Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 20 of 216
Found at i:6205386 original size:17 final size:18
Alignment explanation
Indices: 6205360--6205397 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
6205350 CAAAAATTAA
6205360 TTATAAATTTTGA-ATTT
1 TTATAAATTTTGAGATTT
* *
6205377 TTATATATTTTTAGATTT
1 TTATAAATTTTGAGATTT
6205395 TTA
1 TTA
6205398 AAAAATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTATAAATTTTGAGATTT
Found at i:6205607 original size:26 final size:26
Alignment explanation
Indices: 6205571--6205623 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
6205561 ATATTCTTAG
6205571 ATTTTTTAAAATATTTA-AATATTTTT
1 ATTTTTTAAAATATTTACAA-ATTTTT
*
6205597 ATTTTTTAAAATTTTTACAAATTTTT
1 ATTTTTTAAAATATTTACAAATTTTT
6205623 A
1 A
6205624 ATAATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTTAAAATATTTACAAATTTTT
Found at i:6205623 original size:10 final size:9
Alignment explanation
Indices: 6205534--6205654 Score: 84
Period size: 10 Copynumber: 13.0 Consensus size: 9
6205524 TATTTAATTT
6205534 AATTTTTAA
1 AATTTTTAA
*
6205543 AATGTTTAA
1 AATTTTTAA
6205552 ACATTTTTAA
1 A-ATTTTTAA
* * *
6205562 TATTCTTAG
1 AATTTTTAA
*
6205571 ATTTTTTAA
1 AATTTTTAA
*
6205580 AATATTTAA
1 AATTTTTAA
6205589 ATATTTTT--
1 A-ATTTTTAA
*
6205597 ATTTTTTAA
1 AATTTTTAA
6205606 AATTTTTACA
1 AATTTTTA-A
6205616 AATTTTTAA
1 AATTTTTAA
*
6205625 TAATTTATAA
1 -AATTTTTAA
* *
6205635 GTATGTTTAA
1 -AATTTTTAA
6205645 AAGTTTTTAA
1 AA-TTTTTAA
6205655 GCCACATGAA
Statistics
Matches: 84, Mismatches: 21, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
9 37 0.44
10 41 0.49
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:6207075 original size:18 final size:19
Alignment explanation
Indices: 6207042--6207082 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
6207032 ATGTCTCTAA
6207042 AATAATAACAAGATTA-AC
1 AATAATAACAAGATTATAC
6207060 AATAA-AACAAGTATTATAC
1 AATAATAACAAG-ATTATAC
6207079 AATA
1 AATA
6207083 TCCAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAATAACAAGATTATAC
Found at i:6213819 original size:18 final size:20
Alignment explanation
Indices: 6213798--6213837 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
6213788 CTAAATAAAA
*
6213798 ATAAAAAT-TTATAAAT-TT
1 ATAAAAATATTAGAAATATT
6213816 ATAAAAATATTAGAAATATT
1 ATAAAAATATTAGAAATATT
6213836 AT
1 AT
6213838 TTGACACTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
ATAAAAATATTAGAAATATT
Found at i:6214051 original size:24 final size:24
Alignment explanation
Indices: 6213989--6214056 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
6213979 TAAGAAAAGG
* *
6213989 GTTACAAGAAGATTAAAGGTGAAGA
1 GTTA-AAGAAGATGAAAGGTGAAAA
6214014 GTTAAAGAAGATGAAAGGTGAAAA
1 GTTAAAGAAGATGAAAGGTGAAAA
* * *
6214038 GTTGAGGAATATGAAAGGT
1 GTTAAAGAAGATGAAAGGT
6214057 TGAACATCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
24 34 0.89
25 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.31, T:0.21
Consensus pattern (24 bp):
GTTAAAGAAGATGAAAGGTGAAAA
Found at i:6214880 original size:96 final size:94
Alignment explanation
Indices: 6214768--6215047 Score: 303
Period size: 94 Copynumber: 2.9 Consensus size: 94
6214758 GTTTGTCACT
** * * **
6214768 TAAATTAATTATAAAATTTTCAAAATTAGATTA-ATTTTCGTGTTTATTGTTTTGTAAGAAAAAA
1 TAAATTAATTATAAAATTTT-AAAATTAGATTAGGGTTTAGAGTTTAAGGTTTT-TAAG-AAAAA
* *
6214832 ATCAATTAAATTAGGGTTTAGGGTTACTTGAG
63 ATCAAATAAATTAGGGTTCAGGGTTACTTGAG
* * * * * *
6214864 TAATTTAATTAAAAAATTTTAAAGATCAAATTAGGGTTTAGAG-TTAAGGGTTTTAAGGAAAAAT
1 TAAATTAATTATAAAATTTTAAA-ATTAGATTAGGGTTTAGAGTTTAAGGTTTTTAAGAAAAAAT
6214928 CAAATAAATTAGGGTTCAGGGTTACTTGAG
65 CAAATAAATTAGGGTTCAGGGTTACTTGAG
* * * *
6214958 TAAATTAATTATAAATTTTTAATAAATTAGTTTAGGGTTTAGGGTTTAGGGTTTTTAAGTAAAAA
1 TAAATTAATTATAAAATTTT-A-AAATTAGATTAGGGTTTAGAGTTTAAGGTTTTTAAG-AAAAA
* *
6215023 CTCAAATAAATTAGGGTTCTGGGTT
63 ATCAAATAAATTAGGGTTCAGGGTT
6215048 TAAGGTTACT
Statistics
Matches: 152, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
94 51 0.34
95 23 0.15
96 46 0.30
97 32 0.21
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.40
Consensus pattern (94 bp):
TAAATTAATTATAAAATTTTAAAATTAGATTAGGGTTTAGAGTTTAAGGTTTTTAAGAAAAAATC
AAATAAATTAGGGTTCAGGGTTACTTGAG
Found at i:6214999 original size:7 final size:7
Alignment explanation
Indices: 6214987--6215011 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6214977 TAATAAATTA
6214987 GTTTAGG
1 GTTTAGG
6214994 GTTTAGG
1 GTTTAGG
6215001 GTTTAGG
1 GTTTAGG
6215008 GTTT
1 GTTT
6215012 TTAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:6215472 original size:125 final size:126
Alignment explanation
Indices: 6215080--6215506 Score: 694
Period size: 126 Copynumber: 3.4 Consensus size: 126
6215070 TTGTTAATTT
* **
6215080 AAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
*
6215145 ATTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTG
66 ATTTTTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTG
* *
6215206 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAGAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
* **
6215271 GTTTTTGAGCAAACAGTGTCAAAAACGCTTTAATTAGGATGCTTTGTCAGCAGAAGTACTG
66 ATTTTTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTG
* * *
6215332 AAAGAAGCTCTCACGTGGACGGGCTTTTGCTATAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
* * * *
6215397 -TTTTTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGATGTATTG
66 ATTTTTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTG
*
6215457 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTTGCCCCTGAAAAAA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAA
6215507 GCTCCCACGT
Statistics
Matches: 280, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
125 101 0.36
126 179 0.64
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
ATTTTTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:6219406 original size:11 final size:11
Alignment explanation
Indices: 6219392--6219451 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
6219382 TCTTTTAAAT
6219392 AGAAATTTGAG
1 AGAAATTTGAG
6219403 AGAAATTTGAG
1 AGAAATTTGAG
* *
6219414 AGGAAGTTGAG
1 AGAAATTTGAG
*
6219425 AGGAATTTGAG
1 AGAAATTTGAG
*
6219436 AGAATATTAGAG
1 AGAA-ATTTGAG
6219448 AGAA
1 AGAA
6219452 TATTAGAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
11 33 0.77
12 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (11 bp):
AGAAATTTGAG
Found at i:6219450 original size:12 final size:12
Alignment explanation
Indices: 6219433--6219460 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6219423 AGAGGAATTT
6219433 GAGAGAATATTA
1 GAGAGAATATTA
6219445 GAGAGAATATTA
1 GAGAGAATATTA
6219457 GAGA
1 GAGA
6219461 AAGGATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAGAGAATATTA
Found at i:6219452 original size:22 final size:20
Alignment explanation
Indices: 6219392--6219462 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 20
6219382 TCTTTTAAAT
6219392 AGAAATTTGAGAGAAATTTGAG
1 AGAAA-TTGAGAG-AATTTGAG
*
6219414 AGGAAGTTGAGAGGAATTTGAG
1 A-GAAATTGAGA-GAATTTGAG
6219436 AGAATATTAGAGAGAATATT-AG
1 AGAA-ATT-GAGAGAAT-TTGAG
6219458 AGAAA
1 AGAAA
6219463 GGATTTAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 4 0.10
22 28 0.67
23 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (20 bp):
AGAAATTGAGAGAATTTGAG
Found at i:6234644 original size:54 final size:54
Alignment explanation
Indices: 6234560--6234668 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
6234550 AATACTCAGG
*
6234560 CGGCAGGGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
1 CGGCAGAGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
*
6234614 CGGCAGAGTTGACCATATATTAAAGTCAACCCAAGTGCACTAAGTGCTTAGAAA
1 CGGCAGAGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
6234668 C
1 C
6234669 TTAAGGCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (54 bp):
CGGCAGAGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
Found at i:6241312 original size:151 final size:152
Alignment explanation
Indices: 6241024--6241333 Score: 451
Period size: 151 Copynumber: 2.0 Consensus size: 152
6241014 TCTCGAGCTA
* * * * *
6241024 TTCACTTTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCGTTTCTATTCAGTGCTACTCATAC
1 TTCACATTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCATTACTACTCAGTGCTACTCACAC
* *
6241089 AAGCTGTCAGGTATCTGCAACACATACCAGTATACCCAGGCATTGGTAGAACTTAAGACCAGCAC
66 AAGCTGTCAGGTATCCGCAACACATACCAGTATACCCAGCCATTGGTAGAACTTAAGACCAGCAC
6241154 CCAGATTCACTTTAGTCACACT
131 CCAGATTCACTTTAGTCACACT
* * *
6241176 TTCACATT-ACGGGTCTGCTCACACAAGCTGTCAGTCTTTCATTACTACTCAGTGTTGCTCACAC
1 TTCACATTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCATTACTACTCAGTGCTACTCACAC
* ** * * * *
6241240 AAGCTGTCAGGTATCCGCAATACATGTCGGTATGCTCAGCCATTGGTAGAACTTAAGACTAGCAC
66 AAGCTGTCAGGTATCCGCAACACATACCAGTATACCCAGCCATTGGTAGAACTTAAGACCAGCAC
*
6241305 CCGGATTCACTTTAGTCACACT
131 CCAGATTCACTTTAGTCACACT
6241327 TTCACAT
1 TTCACAT
6241334 AGAACCTTAG
Statistics
Matches: 140, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
151 133 0.95
152 7 0.05
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (152 bp):
TTCACATTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCATTACTACTCAGTGCTACTCACAC
AAGCTGTCAGGTATCCGCAACACATACCAGTATACCCAGCCATTGGTAGAACTTAAGACCAGCAC
CCAGATTCACTTTAGTCACACT
Found at i:6246469 original size:13 final size:14
Alignment explanation
Indices: 6246432--6246463 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6246422 ATGGCCTACA
6246432 ATTTCACGAAATCG
1 ATTTCACGAAATCG
6246446 ATTTCACGAAAT-G
1 ATTTCACGAAATCG
6246459 ATTTC
1 ATTTC
6246464 GTGAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (14 bp):
ATTTCACGAAATCG
Found at i:6257904 original size:18 final size:19
Alignment explanation
Indices: 6257871--6257906 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6257861 TCAAATGAAC
*
6257871 TAAAATCATAAATATGTAA
1 TAAAATAATAAATATGTAA
6257890 TAAAATAAT-AATATGTA
1 TAAAATAATAAATATGTA
6257907 TAGATACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (19 bp):
TAAAATAATAAATATGTAA
Found at i:6260326 original size:112 final size:113
Alignment explanation
Indices: 6260128--6260342 Score: 360
Period size: 112 Copynumber: 1.9 Consensus size: 113
6260118 TTTCATGGAT
* **
6260128 GTCAAAATAAAAAAAAAAGGCCCACATCTAACTTGACTTAAATCTATCCAAAGATTTATTGTGTA
1 GTCAAAATAAAAAAAAAAGGCCCACATCTAACTTGACTTAAAGCTATCCAAAGATTTATTGTACA
* *
6260193 GATTACTATTCAAAGATCTATCTAAATATTTTTTTGAAGATGGAGTGA
66 AATTACTATTCAAAGATCTATCTAAATATTTGTTTGAAGATGGAGTGA
*
6260241 GTCAAAAT-AAAAAAAAAGGCCCACATCTAAGTTGACTTAAAGCTATCCAAAGATTTATTGTACA
1 GTCAAAATAAAAAAAAAAGGCCCACATCTAACTTGACTTAAAGCTATCCAAAGATTTATTGTACA
*
6260305 AATTACTATTCAAATATCTATCTAAATATTTGTTTGAA
66 AATTACTATTCAAAGATCTATCTAAATATTTGTTTGAA
6260343 CATCAGAGTG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
112 87 0.92
113 8 0.08
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (113 bp):
GTCAAAATAAAAAAAAAAGGCCCACATCTAACTTGACTTAAAGCTATCCAAAGATTTATTGTACA
AATTACTATTCAAAGATCTATCTAAATATTTGTTTGAAGATGGAGTGA
Found at i:6262157 original size:15 final size:15
Alignment explanation
Indices: 6262137--6262185 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
6262127 TACTTTTCAA
6262137 TTTTTAAGAATTTAG
1 TTTTTAAGAATTTAG
* *
6262152 TTTTT-ATATTTGTA-
1 TTTTTAAGAATT-TAG
6262166 TTTTTAAGAATTTAG
1 TTTTTAAGAATTTAG
6262181 TTTTT
1 TTTTT
6262186 TTTTTAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (15 bp):
TTTTTAAGAATTTAG
Found at i:6262556 original size:16 final size:16
Alignment explanation
Indices: 6262535--6262566 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6262525 TTTCAGATTT
6262535 ATTAACCACACACACG
1 ATTAACCACACACACG
*
6262551 ATTAACCACAGACACG
1 ATTAACCACACACACG
6262567 TGGCTCACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.34, G:0.09, T:0.12
Consensus pattern (16 bp):
ATTAACCACACACACG
Found at i:6262821 original size:83 final size:83
Alignment explanation
Indices: 6262682--6262847 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
6262672 CCGTCACACA
* *
6262682 GATTGTTAAACTTTCATATTACTTAGAGATAATAAGCAATATTCTTCCATACATTCATAAGTGAA
1 GATTGTTAAACTCTCATATTACTTAGAGAAAATAAGCAATATTCTTCCATACATTCATAAGTGAA
6262747 ACTACACGTATTTAATAC
66 ACTACACGTATTTAATAC
6262765 GATTGTTAAACTCTCATATTACTTAGAGAAAATAAGCAATATTCTTCCATACATTCATAAGTGAA
1 GATTGTTAAACTCTCATATTACTTAGAGAAAATAAGCAATATTCTTCCATACATTCATAAGTGAA
6262830 ACTACACGTATTTAATAC
66 ACTACACGTATTTAATAC
6262848 TCACAATCTC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (83 bp):
GATTGTTAAACTCTCATATTACTTAGAGAAAATAAGCAATATTCTTCCATACATTCATAAGTGAA
ACTACACGTATTTAATAC
Found at i:6264929 original size:19 final size:19
Alignment explanation
Indices: 6264905--6264978 Score: 94
Period size: 19 Copynumber: 3.8 Consensus size: 19
6264895 ATTTTTGAGA
6264905 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
**
6264924 ATATGCAATCCAAGATATG
1 ATATGCAATCTTAGATATG
**
6264943 ATATATATAATCTTAGATATG
1 --ATATGCAATCTTAGATATG
6264964 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
6264979 ATATATGATT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 30 0.67
21 15 0.33
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:6266436 original size:98 final size:98
Alignment explanation
Indices: 6266313--6266509 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
6266303 TTAAAAATAA
* * * *
6266313 TAAAGGAAATATTTCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
6266378 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
6266411 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAATGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
6266476 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
6266509 T
1 T
6266510 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:6275034 original size:42 final size:42
Alignment explanation
Indices: 6274939--6275022 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
6274929 TAAAATGCAA
6274939 CCTTCAGTTAATTTTTGTACTTTTCAAATTTAAAAACACAAT
1 CCTTCAGTTAATTTTTGTACTTTTCAAATTTAAAAACACAAT
6274981 CCTTCAGTTAATTTTTGTACTTTTCAAATTTAAAAACACAAT
1 CCTTCAGTTAATTTTTGTACTTTTCAAATTTAAAAACACAAT
6275023 TCTATTGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (42 bp):
CCTTCAGTTAATTTTTGTACTTTTCAAATTTAAAAACACAAT
Found at i:6275724 original size:22 final size:22
Alignment explanation
Indices: 6275683--6275724 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6275673 CTTGAATTTT
*
6275683 TAAATTCAGAAAGTAGAAAAAC
1 TAAATTCAGAAAATAGAAAAAC
6275705 TAAATTCCAGAAAATA-AAAA
1 TAAATT-CAGAAAATAGAAAA
6275725 TAGGTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (22 bp):
TAAATTCAGAAAATAGAAAAAC
Found at i:6277658 original size:12 final size:13
Alignment explanation
Indices: 6277635--6277676 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
6277625 AAAAAAAGAG
*
6277635 ATTTGACATTATA
1 ATTTTACATTATA
6277648 ATTTT-CATTATA
1 ATTTTACATTATA
*
6277660 TTTTTACATT-TA
1 ATTTTACATTATA
6277672 ATTTT
1 ATTTT
6277677 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTTACATTATA
Found at i:6289414 original size:20 final size:20
Alignment explanation
Indices: 6289391--6289428 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6289381 TTATACTTTT
*
6289391 TAAAATAGCTTTACTTTAGG
1 TAAAATAGATTTACTTTAGG
*
6289411 TAAAATATATTTACTTTA
1 TAAAATAGATTTACTTTA
6289429 ATAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (20 bp):
TAAAATAGATTTACTTTAGG
Found at i:6290259 original size:23 final size:22
Alignment explanation
Indices: 6290232--6290349 Score: 73
Period size: 23 Copynumber: 5.2 Consensus size: 22
6290222 ATCTTACTCA
6290232 TTTTATCATGATGTCATAACATC
1 TTTTATCAT-ATGTCATAACATC
* * *
6290255 TTTTAGC-TATGGTCTTACTCAT-
1 TTTTATCATAT-GTCATA-ACATC
*
6290277 TTTTATCATGATGCCATAACATC
1 TTTTATCAT-ATGTCATAACATC
* * * *
6290300 TTTCAAC-TATGGTCTTACTCAT-
1 TTTTATCATAT-GTCATA-ACATC
6290322 TTTTATCATAATGTCATAACATC
1 TTTTATCAT-ATGTCATAACATC
6290345 TTTTA
1 TTTTA
6290350 GCTATGGACT
Statistics
Matches: 69, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
21 4 0.06
22 28 0.41
23 33 0.48
24 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTTATCATATGTCATAACATC
Found at i:6290296 original size:45 final size:45
Alignment explanation
Indices: 6290195--6290369 Score: 262
Period size: 45 Copynumber: 3.9 Consensus size: 45
6290185 GTGCTTTCAT
* * *
6290195 ATGATGTCATAGCATCTTCCAGCTATGATCTTACTCA-TTTTATC
1 ATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
*
6290239 ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATTTTTATC
1 ATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
* *
6290284 ATGATGCCATAACATCTTTCAACTATGGTCTTACTCATTTTTATC
1 ATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
* * *
6290329 ATAATGTCATAACATCTTTTAGCTATGGACTTACTCATTTT
1 ATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTT
6290370 AGGCATATAG
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 33 0.28
45 85 0.72
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.43
Consensus pattern (45 bp):
ATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
Found at i:6290808 original size:16 final size:17
Alignment explanation
Indices: 6290767--6290811 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
6290757 CATTTTTCTA
6290767 TATTTTTATAATAATATT
1 TATTTTT-TAATAATATT
* *
6290785 TATATTTTAA-AATTTT
1 TATTTTTTAATAATATT
6290801 TATTTTTTAAT
1 TATTTTTTAAT
6290812 TCATATAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 14 0.61
17 3 0.13
18 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTTTAATAATATT
Found at i:6290886 original size:19 final size:19
Alignment explanation
Indices: 6290840--6290896 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
6290830 TTTTAATTTC
6290840 ATAATTTAT-ATAATTATTTT
1 ATAATTTATAATAA-T-TTTT
*
6290860 AGTCATTTATAATAATTTTT
1 A-TAATTTATAATAATTTTT
*
6290880 ATAATTTTTAAATAATT
1 ATAATTTAT-AATAATT
6290897 ATAATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.19
20 13 0.42
21 8 0.26
22 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATAATTTATAATAATTTTT
Found at i:6290893 original size:20 final size:20
Alignment explanation
Indices: 6290865--6290919 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
6290855 ATTTTAGTCA
6290865 TTTATAATAATTTTTATAATT
1 TTTA-AATAATTTTTATAATT
* * *
6290886 TTTAAATAATTATAATATTT
1 TTTAAATAATTTTTATAATT
**
6290906 TTTTTATAATTTTT
1 TTTAAATAATTTTT
6290920 TGCACATTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAAATAATTTTTATAATT
Found at i:6290965 original size:29 final size:30
Alignment explanation
Indices: 6290933--6290990 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
6290923 ACATTTATAC
6290933 TTTTTTT-T-AATCTTTAATA-TTTTTAATA
1 TTTTTTTATAAAT-TTTAATATTTTTTAATA
6290961 TTTTTTTATAAATTTTAATATTTTTTAATA
1 TTTTTTTATAAATTTTAATATTTTTTAATA
6290991 ATTTGAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.26
29 8 0.30
30 12 0.44
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTTTTATAAATTTTAATATTTTTTAATA
Found at i:6290968 original size:20 final size:19
Alignment explanation
Indices: 6290945--6290994 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
6290935 TTTTTTAATC
*
6290945 TTTAATATTTTTAATATTT
1 TTTAATAATTTTAATATTT
*
6290964 TTTTATAAATTTTAATATTT
1 TTTAAT-AATTTTAATATTT
6290984 TTTAATAATTT
1 TTTAATAATTT
6290995 GAAGTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTAATAATTTTAATATTT
Found at i:6290986 original size:10 final size:10
Alignment explanation
Indices: 6290945--6290990 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
6290935 TTTTTTAATC
6290945 TTTAATA-TT
1 TTTAATATTT
6290954 TTTAATATTT
1 TTTAATATTT
* **
6290964 TTTTATAAAT
1 TTTAATATTT
6290974 TTTAATATTT
1 TTTAATATTT
6290984 TTTAATA
1 TTTAATA
6290991 ATTTGAAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTAATATTT
Found at i:6291135 original size:16 final size:16
Alignment explanation
Indices: 6291114--6291146 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6291104 CGTTTGGTTC
6291114 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
6291130 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
6291146 G
1 G
6291147 ACATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:6291503 original size:29 final size:31
Alignment explanation
Indices: 6291470--6291544 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 31
6291460 AAATATAATT
*
6291470 TAAAATAATTATTATTAAATATAA-T-TTAA
1 TAAAATAATTATTATTAAATAAAATTCTTAA
* *
6291499 TAAAA-AATATATAATTTAATAAAATTCTTAA
1 TAAAATAAT-TATTATTAAATAAAATTCTTAA
* *
6291530 TAAAATTATTCTTAT
1 TAAAATAATTATTAT
6291545 ATGAATTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 3 0.08
29 17 0.47
30 1 0.03
31 13 0.36
32 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAAATAATTATTATTAAATAAAATTCTTAA
Found at i:6291581 original size:60 final size:60
Alignment explanation
Indices: 6291396--6291582 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 60
6291386 ATATAATTTA
6291396 ATAAAATTCTTAATATTAAA-TATTCTTATATGAATTTACTAAAATCATAATATATAATACT
1 ATAAAATTCTTAATA--AAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
* * * *
6291457 ATAAAATATAATTTAA-AATAATTATTATTAAATAT-AATTTAAT-AAA--A-AATATATAAT-T
1 ATAAAAT-T--CTTAATAA-AATTATTCTT--ATATGAATTTACTAAAATCATAATATATAATAC
6291515 T
60 T
6291516 AATAAAATTCTTAATAAAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
1 -ATAAAATTCTTAATAAAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
6291577 ATAAAA
1 ATAAAA
6291583 ATAATATATA
Statistics
Matches: 103, Mismatches: 8, Indels: 31
0.73 0.06 0.22
Matches are distributed among these distances:
55 4 0.04
56 7 0.07
57 16 0.16
58 2 0.02
59 3 0.03
60 33 0.32
61 10 0.10
62 3 0.03
63 10 0.10
64 11 0.11
65 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (60 bp):
ATAAAATTCTTAATAAAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
Found at i:6294811 original size:19 final size:19
Alignment explanation
Indices: 6294771--6294817 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
6294761 CACTTAATGC
** *
6294771 TTATATTAA-TATTAATAT
1 TTATATTAATTAAAAATAA
6294789 TTATATTAATTAAAAATAA
1 TTATATTAATTAAAAATAA
6294808 TTATATTAAT
1 TTATATTAAT
6294818 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATATTAATTAAAAATAA
Found at i:6296323 original size:43 final size:43
Alignment explanation
Indices: 6295924--6296306 Score: 586
Period size: 43 Copynumber: 8.9 Consensus size: 43
6295914 TCGCTAAAAG
* * * *
6295924 TCATGACCTTTAGCGGCGCTTTTCCCTCAAACGTCGCTATAAA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
** *
6295967 TCATGACTTTTAGCGATGCTTTTCCCACAAACGCCACTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
*
6296010 TCATGACTTTTAGTGGCGCTTTTCCCACAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
*
6296053 TCATGACTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
*
6296096 TCATGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
*
6296139 TCATGACTTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
6296182 TCATGACTTTTAGTGGCGCTTTTCCCAAAAATGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
6296225 TCATGACTTTTAACGGCGCTTCTCCCACAAACGCCGTTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
** *
6296268 TCATGACTTTTAGCGGTACTTTTCCCACAAATGCCGCTA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
6296307 AAGAATACGA
Statistics
Matches: 309, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 309 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (43 bp):
TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
Found at i:6296655 original size:21 final size:21
Alignment explanation
Indices: 6296631--6296693 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
6296621 TTCTCCTCTG
* *
6296631 CTCTGTTGCTCTCGCTGTTGC
1 CTCTGCTGCTCTCGCTGCTGC
6296652 CTCTGCTGCTCTCGCTGCTGC
1 CTCTGCTGCTCTCGCTGCTGC
* *
6296673 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTGCTCTCGCTGCTGC
6296694 ATCTACTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (21 bp):
CTCTGCTGCTCTCGCTGCTGC
Found at i:6299028 original size:9 final size:9
Alignment explanation
Indices: 6299010--6299139 Score: 116
Period size: 9 Copynumber: 15.3 Consensus size: 9
6299000 GTCTGATGTA
*
6299010 TTATGAAAG
1 TTATGTAAG
6299019 TTATGTAAG
1 TTATGTAAG
6299028 TTATGT-A-
1 TTATGTAAG
*
6299035 TTATGAAAG
1 TTATGTAAG
6299044 TTATGTAAG
1 TTATGTAAG
6299053 TTATGT-A-
1 TTATGTAAG
6299060 TTATGTAAG
1 TTATGTAAG
*
6299069 TTACGTAAG
1 TTATGTAAG
6299078 TTATGTAAG
1 TTATGTAAG
6299087 TTATGT-A-
1 TTATGTAAG
*
6299094 TTAT-TGAAA
1 TTATGT-AAG
* * *
6299103 TAATTTAAA
1 TTATGTAAG
6299112 TTATGTAAG
1 TTATGTAAG
6299121 TTATGT-A-
1 TTATGTAAG
*
6299128 TTATGAAAG
1 TTATGTAAG
6299137 TTA
1 TTA
6299140 CGTATTATTT
Statistics
Matches: 101, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
6 1 0.01
7 20 0.20
8 8 0.08
9 71 0.70
10 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:6299034 original size:25 final size:25
Alignment explanation
Indices: 6299005--6299084 Score: 142
Period size: 25 Copynumber: 3.2 Consensus size: 25
6298995 CATAAGTCTG
6299005 ATGTATTATGAAAGTTATGTAAGTT
1 ATGTATTATGAAAGTTATGTAAGTT
6299030 ATGTATTATGAAAGTTATGTAAGTT
1 ATGTATTATGAAAGTTATGTAAGTT
* *
6299055 ATGTATTATGTAAGTTACGTAAGTT
1 ATGTATTATGAAAGTTATGTAAGTT
6299080 ATGTA
1 ATGTA
6299085 AGTTATGTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (25 bp):
ATGTATTATGAAAGTTATGTAAGTT
Found at i:6299048 original size:34 final size:34
Alignment explanation
Indices: 6299035--6299139 Score: 133
Period size: 34 Copynumber: 3.1 Consensus size: 34
6299025 AAGTTATGTA
*
6299035 TTATGAAAGTTATGTAAGTTATGTATTATGTAAG
1 TTATGAAAGTTATGTAAGTTATGTATTATGAAAG
* *
6299069 TTACGTAAGTTATGTAAGTTATGTATTATTGAAA-
1 TTATGAAAGTTATGTAAGTTATGTATTA-TGAAAG
* *
6299103 TAATTTAAA-TTATGTAAGTTATGTATTATGAAAG
1 TTA-TGAAAGTTATGTAAGTTATGTATTATGAAAG
6299137 TTA
1 TTA
6299140 CGTATTATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 5 0.08
34 49 0.82
35 6 0.10
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (34 bp):
TTATGAAAGTTATGTAAGTTATGTATTATGAAAG
Found at i:6299083 original size:59 final size:59
Alignment explanation
Indices: 6299019--6299282 Score: 218
Period size: 59 Copynumber: 4.4 Consensus size: 59
6299009 ATTATGAAAG
* * * *
6299019 TTATGTAAGTTATGTATTATGAAAGTTATGTAAGTTATGTATTATGTAAGTTACGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTATTATGTAAATAACGTAAA
*
6299078 TTATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATG-AAAGTTACG
1 TTATGTAAGTTATGTATTA-TG-----A---AAATTATGTAAGTTATGTATTATGTAAA-TAACG
6299142 T--A
56 TAAA
* * * * * * * **
6299144 TTATTTAA-ATA-ATATCATCACAA--ATGTAAGTTATGTATTATTTAAATAAATTAAA
1 TTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTATTATGTAAATAACGTAAA
* * **
6299199 TTATGTAAGTTATGTATTATGAAAATAATGTAAGTTATGTATTATTTAAATAATTTAAA
1 TTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTATTATGTAAATAACGTAAA
6299258 TTATGTAAGTTATGTATTATTGAAA
1 TTATGTAAGTTATGTATTA-TGAAA
6299283 TAATTTAAAT
Statistics
Matches: 167, Mismatches: 20, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
53 21 0.13
54 3 0.02
55 10 0.06
56 2 0.01
57 8 0.05
58 1 0.01
59 69 0.41
60 7 0.04
63 1 0.01
64 4 0.02
65 3 0.02
66 7 0.04
67 2 0.01
68 29 0.17
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.45
Consensus pattern (59 bp):
TTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTATTATGTAAATAACGTAAA
Found at i:6299210 original size:34 final size:34
Alignment explanation
Indices: 6299127--6299311 Score: 194
Period size: 34 Copynumber: 5.6 Consensus size: 34
6299117 TAAGTTATGT
* *
6299127 ATTATGAAAGTTACGTATTATTTAAATAATATCATCACA
1 ATTATGTAAGTTATGTATTATTTAAATAA-AT--T-A-A
6299166 A--ATGTAAGTTATGTATTATTTAAATAAATTAA
1 ATTATGTAAGTTATGTATTATTTAAATAAATTAA
*
6299198 ATTATGTAAGTTATGTATTA--T-GA-AAA-T--
1 ATTATGTAAGTTATGTATTATTTAAATAAATTAA
*
6299225 A--ATGTAAGTTATGTATTATTTAAATAATTTAA
1 ATTATGTAAGTTATGTATTATTTAAATAAATTAA
* *
6299257 ATTATGTAAGTTATGTATTATTGAAATAATTTAA
1 ATTATGTAAGTTATGTATTATTTAAATAAATTAA
6299291 ATTATGTAAGTTATGTATTAT
1 ATTATGTAAGTTATGTATTAT
6299312 GAAAGTTATG
Statistics
Matches: 129, Mismatches: 6, Indels: 27
0.80 0.04 0.17
Matches are distributed among these distances:
25 17 0.13
27 2 0.02
28 1 0.01
29 3 0.02
30 4 0.03
31 1 0.01
32 4 0.03
33 1 0.01
34 69 0.53
36 2 0.02
37 24 0.19
39 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (34 bp):
ATTATGTAAGTTATGTATTATTTAAATAAATTAA
Found at i:6299211 original size:9 final size:9
Alignment explanation
Indices: 6299195--6299323 Score: 71
Period size: 9 Copynumber: 15.2 Consensus size: 9
6299185 TTAAATAAAT
6299195 TAAATTATG
1 TAAATTATG
*
6299204 TAAGTTATG
1 TAAATTATG
6299213 T--ATTATG
1 TAAATTATG
* *
6299220 AAAATAATG
1 TAAATTATG
*
6299229 TAAGTTATG
1 TAAATTATG
*
6299238 T--ATTATT
1 TAAATTATG
* *
6299245 TAAATAATT
1 TAAATTATG
6299254 TAAATTATG
1 TAAATTATG
*
6299263 TAAGTTATG
1 TAAATTATG
6299272 T--ATTAT-
1 TAAATTATG
* *
6299278 TGAAATAATT
1 T-AAATTATG
6299288 TAAATTATG
1 TAAATTATG
*
6299297 TAAGTTATG
1 TAAATTATG
6299306 T--ATTATG
1 TAAATTATG
6299313 -AAAGTTATG
1 TAAA-TTATG
6299322 TA
1 TA
6299324 TTATTTAAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 23
0.68 0.15 0.18
Matches are distributed among these distances:
6 1 0.01
7 19 0.21
8 1 0.01
9 66 0.74
10 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (9 bp):
TAAATTATG
Found at i:6299224 original size:25 final size:25
Alignment explanation
Indices: 6299196--6299264 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
6299186 TAAATAAATT
*
6299196 AAATTATGTAAGTTATGTATTATGA
1 AAATAATGTAAGTTATGTATTATGA
**
6299221 AAATAATGTAAGTTATGTATTATTT
1 AAATAATGTAAGTTATGTATTATGA
* *
6299246 AAATAATTTAAATTATGTA
1 AAATAATGTAAGTTATGTA
6299265 AGTTATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (25 bp):
AAATAATGTAAGTTATGTATTATGA
Found at i:6299284 original size:59 final size:59
Alignment explanation
Indices: 6299166--6299298 Score: 223
Period size: 59 Copynumber: 2.3 Consensus size: 59
6299156 TATCATCACA
6299166 AATGTAAGTTATGTATTATTTAAATAAATTAAATTATGTAAGTTATGTATTATGAAAAT
1 AATGTAAGTTATGTATTATTTAAATAAATTAAATTATGTAAGTTATGTATTATGAAAAT
*
6299225 AATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATTATTG-AAAT
1 AATGTAAGTTATGTATTATTTAAATAAATTAAATTATGTAAGTTATGTATTA-TGAAAAT
* *
6299284 AATTTAAATTATGTA
1 AATGTAAGTTATGTA
6299299 AGTTATGTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 68 0.97
60 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (59 bp):
AATGTAAGTTATGTATTATTTAAATAAATTAAATTATGTAAGTTATGTATTATGAAAAT
Found at i:6299298 original size:180 final size:180
Alignment explanation
Indices: 6299019--6299360 Score: 603
Period size: 180 Copynumber: 1.9 Consensus size: 180
6299009 ATTATGAAAG
* * * * *
6299019 TTATGTAAGTTATGTATTATGAAAGTTATGTAAGTTATGTATTATGTAAGTTACGTAAGTTATGT
1 TTATGTAAGTTATGTATTATGAAAATAATGTAAGTTATGTATTATGTAAATAACGTAAATTATGT
6299084 AAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTACGTATTATT
66 AAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTACGTATTATT
6299149 TAAATAATATCATCACAAATGTAAGTTATGTATTATTTAAATAAATTAAA
131 TAAATAATATCATCACAAATGTAAGTTATGTATTATTTAAATAAATTAAA
* **
6299199 TTATGTAAGTTATGTATTATGAAAATAATGTAAGTTATGTATTATTTAAATAATTTAAATTATGT
1 TTATGTAAGTTATGTATTATGAAAATAATGTAAGTTATGTATTATGTAAATAACGTAAATTATGT
*
6299264 AAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTATGTATTATT
66 AAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTACGTATTATT
6299329 TAAATAATATCATCACAAATGTAAGTTATGTA
131 TAAATAATATCATCACAAATGTAAGTTATGTA
6299361 ATAGTCCTAT
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
180 153 1.00
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (180 bp):
TTATGTAAGTTATGTATTATGAAAATAATGTAAGTTATGTATTATGTAAATAACGTAAATTATGT
AAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTACGTATTATT
TAAATAATATCATCACAAATGTAAGTTATGTATTATTTAAATAAATTAAA
Found at i:6300829 original size:13 final size:14
Alignment explanation
Indices: 6300804--6300833 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6300794 GTCATTATCG
6300804 AACATGATAAGCAA
1 AACATGATAAGCAA
6300818 AACATG-TAAGCAA
1 AACATGATAAGCAA
6300831 AAC
1 AAC
6300834 GTGTGTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (14 bp):
AACATGATAAGCAA
Found at i:6302407 original size:7 final size:7
Alignment explanation
Indices: 6302395--6302663 Score: 96
Period size: 7 Copynumber: 36.9 Consensus size: 7
6302385 AGTAATTAAT
6302395 CTAAACC
1 CTAAACC
6302402 CTAAA-C
1 CTAAACC
6302408 CTATAACC
1 CTA-AACC
6302416 ACTAAATCC
1 -CTAAA-CC
6302425 CTTAAACC
1 C-TAAACC
6302433 CTAAACC
1 CTAAACC
* *
6302440 CAAAATC
1 CTAAACC
* *
6302447 ATAAGCC
1 CTAAACC
6302454 CTAAACTC
1 CTAAAC-C
*
6302462 GACTTAAATC
1 --C-TAAACC
*
6302472 GTAAACC
1 CTAAACC
*
6302479 TTAAACC
1 CTAAACC
6302486 CT-AACC
1 CTAAACC
6302492 TCTAAACC
1 -CTAAACC
*
6302500 TTAAACC
1 CTAAACC
6302507 CT-AACC
1 CTAAACC
*
6302513 CTATACC
1 CTAAACC
*
6302520 CTAAACT
1 CTAAACC
*
6302527 GTAAACC
1 CTAAACC
* * *
6302534 GTAATCA
1 CTAAACC
6302541 CTAAACC
1 CTAAACC
*
6302548 CATAATCC
1 C-TAAACC
*
6302556 ATAAACC
1 CTAAACC
* **
6302563 TTAAATA
1 CTAAACC
*
6302570 GT-AACTC
1 CTAAAC-C
*
6302577 ATAAACC
1 CTAAACC
*
6302584 TTAAACC
1 CTAAACC
*
6302591 TTAAACC
1 CTAAACC
*
6302598 ATAAACC
1 CTAAACC
*
6302605 ATAAACC
1 CTAAACC
*
6302612 ATAAACC
1 CTAAACC
*
6302619 ATGTATAATCC
1 --CTA-AA-CC
6302630 CTAAACC
1 CTAAACC
*
6302637 CTAAATC
1 CTAAACC
* *
6302644 TTATACC
1 CTAAACC
*
6302651 CTAAACT
1 CTAAACC
6302658 CTAAAC
1 CTAAAC
6302664 TGTAATGATA
Statistics
Matches: 197, Mismatches: 46, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
6 16 0.08
7 136 0.69
8 22 0.11
9 13 0.07
10 4 0.02
11 6 0.03
ACGTcount: A:0.43, C:0.31, G:0.03, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:6303909 original size:41 final size:41
Alignment explanation
Indices: 6303852--6304001 Score: 212
Period size: 41 Copynumber: 3.7 Consensus size: 41
6303842 TTTAACATAT
*
6303852 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
6303893 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * * *
6303934 TCACCGACACTTAGCCTGCTAAG-TTCATAACCCGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTT-ATAACCTGATTCAGA
*
6303975 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
6304002 AAGTCTGAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.02
41 92 0.96
42 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:6304020 original size:82 final size:83
Alignment explanation
Indices: 6303850--6304026 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 83
6303840 AATTTAACAT
* * *
6303850 ATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAAGCTTATAACCCGATTCAGATCACCGGCACGTAGCCTGCTAG
**
6303915 GTTTATAACCTGATTCAG
66 ACTTATAACCTGATTCAG
* * *
6303933 A-TCACCGACACTTAGCCTGCTAAG-TTCATAACCCGGTTCAGATCACCGGCACTTAGCCTGCTA
1 ATTCACCGGCACTTAGCCTGCTAAGCTT-ATAACCCGATTCAGATCACCGGCACGTAGCCTGCTA
*
6303996 GACTTA-AAGTCTGAATT-A-
65 GACTTATAA-CCTG-ATTCAG
6304014 ATTCACCGGCACT
1 ATTCACCGGCACT
6304027 ACATCTGCTA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
81 5 0.06
82 71 0.89
83 4 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (83 bp):
ATTCACCGGCACTTAGCCTGCTAAGCTTATAACCCGATTCAGATCACCGGCACGTAGCCTGCTAG
ACTTATAACCTGATTCAG
Found at i:6305251 original size:41 final size:41
Alignment explanation
Indices: 6305193--6305409 Score: 335
Period size: 41 Copynumber: 5.3 Consensus size: 41
6305183 AATTTAACAT
* *
6305193 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* ** *
6305234 ATTCATATCACTAGCACTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
6305275 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
6305316 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * * *
6305357 ATTTAGATCACCGGCATTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
6305398 ATTCAAATCACC
1 ATTCAGATCACC
6305410 AATTTCAAAC
Statistics
Matches: 160, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 160 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:6306936 original size:13 final size:13
Alignment explanation
Indices: 6306918--6306942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6306908 CAATCAAATG
6306918 CACACAAAATAAA
1 CACACAAAATAAA
6306931 CACACAAAATAA
1 CACACAAAATAA
6306943 TATTAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:6309056 original size:40 final size:40
Alignment explanation
Indices: 6309011--6309113 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 40
6309001 CTTAATTTTT
*
6309011 GCGGCGTTTTTCAAAAAGCGCCACTAATGCTCGACCTATA
1 GCGGCGTTTTTCAAAAAGCGCCACTAATGATCGACCTATA
* *
6309051 GCGGCGATTTTT-AAGCAGGCGCCACTAATGATCGACCTATA
1 GCGGCG-TTTTTCAA-AAAGCGCCACTAATGATCGACCTATA
*
6309092 GCGGCATTTTTCAAAAAGCGCC
1 GCGGCGTTTTTCAAAAAGCGCC
6309114 GCAAATGCCG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 19 0.35
41 35 0.65
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCACTAATGATCGACCTATA
Found at i:6309225 original size:40 final size:39
Alignment explanation
Indices: 6309166--6309296 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
6309156 TTAAATTTTT
*
6309166 GCGGCGTTTTTAAACAATCACTGCTTATGCTCGACCTATA
1 GCGGCGTTTTT-AACAATCACCGCTTATGCTCGACCTATA
* *
6309206 GCGGCGCTTGTTTAA-AATCACCGCTAATGCTCGACTTATA
1 GCGGCG-TT-TTTAACAATCACCGCTTATGCTCGACCTATA
* * *
6309246 GCGGTGTTTTTAAACAAGCGCCGC-TAGTGCTCGACCTATA
1 GCGGCGTTTTT-AACAATCACCGCTTA-TGCTCGACCTATA
6309286 GCGGCGTTTTT
1 GCGGCGTTTTT
6309297 TAAGAAGCGT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
38 3 0.04
39 5 0.06
40 62 0.81
41 4 0.05
42 3 0.04
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (39 bp):
GCGGCGTTTTTAACAATCACCGCTTATGCTCGACCTATA
Found at i:6309256 original size:154 final size:151
Alignment explanation
Indices: 6308879--6309269 Score: 421
Period size: 154 Copynumber: 2.5 Consensus size: 151
6308869 CGGGTTGTTA
* *
6308879 CACTAATGCTCGACCTATAGCGGCGTTTTTCAAAAACCACCGCTAATGATAGACCTATGGCGGTG
1 CACTAATGCTCGACCTATAGCGGCGTTTTT--AAAACCACCGCTAATGATCGACCTATAGCGGTG
** * * *
6308944 TTTACCAGAAAGCGCCGCTAATGCCACTAAAGCTCAAAATAAAACAACAGCACTGTGCTTAATTT
64 TTTTTCAAAAAGCGCCGCAAATGCCACTAAAGCTCAAAACAAAACAACAGCACTGTGCTTAATTT
*
6309009 TTGCGGCGTTTTTCAAAAAGCGC
129 TTGCGGCGTTTTTCAAAAAGCAC
** * * *
6309032 CACTAATGCTCGACCTATAGCGGCGATTTTTAAGCAGGCGCCACTAATGATCGACCTATAGCGGC
1 CACTAATGCTCGACCTATAGCGGCG-TTTTTAA--AACCACCGCTAATGATCGACCTATAGCGGT
* * * **
6309097 ATTTTTCAAAAAGCGCCGCAAATGCCGCTAAAGCTCAACACAAAATGAC-G-ACGTTGTGCTTAA
63 GTTTTTCAAAAAGCGCCGCAAATGCCACTAAAGCTCAAAACAAAACAACAGCAC--TGTGCTT-A
*
6309160 ATTTTTGCGGCGTTTTT-AAACAATCAC
125 ATTTTTGCGGCGTTTTTCAAA-AAGCAC
** * * * *
6309187 TGCTTATGCTCGACCTATAGCGGCGCTTGTTTAAAATCACCGCTAATGCTCGACTTATAGCGGTG
1 CACTAATGCTCGACCTATAGCGGCG-TT-TTTAAAACCACCGCTAATGATCGACCTATAGCGGTG
6309252 TTTTT-AAACAAGCGCCGC
64 TTTTTCAAA-AAGCGCCGC
6309270 TAGTGCTCGA
Statistics
Matches: 198, Mismatches: 31, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
152 4 0.02
153 29 0.15
154 114 0.58
155 46 0.23
156 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (151 bp):
CACTAATGCTCGACCTATAGCGGCGTTTTTAAAACCACCGCTAATGATCGACCTATAGCGGTGTT
TTTCAAAAAGCGCCGCAAATGCCACTAAAGCTCAAAACAAAACAACAGCACTGTGCTTAATTTTT
GCGGCGTTTTTCAAAAAGCAC
Found at i:6309305 original size:40 final size:39
Alignment explanation
Indices: 6309193--6309337 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 39
6309183 TCACTGCTTA
* * * *
6309193 TGCTCGACCTATAGCGGCGCTTGTTTAAAATCACCGCTAA
1 TGCTCGACCTATAGCGGCG-TTTTTTAAAAGCGCCGCTAG
* * *
6309233 TGCTCGACTTATAGCGGTGTTTTTAAACAAGCGCCGCTAG
1 TGCTCGACCTATAGCGGCGTTTTTTAA-AAGCGCCGCTAG
* *
6309273 TGCTCGACCTATAGCGGCGTTTTTTAAGAAGCGTCACT-G
1 TGCTCGACCTATAGCGGCGTTTTTTAA-AAGCGCCGCTAG
* * *
6309312 ATGCCCGAGCTATAGCGACGTTTTTT
1 -TGCTCGACCTATAGCGGCGTTTTTT
6309338 GTCCAAACGC
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 7 0.08
40 80 0.92
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (39 bp):
TGCTCGACCTATAGCGGCGTTTTTTAAAAGCGCCGCTAG
Found at i:6309326 original size:80 final size:80
Alignment explanation
Indices: 6309166--6309336 Score: 186
Period size: 80 Copynumber: 2.1 Consensus size: 80
6309156 TTAAATTTTT
* * * *
6309166 GCGGCGTTTTTAAACAATCACTGCTTATGCTCGACCTATAGCGGCGCTTGTTTAAAATCACCGCT
1 GCGGCGTTTTTAAACAAGCACCGCTTATGCTCGACCTATAGCGGCGCTTGTTTAAAAGCACCACT
*
6309231 AATGCTCGACTTATA
66 AATGCCCGACTTATA
* * * **
6309246 GCGGTGTTTTTAAACAAGCGCCGC-TAGTGCTCGACCTATAGCGGCG-TTTTTTAAGAAGCGTCA
1 GCGGCGTTTTTAAACAAGCACCGCTTA-TGCTCGACCTATAGCGGCGCTTGTTTAA-AAGCACCA
*
6309309 CTGATGCCCGAGC-TATA
64 CTAATGCCCGA-CTTATA
*
6309326 GCGACGTTTTT
1 GCGGCGTTTTT
6309337 TGTCCAAACG
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
79 9 0.12
80 65 0.87
81 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (80 bp):
GCGGCGTTTTTAAACAAGCACCGCTTATGCTCGACCTATAGCGGCGCTTGTTTAAAAGCACCACT
AATGCCCGACTTATA
Found at i:6310520 original size:18 final size:19
Alignment explanation
Indices: 6310488--6310530 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
6310478 TTTAAAATTT
6310488 TTTTATAAATAATTTAAAA
1 TTTTATAAATAATTTAAAA
* *
6310507 TTTTA-AAATTATTTTAAA
1 TTTTATAAATAATTTAAAA
6310525 TTTTAT
1 TTTTAT
6310531 TTTATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATAAATAATTTAAAA
Found at i:6314214 original size:18 final size:18
Alignment explanation
Indices: 6314179--6314223 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
6314169 GCAATAAGTG
*
6314179 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
6314197 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
6314215 AC-TTTTGAA
1 ACGTTTTGAA
6314224 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:6315674 original size:12 final size:12
Alignment explanation
Indices: 6315657--6315683 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6315647 GGTGGCATTG
6315657 TTTTGTTTTTCT
1 TTTTGTTTTTCT
6315669 TTTTGTTTTTCT
1 TTTTGTTTTTCT
6315681 TTT
1 TTT
6315684 CCATTTTCTA
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:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTGTTTTTCT
Found at i:6316899 original size:5 final size:5
Alignment explanation
Indices: 6316866--6316939 Score: 53
Period size: 5 Copynumber: 14.8 Consensus size: 5
6316856 TTTGTGTAAC
* * *
6316866 TCTGT TCAGT TCTGCT T-TGT T-TCGT TCTGT TCTGC TCTGT TCTGT TCTAT
1 TCTGT TCTGT TCTG-T TCTGT TCT-GT TCTGT TCTGT TCTGT TCTGT TCTGT
** * *
6316916 AATGT TCTGC TCTGT CCTGT TCTG
1 TCTGT TCTGT TCTGT TCTGT TCTG
6316940 GTTGGTTTGT
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
4 3 0.06
5 46 0.88
6 3 0.06
ACGTcount: A:0.05, C:0.23, G:0.19, T:0.53
Consensus pattern (5 bp):
TCTGT
Found at i:6316912 original size:20 final size:20
Alignment explanation
Indices: 6316866--6316913 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
6316856 TTTGTGTAAC
* *
6316866 TCTGTTCAGTTCTGCTTTGT
1 TCTGTTCTGTTCTGCTCTGT
6316886 T-TCGTTCTGTTCTGCTCTGT
1 TCT-GTTCTGTTCTGCTCTGT
6316906 TCTGTTCT
1 TCTGTTCT
6316914 ATAATGTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.02, C:0.23, G:0.19, T:0.56
Consensus pattern (20 bp):
TCTGTTCTGTTCTGCTCTGT
Found at i:6319182 original size:26 final size:24
Alignment explanation
Indices: 6319153--6319220 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
6319143 GCCATGATCA
*
6319153 GTAAGCTCAT-TCTGAGTTGAAGAACG
1 GTAAGCTCATATC-GAGCTG-A-AACG
6319179 GTAAGCTC-TATCGAGCTGAAACG
1 GTAAGCTCATATCGAGCTGAAACG
*
6319202 GTAAGCTCATA-AGAGCTGA
1 GTAAGCTCATATCGAGCTGA
6319221 TATATCAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 19 0.50
24 3 0.08
25 6 0.16
26 10 0.26
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (24 bp):
GTAAGCTCATATCGAGCTGAAACG
Found at i:6326394 original size:40 final size:40
Alignment explanation
Indices: 6326350--6326429 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
6326340 TAAGTAAGCA
6326350 TTAAAGCTTAGTAAGCCCGTATAATAGAATTAAACTTACC
1 TTAAAGCTTAGTAAGCCCGTATAATAGAATTAAACTTACC
*
6326390 TTAAAGCTTAGTAAGCTCGTATAATAGAATTAAACTTACC
1 TTAAAGCTTAGTAAGCCCGTATAATAGAATTAAACTTACC
6326430 ACAATACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (40 bp):
TTAAAGCTTAGTAAGCCCGTATAATAGAATTAAACTTACC
Found at i:6332468 original size:39 final size:38
Alignment explanation
Indices: 6332425--6332509 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
6332415 TTAAAATAAT
* *
6332425 TAAAAATTTAAAAATATTATAAAATATTA-TAGAAAATCA
1 TAAAAATTTAAAAA-ATTATAAAA-ATTACAAAAAAATCA
* * *
6332464 TAAAAAAATTATAAAATTATAAAAATTACAAAAAAATTA
1 T-AAAAATTTAAAAAATTATAAAAATTACAAAAAAATCA
6332503 TAAAAAT
1 TAAAAAT
6332510 ATATAAAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
38 9 0.24
39 18 0.47
40 11 0.29
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (38 bp):
TAAAAATTTAAAAAATTATAAAAATTACAAAAAAATCA
Found at i:6332512 original size:8 final size:9
Alignment explanation
Indices: 6332425--6332517 Score: 73
Period size: 10 Copynumber: 9.6 Consensus size: 9
6332415 TTAAAATAAT
6332425 TAAAAATT-
1 TAAAAATTA
6332433 TAAAAATATTA
1 T-AAAA-ATTA
6332444 TAAAATATTA
1 TAAAA-ATTA
6332454 TAGAAAATCATA
1 TA-AAAAT--TA
*
6332466 AAAAAATTA
1 TAAAAATTA
6332475 T-AAAATTA
1 TAAAAATTA
6332483 TAAAAATTACA
1 TAAAAATT--A
*
6332494 AAAAAATTA
1 TAAAAATTA
6332503 TAAAAATATA
1 TAAAAAT-TA
6332513 TAAAA
1 TAAAA
6332518 GTGAAAAATT
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
8 9 0.13
9 19 0.27
10 23 0.32
11 17 0.24
12 3 0.04
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:6332525 original size:28 final size:28
Alignment explanation
Indices: 6332434--6332519 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 28
6332424 TTAAAAATTT
* *
6332434 AAAAATATTATAAAATATTATAGAAAA-TCAT
1 AAAAAAATTATAAAA-A-TATA-AAAAGT-AC
* *
6332465 AAAAAAATTATAAAATTATAAAAATTAC
1 AAAAAAATTATAAAAATATAAAAAGTAC
6332493 AAAAAAATTATAAAAATATATAAAAGT
1 AAAAAAATTATAAAAATATA-AAAAGT
6332520 GAAAAATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
28 24 0.50
29 10 0.21
31 14 0.29
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAAAAATTATAAAAATATAAAAAGTAC
Found at i:6335630 original size:22 final size:22
Alignment explanation
Indices: 6335581--6335623 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6335571 TGGACAAGCC
*
6335581 ACCACATAATTGCCGATAAACG
1 ACCACATAATTGCAGATAAACG
6335603 ACCACATAATTGCAGATAAAC
1 ACCACATAATTGCAGATAAAC
6335624 TGCCACAGAT
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:0.44, C:0.26, G:0.12, T:0.19
Consensus pattern (22 bp):
ACCACATAATTGCAGATAAACG
Found at i:6335888 original size:18 final size:19
Alignment explanation
Indices: 6335858--6335894 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6335848 TTTGCACAAA
*
6335858 CATCACAATCACATAATAT
1 CATCACAATCACACAATAT
6335877 CATCAC-ATCACACAATAT
1 CATCACAATCACACAATAT
6335895 ACTTTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (19 bp):
CATCACAATCACACAATAT
Found at i:6343530 original size:96 final size:96
Alignment explanation
Indices: 6343366--6343559 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 96
6343356 CTGAAACAAA
*
6343366 TAAATTCAGATTTTGGCTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
1 TAAATTCAGATTTTGACTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
6343431 ACAAAATGCCACCAAAATGACCTCTTTTGTG
66 ACAAAATGCCACCAAAATGACCTCTTTTGTG
6343462 TAAATTCAGATTTTGACTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
1 TAAATTCAGATTTTGACTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
* *
6343527 ACAAAATGCCGCCAAAGTGACCTCTTTTGTG
66 ACAAAATGCCACCAAAATGACCTCTTTTGTG
6343558 TA
1 TA
6343560 GATTAGTTTA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (96 bp):
TAAATTCAGATTTTGACTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
ACAAAATGCCACCAAAATGACCTCTTTTGTG
Found at i:6345980 original size:18 final size:19
Alignment explanation
Indices: 6345939--6345982 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
6345929 TGTTAATTTC
*
6345939 ATGAATTATATAATGTATG
1 ATGAAATATATAATGTATG
*
6345958 ATGAAATATAT-ATTTATG
1 ATGAAATATATAATGTATG
*
6345976 TTGAAAT
1 ATGAAAT
6345983 GAGAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
ATGAAATATATAATGTATG
Found at i:6346118 original size:46 final size:46
Alignment explanation
Indices: 6346051--6346440 Score: 646
Period size: 46 Copynumber: 8.6 Consensus size: 46
6346041 TTTGAGTACT
*
6346051 TCTGATCAAGTGACAAAGTGATAAGTGGTAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
6346097 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
6346143 TCTGATCAAGTGACAAAGTGATAAGTGGAAGCTTTAGCTACACCTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6346189 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACCTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6346235 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6346280 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
6346325 TCTGATTAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6346371 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6346416 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
6346441 ATCATACGTA
Statistics
Matches: 328, Mismatches: 15, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
43 12 0.04
44 5 0.02
45 104 0.32
46 207 0.63
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:6348958 original size:17 final size:18
Alignment explanation
Indices: 6348938--6348972 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6348928 TTTTATTCTA
6348938 GTTTTGGTTT-AAGTTTT
1 GTTTTGGTTTAAAGTTTT
*
6348955 GTTTTGTTTTAAAGTTTT
1 GTTTTGGTTTAAAGTTTT
6348973 AAAGTTTTAT
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:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (18 bp):
GTTTTGGTTTAAAGTTTT
Found at i:6350121 original size:23 final size:23
Alignment explanation
Indices: 6350072--6350121 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6350062 CACACCAAAC
*
6350072 TTTGGACAGCATAAATACATCAA
1 TTTGGACAGCATAAATACAACAA
* * *
6350095 TTTGGGCAGCATATATACAACAG
1 TTTGGACAGCATAAATACAACAA
6350118 TTTG
1 TTTG
6350122 AGCAACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (23 bp):
TTTGGACAGCATAAATACAACAA
Found at i:6350204 original size:23 final size:23
Alignment explanation
Indices: 6350175--6350345 Score: 144
Period size: 23 Copynumber: 7.3 Consensus size: 23
6350165 TTAAGCATCA
* *
6350175 AAATTGGACAGCATATATGTAAC
1 AAATTGGGCAGCATATATGTATC
* * * *
6350198 AAATTGGGCAACATTTAAGCATC
1 AAATTGGGCAGCATATATGTATC
*
6350221 AAAATTGGGCAGCATATATGTAGC
1 -AAATTGGGCAGCATATATGTATC
* * * *
6350245 AAATTGGGTAGCATTTAAGCATC
1 AAATTGGGCAGCATATATGTATC
* *
6350268 AAAATTGGACAGCATATATGTAGC
1 -AAATTGGGCAGCATATATGTATC
* * *
6350292 AAATTGGGCAGCATTTAAGCATC
1 AAATTGGGCAGCATATATGTATC
* * *
6350315 AAAATTGGACAGCATACATGTAAC
1 -AAATTGGGCAGCATATATGTATC
6350339 AAATTGG
1 AAATTGG
6350346 TTCAACTCAT
Statistics
Matches: 112, Mismatches: 33, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
23 60 0.54
24 52 0.46
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (23 bp):
AAATTGGGCAGCATATATGTATC
Found at i:6350227 original size:47 final size:47
Alignment explanation
Indices: 6350158--6350345 Score: 313
Period size: 47 Copynumber: 4.0 Consensus size: 47
6350148 CAGCATATAT
6350158 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* *
6350205 GCAACATTTAAGCATCAAAATTGGGCAGCATATATGTAGCAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* * *
6350252 GTAGCATTTAAGCATCAAAATTGGACAGCATATATGTAGCAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* *
6350299 GCAGCATTTAAGCATCAAAATTGGACAGCATACATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
6350346 TTCAACTCAT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (47 bp):
GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
Found at i:6350327 original size:24 final size:24
Alignment explanation
Indices: 6350162--6350329 Score: 162
Period size: 24 Copynumber: 7.1 Consensus size: 24
6350152 ATATATGCAA
*
6350162 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * * *
6350186 CATATATGTAAC-AAATTGGGCAA
1 CATTTAAGCATCAAAATTGGGCAG
6350209 CATTTAAGCATCAAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * * *
6350233 CATATATGTAGC-AAATTGGGTAG
1 CATTTAAGCATCAAAATTGGGCAG
*
6350256 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * *
6350280 CATATATGTAGC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGGCAG
*
6350303 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
6350327 CAT
1 CAT
6350330 ACATGTAACA
Statistics
Matches: 109, Mismatches: 32, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
23 53 0.49
24 56 0.51
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (24 bp):
CATTTAAGCATCAAAATTGGGCAG
Found at i:6351274 original size:43 final size:42
Alignment explanation
Indices: 6351187--6351310 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 42
6351177 AACTCGTACA
* * * *
6351187 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCACGTATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACAC-AATCG
* *
6351230 ATGTC-ACTGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
* *
6351273 ATGCCAACATCCCAGATGTGGTCTTACACG-ATAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACA
6351311 TCTCGAAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 4 0.06
43 61 0.91
44 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:6357291 original size:23 final size:23
Alignment explanation
Indices: 6357242--6357291 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6357232 CACACCAAAC
*
6357242 TTTGGACAGCATAAATACATCAA
1 TTTGGACAGCATAAATACAACAA
* * *
6357265 TTTGGGCAGCATATATACAACAG
1 TTTGGACAGCATAAATACAACAA
6357288 TTTG
1 TTTG
6357292 AGCAACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (23 bp):
TTTGGACAGCATAAATACAACAA
Found at i:6357374 original size:23 final size:23
Alignment explanation
Indices: 6357345--6357515 Score: 137
Period size: 23 Copynumber: 7.3 Consensus size: 23
6357335 TTAAGCATCA
* *
6357345 AAATTGGACAGCATATATGTAAC
1 AAATTGGGCAGCATATATGTATC
* * * *
6357368 AAATTGGGCAACATTTAAGCATC
1 AAATTGGGCAGCATATATGTATC
*
6357391 AAAATTGGGCAGCATATATGTAGC
1 -AAATTGGGCAGCATATATGTATC
* * * *
6357415 AAATTGGGTAGCATTTAAGCATC
1 AAATTGGGCAGCATATATGTATC
* *
6357438 AAAATTGGACAGCATATATGTAGC
1 -AAATTGGGCAGCATATATGTATC
* *
6357462 AAATTGGGCAGCATTTAAT-CATC
1 AAATTGGGCAGCATAT-ATGTATC
* * *
6357485 AAAATTGGACAGCATACATGTAAC
1 -AAATTGGGCAGCATATATGTATC
6357509 AAATTGG
1 AAATTGG
6357516 TTCAACTCAT
Statistics
Matches: 112, Mismatches: 31, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
23 60 0.54
24 52 0.46
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (23 bp):
AAATTGGGCAGCATATATGTATC
Found at i:6357397 original size:47 final size:47
Alignment explanation
Indices: 6357328--6357515 Score: 304
Period size: 47 Copynumber: 4.0 Consensus size: 47
6357318 CAGCATATAT
6357328 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* *
6357375 GCAACATTTAAGCATCAAAATTGGGCAGCATATATGTAGCAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* * *
6357422 GTAGCATTTAAGCATCAAAATTGGACAGCATATATGTAGCAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* * *
6357469 GCAGCATTTAATCATCAAAATTGGACAGCATACATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
6357516 TTCAACTCAT
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (47 bp):
GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
Found at i:6357398 original size:24 final size:24
Alignment explanation
Indices: 6357332--6357499 Score: 153
Period size: 24 Copynumber: 7.1 Consensus size: 24
6357322 ATATATGCAA
*
6357332 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * * *
6357356 CATATATGTAAC-AAATTGGGCAA
1 CATTTAAGCATCAAAATTGGGCAG
6357379 CATTTAAGCATCAAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * * *
6357403 CATATATGTAGC-AAATTGGGTAG
1 CATTTAAGCATCAAAATTGGGCAG
*
6357426 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * *
6357450 CATATATGTAGC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGGCAG
* *
6357473 CATTTAATCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
6357497 CAT
1 CAT
6357500 ACATGTAACA
Statistics
Matches: 108, Mismatches: 33, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
23 52 0.48
24 56 0.52
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (24 bp):
CATTTAAGCATCAAAATTGGGCAG
Found at i:6358451 original size:43 final size:44
Alignment explanation
Indices: 6358364--6358477 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 44
6358354 AACTCGTACA
* * *
6358364 ATGCCAA-TGTCCCAGACGTGGTCTTACATGTAATCACGTATCG
1 ATGCCAACTGTCCCAGACGTGGTCTTACACGTAAACACGAATCG
*
6358407 ATGGC-ACTGTCCCAGACAG-GGTCTTACACGTAAACAC-AAGTCG
1 ATGCCAACTGTCCCAGAC-GTGGTCTTACACGTAAACACGAA-TCG
*
6358450 ATGCCAAC-GTCCCAGATGTGGTCTTACA
1 ATGCCAACTGTCCCAGACGTGGTCTTACA
6358478 TGATAACACA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 3 0.05
43 54 0.90
44 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACGTGGTCTTACACGTAAACACGAATCG
Found at i:6359649 original size:14 final size:15
Alignment explanation
Indices: 6359630--6359658 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6359620 TCACGAAACT
6359630 TTCACACAT-ATAAA
1 TTCACACATAATAAA
6359644 TTCACACATAATAAA
1 TTCACACATAATAAA
6359659 CACATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:6361924 original size:36 final size:36
Alignment explanation
Indices: 6361884--6361992 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
6361874 GCTAAGCTAC
*
6361884 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
* *
6361920 CACTTATCACTTTTTCGCTTGATCAGATAAATGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
6361956 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
6361992 C
1 C
6361993 TAAAGTTACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
Found at i:6362007 original size:46 final size:46
Alignment explanation
Indices: 6361956--6362074 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
6361946 ATAAATGTAG
* * *
6361956 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGTTAC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
*
6362002 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
6362048 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
6362075 AGTACTCAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:6363746 original size:24 final size:24
Alignment explanation
Indices: 6363698--6363744 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6363688 ACTGGTCATA
*
6363698 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
6363722 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
6363745 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:6364787 original size:27 final size:27
Alignment explanation
Indices: 6364747--6365102 Score: 351
Period size: 27 Copynumber: 13.2 Consensus size: 27
6364737 AGAGGTCGAT
6364747 AAATGA-TCGAAATACCCCCATAGGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
* * * *
6364774 AATTGACTAAAATAACCCCGTAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
6364801 AAATAACTGAAATACCCCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
** *
6364828 AAATGACCAAAATACCCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
** * *
6364855 AAATGACCAAAATACCCTCATAGTGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
6364882 GAATGACTGAAATACCCCAATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
6364909 AAATAACCGAAATACCCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* ***
6364936 AAAT-AATCGAAATA-CCCCATAAAATA
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
6364962 AAATGACTGAAATACCTCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
6364989 AAATGACCGAAATACCCCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * * *
6365016 GAATGACCGAAATACCCTCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
6365043 GAATGA-TCGAAATATCCCCATAAGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
*
6365070 AAATGACTGAAATACCCCCATAGAGTA
1 AAATGACTGAAATACCCCCATAGGGTA
6365097 AAATGA
1 AAATGA
6365103 TTGTTATACT
Statistics
Matches: 274, Mismatches: 49, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
26 19 0.07
27 253 0.92
28 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:6364891 original size:81 final size:79
Alignment explanation
Indices: 6364747--6365102 Score: 408
Period size: 81 Copynumber: 4.4 Consensus size: 79
6364737 AGAGGTCGAT
* * * * *
6364747 AAATGATCGAAATACCCCCATAGGGTAAATTGACTAAAATAACCCCGTAGGGTAAAATAACTGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAAT-ACCCCATA-GGTAAAATGACTGAA
6364812 ATACCCCCATAAGGTA
64 ATACCCCCATAAGGTA
* * *
6364828 AAATGACCAAAATACCCCTATAGGGTAAAATGACCAAAATACCCTCATAGTGTAGAATGACTGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAG-GTAAAATGACTGAA
* *
6364893 ATACCCCAATAGGGTA
64 ATACCCCCATAAGGTA
* * * * * **
6364909 AAATAACCGAAATACCCCTATAGGGTAAAATAATCGAAATACCCCATAAAATAAAATGACTGAAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCAT-AGGTAAAATGACTGAAA
*
6364974 TACCTCCATAAGGTA
65 TACCCCCATAAGGTA
* * * *
6364989 AAATGACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAAGGTAGAATGA-TCGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CAT-AGGTAAAATGACT-GA
*
6365053 AATATCCCCATAAGGTA
63 AATACCCCCATAAGGTA
* *
6365070 AAATGACTGAAATACCCCCATAGAGTAAAATGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGA
6365103 TTGTTATACT
Statistics
Matches: 234, Mismatches: 36, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
80 72 0.31
81 162 0.69
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (79 bp):
AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGTAAAATGACTGAAAT
ACCCCCATAAGGTA
Found at i:6365373 original size:26 final size:26
Alignment explanation
Indices: 6365337--6365413 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
6365327 TTTACCACAT
*
6365337 ATACTGTTACTGGTAGCTTTGCTGCG
1 ATACTGATACTGGTAGCTTTGCTGCG
* *
6365363 ATACTGATACTGGCAGCTCTGCTGCG
1 ATACTGATACTGGTAGCTTTGCTGCG
*
6365389 ATGCT-ATTACTGGTAGCTTTGCTGC
1 ATACTGA-TACTGGTAGCTTTGCTGC
6365414 AATATTTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 43 0.98
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGTAGCTTTGCTGCG
Found at i:6365554 original size:28 final size:28
Alignment explanation
Indices: 6365506--6365599 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
6365496 TACTGCACTG
*
6365506 CACTGCTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
6365534 CATTGATT-CTGTATTGGGCTAAAGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
* *
6365562 CACTGTTACTATATTGGGCTAAGGCCTA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
6365590 CACTG-TACTG
1 CACTGTTACTG
6365600 CCACTGAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.11
28 49 0.88
29 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:6368253 original size:27 final size:27
Alignment explanation
Indices: 6368233--6368580 Score: 320
Period size: 27 Copynumber: 12.9 Consensus size: 27
6368223 TAAAATAATT
** *
6368233 GAAATACCCCTGTAGGGTAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
* * *
6368260 GAAATACCACCGTATGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
* * * *
6368287 AAAATACCCTCATAGGGTAAAATAACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *** **
6368314 GAAATACCCTCAATAAAATAAAATGATT
1 GAAATACCC-CCATAGGGTAAAATGACC
** * * *
6368342 GAAATACCCTTATCGGGTAGAATAACC
1 GAAATACCCCCATAGGGTAAAATGACC
* * *
6368369 AAAATACCCCCATAGAGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
* * * * * *
6368396 AAAATACCCCTATAAGATAGAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
* *
6368423 GAAATACCCCCCATAAGGTAAAATGACA
1 GAAATA-CCCCCATAGGGTAAAATGACC
*
6368451 GAAATACCCCCATAGGGTAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
*
6368478 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *
6368505 GAAATACCCCCATAGGGTAAAATAACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *
6368532 GAAATACCCCC-TAGGATAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
*
6368558 GAAATACCCCCATAAGGTAAAAT
1 GAAATACCCCCATAGGGTAAAAT
6368581 AACTATTATA
Statistics
Matches: 256, Mismatches: 62, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
26 22 0.09
27 192 0.75
28 42 0.16
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (27 bp):
GAAATACCCCCATAGGGTAAAATGACC
Found at i:6368427 original size:109 final size:109
Alignment explanation
Indices: 6368222--6368580 Score: 370
Period size: 109 Copynumber: 3.3 Consensus size: 109
6368212 CCCTTACAGG
* * * * *
6368222 ATAAAATAATTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCACCGTATGGTAAAATGACC
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATA-GGTAAAATGACT
* * *
6368287 AAAATA-CCCTCATAGGGTAAAATAACTGAAATACCCTCAATAAA
65 AAAATACCCCTCATAAGATAAAATAACTGAAATACCCCCAATAAA
* * * * * *
6368331 ATAAAATGATTGAAATACCCTTATCGGGTAGAATAACCAAAATACCCCCATAGAGTAAAATGACT
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAG-GTAAAATGACT
* * * *
6368396 AAAATACCCCT-ATAAGATAGAATGA-TCGAAATACCCCCCATAAG
65 AAAATACCCCTCATAAGATAAAATAACT-GAAATACCCCCAATAAA
* ** *
6368440 GTAAAATGACAGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACT
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATA-GGTAAAATGACT
* * * **
6368505 GAAATACCCC-CATAGGGTAAAATAACTGAAATACCCCC--TAGG
65 AAAATACCCCTCATAAGATAAAATAACTGAAATACCCCCAATAAA
* * *
6368547 ATAAAATGATCGAAATACCCCCATAAGGTAAAAT
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAAT
6368581 AACTATTATA
Statistics
Matches: 206, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
107 33 0.16
108 2 0.01
109 165 0.80
110 6 0.03
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (109 bp):
ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAGGTAAAATGACTA
AAATACCCCTCATAAGATAAAATAACTGAAATACCCCCAATAAA
Found at i:6368884 original size:23 final size:24
Alignment explanation
Indices: 6368835--6368884 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
6368825 GTGATATTGA
*
6368835 TACTGGCAGCTTTGTTGCGATGCTAT
1 TACTGGCAGCTTTGCTGCGA--CTAT
*
6368861 TACTGGTAGCTTTGCTGCGA-TAT
1 TACTGGCAGCTTTGCTGCGACTAT
6368884 T
1 T
6368885 GGTGTGTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
26 18 0.82
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (24 bp):
TACTGGCAGCTTTGCTGCGACTAT
Found at i:6369039 original size:28 final size:28
Alignment explanation
Indices: 6368987--6369078 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 28
6368977 TGCACTGCAT
* *
6368987 TGTTACTGTATTGGGCAAAGACCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
6369015 TGATT-TTGTATTGGGCTAAGGCCCACAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
* *
6369043 TGTTACTGTATTAGGCTAAGGCCCAAAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
6369071 TG-TACTGT
1 TGTTACTGT
6369079 CACTGAATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.14
28 46 0.82
29 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:6370747 original size:23 final size:23
Alignment explanation
Indices: 6370716--6370791 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
6370706 GCACATAAGT
6370716 GCTA-CACTGATATGTAGCCGAA
1 GCTACCACTGATATGTAGCCGAA
*
6370738 GCTACCACTGATATGTAGCCGTA
1 GCTACCACTGATATGTAGCCGAA
* *
6370761 GCTACCACTGAAATGTAGCTGAA
1 GCTACCACTGATATGTAGCCGAA
6370784 GCTACCAC
1 GCTACCAC
6370792 AGATCAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 4 0.08
23 45 0.92
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
GCTACCACTGATATGTAGCCGAA
Found at i:6379261 original size:30 final size:30
Alignment explanation
Indices: 6379227--6379286 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6379217 GAATTGGATC
6379227 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
* *
6379257 AAATCAAATTTTCATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
6379287 TATTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:6384618 original size:49 final size:49
Alignment explanation
Indices: 6384561--6384664 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
6384551 TCATGTGTTA
* * *
6384561 TAATTTTATAAAGTGTTGATCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
*
6384610 TAATTTTATAAAGTTTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
6384659 TAATTT
1 TAATTT
6384665 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:6386087 original size:21 final size:21
Alignment explanation
Indices: 6386046--6386088 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6386036 AATAAAGTAG
*
6386046 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
6386067 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
6386088 A
1 A
6386089 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:6386153 original size:28 final size:28
Alignment explanation
Indices: 6386117--6386317 Score: 83
Period size: 28 Copynumber: 6.9 Consensus size: 28
6386107 TAATATTAAG
*
6386117 AATTTTATTAAATTATATATTTTTATTA
1 AATTATATTAAATTATATATTTTTATTA
* * *
6386145 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTAAATTATATATTTTTATTA
*
6386171 AATTATATT---TTATAGTATTATATATTA
1 AATTATATTAAATTATA-TATT-TTTATTA
* * * *
6386198 TGATTTTAGTAAATTCATATAAGAATATTAATATTAA
1 -AATTATATTAAATT-ATAT----AT-TT-TTATT-A
*
6386235 GAATTTTATTAAATTATATATTTTTATTA
1 -AATTATATTAAATTATATATTTTTATTA
* * * *
6386264 AATTATATTTAA-TA-ATAATTATGTTA
1 AATTATATTAAATTATATATTTTTATTA
* *
6386290 AAATATGATTAAATTATTTATTATTTAT
1 AATTAT-ATTAAATTATATATT-TTTAT
6386318 ATTAATAATC
Statistics
Matches: 128, Mismatches: 25, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
23 4 0.03
25 3 0.02
26 27 0.21
27 15 0.12
28 32 0.25
29 4 0.03
30 7 0.05
31 5 0.04
32 5 0.04
35 3 0.02
36 10 0.08
37 13 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTATATTAAATTATATATTTTTATTA
Found at i:6386176 original size:119 final size:119
Alignment explanation
Indices: 6386053--6386291 Score: 453
Period size: 119 Copynumber: 2.0 Consensus size: 119
6386043 TAGATTATAT
6386053 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-TTAATATTAAG
*
6386117 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
65 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
6386172 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTAATATTAAGA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTAATATTAAGA
6386237 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
6386291 A
1 A
6386292 ATATGATTAA
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
119 71 0.60
120 47 0.40
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (119 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTAATATTAAGA
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:6386246 original size:18 final size:18
Alignment explanation
Indices: 6386223--6386270 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
6386213 CATATAAGAA
6386223 TATTAATATTA-AGAATTT
1 TATTAA-ATTATAGAATTT
* *
6386241 TATTAAATTATATATTTT
1 TATTAAATTATAGAATTT
6386259 TATTAAATTATA
1 TATTAAATTATA
6386271 TTTAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTAAATTATAGAATTT
Found at i:6388234 original size:18 final size:20
Alignment explanation
Indices: 6388199--6388239 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
6388189 ATATTATTTT
*
6388199 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
*
6388219 AAAATAT-TA-AAAACATTA
1 AAAATATATATAAAACATCA
6388237 AAA
1 AAA
6388240 TAAATGTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:6391472 original size:31 final size:33
Alignment explanation
Indices: 6391429--6391492 Score: 114
Period size: 31 Copynumber: 2.0 Consensus size: 33
6391419 GAGTCTCTTT
6391429 TTTTTCCCTAATTTGGTACCTAAACTTG-AAAA
1 TTTTTCCCTAATTTGGTACCTAAACTTGTAAAA
6391461 TTTTT-CCTAATTTGGTACCTAAACTTGTAAAA
1 TTTTTCCCTAATTTGGTACCTAAACTTGTAAAA
6391493 CATATACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.42
Consensus pattern (33 bp):
TTTTTCCCTAATTTGGTACCTAAACTTGTAAAA
Found at i:6392401 original size:20 final size:19
Alignment explanation
Indices: 6392376--6392417 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6392366 AAATAATTTC
*
6392376 TAGAAAATATTAATTTTTTT
1 TAGAAAA-ATTAATATTTTT
*
6392396 TAGAAAAGTTAATATTTTT
1 TAGAAAAATTAATATTTTT
6392415 TAG
1 TAG
6392418 TGTTTGGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
TAGAAAAATTAATATTTTT
Found at i:6394231 original size:19 final size:18
Alignment explanation
Indices: 6394191--6394231 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
6394181 ATTGCCTCTA
6394191 AATAATAACAAAATTAAC
1 AATAATAACAAAATTAAC
6394209 AATAA-AACAAAAGTTATAC
1 AATAATAACAAAA-TTA-AC
6394228 AATA
1 AATA
6394232 TCCAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAATAACAAAATTAAC
Found at i:6395368 original size:2 final size:2
Alignment explanation
Indices: 6395361--6395385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6395351 CTAGTAATTA
6395361 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6395386 ATACTAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6403411 original size:23 final size:24
Alignment explanation
Indices: 6403385--6403450 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
6403375 GCGCATTCTA
* *
6403385 TTTGGCCTGTGTGGTGTA-TTTTG
1 TTTGGCCTTTGTGGTGTACTTATG
*
6403408 TTTGGCCTTTGTGGCGTACTTATG
1 TTTGGCCTTTGTGGTGTACTTATG
*
6403432 TTTGGCCTTTGTGATGTAC
1 TTTGGCCTTTGTGGTGTAC
6403451 CCTATATGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 16 0.43
24 21 0.57
ACGTcount: A:0.08, C:0.14, G:0.30, T:0.48
Consensus pattern (24 bp):
TTTGGCCTTTGTGGTGTACTTATG
Found at i:6403438 original size:24 final size:24
Alignment explanation
Indices: 6403385--6403499 Score: 90
Period size: 23 Copynumber: 4.8 Consensus size: 24
6403375 GCGCATTCTA
* * *
6403385 TTTGGCCTGTGTGGTGTA-TTTTG
1 TTTGGCCTTTGTGGCGTACTTATG
6403408 TTTGGCCTTTGTGGCGTACTTATG
1 TTTGGCCTTTGTGGCGTACTTATG
** * *
6403432 TTTGGCCTTTGTGATGTACCCTATA
1 TTTGGCCTTTGTGGCGTA-CTTATG
* * * * *
6403457 TGTCGTCTTTGTGGCATA-TTCTG
1 TTTGGCCTTTGTGGCGTACTTATG
*
6403480 TTGGGCCTTTGTGGCGTACT
1 TTTGGCCTTTGTGGCGTACT
6403500 CTGCTAAGTT
Statistics
Matches: 68, Mismatches: 21, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
23 31 0.46
24 21 0.31
25 16 0.24
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (24 bp):
TTTGGCCTTTGTGGCGTACTTATG
Found at i:6411333 original size:27 final size:27
Alignment explanation
Indices: 6411303--6411367 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
6411293 ACAACAATTC
**
6411303 CAACAGCAACAACTCCTCCAACAACAA
1 CAACAGCAACAACAACTCCAACAACAA
** *
6411330 CAACAGCAACTGCAACTTCAACAACAA
1 CAACAGCAACAACAACTCCAACAACAA
*
6411357 CAAGAGCAACA
1 CAACAGCAACA
6411368 TGAACAACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.35, G:0.08, T:0.08
Consensus pattern (27 bp):
CAACAGCAACAACAACTCCAACAACAA
Found at i:6411365 original size:21 final size:21
Alignment explanation
Indices: 6411321--6411376 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
6411311 ACAACTCCTC
* * *
6411321 CAACAACAACAACAGCAACTG
1 CAACATCAACAACAACAACAG
* *
6411342 CAACTTCAACAACAACAAGAG
1 CAACATCAACAACAACAACAG
*
6411363 CAACATGAACAACA
1 CAACATCAACAACA
6411377 GTTACAGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.54, C:0.30, G:0.09, T:0.07
Consensus pattern (21 bp):
CAACATCAACAACAACAACAG
Found at i:6414052 original size:23 final size:24
Alignment explanation
Indices: 6414005--6414050 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
6413995 GAAAAATATT
6414005 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
6414029 AAATATA-ATAATTTTTTATTTT
1 AAATATATAT-ATTTTTTATTTT
6414051 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:6414161 original size:9 final size:9
Alignment explanation
Indices: 6414147--6414174 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6414137 TTTTGTTACA
6414147 ACAATTAAT
1 ACAATTAAT
6414156 ACAATTAAT
1 ACAATTAAT
6414165 ACAATTAAT
1 ACAATTAAT
6414174 A
1 A
6414175 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:6414196 original size:68 final size:68
Alignment explanation
Indices: 6414117--6414394 Score: 515
Period size: 68 Copynumber: 4.1 Consensus size: 68
6414107 TCAAGTTTGT
*
6414117 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
6414182 AAA
66 AAA
6414185 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
6414250 AAA
66 AAA
6414253 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
6414318 AAA
66 AAA
*
6414321 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAGTACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
6414384 AAT
66 AAA
6414387 TTTACTAA
1 TTTACTAA
6414395 CAATTAATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 27 0.13
67 1 0.00
68 179 0.86
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:6414227 original size:9 final size:9
Alignment explanation
Indices: 6414215--6414242 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6414205 TTTTATTACA
6414215 ACAATTAAT
1 ACAATTAAT
6414224 ACAATTAAT
1 ACAATTAAT
6414233 ACAATTAAT
1 ACAATTAAT
6414242 A
1 A
6414243 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:6414295 original size:9 final size:9
Alignment explanation
Indices: 6414283--6414310 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6414273 TTTTATTACA
6414283 ACAATTAAT
1 ACAATTAAT
6414292 ACAATTAAT
1 ACAATTAAT
6414301 ACAATTAAT
1 ACAATTAAT
6414310 A
1 A
6414311 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:6414404 original size:16 final size:16
Alignment explanation
Indices: 6414383--6414424 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6414373 AATAATTTGA
*
6414383 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
6414399 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
6414415 TAGTTTTAAT
1 TAATTTTAAT
6414425 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Done.