Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001674.1 Hibiscus syriacus cultivar Beakdansim tig00003348_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 384960
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
File 1 of 2
Found at i:5048 original size:45 final size:45
Alignment explanation
Indices: 4968--5367 Score: 281
Period size: 45 Copynumber: 8.9 Consensus size: 45
4958 CAGGTTGAGG
* * * * * *
4968 ATGACATTACTGAAAGGTAGACTCCTC-TCAACGAGAAAGTCACGA
1 ATGACATCACTAAAAGATTGACTCCTCTTC-GCGAGAAAGTCAAGA
* * * *
5013 ATGACATCATTAAAAAATTGACTTCTCTTCGCGAGAAAATCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGA
* * * * * *
5058 ATAACATCACTGAAGGATTGGA-TCCTCTTCTCGAGATATTCAAGA
1 ATGACATCACTAAAAGATT-GACTCCTCTTCGCGAGAAAGTCAAGA
* * * * **
5103 ATGACATTACTGAAAGGTTGACTCCTATTCGAAAGAAAGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGA
* * * * * * * * *
5148 ATGGCACCAGTAAAATG-TCGACTTCTCTCCGCAATAAAGTCACGA
1 ATGACATCACTAAAA-GATTGACTCCTCTTCGCGAGAAAGTCAAGA
* *
5193 ATGCCATTACTAAAAGGA-TGA--CCTCTTCGCGAGAAAGTCAAGA
1 ATGACATCACTAAAA-GATTGACTCCTCTTCGCGAGAAAGTCAAGA
* * ** *
5236 ATGACATCACTAAAAGATTGACTCTTATTCATGAGAATGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGA
* * * * * *
5281 ATGATATCACTATAAGGTTGACTCCTCTTTGCGAGAAAATTAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGA
* * * * *
5326 ATAATATCACTAAAAGGTTGACTCCTCTTTGGGAGAAAGTCA
1 ATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCA
5368 CGTTGAGGTT
Statistics
Matches: 272, Mismatches: 75, Indels: 16
0.75 0.21 0.04
Matches are distributed among these distances:
42 2 0.01
43 33 0.12
44 2 0.01
45 230 0.85
46 5 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (45 bp):
ATGACATCACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGA
Found at i:7992 original size:6 final size:6
Alignment explanation
Indices: 7981--8005 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7971 AATACAAAGG
7981 TGCAAA TGCAAA TGCAAA TGCAAA T
1 TGCAAA TGCAAA TGCAAA TGCAAA T
8006 ATTGTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (6 bp):
TGCAAA
Found at i:9574 original size:15 final size:17
Alignment explanation
Indices: 9550--9587 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
9540 AATGTATTTT
9550 AAAATAA-TTTTAAGA-
1 AAAATAATTTTTAAGAC
*
9565 AAAATCATTTTTAAGAC
1 AAAATAATTTTTAAGAC
9582 AAAATA
1 AAAATA
9588 GGTTCATGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATAATTTTTAAGAC
Found at i:10828 original size:137 final size:136
Alignment explanation
Indices: 10582--10829 Score: 370
Period size: 137 Copynumber: 1.8 Consensus size: 136
10572 TCTGATTAGG
* * * *
10582 AAAAAATAGTTTTCAAGTTGAAATGGGCATGTTTTAAAATGAATCAAAAGTATAAGAATTTATGT
1 AAAAAATAGTATTCAAGTTGAAATAGACATGTTTTAAAATGAAACAAAAGTATAAGAATTTATGT
* * * *
10647 TCTCTGAATGTTTGTCAAGTTGATGTTACATATTTAGCTCGTATTTCAAAATGTATACGGGTTGT
66 TCTCTGAATATCTGTCAAGCTGATGTGACATATTTAGCTCGTATTTCAAAATGTATACGGGTTGT
10712 GGTAAC
131 GGTAAC
* * *
10718 AAAAAAGTAGTATTCAAGTTGAAATAGACATGTTTTAAAATGAAACAAAATTTTAAGCATTTATG
1 AAAAAA-TAGTATTCAAGTTGAAATAGACATGTTTTAAAATGAAACAAAAGTATAAGAATTTATG
* *
10783 TTCTCTGAATATCTGTCAAGCTGATGTGACATATTTAGTTTGTATTT
65 TTCTCTGAATATCTGTCAAGCTGATGTGACATATTTAGCTCGTATTT
10830 TGAAACATAT
Statistics
Matches: 98, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
136 6 0.06
137 92 0.94
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (136 bp):
AAAAAATAGTATTCAAGTTGAAATAGACATGTTTTAAAATGAAACAAAAGTATAAGAATTTATGT
TCTCTGAATATCTGTCAAGCTGATGTGACATATTTAGCTCGTATTTCAAAATGTATACGGGTTGT
GGTAAC
Found at i:12494 original size:21 final size:19
Alignment explanation
Indices: 12456--12501 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
12446 AATTAATCCT
12456 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
12476 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
12497 A-TAAT
1 ACTAAT
12502 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:16595 original size:21 final size:20
Alignment explanation
Indices: 16554--16600 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
16544 GTGATTAAGG
* *
16554 AATTTTTAGTGAATTAGTGAA
1 AATTTTAAGTGAATGAGTG-A
16575 AATTTTAAGTGAAATGA-TGA
1 AATTTTAAGTG-AATGAGTGA
16595 AATTTT
1 AATTTT
16601 GTTAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (20 bp):
AATTTTAAGTGAATGAGTGA
Found at i:17393 original size:23 final size:23
Alignment explanation
Indices: 17367--17414 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
17357 TAGAGCATTC
17367 TATGTGGTCATTCGGGACAAATA
1 TATGTGGTCATTCGGGACAAATA
17390 TATGTGGTCATTCGGGACAAATA
1 TATGTGGTCATTCGGGACAAATA
17413 TA
1 TA
17415 AGGCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (23 bp):
TATGTGGTCATTCGGGACAAATA
Found at i:24286 original size:23 final size:23
Alignment explanation
Indices: 24256--24347 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
24246 AGTCGACGGT
*
24256 TCTATGTGGTCCTTCAGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
24279 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* * * *
24302 CCTATATGATCTTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
24325 CCTATGT-GTCATTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
24347 T
1 T
24348 ATGTGGCACT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 13 0.22
23 47 0.78
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:25904 original size:30 final size:31
Alignment explanation
Indices: 25870--25988 Score: 106
Period size: 30 Copynumber: 3.9 Consensus size: 31
25860 CAATAAAAAA
* *
25870 TTTATTTAAA-TTCATGAGTCAAATTAATAT
1 TTTATCTAAAGTTCATGAATCAAATTAATAT
*
25900 TTTATCTAAAGTT--TGAATATCAAATTGATA-
1 TTTATCTAAAGTTCATG-A-ATCAAATTAATAT
* * *
25930 TTTATCTAAATTTTATTG-ATTAAATTAATAT
1 TTTATCTAAAGTTCA-TGAATCAAATTAATAT
25961 TTTATCTAAA-TTCTATGAATCAAATTAA
1 TTTATCTAAAGTTC-ATGAATCAAATTAA
25989 AAATTAAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
29 2 0.03
30 36 0.50
31 32 0.44
33 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTATCTAAAGTTCATGAATCAAATTAATAT
Found at i:25923 original size:31 final size:31
Alignment explanation
Indices: 25883--25988 Score: 112
Period size: 31 Copynumber: 3.4 Consensus size: 31
25873 ATTTAAATTC
25883 ATGAGTCAAATTAATATTTTATCTAAAGTTTGA
1 ATGA-TCAAATTAATATTTTATCTAAA-TTTGA
* *
25916 AT-ATCAAATTGATA-TTTATCTAAATTTTA
1 ATGATCAAATTAATATTTTATCTAAATTTGA
* *
25945 TTGATTAAATTAATATTTTATCTAAATTCT--
1 ATGATCAAATTAATATTTTATCTAAATT-TGA
25975 ATGAATCAAATTAA
1 ATG-ATCAAATTAA
25989 AAATTAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 5 0.08
30 22 0.35
31 31 0.50
32 2 0.03
33 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (31 bp):
ATGATCAAATTAATATTTTATCTAAATTTGA
Found at i:25935 original size:15 final size:15
Alignment explanation
Indices: 25917--25972 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
25907 AAAGTTTGAA
25917 TATC-AAATTGATATT
1 TATCTAAATT-ATATT
*
25932 TATCTAAATTTTATT
1 TATCTAAATTATATT
*
25947 GAT-TAAATTAATATTT
1 TATCTAAATT-ATA-TT
25963 TATCTAAATT
1 TATCTAAATT
25973 CTATGAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.18
15 12 0.36
16 9 0.27
17 6 0.18
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (15 bp):
TATCTAAATTATATT
Found at i:26513 original size:22 final size:22
Alignment explanation
Indices: 26471--26515 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
26461 ATAAATATTA
* *
26471 ATTTAATTATTGTATGTATAAT
1 ATTTAAATATTATATGTATAAT
26493 ATTTAAATATTATAT-TAATAAT
1 ATTTAAATATTATATGT-ATAAT
26515 A
1 A
26516 ATTATTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTAAATATTATATGTATAAT
Found at i:30002 original size:30 final size:31
Alignment explanation
Indices: 29968--30026 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
29958 TAAAAATTTT
29968 GGGACC-ATTCTG-TAATGTTT-GAAAAGTTAG
1 GGGACCAATT-TGATAAT-TTTGGAAAAGTTAG
29998 GGGACCAATTTGATAATTTTGGAAAAGTT
1 GGGACCAATTTGATAATTTTGGAAAAGTT
30027 GTGAATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.34
Consensus pattern (31 bp):
GGGACCAATTTGATAATTTTGGAAAAGTTAG
Found at i:38108 original size:31 final size:31
Alignment explanation
Indices: 38062--38154 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
38052 GTGTCCGACC
* *
38062 ATCAAAATGACATTTTATCTAAATTTCAAGG
1 ATCAAATTGATATTTTATCTAAATTTCAAGG
*
38093 ATCAAATTGATATTTTATGTAAAGTTT-AGAGGG
1 ATCAAATTGATATTTTATCTAAA-TTTCA-A-GG
*
38126 A-CAAATTTATATTTTATCATAAA-TTCAAG
1 ATCAAATTGATATTTTATC-TAAATTTCAAG
38155 AGTCAAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
30 1 0.02
31 24 0.46
32 20 0.38
33 7 0.13
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (31 bp):
ATCAAATTGATATTTTATCTAAATTTCAAGG
Found at i:46493 original size:11 final size:11
Alignment explanation
Indices: 46474--46506 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
46464 GTGATTTTTA
46474 TTTTATTATTT
1 TTTTATTATTT
*
46485 TTTTGTTATTT
1 TTTTATTATTT
46496 TTTTA-TATTT
1 TTTTATTATTT
46506 T
1 T
46507 AATTTTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:47923 original size:21 final size:21
Alignment explanation
Indices: 47890--47947 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
47880 ATCCCTTTTC
*
47890 AAAAGGATTGATCCCTCGGGG
1 AAAAAGATTGATCCCTCGGGG
*
47911 AAAAAGATCGATCCCTCGGGG
1 AAAAAGATTGATCCCTCGGGG
47932 AAAAAGATTGATCCCT
1 AAAAAGATTGATCCCT
47948 TGAAAGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (21 bp):
AAAAAGATTGATCCCTCGGGG
Found at i:53856 original size:21 final size:21
Alignment explanation
Indices: 53832--53884 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
53822 ATTCCTTTTC
*
53832 AAAAAGATCAATCCCTCCGGA
1 AAAAAGATCAATCCCTCAGGA
* *
53853 AAAAATATCGATCCCTCAGGA
1 AAAAAGATCAATCCCTCAGGA
53874 AAAAAGATCAA
1 AAAAAGATCAA
53885 CCCCCAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAAGATCAATCCCTCAGGA
Found at i:56901 original size:90 final size:89
Alignment explanation
Indices: 56784--56960 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
56774 TAATCACGAA
* * *
56784 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
56849 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
56874 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
56939 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
56961 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 34 0.41
90 49 0.59
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:65648 original size:30 final size:30
Alignment explanation
Indices: 65614--65674 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
65604 TGCAAAGTCC
** *
65614 AGAAATTAAAAAATGAAATTATTTAGGCCT
1 AGAAATTAAAAAACAAAATGATTTAGGCCT
*
65644 AGAAATTAAAAAACAAAATGGTTTAGGCCT
1 AGAAATTAAAAAACAAAATGATTTAGGCCT
65674 A
1 A
65675 CTTGCATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (30 bp):
AGAAATTAAAAAACAAAATGATTTAGGCCT
Found at i:69283 original size:265 final size:261
Alignment explanation
Indices: 68734--69468 Score: 769
Period size: 265 Copynumber: 2.8 Consensus size: 261
68724 AGGTTGCTCT
* * * * * ** *
68734 TAAAAGGTTACCATAGTTTAAGTTGATGGGGCCTTAGACATTCCCACGATAGGAAAATAAGTTAA
1 TAAAATGTTAACAAAGTTTAAGATGATGGGGCCTTAGA-TTTTTCACGATAAGAAAATAAGTTAA
* * *
68799 AAGCTGAAAAA-GTTATAAATATATATAAGAAATACGGTGTCGCCCAATAATGTCATGGTTCACT
65 AAGCT-AAAAATGTTATGAATATATATAAGAAATACGTTGTCGCCTAATAATGTCATGGTTCACT
* * * *
68863 AAGTAATATGTTGCGATC-TGTAAAGTTAATATTTTTATTAATAAAATAGGTTGCACCCAAGAAT
129 AAGAAATAGGTTGTGA-CATGTAATGTTAATATTTTTATTAATAAAATAGGTT--ACCCAAGAAT
* * * * * *
68927 GTCATGGTTCACTAGGAAAGCAGGTTAGGATCTGGAATTTTAATAGTTTTAATAATAAAATGGGT
191 GTCATGGTTCACTAGGAAAACAGGTTAGAATATGAAATCTTAATAGTTTTAATAATAAAATGGAT
68992 TAATCC
256 TAATCC
* * * *
68998 TAAAATGTTATCAGAGTTTAAGCTGATGGGGCCTTGGATTTTTCAACGATAAGAAAATAAGTTAA
1 TAAAATGTTAACAAAGTTTAAGATGATGGGGCCTTAGATTTTTC-ACGATAAGAAAATAAGTTAA
* * * *
69063 AAGCTAAAAATGTCATGAATATATATAAAAAATATGTTTTCGCCTAATAATGTCATGTGCTTCAC
65 AAGCTAAAAATGTTATGAATATATATAAGAAATACGTTGTCGCCTAATAATGTCATG-G-TTCAC
* * *
69128 TAAAAAATGGGTTGTGACATGTAATGTTAATATTTGTATTAATAAAATAGGTTACGCCAAGAATG
128 TAAGAAATAGGTTGTGACATGTAATGTTAATATTTTTATTAATAAAATAGGTTAC-CCAAGAATG
* * *
69193 TCATGGCTT-ACTAGGAAAACATG-TAGCAATATGAAATCTTAATATTTTTAATAATAAAATTGA
192 TCATGG-TTCACTAGGAAAACAGGTTAG-AATATGAAATCTTAATAGTTTTAATAATAAAATGGA
*
69256 TT-GTGCC
255 TTAAT-CC
* **** *
69263 TAAAATGTTAACAAAGTTTAAGATAATGGAATATTAGATTTCCTCAC-AGTAAGAAAATAAGTTA
1 TAAAATGTTAACAAAGTTTAAGATGATGGGGCCTTAGATTT-TTCACGA-TAAGAAAATAAGTTA
* * *
69327 AAAGGTGAAAATGTTATGAATATAAATAAGAAATACGTATGT-G-CTCAATAATGTCATGGTTCA
64 AAAGCTAAAAATGTTATGAATATATATAAGAAATACGT-TGTCGCCT-AATAATGTCATGGTTCA
* *
69390 CTAAGAAATAGGTTATG--A--T-ATG-TAATATTTTTATTAATAAAATAGGTTGCTCCCAAGAA
127 CTAAGAAATAGGTTGTGACATGTAATGTTAATATTTTTATTAATAAAATAGGTT--ACCCAAGAA
* *
69449 TGTTATGGTTCACTAAGAAA
190 TGTCATGGTTCACTAGGAAA
69469 GTAGGTTGCG
Statistics
Matches: 398, Mismatches: 57, Indels: 38
0.81 0.12 0.08
Matches are distributed among these distances:
257 27 0.07
258 25 0.06
259 2 0.01
261 1 0.00
263 26 0.07
264 106 0.27
265 156 0.39
266 55 0.14
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (261 bp):
TAAAATGTTAACAAAGTTTAAGATGATGGGGCCTTAGATTTTTCACGATAAGAAAATAAGTTAAA
AGCTAAAAATGTTATGAATATATATAAGAAATACGTTGTCGCCTAATAATGTCATGGTTCACTAA
GAAATAGGTTGTGACATGTAATGTTAATATTTTTATTAATAAAATAGGTTACCCAAGAATGTCAT
GGTTCACTAGGAAAACAGGTTAGAATATGAAATCTTAATAGTTTTAATAATAAAATGGATTAATC
C
Found at i:69549 original size:81 final size:77
Alignment explanation
Indices: 69407--69595 Score: 226
Period size: 81 Copynumber: 2.4 Consensus size: 77
69397 ATAGGTTATG
*
69407 ATATGTAATATTTTTATTAATAAAATAGGTTGCTCCCAAGAATGTTATGGTTCACTAAGAAAGTA
1 ATAT-TAATATTTTTATTAATAAAATAGGTTGCTCCCAAGAATGTTATGGTTCAATAAGAAA-TA
69472 GGTTGCGATATGTAAT
64 GGTTGCGATATGT--T
*
69488 ATAATGTTAATA-TTTT-TTAATAAAATAGGTTG-TACCCAAGAATG-TATGGTTTTGAAT-AGA
1 AT-A--TTAATATTTTTATTAATAAAATAGGTTGCT-CCCAAGAATGTTATGG--TTCAATAAGA
*
69548 AATAGGTTGTGATATGTT
60 AATAGGTTGCGATATGTT
69566 ATATTAATATTTTTATTAATAAAATAGGTT
1 ATATTAATATTTTTATTAATAAAATAGGTT
69596 ACGCAAAAAA
Statistics
Matches: 97, Mismatches: 3, Indels: 20
0.81 0.03 0.17
Matches are distributed among these distances:
75 6 0.06
76 4 0.04
77 16 0.16
78 3 0.03
80 20 0.21
81 33 0.34
82 9 0.09
83 5 0.05
84 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (77 bp):
ATATTAATATTTTTATTAATAAAATAGGTTGCTCCCAAGAATGTTATGGTTCAATAAGAAATAGG
TTGCGATATGTT
Found at i:71109 original size:98 final size:98
Alignment explanation
Indices: 70986--71167 Score: 249
Period size: 98 Copynumber: 1.9 Consensus size: 98
70976 TTGTATAACC
* * *
70986 TTTTCATAATATATATAGTTTCAGCCTATAAATTAAT-CAGTTAACATAACAACAAGACACAACC
1 TTTTCATAATATACACAGTTTCAGCCTATAAATT-ATCCAATTAACATAACAACAAGACACAACC
* *
71050 TATAATATTATCCAGGAAACTAGGTTTGCATTTT
65 TACAATATTATCCAAGAAACTAGGTTTGCATTTT
* * ***
71084 TTTTCATAATATACACGGTTTCAGCCTATAACTTATCCAATTAACATAACAACAAGGTGCAACCT
1 TTTTCATAATATACACAGTTTCAGCCTATAAATTATCCAATTAACATAACAACAAGACACAACCT
*
71149 ACAATGTTATCCAAGAAAC
66 ACAATATTATCCAAGAAAC
71168 AAAGTTTTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 2 0.03
98 70 0.97
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (98 bp):
TTTTCATAATATACACAGTTTCAGCCTATAAATTATCCAATTAACATAACAACAAGACACAACCT
ACAATATTATCCAAGAAACTAGGTTTGCATTTT
Found at i:76448 original size:945 final size:943
Alignment explanation
Indices: 74570--76469 Score: 2922
Period size: 945 Copynumber: 2.0 Consensus size: 943
74560 AATAATGCTC
* *
74570 TCACAAAGCCTCATTAGTTCACTCTAAGGAAACTTTAATGTCACTCAATCCGCTCGTGTTTGCAC
1 TCACAAAGCCTCATGAGTTCACTCTAAGGAAACTTTAATGTCACTCAATCCACTCGTGTTTGCAC
*
74635 TGTAGTACTTCAAGGCTTTTACTAGCCCTCTTCTAGTCTCCCACGCTCAAGCCTTTTTCCTCTCA
66 TCTAGTACTTCAAGGCTTTTACTAGCCCTCTTCTAGTCTCCCACGCTCAAGCCTTTTTCCTCTCA
* * *
74700 ATCTCTTTCTCTCCAGTTCTATGCAACTTTACTCAAAACTATACCAAGTAAAGTTTACTTGTTGT
131 ATCTCTTTATCTCAAGTTCTAAGCAACTTTACTCAAAACTATACCAAGTAAAGTTTACTTGTTGT
* *
74765 GTGTCGGCTACAAAAGGGTTAGTAGGAATGGAAAACAAAATATAATGAAAAGGGTGGCTTAGAAA
196 GCGTCAGCTACAAAAGGGTTAGTAGGAATGGAAAACAAAATATAATGAAAAGGGTGGCTTAGAAA
* *
74830 AAAGAAAGAAGAGAATAAAGGGGTTACTTACACAAAGTCACTTCACAACCTTTCTATCACCACAA
261 AAAGAAAGAAGAGAATAAAGGGGTTACCTACACAAAGTCACTTAACAACCTTTCTATCACCACAA
* *
74895 TCAATTTTAGATGCTTACTTGGAATGGCTTGGTGATGAGACTTGTTGTTGTGGGCATTCAACTTT
326 TCAATTTTAGATGCTTACTTGAAATGGCTTGGTGATGAGACTTGTTGTTGTAGGCATTCAACTTT
* *
74960 CTTTCCAATTTTCTTTTCTTTTCTTCTTTTTGTTTCTTCTTTGAGTGCTTTGTAATTTTCTTTGG
391 CTTTCCAATTTTCTTTTCTTTTCTTCTTTTTGTTTCTTCTTTGAGTGCTTTGCAATTTTCTTTGC
*
75025 TGATTTGTTTATTTCTTCTTTTGCACATCACTTGCACTTCTTTTTGTATTTTATTGTTGTTGTTG
456 TGATTTGTTTATATCTTC--TT----ATCACTTGCACTTCTTTTTGTATTTTATTGTTGTTGTTG
* * *
75090 TTGCACATTGCTTCTTCCACCAAAGCTCTGAATATCACTTGATGTAAGGTATTTCTACCTTAAAT
515 TTGCACATTGCTTCTTCCACCAAAGCTCAGAATACCACTTGATGTAAGGTATTTCTAACTTAAAT
* *
75155 TGATTGTGGATCTAGGAAGAACGCAAAACAACCTGTATAAGTGAATGGCTCAGAGAGATGGTTTG
580 TGATTGTGGATCTAGGAAGAACGCAAAACAACCTGCATAAGTGAATGGCTCAAAGAGATGGTTTG
* * *
75220 GTAGTTAATGTAAAGGTTAAATGGAGGGTTATTTATATTATGAGAAATGATAGAGGAAGTATGAT
645 GTAGTTAATGTAAAGGTGAAATGGAGGGCTATTTATATTATGAGAAATGATAGAGGAAGTAAGAT
* * * * *
75285 GATATGGCTATGGTTTGATTTATGAAAGAAAGTACGTTTGGTGAGTATATTATCTAAGAAAAACT
710 GATATGGCTATGGTTTGATTTATAAAAGAAAGTACATTTGGTGAGGATAGTATCTAAGAAAAACC
* * *
75350 AAGGAAGAACCAGTGCTACAATGACCAAAGACCCAACCTTATAAATATTTCTAAGGGGTGGTAAC
775 AAGGAAGAACCAATGCTACAATAACAAAAGACCCAACCTTATAAATATTTCTAAGGGGTGGTAAC
* * *
75415 AAAGGATTTGGACCCACTATCTATAGGGAGATAGGAACCACAAGTATCAATGACAAATGGGTTGA
840 AAAGGACTTGGACCCACTATCTATAGGGAGAAAGGAACCACAAGTATCAATGACAAAGGGGTTGA
* *
75480 CGCCACAACTAATTAAATTACTTGATAAGTTGATAAATG
905 CGCAACAACTAATTAAATTACTTGATAAGTTGATAAAAG
** *
75519 TCACAAAGCCTCATGAGTTTGCTCTAAGGAAA-TTTGAATGTCACTCAATCCACTCGTGTTTTCA
1 TCACAAAGCCTCATGAGTTCACTCTAAGGAAACTTT-AATGTCACTCAATCCACTCGTGTTTGCA
* *
75583 CTCTACG-ACTTCAAGGCTTTTATTAGTCCTCTTCTAGTCTCCCACGCTCAAGCCTTTTTCCTCT
65 CTCTA-GTACTTCAAGGCTTTTACTAGCCCTCTTCTAGTCTCCCACGCTCAAGCCTTTTTCCTCT
* *
75647 CAATCTCTTTATCTCAAGTTCTAAGTAACTTTACTCAAAATTATACCAAGTAAAGTTTACTTGTT
129 CAATCTCTTTATCTCAAGTTCTAAGCAACTTTACTCAAAACTATACCAAGTAAAGTTTACTTGTT
* * *
75712 GTGCGTTAGCTACAAAAGGGTTAGTAGGAATGGAAAGCAAAATATAATGAAAATGGTGGCTTAGA
194 GTGCGTCAGCTACAAAAGGGTTAGTAGGAATGGAAAACAAAATATAATGAAAAGGGTGGCTTAGA
* * *
75777 AATAAGAAAGAAGAGAATAAAGGGGTTGCCTACACAAAGTCACTTAACAACCTTTCTGTCACCAC
259 AAAAAGAAAGAAGAGAATAAAGGGGTTACCTACACAAAGTCACTTAACAACCTTTCTATCACCAC
* *
75842 AATCAATTTTAGATGCTTACTTGAAATGGCTTGGTGATGAGACTTGTTGTTGTATGCTTTCAACT
324 AATCAATTTTAGATGCTTACTTGAAATGGCTTGGTGATGAGACTTGTTGTTGTAGGCATTCAACT
**
75907 TT-TTTGGTAATTTTCTTTTCTTTTCTTTTCTTCTTTTTGTTTCTTCTTTGAGTGCTTTGCAATT
389 TTCTTT-CCAA-----TTTTCTTTTCTTTTCTTCTTTTTGTTTCTTCTTTGAGTGCTTTGCAATT
*
75971 TTCTTTGCTG-TTT-TTT-TAT-TTC-T-TCACTTGCACTTCTTTTTGTATTTTGTTGTTGTTGT
448 TTCTTTGCTGATTTGTTTATATCTTCTTATCACTTGCACTTCTTTTTGTATTTTATTGTTGTTGT
** * *
76030 TGTTGTTGCATGTTCTTTCTTCCACCAAAGCTCAGAATACCGCTTGATGTAAGGTATTTCTAACT
513 TGTTG-CACAT-TGC-TTCTTCCACCAAAGCTCAGAATACCACTTGATGTAAGGTATTTCTAACT
*
76095 TATATTGATTGTGGATCTAGGAAGGAA-GCAAAACAACCTGCATAAGTGAATGGCTCAAAGAGAT
575 TAAATTGATTGTGGATCTAGGAA-GAACGCAAAACAACCTGCATAAGTGAATGGCTCAAAGAGAT
* * * *
76159 GGTTTGGTAGTTGATGTAAAGGTGAAATGGAGGGCTATTTATGTTATGAGAAATGGTAGCGGAAG
639 GGTTTGGTAGTTAATGTAAAGGTGAAATGGAGGGCTATTTATATTATGAGAAATGATAGAGGAAG
* * *
76224 TAAGATGATATGGCTATGGTTTGGTTTATAAAAGAAAGTACATTTGGTGTGGATGGTATCTAAGA
704 TAAGATGATATGGCTATGGTTTGATTTATAAAAGAAAGTACATTTGGTGAGGATAGTATCTAAGA
* *
76289 AAAACCAAGGAAGAACCAATGCTACAATAAGAAAAGACCCAACCTTATAAATCTTTCTAAGGGGT
769 AAAACCAAGGAAGAACCAATGCTACAATAACAAAAGACCCAACCTTATAAATATTTCTAAGGGGT
76354 GGTAACAAAGGACTTGGACCCACTATCTATAGGGA-AAAGGGAACCACAAGTATCAATGACAAAG
834 GGTAACAAAGGACTTGGACCCACTATCTATAGGGAGAAA-GGAACCACAAGTATCAATGACAAAG
* *
76418 GGGTTGATGCAACAAGTAATTAAATTACTTGATAAGTTGATAAAAG
898 GGGTTGACGCAACAACTAATTAAATTACTTGATAAGTTGATAAAAG
76464 TCACAA
1 TCACAA
76470 GGACTTAAGA
Statistics
Matches: 868, Mismatches: 70, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
942 40 0.05
943 3 0.00
944 4 0.00
945 383 0.44
946 3 0.00
947 1 0.00
948 6 0.01
949 359 0.41
950 4 0.00
951 2 0.00
952 3 0.00
953 3 0.00
954 57 0.07
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (943 bp):
TCACAAAGCCTCATGAGTTCACTCTAAGGAAACTTTAATGTCACTCAATCCACTCGTGTTTGCAC
TCTAGTACTTCAAGGCTTTTACTAGCCCTCTTCTAGTCTCCCACGCTCAAGCCTTTTTCCTCTCA
ATCTCTTTATCTCAAGTTCTAAGCAACTTTACTCAAAACTATACCAAGTAAAGTTTACTTGTTGT
GCGTCAGCTACAAAAGGGTTAGTAGGAATGGAAAACAAAATATAATGAAAAGGGTGGCTTAGAAA
AAAGAAAGAAGAGAATAAAGGGGTTACCTACACAAAGTCACTTAACAACCTTTCTATCACCACAA
TCAATTTTAGATGCTTACTTGAAATGGCTTGGTGATGAGACTTGTTGTTGTAGGCATTCAACTTT
CTTTCCAATTTTCTTTTCTTTTCTTCTTTTTGTTTCTTCTTTGAGTGCTTTGCAATTTTCTTTGC
TGATTTGTTTATATCTTCTTATCACTTGCACTTCTTTTTGTATTTTATTGTTGTTGTTGTTGCAC
ATTGCTTCTTCCACCAAAGCTCAGAATACCACTTGATGTAAGGTATTTCTAACTTAAATTGATTG
TGGATCTAGGAAGAACGCAAAACAACCTGCATAAGTGAATGGCTCAAAGAGATGGTTTGGTAGTT
AATGTAAAGGTGAAATGGAGGGCTATTTATATTATGAGAAATGATAGAGGAAGTAAGATGATATG
GCTATGGTTTGATTTATAAAAGAAAGTACATTTGGTGAGGATAGTATCTAAGAAAAACCAAGGAA
GAACCAATGCTACAATAACAAAAGACCCAACCTTATAAATATTTCTAAGGGGTGGTAACAAAGGA
CTTGGACCCACTATCTATAGGGAGAAAGGAACCACAAGTATCAATGACAAAGGGGTTGACGCAAC
AACTAATTAAATTACTTGATAAGTTGATAAAAG
Found at i:80223 original size:24 final size:24
Alignment explanation
Indices: 80192--80249 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
80182 CTTCCATTTC
80192 ATGAATGAAATGAATCAA-GGTTAA
1 ATGAATGAAATGAAT-AATGGTTAA
80216 ATGAATGAAATGAATAATGGTTAA
1 ATGAATGAAATGAATAATGGTTAA
80240 ATGAATGAAA
1 ATGAATGAAA
80250 GGCTATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.26
Consensus pattern (24 bp):
ATGAATGAAATGAATAATGGTTAA
Found at i:84392 original size:15 final size:15
Alignment explanation
Indices: 84373--84428 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
84363 TTTATGGGGT
* *
84373 AAGAAGACAACGTCT
1 AAGAAGAAAACGTCA
84388 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
84403 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
84418 AAGAAGGAAAA
1 AAGAA-GAAAA
84429 AGAAAGCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 33 0.87
16 5 0.13
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.07
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:86426 original size:20 final size:20
Alignment explanation
Indices: 86401--86443 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
86391 TCACGATGAA
86401 GACTCTAAACAAAGAGGTCC
1 GACTCTAAACAAAGAGGTCC
86421 GACTCTAAACAAAGAGGTCC
1 GACTCTAAACAAAGAGGTCC
86441 GAC
1 GAC
86444 AATAAAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (20 bp):
GACTCTAAACAAAGAGGTCC
Found at i:86449 original size:20 final size:20
Alignment explanation
Indices: 86406--86449 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
86396 ATGAAGACTC
**
86406 TAAACAAAGAGGTCCGACTC
1 TAAACAAAGAGGTCCGACAA
86426 TAAACAAAGAGGTCCGACAA
1 TAAACAAAGAGGTCCGACAA
86446 TAAA
1 TAAA
86450 GGGAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (20 bp):
TAAACAAAGAGGTCCGACAA
Found at i:88324 original size:38 final size:38
Alignment explanation
Indices: 88273--88364 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 38
88263 AGAACTTGTT
* *
88273 GAAAAAGAAGAGGAGAAAGGAGAAAGGACACCGAAGAC
1 GAAAAAAAAGAGGAGAAAGGAGAAAGGAAACCGAAGAC
88311 GAAAAAAAAGAGGAGAAAGGAGAAAGGAAACCGAAGAC
1 GAAAAAAAAGAGGAGAAAGGAGAAAGGAAACCGAAGAC
*
88349 G-GAAAAAAGA-GAGAAA
1 GAAAAAAAAGAGGAGAAA
88365 AGGAAGAGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
36 6 0.12
37 8 0.16
38 37 0.73
ACGTcount: A:0.60, C:0.08, G:0.33, T:0.00
Consensus pattern (38 bp):
GAAAAAAAAGAGGAGAAAGGAGAAAGGAAACCGAAGAC
Found at i:88957 original size:12 final size:12
Alignment explanation
Indices: 88937--88967 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
88927 TAATCCCGGG
*
88937 TTTGTTTTTTCA
1 TTTGATTTTTCA
88949 TTTGATTTTTCA
1 TTTGATTTTTCA
88961 TTTGATT
1 TTTGATT
88968 ATCAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTGATTTTTCA
Found at i:90792 original size:2 final size:2
Alignment explanation
Indices: 90785--90848 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
90775 TCAATCTACA
90785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
90826 AT AT TT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
90849 ATTTACGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:91011 original size:85 final size:85
Alignment explanation
Indices: 90896--91056 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 85
90886 GTCTTTTTTA
* *
90896 ATGACGTGTGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
1 ATGACGGGGGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
90961 AATGTATGTCAAGCAGATTT
66 AATGTATGTCAAGCAGATTT
* * *
90981 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACA
1 ATGACGGGGGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
*
91046 AATGTGTGTCA
66 AATGTATGTCA
91057 TCTTAAATTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (85 bp):
ATGACGGGGGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
AATGTATGTCAAGCAGATTT
Found at i:91068 original size:85 final size:85
Alignment explanation
Indices: 90896--91118 Score: 256
Period size: 85 Copynumber: 2.6 Consensus size: 85
90886 GTCTTTTTTA
* *
90896 ATGACGTGTGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
1 ATGACGAGGGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
*
90961 AATGTATGTCAAGCAGATTT
66 AATGTATGTCAAGCAGAATT
* * * *
90981 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACA
1 ATGACGAGGGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
* *
91046 AATGTGTGTC-ATCTTA-AATT
66 AATGTATGTCAAGC--AGAATT
* * * **
91066 ATGATGAGGGCTTTAATGACACTCAATG-AACGTCATTA-ATGCACGTCATAAAT
1 ATGACGAGGGCTTAAATGACACGCAATGTAA-GTCA-TACATGCGTGTCATAAAT
91119 GTGTGTCATA
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
84 4 0.03
85 112 0.94
86 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (85 bp):
ATGACGAGGGCTTAAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
AATGTATGTCAAGCAGAATT
Found at i:91126 original size:13 final size:13
Alignment explanation
Indices: 91110--91154 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
91100 ATTAATGCAC
91110 GTCATAAATGTGT
1 GTCATAAATGTGT
91123 GTCATAAATGTGT
1 GTCATAAATGTGT
* *
91136 GGCATAAATGCGT
1 GTCATAAATGTGT
91149 GTCATA
1 GTCATA
91155 GATTTATGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (13 bp):
GTCATAAATGTGT
Found at i:92879 original size:7 final size:7
Alignment explanation
Indices: 92869--92896 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
92859 AAGAAAAGAA
92869 AAAATAT
1 AAAATAT
92876 AAAATAT
1 AAAATAT
92883 AAAATAT
1 AAAATAT
92890 AAAATAT
1 AAAATAT
92897 TGTCGAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:94767 original size:18 final size:18
Alignment explanation
Indices: 94744--94781 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
94734 TTTTAAGATT
94744 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
94762 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
94780 TT
1 TT
94782 CGAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:95201 original size:24 final size:23
Alignment explanation
Indices: 95125--95203 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
95115 ACCATGTTAG
*
95125 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTAC-TCACATAGTA
*
95149 GTATCGAT-C--CTCAC-TAGATG
1 GTATCGATACTACTCACATAG-TA
*
95169 GTATTGATACTACTACACATAGTA
1 GTATCGATACTACT-CACATAGTA
95193 GTATCGATACT
1 GTATCGATACT
95204 CCCTGGCCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 3 0.07
20 11 0.25
21 2 0.05
23 3 0.07
24 22 0.50
25 3 0.07
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (23 bp):
GTATCGATACTACTCACATAGTA
Found at i:95222 original size:44 final size:44
Alignment explanation
Indices: 95125--95222 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
95115 ACCATGTTAG
** * **
95125 GTATCGATACTACTTTACATAGTAGTATCGATCCTCACTAGATG
1 GTATCGATACTACTACACATAGTAGTATCGATACTCACTAGACA
* * * *
95169 GTATTGATACTACTACACATAGTAGTATCGATACTCCCTGGCCA
1 GTATCGATACTACTACACATAGTAGTATCGATACTCACTAGACA
95213 GTATCGATAC
1 GTATCGATAC
95223 CGTTGGGTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (44 bp):
GTATCGATACTACTACACATAGTAGTATCGATACTCACTAGACA
Found at i:97640 original size:16 final size:16
Alignment explanation
Indices: 97613--97658 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
97603 AAATCGGAGT
97613 ACAAAAAGAAAGAAAAG
1 ACAAAAA-AAAGAAAAG
97630 ACAAAAAAAAGAAAAAG
1 ACAAAAAAAAG-AAAAG
*
97647 A-AGAAAAAAGAA
1 ACAAAAAAAAGAA
97659 GAAAAAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 13 0.48
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.00
Consensus pattern (16 bp):
ACAAAAAAAAGAAAAG
Found at i:97641 original size:11 final size:10
Alignment explanation
Indices: 97615--97664 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
97605 ATCGGAGTAC
97615 AAAAAG-AAA
1 AAAAAGAAAA
*
97624 GAAAAGACAAA
1 AAAAAGA-AAA
97635 AAAAAG-AAA
1 AAAAAGAAAA
*
97644 AAGAAGAAAA
1 AAAAAGAAAA
*
97654 AAGAAGAAAA
1 AAAAAGAAAA
97664 A
1 A
97665 GAAGAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 13 0.37
10 14 0.40
11 8 0.23
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:97644 original size:25 final size:25
Alignment explanation
Indices: 97615--97667 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
97605 ATCGGAGTAC
*
97615 AAAAAGAAAGAAAAGACAAAAAAAAG
1 AAAAAG-AAGAAAAAACAAAAAAAAG
* *
97641 AAAAAGAAGAAAAAAGAAGAAAAAG
1 AAAAAGAAGAAAAAACAAAAAAAAG
97666 AA
1 AA
97668 GAATTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAAAGAAGAAAAAACAAAAAAAAG
Found at i:97654 original size:19 final size:19
Alignment explanation
Indices: 97615--97670 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
97605 ATCGGAGTAC
97615 AAAAAGAAAGAA-AAGACAAA
1 AAAAAGAAA-AAGAAGA-AAA
97635 AAAAAGAAAAAGAAGAAAA
1 AAAAAGAAAAAGAAGAAAA
*
97654 AAGAAGAAAAAGAAGAA
1 AAAAAGAAAAAGAAGAA
97671 TTTCAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 21 0.62
20 13 0.38
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAGAAAA
Found at i:97666 original size:16 final size:16
Alignment explanation
Indices: 97621--97667 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
97611 GTACAAAAAG
*
97621 AAAG-AAAAGACAAAAA
1 AAAGAAAAAGA-AGAAA
97637 AAAGAAAAAGAAGAAA
1 AAAGAAAAAGAAGAAA
97653 AAAGAAGAAA-AAGAA
1 AAAGAA-AAAGAAGAA
97668 GAATTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAGAAA
Found at i:97668 original size:9 final size:9
Alignment explanation
Indices: 97615--97670 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
97605 ATCGGAGTAC
97615 AAAAAGAA-
1 AAAAAGAAG
97623 AGAAAAGACA-
1 A-AAAAGA-AG
97633 AAAAA-AAG
1 AAAAAGAAG
97641 AAAAAGAAG
1 AAAAAGAAG
97650 AAAAAAGAAG
1 -AAAAAGAAG
97660 AAAAAGAAG
1 AAAAAGAAG
97669 AA
1 AA
97671 TTTCAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
7 1 0.02
8 7 0.16
9 24 0.56
10 11 0.26
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:115722 original size:44 final size:44
Alignment explanation
Indices: 115545--115726 Score: 135
Period size: 43 Copynumber: 4.2 Consensus size: 44
115535 TTTTTGTTAC
* * * * *
115545 AAACGCCGTTATATACCA-ACCTTTACCGACGTTTGTATACT-A
1 AAACGCCGCTATATACCAGACCTTTAGCGGCATTTGTACACTAA
* * * *
115587 AAATGCCGCTATATACCAGACCATCAGCGGCATTTGTATACTAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCATTTGTACACTAA
* * * * *
115631 AAATGCCG-T-TATACCATATCTTTATCTGCATTT-TATC-CTAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCATTTGTA-CACTAA
* ** *
115672 AGACGCCGCTATATACC-GAATTTTTAGCGGCGTTTGTACACTAA
1 AAACGCCGCTATATACCAG-ACCTTTAGCGGCATTTGTACACTAA
115716 AAACGCCGCTA
1 AAACGCCGCTA
115727 AATGTCAAAA
Statistics
Matches: 110, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
41 12 0.11
42 35 0.32
43 38 0.35
44 25 0.23
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (44 bp):
AAACGCCGCTATATACCAGACCTTTAGCGGCATTTGTACACTAA
Found at i:122338 original size:8 final size:8
Alignment explanation
Indices: 122310--122374 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
122300 AAAATTTACC
122310 AAAAATACT
1 AAAAATA-T
122319 -AAAATAT
1 AAAAATAT
*
122326 -TAAATAT
1 AAAAATAT
122333 AAAAAT-T
1 AAAAATAT
122340 AAGAAA-AT
1 AA-AAATAT
122348 AAAAA-AT
1 AAAAATAT
*
122355 AAAGATAT
1 AAAAATAT
*
122363 AAAACTAT
1 AAAAATAT
122371 AAAA
1 AAAA
122375 GGAAAGTAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 19 0.40
8 28 0.60
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:123758 original size:37 final size:37
Alignment explanation
Indices: 123556--123912 Score: 167
Period size: 37 Copynumber: 9.6 Consensus size: 37
123546 GTTTTCAAGG
* * ** * *
123556 GAAAATATCTCAAGGGAGATGAACTTTTTGTTTCAAGA
1 GAAACTATCTCAAGTGAGAT-AAAATTATGTTTCGAGA
* * * *
123594 GAAAATGTCTCAAGTGAGATGAAAA-T-T-TTTCAAAGG
1 GAAACTATCTCAAGTGAGAT-AAAATTATGTTTC-GAGA
* * *
123630 GAGA-TATCTTAAGTGAGATAAAATT-TGTTTCTAGA
1 GAAACTATCTCAAGTGAGATAAAATTATGTTTCGAGA
* * * * * * * *
123665 AAAACTGTCCCGAGTGAGACAAAA-AATTTTATTGAGGA
1 GAAACTATCTCAAGTGAGATAAAATTATGTT-TCGA-GA
* * *
123703 AAAATTATCTCGAGTGAGATAAAATTATGTTTCGAGA
1 GAAACTATCTCAAGTGAGATAAAATTATGTTTCGAGA
* * * *
123740 GAAACTATCTCAACTGAGACAAAACTAT-TTTTGAGGA
1 GAAACTATCTCAAGTGAGATAAAATTATGTTTCGA-GA
* * * *
123777 AAAACTATCT-AAGGCGAGATAAAATTTTGTTTCGAGG
1 GAAACTATCTCAA-GTGAGATAAAATTATGTTTCGAGA
* * *
123814 GAAACTATCTCAAGTGAG--ACAATTATTGTTTTTGTGAA
1 GAAACTATCTCAAGTGAGATAAAATTA-TG-TTTCGAG-A
* * ** *
123852 TAAATTATCTCTTGTGAGATAAAATTATGTTCCGAGA
1 GAAACTATCTCAAGTGAGATAAAATTATGTTTCGAGA
* * *
123889 GAAACTGTCTCGAGTGAGACAAAA
1 GAAACTATCTCAAGTGAGATAAAA
123913 ATTTCAAGTG
Statistics
Matches: 238, Mismatches: 64, Indels: 35
0.71 0.19 0.10
Matches are distributed among these distances:
34 4 0.02
35 28 0.12
36 37 0.16
37 86 0.36
38 71 0.30
39 6 0.03
40 6 0.03
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Consensus pattern (37 bp):
GAAACTATCTCAAGTGAGATAAAATTATGTTTCGAGA
Found at i:123761 original size:75 final size:73
Alignment explanation
Indices: 123428--123916 Score: 293
Period size: 74 Copynumber: 6.7 Consensus size: 73
123418 ACATCACAAA
* * * * * ** * *
123428 TGAGATGAAATTTTGTTTCGAGGGAAACTGTCTCAATTGTA-AC-AAAATATTTTCAAGGGATAA
1 TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAAGTG-AGACAAAAAT-TTTTTGAGGAAAAA
123491 -TATCTCAAG
64 TTATCTCAAG
** * * * * * ** *
123500 TGATGA-AATTTTCAT-TTTTGAGAGAAACTATCACGAGT--GACAGAAAGTTTTCAAGGGAAAA
1 TGA-GATAAAATT-ATGTTTCGAGAGAAACTATCTCAAGTGAGACAAAAATTTTTTGAGGAAAAA
123561 -TATCTCAAG
64 TTATCTCAAG
* ** * * * * ** ** * *
123570 GGAGATGAACTTTTTGTTTCAAGAGAAAATGTCTCAAGTGAGATGAAAATTTTTCAAAGG-GAGA
1 TGAGAT-AAAATTATGTTTCGAGAGAAACTATCTCAAGTGAGACAAAAATTTTT-TGAGGAAAAA
*
123634 -TATCTTAAG
64 TTATCTCAAG
* * * * *
123643 TGAGATAAAATT-TGTTTCTAGAAAAACTGTCCCGAGTGAGACAAAAAATTTTATTGAGGAAAAA
1 TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAAGTGAGAC-AAAAATTTT-TTGAGGAAAAA
*
123707 TTATCTCGAG
64 TTATCTCAAG
* * *
123717 TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAACTGAGACAAAACTATTTTTGAGGAAAAAC
1 TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAAGTGAGACAAAAAT-TTTTTGAGGAAAAAT
123782 TATCT-AAGG
65 TATCTCAA-G
* * * * * *
123791 CGAGATAAAATTTTGTTTCGAGGGAAACTATCTCAAGTGAGACAATTATTGTTTTTG-TGAATAA
1 TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAAGTGAGACAA-AAAT-TTTTTGAGGAA-AA
**
123855 ATTATCTCTTG
63 ATTATCTCAAG
* * *
123866 TGAGATAAAATTATGTTCCGAGAGAAACTGTCTCGAGTGAGACAAAAATTT
1 TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAAGTGAGACAAAAATTT
123917 CAAGTGAAAC
Statistics
Matches: 323, Mismatches: 74, Indels: 39
0.74 0.17 0.09
Matches are distributed among these distances:
69 2 0.01
70 27 0.08
71 49 0.15
72 38 0.12
73 33 0.10
74 91 0.28
75 83 0.26
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (73 bp):
TGAGATAAAATTATGTTTCGAGAGAAACTATCTCAAGTGAGACAAAAATTTTTTGAGGAAAAATT
ATCTCAAG
Found at i:125641 original size:2 final size:2
Alignment explanation
Indices: 125634--125685 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
125624 ATATTGGTTG
125634 AT AT AT AT AT 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 AT AT AT AT AT
*
125676 AT AT GT AT AT
1 AT AT AT AT AT
125686 TTTATGACCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130921 original size:47 final size:47
Alignment explanation
Indices: 130868--130982 Score: 221
Period size: 47 Copynumber: 2.4 Consensus size: 47
130858 TAAAGGTCAT
130868 TTTTCTCCTCTCACGAGGACATCATCAAATTTTCTTTCTCAAGATCA
1 TTTTCTCCTCTCACGAGGACATCATCAAATTTTCTTTCTCAAGATCA
130915 TTTTCTCCTCTCACGAGGACATCATCAAATTTTCTTTCTCAAGATCA
1 TTTTCTCCTCTCACGAGGACATCATCAAATTTTCTTTCTCAAGATCA
*
130962 TTTTCTCCTCTCATGAGGACA
1 TTTTCTCCTCTCACGAGGACA
130983 AATTCAAGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (47 bp):
TTTTCTCCTCTCACGAGGACATCATCAAATTTTCTTTCTCAAGATCA
Found at i:133475 original size:16 final size:16
Alignment explanation
Indices: 133454--133484 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
133444 GTCGAAAGGC
133454 TCATTTTCGATAAGTA
1 TCATTTTCGATAAGTA
133470 TCATTTTCGATAAGT
1 TCATTTTCGATAAGT
133485 CTAAATATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (16 bp):
TCATTTTCGATAAGTA
Found at i:134395 original size:27 final size:27
Alignment explanation
Indices: 134336--134396 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 27
134326 ATTTTCAAAT
134336 GAAAAATGAGATCAATCAAACTAATAA
1 GAAAAATGAGATCAATCAAACTAATAA
134363 GAAAAATTGAGATCAATCAAACTAATAA
1 GAAAAA-TGAGATCAATCAAACTAATAA
134391 GAAAAA
1 GAAAAA
134397 AATAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.18
Consensus pattern (27 bp):
GAAAAATGAGATCAATCAAACTAATAA
Found at i:140509 original size:32 final size:32
Alignment explanation
Indices: 140426--140514 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
140416 GACGCTCATG
* *
140426 TGCATTATCTGAATGCAACACTAACTCTACTA
1 TGCATTATCTGAATGCAATACTGACTCTACTA
* * * *
140458 TGTATTATTTGAATACAATACTGACTCTATTA
1 TGCATTATCTGAATGCAATACTGACTCTACTA
*
140490 TGCATTATCTAAATGCAATACTGAC
1 TGCATTATCTGAATGCAATACTGAC
140515 ATTGTAAAGC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (32 bp):
TGCATTATCTGAATGCAATACTGACTCTACTA
Found at i:144049 original size:13 final size:13
Alignment explanation
Indices: 144033--144057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
144023 TCTTTCTTTC
144033 TTTTTATATTTTA
1 TTTTTATATTTTA
144046 TTTTTATATTTT
1 TTTTTATATTTT
144058 GAGTATTGGT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATATTTTA
Found at i:144472 original size:2 final size:2
Alignment explanation
Indices: 144465--144699 Score: 186
Period size: 2 Copynumber: 130.0 Consensus size: 2
144455 TTTTGTCCTA
* *
144465 AT AT AT AT AT -T AT AT AGT AT AT AT AT GT -T AT AC A- AT -T AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
144504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AGT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
144546 AT AT AT -T AT -T AT -T AT AT A- AT -T AT AT A- AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144580 AT A- AT -T AT GAT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
144621 AT AT AT AT AT AT AT -T AT -T AT AT CT -T AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
144659 -T AT -T AT -T AT AT -T TT AT AT AT -T AT AT -T AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144693 AT -T AT AT
1 AT AT AT AT
144700 TGATTTTTAT
Statistics
Matches: 194, Mismatches: 6, Indels: 66
0.73 0.02 0.25
Matches are distributed among these distances:
1 29 0.15
2 157 0.81
3 8 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (2 bp):
AT
Found at i:144487 original size:16 final size:15
Alignment explanation
Indices: 144465--144699 Score: 212
Period size: 14 Copynumber: 16.0 Consensus size: 15
144455 TTTTGTCCTA
144465 ATATATATATTATAT
1 ATATATATATTATAT
* *
144480 A-GTATATA-TATGT
1 ATATATATATTATAT
*
144493 -TATACA-ATTATAT
1 ATATATATATTATAT
144506 ATATATATA-TATAT
1 ATATATATATTATAT
144520 ATATATATA-TATAT
1 ATATATATATTATAT
*
144534 ATATGTAGTATTATAT
1 ATATATA-TATTATAT
144550 AT-TAT-TATTATAT
1 ATATATATATTATAT
144563 A-ATTATATAATTATAT
1 ATA-TATAT-ATTATAT
*
144579 -TATA-ATTATGATAT
1 ATATATA-TATTATAT
144593 AGTATATATATATATAT
1 A-TATATATAT-TATAT
144610 ATATATATATTATAT
1 ATATATATATTATAT
144625 ATATATATATTATTAT
1 ATATATATATTA-TAT
*
144641 ATCTTATATATTATAT
1 AT-ATATATATTATAT
144657 AT-TAT-TATTATAT
1 ATATATATATTATAT
*
144670 -TTTATATATTATAT
1 ATATATATATTATAT
144684 -TATTATTATATTATAT
1 ATA-TA-TATATTATAT
144700 TGATTTTTAT
Statistics
Matches: 186, Mismatches: 12, Indels: 43
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.01
13 31 0.17
14 58 0.31
15 29 0.16
16 51 0.27
17 15 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (15 bp):
ATATATATATTATAT
Found at i:144496 original size:27 final size:26
Alignment explanation
Indices: 144466--144699 Score: 194
Period size: 27 Copynumber: 9.2 Consensus size: 26
144456 TTTGTCCTAA
*
144466 TATATATATTATATAGTATATATATGT
1 TATATATATTATATATTATATATAT-T
* *
144493 TATACA-ATTATATA-TATATATATA
1 TATATATATTATATATTATATATATT
* *
144517 TATATATA-TATATA-TATATATGTAG
1 TATATATATTATATATTATATATAT-T
144542 TATTATATATTAT-TATTATATA-ATT
1 TA-TATATATTATATATTATATATATT
*
144567 ATATAATTATATTATA-ATTATGATATA-G
1 -TAT-A-TATATTATATATTAT-ATATATT
144595 TATATATA-TATATA-TATATATATAT
1 TATATATATTATATATTATATATAT-T
*
144620 TATATATA-TATATATTAT-TATATC
1 TATATATATTATATATTATATATATT
144644 T-TATATATTATATATTATTATTATATT
1 TATATATATTATATATTA-TA-TATATT
144671 T-TATATATTATATTATTAT-TATA-T
1 TATATATATTATA-TATTATATATATT
144695 TATAT
1 TATAT
144700 TGATTTTTAT
Statistics
Matches: 175, Mismatches: 11, Indels: 44
0.76 0.05 0.19
Matches are distributed among these distances:
23 11 0.06
24 38 0.22
25 45 0.26
26 24 0.14
27 48 0.27
28 8 0.05
29 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (26 bp):
TATATATATTATATATTATATATATT
Found at i:144512 original size:8 final size:8
Alignment explanation
Indices: 144465--144699 Score: 186
Period size: 7 Copynumber: 32.5 Consensus size: 8
144455 TTTTGTCCTA
144465 ATATATAT
1 ATATATAT
144473 AT-TATAT
1 ATATATAT
144480 AGTATATAT
1 A-TATATAT
*
144489 ATGT-TAT
1 ATATATAT
*
144496 ACA-AT-T
1 ATATATAT
144502 ATATATAT
1 ATATATAT
144510 ATATATAT
1 ATATATAT
144518 ATATATAT
1 ATATATAT
144526 ATATATAT
1 ATATATAT
*
144534 ATATGTAGT
1 ATATATA-T
144543 AT-TATAT
1 ATATATAT
144550 AT-TAT-T
1 ATATATAT
144556 AT-TATAT
1 ATATATAT
144563 A-AT-TAT
1 ATATATAT
144569 ATA-AT-T
1 ATATATAT
144575 ATAT-TAT
1 ATATATAT
144582 A-AT-TAT
1 ATATATAT
144588 GATATAGTAT
1 -ATATA-TAT
144598 ATATATAT
1 ATATATAT
144606 ATATATAT
1 ATATATAT
144614 ATATAT-T
1 ATATATAT
144621 ATATATAT
1 ATATATAT
144629 ATATAT-T
1 ATATATAT
144636 AT-TATAT
1 ATATATAT
*
144643 CT-TATAT
1 ATATATAT
144650 AT-TATAT
1 ATATATAT
144657 AT-TAT-T
1 ATATATAT
144663 AT-TATAT
1 ATATATAT
*
144670 -TTTATAT
1 ATATATAT
144677 AT-TATAT
1 ATATATAT
144684 -TAT-TAT
1 ATATATAT
144690 -TATAT-T
1 ATATATAT
144696 ATAT
1 ATAT
144700 TGATTTTTAT
Statistics
Matches: 195, Mismatches: 8, Indels: 49
0.77 0.03 0.19
Matches are distributed among these distances:
6 41 0.21
7 71 0.36
8 66 0.34
9 14 0.07
10 3 0.02
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (8 bp):
ATATATAT
Found at i:149034 original size:54 final size:54
Alignment explanation
Indices: 148948--149131 Score: 278
Period size: 54 Copynumber: 3.4 Consensus size: 54
148938 ATTACACCTA
** *
148948 AGTGCCAAAATTATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
1 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACAT
* *
149002 AGTACCAAAATGGTAATTCACAAACTCATTATGAATTACATGGGTTACACACAT
1 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACAT
* * *
149056 AGTGCGAAAATGGTAATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
1 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACAT
* *
149110 AGTGCCGAAATGGTAATACACA
1 AGTGCCAAAATGGTAATTCACA
149132 TAGTACTAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (54 bp):
AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACAT
Found at i:158744 original size:2 final size:2
Alignment explanation
Indices: 158735--159032 Score: 446
Period size: 2 Copynumber: 156.0 Consensus size: 2
158725 AGTATATAAA
* *
158735 AT AT -T AT AT AGT AT AT AT AT AT GT -T AT AC A- AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
158775 AT AT AT AT AT 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 AT AT AT AT AT
158817 AT AT AT AT AT 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 AT AT AT AT AT
158859 AT AT AT AT AT 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 AT AT AT AT AT
*
158901 AT -T AT AT AT -T AT AT AT AT TT AT AT AT AT AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
158939 AT AT AT -T AT -T AT AT -T AT -T AT -T AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
158975 AT AT AT AT AT AT AT TT AT -T AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159015 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
159033 TAATTTTATC
Statistics
Matches: 274, Mismatches: 6, Indels: 32
0.88 0.02 0.10
Matches are distributed among these distances:
1 15 0.05
2 257 0.94
3 2 0.01
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:162488 original size:653 final size:653
Alignment explanation
Indices: 161191--162502 Score: 2351
Period size: 654 Copynumber: 2.0 Consensus size: 653
161181 CTAATCAAGA
* *
161191 TTGCTTTTATTTGAAATCATGTTTATCTTCCCTGCTATGGACCTTCAGATTGAATTTGGATACGT
1 TTGCTTTTATTTGAAATAATGTTTATCTTCCCTGCTATGGACCTTCAGATTGAATTTGGATACAT
161256 GATTTTATGTTTGTGGATAGTTTCTCATGACACTCAACTCTGATTTGCGATTCTCAGTGGTTTTC
66 GATTTTATGTTTGTGGATAGTTTCTCATGACACTCAACTCTGATTTGCGATTCTCAGTGGTTTTC
*
161321 CAATAGCTTAATTCTCATTTTTGGTTTGTTTACCGATGCAGTCAGATTTATTCGTATCTATTTTT
131 CAATAGCTTAATTCTCATTTTTGGTTCGTTTACCGATGCAGTCAGATTTATTCGTATCTATTTTT
*
161386 GTTCGAGTCTTTTGGTTGGGTTTTTAACCTTTTCCATGTATTCCTTATAATCTAAAGTGGCTAGT
196 GTTCGAGTCTTTTGGTTGGGTTTTTAACCTTTTCCATGTATTCCTTATAATCTAAAATGGCTAGT
*
161451 TTCAATATTATAGGAAAAGTTTAAATTATGTATTTAGTTTATAATTATAGTTGTAAACTCTTAGG
261 TTCAATATTATAGGAAAAGTTCAAATTATGTATTTAGTTTATAATTATAGTTGTAAACTCTTAGG
161516 GATCATTTGGTTCATGGAATATAATATTACCTTTGGGAATAAGATTACTAGAATGTTACATTACT
326 GATCATTTGGTTCATGGAATATAATATTACCTTTGGGAATAAGATTACTAGAATGTTACATTACT
*
161581 TAACATATTACTATGAATGTTATATTACCTTGTTTGATTTGTTTAGCAGGAATGTAAGATTATAG
391 TAACATATTAATATGAATGTTATATTACCTTGTTTGATTTGTTTAGCAGGAATGTAAGATTATAG
161646 TGTTTGGTTGAAGGAATATAAGATAGAAAAAATGTATGTTTTATCAAATTATCCTTGAGATATAT
456 TGTTTGGTTGAAGGAATATAAGATAGAAAAAATGTATGTTTTATCAAATTATCCTTGAGATATAT
*
161711 TTTCTTTTTTTAGTATAACCACCGGTTTCCAATCTATTGATCGACTAATCTGGATCGGGTAATGC
521 TTTCTTTTTTTAGTATAACCACCGATTTCCAATCTATTGATCGACTAATCTGGATCGGGTAATGC
* * * *
161776 AGGGGTAAGGGCGACCCTCTCAACCCAGTTTACTCCAATCGCGATCATTAGGATTCATACCCCTG
586 AGAGGTAAGGGCGACCCTCTCAACCCAGTTTACTCCAAACACGATCATCAGGATTCATACCCCTG
161841 ATC
651 ATC
* *
161844 TTGCTTTTCTTTGAAATAATGTTTATTTTCCCTGCTATGGACCTTCAGATTGAATTTGGA-AGCA
1 TTGCTTTTATTTGAAATAATGTTTATCTTCCCTGCTATGGACCTTCAGATTGAATTTGGATA-CA
*
161908 TGATTTTATGTTTGTGGATAGTTTCTCATGACACTCAACTCTGATTTGCGGTTCTC-GATGGTTT
65 TGATTTTATGTTTGTGGATAGTTTCTCATGACACTCAACTCTGATTTGCGATTCTCAG-TGGTTT
* * * *
161972 TTCAATAGCTTAATTCTCTTTTTTTGGTTCGTTTGCCGATGCAGTCAGATTTATTTGTATCTATT
129 TCCAATAGCTTAATTCTC-ATTTTTGGTTCGTTTACCGATGCAGTCAGATTTATTCGTATCTATT
162037 TTTGTTCGAGTCTTTTGGTTGGGTTTTTAACCTTTTCCATGTATTCCTTATAATCTAAAATGGCT
193 TTTGTTCGAGTCTTTTGGTTGGGTTTTTAACCTTTTCCATGTATTCCTTATAATCTAAAATGGCT
* *
162102 AGTTTCAATGTTATAGGAAAAGTTCAAATTATGTATTTAGTTTATAATTGTAGTTGTAAACTCTT
258 AGTTTCAATATTATAGGAAAAGTTCAAATTATGTATTTAGTTTATAATTATAGTTGTAAACTCTT
*
162167 AGGGATCATTTGGTTCATGGAATATAATATTACCTTTGGGAATAAGATTACTGGAATGTTACATT
323 AGGGATCATTTGGTTCATGGAATATAATATTACCTTTGGGAATAAGATTACTAGAATGTTACATT
*
162232 ACTTAACATATTAATGTGAATGTTATATTACCTTGTTTGATTTGTTTAGCAGGAATGTAAGATTA
388 ACTTAACATATTAATATGAATGTTATATTACCTTGTTTGATTTGTTTAGCAGGAATGTAAGATTA
*
162297 TAGTGTTTGGTTGAAGGAATATAATATAGAAAAAATGTATGTTTTATCAAATTATCCTTGAGATA
453 TAGTGTTTGGTTGAAGGAATATAAGATAGAAAAAATGTATGTTTTATCAAATTATCCTTGAGATA
162362 T-TTTTCTTTTTTTAGTATAACCACCGATTTCCAATCTATTGATCGACTAATCTGGATCGGGTAA
518 TATTTTCTTTTTTTAGTATAACCACCGATTTCCAATCTATTGATCGACTAATCTGGATCGGGTAA
* *
162426 TGTAGAGGTAAGGGCGACCCTCTCAACCCAGTTTACTCCAAACACGATCGTCAGGATTCATACCC
583 TGCAGAGGTAAGGGCGACCCTCTCAACCCAGTTTACTCCAAACACGATCATCAGGATTCATACCC
162491 CTGATC
648 CTGATC
162497 TTGCTT
1 TTGCTT
162503 AATAAAATTT
Statistics
Matches: 631, Mismatches: 25, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
652 2 0.00
653 269 0.43
654 360 0.57
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (653 bp):
TTGCTTTTATTTGAAATAATGTTTATCTTCCCTGCTATGGACCTTCAGATTGAATTTGGATACAT
GATTTTATGTTTGTGGATAGTTTCTCATGACACTCAACTCTGATTTGCGATTCTCAGTGGTTTTC
CAATAGCTTAATTCTCATTTTTGGTTCGTTTACCGATGCAGTCAGATTTATTCGTATCTATTTTT
GTTCGAGTCTTTTGGTTGGGTTTTTAACCTTTTCCATGTATTCCTTATAATCTAAAATGGCTAGT
TTCAATATTATAGGAAAAGTTCAAATTATGTATTTAGTTTATAATTATAGTTGTAAACTCTTAGG
GATCATTTGGTTCATGGAATATAATATTACCTTTGGGAATAAGATTACTAGAATGTTACATTACT
TAACATATTAATATGAATGTTATATTACCTTGTTTGATTTGTTTAGCAGGAATGTAAGATTATAG
TGTTTGGTTGAAGGAATATAAGATAGAAAAAATGTATGTTTTATCAAATTATCCTTGAGATATAT
TTTCTTTTTTTAGTATAACCACCGATTTCCAATCTATTGATCGACTAATCTGGATCGGGTAATGC
AGAGGTAAGGGCGACCCTCTCAACCCAGTTTACTCCAAACACGATCATCAGGATTCATACCCCTG
ATC
Found at i:162825 original size:100 final size:95
Alignment explanation
Indices: 162659--162851 Score: 314
Period size: 100 Copynumber: 2.0 Consensus size: 95
162649 TGTAAGTATG
* *
162659 TATTTATTTTTAGGTTGAGAAATGTACATTATCGGTGTAAGTATAATTGCTACGCTTCTTTATTT
1 TATTTATTTTTAGGTTGAGAAATGTACATTACCGGTGTAAGTATAATTGCTACACTTCTTTATTT
*
162724 ATGCTACATGTATGAGTTGTATAAAAAAGT
66 ATGCTACATGTATGAGTTGTACAAAAAAGT
162754 TATTTATTTTTAGGTTGAGAAATGTACATACTTACACCGGTGTAAGTATAATTGCTACACTTCTT
1 TATTTATTTTTAGGTTGAGAAATGTAC--A-TT--ACCGGTGTAAGTATAATTGCTACACTTCTT
162819 TATTTATGCTACATGTATGAGTTGTACAAAAAA
61 TATTTATGCTACATGTATGAGTTGTACAAAAAA
162852 ATATTATATC
Statistics
Matches: 90, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
95 27 0.30
97 1 0.01
98 2 0.02
100 60 0.67
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (95 bp):
TATTTATTTTTAGGTTGAGAAATGTACATTACCGGTGTAAGTATAATTGCTACACTTCTTTATTT
ATGCTACATGTATGAGTTGTACAAAAAAGT
Found at i:167800 original size:16 final size:14
Alignment explanation
Indices: 167764--167801 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
167754 TATACCTTTA
*
167764 ATGACACATGGACG
1 ATGACACACGGACG
167778 ATGACACACGGACG
1 ATGACACACGGACG
167792 ATGACACACG
1 ATGACACACG
167802 CTAATTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.26, T:0.11
Consensus pattern (14 bp):
ATGACACACGGACG
Found at i:172397 original size:2 final size:2
Alignment explanation
Indices: 172386--172429 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
172376 TCAATTTACA
172386 AT AT -T AT AT 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 AT AT AT AT AT
172427 AT A
1 AT A
172430 ATTTACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172598 original size:85 final size:85
Alignment explanation
Indices: 172449--172614 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
172439 ATACAATCAC
* * *
172449 GACACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACACAATGTAACTCATA
1 GACACACAAATGTGTGTCATCTTATTTAATGACGTGGGCTTCAATGACACACAATGTAACTCATA
* * *
172514 CATGCTTGTCATAAATTTAT
66 AATGCGTATCATAAATTTAT
* * *
172534 GACACACAAATGTGTGTCATCTTAATTT-ATGACAG-GGGCTTCAATGACGCTCAATG-CACGTC
1 GACACACAAATGTGTGTCATCTT-ATTTAATGAC-GTGGGCTTCAATGACACACAATGTAAC-TC
172596 ATAAATGCGTATCATAAAT
63 ATAAATGCGTATCATAAAT
172615 GTGAGTCATA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 2 0.03
85 63 0.91
86 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTATTTAATGACGTGGGCTTCAATGACACACAATGTAACTCATA
AATGCGTATCATAAATTTAT
Found at i:172610 original size:13 final size:13
Alignment explanation
Indices: 172594--172642 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
172584 TCAATGCACG
172594 TCATAAATGCGTA
1 TCATAAATGCGTA
*
172607 TCATAAATGTG-A
1 TCATAAATGCGTA
*
172619 GTCATAAATGCGTG
1 -TCATAAATGCGTA
*
172633 TCATCAATGC
1 TCATAAATGC
172643 ACGTCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 29 0.97
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (13 bp):
TCATAAATGCGTA
Found at i:172615 original size:26 final size:26
Alignment explanation
Indices: 172586--172653 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
172576 AATGACGCTC
172586 AATGCACGTCATAAATGCGTATCATA
1 AATGCACGTCATAAATGCGTATCATA
* * *
172612 AATGTGA-GTCATAAATGCGTGTCATC
1 AATG-CACGTCATAAATGCGTATCATA
172638 AATGCACGTCATAAAT
1 AATGCACGTCATAAAT
172654 TTATGACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 34 0.94
27 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (26 bp):
AATGCACGTCATAAATGCGTATCATA
Found at i:174268 original size:17 final size:17
Alignment explanation
Indices: 174247--174287 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
174237 TTGGTTCATC
174247 AATTAAACTAGTCCATT
1 AATTAAACTAGTCCATT
* *
174264 CATTAAACTAGTTCATT
1 AATTAAACTAGTCCATT
174281 AATTAAA
1 AATTAAA
174288 TTAACTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (17 bp):
AATTAAACTAGTCCATT
Found at i:176740 original size:41 final size:41
Alignment explanation
Indices: 176450--176742 Score: 349
Period size: 41 Copynumber: 7.1 Consensus size: 41
176440 CCATGATTGA
* * *
176450 ATTGAATTGAATTGAATTGTGAATTATTGCATGTTGTCGTG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCATG
*
176491 ATCGAATT-AAGTCGAATTGTGAATTATTGCATGTTGCCATG
1 ATTGAATTGAA-TCGAATTGTGAATTATTGCATGTTGCCATG
* * * ***
176532 ATCGAATT-AAGCTGAATTTTGAATTATTGCATGCCACCATG
1 ATTGAATTGAATC-GAATTGTGAATTATTGCATGTTGCCATG
* * *
176573 ATTGAATTGAATCAAATTCTGAATTATTGCATGCTGCCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCATG
* *
176614 ATTGAATTGAATCGAATTGTAAAGTATTGCATGTTGCCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCATG
* * * *
176655 ATCGAATTGAGTCGAATGGTGAATTATTGCATGTTGACATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCATG
* *
176696 ATTGAATTGAATCGAATTGTAAATTATTGCATGCTT-CCAAG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATG-TTGCCATG
176737 ATTGAA
1 ATTGAA
176743 CTCGACTGAA
Statistics
Matches: 216, Mismatches: 32, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
40 3 0.01
41 208 0.96
42 5 0.02
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (41 bp):
ATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCATG
Found at i:181108 original size:23 final size:23
Alignment explanation
Indices: 181078--181122 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
181068 AATAATTTTG
181078 TCTTTGTGACACGTTTATCTCTA
1 TCTTTGTGACACGTTTATCTCTA
*
181101 TCTTTGTGGCACGTTTATCTCT
1 TCTTTGTGACACGTTTATCTCT
181123 GCCTTTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.49
Consensus pattern (23 bp):
TCTTTGTGACACGTTTATCTCTA
Found at i:181128 original size:23 final size:23
Alignment explanation
Indices: 181079--181128 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
181069 ATAATTTTGT
*
181079 CTTTGTGACACGTTTATCTCTAT
1 CTTTGTGACACGTTTATCTCTAC
* *
181102 CTTTGTGGCACGTTTATCTCTGC
1 CTTTGTGACACGTTTATCTCTAC
181125 CTTT
1 CTTT
181129 TGATAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (23 bp):
CTTTGTGACACGTTTATCTCTAC
Found at i:191641 original size:41 final size:41
Alignment explanation
Indices: 191594--191872 Score: 308
Period size: 41 Copynumber: 6.8 Consensus size: 41
191584 TAATTTTAGA
* * *
191594 ACAAACGCCGCTAAAGACT-GTACTTTAGTGACGTTTGTTCT
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT-TTAT
* * * * *
191635 AAAAACGCCGCTAAAGACTCATACTTTAGTGGCCTTTCTAT
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* ** * *
191676 ACAAACACTACTATAGACTCGTACTTTAGTGGCATTTTTAC
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
191717 ACAAATGCCGCTAAAGACTCGTACTTCAGTGGCGTTTTTAC
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
191758 ATAAACGTCGTTATAGACTCGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
191799 ACAAACGTCGTTATAGACTTGTACTTTAGTGGTGTTTTTAT
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* *
191840 ACAAATGCCGCTATAGACTTGTACTTTAGTGGC
1 ACAAACGCCGCTATAGACTCGTACTTTAGTGGC
191873 CGCTATAGAC
Statistics
Matches: 201, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
41 187 0.93
42 14 0.07
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (41 bp):
ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
Found at i:191776 original size:123 final size:122
Alignment explanation
Indices: 191594--191872 Score: 339
Period size: 123 Copynumber: 2.3 Consensus size: 122
191584 TAATTTTAGA
* *
191594 ACAAACGCCGCTAAAGACTGTACTTTAGTGACGTTTGTTCTAAAAACGCCGCTAAAGACTCATAC
1 ACAAATGCCGCTAAAGACTGTACTTTAGTGGCGTTTGTTCTAAAAACGCCGCTAAAGACTCATAC
191659 TTTAGTGGCCTTTCTATACAAACACTAC-TATAGACTCGTACTTTAGTGGCATTTTTAC
66 TTTAGTGGCCTTTCTATACAAAC-CT-CGTATAGACTCGTACTTTAGTGGCATTTTTAC
* * * * * *
191717 ACAAATGCCGCTAAAGACTCGTACTTCAGTGGCGTTT-TTAC-ATAAACGTCGTTATAGACTCGT
1 ACAAATGCCGCTAAAGACT-GTACTTTAGTGGCGTTTGTT-CTAAAAACGCCGCTAAAGACTCAT
* * * * ** *
191780 ACTTTAGTGGCGTTTTTATACAAACGTCGTTATAGACTTGTACTTTAGTGGTGTTTTTAT
64 ACTTTAGTGGCCTTTCTATACAAACCTCG-TATAGACTCGTACTTTAGTGGCATTTTTAC
*
191840 ACAAATGCCGCTATAGACTTGTACTTTAGTGGC
1 ACAAATGCCGCTAAAGAC-TGTACTTTAGTGGC
191873 CGCTATAGAC
Statistics
Matches: 134, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
121 1 0.01
122 1 0.01
123 115 0.86
124 17 0.13
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (122 bp):
ACAAATGCCGCTAAAGACTGTACTTTAGTGGCGTTTGTTCTAAAAACGCCGCTAAAGACTCATAC
TTTAGTGGCCTTTCTATACAAACCTCGTATAGACTCGTACTTTAGTGGCATTTTTAC
Found at i:191880 original size:25 final size:25
Alignment explanation
Indices: 191846--191897 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
191836 TTATACAAAT
*
191846 GCCGCTATAGACTTGTACTTTAGTG
1 GCCGCTATAGACTCGTACTTTAGTG
191871 GCCGCTATAGACTCGTACTTTAGTG
1 GCCGCTATAGACTCGTACTTTAGTG
191896 GC
1 GC
191898 GTTTTTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (25 bp):
GCCGCTATAGACTCGTACTTTAGTG
Found at i:191893 original size:66 final size:66
Alignment explanation
Indices: 191810--191938 Score: 195
Period size: 66 Copynumber: 2.0 Consensus size: 66
191800 CAAACGTCGT
* * * * *
191810 TATAGACTTGTACTTTAGTGGTGTTTTTATACAAATGCCGCTATAGACTTGTACTTTAGTGGCCG
1 TATAGACTCGTACTTTAGTGGCGTTTTTATACAAATGCCACTAAAGACTCGTACTTTAGTGGCCG
191875 C
66 C
* *
191876 TATAGACTCGTACTTTAGTGGCGTTTTTATACAAATGTCATTAAAGACTCGTACTTTAGTGGC
1 TATAGACTCGTACTTTAGTGGCGTTTTTATACAAATGCCACTAAAGACTCGTACTTTAGTGGC
191939 GTTTACACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (66 bp):
TATAGACTCGTACTTTAGTGGCGTTTTTATACAAATGCCACTAAAGACTCGTACTTTAGTGGCCG
C
Found at i:197889 original size:30 final size:30
Alignment explanation
Indices: 197852--197942 Score: 98
Period size: 31 Copynumber: 3.1 Consensus size: 30
197842 TCATTTAAAG
*
197852 TTTTTTTTGTCAAAATAAGTATCAAAACTTA
1 TTTTTTTTGTCAAAATAAGTATCAAAA-GTA
* *
197883 TTTTTTTTGTCAAAATAGGTATCTAAAGTA
1 TTTTTTTTGTCAAAATAAGTATCAAAAGTA
* *
197913 --TTTTTGGTCAAAAT-AGATATCTAAAGTA
1 TTTTTTTTGTCAAAATAAG-TATCAAAAGTA
197941 TT
1 TT
197943 CAATTTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.02
28 24 0.46
30 2 0.04
31 25 0.48
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (30 bp):
TTTTTTTTGTCAAAATAAGTATCAAAAGTA
Found at i:197925 original size:28 final size:28
Alignment explanation
Indices: 197847--197942 Score: 111
Period size: 28 Copynumber: 3.3 Consensus size: 28
197837 CACCTTCATT
* *
197847 TAAAGTTTTTTTTGTCAAAATAAGTATC
1 TAAAGTATTTTTTGTCAAAATAGGTATC
* *
197875 AAAACTTATTTTTTTTGTCAAAATAGGTATC
1 TAAA-GTA--TTTTTTGTCAAAATAGGTATC
* *
197906 TAAAGTATTTTTGGTCAAAATAGATATC
1 TAAAGTATTTTTTGTCAAAATAGGTATC
197934 TAAAGTATT
1 TAAAGTATT
197943 CAATTTTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
28 31 0.54
29 1 0.02
30 2 0.04
31 23 0.40
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (28 bp):
TAAAGTATTTTTTGTCAAAATAGGTATC
Found at i:199390 original size:21 final size:21
Alignment explanation
Indices: 199338--199392 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
199328 ATACTAATAG
*
199338 GGGTATCGGTACTTGACCCTA
1 GGGTATCGATACTTGACCCTA
* * *
199359 GAGTGTAGATACTTGACCCTA
1 GGGTATCGATACTTGACCCTA
199380 GGGTATCGATACT
1 GGGTATCGATACT
199393 ACTCACTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACTTGACCCTA
Found at i:203779 original size:18 final size:18
Alignment explanation
Indices: 203727--203779 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
203717 TAAAATACCA
203727 AAAATTAATAAT-ATAATT
1 AAAA-TAATAATAATAATT
* * *
203745 AAAATAATTACATTAATT
1 AAAATAATAATAATAATT
203763 AAAATAATAATAATAAT
1 AAAATAATAATAATAAT
203780 ACTAACATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATAATAATAATAATT
Found at i:204443 original size:30 final size:31
Alignment explanation
Indices: 204402--204473 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
204392 AGGTGAATCT
* *
204402 GTCAAAAATTTGTGA-CGATCCACATATTTC
1 GTCACAAATTTGTGATCGATCCACATATTCC
* *
204432 GTCACAAATTTGTGATGGGTCCACATATTCC
1 GTCACAAATTTGTGATCGATCCACATATTCC
*
204463 ATCACAAATTT
1 GTCACAAATTT
204474 AAAAAATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 14 0.39
31 22 0.61
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (31 bp):
GTCACAAATTTGTGATCGATCCACATATTCC
Found at i:209344 original size:20 final size:21
Alignment explanation
Indices: 209298--209358 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
209288 TTCCCCTGTG
*
209298 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
209321 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
209341 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
209359 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:216243 original size:50 final size:51
Alignment explanation
Indices: 216186--216346 Score: 144
Period size: 65 Copynumber: 2.9 Consensus size: 51
216176 TGAACAAAAG
216186 TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTTTTTTT-AT
1 TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTTTTTTTAAT
* * * * *
216236 TTCCGACGGAATGATTATTCCATCACAAATTAAATTGGTATATTTTAATTAAATTTGAACAAAAT
1 TTCCGACGGAATCATTGTCCCGTCATAAATTAAATT-G-ATA-TTT--TT---TTT------AAT
216301 TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTTTTT
1 TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTTTTT
216347 ATTGAAATGA
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
50 31 0.36
51 1 0.01
52 3 0.03
53 3 0.03
55 2 0.02
57 1 0.01
58 3 0.03
60 2 0.02
62 3 0.03
63 3 0.03
64 1 0.01
65 33 0.38
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (51 bp):
TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTTTTTTTAAT
Found at i:216255 original size:115 final size:115
Alignment explanation
Indices: 216113--216346 Score: 423
Period size: 115 Copynumber: 2.0 Consensus size: 115
216103 TAGTTAGTTA
*
216113 TTTTTTATTTCTGACGAAATGAGTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTG
1 TTTTTTATTTCCGACGAAATGAGTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTG
216178 AACAAAAGTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATT
66 AACAAAAGTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATT
* * *
216228 TTTTTTATTTCCGACGGAATGATTATTCCATCACAAATTAAATTGGTATATTTTAATTAAATTTG
1 TTTTTTATTTCCGACGAAATGAGTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTG
*
216293 AACAAAATTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATT
66 AACAAAAGTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATT
216343 TTTT
1 TTTT
216347 ATTGAAATGA
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (115 bp):
TTTTTTATTTCCGACGAAATGAGTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTG
AACAAAAGTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATT
Found at i:217895 original size:14 final size:14
Alignment explanation
Indices: 217878--217964 Score: 54
Period size: 14 Copynumber: 6.2 Consensus size: 14
217868 TTTTTATTTA
217878 TTTAATTTTAGTCC
1 TTTAATTTTAGTCC
* * *
217892 TTTAATTTCATTAC
1 TTTAATTTTAGTCC
*
217906 TTTAATTTTTTGT-C
1 TTTAA-TTTTAGTCC
*
217920 TTTTATTTT--TCCC
1 TTTAATTTTAGT-CC
* *
217933 TTTATTTTTCAGTAC
1 TTTAATTTT-AGTCC
*
217948 GTTAATTTTAGTCC
1 TTTAATTTTAGTCC
217962 TTT
1 TTT
217965 GATTATTGCA
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
11 1 0.02
13 12 0.23
14 27 0.51
15 12 0.23
16 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTAATTTTAGTCC
Found at i:218917 original size:18 final size:20
Alignment explanation
Indices: 218883--218922 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
218873 CTTTCAATTA
218883 TTTATTATTTATTATTTTAT
1 TTTATTATTTATTATTTTAT
218903 TTTATT-TTT-TTATTTTAT
1 TTTATTATTTATTATTTTAT
218921 TT
1 TT
218923 CATATCGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.55
19 3 0.15
20 6 0.30
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTATTATTTATTATTTTAT
Found at i:218922 original size:13 final size:13
Alignment explanation
Indices: 218890--218922 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
218880 TTATTTATTA
*
218890 TTTATTATTTTAT
1 TTTATTTTTTTAT
218903 TTTATTTTTTTAT
1 TTTATTTTTTTAT
218916 TTTATTT
1 TTTATTT
218923 CATATCGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:220326 original size:3 final size:3
Alignment explanation
Indices: 220318--220343 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
220308 CATTCATTAA
220318 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
220344 GATAAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:223246 original size:474 final size:472
Alignment explanation
Indices: 222354--223287 Score: 1575
Period size: 474 Copynumber: 2.0 Consensus size: 472
222344 TAAATGTGGG
* *
222354 GTTTCCTGACCATCCAAGACACCAAGACTATAATAGGATCTTCTCGATTAGCTTAATAAATTCTA
1 GTTTCCTGACCATCCAAGACACCAAGACTATAATAGGATCTTCTCGATTAACTTAAGAAATTCTA
* *
222419 AATATGAATATTTAAAAGGTTAATAAATTATTATTATTATAGATTACACAATAAAGCTGAGCTAT
66 AATATGAATACTCAAAAGGTTAATAAATTATTATTATTATAGATTACACAATAAAGCTGAGCTAT
222484 TCCACTAAAGCAATTGGTTATAGAGGAAACTAAAATGCCCTTGCTTTATGAATAGATTGCATTCA
131 TCCACTAAAGCAATTGGTTATAGAGGAAACTAAAATGCCCTTGCTTTATGAATAGATTGCATTCA
* *
222549 AGCCATGACATTGCTCGGGTACTTGAAAATTTAGTGTTTACTCCACTGGATTGTCAAGTCGAAGA
196 AACCATGACATTGCTCGGGTACTTGAAAATTTAGTGTTTACTCCACTGGATTGTCAAGTAGAAGA
* *
222614 CATTGTGACGAGATGAACCCTTCAGCTATGCCTGAACAAAGGTAAACTAAATAAATTCCAAACAA
261 CATTGTGACGAGATGAACCCTTCAGCTATGCCTGAACAAAGGAAAACAAAATAAATTCCAAACAA
*
222679 TAAAGGTTATGTTGTATATGATTGATCTAATAATGAGTTTCGATGAAAATGGACTAAAAGAGTTG
326 TAAAGGTTATGATGTATATGATTGATCTAATAATGAGTTTCGATGAAAATGGACTAAAAGAGTTG
222744 AGGAACACCTATTATAGTCAACTTCACATAAGAACTCAGGAATTC-TTTTTTTAGACTGATGTCT
391 AGGAACACCTATTATAGTCAACTTCACATAAGAACTCAGGAATTCTTTTTTTTAGACTGATGTCT
222808 CTGCAATCTAATAATGA
456 CTGCAATCTAATAATGA
* *
222825 GTTTCTTGACCATCCAAGACACCTAGACTATAATAGGATCTTCTCGATTAACTTAAGAAATTCTA
1 GTTTCCTGACCATCCAAGACACCAAGACTATAATAGGATCTTCTCGATTAACTTAAGAAATTCTA
*
222890 AATCTGAATACTCAAAAGGTTAATAAATTATTATTATTATTATAGATTACACAATAAAGCTGAGC
66 AATATGAATACTCAAAAGGTTAAT-AA--ATTATTATTATTATAGATTACACAATAAAGCTGAGC
*
222955 TATTCCACTAAAGCAATTGGTTATAGAGGAAACTCAAATGCCC-TGACTTTATGAATAGATTGCA
128 TATTCCACTAAAGCAATTGGTTATAGAGGAAACTAAAATGCCCTTG-CTTTATGAATAGATTGCA
** * *
223019 TTCAAACCATGACATTGCTCGGGTACTTGGCAATTTAGTGTTTGCTCTACTGGATTGTCAAGTAG
192 TTCAAACCATGACATTGCTCGGGTACTTGAAAATTTAGTGTTTACTCCACTGGATTGTCAAGTAG
*
223084 AAGACATTGTGACGATATGAACCCTTCAGCTATGCCTGAACAAAGGAAAACAAAATAAATTCCAA
257 AAGACATTGTGACGAGATGAACCCTTCAGCTATGCCTGAACAAAGGAAAACAAAATAAATTCCAA
* * * *
223149 ACAATAAAGGTTATGATGTCTATGCTTGATCTAATAATGAGTTTTGATGAAAATGGACTAAAGGA
322 ACAATAAAGGTTATGATGTATATGATTGATCTAATAATGAGTTTCGATGAAAATGGACTAAAAGA
* * * * *
223214 GTTGAGGAACACTTGTTATAGTCAATTTCACATAAGCACTCATGAATTCTTTTTTTTAGACTGAT
387 GTTGAGGAACACCTATTATAGTCAACTTCACATAAGAACTCAGGAATTCTTTTTTTTAGACTGAT
223279 GTCTCTGCA
452 GTCTCTGCA
223288 CTACCTCTGC
Statistics
Matches: 431, Mismatches: 27, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
471 82 0.19
472 2 0.00
473 2 0.00
474 321 0.74
475 24 0.06
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (472 bp):
GTTTCCTGACCATCCAAGACACCAAGACTATAATAGGATCTTCTCGATTAACTTAAGAAATTCTA
AATATGAATACTCAAAAGGTTAATAAATTATTATTATTATAGATTACACAATAAAGCTGAGCTAT
TCCACTAAAGCAATTGGTTATAGAGGAAACTAAAATGCCCTTGCTTTATGAATAGATTGCATTCA
AACCATGACATTGCTCGGGTACTTGAAAATTTAGTGTTTACTCCACTGGATTGTCAAGTAGAAGA
CATTGTGACGAGATGAACCCTTCAGCTATGCCTGAACAAAGGAAAACAAAATAAATTCCAAACAA
TAAAGGTTATGATGTATATGATTGATCTAATAATGAGTTTCGATGAAAATGGACTAAAAGAGTTG
AGGAACACCTATTATAGTCAACTTCACATAAGAACTCAGGAATTCTTTTTTTTAGACTGATGTCT
CTGCAATCTAATAATGA
Found at i:225009 original size:139 final size:139
Alignment explanation
Indices: 224754--225424 Score: 862
Period size: 139 Copynumber: 4.8 Consensus size: 139
224744 GGATAAACCA
** * * * *
224754 ATCAACATTTTTAGTGGAGAGTTCATAATGAAAAGAACTCATTCAATG-AGTGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAG-AAGAAGAAGTTCA
* * * *
224818 TAGTAAGAAGAACTTGTTCAACCTCAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCT
224883 CACTCGAGGG
130 CACTCGAGGG
* * ** * *
224893 ATGACCATTTCCAGTGGATTGTTCATAATGAGAAGAACTCATCCGATGATGAAGAATAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAAGAAGTTCAT
* * * *
224958 AATGAGAATAACTTGTTCAACCTTAACTCGATTCCTCACATATGGAGTTGAATCAACAACACGTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTC
* * **
225023 TCTTGAATG
131 ACTCGAGGG
* * * *
225032 ATCAACATTTCCAGTGGAGAGTTTATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAAGAAGTTCAT
* *
225097 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATTAACAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTC
225162 ACTCGAGGG
131 ACTCGAGGG
* * *
225171 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAAGGAGAAAAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAAGAAGTTCAT
* *
225236 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAATA-TTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTC
* *
225300 GCTCGTGGG
131 ACTCGAGGG
* * * * * * *
225309 ATCAATATGTCAAGTGGAGAGTTAATAATAAGAAGAACTCAACCGA-CAAGAGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGA-AGAAGAAGTTCA
* * * *
225373 TAATAAGAAGAACTTGTTCAACCTTATCTCGTTTCCATCACATAAGGAGTTG
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTG
225425 GAACATAACC
Statistics
Matches: 461, Mismatches: 68, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
137 3 0.01
138 90 0.20
139 367 0.80
140 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (139 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACAACACCTC
ACTCGAGGG
Found at i:226946 original size:21 final size:21
Alignment explanation
Indices: 226920--226967 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
226910 ACTAACTTTT
* ** *
226920 CTAACTTCTAACTTCTAATCA
1 CTAACTGCTAACCGCTAACCA
226941 CTAACTGCTAACCGCTAACCA
1 CTAACTGCTAACCGCTAACCA
226962 CTAACT
1 CTAACT
226968 ATTTATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.29
Consensus pattern (21 bp):
CTAACTGCTAACCGCTAACCA
Found at i:227191 original size:14 final size:14
Alignment explanation
Indices: 227153--227179 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
227143 TTACTTTTAT
227153 TCATTTAATTTCAG
1 TCATTTAATTTCAG
227167 TCATTTAATTTCA
1 TCATTTAATTTCA
227180 TTACTTTAAT
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:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (14 bp):
TCATTTAATTTCAG
Found at i:229141 original size:3 final size:3
Alignment explanation
Indices: 229133--229175 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
229123 ATATTAAATA
229133 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TACT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
229176 AATATGTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:230398 original size:29 final size:30
Alignment explanation
Indices: 230364--230429 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
230354 ATTTTGATAC
* *
230364 TTAAGTTTCTGTTATT-TTATTTTAGTCAT
1 TTAAGTTTCTATTATTGTTATTTTAATCAT
* *
230393 TTAAGTTTCTATTTTTGTTATTTTAATCCT
1 TTAAGTTTCTATTATTGTTATTTTAATCAT
230423 TTAAGTT
1 TTAAGTT
230430 AATGTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.21, C:0.08, G:0.09, T:0.62
Consensus pattern (30 bp):
TTAAGTTTCTATTATTGTTATTTTAATCAT
Found at i:230683 original size:16 final size:17
Alignment explanation
Indices: 230646--230684 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
230636 TGCAAACTAA
230646 TTTTTATCTTAAAAATG
1 TTTTTATCTTAAAAATG
* *
230663 ATTTT-TCTTAAAATTG
1 TTTTTATCTTAAAAATG
230679 TTTTTA
1 TTTTTA
230685 AAAGACGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 2
0.78 0.13 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTTTATCTTAAAAATG
Found at i:231602 original size:19 final size:20
Alignment explanation
Indices: 231574--231611 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
231564 TCCCACTAAC
231574 TTTTCCTTCATTTT-TTTTG
1 TTTTCCTTCATTTTATTTTG
*
231593 TTTTCTTTCATTTTATTTT
1 TTTTCCTTCATTTTATTTT
231612 TATTATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTCCTTCATTTTATTTTG
Found at i:233514 original size:19 final size:19
Alignment explanation
Indices: 233492--233538 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
233482 CAAAAAGAGG
233492 AAGAAAAAAGAAAAAAACA
1 AAGAAAAAAGAAAAAAACA
* * *
233511 AAGAGAAAATAAAAAAAGA
1 AAGAAAAAAGAAAAAAACA
*
233530 AACAAAAAA
1 AAGAAAAAA
233539 CAAAGGAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (19 bp):
AAGAAAAAAGAAAAAAACA
Found at i:233536 original size:12 final size:12
Alignment explanation
Indices: 233495--233538 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 12
233485 AAAGAGGAAG
233495 AAAAAAGAAAAA
1 AAAAAAGAAAAA
233507 AACAAAGAGAAAATA
1 AA-AAA-AGAAAA-A
233522 AAAAAAGAAACAA
1 AAAAAAGAAA-AA
233535 AAAA
1 AAAA
233539 CAAAGGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.07
13 13 0.46
14 10 0.36
15 3 0.11
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:234664 original size:31 final size:32
Alignment explanation
Indices: 234614--234699 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
234604 AGGAACAATG
* *
234614 GGGGCATCTTTGAAGATTCAACCTCAAATATT
1 GGGGCATCTTTGGAGATTCAACATCAAATATT
**
234646 GGGGCAT-TTTGGAGATTCAACATTGAATATT
1 GGGGCATCTTTGGAGATTCAACATCAAATATT
*
234677 GGGGCATCTTTGGGGATTCAACA
1 GGGGCATCTTTGGAGATTCAACA
234700 CCCTAATGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 27 0.56
32 21 0.44
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (32 bp):
GGGGCATCTTTGGAGATTCAACATCAAATATT
Found at i:235123 original size:45 final size:46
Alignment explanation
Indices: 235062--235148 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
235052 TTACTCAAGA
235062 TTGGATTTTCAACTTCACGAA-GAAGGATATCCAACTCAAAACCAAT
1 TTGGATTTTCAACTTCAC-AACGAAGGATATCCAACTCAAAACCAAT
* *
235108 TTGGA-TTTCAACTTCACAACGAAGGATATTCAATTCAAAAC
1 TTGGATTTTCAACTTCACAACGAAGGATATCCAACTCAAAAC
235149 TAACTTCACA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 2 0.05
45 31 0.82
46 5 0.13
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (46 bp):
TTGGATTTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAAT
Found at i:235140 original size:22 final size:22
Alignment explanation
Indices: 235064--235144 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
235054 ACTCAAGATT
*
235064 GGATTTTCAACTTCACGAA-GAA
1 GGATATTCAACTTCAC-AACGAA
* * *
235086 GGATATCCAAC-TCAAAACCAA
1 GGATATTCAACTTCACAACGAA
235107 TTTGGAT-TTCAACTTCACAACGAA
1 ---GGATATTCAACTTCACAACGAA
235131 GGATATTCAA-TTCA
1 GGATATTCAACTTCA
235145 AAACTAACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
22 14 0.30
23 5 0.11
24 12 0.26
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (22 bp):
GGATATTCAACTTCACAACGAA
Found at i:235357 original size:201 final size:202
Alignment explanation
Indices: 234945--235359 Score: 690
Period size: 201 Copynumber: 2.1 Consensus size: 202
234935 GATGGTGGTT
* * * * * *
234945 GCTCAACTTCACAGCGAATGAGCGACTGTCCACAAACAACTTTCCAGTTTCATTCATAGTCAATT
1 GCTCAACTTCACAGCAAAGGAGCAACTGTCAACAAACAACTTTCCAGTTTCATTAAGAGTCAATT
235010 TCAACTTCACAACAAAGGATATTGAACTCGAAGTGACACAATTTACTCAAGATTGGATTTTCAAC
66 TCAACTTCACAACAAAGGATATTGAACTCGAAGTGACACAATTTACTCAAGATTGGATTTTCAAC
235075 TTCACGAAGAAGGATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAACGAAGGATATTCA
131 TTCACGAAGAAGGATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAACGAAGGATATTCA
235140 ATTCAAA
196 ATTCAAA
* *
235147 ACT-AACTTCACAGCAAAGGGGCAACTGTCAACAAACAACTTTCCAGTTTCATTAAGAGTCAATT
1 GCTCAACTTCACAGCAAAGGAGCAACTGTCAACAAACAACTTTCCAGTTTCATTAAGAGTCAATT
* *
235211 TCAACTTCACAACGAAGGATATTGAACTTGAAGTGACACAATTTACTCAAGATTGGA-TTTCAAC
66 TCAACTTCACAACAAAGGATATTGAACTCGAAGTGACACAATTTACTCAAGATTGGATTTTCAAC
* * * *
235275 TTCACGACGAAGGATATCCAACTCAAAACCAATTTGGATTTCAACTTCATAATGAATGATATTCA
131 TTCACGAAGAAGGATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAACGAAGGATATTCA
235340 ATTCAAA
196 ATTCAAA
235347 GCTCAACTTCACA
1 GCTCAACTTCACA
235360 ATGAATGAGC
Statistics
Matches: 197, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
200 77 0.39
201 118 0.60
202 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (202 bp):
GCTCAACTTCACAGCAAAGGAGCAACTGTCAACAAACAACTTTCCAGTTTCATTAAGAGTCAATT
TCAACTTCACAACAAAGGATATTGAACTCGAAGTGACACAATTTACTCAAGATTGGATTTTCAAC
TTCACGAAGAAGGATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAACGAAGGATATTCA
ATTCAAA
Found at i:235589 original size:115 final size:119
Alignment explanation
Indices: 235308--235702 Score: 462
Period size: 115 Copynumber: 3.3 Consensus size: 119
235298 CAAAACCAAT
* * * *
235308 TTGGATTTCAACTTCATAATGAATGATAT-TCAATTCAAAGCTCAACTTCACAATGAATGAGCCA
1 TTGGATTTCAACTTCACAACGAAGGATATCT-AATTCAAAGCTCAACTTCACAACGAATGAGCCA
* * * *
235372 TCCACGATTTCAACTTTACGACGAAGGATATCGTGCCCACAAGCAGCCATGCAACCC
65 TCCACGATTTCAAC-TTACAACGAA-GATATCGTGCCCACAAGCAGCAATGTAACCA
* * * * * *
235429 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTTATAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * *
235494 CCACGATTTTAACTT-C-ACG-A-ATATTGTGCCCACAAGCAACAATGTAACCA
66 CCACGATTTCAACTTACAACGAAGATATCGTGCCCACAAGCAGCAATGTAACCA
* * *
235544 TTGGATTTCAACTTCACGACGAAGGATATCTAATTGAAAGATCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * *
235609 CAACGATTTCAATTTCACAACGAAGGATATCGTGCCCACAAGCAGCAAT-TCAA-GA
66 CCACGATTTCAACTT-ACAACGAA-GATATCGTGCCCACAAGCAGCAATGT-AACCA
* *
235664 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
1 TTGGATTTCAACTTCACAACGAAGGATATCTAATTCAAA
235703 ACCAATTTGG
Statistics
Matches: 235, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
115 95 0.40
117 2 0.01
118 6 0.03
119 2 0.01
120 39 0.17
121 91 0.39
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (119 bp):
TTGGATTTCAACTTCACAACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAACTTACAACGAAGATATCGTGCCCACAAGCAGCAATGTAACCA
Found at i:236011 original size:85 final size:83
Alignment explanation
Indices: 235904--236228 Score: 341
Period size: 85 Copynumber: 3.8 Consensus size: 83
235894 GTACATCAAA
* * *
235904 CTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAGTTCAAAGGC
1 CTCAA-GCGAGAAGAGCTATCTGTCAGC-AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
235969 ACATCAAATTTACATCATAG
64 ACATCAAATTTACAGCATAG
* * * * *
235989 CTCAAGTTGAGAAAAGCTATCTGTCTACCAAGACCTTCGATTTCGATTACATTTAGCTCAAAGGC
1 CTCAAG-CGAGAAGAGCTATCTGTC-AGCAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
236054 ACATCAAATTTACAGCATAA
64 ACATCAAATTTACAGCATAG
* *
236074 CTTAAAGCGAGAAGAGCTATATGTCAGCAA-ACCTTCGAGTTCGATTACATTCAGCTCATGAA--
1 C-TCAAGCGAGAAGAGCTATCTGTCAGCAAGACCTTCGAGTTCGATTACATTCAGCTCA--AAGG
* *
236136 CATATCTAATTTACAGCATAG
63 CACATCAAATTTACAGCATAG
* * ** * * * *
236157 CTCAAGGCGAGAAGGGCTATCTGTCAACAAGAATTTTCAAGTTCGATTTCATTCAGTTCGAAGGC
1 CTCAA-GCGAGAAGAGCTATCTGTCAGCAAG-ACCTTCGAGTTCGATTACATTCAGCTCAAAGGC
*
236222 ATATCAA
64 ACATCAA
236229 CCGCATGGTA
Statistics
Matches: 199, Mismatches: 31, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
82 3 0.02
83 68 0.34
84 5 0.03
85 117 0.59
86 6 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (83 bp):
CTCAAGCGAGAAGAGCTATCTGTCAGCAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAC
ATCAAATTTACAGCATAG
Found at i:236204 original size:168 final size:169
Alignment explanation
Indices: 235910--236228 Score: 385
Period size: 168 Copynumber: 1.9 Consensus size: 169
235900 CAAACTCAAG
* * * *
235910 GCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAGTTCAAAGGCACATCA
1 GCGAGAAGAGCTATATGTCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTCAAA-GCACATCA
* ** * * *
235975 AATTTACATCATAGCTCAAGTTGAGAAAAGCTATCTGTCTACCAAGACCTTCGATTTCGATTACA
65 AATTTACAGCATAGCTCAAGGCGAGAAAAGCTATCTGTCTAACAAGACCTTCAAGTTCGATTACA
*
236040 TTTAGCTCAAAGGCACATCAAATTTACAGCATAACTTAAA
130 TTCAGCTCAAAGGCACATCAAATTTACAGCATAACTTAAA
*
236080 GCGAGAAGAGCTATATGTCAGC-AA-ACCTTCGAGTTCGATTACATTCAGCTCATGAA-CATATC
1 GCGAGAAGAGCTATATGTCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTCA--AAGCACATC
* ** ** *
236142 TAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTC-AACAAGAATTTTCAAGTTCGATTT
64 AAATTTACAGCATAGCTCAAGGCGAGAAAAGCTATCTGTCTAACAAG-ACCTTCAAGTTCGATTA
* * *
236206 CATTCAGTTCGAAGGCATATCAA
128 CATTCAGCTCAAAGGCACATCAA
236229 CCGCATGGTA
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
167 5 0.04
168 97 0.78
169 2 0.02
170 21 0.17
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (169 bp):
GCGAGAAGAGCTATATGTCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGCACATCAA
ATTTACAGCATAGCTCAAGGCGAGAAAAGCTATCTGTCTAACAAGACCTTCAAGTTCGATTACAT
TCAGCTCAAAGGCACATCAAATTTACAGCATAACTTAAA
Found at i:237764 original size:29 final size:30
Alignment explanation
Indices: 237730--237792 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
237720 ATTTTGATAC
*
237730 TTAAGTTTCTATTATT-TTATTTTAGTCAT
1 TTAAGTTTCTATTATTGTTATTTTAATCAT
* *
237759 TTAAGTTTCTATTTTTGTTATTTTAATCCT
1 TTAAGTTTCTATTATTGTTATTTTAATCAT
237789 TTAA
1 TTAA
237793 ATTAATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.62
Consensus pattern (30 bp):
TTAAGTTTCTATTATTGTTATTTTAATCAT
Found at i:237872 original size:6 final size:6
Alignment explanation
Indices: 237861--237888 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
237851 GAATCAAGTC
237861 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
237889 CGTAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:239423 original size:11 final size:11
Alignment explanation
Indices: 239407--239444 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
239397 TTAGATGGTA
*
239407 AAATAATAATT
1 AAATAATAAAT
239418 AAATAATAAAT
1 AAATAATAAAT
239429 AAATAAATAAAT
1 AAAT-AATAAAT
239441 AAAT
1 AAAT
239445 TGAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:239431 original size:4 final size:4
Alignment explanation
Indices: 239407--239444 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
239397 TTAGATGGTA
*
239407 AAAT -AAT AATT AAAT -AAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
239445 TGAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:249324 original size:20 final size:20
Alignment explanation
Indices: 249295--249350 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
249285 TTTCAGAGTA
*
249295 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
249315 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
249335 ATGCATCGATGCACCA
1 ATGCATCGATGCACCA
249351 TGAATTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:249393 original size:65 final size:64
Alignment explanation
Indices: 249317--249522 Score: 192
Period size: 65 Copynumber: 3.2 Consensus size: 64
249307 ACCAATCCAT
249317 GCATCGATGCACCAATCCATGCATCGATGCACCATGA-ATTAAATTG-AACATCGAATGCATTTC
1 GCATCGATGCACC-ATCCATGCATCGATGCACC-TGAGATTAAA-TGAAACATCGAATGCATTTC
249380 AA
63 AA
* ** *
249382 GCATCGATGCA-CATACCATGCACCGATGCA-CTGAGGATTTTATGAAAACATCGAATGCATTTG
1 GCATCGATGCACCAT-CCATGCATCGATGCACCTGA-GATTAAATG-AAACATCGAATGCATTTC
*
249445 AT
63 AA
* * * *
249447 GCATCGATGCACCAGCCATGCATCGATGCACTCTG-GCTATT--TTGAAACATCGAATGCACTTG
1 GCATCGATGCACCATCCATGCATCGATGCAC-CTGAG--ATTAAATGAAACATCGAATGCATTTC
*
249509 AT
63 AA
249511 GCATCGATGCAC
1 GCATCGATGCAC
249523 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 50 0.41
65 56 0.46
66 2 0.02
67 6 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (64 bp):
GCATCGATGCACCATCCATGCATCGATGCACCTGAGATTAAATGAAACATCGAATGCATTTCAA
Found at i:249522 original size:17 final size:19
Alignment explanation
Indices: 249494--249542 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
249484 TATTTTGAAA
249494 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
249512 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
249531 CACCGATGCACT
1 CATCGATGCACT
249543 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:249538 original size:64 final size:63
Alignment explanation
Indices: 249363--249542 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 63
249353 AATTAAATTG
* * *
249363 AACATCGAATGCATTTCAAGCATCGATGCACATACCA-TGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T--CAGTGCACCGATGCACTCAGGATTTTATGA
249427 A
63 A
* * *
249428 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACTCAGGAT-TTTATG
249491 -A
62 AA
*
249492 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACT
249543 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 8, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
61 2 0.02
64 44 0.44
65 48 0.48
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTCAGGATTTTATGAA
Found at i:250669 original size:31 final size:31
Alignment explanation
Indices: 250635--250693 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
250625 ATGTTTCAAA
*
250635 AAAAATATTTTTAAA-CTATATATTATATTT
1 AAAAACATTTTTAAAACTATATATTATATTT
*
250665 AAAAACGTTTTTAAAACTATATATTATAT
1 AAAAACATTTTTAAAACTATATATTATAT
250694 GGTTTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (31 bp):
AAAAACATTTTTAAAACTATATATTATATTT
Found at i:250891 original size:38 final size:34
Alignment explanation
Indices: 250800--250900 Score: 98
Period size: 35 Copynumber: 2.8 Consensus size: 34
250790 AAATGATTTC
* *
250800 AAAACTATATACTATATAATTTTCAAAATGTTTT
1 AAAACTATATAATATATAATTTTCAAAACGTTTT
*
250834 AAAACTTATATATTGTATATAAGTTTTCAAAAACGTTTT
1 AAAAC-TATATA--ATATATAA-TTTTC-AAAACGTTTT
250873 AAAAAACTATATAATATAT-A-TTTCAAAA
1 --AAAACTATATAATATATAATTTTCAAAA
250901 AATATTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
34 9 0.16
35 10 0.18
37 8 0.14
38 10 0.18
39 9 0.16
40 6 0.11
41 5 0.09
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (34 bp):
AAAACTATATAATATATAATTTTCAAAACGTTTT
Found at i:250922 original size:37 final size:36
Alignment explanation
Indices: 250875--250944 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
250865 AACGTTTTAA
250875 AAAACTATATAATATATATTTCAAAAAATATTTTTTG
1 AAAACTATATAATATATATTTC-AAAAATATTTTTTG
* *
250912 AAAACTATATACTATATTTTTCAAAAATATTTT
1 AAAACTATATAATATATATTTCAAAAATATTTT
250945 CAAAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (36 bp):
AAAACTATATAATATATATTTCAAAAATATTTTTTG
Found at i:255577 original size:90 final size:88
Alignment explanation
Indices: 255423--255601 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 88
255413 CCTAACACAC
*
255423 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTATTATTTCAAATTAATTAAATATATAT
1 CCTTTCATAGCCAAGTTACCCTAATCATATTAGGGTTTATTATTTCAAATTAATTAAATATATAT
* *
255488 TTAATTAATTGGAATTTAATATT
66 TTAATTAATTGAAATTAAATATT
* * * *
255511 CCTTTCATATCCAAGTTACCCTATTTATATTAGGGATTTTATTATTTCAAATTAATTAAATTTAT
1 CCTTTCATAGCCAAGTTACCCTAATCATATTAGGG--TTTATTATTTCAAATTAATTAAATATAT
255576 ATTTAATTAATTGAAATTAAATATT
64 ATTTAATTAATTGAAATTAAATATT
255601 C
1 C
255602 GGATTATTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 31 0.38
90 51 0.62
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (88 bp):
CCTTTCATAGCCAAGTTACCCTAATCATATTAGGGTTTATTATTTCAAATTAATTAAATATATAT
TTAATTAATTGAAATTAAATATT
Found at i:269352 original size:2 final size:2
Alignment explanation
Indices: 269345--269370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
269335 GTCCAATCGC
269345 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
269371 AGACACATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:271337 original size:124 final size:124
Alignment explanation
Indices: 271168--271391 Score: 351
Period size: 124 Copynumber: 1.8 Consensus size: 124
271158 CCTTCTTCTA
*
271168 AAGGATGCTTAATCTGGTGATGATCTCATTCATTCCTCTAGAAGACGTTGAGTCAAGGGATGATC
1 AAGGATGCTGAATCTGGTGATGATCTCATTCATTCCTCTAGAAGACGTTGAGTCAAGGGATGATC
* * *
271233 TTACTCCTTCTTCTGAAGGACGCTAAGTTGTAATTCGGGGTGATCCCCTCCTTTTGTTG
66 TTACTCCTTCGTCTGAAGAACGCTAAGTCGTAATTCGGGGTGATCCCCTCCTTTTGTTG
* * * *
271292 AAGGATGCTGAATCTGGTGATGATCTCATTCTTTCCT-TTGAAAGACGTTGAGTCATGGGATTAT
1 AAGGATGCTGAATCTGGTGATGATCTCATTCATTCCTCTAG-AAGACGTTGAGTCAAGGGATGAT
*
271356 CTTACTCCTTCGTCTGAAGAACTCTAAGTCGTAATT
65 CTTACTCCTTCGTCTGAAGAACGCTAAGTCGTAATT
271392 GGATTATTGC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 2 0.02
124 88 0.98
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (124 bp):
AAGGATGCTGAATCTGGTGATGATCTCATTCATTCCTCTAGAAGACGTTGAGTCAAGGGATGATC
TTACTCCTTCGTCTGAAGAACGCTAAGTCGTAATTCGGGGTGATCCCCTCCTTTTGTTG
Found at i:271604 original size:50 final size:50
Alignment explanation
Indices: 271524--271634 Score: 152
Period size: 50 Copynumber: 2.2 Consensus size: 50
271514 TGGAGAATGT
271524 TTGACTTCTCTACAAAAAAAAGTCAAATTGAAGATGACATCACT-AAAAGG
1 TTGACTTCTCTACAAAAAAAAGTCAAATTGAAGATGACATCACTGAAAA-G
* * * * *
271574 TTGACTTCTCTACACAAAAAAGTTATATTGAAGATGATATCATTGAAAAG
1 TTGACTTCTCTACAAAAAAAAGTCAAATTGAAGATGACATCACTGAAAAG
*
271624 TTGACTCCTCT
1 TTGACTTCTCT
271635 CCATGAGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 50 0.93
51 4 0.07
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (50 bp):
TTGACTTCTCTACAAAAAAAAGTCAAATTGAAGATGACATCACTGAAAAG
Found at i:271723 original size:50 final size:50
Alignment explanation
Indices: 271619--271724 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
271609 GATATCATTG
* *
271619 AAAA-GTTGACTCCTCTCCATGAGAAAGTCAGGTTGAGAATACCATCACT
1 AAAAGGTTAACTCCTCTCCAGGAGAAAGTCAGGTTGAGAATACCATCACT
* * * *
271668 GAAAGGTTAACTCTTCTCCAGGAGAAAGTCAGGTTGAGGATGA-CATTACT
1 AAAAGGTTAACTCCTCTCCAGGAGAAAGTCAGGTTGAGAAT-ACCATCACT
271718 AAAAGGT
1 AAAAGGT
271725 GGACTCCTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 3 0.06
50 44 0.92
51 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGGTTAACTCCTCTCCAGGAGAAAGTCAGGTTGAGAATACCATCACT
Found at i:271807 original size:45 final size:45
Alignment explanation
Indices: 271741--272043 Score: 200
Period size: 45 Copynumber: 6.7 Consensus size: 45
271731 CTATCCACGA
* * * **
271741 AAAGTTCACGAATGACATCACTAAAAAATTGACTTCACTTCGTGAG
1 AAAG-TCAAGAATAACATCACTAAAAGATTGACTTCACTTCGCAAG
* * * * * *
271787 AAAGTCAAGAATAACTTCACTGAAAGATTG-GTTCCTCTTTGGAAG
1 AAAGTCAAGAATAACATCACTAAAAGATTGACTT-CACTTCGCAAG
** * * * * *
271832 TTATTCAAGAATGACATCACTGAAAGGTTGACTT-ATCTTTGCAAG
1 AAAGTCAAGAATAACATCACTAAAAGATTGACTTCA-CTTCGCAAG
* * * *
271877 AAAGTCAAGAATAACATCACTAAAAGGTTGAGTCCTCTTCGCAAG
1 AAAGTCAAGAATAACATCACTAAAAGATTGACTTCACTTCGCAAG
* * ** *
271922 AAAGTCAAGAATAACATCACTAAAAGACTAAC-TCTTTTTCGTAAG
1 AAAGTCAAGAATAACATCACTAAAAGATTGACTTC-ACTTCGCAAG
* * * * * * *
271967 AAAGTCAATAATGACATCAATAAAAGATTTACTCCACTTCTCGAG
1 AAAGTCAAGAATAACATCACTAAAAGATTGACTTCACTTCGCAAG
* ** *
272012 AAAGTTAAGAAT-GTATCACTAAAAGGTTGACT
1 AAAGTCAAGAATAACATCACTAAAAGATTGACT
272044 CTTCTTTGTA
Statistics
Matches: 198, Mismatches: 53, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
44 18 0.09
45 173 0.87
46 7 0.04
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (45 bp):
AAAGTCAAGAATAACATCACTAAAAGATTGACTTCACTTCGCAAG
Done.