alignment explanation
Indices: 1381614--1381646 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1381604 AAAATATTTC
*
1381614 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTAGAT
1381629 TTTCCCGTTCTAGAT
1 TTTCCCGTTCTAGAT
1381644 TTT
1 TTT
1381647 GATCTTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.12, T:0.55
Consensus pattern (15 bp):
TTTCCCGTTCTAGAT
Found at i:1383731 original size:12 final size:12
Alignment explanation
Indices: 1383714--1383740 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1383704 TTATTTCTTT
1383714 TATTTTTTAAAA
1 TATTTTTTAAAA
1383726 TATTTTTTAAAA
1 TATTTTTTAAAA
1383738 TAT
1 TAT
1383741 AATTTTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTTTAAAA
Found at i:1385873 original size:226 final size:227
Alignment explanation
Indices: 1385476--1385925 Score: 875
Period size: 226 Copynumber: 2.0 Consensus size: 227
1385466 AAAAAGGTGG
1385476 GATGAGTTGTTGTCCCTCCCATTCTTATATCTAAATACTTTATTAAACATCGTTCTTTCATCGTA
1 GATGAGTTGTTGTCCCTCCCATTC-T-TATCTAAATACTTTATTAAACATCGTTCTTTCATCGTA
1385541 AATAAAAATAACCCCTCATAATGTTTGATCATATCTCCGACTCTATTCCATGCTCGCCAAAGTTG
64 AATAAAAATAACCCCTCATAATGTTTGATCATATCTCCGACTCTATTCCATGCTCGCCAAAGTTG
1385606 CACCGATCGAGCCAAGTAGCACATAGGGTTATTCTGGTGCATTTAGTGTAACTAATTCCCATTTT
129 CACCGATCGAGCCAAGTAGCACATAGGGTTATTCTGGTGCATTTAGTGTAACTAATTCCCATTTT
1385671 GAAGGATTCTGTGTGGAATGTTGTCAAGAGTTTT
194 GAAGGATTCTGTGTGGAATGTTGTCAAGAGTTTT
1385705 GATGAGTTGTTGTCCCTCCCATTC-TATCTAAATACTTTATTAAACATCGTTCTTTCATCGTAAA
1 GATGAGTTGTTGTCCCTCCCATTCTTATCTAAATACTTTATTAAACATCGTTCTTTCATCGTAAA
1385769 TAAAAATAACCCCTCATAATGTTTGATCATATCTCCGACTCTATTCCATGCTCGCCAAAGTTGCA
66 TAAAAATAACCCCTCATAATGTTTGATCATATCTCCGACTCTATTCCATGCTCGCCAAAGTTGCA
1385834 CCGATCGAGCCAAGTAGCACATAGGGTTATTCTGGTGCATTTAGTGTAACTAATTCCCATTTTGA
131 CCGATCGAGCCAAGTAGCACATAGGGTTATTCTGGTGCATTTAGTGTAACTAATTCCCATTTTGA
1385899 AGGATTCTGTGTGGAATGTTGTCAAGA
196 AGGATTCTGTGTGGAATGTTGTCAAGA
1385926 CGAGTTTTGA
Statistics
Matches: 221, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
226 197 0.89
229 24 0.11
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (227 bp):
GATGAGTTGTTGTCCCTCCCATTCTTATCTAAATACTTTATTAAACATCGTTCTTTCATCGTAAA
TAAAAATAACCCCTCATAATGTTTGATCATATCTCCGACTCTATTCCATGCTCGCCAAAGTTGCA
CCGATCGAGCCAAGTAGCACATAGGGTTATTCTGGTGCATTTAGTGTAACTAATTCCCATTTTGA
AGGATTCTGTGTGGAATGTTGTCAAGAGTTTT
Found at i:1394275 original size:20 final size:20
Alignment explanation
Indices: 1394250--1394320 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1394240 CCAAGAGACT
*
1394250 AGTATCGATACTATAAGACC
1 AGTATCGATACTATAAGGCC
*
1394270 AATATCGATACTATAAGGCC
1 AGTATCGATACTATAAGGCC
*
1394290 AGTATCAATACTATAAGGCC
1 AGTATCGATACTATAAGGCC
1394310 AGTATCGATAC
1 AGTATCGATAC
1394321 CCTCATCTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTATAAGGCC
Found at i:1396552 original size:21 final size:21
Alignment explanation
Indices: 1396526--1396570 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1396516 TTCTATTATG
1396526 CTCCCTAAGAAGTCAATAACC
1 CTCCCTAAGAAGTCAATAACC
*
1396547 CTCCCTAATAAGTCAATAACC
1 CTCCCTAAGAAGTCAATAACC
1396568 CTC
1 CTC
1396571 GTTAGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.22
Consensus pattern (21 bp):
CTCCCTAAGAAGTCAATAACC
Found at i:1412340 original size:19 final size:19
Alignment explanation
Indices: 1412310--1412399 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
1412300 GAAAGCAATT
1412310 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
* *
1412329 AGTACTTCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
1412348 AGTGCATCGATGCATAAGA
1 AGTGCATCGATGCATAAGG
* *
1412367 AGTCCATCGATGTATAAGG
1 AGTGCATCGATGCATAAGG
1412386 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1412400 CCTGCCTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:1412693 original size:13 final size:13
Alignment explanation
Indices: 1412675--1412700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1412665 TAAGGTGAGT
1412675 GTATATGATTATA
1 GTATATGATTATA
1412688 GTATATGATTATA
1 GTATATGATTATA
1412701 TGGAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
GTATATGATTATA
Found at i:1416640 original size:19 final size:19
Alignment explanation
Indices: 1416616--1416667 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1416606 GAATGCAATT
1416616 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1416635 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
1416654 AGTGCATCAATGCA
1 AGTGCATCGATGCA
1416668 ACTACTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:1421645 original size:30 final size:30
Alignment explanation
Indices: 1421595--1421655 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
1421585 AATTACATGA
*
1421595 AAAGAAGCTATATGTCTATATGTATATGTG
1 AAAGAAGCTATATGTCTATATGAATATGTG
1421625 AAAGAAGCTATGA-G-CTTATATGAATATGTG
1 AAAGAAGCTAT-ATGTC-TATATGAATATGTG
1421655 A
1 A
1421656 TATGAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 26 0.93
31 1 0.04
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (30 bp):
AAAGAAGCTATATGTCTATATGAATATGTG
Found at i:1425970 original size:18 final size:18
Alignment explanation
Indices: 1425947--1425998 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
1425937 GGGTCTACGA
1425947 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
1425965 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
1425983 GGTCCTTCGTGACATA
1 GGTCCTTCGGGACATA
1425999 TGTGTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:1430105 original size:3 final size:3
Alignment explanation
Indices: 1430092--1430170 Score: 113
Period size: 3 Copynumber: 25.7 Consensus size: 3
1430082 AATTTTTTCA
* * *
1430092 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1430140 TAT TAT TAT TAT ATAT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TA
1430171 AATAAAAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
3 62 0.90
4 7 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1430338 original size:26 final size:26
Alignment explanation
Indices: 1430299--1430365 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
1430289 TAAACCTAGC
*
1430299 TCCCAGCTGCCGCCTTATCCAAGAGT
1 TCCCAGCAGCCGCCTTATCCAAGAGT
*
1430325 TCTCAGCAGCCGCCTTATCCAAGAGT
1 TCCCAGCAGCCGCCTTATCCAAGAGT
1430351 TCCCAGCAGCCGCCT
1 TCCCAGCAGCCGCCT
1430366 CTGTCGACGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (26 bp):
TCCCAGCAGCCGCCTTATCCAAGAGT
Found at i:1431397 original size:32 final size:33
Alignment explanation
Indices: 1431361--1431442 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
1431351 AATCACTAAA
*
1431361 TTTAATACTTTTATTTATTTTTAACTAC-A-AGT
1 TTTAATA-TTTTATTTATTTTTAAATACTATAGT
1431393 TTTAATA-TTT-TTTATATTTTAAATACTATAGT
1 TTTAATATTTTATTTAT-TTTTAAATACTATAGT
1431425 TTT-A-ATTTTATTTATTTT
1 TTTAATATTTTATTTATTTT
1431443 AGTCATTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
29 5 0.11
30 13 0.30
31 8 0.18
32 18 0.41
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTAATATTTTATTTATTTTTAAATACTATAGT
Found at i:1431433 original size:30 final size:30
Alignment explanation
Indices: 1431374--1431443 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
1431364 AATACTTTTA
*
1431374 TTTAT-TTTTAACTACAAGTTTTAATATTT
1 TTTATATTTTAAATACAAGTTTTAATATTT
1431403 TTTATATTTTAAATACTATAGTTTTAAT-TTT
1 TTTATATTTTAAATAC-A-AGTTTTAATATTT
*
1431434 ATT-TATTTTA
1 TTTATATTTTA
1431444 GTCATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 5 0.14
30 16 0.44
31 6 0.17
32 9 0.25
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTATATTTTAAATACAAGTTTTAATATTT
Found at i:1432527 original size:18 final size:18
Alignment explanation
Indices: 1432504--1432542 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1432494 ATTACTGTTT
1432504 TTATTTCATTTTCAAGTA
1 TTATTTCATTTTCAAGTA
*
1432522 TTATTTCATTTTGAAGTA
1 TTATTTCATTTTCAAGTA
1432540 TTA
1 TTA
1432543 AATTTCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (18 bp):
TTATTTCATTTTCAAGTA
Found at i:1433875 original size:22 final size:22
Alignment explanation
Indices: 1433847--1433893 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1433837 AATTCAACTG
1433847 TTGAGCATGAATGGAAACTAAC
1 TTGAGCATGAATGGAAACTAAC
1433869 TTGAGCATGAATGGAAACTAAC
1 TTGAGCATGAATGGAAACTAAC
1433891 TTG
1 TTG
1433894 GCTTTAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (22 bp):
TTGAGCATGAATGGAAACTAAC
Found at i:1433962 original size:43 final size:41
Alignment explanation
Indices: 1433901--1433985 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 41
1433891 TTGGCTTTAG
* *
1433901 TGAAGTTAGGAGGGAAAGTTA-TCCCCTATATGTAAAGTTTTGT
1 TGAAGATAGGACGGAAAG-TAGTCCCCTATA--TAAAGTTTTGT
*
1433944 TGAAGATAGGACGGAAAGTAGTCCTCTATATAAAGTTTTGT
1 TGAAGATAGGACGGAAAGTAGTCCCCTATATAAAGTTTTGT
1433985 T
1 T
1433986 TGATGCACGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 12 0.32
42 2 0.05
43 24 0.63
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (41 bp):
TGAAGATAGGACGGAAAGTAGTCCCCTATATAAAGTTTTGT
Found at i:1436955 original size:9 final size:9
Alignment explanation
Indices: 1436941--1436980 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
1436931 TTATACAGTC
1436941 AAAAAAAGG
1 AAAAAAAGG
1436950 -AAAAAAGG
1 AAAAAAAGG
*
1436958 AAAAAAAAG
1 AAAAAAAGG
*
1436967 AAGAAAAGG
1 AAAAAAAGG
1436976 AAAAA
1 AAAAA
1436981 TTTAACCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:1436964 original size:18 final size:18
Alignment explanation
Indices: 1436941--1436980 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1436931 TTATACAGTC
*
1436941 AAAAAAAGGAA-AAAAGG
1 AAAAAAAAGAAGAAAAGG
1436958 AAAAAAAAGAAGAAAAGG
1 AAAAAAAAGAAGAAAAGG
1436976 AAAAA
1 AAAAA
1436981 TTTAACCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAGAAAAGG
Found at i:1437143 original size:27 final size:28
Alignment explanation
Indices: 1437105--1437160 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
1437095 TGGAAATGAA
1437105 CCAAAAAAATTGGCAGTCTAGA-GGATC
1 CCAAAAAAATTGGCAGTCTAGAGGGATC
1437132 CCAAAAAAATTGGCAGTCTAGAGGGATC
1 CCAAAAAAATTGGCAGTCTAGAGGGATC
1437160 C
1 C
1437161 AGATTATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (28 bp):
CCAAAAAAATTGGCAGTCTAGAGGGATC
Found at i:1437546 original size:32 final size:32
Alignment explanation
Indices: 1437506--1437566 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1437496 TAGAAACAAG
*
1437506 AAGTATCTCTACGAGATGAGCATAACAACGAA
1 AAGTATCTCTACAAGATGAGCATAACAACGAA
*
1437538 AAGTATCTCTACAATATGAGCATAACAAC
1 AAGTATCTCTACAAGATGAGCATAACAAC
1437567 TATTTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (32 bp):
AAGTATCTCTACAAGATGAGCATAACAACGAA
Found at i:1440130 original size:75 final size:75
Alignment explanation
Indices: 1440036--1440208 Score: 265
Period size: 75 Copynumber: 2.3 Consensus size: 75
1440026 ATCAACAATA
* *
1440036 AGCAAATGCTGAGGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACGCATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACGCATTTTGAA
*
1440101 TGTTTGTATC
66 TGCTTGTATC
* * *
1440111 AGCAAATGCTGGGGAATGCTGAAAGCCCATTTCAATCAAAATGAGGAATGTTGACGCATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACGCATTTTGAA
*
1440176 TGCTTGTATT
66 TGCTTGTATC
* *
1440186 GGCAAATGTTGGGGCATGCTGAA
1 AGCAAATGCTGGGGCATGCTGAA
1440209 GGCCTATATC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACGCATTTTGAA
TGCTTGTATC
Found at i:1442234 original size:45 final size:45
Alignment explanation
Indices: 1442170--1442790 Score: 1028
Period size: 45 Copynumber: 13.8 Consensus size: 45
1442160 CTATTTCCCA
* *
1442170 CATCTGTAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1442215 CATCTGTAAGTCATTCAGTGCATGATGATTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1442260 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1442305 CATCTGTAAGTCCTTCGGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1442350 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGGT
1442396 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1442441 CATCTGTATGCCCTTCAGTACATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1442486 CATCTGTAAGTCTTTCAGTGCATAATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
**
1442531 CATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1442576 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1442621 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1442666 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1442711 CATCTGTAAGTCCTTCAATGCATGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1442756 CATCT-TAAGTCATTCAGTTCATGATGTTTTCAAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA
1442791 TTTTCACCTT
Statistics
Matches: 537, Mismatches: 38, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
44 26 0.05
45 467 0.87
46 44 0.08
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1442668 original size:25 final size:25
Alignment explanation
Indices: 1442640--1442709 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 25
1442630 GTCCTTTAGT
1442640 GCATGATGTTTTCAAAACCTTCGGG
1 GCATGATGTTTTCAAAACCTTCGGG
* ** * *
1442665 GCAT-CTG---T-AAGTCCTTCAGT
1 GCATGATGTTTTCAAAACCTTCGGG
1442685 GCATGATGTTTTCAAAACCTTCGGG
1 GCATGATGTTTTCAAAACCTTCGGG
1442710 TCATCTGTAA
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
20 12 0.40
21 3 0.10
24 3 0.10
25 12 0.40
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (25 bp):
GCATGATGTTTTCAAAACCTTCGGG
Found at i:1442936 original size:3 final size:3
Alignment explanation
Indices: 1442909--1442965 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
1442899 TTTTTTCATT
* * * **
1442909 TTA TTT TTA TTT TTA TTA TTT TTA TTA TTA TTA TTA TTA AAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1442957 TTA TTA TTA
1 TTA TTA TTA
1442966 AATAAAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1444165 original size:32 final size:33
Alignment explanation
Indices: 1444129--1444210 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
1444119 AATCACTAAA
*
1444129 TTTAATACTTTTATTTATTTTTAACTAC-A-AGT
1 TTTAATA-TTTTATTTATTTTTAAATACTATAGT
1444161 TTTAATA-TTT-TTTATATTTTAAATACTATAGT
1 TTTAATATTTTATTTAT-TTTTAAATACTATAGT
1444193 TTT-A-ATTTTATTTATTTT
1 TTTAATATTTTATTTATTTT
1444211 AGTCATTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
29 5 0.11
30 13 0.30
31 8 0.18
32 18 0.41
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTAATATTTTATTTATTTTTAAATACTATAGT
Found at i:1444201 original size:30 final size:30
Alignment explanation
Indices: 1444142--1444211 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
1444132 AATACTTTTA
*
1444142 TTTAT-TTTTAACTACAAGTTTTAATATTT
1 TTTATATTTTAAATACAAGTTTTAATATTT
1444171 TTTATATTTTAAATACTATAGTTTTAAT-TTT
1 TTTATATTTTAAATAC-A-AGTTTTAATATTT
*
1444202 ATT-TATTTTA
1 TTTATATTTTA
1444212 GTCATTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 5 0.14
30 16 0.44
31 6 0.17
32 9 0.25
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTATATTTTAAATACAAGTTTTAATATTT
Found at i:1448288 original size:22 final size:24
Alignment explanation
Indices: 1448249--1448292 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
1448239 TACACCTATC
1448249 AAAATAATCTATTAATCACTTTAAA
1 AAAATAATCTATTAATCA-TTTAAA
1448274 AAAATAAT-T-TT-ATCATTTA
1 AAAATAATCTATTAATCATTTA
1448293 CCTCATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 2 0.11
24 1 0.05
25 8 0.42
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATAATCTATTAATCATTTAAA
Found at i:1455554 original size:31 final size:31
Alignment explanation
Indices: 1455519--1455581 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1455509 TCAATATAGT
* *
1455519 TTAAAAAATTATACAA-TACTTATTAAATTTA
1 TTAAAAAATTATAAAATTA-TTAATAAATTTA
*
1455550 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAATTATTAATAAATTTA
1455581 T
1 T
1455582 CTAGATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAATAAATTTA
Found at i:1458728 original size:17 final size:16
Alignment explanation
Indices: 1458708--1458751 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
1458698 GTATTAATTC
1458708 TAAAAATAATTAGATGA
1 TAAAAATAATTA-ATGA
*
1458725 TAAAAATAA--AATTA
1 TAAAAATAATTAATGA
1458739 TAAAAATAATTAA
1 TAAAAATAATTAA
1458752 CCGACTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 2 0.08
17 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
TAAAAATAATTAATGA
Found at i:1458847 original size:18 final size:18
Alignment explanation
Indices: 1458803--1458848 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1458793 AGCTCCCAAC
1458803 AATC-TAATATAAAAATA
1 AATCATAATATAAAAATA
*
1458820 AGCTCA-AATATAAAAATA
1 A-ATCATAATATAAAAATA
1458838 AATCATAATAT
1 AATCATAATAT
1458849 TTCCAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (18 bp):
AATCATAATATAAAAATA
Found at i:1461610 original size:69 final size:70
Alignment explanation
Indices: 1461498--1461641 Score: 229
Period size: 69 Copynumber: 2.1 Consensus size: 70
1461488 ATAATACCCT
* * *
1461498 TGAATTAAGGGAATGCCTTATACTTTCTCGGTTCATTGATATTCTCGAAGCACGTGATTTTTGAT
1 TGAATTAAGGGAATGACTTATACTTTCTCGGTTCATTGATATTCTCGAAGCACATGATTTTCGAT
1461563 ATTAC
66 ATTAC
*
1461568 TGAATTAAGGG-ATGACTTATA-TGTTCTCGGTTCATTGATATTCTCGAAGCACATGATTTTCGC
1 TGAATTAAGGGAATGACTTATACT-TTCTCGGTTCATTGATATTCTCGAAGCACATGATTTTCGA
1461631 TATTAC
65 TATTAC
1461637 TGAAT
1 TGAAT
1461642 CTGGCTTACT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
68 1 0.01
69 57 0.83
70 11 0.16
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (70 bp):
TGAATTAAGGGAATGACTTATACTTTCTCGGTTCATTGATATTCTCGAAGCACATGATTTTCGAT
ATTAC
Found at i:1463798 original size:201 final size:198
Alignment explanation
Indices: 1463402--1463967 Score: 611
Period size: 200 Copynumber: 2.8 Consensus size: 198
1463392 CAATATCAGT
* ** * * *
1463402 CTCAACTAAAAGGTAAGTTGTAATACTACACCACTAAGATTTAAAATTAAAAAAAATCCGGTTAA
1 CTCAACTAAAAGATAAGTTGTAATACTACACCTTTAAGCTTTAAAATTAAAAAAAATTCGATTAA
* * * *
1463467 CTTCTTGGAAATACCCCTCCAACATGCTTAACAAGCCATTTTAACTTGTTT-TTCATGCACAAAA
66 CTTCTCGGAAATACCCCTCAAACATGC-TATCAAGCCATTTT-AGTT-TTTCTTCATGCACAAAA
* * * * *
1463531 CC-AAGCTTTGGAATCATTTTCAACGCGATTTTTGCCTCACTTATAATGTCTTGAATGTGCTGAT
128 CCAAAGCTTTGGAACCATTTTCAACGCAATTTTTACCCCACTTACAATGTCTTGAATGTGCTGAT
1463595 ATTACC
193 ATTACC
* * *
1463601 CTCAACTAAAAGATAAGTTGTAATACAAAACCTTTAAGCTTTAAAATTATAAAAAAATTCAATTA
1 CTCAACTAAAAGATAAGTTGTAATACTACACCTTTAAGCTTTAAAATTA-AAAAAAATTCGATTA
* * * * *
1463666 TCTTCTCAGAAATACCCCTCAAACATGTCTATCAAGCCAGTCTAGTTATTTCTTCATGCGCAAAA
65 ACTTCTCGGAAATACCCCTCAAACATG-CTATCAAGCCATTTTAGTT-TTTCTTCATGCACAAAA
* * * *
1463731 CCAAAGGTTTGGAACCATTTTCAACGCAATTTTTACCCCATTTACAATGTCTTGTATGTGTTGAT
128 CCAAAGCTTTGGAACCATTTTCAACGCAATTTTTACCCCACTTACAATGTCTTGAATGTGCTGAT
*
1463796 ATTATC
193 ATTACC
* * * * * *
1463802 CTCAATTGAAAGATAAGTTGTAATACTACGCCTTCAAGCTTAAAAATTAGAAAAAAA-TGGATTA
1 CTCAACTAAAAGATAAGTTGTAATACTACACCTTTAAGCTTTAAAATTA-AAAAAAATTCGATTA
* * * ** * * *
1463866 CCTTCTCGGAAATAACCCTCGAGTATGCCTATCAAGCAATTTTAGCTTGTTCTTCATGCACAAAG
65 ACTTCTCGGAAATACCCCTCAAACATG-CTATCAAGCCATTTTAG-TTTTTCTTCATGCACAAAA
* *
1463931 CCAAA-CTTAT-AAACCATTTTCAACGCAATGTTTACCC
128 CCAAAGCTT-TGGAACCATTTTCAACGCAATTTTTACCC
1463968 GCATACAATA
Statistics
Matches: 306, Mismatches: 55, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
199 76 0.25
200 120 0.39
201 110 0.36
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (198 bp):
CTCAACTAAAAGATAAGTTGTAATACTACACCTTTAAGCTTTAAAATTAAAAAAAATTCGATTAA
CTTCTCGGAAATACCCCTCAAACATGCTATCAAGCCATTTTAGTTTTTCTTCATGCACAAAACCA
AAGCTTTGGAACCATTTTCAACGCAATTTTTACCCCACTTACAATGTCTTGAATGTGCTGATATT
ACC
Found at i:1464658 original size:50 final size:50
Alignment explanation
Indices: 1464599--1464711 Score: 145
Period size: 50 Copynumber: 2.3 Consensus size: 50
1464589 TTAGCAGGAA
* * * * *
1464599 AGCGCGCCCCCTGCACTGCGTTATATGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGATATACGCTGATCTAGCGCCACGTGGGTAT
* * * *
1464649 AGCGCGCCCCCTTCCCCGCGATATACGGTGATCTAGCGCCACGTTGGTAT
1 AGCGCGCCCCCTGCACCGCGATATACGCTGATCTAGCGCCACGTGGGTAT
1464699 AGCGCGCCCCCTG
1 AGCGCGCCCCCTG
1464712 ATCCACGCTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.14, C:0.35, G:0.28, T:0.22
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGATATACGCTGATCTAGCGCCACGTGGGTAT
Found at i:1468601 original size:15 final size:15
Alignment explanation
Indices: 1468583--1468626 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1468573 TTGTCATCAT
*
1468583 CATCGTCGTCGTCAC
1 CATCGTCATCGTCAC
* *
1468598 CATCGTCAACGTTAC
1 CATCGTCATCGTCAC
1468613 CATCGTCATCGTCA
1 CATCGTCATCGTCA
1468627 TCGTCGTCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.36, G:0.16, T:0.27
Consensus pattern (15 bp):
CATCGTCATCGTCAC
Found at i:1469028 original size:18 final size:18
Alignment explanation
Indices: 1468993--1469028 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1468983 CGATGGCGGC
* *
1468993 ATCATATATGGTTGCGGT
1 ATCATATATGGCTCCGGT
1469011 ATCATATATGGCTCCGGT
1 ATCATATATGGCTCCGGT
1469029 GGCTGCTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (18 bp):
ATCATATATGGCTCCGGT
Found at i:1470627 original size:111 final size:111
Alignment explanation
Indices: 1470490--1470711 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
1470480 ATTACAAAAA
* *
1470490 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * * *
1470555 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTAGCAGCAAAGTGTAGAGATAT
1470601 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1470666 AATTAAAACATTAAAATGTTACCGTAGCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTAGCAGCAAAGTGTAGAGATAT
1470712 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTAGCAGCAAAGTGTAGAGATAT
Found at i:1470850 original size:12 final size:10
Alignment explanation
Indices: 1470836--1470876 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1470826 ACCTTAAAAA
*
1470836 GAGAGTATTT
1 GAGAGAATTT
1470846 GAGAGAAATTT
1 GAGAG-AATTT
1470857 -AGAGAATTT
1 GAGAGAATTT
1470866 GAGAGAATTT
1 GAGAGAATTT
1470876 G
1 G
1470877 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1471714 original size:14 final size:15
Alignment explanation
Indices: 1471687--1471717 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1471677 TAAGCAGTAC
1471687 GTTTAAACTATTATA
1 GTTTAAACTATTATA
1471702 GTTTAAA-TATTATA
1 GTTTAAACTATTATA
1471716 GT
1 GT
1471718 GGATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (15 bp):
GTTTAAACTATTATA
Found at i:1474920 original size:172 final size:172
Alignment explanation
Indices: 1474636--1474980 Score: 658
Period size: 172 Copynumber: 2.0 Consensus size: 172
1474626 AGTCGAGCTG
1474636 TGTTAACTACAGACTTTGTCGAGGTGCATATTTCTTTCCTGCAAATGGAAAAACAGATTCATTAA
1 TGTTAACTACAGACTTTGTCGAGGTGCATATTTCTTTCCTGCAAATGGAAAAACAGATTCATTAA
1474701 TGTAACATGGCGAGAAACATATACTCGTCCATCGGGTGCCAAGCATTGGAA-CCTTTGTGTTGAG
66 TGTAACATGGCGAGAAACATATACTCGTCCATCGGGTGCCAAGCATTGGAACCCTTTGTGTTGAG
1474765 GGCT-ACTCCCAAATATGTGCATACTTGAGACCTGAAGGACA
131 GGCTAACTCCCAAATATGTGCATACTTGAGACCTGAAGGACA
1474806 TGTTAACTACAGACTTTGTCGAGGTGCATATTTCTTTCCCTGCAAATGGAAAAACAGATTCATTA
1 TGTTAACTACAGACTTTGTCGAGGTGCATATTTCTTT-CCTGCAAATGGAAAAACAGATTCATT-
1474871 AATGTAACATGGCGAGAAACATATACTCGTCCATCGGGTGCCAAGCATTGGAACCCTTTGTGTTG
64 AATGTAACATGGCGAGAAACATATACTCGTCCATCGGGTGCCAAGCATTGGAACCCTTTGTGTTG
1474936 AGGGCTAACTCCCAAATATGTGCATACTTGAGACCTGAAGGACA
129 AGGGCTAACTCCCAAATATGTGCATACTTGAGACCTGAAGGACA
1474980 T
1 T
1474981 CTTATGCCTT
Statistics
Matches: 171, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
170 37 0.22
171 26 0.15
172 53 0.31
173 17 0.10
174 38 0.22
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (172 bp):
TGTTAACTACAGACTTTGTCGAGGTGCATATTTCTTTCCTGCAAATGGAAAAACAGATTCATTAA
TGTAACATGGCGAGAAACATATACTCGTCCATCGGGTGCCAAGCATTGGAACCCTTTGTGTTGAG
GGCTAACTCCCAAATATGTGCATACTTGAGACCTGAAGGACA
Found at i:1476489 original size:17 final size:18
Alignment explanation
Indices: 1476461--1476507 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1476451 TTAAATTGAA
1476461 CATCGAATGCATTT-CATG
1 CATCG-ATGCATTTACATG
1476479 CATCGATGCATTTACCATG
1 CATCGATGCATTTA-CATG
*
1476498 CACCGATGCA
1 CATCGATGCA
1476508 CTAAGGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.31
18 5 0.19
19 13 0.50
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
CATCGATGCATTTACATG
Found at i:1476551 original size:46 final size:45
Alignment explanation
Indices: 1476495--1476600 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
1476485 TGCATTTACC
* *
1476495 ATGCACCGATGCACTAAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTAAGGATATTT-TG-AAACATCGAATGCACTTG
** * *
1476541 ATGCATCGATGCACTCTGGCTATTTTGAAACATTGAATGCACTTG
1 ATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCACTTG
*
1476586 ATGCATCGTTGCACT
1 ATGCATCGATGCACT
1476601 CTTAGTGCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 30 0.58
46 19 0.37
47 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (45 bp):
ATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCACTTG
Found at i:1487392 original size:26 final size:24
Alignment explanation
Indices: 1487355--1487402 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1487345 ATTGAAAAAA
1487355 TATAAAAATTTAGTAATATATAAATT
1 TATAAAAATTTAG-AATA-ATAAATT
*
1487381 TATAAAATTTTAGAATAATAAA
1 TATAAAAATTTAGAATAATAAA
1487403 AAATAGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TATAAAAATTTAGAATAATAAATT
Found at i:1491375 original size:65 final size:66
Alignment explanation
Indices: 1491289--1491420 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 66
1491279 CCTACACACG
1491289 TCAGAAACATATTAAACACTCAACATTCTCTCTACCTTTTCTTCCTCCCCAAAAAAAGACT-AAC
1 TCAGAAACATATTAAACACTCAACATTCTCTCTACCTTTTCTTCCTCCCCAAAAAAAGACTGAAC
1491353 A
66 A
* * *
1491354 TCAGCAACATATTCAACACTCAACATTCTCTCTACTTTTTCTTCCTCCCCAAAAAAAGACTGAAC
1 TCAGAAACATATTAAACACTCAACATTCTCTCTACCTTTTCTTCCTCCCCAAAAAAAGACTGAAC
1491419 A
66 A
1491420 T
1 T
1491421 TAACTATAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 58 0.92
66 5 0.08
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (66 bp):
TCAGAAACATATTAAACACTCAACATTCTCTCTACCTTTTCTTCCTCCCCAAAAAAAGACTGAAC
A
Found at i:1495125 original size:33 final size:33
Alignment explanation
Indices: 1495083--1495156 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1495073 GTAAGGGGTT
*
1495083 GTTTGTTTGCCTCTTAATGGAATCATTCAGCAC
1 GTTTGTTTGCCTCTTAATGGAACCATTCAGCAC
*
1495116 GTTTGTTTGCCTCTTAATGGAACCATTCAGCGC
1 GTTTGTTTGCCTCTTAATGGAACCATTCAGCAC
1495149 GTTTGTTT
1 GTTTGTTT
1495157 CGCACCTCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (33 bp):
GTTTGTTTGCCTCTTAATGGAACCATTCAGCAC
Found at i:1495206 original size:23 final size:23
Alignment explanation
Indices: 1495174--1495239 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
1495164 CTGAATGATT
*
1495174 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
1495197 CAGTGTTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
1495220 CAGTGTTGACTGATTCAGCA
1 CAGTGTTGACTGATTCAGCA
1495240 TAGAAGTACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (23 bp):
CAGTGTTGACTGATTCAGCAAAA
Found at i:1498679 original size:13 final size:13
Alignment explanation
Indices: 1498661--1498725 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
1498651 GTCATAAATC
*
1498661 TATGACACGCATT
1 TATGACGCGCATT
*
1498674 TATGACGCACATT
1 TATGACGCGCATT
*
1498687 TATGACACGCATT
1 TATGACGCGCATT
*
1498700 TATGACGCACATT
1 TATGACGCGCATT
1498713 TATGACGCGCATT
1 TATGACGCGCATT
1498726 GCGCGTCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1498691 original size:26 final size:26
Alignment explanation
Indices: 1498661--1498725 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
1498651 GTCATAAATC
1498661 TATGACACGCATTTATGACGCACATT
1 TATGACACGCATTTATGACGCACATT
1498687 TATGACACGCATTTATGACGCACATT
1 TATGACACGCATTTATGACGCACATT
*
1498713 TATGACGCGCATT
1 TATGACACGCATT
1498726 GCGCGTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (26 bp):
TATGACACGCATTTATGACGCACATT
Found at i:1502979 original size:16 final size:17
Alignment explanation
Indices: 1502945--1502982 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1502935 GAAATGCATT
* *
1502945 TTTTTTTCTTTCATGTC
1 TTTTTTTCTCTCATCTC
1502962 TTTTTTTCTCTC-TCTC
1 TTTTTTTCTCTCATCTC
1502978 TTTTT
1 TTTTT
1502983 CTTTCGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTTCTCTCATCTC
Found at i:1517190 original size:18 final size:18
Alignment explanation
Indices: 1517167--1517209 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1517157 CTTTAAATTA
**
1517167 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTAACT
*
1517185 TTTATTTAATTCTTAACT
1 TTTATTTAATTATTAACT
1517203 TTTATTT
1 TTTATTT
1517210 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTAACT
Found at i:1522136 original size:26 final size:27
Alignment explanation
Indices: 1522085--1522137 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1522075 AAGTAGTATT
*
1522085 GATATTGTTCTTTGCAGTATCGATACC
1 GATACTGTTCTTTGCAGTATCGATACC
*
1522112 GATACTGTTC-TTGGAGTATCGATACC
1 GATACTGTTCTTTGCAGTATCGATACC
1522138 ATAGGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (27 bp):
GATACTGTTCTTTGCAGTATCGATACC
Found at i:1524203 original size:20 final size:20
Alignment explanation
Indices: 1524165--1524215 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1524155 ACCGTGATTG
*
1524165 CGGCCGTCGCGGGCGCTATTA
1 CGGCCGTCGC-GACGCTATTA
* *
1524186 CGGTCGTCGCGACGCTATTG
1 CGGCCGTCGCGACGCTATTA
1524206 CGGCCGTCGC
1 CGGCCGTCGC
1524216 CGGTAACTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.08, C:0.35, G:0.37, T:0.20
Consensus pattern (20 bp):
CGGCCGTCGCGACGCTATTA
Found at i:1525914 original size:18 final size:18
Alignment explanation
Indices: 1525891--1525934 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1525881 AAGCTTTTAG
1525891 AGAGTTCTACACTTCTCT
1 AGAGTTCTACACTTCTCT
* *
1525909 AGAGTTCTATATTTCTCT
1 AGAGTTCTACACTTCTCT
1525927 AGAGTTCT
1 AGAGTTCT
1525935 TTGGAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (18 bp):
AGAGTTCTACACTTCTCT
Found at i:1529882 original size:101 final size:101
Alignment explanation
Indices: 1529707--1529909 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
1529697 CTTCACCAAG
1529707 AAGGCTATCACTAACGGTATCCATGGCGAGCTTTCCTTCCGGAGCTGAATTACTAAATGTAACAA
1 AAGGCTATCACTAACGGTATCCATGGCGAGCTTTCCTTCCGGAGCTGAATTACTAAATGTAACAA
1529772 CGAGTGTATCCCAACTTTTCGGTAAGGAACTAATGA
66 CGAGTGTATCCCAACTTTTCGGTAAGGAACTAATGA
1529808 AAGGCTATCACTAACGGTATCCATGGCGAGCTTTCCTTCCGGAGCTGAATTACTAAATGTAACAA
1 AAGGCTATCACTAACGGTATCCATGGCGAGCTTTCCTTCCGGAGCTGAATTACTAAATGTAACAA
1529873 CGAGTGTATCCCAACTTTTCGGTAAGGAACTAATGA
66 CGAGTGTATCCCAACTTTTCGGTAAGGAACTAATGA
1529909 A
1 A
1529910 TAGAATGGCT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (101 bp):
AAGGCTATCACTAACGGTATCCATGGCGAGCTTTCCTTCCGGAGCTGAATTACTAAATGTAACAA
CGAGTGTATCCCAACTTTTCGGTAAGGAACTAATGA
Found at i:1530999 original size:20 final size:20
Alignment explanation
Indices: 1530950--1531002 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1530940 GAATTCTCCG
* *
1530950 GAATATTCTAGAAAATTCTA
1 GAATTTTCTAGAAAACTCTA
* * *
1530970 CACTTCTCTAGAAAACTCTA
1 GAATTTTCTAGAAAACTCTA
1530990 GAATTTTCTAGAA
1 GAATTTTCTAGAA
1531003 CCTCTCCAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (20 bp):
GAATTTTCTAGAAAACTCTA
Found at i:1530999 original size:40 final size:40
Alignment explanation
Indices: 1530915--1531002 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
1530905 TTACACAAGC
* * ** *
1530915 TTCTAGAGAGTTCTACACTTCTCTAGAATTCTCCGGAATA
1 TTCTAGAAAATTCTACACTTCTCTAGAAAACTCCAGAATA
* *
1530955 TTCTAGAAAATTCTACACTTCTCTAGAAAACTCTAGAATT
1 TTCTAGAAAATTCTACACTTCTCTAGAAAACTCCAGAATA
1530995 TTCTAGAA
1 TTCTAGAA
1531003 CCTCTCCAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (40 bp):
TTCTAGAAAATTCTACACTTCTCTAGAAAACTCCAGAATA
Found at i:1540986 original size:51 final size:51
Alignment explanation
Indices: 1540913--1541026 Score: 185
Period size: 51 Copynumber: 2.2 Consensus size: 51
1540903 AGTATGATGA
* *
1540913 TGGTGGTGGCGGTGGATATGGTCCGTC-TAAGGCGGGTGGTTGATGGTAGTT
1 TGGTGGTGGCGGCGGATATGGTCCG-CGAAAGGCGGGTGGTTGATGGTAGTT
1540964 TGGTGGTGGCGGCGGATATGGTCCGCGAAAGGCGGGTGGTTGATGGTAGTT
1 TGGTGGTGGCGGCGGATATGGTCCGCGAAAGGCGGGTGGTTGATGGTAGTT
*
1541015 TGGTGTTGGCGG
1 TGGTGGTGGCGG
1541027 GTAGTGCTGA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 1 0.02
51 58 0.98
ACGTcount: A:0.11, C:0.11, G:0.49, T:0.29
Consensus pattern (51 bp):
TGGTGGTGGCGGCGGATATGGTCCGCGAAAGGCGGGTGGTTGATGGTAGTT
Found at i:1543530 original size:55 final size:55
Alignment explanation
Indices: 1543469--1543577 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
1543459 TATATTTTTA
1543469 TTAACATGCTAAATTATTGTAACTAAATAATAATTCAAGTTTAAAAATAAATTAT
1 TTAACATGCTAAATTATTGTAACTAAATAATAATTCAAGTTTAAAAATAAATTAT
* *
1543524 TTAACATGTTAAATTATTGTAATTAAATAATAATTCAAGTTTAAAAATAAATTA
1 TTAACATGCTAAATTATTGTAACTAAATAATAATTCAAGTTTAAAAATAAATTA
1543578 GATTTTTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (55 bp):
TTAACATGCTAAATTATTGTAACTAAATAATAATTCAAGTTTAAAAATAAATTAT
Found at i:1547201 original size:51 final size:51
Alignment explanation
Indices: 1547124--1547230 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 51
1547114 AGATTGATGA
* *
1547124 ACATCCTAACATAGTTAGGTTGCATGAGGTATGTGTTGTTTTAAGTATTGT
1 ACATCCTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAAGTAGTGT
* *
1547175 ACATCTTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAATTAGTGT
1 ACATCCTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAAGTAGTGT
1547226 ACATC
1 ACATC
1547231 ATACTTTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.41
Consensus pattern (51 bp):
ACATCCTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAAGTAGTGT
Found at i:1548223 original size:21 final size:21
Alignment explanation
Indices: 1548193--1548268 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
1548183 TGATACATGG
*
1548193 GGTATTGATACCTATATGAAC
1 GGTATCGATACCTATATGAAC
* *
1548214 AGTATCGATACC-ATATGGTAC
1 GGTATCGATACCTATAT-GAAC
* * *
1548235 TGGTATCGATACCTATGTGGAG
1 -GGTATCGATACCTATATGAAC
1548257 GGTATCGATACC
1 GGTATCGATACC
1548269 CAGAAAACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.09
21 25 0.56
22 13 0.29
23 3 0.07
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCTATATGAAC
Found at i:1548752 original size:21 final size:21
Alignment explanation
Indices: 1548722--1548797 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
1548712 TGATACATGG
*
1548722 GGTATTGATACCTATATGAAC
1 GGTATCGATACCTATATGAAC
* *
1548743 AGTATCGATACC-ATATGGTAC
1 GGTATCGATACCTATAT-GAAC
* * *
1548764 TGGTATCGATACCTATGTGGAG
1 -GGTATCGATACCTATATGAAC
1548786 GGTATCGATACC
1 GGTATCGATACC
1548798 CAGAAAACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.09
21 25 0.56
22 13 0.29
23 3 0.07
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCTATATGAAC
Found at i:1548798 original size:529 final size:529
Alignment explanation
Indices: 1547800--1548845 Score: 2011
Period size: 529 Copynumber: 2.0 Consensus size: 529
1547790 ACAATAAGAT
*
1547800 GAGTGAATTAAGAAGGGATTTGTAAAATGAGTTTTAAGATGAATTGTTGATATGGTTTAGTTTTT
1 GAGTGAATTAAGAAGGGATTTGTAAAATGAGTTTTAAGATGAATTGTTGACATGGTTTAGTTTTT
*
1547865 AGATTTTTGATAAGATTTTTGACTTGTCATAAGAAGGATTAAGAAGTTTAAAGCATTAGAATTGA
66 AGAGTTTTGATAAGATTTTTGACTTGTCATAAGAAGGATTAAGAAGTTTAAAGCATTAGAATTGA
*
1547930 ATTTAGAACATATGGAAAGTTTGATGAAATTCTTTGATTCAAGAGTTATAGTGAGATATTGAGTA
131 ATTTAGAACATATGGAAAGTTTGATGAAATTCTTTGATTCAAGAGTTATAGTGAGATATTGAGGA
1547995 TAATGAAGTATTATAGTACTTAAAGAGGGTTTATATATGTATATATAAGTTTAAGGTATAAGAAG
196 TAATGAAGTATTATAGTACTTAAAGAGGGTTTATATATGTATATATAAGTTTAAGGTATAAGAAG
1548060 AGGTTAAAAAGTAGAATTTAGGGTCAAAGTGTTAAATTTTCAGACTTAAAAATGAAAATCTGGGT
261 AGGTTAAAAAGTAGAATTTAGGGTCAAAGTGTTAAATTTTCAGACTTAAAAATGAAAATCTGGGT
*
1548125 AAGGGGTATCGGTACCTGTTGAGTGGGTACCGATGCTACAAGGCTATTTATGAAGAACTGATACA
326 AAGGGGTATCGGTACCTATTGAGTGGGTACCGATGCTACAAGGCTATTTATGAAGAACTGATACA
1548190 TGGGGTATTGATACCTATATGAACAGTATCGATACCATATGGTACTGGTATCGATACCTATGTGG
391 TGGGGTATTGATACCTATATGAACAGTATCGATACCATATGGTACTGGTATCGATACCTATGTGG
*
1548255 AGGGTATCGATACCCAGAAAACTTTGAAGCTAAATTTGGTATCGGTACCTGGGTAGGGTATCGAT
456 AGGGTATCGATACCCAGAAAACTTTGAAGCTAAATTTGGTATCGGTACCTGGGAAGGGTATCGAT
1548320 ACCTATGTG
521 ACCTATGTG
* *
1548329 GAGTGAATTAGGAAGGGATTTGTAAAATGAGTTTTAAGATGAATTGTTGACATGGTTTGGTTTTT
1 GAGTGAATTAAGAAGGGATTTGTAAAATGAGTTTTAAGATGAATTGTTGACATGGTTTAGTTTTT
*
1548394 AGAGTTTTGATAAGATTTTTGACTTTTCATAAGAAGGATTAAGAAGTTTAAAGCATTAGAATTGA
66 AGAGTTTTGATAAGATTTTTGACTTGTCATAAGAAGGATTAAGAAGTTTAAAGCATTAGAATTGA
1548459 ATTTAGAACATATGGAAAGTTTGATGAAATTCTTTGATTCAAGAGTTATAGTGAGATATTGAGGA
131 ATTTAGAACATATGGAAAGTTTGATGAAATTCTTTGATTCAAGAGTTATAGTGAGATATTGAGGA
*
1548524 TAATGAAGTATTATAGTGCTTAAAGAGGGTTTATATATGTATATATAAGTTTAAGGTATAAGAAG
196 TAATGAAGTATTATAGTACTTAAAGAGGGTTTATATATGTATATATAAGTTTAAGGTATAAGAAG
1548589 AGGTTAAAAAGTAGAATTTAGGGTCAAAGTGTTAAATTTTCAGACTTAAAAATGAAAATCTGGGT
261 AGGTTAAAAAGTAGAATTTAGGGTCAAAGTGTTAAATTTTCAGACTTAAAAATGAAAATCTGGGT
1548654 AAGGGGTATCGGTACCTATTGAGTGGGTACCGATGCTACAAGGCTATTTATGAAGAACTGATACA
326 AAGGGGTATCGGTACCTATTGAGTGGGTACCGATGCTACAAGGCTATTTATGAAGAACTGATACA
1548719 TGGGGTATTGATACCTATATGAACAGTATCGATACCATATGGTACTGGTATCGATACCTATGTGG
391 TGGGGTATTGATACCTATATGAACAGTATCGATACCATATGGTACTGGTATCGATACCTATGTGG
1548784 AGGGTATCGATACCCAGAAAACTTTGAAGCTAAATTTGGTATCGGTACCTGGGAAGGGTATC
456 AGGGTATCGATACCCAGAAAACTTTGAAGCTAAATTTGGTATCGGTACCTGGGAAGGGTATC
1548846 AGTACCTTAG
Statistics
Matches: 508, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
529 508 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.33
Consensus pattern (529 bp):
GAGTGAATTAAGAAGGGATTTGTAAAATGAGTTTTAAGATGAATTGTTGACATGGTTTAGTTTTT
AGAGTTTTGATAAGATTTTTGACTTGTCATAAGAAGGATTAAGAAGTTTAAAGCATTAGAATTGA
ATTTAGAACATATGGAAAGTTTGATGAAATTCTTTGATTCAAGAGTTATAGTGAGATATTGAGGA
TAATGAAGTATTATAGTACTTAAAGAGGGTTTATATATGTATATATAAGTTTAAGGTATAAGAAG
AGGTTAAAAAGTAGAATTTAGGGTCAAAGTGTTAAATTTTCAGACTTAAAAATGAAAATCTGGGT
AAGGGGTATCGGTACCTATTGAGTGGGTACCGATGCTACAAGGCTATTTATGAAGAACTGATACA
TGGGGTATTGATACCTATATGAACAGTATCGATACCATATGGTACTGGTATCGATACCTATGTGG
AGGGTATCGATACCCAGAAAACTTTGAAGCTAAATTTGGTATCGGTACCTGGGAAGGGTATCGAT
ACCTATGTG
Found at i:1554301 original size:23 final size:23
Alignment explanation
Indices: 1554270--1554361 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 23
1554260 AGGGTTCTAC
* * *
1554270 GGTCATTCGGGACAATTCTATGT
1 GGTCCTTCGGGACATTTCTACGT
*
1554293 GGTCCTTCGAGACATTTCTACGT
1 GGTCCTTCGGGACATTTCTACGT
* *
1554316 AGTCCTTCAGGACATTTCTACGT
1 GGTCCTTCGGGACATTTCTACGT
1554339 GG-CACTTCGGTG-CATATTCTACG
1 GGTC-CTTCGG-GACAT-TTCTACG
1554362 CGACACTTCG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.02
23 48 0.84
24 8 0.14
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.34
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTACGT
Found at i:1554361 original size:24 final size:23
Alignment explanation
Indices: 1554331--1554389 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
1554321 TTCAGGACAT
1554331 TTCTACGTGGCACTTCGGTGCATA
1 TTCTACGTGGCACTTCGGTGCA-A
* *
1554355 TTCTACGCGACACTTCGGTGCAA
1 TTCTACGTGGCACTTCGGTGCAA
*
1554378 TTCTATGTGGCA
1 TTCTACGTGGCA
1554390 ATTTCGACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (23 bp):
TTCTACGTGGCACTTCGGTGCAA
Found at i:1561266 original size:23 final size:23
Alignment explanation
Indices: 1561205--1561260 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1561195 GAGTCAAGGG
* *
1561205 TTCTACGCGGTCTTTC-GAGACAT
1 TTCTACGTGGTCCTTCAG-GACAT
*
1561228 TTCTTCGTGGTCCTTCAGGACAT
1 TTCTACGTGGTCCTTCAGGACAT
1561251 TTCTACGTGG
1 TTCTACGTGG
1561261 CACTTCGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.38
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCAGGACAT
Found at i:1561309 original size:23 final size:23
Alignment explanation
Indices: 1561251--1561309 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1561241 TTCAGGACAT
*
1561251 TTCTACGTGGCACTTCGGTGCATA
1 TTCTACGTGACACTTCGGT-CATA
*
1561275 TTCTACGCGACACTTCGGT-ATAA
1 TTCTACGTGACACTTCGGTCAT-A
*
1561298 TTCTATGTGACA
1 TTCTACGTGACA
1561310 ATTTTGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.07
23 11 0.37
24 17 0.57
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (23 bp):
TTCTACGTGACACTTCGGTCATA
Found at i:1561993 original size:4 final size:4
Alignment explanation
Indices: 1561986--1562102 Score: 50
Period size: 4 Copynumber: 29.8 Consensus size: 4
1561976 ATAGTAAGTA
* * * * * *
1561986 AAAT AAAT --AT AAAA AAAT AAAG AAAA AGAAG AAAA AAAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* *
1562033 AAAAC AAAT AAAT AAA- ATAAT -AAT AAA- AAAGT -AA- AAAT AAAT ATAT
1 -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
* *
1562079 ATAT ATAAT AAAT ATAT AAAT AAA
1 AAAT A-AAT AAAT AAAT AAAT AAA
1562103 AATAGTAATA
Statistics
Matches: 86, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
2 2 0.02
3 9 0.10
4 66 0.77
5 9 0.10
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1562012 original size:13 final size:13
Alignment explanation
Indices: 1561985--1562075 Score: 69
Period size: 13 Copynumber: 6.8 Consensus size: 13
1561975 AATAGTAAGT
1561985 AAAATAAATATAAA
1 AAAATAAATA-AAA
*
1561999 AAAATAAAGAAAA
1 AAAATAAATAAAA
* *
1562012 AGAAGAAA-AAAA
1 AAAATAAATAAAA
* *
1562024 TATATAAATAAAA
1 AAAATAAATAAAA
*
1562037 CAAATAAATAAAA
1 AAAATAAATAAAA
1562050 TAATAATAAA-AAAGTA
1 -AA-AATAAATAAA--A
1562066 AAAATAAATA
1 AAAATAAATA
1562076 TATATATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
12 8 0.13
13 24 0.39
14 19 0.31
15 9 0.15
16 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:1562036 original size:25 final size:24
Alignment explanation
Indices: 1562002--1562079 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 24
1561992 ATATAAAAAA
*
1562002 ATAAAGAAAAAGAAGAAAAAAATAT
1 ATAAATAAAAAGAA-AAAAAAATAT
1562027 ATAAATAAAACA-AATAAATAAAATA-
1 ATAAATAAAA-AGAA-AAA-AAAATAT
*
1562052 AT-AATAAAAAAGTAAAAATAAATAT
1 ATAAAT-AAAAAG-AAAAAAAAATAT
1562077 ATA
1 ATA
1562080 TATATAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
24 9 0.21
25 25 0.58
26 9 0.21
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (24 bp):
ATAAATAAAAAGAAAAAAAAATAT
Found at i:1562047 original size:17 final size:16
Alignment explanation
Indices: 1561985--1562104 Score: 59
Period size: 17 Copynumber: 7.1 Consensus size: 16
1561975 AATAGTAAGT
1561985 AAAATAAAT--ATAAA
1 AAAATAAATAAATAAA
*
1561999 AAAATAAAGAAA-AAGA
1 AAAATAAATAAATAA-A
* *
1562015 AGAAAAAAATATATAAA
1 A-AAATAAATAAATAAA
*
1562032 TAAAACAAATAAATAAA
1 -AAAATAAATAAATAAA
* *
1562049 ATAAT-AATAAAAAAGTA
1 AAAATAAATAAATAA--A
1562066 AAAATAAATATATATATATA
1 AAAATAAATA-A-ATA-A-A
*
1562086 ATAAATATATAAATAAA
1 A-AAATAAATAAATAAA
1562103 AA
1 AA
1562105 TAGTAATATA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
14 8 0.10
15 10 0.12
16 7 0.09
17 29 0.36
18 8 0.10
19 4 0.05
20 6 0.07
21 9 0.11
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAATAAATAAATAAA
Found at i:1562062 original size:50 final size:51
Alignment explanation
Indices: 1561994--1562107 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 51
1561984 TAAAATAAAT
*
1561994 ATAAAAAAATAA-AGAAAAAG-AAGAAAAAAATATATAAATAAAACAAATAA
1 ATAAAATAATAATAGAAAAAGTAA-AAAAAAATATATAAATAAAACAAATAA
* * * * *
1562044 ATAAAATAATAATA-AAAAAGTAAAAATAAATATATATATATAATAAATAT
1 ATAAAATAATAATAGAAAAAGTAAAAAAAAATATATAAATAAAACAAATAA
*
1562094 AT-AAATAAAAATAG
1 ATAAAATAATAATAG
1562108 TAATATATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
49 10 0.19
50 41 0.76
51 3 0.06
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (51 bp):
ATAAAATAATAATAGAAAAAGTAAAAAAAAATATATAAATAAAACAAATAA
Found at i:1562092 original size:41 final size:41
Alignment explanation
Indices: 1562047--1562171 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 41
1562037 CAAATAAATA
*
1562047 AAATAATAATAAAAAAGTAAAAATAAATATATATATATAAT
1 AAATAATAATAAAAAAGTAAATATAAATATATATATATAAT
*
1562088 AAATATATAAATAAAAATAGT-AATATATATATATATATA-AAT
1 AAATA-AT-AATAAAAA-AGTAAATATAAATATATATATATAAT
*
1562130 AAACTGATAATAAAAAA--AATATATAATATATATATATATAAT
1 AAA-TAATAATAAAAAAGTAA-ATATAA-ATATATATATATAAT
1562172 CTAAAAATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
39 1 0.01
40 6 0.08
41 24 0.33
42 13 0.18
43 25 0.35
44 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (41 bp):
AAATAATAATAAAAAAGTAAATATAAATATATATATATAAT
Found at i:1562181 original size:15 final size:15
Alignment explanation
Indices: 1562019--1562184 Score: 87
Period size: 15 Copynumber: 11.7 Consensus size: 15
1562009 AAAAGAAGAA
1562019 AAAAATATATAA-AT
1 AAAAATATATAATAT
1562033 AAAACA-A-ATAA-AT
1 AAAA-ATATATAATAT
1562046 -AAAATA-ATAATA-
1 AAAAATATATAATAT
1562058 AAAAAGTA-A-AA-AT
1 AAAAA-TATATAATAT
*
1562071 AAATATATAT-ATAT
1 AAAAATATATAATAT
1562085 AATAAATATATAA-AT
1 AA-AAATATATAATAT
*
1562100 AAAAATA-GTAATAT
1 AAAAATATATAATAT
*
1562114 --ATATATAT-ATAT
1 AAAAATATATAATAT
*
1562126 AAATAA-ACTGATAATAAA
1 AAA-AATA-T-ATAAT-AT
1562144 AAAAATATATAATAT
1 AAAAATATATAATAT
* * *
1562159 ATATATATATAATCT
1 AAAAATATATAATAT
1562174 AAAAATATATA
1 AAAAATATATA
1562185 TACTAAAGTA
Statistics
Matches: 118, Mismatches: 13, Indels: 41
0.69 0.08 0.24
Matches are distributed among these distances:
11 1 0.01
12 19 0.16
13 23 0.19
14 21 0.18
15 36 0.31
16 8 0.07
17 5 0.04
18 5 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAATATATAATAT
Found at i:1562186 original size:2 final size:2
Alignment explanation
Indices: 1562073--1562169 Score: 51
Period size: 2 Copynumber: 49.5 Consensus size: 2
1562063 GTAAAAATAA
* * * *
1562073 AT AT AT AT AT AT A- AT AA AT AT AT AA AT AA AA AT AGT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
1562114 AT AT AT AT AT AT AA AT AA ACT GAT A- AT A- AA AA AA AT AT AT A-
1 AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT
1562155 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1562170 ATCTAAAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
1 5 0.07
2 67 0.88
3 3 0.04
4 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (2 bp):
AT
Found at i:1563347 original size:39 final size:39
Alignment explanation
Indices: 1563293--1563370 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1563283 CGAGGGTTTG
*
1563293 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
* * *
1563332 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTTTTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
1563371 TTCAAGATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (39 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
Found at i:1563377 original size:35 final size:39
Alignment explanation
Indices: 1563293--1563382 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
1563283 CGAGGGTTTG
* *
1563293 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTGTGTGT
*
1563332 GTGTTTCAAGAGAAACAATTTC-GAGGGTTTTT-T-T-T
1 GTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTGTGTGT
*
1563367 GTGTTTCAAGATAAAC
1 GTGTTTCAAGAGAAAC
1563383 TTAGTTCTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 16 0.34
36 1 0.02
37 1 0.02
38 8 0.17
39 21 0.45
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (39 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTGTGTGT
Found at i:1563534 original size:37 final size:37
Alignment explanation
Indices: 1563443--1563545 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
1563433 AAGATATTCA
1563443 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* *
1563480 AA-AATTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1563516 AAGATTTTGTTTCAAGGGAAACTGTCTCAA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAA
1563546 AACTCGTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (37 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
Found at i:1563725 original size:102 final size:102
Alignment explanation
Indices: 1563583--1563822 Score: 365
Period size: 102 Copynumber: 2.4 Consensus size: 102
1563573 ATATTTTGTG
* * * *
1563583 TTTCAAGGGAAACGTTTTCAAGGTTTATATTTCAAAAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * *
1563648 GTTTCAATGGAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
*
1563685 TTTCTAA-GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTC-AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* * *
1563749 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
65 TGTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
1563787 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1563823 GGAGACAAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
101 2 0.02
102 121 0.97
103 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:1563763 original size:37 final size:36
Alignment explanation
Indices: 1563712--1563798 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
1563702 TCAATGTTTA
* ** * *
1563712 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAA-TT
*
1563749 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
*
1563785 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1563799 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
Done.