Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 2 of 26
Found at i:269360 original size:21 final size:22
Alignment explanation
Indices: 269325--269368 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
269315 CTCTTAAAGT
269325 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
269347 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
269368 A
1 A
269369 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:271117 original size:15 final size:15
Alignment explanation
Indices: 271097--271127 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
271087 TAAATATGAA
271097 ATGTGATTAAGATTG
1 ATGTGATTAAGATTG
*
271112 ATGTGATTGAGATTG
1 ATGTGATTAAGATTG
271127 A
1 A
271128 CCTATCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (15 bp):
ATGTGATTAAGATTG
Found at i:279754 original size:17 final size:17
Alignment explanation
Indices: 279732--279765 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
279722 GTTAAGGTGT
*
279732 TTTCTTCATGTTTTTTC
1 TTTCTTCATGTTATTTC
*
279749 TTTCTTTATGTTATTTC
1 TTTCTTCATGTTATTTC
279766 CTTTTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTCTTCATGTTATTTC
Found at i:282614 original size:16 final size:17
Alignment explanation
Indices: 282582--282614 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
282572 TAGCACTGAC
282582 CATGATTTGATTTCTCTG
1 CATGATTTGA-TTCTCTG
282600 CATGATTTG-TTCTCT
1 CATGATTTGATTCTCT
282615 ACCCTTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.52
Consensus pattern (17 bp):
CATGATTTGATTCTCTG
Found at i:289033 original size:48 final size:49
Alignment explanation
Indices: 288980--289081 Score: 111
Period size: 52 Copynumber: 2.0 Consensus size: 49
288970 CGCAATTGTG
*
288980 ATTTA-TTGCTTGCATTT-AGC-TCGGCAAAATATTTTACCTTGATTCATT
1 ATTTATTTGCTTGCATTTGA-CTTAGG-AAAATATTTTACCTTGATTCATT
* *
289028 ATTTATGCTTTGCTTTCATTTGACTTAGGAAAATATTTTACCTTGATTTATT
1 ATTTA---TTTGCTTGCATTTGACTTAGGAAAATATTTTACCTTGATTCATT
289080 AT
1 AT
289082 ATGTTCTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
48 5 0.11
52 36 0.80
53 4 0.09
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (49 bp):
ATTTATTTGCTTGCATTTGACTTAGGAAAATATTTTACCTTGATTCATT
Found at i:292903 original size:24 final size:24
Alignment explanation
Indices: 292858--292901 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
292848 CTTTGGCTCA
292858 TTATTTACATAGAACTGACTTCTG
1 TTATTTACATAGAACTGACTTCTG
292882 TTATTTA-A-AGAACTGA-TTCT
1 TTATTTACATAGAACTGACTTCT
292902 TCCTTCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 1 0.05
24 7 0.35
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (24 bp):
TTATTTACATAGAACTGACTTCTG
Found at i:298330 original size:73 final size:72
Alignment explanation
Indices: 298243--298408 Score: 197
Period size: 73 Copynumber: 2.3 Consensus size: 72
298233 TCGACAAAAT
* * * *
298243 GCTCTTAGTTGACTAACATTGCCACTTAGTCGATTAAGTCGTGTCTGTCTCTGAACCTAATTTTT
1 GCTCTTAGTCGACTAACATTGCCACTTAGTCGATTAAGTCGTGTCTATCTCTGAACCCAATTTCT
298308 AGCAGTAA
66 -GCAGTAA
*** ** * * * *
298316 GCTCTTAGTCGACTAACAAAACTTCTTAGTCGATTAAGTCGTTTTTATCTTTGAACCCAGTTTCT
1 GCTCTTAGTCGACTAACATTGCCACTTAGTCGATTAAGTCGTGTCTATCTCTGAACCCAATTTCT
*
298381 GGAGTAA
66 GCAGTAA
298388 GCTCTTAGTCGACTAACATTG
1 GCTCTTAGTCGACTAACATTG
298409 TCTCTTGGTA
Statistics
Matches: 76, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
72 24 0.32
73 52 0.68
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (72 bp):
GCTCTTAGTCGACTAACATTGCCACTTAGTCGATTAAGTCGTGTCTATCTCTGAACCCAATTTCT
GCAGTAA
Found at i:307889 original size:73 final size:73
Alignment explanation
Indices: 307729--307868 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 73
307719 AATATTGCCA
* * * *
307729 CTTAGTCGATTAAGTCGTATTTGTCTCTGAATCCAGTTTTTGGCAGTATACTTTTAGTCGACTAA
1 CTTAGTCGATTAAGTCGTATTTGTCTCTGAATCAAATTTCTGGCAGTATACTTTGAGTCGACTAA
307794 CAAAACTT
66 CAAAACTT
* *
307802 CTTAGTCGATTAAGTTGTTTTTGTCTCTGAATCAAATTTCTGGCAGTA-AGCTTTGAGTCGACTA
1 CTTAGTCGATTAAGTCGTATTTGTCTCTGAATCAAATTTCTGGCAGTATA-CTTTGAGTCGACTA
307866 ACA
65 ACA
307869 CTGTCTCTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.02
73 59 0.98
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (73 bp):
CTTAGTCGATTAAGTCGTATTTGTCTCTGAATCAAATTTCTGGCAGTATACTTTGAGTCGACTAA
CAAAACTT
Found at i:310224 original size:58 final size:57
Alignment explanation
Indices: 310109--310228 Score: 132
Period size: 58 Copynumber: 2.1 Consensus size: 57
310099 AAGGTCCCAT
** * * **
310109 CTTTGCATGCATAACATCTATTAAATCTTATAAAAGAAATGTATGACATGCGTACTA
1 CTTTGCATGCATAACATCTATTAAATCACATAAAAGAAATCTATCACATGCAAACTA
** * * *
310166 CTTTGCATTGCATAGTATTTATTAAATCACATAAAATAAATCTATCATATGCAAACTA
1 CTTTGCA-TGCATAACATCTATTAAATCACATAAAAGAAATCTATCACATGCAAACTA
310224 CTTTG
1 CTTTG
310229 GATGATTATA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
57 7 0.14
58 44 0.86
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (57 bp):
CTTTGCATGCATAACATCTATTAAATCACATAAAAGAAATCTATCACATGCAAACTA
Found at i:313719 original size:29 final size:30
Alignment explanation
Indices: 313686--313754 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
313676 GAAACAGCCC
*
313686 TAGTAACTAAATAAGATATA-CAATATCCA
1 TAGTAACTAAACAAGATATATCAATATCCA
* * *
313715 TAGTAGCTAAGCAAGATATATTGAATATCCA
1 TAGTAACTAAACAAGATATA-TCAATATCCA
*
313746 TAATAACTA
1 TAGTAACTA
313755 GCACATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.53
31 15 0.47
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (30 bp):
TAGTAACTAAACAAGATATATCAATATCCA
Found at i:314861 original size:19 final size:19
Alignment explanation
Indices: 314834--314875 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
314824 GAGAAGAGAC
* *
314834 AATTATAAAGCTTGATGCT
1 AATTATAAAGCTAGATACT
*
314853 AATTTTAAAGCTAGATACT
1 AATTATAAAGCTAGATACT
314872 AATT
1 AATT
314876 GAGAAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AATTATAAAGCTAGATACT
Found at i:331054 original size:92 final size:92
Alignment explanation
Indices: 330897--331073 Score: 291
Period size: 92 Copynumber: 1.9 Consensus size: 92
330887 TTTATTCTTG
* *
330897 TGAGTGATTTATTAATGACAAACATTTTTGTCCTGCACACTTAAGTAGTAAAGTTAGACATAAAT
1 TGAGTGATTTATTAATGACAAACATTTTTGTCCTACACACTCAAGTAGTAAAGTTAGACATAAAT
* *
330962 GAGTGGGAATGTTTTATTATTTGCTTT
66 GAGTAGGAATATTTTATTATTTGCTTT
* * *
330989 TGAGTGATTTATTAATGACATACATTTTTGTCCTACACACTCAAGTAGTAAATTTAGATATAAAT
1 TGAGTGATTTATTAATGACAAACATTTTTGTCCTACACACTCAAGTAGTAAAGTTAGACATAAAT
331054 GAGTAGGAATATTTTATTAT
66 GAGTAGGAATATTTTATTAT
331074 CATCAAAAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 78 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (92 bp):
TGAGTGATTTATTAATGACAAACATTTTTGTCCTACACACTCAAGTAGTAAAGTTAGACATAAAT
GAGTAGGAATATTTTATTATTTGCTTT
Found at i:346091 original size:19 final size:18
Alignment explanation
Indices: 346052--346093 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
346042 TTTTAGTTAT
*
346052 TTTTA-TAATTAGTTTAT
1 TTTTATTAATTAGTTTAA
*
346069 TTTTATTAAGTTATTTTAA
1 TTTTATTAA-TTAGTTTAA
346088 TTTTAT
1 TTTTAT
346094 GTTTATTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTATTAATTAGTTTAA
Found at i:354135 original size:20 final size:21
Alignment explanation
Indices: 354097--354143 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
354087 AAGTAATTTA
*
354097 AAAC-AAAATAACATAAAATT
1 AAACTAAAATAACATAAAATC
*
354117 AAACTAAAATAAC-TTAAATC
1 AAACTAAAATAACATAAAATC
354137 AAACTAA
1 AAACTAA
354144 TCAACATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACTAAAATAACATAAAATC
Found at i:370337 original size:15 final size:16
Alignment explanation
Indices: 370312--370342 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
370302 CCTGCCGAGC
370312 CATCTTGCGTGCCGCG
1 CATCTTGCGTGCCGCG
370328 CATC-TGCGTGCCGCG
1 CATCTTGCGTGCCGCG
370343 TACTGGCGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.06, C:0.39, G:0.32, T:0.23
Consensus pattern (16 bp):
CATCTTGCGTGCCGCG
Found at i:374573 original size:2 final size:2
Alignment explanation
Indices: 374566--374594 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
374556 TGTATACTAT
374566 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
374595 TATGTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:375039 original size:26 final size:26
Alignment explanation
Indices: 375003--375091 Score: 142
Period size: 26 Copynumber: 3.4 Consensus size: 26
374993 TGATCTGTGA
*
375003 TTATACGTGGTAAGGCCACCGGATTG
1 TTATACGTGGTAAGGCCACAGGATTG
*
375029 TTATACGTGGTAAGGCCACGGGATTG
1 TTATACGTGGTAAGGCCACAGGATTG
* *
375055 TTATACGTGGCAAGGCCACAGGGTTG
1 TTATACGTGGTAAGGCCACAGGATTG
375081 TTATACGTGGT
1 TTATACGTGGT
375092 TGCGAGCACA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (26 bp):
TTATACGTGGTAAGGCCACAGGATTG
Found at i:379528 original size:33 final size:33
Alignment explanation
Indices: 379490--379570 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
379480 TGTAAGGATG
*
379490 CTTGATCTTGTAAAAAGCATTGTAAATATTTCA
1 CTTGATCTTGTAAAAAGCATTGTAAAGATTTCA
* * * *
379523 CTTGATCCTGTAAAAAGCATTGTAAGGGTTTCG
1 CTTGATCTTGTAAAAAGCATTGTAAAGATTTCA
379556 CTTGATCTTGTAAAA
1 CTTGATCTTGTAAAA
379571 CCCTCATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (33 bp):
CTTGATCTTGTAAAAAGCATTGTAAAGATTTCA
Found at i:379756 original size:37 final size:36
Alignment explanation
Indices: 379712--379782 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 36
379702 ATTTAGGTTA
*
379712 GAAAATATTTTACCTTGATTTATTAATTTTTTCTTAG
1 GAAAATATTTTACCTTGAATTATT-ATTTTTTCTTAG
*
379749 GAAAATATTTTATCTTGAATTATTATTTTTTCTT
1 GAAAATATTTTACCTTGAATTATTATTTTTTCTT
379783 GCACTTGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (36 bp):
GAAAATATTTTACCTTGAATTATTATTTTTTCTTAG
Found at i:379842 original size:47 final size:46
Alignment explanation
Indices: 379744--379924 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 46
379734 TTAATTTTTT
* * * *
379744 CTTAGGAAAATATTTTA-TCTTGAATTATTATTTTTTC-TTGCACTTGA
1 CTTAGAAAAATATTTTACT-TTGATTTATTATTTGTTCATT--ATTTGA
*
379791 CTTAGAAAAATATTCTTACTTTGATTTATTATTTGTTCATTATTTGG
1 CTTAGAAAAATATT-TTACTTTGATTTATTATTTGTTCATTATTTGA
* * *
379838 CTTAGAAAAATATTTTTCTTTAACTTATTATTTGTTCATTATTTGA
1 CTTAGAAAAATATTTTACTTTGATTTATTATTTGTTCATTATTTGA
* * * * *
379884 CTTGGGAAAATATCTTTACTTTGATGTGTTATTTGCTCATT
1 CTTAGAAAAATAT-TTTACTTTGATTTATTATTTGTTCATT
379925 TCAATTTATT
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 39 0.35
47 52 0.46
48 19 0.17
49 3 0.03
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (46 bp):
CTTAGAAAAATATTTTACTTTGATTTATTATTTGTTCATTATTTGA
Found at i:379908 original size:93 final size:93
Alignment explanation
Indices: 379744--379924 Score: 224
Period size: 93 Copynumber: 1.9 Consensus size: 93
379734 TTAATTTTTT
* *
379744 CTTAGGAAAATATTTTATCTTGAATTATTATTTTTTCTTGCACTTGACTTAGAAAAATATTCTTA
1 CTTAGAAAAATATTTTATCTTGAATTATTATTTGTTCTT-CACTTGACTTAGAAAAATATTCTTA
* *
379809 CTTTGATTTATTATTTGTTCATTATTTGG
65 CTTTGATGTATTATTTGCTCATTATTTGG
* * * *
379838 CTTAGAAAAATATTTT-TCTTTAACTTATTATTTGTTCATT-ATTTGACTTGGGAAAATA-TCTT
1 CTTAGAAAAATATTTTATCTTGAA-TTATTATTTGTTC-TTCACTTGACTTAGAAAAATATTC-T
*
379900 TACTTTGATGTGTTATTTGCTCATT
63 TACTTTGATGTATTATTTGCTCATT
379925 TCAATTTATT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
92 2 0.03
93 44 0.59
94 27 0.36
95 2 0.03
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (93 bp):
CTTAGAAAAATATTTTATCTTGAATTATTATTTGTTCTTCACTTGACTTAGAAAAATATTCTTAC
TTTGATGTATTATTTGCTCATTATTTGG
Found at i:381375 original size:24 final size:24
Alignment explanation
Indices: 381347--381397 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
381337 TTTTAGAATC
381347 TATTTATGTACATAAATATACTAT
1 TATTTATGTACATAAATATACTAT
*
381371 TATTTATGTTCATAAATATACTAT
1 TATTTATGTACATAAATATACTAT
381395 TAT
1 TAT
381398 GTATTAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTATGTACATAAATATACTAT
Found at i:389485 original size:33 final size:32
Alignment explanation
Indices: 389426--389525 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 32
389416 GTTTCGTTTT
* * *
389426 ATCCCATAAAAAGGCTTGGAATGGTTTCACTTG
1 ATCCCAT-AAAAGGATTGTAAGGGTTTCACTTG
389459 ATCCCATAAAAGGTATTGTAAGGGTTTCACTTG
1 ATCCCATAAAAGG-ATTGTAAGGGTTTCACTTG
* * *
389492 ATCTCGT-AAAGCATTGTAAGGGTTTCACTTG
1 ATCCCATAAAAGGATTGTAAGGGTTTCACTTG
389523 ATC
1 ATC
389526 TTGTAAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
31 22 0.37
32 10 0.17
33 28 0.47
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (32 bp):
ATCCCATAAAAGGATTGTAAGGGTTTCACTTG
Found at i:389511 original size:31 final size:32
Alignment explanation
Indices: 389435--389532 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 32
389425 TATCCCATAA
* * * *
389435 AAAGGC-TTGGAATGGTTTCACTTGATCCCAT
1 AAAGGCATTGTAAGGGTTTCACTTGATCTCGT
*
389466 AAAAGGTATTGTAAGGGTTTCACTTGATCTCGT
1 -AAAGGCATTGTAAGGGTTTCACTTGATCTCGT
*
389499 AAA-GCATTGTAAGGGTTTCACTTGATCTTGT
1 AAAGGCATTGTAAGGGTTTCACTTGATCTCGT
389530 AAA
1 AAA
389533 AAGTCTCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
31 29 0.50
32 8 0.14
33 21 0.36
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (32 bp):
AAAGGCATTGTAAGGGTTTCACTTGATCTCGT
Found at i:389694 original size:35 final size:36
Alignment explanation
Indices: 389655--389722 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
389645 TTTCGCATTG
*
389655 AGATTTATT-ATTTAACTTAGGAAAATATTTTACCT
1 AGATTCATTAATTTAACTTAGGAAAATATTTTACCT
** * *
389690 AGATTCATTAATTTTTCTTGGGAAATTATTTTA
1 AGATTCATTAATTTAACTTAGGAAAATATTTTA
389723 TCTTGAACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 8 0.30
36 19 0.70
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (36 bp):
AGATTCATTAATTTAACTTAGGAAAATATTTTACCT
Found at i:389887 original size:47 final size:47
Alignment explanation
Indices: 389749--389887 Score: 197
Period size: 47 Copynumber: 3.0 Consensus size: 47
389739 TTTCTTACAC
* * * *
389749 TTGACTTAGGAAAGTATTTTTACTCTAATTTATTATTTGTTCATCAT
1 TTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTAT
** *
389796 TTGACTTAAAAAAATATTTTTACTTTGATTTATTATTTATTCATTAT
1 TTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTAT
* *
389843 TTGACTTAGGAAAATATCTTTGCTTTGATTTATTATTTGTTCATT
1 TTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATT
389888 TCAATTTATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 80 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (47 bp):
TTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTAT
Found at i:393966 original size:2 final size:2
Alignment explanation
Indices: 393959--393990 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
393949 TTGCGTCTTT
393959 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
393991 ATTAAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:397085 original size:251 final size:250
Alignment explanation
Indices: 396518--397201 Score: 806
Period size: 251 Copynumber: 2.7 Consensus size: 250
396508 AAGTAAAGTA
* * * * * *
396518 ATAAGAATTGACATAAAAACTAATAAAGATAGAATAACTAAATTTAAAATTTTAATATAAATGTG
1 ATAAGAATTGACATAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAATGTAAATGTG
* ** * * * *
396583 TAAAAGTTAACGTAACAAGCCAATT-A--AAAAAATTTTAATTTTAATGAAAAATAAATATTTAA
66 TGAAAGTTAACGTAACAAGTAAATTAAGTAAAAAAATCTAATTTTAGTGAAAAATAAATATTTAT
* * * *
396645 ATTTATATTCTCGGACTAAAATTCTTTAACAATGTATCAATTTTAATTTTTAAATAAAAATAAAA
131 ATTTATATTCTCGGATTAAAAGTCTTTAACAATATATAAATTTTAATTTTTAAATAAAAATAAAA
* * ** * *
396710 ATAATAAAAATGATTATAGTTCAAAATTGACATAGCCAAACTTTGACGTAAAACT
196 ATAATAAAAATAATTATAATTCAAAATTGACATAGAAAAACCTTAACGTAAAACT
* * * * * * * *
396765 GTAACAATTAACATAAAAATTTATAAAAGTGAAATAACTAAATTTTAAATCTTAACGTAAATATG
1 ATAAGAATTGACATAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAATGTAAATGTG
* **
396830 TGAAAGTTAACATAACAAGTTGATTAAGTAAAAAAATCTAATTTTAGTGAAAAATAAATATTTAT
66 TGAAAGTTAACGTAACAAGTAAATTAAGTAAAAAAATCTAATTTTAGTGAAAAATAAATATTTAT
** *
396895 ATTTATATTCTCATATTAAAAGTGTTTAACAATATATAAATTTTAATTTTTAAATAAAAAATAAT
131 ATTTATATTCTCGGATTAAAAGTCTTTAACAATATATAAATTTTAATTTTTAAAT-AAAAATAA-
* *
396960 AAA-GATAAAAATAATTATAATGT-AAAATTGACATA-AAAAAGCCTTAACATTAAAA-T
194 AAATAATAAAAATAATTATAAT-TCAAAATTGACATAGAAAAA-CCTTAAC-GTAAAACT
* * * *
397016 ATGAGAATTGACGTAAAAACTTATAAAGGTGGAATAATTAAATTTTAAATCTTAATGTAAACGTG
1 ATAAGAATTGACATAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAATGTAAATGTG
* * *
397081 TGAAAGCTAACGTAACAAATAAATTAAGTAAAAAAAATCTAATTTTTGTGAAAAATAAATATTTA
66 TGAAAGTTAACGTAACAAGTAAATTAAGT-AAAAAAATCTAATTTTAGTGAAAAATAAATATTTA
* * ** *
397146 TATTTATATTCTTGGATTAAAAGTTTTTAATGATATATAAATTTTAGTTTTTAAAT
130 TATTTATATTCTCGGATTAAAAGTCTTTAACAATATATAAATTTTAATTTTTAAAT
397202 TTTGACGTAA
Statistics
Matches: 365, Mismatches: 63, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
247 71 0.19
248 1 0.00
250 83 0.23
251 118 0.32
252 92 0.25
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (250 bp):
ATAAGAATTGACATAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAATGTAAATGTG
TGAAAGTTAACGTAACAAGTAAATTAAGTAAAAAAATCTAATTTTAGTGAAAAATAAATATTTAT
ATTTATATTCTCGGATTAAAAGTCTTTAACAATATATAAATTTTAATTTTTAAATAAAAATAAAA
ATAATAAAAATAATTATAATTCAAAATTGACATAGAAAAACCTTAACGTAAAACT
Found at i:403442 original size:36 final size:36
Alignment explanation
Indices: 403374--403443 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
403364 TTAGAATGCT
* * *
403374 TTGAATTTAAAATTGATCTTAGAGGAGCTTGGTTGG
1 TTGAATTTAAAATTGATCTCAAAAGAGCTTGGTTGG
*
403410 TTGAATTTAAAATTGATCTCAAAAGAGGTTGGTT
1 TTGAATTTAAAATTGATCTCAAAAGAGCTTGGTT
403444 AAGAAATACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (36 bp):
TTGAATTTAAAATTGATCTCAAAAGAGCTTGGTTGG
Found at i:410860 original size:15 final size:16
Alignment explanation
Indices: 410840--410872 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
410830 GGCTGTACTG
410840 CACTGAAAGGC-TTAT
1 CACTGAAAGGCTTTAT
410855 CACTGAAAGGCTTTAT
1 CACTGAAAGGCTTTAT
410871 CA
1 CA
410873 AATTCTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (16 bp):
CACTGAAAGGCTTTAT
Found at i:417481 original size:2 final size:2
Alignment explanation
Indices: 417474--417498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
417464 AAATTTGCAA
417474 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
417499 AAAGCTTTGT
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:421506 original size:13 final size:13
Alignment explanation
Indices: 421488--421512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
421478 TTACACTCCA
421488 ATCTTTATATCCT
1 ATCTTTATATCCT
421501 ATCTTTATATCC
1 ATCTTTATATCC
421513 ATTATTAGGC
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:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (13 bp):
ATCTTTATATCCT
Found at i:430617 original size:17 final size:17
Alignment explanation
Indices: 430595--430635 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
430585 TTATGAACAT
430595 TTCTATAAGAATATTTA
1 TTCTATAAGAATATTTA
*
430612 TTCTATAAGAATCTTTA
1 TTCTATAAGAATATTTA
*
430629 GTCTATA
1 TTCTATA
430636 TTCCACCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (17 bp):
TTCTATAAGAATATTTA
Found at i:435914 original size:2 final size:2
Alignment explanation
Indices: 435909--435936 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
435899 TCCCCCCCAT
435909 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
435937 TTTTCCTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:436306 original size:15 final size:15
Alignment explanation
Indices: 436286--436316 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
436276 TTTGTATTAT
436286 TGAGTGGGTAGCATC
1 TGAGTGGGTAGCATC
436301 TGAGTGGGTAGCATC
1 TGAGTGGGTAGCATC
436316 T
1 T
436317 AGGTGCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.39, T:0.29
Consensus pattern (15 bp):
TGAGTGGGTAGCATC
Found at i:442475 original size:36 final size:36
Alignment explanation
Indices: 442422--442540 Score: 95
Period size: 36 Copynumber: 3.3 Consensus size: 36
442412 CCTTTGTGAC
* *
442422 TTTGTTCCTT-ACTAATTGCTTTAGCAATGTGCA-TGA
1 TTTGTT-CTTCACCAATTGCTTTAGCAATGAG-ATTGA
* *
442458 TTTGTTCTTCACCAATTG-TTTCAACATTGAGATTGA
1 TTTGTTCTTCACCAATTGCTTT-AGCAATGAGATTGA
*
442494 TTTGATTC-TCTACCAATTGCTTTAGCATTGAG-TGTGA
1 TTTG-TTCTTC-ACCAATTGCTTTAGCAATGAGAT-TGA
*
442531 TTTGATCTTC
1 TTTGTTCTTC
442541 CATTAGATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
35 7 0.10
36 31 0.45
37 28 0.41
38 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (36 bp):
TTTGTTCTTCACCAATTGCTTTAGCAATGAGATTGA
Found at i:442511 original size:37 final size:37
Alignment explanation
Indices: 442455--442540 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
442445 GCAATGTGCA
442455 TGATTTG-TTCTTCACCAATTG-TTTCAACATTGAGAT-
1 TGATTTGATTCTTCACCAATTGCTTT-AACATTGAG-TG
*
442491 TGATTTGATTC-TCTACCAATTGCTTTAGCATTGAGTG
1 TGATTTGATTCTTC-ACCAATTGCTTTAACATTGAGTG
442528 TGATTTGA-TCTTC
1 TGATTTGATTCTTC
442541 CATTAGATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
36 12 0.27
37 29 0.66
38 3 0.07
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (37 bp):
TGATTTGATTCTTCACCAATTGCTTTAACATTGAGTG
Found at i:447831 original size:39 final size:39
Alignment explanation
Indices: 447777--447890 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 39
447767 TCCTACATTG
* *
447777 TAACTTTGATATTTCATTAATGGCTTTGGCACTGGACGA
1 TAACTTTGATATTTCATTAGTGGCTTTAGCACTGGACGA
* *
447816 TAACTTT-ACTATTTCATTAGTGGCTTTTGCATTGGACGA
1 TAACTTTGA-TATTTCATTAGTGGCTTTAGCACTGGACGA
* * *
447855 TGACTTTGATATTTCGTTAGTAGCTTTAGCACTGGA
1 TAACTTTGATATTTCATTAGTGGCTTTAGCACTGGA
447891 TGTATTTGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
38 1 0.02
39 63 0.97
40 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (39 bp):
TAACTTTGATATTTCATTAGTGGCTTTAGCACTGGACGA
Found at i:474805 original size:15 final size:15
Alignment explanation
Indices: 474785--474821 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
474775 TGGAAGGCTT
474785 AGAAGCTGGCATCAA
1 AGAAGCTGGCATCAA
474800 AGAAGCTGGCATCAA
1 AGAAGCTGGCATCAA
474815 AGAAGCT
1 AGAAGCT
474822 AAAATATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (15 bp):
AGAAGCTGGCATCAA
Found at i:488102 original size:40 final size:40
Alignment explanation
Indices: 488049--488127 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
488039 TTGTGAAAGA
* *
488049 CACCAACCATGGCAAGGTTAGAAACCCCACTAAGGTGAAC
1 CACCAACCATGGCAAGGTTAAAAAACCCACTAAGGTGAAC
* *
488089 CACCAATCTTGGCAAGGTTAAAAAACCCACTAAGGTGAA
1 CACCAACCATGGCAAGGTTAAAAAACCCACTAAGGTGAA
488128 GAATAGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.15
Consensus pattern (40 bp):
CACCAACCATGGCAAGGTTAAAAAACCCACTAAGGTGAAC
Found at i:490596 original size:20 final size:20
Alignment explanation
Indices: 490568--490605 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
490558 ACTAATGTCA
*
490568 AGGCGTTGTAAAAGACACTT
1 AGGCATTGTAAAAGACACTT
490588 AGGCATTGTAAAAGACAC
1 AGGCATTGTAAAAGACAC
490606 CAATCGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (20 bp):
AGGCATTGTAAAAGACACTT
Found at i:500870 original size:21 final size:21
Alignment explanation
Indices: 500844--500892 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
500834 AAAGGGTTGG
*
500844 ATTTATTGAAATATACAATGT
1 ATTTATCGAAATATACAATGT
*
500865 ATTTATCGAAATGTACAATGT
1 ATTTATCGAAATATACAATGT
500886 ATTTATC
1 ATTTATC
500893 TCATACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (21 bp):
ATTTATCGAAATATACAATGT
Found at i:521942 original size:2 final size:2
Alignment explanation
Indices: 521935--521973 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
521925 TTGTTTCTTT
*
521935 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
521974 TTCTGGTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:532388 original size:24 final size:25
Alignment explanation
Indices: 532361--532408 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
532351 CGTAATCGCG
*
532361 TATATC-ACTTGTGG-CTTAGCCACA
1 TATATCAACTCGTGGCCTT-GCCACA
532385 TATATCAACTCGTGGCCTTGCCAC
1 TATATCAACTCGTGGCCTTGCCAC
532409 GTAAATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 12 0.57
26 3 0.14
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (25 bp):
TATATCAACTCGTGGCCTTGCCACA
Found at i:544247 original size:18 final size:20
Alignment explanation
Indices: 544224--544262 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
544214 AGGTAAAAGG
544224 AATA-TTTT-TAAATAAAAT
1 AATATTTTTATAAATAAAAT
544242 AATATTTTTATAAATAAAAT
1 AATATTTTTATAAATAAAAT
544262 A
1 A
544263 TTAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTTATAAATAAAAT
Found at i:544256 original size:15 final size:17
Alignment explanation
Indices: 544224--544273 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
544214 AGGTAAAAGG
544224 AATATTTTTAAATAAAAT
1 AATATTTTT-AATAAAAT
544242 AATATTTTT-AT-AAAT
1 AATATTTTTAATAAAAT
* *
544257 AA-AATATTAATAAAAT
1 AATATTTTTAATAAAAT
544273 A
1 A
544274 TTACTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 7 0.25
18 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTTTTAATAAAAT
Found at i:550040 original size:26 final size:26
Alignment explanation
Indices: 550011--550063 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
550001 AAGCTTAGAA
550011 GTATGGTGGTTTAAAGCAAGACAAAT
1 GTATGGTGGTTTAAAGCAAGACAAAT
550037 GTATGGTGGTTTAAAGCAAGACAAAT
1 GTATGGTGGTTTAAAGCAAGACAAAT
550063 G
1 G
550064 AGGGGTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (26 bp):
GTATGGTGGTTTAAAGCAAGACAAAT
Found at i:572997 original size:32 final size:32
Alignment explanation
Indices: 572961--573024 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
572951 TGGGAATTAA
572961 CCCTTCATGCCTTAATTCACAAAAATACATTC
1 CCCTTCATGCCTTAATTCACAAAAATACATTC
* ** *
572993 CCCTTTATGCCTTAATTCGTAAAAATGCATTC
1 CCCTTCATGCCTTAATTCACAAAAATACATTC
573025 TTTTGGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (32 bp):
CCCTTCATGCCTTAATTCACAAAAATACATTC
Found at i:573250 original size:32 final size:32
Alignment explanation
Indices: 573212--573310 Score: 161
Period size: 30 Copynumber: 3.2 Consensus size: 32
573202 CGATTTCACA
*
573212 TATAACCTTTATCTACACTTTTTCTATGAAGG
1 TATAACCTTTATCTACACTTTTTCTATGGAGG
573244 TATAACCTTTATCTAC-C-TTTTCTATGGAGG
1 TATAACCTTTATCTACACTTTTTCTATGGAGG
573274 TATAACCTTTATC--CACTTTTTCTATGGAGG
1 TATAACCTTTATCTACACTTTTTCTATGGAGG
573304 TATAACC
1 TATAACC
573311 AAAAACAGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 45 0.70
31 1 0.02
32 16 0.25
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.42
Consensus pattern (32 bp):
TATAACCTTTATCTACACTTTTTCTATGGAGG
Found at i:578083 original size:8 final size:8
Alignment explanation
Indices: 578063--578149 Score: 117
Period size: 8 Copynumber: 11.1 Consensus size: 8
578053 AAATTCGGCT
578063 AGGAAGTAA
1 AGGAAG-AA
578072 AGGAAGAA
1 AGGAAGAA
578080 AGGAAGAA
1 AGGAAGAA
578088 AGGAAGAA
1 AGGAAGAA
*
578096 AGAAAGAA
1 AGGAAGAA
578104 AGG-AGAA
1 AGGAAGAA
578111 AGGAAGAA
1 AGGAAGAA
578119 AGGAAGAA
1 AGGAAGAA
* *
578127 AGGGAGAG
1 AGGAAGAA
578135 AGG-AGAA
1 AGGAAGAA
578142 A-GAAGAA
1 AGGAAGAA
578149 A
1 A
578150 AGAGAATGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
6 1 0.01
7 16 0.23
8 48 0.68
9 6 0.08
ACGTcount: A:0.61, C:0.00, G:0.38, T:0.01
Consensus pattern (8 bp):
AGGAAGAA
Found at i:578100 original size:4 final size:4
Alignment explanation
Indices: 578070--578128 Score: 57
Period size: 4 Copynumber: 15.0 Consensus size: 4
578060 GCTAGGAAGT
* * * * *
578070 AAAG GAAG AAAG GAAG AAAG GAAG AAAG AAAG AAAG -GAG AAAG GAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
578117 AAAG GAAG AAAG
1 AAAG AAAG AAAG
578129 GGAGAGAGGA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
3 2 0.05
4 40 0.95
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:578113 original size:31 final size:31
Alignment explanation
Indices: 578070--578149 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
578060 GCTAGGAAGT
578070 AAAGGAAGAAAGGAAGAAAGGAAGAAAGAAAG
1 AAAGG-AGAAAGGAAGAAAGGAAGAAAGAAAG
**
578102 AAAGGAGAAAGGAAGAAAGGAAGAAAGGGAG
1 AAAGGAGAAAGGAAGAAAGGAAGAAAGAAAG
*
578133 AGAGGAGAAA-GAAGAAA
1 AAAGGAGAAAGGAAGAAA
578150 AGAGAATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 7 0.16
31 33 0.73
32 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (31 bp):
AAAGGAGAAAGGAAGAAAGGAAGAAAGAAAG
Found at i:578151 original size:23 final size:23
Alignment explanation
Indices: 578063--578149 Score: 106
Period size: 23 Copynumber: 3.7 Consensus size: 23
578053 AAATTCGGCT
*
578063 AGGAAGTAAAGGAAGAAAGGAAGAA
1 AGGAAG-AAA-GAAGAAAGGGAGAA
578088 AGGAAGAAAGAAAGAAA-GGAGAA
1 AGGAAGAAAG-AAGAAAGGGAGAA
*
578111 AGGAAGAAAGGAAGAAAGGGAGAG
1 AGGAAGAAA-GAAGAAAGGGAGAA
578135 AGG-AGAAAGAAGAAA
1 AGGAAGAAAGAAGAAA
578150 AGAGAATGTG
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
22 7 0.12
23 26 0.46
24 18 0.32
25 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.38, T:0.01
Consensus pattern (23 bp):
AGGAAGAAAGAAGAAAGGGAGAA
Found at i:578863 original size:18 final size:19
Alignment explanation
Indices: 578840--578883 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
578830 AGGTAGAAAG
578840 AATATTTTTA-AATAAAAT
1 AATATTTTTAGAATAAAAT
578858 AATATTTTTATGAATAAAAT
1 AATATTTTTA-GAATAAAAT
578878 AATATT
1 AATATT
578884 AAAATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATATTTTTAGAATAAAAT
Found at i:595441 original size:15 final size:16
Alignment explanation
Indices: 595417--595457 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
595407 TTCAAGAAGG
595417 TTAA-GATATCT-TTC
1 TTAATGATATCTATTC
595431 TTAATGATATCTATTC
1 TTAATGATATCTATTC
595447 TTAATAGATAT
1 TTAAT-GATAT
595458 TTGAGAACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 8 0.33
17 5 0.21
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (16 bp):
TTAATGATATCTATTC
Found at i:630161 original size:35 final size:35
Alignment explanation
Indices: 630068--630193 Score: 123
Period size: 35 Copynumber: 3.7 Consensus size: 35
630058 ATTGTTGAAA
*** *
630068 GGTTTCACTTAATCCCATGAAAAAGCTATTAAAAG
1 GGTTTCACTTAATCTTGTGAAAAAGCTATTATAAG
** *
630103 GGTTTCAC-TATATCTCATTAAAAAGCTATTATAAG
1 GGTTTCACTTA-ATCTTGTGAAAAAGCTATTATAAG
* * *
630138 GGTTTCGCTTAATCTTGTGAAAAAGTTATTATGAG
1 GGTTTCACTTAATCTTGTGAAAAAGCTATTATAAG
*
630173 GG-TTCACTTTATCTTGT-AAAA
1 GGTTTCACTTAATCTTGTGAAAA
630194 TGCTCATTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
33 4 0.05
34 15 0.19
35 57 0.73
36 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (35 bp):
GGTTTCACTTAATCTTGTGAAAAAGCTATTATAAG
Found at i:631136 original size:2 final size:2
Alignment explanation
Indices: 631129--631157 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
631119 TTGTGTAGAC
631129 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
631158 GTAAAGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:637207 original size:17 final size:17
Alignment explanation
Indices: 637185--637217 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
637175 TTATTTCTTC
637185 TTTTTC-TTTCTATTTTG
1 TTTTTCATTT-TATTTTG
637202 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
637218 CTATTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:637414 original size:18 final size:18
Alignment explanation
Indices: 637387--637426 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
637377 AATGATTAAT
*
637387 TTATGGGTTACTTATGAA
1 TTATGGGTTACTTATAAA
*
637405 TTATGTGTTACTTATAAA
1 TTATGGGTTACTTATAAA
637423 TTAT
1 TTAT
637427 TTGTGAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (18 bp):
TTATGGGTTACTTATAAA
Found at i:638770 original size:31 final size:29
Alignment explanation
Indices: 638730--638794 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
638720 ATATTATGTG
*
638730 TTAGTTATTATACATATTTAATATATCTTAC
1 TTAGCTATTATACATA-TT-ATATATCTTAC
** *
638761 TTAGCTATTATGGATATTATATATCTTAT
1 TTAGCTATTATACATATTATATATCTTAC
638790 TTAGC
1 TTAGC
638795 CACTATGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.50
30 2 0.07
31 13 0.43
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.51
Consensus pattern (29 bp):
TTAGCTATTATACATATTATATATCTTAC
Found at i:642343 original size:4 final size:4
Alignment explanation
Indices: 642334--642363 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
642324 GTTAAATTGG
642334 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
642364 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:642633 original size:12 final size:12
Alignment explanation
Indices: 642616--642645 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
642606 AAAAAATCTT
642616 CTCTTTGATGGA
1 CTCTTTGATGGA
642628 CTCTTTGATGGA
1 CTCTTTGATGGA
642640 CTCTTT
1 CTCTTT
642646 TCATGCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (12 bp):
CTCTTTGATGGA
Found at i:642976 original size:17 final size:18
Alignment explanation
Indices: 642954--642987 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
642944 AAGTCATTTA
*
642954 AAAAAATTAAT-TTTAAT
1 AAAAAATAAATATTTAAT
642971 AAAAAATAAATATTTAA
1 AAAAAATAAATATTTAA
642988 ATTTATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAATAAATATTTAAT
Found at i:643312 original size:244 final size:247
Alignment explanation
Indices: 642877--643535 Score: 798
Period size: 244 Copynumber: 2.7 Consensus size: 247
642867 GAACTGACAA
** ** * *
642877 AAAAACTCGTAAAAGTAGAATAACTAAATTGAAAATCTTAATGTAAATGTGTAAAAGTTAACGTA
1 AAAAACTTATAAAAGTAGAATAACTAAATTTTAAATCTTAATATAAATGTGTAAAAG-TAACATA
* * * *
642942 ACAAG-TCA-T---TTAAAAAAATTAATTTTAATAAAAAATAAATATTTAAATTTATATTCTCAA
65 ACAAGTTAATTAAGTTAAAAAATTTAATTTTAGTGAAAAATAAATATTTAAATTTATA-T-TCAA
* * * * * * *
643002 ATTACAATTGTTTAATGATATACAAATTTTATTTTTTAAATAAAAATATTAATAATAAAGATAAT
128 ATTAAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAAAATAATAATAATAAAAATAAT
* *
643067 TATAGTTCAAAATTGACATAGATAAA-TCTTGA-CTAAAACTGTAATAATTGACGT
193 TATAGTTCAAAATTGACATAGA-AAAGCCTTGATCTAAAACTGTAAGAATTGACGT
*
643121 AAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAATATAAATGTGTAAAAGTAACATAA
1 AAAAACTTATAAAAGTAGAATAACTAAATTTTAAATCTTAATATAAATGTGTAAAAGTAACATAA
* * *
643186 CAAGTTAATTAAGTTAAAAAATTTAATTTTAGCGAAAAATAAACATTTATA-TT-TATTCAAATT
66 CAAGTTAATTAAGTTAAAAAATTTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCAAATT
*
643249 AAAAGTGTTTAACAATATATAAATTTTAATTTTTAAATAAAGAATAATAA-AATAAAAATAATTA
131 AAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAA-AATAATAATAATAAAAATAATTA
* * * * *
643313 TAGTTCAAAATTGATATAGAAAAGCCTTGATGTTAAATTGTGAGAATTGACGT
195 TAGTTCAAAATTGACATAGAAAAGCCTTGATCTAAAACTGTAAGAATTGACGT
* * * * **
643366 AAAAACTTATAAAGGTAGAATAACAAAATTTTAAATCTTAATATAAACGTGTGACATTTAACATA
1 AAAAACTTATAAAAGTAGAATAACTAAATTTTAAATCTTAATATAAATGTGT-AAAAGTAACATA
* * *
643431 ACAAGTCAATTAAGTGAAAAAAATTTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTTA
65 ACAAGTTAATTAAGT-TAAAAAATTTAATTTTAGTGAAAAATAAATATTTAAATTTATATTC--A
* * *
643496 AACTAAAAGTATTTAGCGATATATAAATTTTAATTTTTAA
127 AATTAAAAGTGTTTAACGATATATAAATTTTAATTTTTAA
643536 GTTTTGATGT
Statistics
Matches: 355, Mismatches: 46, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
243 14 0.04
244 132 0.37
245 74 0.21
246 25 0.07
247 34 0.10
248 34 0.10
249 5 0.01
251 37 0.10
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (247 bp):
AAAAACTTATAAAAGTAGAATAACTAAATTTTAAATCTTAATATAAATGTGTAAAAGTAACATAA
CAAGTTAATTAAGTTAAAAAATTTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCAAATT
AAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAAAATAATAATAATAAAAATAATTAT
AGTTCAAAATTGACATAGAAAAGCCTTGATCTAAAACTGTAAGAATTGACGT
Found at i:643932 original size:691 final size:692
Alignment explanation
Indices: 642895--644186 Score: 1584
Period size: 691 Copynumber: 1.9 Consensus size: 692
642885 GTAAAAGTAG
* * *
642895 AATAACTAAATTGAAAATCTTAATGTAAATGTGTAAAAGTTAACGTAACAAGTCATTTAAAAAAA
1 AATAACTAAATTGAAAATCTTAACGTAAATCTGTAAAAGTTAACGTAACAAATCATTTAAAAAAA
* * * ** **
642960 TTAATTTTAATAAAAAATAAATATTTAAATTTATATTCTCAAATTACAATTGTTTAATGATATAC
66 TTAATTTTAAT-AAAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTGGATAACAATATAC
* * *
643025 AAATTTTATTTTTTAAATAAAAATATTAATAATAAAGATAATTATAGTTCAAAATTGACATAGAT
130 AAATTTTAATTTTTAAATAAAAATAATAATAATAAAGATAATTATAGTTCAAAATTCACATAGAT
* * * *
643090 AAATCTTGACTAAAACTGTAATAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAA
195 AAACCTTGAATAAAACTATAACAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAA
* * * *
643155 ATCTTAATATAAATGTGTAAAAGTAACATAACAAGTTAATTAAGTTAAAAAATTTAATTTTAGCG
260 ATCTTAACATAAATATGTAAAAGTAACATAACAAGTTAATTAAGTAAAAAAATTTAATTTTAACG
* * *
643220 AAAAATAAACATTTATA-TT-TA-T-TCAAATTAAAAGTGTTTAACAATATAT-AAATTTTAATT
325 AAAAATAAACATTTATATTTATATTATCAAATTAAAAGTATGTAACAAT-TATCAAATTTTAACT
* *
643280 TTTAAATAAAGAATAATAA-AATAAAAATAATTAT-AGTTCAAAATTGATATAGAAAAGCCTTGA
389 TTTAAATAAAGAATAATAAGAATAAAAATAATTATCA-TTCAAAATTGACATAAAAAAGCCTTGA
* * * * * * * * *
643343 TGTTAAATTGTGAGAATTGACGTAAAAACTTATAAAGGTAGAATAACAAAATTTTAAATCTTAAT
453 CGTAAAACTATAAGAATTGAAGTAAAAACTTATAAAAGTAGAATAACAAAATTTTAAATATTAAC
* * * *
643408 ATAAACGTGTGACATTTAACATAACAAGTCAATTAAGTGAAAAAAATTTAATTTTAGTGAAAAAC
518 ATAAACATGTAACAGTTAACATAACAAGTCAATTAAGT-AAAAAAATTTAATTTTAATGAAAAAC
*
643473 AAATATTTAAATTTATATTCTTAAACTAAAAGTATTTAGCGATATATAAATTTTAATTTTTAAGT
582 AAACATTTAAATTTATATTCTTAAACTAAAAGTATTTAGCGATATATAAATTTTAATTTTTAAGT
643538 TTTGATGTATAACTGTAGCAATTGACGTAAAAACTTATAAAGATAA
647 TTTGATGTATAACTGTAGCAATTGACGTAAAAACTTATAAAGATAA
** *
643584 AATAACTAAATTTTAAATCTTAACGTAAATCTGTAAGAGTTAACGTAACAAATCAATTAAGTAAA
1 AATAACTAAATTGAAAATCTTAACGTAAATCTGTAAAAGTTAACGTAACAAATC-ATT---TAAA
* * * ****
643649 AAAATCTAATTTTAGT-GAAA-AAATATTTAAATTTATATTTTTGGGCTAAAAGTGGATAACAAT
62 AAAAT-TAATTTTAATAAAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTGGATAACAAT
* * *
643712 ATATAAATTTTAATTTTTAAATAAAGAATAATAATGAA-AAA-A-AATTATATTTCAATATTCAC
126 ATACAAATTTTAATTTTTAAATAAA-AATAATAAT-AATAAAGATAATTATAGTTCAAAATTCAC
* *
643774 ATAGATAAGCCTTGAAATAAAACTATAACAATTGACGTAAAAACTTATAAATGTGGAATAACTAA
189 ATAGATAAACCTTG-AATAAAACTATAACAATTGACGTAAAAACTTATAAAAGTGGAATAACTAA
* * * * ** *
643839 ATTTTAAATTTTAACGTAAATATTTAAAAGTTTATGTAATAAGTTAATTAAG-AAAAAAATTTAA
253 ATTTTAAATCTTAACATAAATATGTAAAAG-TAACATAACAAGTTAATTAAGTAAAAAAATTTAA
* * * *** ** *
643903 TTTTAATGAAAAATAAATATTTTTATTTATATTATCGGGTTAAAAGTATGTAATGATTTTCAAAT
317 TTTTAACGAAAAATAAACATTTATATTTATATTATCAAATTAAAAGTATGTAACAATTATCAAAT
* *
643968 TTTTACTTTTAAATAAAGAATAATAAGGATAAAAATAATTATCATTCAAAATTGACATAAAAAAG
382 TTTAACTTTTAAATAAAGAATAATAAGAATAAAAATAATTATCATTCAAAATTGACATAAAAAAG
* * * *
644033 TCTTGACGTAAAACTATAAGAATTGAAGTAAAAATTTATAAAAGTGGAATAACTAAATTTTAAAT
447 CCTTGACGTAAAACTATAAGAATTGAAGTAAAAACTTATAAAAGTAGAATAACAAAATTTTAAAT
* * * * * * * *
644098 ATTAACGTAAATATGTAAGAGTTAACGTAATAAGTTAATTACGTAAAAAAGTTTAATTTTAATGA
512 ATTAACATAAACATGTAACAGTTAACATAACAAGTCAATTAAGTAAAAAAATTTAATTTTAATGA
* * *
644163 AAAATAAGCATTTATATTTATATT
577 AAAACAAACATTTAAATTTATATT
644187 ATCGGGCTAA
Statistics
Matches: 499, Mismatches: 88, Indels: 26
0.81 0.14 0.04
Matches are distributed among these distances:
689 48 0.10
690 32 0.06
691 158 0.32
692 33 0.07
693 13 0.03
694 12 0.02
695 83 0.17
696 119 0.24
697 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (692 bp):
AATAACTAAATTGAAAATCTTAACGTAAATCTGTAAAAGTTAACGTAACAAATCATTTAAAAAAA
TTAATTTTAATAAAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTGGATAACAATATACA
AATTTTAATTTTTAAATAAAAATAATAATAATAAAGATAATTATAGTTCAAAATTCACATAGATA
AACCTTGAATAAAACTATAACAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAA
TCTTAACATAAATATGTAAAAGTAACATAACAAGTTAATTAAGTAAAAAAATTTAATTTTAACGA
AAAATAAACATTTATATTTATATTATCAAATTAAAAGTATGTAACAATTATCAAATTTTAACTTT
TAAATAAAGAATAATAAGAATAAAAATAATTATCATTCAAAATTGACATAAAAAAGCCTTGACGT
AAAACTATAAGAATTGAAGTAAAAACTTATAAAAGTAGAATAACAAAATTTTAAATATTAACATA
AACATGTAACAGTTAACATAACAAGTCAATTAAGTAAAAAAATTTAATTTTAATGAAAAACAAAC
ATTTAAATTTATATTCTTAAACTAAAAGTATTTAGCGATATATAAATTTTAATTTTTAAGTTTTG
ATGTATAACTGTAGCAATTGACGTAAAAACTTATAAAGATAA
Found at i:644105 original size:250 final size:250
Alignment explanation
Indices: 643557--645840 Score: 1943
Period size: 251 Copynumber: 9.3 Consensus size: 250
643547 TAACTGTAGC
** * *
643557 AATTGACGTAAAAACTTAT-AAAGATAAAATAACTAAATTTTAAATCTTAACGTAAATCTGTAAG
1 AATTGACGTAAAAACTTATAAAAG-TGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAG
* * * * *
643621 AGTTAACGTAACAAATCAATTAAGTAAAAAAATCTAATTTTAGT--GAAA-AAATATTTAAATTT
65 AGTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTT
* * *** * * *
643683 ATATTTTTGGGCTAAAAGTGGATAACAATATAT-AAATTTTAATTTTTAAATAAAGAATAATAAT
130 ATATTATAGGGCTAAAAGTATTTAACGAT-TTTCAAATTTTAATTTTTAAATAAA-AATAATAAG
* * * * * ** *
643747 GA-AAAAA-AATTATA-TTTCAATATTCACATAGATAAGCCTTGAAATAAAACTATAAC
193 GATAAAAATAATTATAGTTT-AAAATTGATATAGAAAAGTCTTGACGTAAAACTATAAG
* * * * * *
643803 AATTGACGTAAAAACTTATAAATGTGGAATAACTAAATTTTAAATTTTAACGTAAATATTTAAAA
1 AATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGA
* * * * **
643868 GTTTATGTAATAAGTTAATTAAG-AAAAAAATTTAATTTTAATGAAAAATAAATATTTTTATTTA
66 GTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTTA
* * * * * *
643932 TATTATCGGGTTAAAAGTATGTAATGATTTTCAAATTTTTACTTTTAAATAAAGAATAATAAGGA
131 TATTATAGGGCTAAAAGTATTTAACGATTTTCAAATTTTAATTTTTAAATAAA-AATAATAAGGA
* * *
643997 TAAAAATAATTATCA-TTCAAAATTGACATAAAAAAGTCTTGACGTAAAACTATAAG
195 TAAAAATAATTAT-AGTTTAAAATTGATATAGAAAAGTCTTGACGTAAAACTATAAG
* * * * *
644053 AATTGAAGTAAAAATTTATAAAAGTGGAATAACTAAATTTTAAATATTAACGTAAATATGTAAGA
1 AATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGA
* * * * ** *
644118 GTTAACGTAATAAGTTAATTACGTAAAAAAGTTTAATTTTAATGAAAAATAAGCATTTATATTTA
66 GTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTTA
* * * * * *
644183 TATTATCGGGCTAAATGTATGTAAC-AATATAATAATTTTAATTTTTAAATAAAAATAATAAGGA
131 TATTATAGGGCTAAAAGTATTTAACGATTTTCA-AATTTTAATTTTTAAATAAAAATAATAAGGA
* * * * * *
644247 TAAAAATAATTATGGTTTAAAATTAATATAGATAAGTCTTGATGTAAAACTGTAAA
195 TAAAAATAATTATAGTTTAAAATTGATATAGAAAAGTCTTGACGTAAAACTATAAG
* * * * *
644303 AATTGACCTAAAAATTTAT-AAAGTTGGAATAACTAAATTTTAAATCTTAACATAAACGTGTGAA
1 AATTGACGTAAAAACTTATAAAAG-TGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAG
** * * * *
644367 AGTTAACGTAACCAATCAATTAAGTAAAAAAAATCTAATTATAGT-AAAAATAAATATTTAAATT
65 AGTTAACGTAATAAATTAATTAAGT-AAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATT
* ** * * * ** *
644431 TATATTTTAGTCCTAAAAGTGTTTAATGATATGAAAATTTTAATTTTTAAATAAAAAAGAATAAG
129 TATATTATAGGGCTAAAAGTATTTAACGATTTTCAAATTTTAATTTTTAAAT-AAAAATAATAAG
* * * * * *
644496 GATTAAAATAATTATAGTTTAAAATAGACATAGAAAAATCTTGAAGTAAAATTATAAG
193 GATAAAAATAATTATAGTTTAAAATTGATATAGAAAAGTCTTGACGTAAAACTATAAG
* * * * * * * *
644554 AATTGACGTAAAAACTTAT-ATAGATGAAATAATTAAATTTCAAATCTTAACATAAATATATGGG
1 AATTGACGTAAAAACTTATAAAAG-TGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAG
* * * *
644618 AGTTAACATAATAAGTCAATTAAGTAAAAAAA-TTAATTTTATTAAAAAATAAATATTTAAATTT
65 AGTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTT
* * ** * *
644682 ATATTCTTGGAATAAAAGTATTTAACGATATACAAATTTTAA---TT---T-----T--TAA--A
130 ATATTATAGGGCTAAAAGTATTTAACGATTTTCAAATTTTAATTTTTAAATAAAAATAATAAGGA
* * * *
644732 TAAAAATAATTATAGTTTAAAATTTATATAGATAAG-CTTTGACATAAAACTGTAAG
195 TAAAAATAATTATAGTTTAAAATTGATATAGAAAAGTC-TTGACGTAAAACTATAAG
* * *
644788 AATTGACGTAAAAACTTATAAAGGTAGAATAACTAAATTTTAAATCTTAACGAAAATGTGTGAGA
1 AATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGA
* * ** *
644853 GTTAACGTAATAAATTAATTAAGTGAAAAAGTTTAATTTTAATAAAAAATAAGCATTTATATTTA
66 GTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTTA
* * * * *
644918 TATTATCGAGCTAAAAATATATAAC-AGTATAT-AAATTTTAA-TTTT---T----A-AAT----
131 TATTATAGGGCTAAAAGTATTTAACGA-T-TTTCAAATTTTAATTTTTAAATAAAAATAATAAGG
* * *
644968 AT--AAATAATTATAGTTTAAAATTGATATAGATAAGTCTTAACGTAAAACTGTAAG
194 ATAAAAATAATTATAGTTTAAAATTGATATAGAAAAGTCTTGACGTAAAACTATAAG
* * * * *
645023 AACTGACGTAAAAACTTATAAAAATAGAATAACTAAATTTTAAATC-T----TAAACGTGTAAGA
1 AATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGA
* * * * *
645083 GTTAACATAACAAATCAATTAAGTAAAAAAAATTTAATTTTAGTAAAAAATTAATATTTAAATTT
66 GTTAACGTAATAAATTAATTAAGT-AAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTT
* * * * *
645148 ATA-TACTAGGACTAAAAGTATTTAACGATATACAAATTTTAATCTTTAAATAAAGAATAATAAT
130 ATATTA-TAGGGCTAAAAGTATTTAACGATTTTCAAATTTTAATTTTTAAATAAA-AATAATAAG
* * *
645212 GATAAAAATAATTATAGTTTAAAATGGATATAGAAAAGTCTTGATC-TAAAATTGTAAG
193 GATAAAAATAATTATAGTTTAAAATTGATATAGAAAAGTCTTGA-CGTAAAACTATAAG
* * * * * * *
645270 AATTGAAGTAAAAATTTAT-AAAGATGAAATAATTAAATTTCAAATCCTAACATAAATGTGTGAG
1 AATTGACGTAAAAACTTATAAAAG-TGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAG
* * * * *
645334 AGTTAACATAACAAATCT-ATTAAGTAAAAAAATCTAACTTTATTAAAAAATAAATATTTAAATT
65 AGTTAACGTAATAAAT-TAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATT
* * ** * * * * * *
645398 TATATTCTTGGAATAAAAGTATTTAAAGATATACAAATTTTAATTTTTAAATAAAAAATTATTAT
129 TATATTATAGGGCTAAAAGTATTTAACGATTTTCAAATTTTAATTTTTAAAT-AAAAATAATAAG
* ** * * * *
645463 AATAAAAATAATTATAACTCAAAATTGGA-ATA-AATAAATCTTGATGTAAAACTATAAC
193 GATAAAAATAATTATAGTTTAAAATT-GATATAGAA-AAGTCTTGACGTAAAACTATAAG
* * *
645521 AATTGACGTAAAAACTTTATAAAGGTAGAATAACTAAATTTTAAATCTTAACATAAATGTGTGAG
1 AATTGACGTAAAAAC-TTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAG
* * ** *
645586 AGTTAACGTAATAAGTTAATTAAGTAAAAAAATATAATTTTAATAAAAAATAAGCATTTATATTT
65 AGTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTT
* * * *
645651 ATATTATAGAGTTAAAAGTATATAACGATATTT-AAATTTTTA-TTTTAAAT-AAAA-AAT-A--
130 ATATTATAGGGCTAAAAGTATTTAACGAT-TTTCAAATTTTAATTTTTAAATAAAAATAATAAGG
* ** * ** * *
645709 ATAAAGATAATTATAG-TTAAAAGTT-ACTATTA-AAAAAACTTGACATAAAGTTGTAAA
194 ATAAAAATAATTATAGTTTAAAA-TTGA-TA-TAGAAAAGTCTTGACGTAAAACTATAAG
* * * * * * * * *
645766 AATTAACGTAAAATCTTATAAAAGTGAAATAACCAAAATTAAAATCTTAACGTAAATATGTAAAA
1 AATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGA
645831 GTTAACGTAA
66 GTTAACGTAA
645841 CAAGTGATAA
Statistics
Matches: 1675, Mismatches: 295, Indels: 138
0.79 0.14 0.07
Matches are distributed among these distances:
230 33 0.02
231 61 0.04
232 4 0.00
233 1 0.00
234 124 0.07
235 151 0.09
236 4 0.00
237 5 0.00
239 1 0.00
240 1 0.00
241 3 0.00
243 1 0.00
244 56 0.03
245 65 0.04
246 79 0.05
247 92 0.05
248 67 0.04
249 21 0.01
250 361 0.22
251 379 0.23
252 162 0.10
253 4 0.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (250 bp):
AATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGA
GTTAACGTAATAAATTAATTAAGTAAAAAAATTTAATTTTAATAAAAAATAAATATTTAAATTTA
TATTATAGGGCTAAAAGTATTTAACGATTTTCAAATTTTAATTTTTAAATAAAAATAATAAGGAT
AAAAATAATTATAGTTTAAAATTGATATAGAAAAGTCTTGACGTAAAACTATAAG
Found at i:644414 original size:20 final size:19
Alignment explanation
Indices: 644380--644421 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
644370 TAACGTAACC
644380 AATCAATTAAGTAAAAA-A
1 AATCAATTAAGTAAAAATA
644398 AATCTAATTATAGTAAAAATA
1 AATC-AATTA-AGTAAAAATA
644419 AAT
1 AAT
644422 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 8 0.38
21 4 0.19
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (19 bp):
AATCAATTAAGTAAAAATA
Found at i:645909 original size:29 final size:28
Alignment explanation
Indices: 645877--645956 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
645867 ATTAATTAAT
*
645877 TAATTATA-ATTTTAATATTAAAAAAATAA
1 TAATTATATATTTTAA-AAT-AAAAAATAA
645906 TAATCT-TATATTTTAAAATAAAAAATAA
1 TAAT-TATATATTTTAAAATAAAAAATAA
*
645934 -AATTAAATAACTTTTAAAATAAA
1 TAATTATAT-A-TTTTAAAATAAA
645957 TTAAATGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 10 0.23
29 20 0.45
30 8 0.18
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (28 bp):
TAATTATATATTTTAAAATAAAAAATAA
Found at i:645973 original size:21 final size:22
Alignment explanation
Indices: 645926--645974 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
645916 TTTTAAAATA
645926 AAAAATAAAATTAAATAACTTT
1 AAAAATAAAATTAAATAACTTT
*
645948 TAAAAT-AAATTAAATGAA-TTT
1 AAAAATAAAATTAAAT-AACTTT
645969 AAAAAT
1 AAAAAT
645975 TATCTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATAAAATTAAATAACTTT
Found at i:646645 original size:2 final size:2
Alignment explanation
Indices: 646638--646668 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
646628 AAGGAAACCT
*
646638 TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
646669 GCCCCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:648083 original size:2 final size:2
Alignment explanation
Indices: 648078--648106 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
648068 CAAAAAAAAT
648078 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
648107 AAGAATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:654164 original size:5 final size:5
Alignment explanation
Indices: 654151--654193 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
654141 TTTTCGTCAC
* * * *
654151 TTTCC TTTCT TTTCT TTTCT TTTTT TTTTT TTTCT CTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
654194 ATGGATGGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:656492 original size:16 final size:16
Alignment explanation
Indices: 656471--656503 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
656461 CTATGAAAAT
656471 ACTAGAGACAATGAGC
1 ACTAGAGACAATGAGC
656487 ACTAGAGACAATGAGC
1 ACTAGAGACAATGAGC
656503 A
1 A
656504 TAAAAAAAGA
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:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
ACTAGAGACAATGAGC
Found at i:666771 original size:34 final size:34
Alignment explanation
Indices: 666699--666763 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
666689 TTGCTTTTAT
* *
666699 AAAAAGGCATTATGAAGGTTGTGCTTGAGCCCAA
1 AAAAAGGCATTATGAAGGTTATACTTGAGCCCAA
*
666733 AAAAAGGCATTGTGAAGGTTATACTTGAGCC
1 AAAAAGGCATTATGAAGGTTATACTTGAGCC
666764 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (34 bp):
AAAAAGGCATTATGAAGGTTATACTTGAGCCCAA
Found at i:667128 original size:27 final size:27
Alignment explanation
Indices: 667098--667200 Score: 89
Period size: 27 Copynumber: 3.8 Consensus size: 27
667088 CCTAAGGGTA
*
667098 TTCCAAGTGTAGAAATGCCCAAAGGTG
1 TTCCAAGTATAGAAATGCCCAAAGGTG
* ** **
667125 TTCCTAGTATAGAAGCGCCCAGGGGTG
1 TTCCAAGTATAGAAATGCCCAAAGGTG
* * ** *
667152 TTCCTAGTACAGAAGGGCCCAAAGGCG
1 TTCCAAGTATAGAAATGCCCAAAGGTG
* *
667179 TTCCAAGCATGGAAATGCCCAA
1 TTCCAAGTATAGAAATGCCCAA
667201 GGGCATTCCC
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.19
Consensus pattern (27 bp):
TTCCAAGTATAGAAATGCCCAAAGGTG
Found at i:667370 original size:27 final size:27
Alignment explanation
Indices: 667340--667401 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
667330 GCCCAAGGGC
* *
667340 GTTCCAAGCACAGAAATGCTTAGGGAT
1 GTTCCAAGCACAGAAATGCCTAGAGAT
*
667367 GTTCCAAGCGCAGAAATGCCTAGAGAT
1 GTTCCAAGCACAGAAATGCCTAGAGAT
*
667394 ATTCCAAG
1 GTTCCAAG
667402 TGTAGAAGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
GTTCCAAGCACAGAAATGCCTAGAGAT
Found at i:668764 original size:52 final size:52
Alignment explanation
Indices: 668505--668765 Score: 283
Period size: 52 Copynumber: 5.0 Consensus size: 52
668495 ATATTACACT
* * * * * *
668505 ATTGGCCGTAAGCTTTATCACTCACTTCTTGGACACAGTTTGCTATTTACAT
1 ATTGGCTGCAAGCTTTATCACTCACTTCTTGGCCATAGTTTGCTATTCACAA
* * * * * *
668557 ATTGGCAGTAAGCTTTATTACTCACTTTTTGGCTATAGTTTACTATTCACAA
1 ATTGGCTGCAAGCTTTATCACTCACTTCTTGGCCATAGTTTGCTATTCACAA
* ** * *
668609 ATTGGCTGCCAA--TTTAATCGCTCACTTCTTGGTTATAGTTTGCTATCCACAT
1 ATTGGCTG-CAAGCTTT-ATCACTCACTTCTTGGCCATAGTTTGCTATTCACAA
* * *
668661 ATTGGCTACAAGCTTAATCACTCACTTCTTGGTCATAGTTTGCTATTCACAA
1 ATTGGCTGCAAGCTTTATCACTCACTTCTTGGCCATAGTTTGCTATTCACAA
* * *
668713 ATTAGCTGCAAGCTTTATCACTCACTTCTTAGCCATGGTTTGCTATTCACAA
1 ATTGGCTGCAAGCTTTATCACTCACTTCTTGGCCATAGTTTGCTATTCACAA
668765 A
1 A
668766 AAGGCCGCAG
Statistics
Matches: 175, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
51 6 0.03
52 165 0.94
53 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (52 bp):
ATTGGCTGCAAGCTTTATCACTCACTTCTTGGCCATAGTTTGCTATTCACAA
Found at i:668787 original size:104 final size:104
Alignment explanation
Indices: 668576--668788 Score: 227
Period size: 104 Copynumber: 2.0 Consensus size: 104
668566 AAGCTTTATT
* * * *
668576 ACTCACTTTTTGGCTATAGTTTACTATTCACAAATTGGCTGCCAATTTAATCGCTCACTTCTTGG
1 ACTCACTTCTTGGCTATAGTTTACTATTCACAAATTAGCTGCCAATTTAATCACTCACTTCTTAG
** * ** * *
668641 TTATAGTTTGCTATCCACATATTGGCTACAAGCTTAATC
66 CCATAGTTTGCTATCCACAAAAAGGCCACAAGCTTAAAC
*
668680 ACTCACTTCTTGG-TCATAGTTTGCTATTCACAAATTAGCTG-CAAGCTTT-ATCACTCACTTCT
1 ACTCACTTCTTGGCT-ATAGTTTACTATTCACAAATTAGCTGCCAA--TTTAATCACTCACTTCT
* * *
668742 TAGCCATGGTTTGCTATTCACAAAAAGGCCGC-AGCATTAAAC
63 TAGCCATAGTTTGCTATCCACAAAAAGGCCACAAGC-TTAAAC
668784 ACTCA
1 ACTCA
668789 TGTAATATGT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
103 7 0.08
104 80 0.89
105 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (104 bp):
ACTCACTTCTTGGCTATAGTTTACTATTCACAAATTAGCTGCCAATTTAATCACTCACTTCTTAG
CCATAGTTTGCTATCCACAAAAAGGCCACAAGCTTAAAC
Found at i:673600 original size:18 final size:19
Alignment explanation
Indices: 673579--673614 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
673569 TTTATTGCCC
673579 GCAACACATCTT-TCTCAA
1 GCAACACATCTTGTCTCAA
*
673597 GCAACCCATCTTGTCTCA
1 GCAACACATCTTGTCTCA
673615 CTCTTGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (19 bp):
GCAACACATCTTGTCTCAA
Found at i:682391 original size:109 final size:112
Alignment explanation
Indices: 682143--682460 Score: 326
Period size: 112 Copynumber: 2.9 Consensus size: 112
682133 CCTTGAACAG
* * * * * * * *
682143 GTCTTTTTACCATGGTGGAAAATACAATTTGAATAGGA-CTGTAACTCTGCCAATCAAAATATAT
1 GTCTTTTTACCATGGTGGAAAGTACAATTTG-A-ACGATTTGTGATTCTACCAACCAAAACATAT
* ** * * *
682207 TTTGTCGTTACAAAACTT-TTTTGGTTTTTGA-TTTTTTCATTGACCAA
64 TGTAACATTACAAAACTTGATTTGGTCTTTGATTTTTTTCATTGACCAA
* *
682254 GTCTTTTTACCATGGTGGAAAGTACAATTT-AA-GGTTTGTGATTCTACCAACCAAAATATATTG
1 GTCTTTTTACCATGGTGGAAAGTACAATTTGAACGATTTGTGATTCTACCAACCAAAACATATTG
*
682317 TAATATTACAAAACTTGATTTGGTCTTTGATTTTTTTCATTGACC-A
66 TAACATTACAAAACTTGATTTGGTCTTTGATTTTTTTCATTGACCAA
* *** * *
682363 TTCTTTTTATTGTGGTGGGAAA-TGCAATTTGAATCGATTTGTGATTCTACCGACCAAAACATAT
1 GTCTTTTTACCATGGT-GGAAAGTACAATTTGAA-CGATTTGTGATTCTACCAACCAAAACATAT
* *
682427 TTTACCATTACAAAACTTGATTTGGTCTTTGATT
64 TGTAACATTACAAAACTTGATTTGGTCTTTGATT
682461 CAGAACAAAC
Statistics
Matches: 175, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
107 1 0.01
108 35 0.20
109 32 0.18
110 21 0.12
111 29 0.17
112 57 0.33
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (112 bp):
GTCTTTTTACCATGGTGGAAAGTACAATTTGAACGATTTGTGATTCTACCAACCAAAACATATTG
TAACATTACAAAACTTGATTTGGTCTTTGATTTTTTTCATTGACCAA
Found at i:687673 original size:18 final size:19
Alignment explanation
Indices: 687646--687690 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
687636 ATCATCACTA
* *
687646 ACATGGCACTT-TGTGATG
1 ACATGACACTTATCTGATG
687664 ACATGACACTTATCTGATG
1 ACATGACACTTATCTGATG
*
687683 ACGTGACA
1 ACATGACA
687691 TGCCACATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (19 bp):
ACATGACACTTATCTGATG
Found at i:687793 original size:13 final size:12
Alignment explanation
Indices: 687772--687796 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
687762 ATAACAAATC
687772 AAAAATTTTTTT
1 AAAAATTTTTTT
687784 AAAAATTTTTTT
1 AAAAATTTTTTT
687796 A
1 A
687797 TGTCATGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAAAATTTTTTT
Found at i:688533 original size:15 final size:15
Alignment explanation
Indices: 688509--688538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
688499 AAATGCAGTC
*
688509 TTTAATCTAAAAAAT
1 TTTAACCTAAAAAAT
688524 TTTAACCTAAAAAAT
1 TTTAACCTAAAAAAT
688539 ATAACATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAACCTAAAAAAT
Found at i:689164 original size:31 final size:29
Alignment explanation
Indices: 689090--689171 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 29
689080 TATGTTTCAA
*
689090 ATATTTTTTTCAATTTAGTCTCTCAACAT
1 ATATTTTTTTCAATTTAATCTCTCAACAT
* *
689119 CTCAATTTTGTTCAATTTAATCTCT-ATACAAT
1 AT--ATTTTTTTCAATTTAATCTCTCA-AC-AT
689151 ATATTTTTCTTCAATTTAATC
1 ATATTTTT-TTCAATTTAATC
689172 GTTATGACGT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.02
30 6 0.14
31 33 0.77
32 3 0.07
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATTTTTTTCAATTTAATCTCTCAACAT
Found at i:692129 original size:34 final size:34
Alignment explanation
Indices: 692085--692153 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
692075 GAGTTAGAAA
*
692085 AAGGTTAATTAGCTCATTCAGTGTGAGAGTATTT
1 AAGGTCAATTAGCTCATTCAGTGTGAGAGTATTT
692119 AAGGTCAATTAGCTCATTCAGTGTGAGAGTATTT
1 AAGGTCAATTAGCTCATTCAGTGTGAGAGTATTT
692153 A
1 A
692154 GATTCTTCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.36
Consensus pattern (34 bp):
AAGGTCAATTAGCTCATTCAGTGTGAGAGTATTT
Found at i:697017 original size:17 final size:17
Alignment explanation
Indices: 696994--697051 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
696984 AGAATCCCAA
696994 ACTAAATAAAATAAAAT
1 ACTAAATAAAATAAAAT
* * *
697011 CCTAAATCAACTAAAAT
1 ACTAAATAAAATAAAAT
* *
697028 AATAAATAAAATAGAAT
1 ACTAAATAAAATAAAAT
*
697045 TCTAAAT
1 ACTAAAT
697052 GCACCAACAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (17 bp):
ACTAAATAAAATAAAAT
Found at i:699569 original size:8 final size:8
Alignment explanation
Indices: 699556--699613 Score: 82
Period size: 8 Copynumber: 7.2 Consensus size: 8
699546 TAGGCCAATT
*
699556 CTTTCTCC
1 CTTTCTTC
699564 CTTTCTTC
1 CTTTCTTC
699572 CTTTC-TC
1 CTTTCTTC
*
699579 CTTTCTTT
1 CTTTCTTC
699587 CTTTCTTC
1 CTTTCTTC
699595 CTTTCTTC
1 CTTTCTTC
699603 CTTTGCTTC
1 CTTT-CTTC
699612 CT
1 CT
699614 AACCAAATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.16
8 32 0.71
9 6 0.13
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (8 bp):
CTTTCTTC
Found at i:699582 original size:23 final size:24
Alignment explanation
Indices: 699556--699606 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
699546 TAGGCCAATT
699556 CTTTCTCCCTTTCTTCCTTTC-TC
1 CTTTCTCCCTTTCTTCCTTTCTTC
**
699579 CTTTCTTTCTTTCTTCCTTTCTTC
1 CTTTCTCCCTTTCTTCCTTTCTTC
699603 CTTT
1 CTTT
699607 GCTTCCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (24 bp):
CTTTCTCCCTTTCTTCCTTTCTTC
Found at i:699659 original size:24 final size:24
Alignment explanation
Indices: 699604--699661 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
699594 CCTTTCTTCC
*
699604 TTTGCTTCCTAACCAAATCTCTCT
1 TTTGCTTTCTAACCAAATCTCTCT
*
699628 TTTGCTTTCTAGCCAAATCTCTCT
1 TTTGCTTTCTAACCAAATCTCTCT
699652 TTTGCTTTCT
1 TTTGCTTTCT
699662 CAAAAGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.48
Consensus pattern (24 bp):
TTTGCTTTCTAACCAAATCTCTCT
Found at i:699977 original size:21 final size:21
Alignment explanation
Indices: 699939--699978 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
699929 TGAATTTGCC
699939 AAATCCCAAACAACCTTAATT
1 AAATCCCAAACAACCTTAATT
*
699960 AAATCTCCAACCAA-CTTAA
1 AAATC-CCAAACAACCTTAA
699979 GCTCAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCCAAACAACCTTAATT
Found at i:703496 original size:19 final size:19
Alignment explanation
Indices: 703447--703494 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
703437 TTAATATTTT
703447 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
703466 AATATTATTTTATTTA-AA
1 AATATTATTTTATTCATAA
*
703484 AATATTCTTTT
1 AATATTATTTT
703495 TACTTGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:727932 original size:91 final size:93
Alignment explanation
Indices: 727805--727992 Score: 263
Period size: 91 Copynumber: 2.0 Consensus size: 93
727795 AAAACTGCCT
*
727805 CATATCTGACTATAAGAAAATAGGTTAGATAAAATAAATG-TCCATAATTTAGCCATGAA-TTTT
1 CATATCTGACTATAAGAAAACAGGTTAGATAAAATAAATGCTCCATAATTTAGCCATGAACTTTT
* *
727868 AATTACTTCCCAACATAAATAAAGGCTG
66 AATTACTACCCAACACAAATAAAGGCTG
* * *
727896 CATATCTGACTGTAAGATAACAGGTTAGATAGAATAAATGTCCTCCATAATTTAGCCATGAACTT
1 CATATCTGACTATAAGAAAACAGGTTAGATAAAATAAATG--CTCCATAATTTAGCCATGAACTT
** *
727961 TTAATTACTACCCAGGACAAATGAAGGCTG
64 TTAATTACTACCCAACACAAATAAAGGCTG
727991 CA
1 CA
727993 ACCTATGGGT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
91 36 0.43
94 19 0.23
95 29 0.35
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (93 bp):
CATATCTGACTATAAGAAAACAGGTTAGATAAAATAAATGCTCCATAATTTAGCCATGAACTTTT
AATTACTACCCAACACAAATAAAGGCTG
Found at i:739968 original size:85 final size:85
Alignment explanation
Indices: 739845--740093 Score: 374
Period size: 85 Copynumber: 2.9 Consensus size: 85
739835 AATATCAATG
* * * *
739845 TTTAATTCTAGCATATTGCCAATCATTTTAATTAAAAATTCAAAAAATAATTCTCAACATTAATT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATTCAAACAATAATTCTAAACATTAATT
*
739910 CCCAAACATAATTTTTAATA
66 CCCAAACATAATTCTTAATA
* *
739930 TTTAATTCTAACATATTATCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATTAATT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATTCAAACAATAATTCTAAACATTAATT
* *
739995 CTCAAACATAATTCTTAATG
66 CCCAAACATAATTCTTAATA
* * *
740015 TTTAATTCTAACATATTACCAATCATTTTAATT-AAAACTCAAACAATGATTCTAAATATTAATT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATTCAAACAATAATTCTAAACATTAATT
*
740079 CCTAAACATAATTCT
66 CCCAAACATAATTCT
740094 AGCATCAAAT
Statistics
Matches: 148, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
84 40 0.27
85 108 0.73
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.39
Consensus pattern (85 bp):
TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATTCAAACAATAATTCTAAACATTAATT
CCCAAACATAATTCTTAATA
Found at i:739993 original size:13 final size:13
Alignment explanation
Indices: 739970--740009 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
739960 ATTAAAAATC
739970 CAAACAATAATTCT
1 CAAAC-ATAATTCT
739984 -AAACATTAATTCT
1 CAAACA-TAATTCT
739997 CAAACATAATTCT
1 CAAACATAATTCT
740010 TAATGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 18 0.75
14 5 0.21
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (13 bp):
CAAACATAATTCT
Found at i:755337 original size:71 final size:71
Alignment explanation
Indices: 755195--755341 Score: 167
Period size: 71 Copynumber: 2.1 Consensus size: 71
755185 ATAAATATGA
* * *
755195 AATTTGTAGGCAACATGTGCTAGTAGTTGGTTTTTCGATTTTCCTTTTCTTGTTCTTGGTGTCCA
1 AATTTGTAGACAACATGTGCTAGTAGTTGGCTTTTCGATTTTCCTCTTCTTGTTCTTGGTGTCCA
755260 TAGTTG
66 TAGTTG
* * *
755266 AGATTTGTAGACAACCTGTGCT-GTTTGTTGGCTTTT-GATTTTCCTCTTGTTG-TCATCT-GTG
1 A-ATTTGTAGACAACATGTGCTAG-TAGTTGGCTTTTCGATTTTCCTCTTCTTGTTC-T-TGGTG
*
755327 TCCATGGTTG
62 TCCATAGTTG
755337 AATTT
1 AATTT
755342 ACTTTTGCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
70 6 0.09
71 30 0.46
72 29 0.45
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (71 bp):
AATTTGTAGACAACATGTGCTAGTAGTTGGCTTTTCGATTTTCCTCTTCTTGTTCTTGGTGTCCA
TAGTTG
Found at i:760100 original size:22 final size:22
Alignment explanation
Indices: 760075--760116 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
760065 TTAATTAAAT
*
760075 AATTTAATTAATTAAGTTTAGC
1 AATTTAATTAAATAAGTTTAGC
*
760097 AATTTAATTAAATAATTTTA
1 AATTTAATTAAATAAGTTTA
760117 ATCAATNNNN
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTTAATTAAATAAGTTTAGC
Found at i:760183 original size:14 final size:14
Alignment explanation
Indices: 760164--760190 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
760154 TCAATTATTA
760164 AAATAACTTAATTT
1 AAATAACTTAATTT
760178 AAATAACTTAATT
1 AAATAACTTAATT
760191 ATTTAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAACTTAATTT
Found at i:760194 original size:17 final size:17
Alignment explanation
Indices: 760156--760196 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 17
760146 AAATTTAATC
*
760156 AATTATTAAAATAACTT
1 AATTATTTAAATAACTT
760173 -A--ATTTAAATAACTT
1 AATTATTTAAATAACTT
760187 AATTATTTAA
1 AATTATTTAA
760197 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 1 0.05
17 6 0.30
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATTTAAATAACTT
Found at i:766428 original size:54 final size:53
Alignment explanation
Indices: 766364--766550 Score: 178
Period size: 57 Copynumber: 3.3 Consensus size: 53
766354 TCTTATCTTT
* *
766364 AATTAAGACAAAATGTTTTATCTTGTCTAAATTGAGACAAATATGTTTTGTCTA
1 AATTAAGACAAAATGTTTT-TCTTGTCTAAATTAAGACAAATATGTTTTCTCTA
* * * *
766418 GATTAAGACAAAATATTTTTCTTGTCTTAAATTAAGGCAAATATATTTTCTTCTCTA
1 AATTAAGACAAAATGTTTTTCTTGTC-TAAATTAAGAC-AA-ATATGTT-TTCTCTA
* *
766475 AATTAAGACCAAACATG-ATTTCTTGTCTAAATTAAGACATAATATGATTTTTTATCTA
1 AATTAAGA-CAAA-ATGTTTTTCTTGTCTAAATTAAGACA-AATATG---TTTTCTCTA
*
766533 AATTAACACAAACATGTT
1 AATTAAGACAAA-ATGTT
766551 AAAATTGTCA
Statistics
Matches: 108, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
53 7 0.06
54 26 0.24
55 2 0.02
56 11 0.10
57 32 0.30
58 26 0.24
59 4 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (53 bp):
AATTAAGACAAAATGTTTTTCTTGTCTAAATTAAGACAAATATGTTTTCTCTA
Found at i:766453 original size:29 final size:29
Alignment explanation
Indices: 766364--766544 Score: 164
Period size: 29 Copynumber: 6.4 Consensus size: 29
766354 TCTTATCTTT
*
766364 AATTAAGACAAAATGT-TTTATCTTGTCTA
1 AATTAAGACAAAATATATTT-TCTTGTCTA
* *
766393 AATTGAGAC--AA-ATATGTT-TTGTCTA
1 AATTAAGACAAAATATATTTTCTTGTCTA
*
766418 GATTAAGACAAAATAT-TTTTCTTGTCTTA
1 AATTAAGACAAAATATATTTTCTTGTC-TA
* *
766447 AATTAAGGC-AAATATATTTTCTTCTCTA
1 AATTAAGACAAAATATATTTTCTTGTCTA
* *
766475 AATTAAGACCAAACATGA-TTTCTTGTCTA
1 AATTAAGACAAAATAT-ATTTTCTTGTCTA
* *
766504 AATTAAGACATAATATGATTTT-TTATCTA
1 AATTAAGACAAAATAT-ATTTTCTTGTCTA
*
766533 AATTAACACAAA
1 AATTAAGACAAA
766545 CATGTTAAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
25 14 0.11
26 2 0.02
27 9 0.07
28 23 0.19
29 72 0.58
30 4 0.03
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (29 bp):
AATTAAGACAAAATATATTTTCTTGTCTA
Found at i:766533 original size:58 final size:57
Alignment explanation
Indices: 766384--766548 Score: 180
Period size: 57 Copynumber: 2.9 Consensus size: 57
766374 AAATGTTTTA
* * * * * *
766384 TCTTGTCTAAATTGAGACAAATATG---TTTTGTCTAGATTAAGACAAAATAT-TTT
1 TCTTGTCTAAATTAAGACAAATATGATTTTTTATCTAAATTAAGACCAAACATGATT
* *
766437 TCTTGTCTTAAATTAAGGCAAATAT-ATTTTCTTCTCTAAATTAAGACCAAACATGATT
1 TCTTGTC-TAAATTAAGACAAATATGATTTT-TTATCTAAATTAAGACCAAACATGATT
*
766495 TCTTGTCTAAATTAAGACATAATATGATTTTTTATCTAAATTAACA-CAAACATG
1 TCTTGTCTAAATTAAGACA-AATATGATTTTTTATCTAAATTAAGACCAAACATG
766549 TTAAAATTGT
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
53 7 0.07
54 15 0.16
56 2 0.02
57 38 0.40
58 27 0.29
59 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (57 bp):
TCTTGTCTAAATTAAGACAAATATGATTTTTTATCTAAATTAAGACCAAACATGATT
Found at i:769863 original size:15 final size:15
Alignment explanation
Indices: 769845--769874 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
769835 GGCCCTATCT
769845 TTACAAACCCTTTCC
1 TTACAAACCCTTTCC
*
769860 TTACAAATCCTTTCC
1 TTACAAACCCTTTCC
769875 ATTTCTCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
TTACAAACCCTTTCC
Found at i:772779 original size:21 final size:19
Alignment explanation
Indices: 772753--772793 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
772743 AATTTAAAAC
772753 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
772774 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
772793 A
1 A
772794 CTTAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:774206 original size:58 final size:58
Alignment explanation
Indices: 774098--774210 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
774088 CATCTTAGCA
* ** *
774098 TGCATAGCATTGATTAAATTACATAAAATAAATCTATTATGTGCATACTACTTTGCAT
1 TGCATAGCATTGATTAAATTACATAAAATAAATCTATCACATGCAAACTACTTTGCAT
* * ** *
774156 TGCATAGTATTTATTAAATTGTATAAAATAAATCTATCGCATGCAAACTACTTTG
1 TGCATAGCATTGATTAAATTACATAAAATAAATCTATCACATGCAAACTACTTTG
774211 GATGATTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (58 bp):
TGCATAGCATTGATTAAATTACATAAAATAAATCTATCACATGCAAACTACTTTGCAT
Found at i:777533 original size:3 final size:3
Alignment explanation
Indices: 777527--777561 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
777517 TTATTAGACC
777527 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
777562 TTTTGTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:777611 original size:18 final size:18
Alignment explanation
Indices: 777578--777612 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
777568 AATAGATAAT
*
777578 ATTATATAAATGTATATC
1 ATTATATAAATATATATC
*
777596 ATTATATAATTATATAT
1 ATTATATAAATATATAT
777613 GTATTAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTATATAAATATATATC
Found at i:778569 original size:12 final size:12
Alignment explanation
Indices: 778532--778566 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
778522 GATTCCTTAC
778532 TTAGTGACAAAA
1 TTAGTGACAAAA
*
778544 TTAGTGACGAAA
1 TTAGTGACAAAA
778556 TT-GTGACAAAA
1 TTAGTGACAAAA
778567 ATTTAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (12 bp):
TTAGTGACAAAA
Found at i:785096 original size:30 final size:30
Alignment explanation
Indices: 785062--785136 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
785052 ATATCTTAAT
785062 TGAAGATGAAGAAGATGACATGCAAAGAGA
1 TGAAGATGAAGAAGATGACATGCAAAGAGA
** * *
785092 TGAAGATTCAGAAGATGACATGGAAGGAGA
1 TGAAGATGAAGAAGATGACATGCAAAGAGA
785122 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
785137 AAAAGATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.48, C:0.05, G:0.32, T:0.15
Consensus pattern (30 bp):
TGAAGATGAAGAAGATGACATGCAAAGAGA
Found at i:785132 original size:15 final size:15
Alignment explanation
Indices: 785062--785148 Score: 63
Period size: 15 Copynumber: 5.8 Consensus size: 15
785052 ATATCTTAAT
785062 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
*
785077 TG-ACATGCAA-AGAGA
1 TGAAGATG-AAGA-AGA
**
785092 TGAAGATTCAGAAGA
1 TGAAGATGAAGAAGA
* *
785107 TG-ACATGGAAGGAGA
1 TGAAGAT-GAAGAAGA
785122 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
**
785137 AAAAGATGAAGA
1 TGAAGATGAAGA
785149 CGAAGATGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.15
15 39 0.72
16 7 0.13
ACGTcount: A:0.51, C:0.05, G:0.31, T:0.14
Consensus pattern (15 bp):
TGAAGATGAAGAAGA
Found at i:790097 original size:2 final size:2
Alignment explanation
Indices: 790090--790121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
790080 TAATGACTAC
790090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
790122 GCATGCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:790895 original size:15 final size:15
Alignment explanation
Indices: 790862--790909 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
790852 GATTGAAAAC
*
790862 GAAAAAGATGACA-TG
1 GAAAAAGATGA-AGTA
790877 GAAAAAGATGAAGTA
1 GAAAAAGATGAAGTA
* *
790892 GAAATAGATGAAGAA
1 GAAAAAGATGAAGTA
790907 GAA
1 GAA
790910 CTTAAAGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.12
Consensus pattern (15 bp):
GAAAAAGATGAAGTA
Found at i:791453 original size:111 final size:110
Alignment explanation
Indices: 791145--791465 Score: 543
Period size: 110 Copynumber: 2.9 Consensus size: 110
791135 GTTAGTATGG
* * * * * * *
791145 CATGTTTTTGTTAACAGTTTTTATTGCAAACATGTATGGGAATTAGTCTTGATTCTTACACTTTG
1 CATGTTCTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATATTTTG
791210 ATGATGATTTTGATAATTTGTTTCAATTTCTTTTATCATGGCTTC
66 ATGATGATTTTGATAATTTGTTTCAATTTCTTTTATCATGGCTTC
791255 CATGTTCTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATATTTTG
1 CATGTTCTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATATTTTG
791320 ATGATGATTTTGATAATTTGTTTCAATTTCTTTTATCATGGCTTC
66 ATGATGATTTTGATAATTTGTTTCAATTTCTTTTATCATGGCTTC
* *
791365 CATGTTCTTATTAACATTTTTTTATTATAAACATGAATGGGAATTAGTCTTAATTCTTATATTTT
1 CATGTTCTTGTTAACA-TTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATATTTT
*
791430 GATGATGATTTTGATAGTTTGTTTCAATTTCTTTTA
65 GATGATGATTTTGATAATTTGTTTCAATTTCTTTTA
791466 GCTTATGTAT
Statistics
Matches: 200, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
110 118 0.59
111 82 0.41
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.51
Consensus pattern (110 bp):
CATGTTCTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATATTTTG
ATGATGATTTTGATAATTTGTTTCAATTTCTTTTATCATGGCTTC
Found at i:797873 original size:16 final size:16
Alignment explanation
Indices: 797852--797885 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
797842 TATTGCAAGT
797852 AACAATACTGGTAGAC
1 AACAATACTGGTAGAC
*
797868 AACAATACTTGTAGAC
1 AACAATACTGGTAGAC
797884 AA
1 AA
797886 TTTGGAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (16 bp):
AACAATACTGGTAGAC
Found at i:798691 original size:21 final size:20
Alignment explanation
Indices: 798650--798700 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
798640 AAAAAAAAAA
798650 AAAAAAGAA-AAA-CCAACC
1 AAAAAAGAACAAATCCAACC
798668 AAAAGAA-AACAAATCCAACAC
1 AAAA-AAGAACAAATCCAAC-C
798689 AAAAAAGAACAA
1 AAAAAAGAACAA
798701 GTAATAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 7 0.25
21 10 0.36
ACGTcount: A:0.73, C:0.20, G:0.06, T:0.02
Consensus pattern (20 bp):
AAAAAAGAACAAATCCAACC
Found at i:808577 original size:26 final size:26
Alignment explanation
Indices: 808539--808588 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
808529 ATTAATCTAG
808539 AAAAACTA-ATTTTTGTAATATAAACA
1 AAAAACTATATTTTTGTAA-ATAAACA
* *
808565 AAAAATTATTTTTTTGTAAATAAA
1 AAAAACTATATTTTTGTAAATAAA
808589 TTTTTGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
AAAAACTATATTTTTGTAAATAAACA
Found at i:808814 original size:277 final size:277
Alignment explanation
Indices: 808320--808828 Score: 910
Period size: 277 Copynumber: 1.8 Consensus size: 277
808310 GAATTATTCT
*
808320 AAATTTTTTATTTCAAACTTTGCATCAAATTGATATATAAACAAAAACAATTTTTGTAATCTTCA
1 AAATTTTTTATTTCAAACTTTGCATCAAATTGACATATAAACAAAAACAATTTTTGTAATCTTCA
* *
808385 ACAACTAAACATAAAACTAGGTTAAATCAATTAAAAGAGGCTGTGATACCACTGTTAGGGATTCA
66 ACAACTAAACATAAAACTAGATTAAATCAATTAAAAGAGGCTATGATACCACTGTTAGGGATTCA
*
808450 AATCATGTTAAGATAGATCATACGTAACAGAATATTATTATAATTTTAATCTTTTAAGTCATGGA
131 AATCATGTTAAGATAGATCATACGTAACAGAATATTATTATAATTTTAATCCTTTAAGTCATGGA
* *
808515 TCACTTTAATTGAAATTAATCTAGAAAAACTAATTTTTGTAATATAAACAAAAAATTATTTTTTT
196 TCACTTTAATTGAAATTAATCTAAAAAAACCAATTTTTGTAATATAAACAAAAAATTATTTTTTT
808580 GTAAATAAATTTTTGTA
261 GTAAATAAATTTTTGTA
* * *
808597 AAATTTTTTTTTTCAAACTTTGCATCAAATTGACATATAAATAAAAACAGTTTTTGTAATCTTCA
1 AAATTTTTTATTTCAAACTTTGCATCAAATTGACATATAAACAAAAACAATTTTTGTAATCTTCA
*
808662 ACAACTAAACATAAAACTAGATTAAATCAATTAAAAGAGGCTATGATACCACTGTTAGGGATTCG
66 ACAACTAAACATAAAACTAGATTAAATCAATTAAAAGAGGCTATGATACCACTGTTAGGGATTCA
* *
808727 AATCATGTTAAGATGGATCATACGTAGCAGAATATTATTATAATTTTAATCCTTTAAGTCATGGA
131 AATCATGTTAAGATAGATCATACGTAACAGAATATTATTATAATTTTAATCCTTTAAGTCATGGA
808792 TCACTTTAATTGAAATTAATCTAAAAAAACCAATTTT
196 TCACTTTAATTGAAATTAATCTAAAAAAACCAATTTT
808829 GATATATCCC
Statistics
Matches: 220, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
277 220 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (277 bp):
AAATTTTTTATTTCAAACTTTGCATCAAATTGACATATAAACAAAAACAATTTTTGTAATCTTCA
ACAACTAAACATAAAACTAGATTAAATCAATTAAAAGAGGCTATGATACCACTGTTAGGGATTCA
AATCATGTTAAGATAGATCATACGTAACAGAATATTATTATAATTTTAATCCTTTAAGTCATGGA
TCACTTTAATTGAAATTAATCTAAAAAAACCAATTTTTGTAATATAAACAAAAAATTATTTTTTT
GTAAATAAATTTTTGTA
Found at i:816353 original size:30 final size:29
Alignment explanation
Indices: 816269--816428 Score: 153
Period size: 30 Copynumber: 5.4 Consensus size: 29
816259 CTTTAACATA
* *
816269 TTTGTCTTAATTTAGACAA-CAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAAATATG
* *
816297 TTTGGTTTTAATTTAGACAAAAAAAAATATG
1 TTT-GTCTTAATTTAGAC-AAGAAAAATATG
* *
816328 TTTGTCTTCATTTAAGACAAGAAAAATATTT
1 TTTGTCTTAATTT-AGACAAGAAAAATA-TG
* * * *
816359 TTTTTCTGAATCTAGACAAG-AAAATATA
1 TTTGTCTTAATTTAGACAAGAAAAATATG
* *
816387 TTTGTCTCAATTTAGACAAGATAAAATATT
1 TTTGTCTTAATTTAGACAAGA-AAAATATG
816417 TTTGTCTTAATT
1 TTTGTCTTAATT
816429 AAAAATAAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
28 21 0.19
29 19 0.18
30 44 0.41
31 24 0.22
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (29 bp):
TTTGTCTTAATTTAGACAAGAAAAATATG
Found at i:823864 original size:17 final size:20
Alignment explanation
Indices: 823831--823870 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
823821 TGGTTTTAGA
823831 TAATACATTTTTGATAAG-C
1 TAATACATTTTTGATAAGTC
823850 TAATA-ATTTTT-ATAAGTC
1 TAATACATTTTTGATAAGTC
823868 TAA
1 TAA
823871 CTGTTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 5 0.25
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TAATACATTTTTGATAAGTC
Found at i:824625 original size:25 final size:25
Alignment explanation
Indices: 824597--824656 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
824587 GTGGTCGCAA
* * *
824597 CCATGTATATCAACTCGTGGCCTTG
1 CCATGTATAACAACCCATGGCCTTG
824622 CCATGTATAACAACCCATGGCCTTG
1 CCATGTATAACAACCCATGGCCTTG
* *
824647 CTATGCATAA
1 CCATGTATAA
824657 TCACAGACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (25 bp):
CCATGTATAACAACCCATGGCCTTG
Found at i:825161 original size:25 final size:25
Alignment explanation
Indices: 825125--825173 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
825115 CCAGCTCATG
*
825125 CTTTCCACAATAATAGTTTATAAAT
1 CTTTCCACAATAATAGTATATAAAT
*
825150 CTTT-CACGAATAGTAGTATATAAA
1 CTTTCCAC-AATAATAGTATATAAA
825174 ACATCATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (25 bp):
CTTTCCACAATAATAGTATATAAAT
Done.