Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 61 of 193
Found at i:19190052 original size:40 final size:42
Alignment explanation
Indices: 19189992--19190081 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 42
19189982 TCATGTCAGC
* *
19189992 AAATGATTTTAAAATTATTAAAGTT-TTTTTTAAAAAT-ATA
1 AAATTATTTTAAAATTATTAAAATTATTTTTTAAAAATAATA
**
19190032 AAATTATTTTAAAATTATTAAAATTATTTTTTTGAAATAATA
1 AAATTATTTTAAAATTATTAAAATTATTTTTTAAAAATAATA
19190074 AAATTATT
1 AAATTATT
19190082 AAATAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 23 0.52
41 10 0.23
42 11 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (42 bp):
AAATTATTTTAAAATTATTAAAATTATTTTTTAAAAATAATA
Found at i:19190677 original size:18 final size:18
Alignment explanation
Indices: 19190650--19190692 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19190640 CAAAAGCCCA
* *
19190650 AGCTTTTTCCCAGTATTG
1 AGCTTGTTCCCAGTACTG
19190668 AGCTTGTTCCCAGTACTG
1 AGCTTGTTCCCAGTACTG
*
19190686 TGCTTGT
1 AGCTTGT
19190693 GATTTTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (18 bp):
AGCTTGTTCCCAGTACTG
Found at i:19191033 original size:9 final size:9
Alignment explanation
Indices: 19191019--19191100 Score: 84
Period size: 9 Copynumber: 9.2 Consensus size: 9
19191009 TATTTCAAAA
19191019 AATAATTTT
1 AATAATTTT
19191028 AATAATTTT
1 AATAATTTT
19191037 AAATTAATTTT
1 -AA-TAATTTT
*
19191048 AAAAATTTT
1 AATAATTTT
19191057 AAATTAATTTT
1 -AA-TAATTTT
19191068 AATAATTTT
1 AATAATTTT
19191077 AA-AA----
1 AATAATTTT
19191081 AATAATTTT
1 AATAATTTT
19191090 AATAATTTT
1 AATAATTTT
19191099 AA
1 AA
19191101 AATCATTTGC
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
8 2 0.03
9 35 0.56
10 8 0.13
11 13 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATAATTTT
Found at i:19191108 original size:20 final size:20
Alignment explanation
Indices: 19191017--19191108 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
19191007 ATTATTTCAA
19191017 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
* *
19191037 AAATTAATTTTAAAAATTTT
1 AAAATAATTTTAATAATTTT
*
19191057 AAATTAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
19191077 AAAAAATAATTTTAATAATTTT
1 --AAAATAATTTTAATAATTTT
*
19191099 AAAATCATTT
1 AAAATAATTT
19191109 GCTGACGTGG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 46 0.71
22 19 0.29
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATAATTTTAATAATTTT
Found at i:19193823 original size:21 final size:21
Alignment explanation
Indices: 19193799--19193854 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19193789 TTAGAGTTTG
*
19193799 TTGTATCGGTAGAAGT-GTAAA
1 TTGTATCGGTAGAAGTCAT-AA
* *
19193820 TTGTATCGGTAGTAGTCATAT
1 TTGTATCGGTAGAAGTCATAA
19193841 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
19193855 CCTTTCTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.38
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAA
Found at i:19201330 original size:26 final size:26
Alignment explanation
Indices: 19201265--19201336 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
19201255 TTCAGAATTG
*
19201265 TGCCCAAAATTGTCACTACATGACGA
1 TGCCCAAAATTGTCACTGCATGACGA
* * *
19201291 TGTCCAAAAATGTCGCTGCATGA-GCA
1 TGCCCAAAATTGTCACTGCATGACG-A
*
19201317 TGCCCAGAATTGTCACTGCA
1 TGCCCAAAATTGTCACTGCA
19201337 GGAACTCGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (26 bp):
TGCCCAAAATTGTCACTGCATGACGA
Found at i:19201492 original size:13 final size:13
Alignment explanation
Indices: 19201474--19201498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19201464 GCTGTCCAGT
19201474 CTGGTATAACCAA
1 CTGGTATAACCAA
19201487 CTGGTATAACCA
1 CTGGTATAACCA
19201499 TAAACAGCTC
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
CTGGTATAACCAA
Found at i:19209329 original size:52 final size:49
Alignment explanation
Indices: 19209248--19209349 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 49
19209238 GCTTGTTCTC
*
19209248 TCTTTCTTTTTTTTTCTTTTTTTCTTTTCTCTCTTGATAATTTTCTCTT
1 TCTTTCTTTTTTTTTCTCTTTTTCTTTTCTCTCTTGATAATTTTCTCTT
* *
19209297 TCTTTCTATTTTTTCCTTCTCTTTTTCTTTTCTCTCTTGCTCATTTTCTCTT
1 TCTTTCT-TTTTTT--TTCTCTTTTTCTTTTCTCTCTTGATAATTTTCTCTT
19209349 T
1 T
19209350 ATTTTGTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
49 7 0.15
50 6 0.13
52 34 0.72
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.71
Consensus pattern (49 bp):
TCTTTCTTTTTTTTTCTCTTTTTCTTTTCTCTCTTGATAATTTTCTCTT
Found at i:19220966 original size:27 final size:27
Alignment explanation
Indices: 19220936--19221026 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
19220926 AACACTATGA
*
19220936 ATGGTGAACTCAGAAGGAATAGAATTC
1 ATGGCGAACTCAGAAGGAATAGAATTC
**
19220963 ATGGCGAACTCCTAAGGAATAGAATTC
1 ATGGCGAACTCAGAAGGAATAGAATTC
* *
19220990 ATGGTGAACTCTGAAGGAAT-GAAATTC
1 ATGGCGAACTCAGAAGGAATAG-AATTC
*
19221017 TTGGCGAACT
1 ATGGCGAACT
19221027 AGGAATGAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 1 0.02
27 54 0.98
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (27 bp):
ATGGCGAACTCAGAAGGAATAGAATTC
Found at i:19224652 original size:138 final size:138
Alignment explanation
Indices: 19224191--19224748 Score: 775
Period size: 138 Copynumber: 4.1 Consensus size: 138
19224181 TAGAAGAATG
* * * * *
19224191 AATTATATTCTTTCCAAAAGAAAATTAATTTTCATGTATTTCATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATCAATTTCCATGTCTTTCATATTTTGACTGAAATTAATTAA
* * * * * * *
19224256 TATAAATGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATAAATAAAATC
66 TATAATTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAAATT
19224321 CATATATT
131 CATATATT
* *
19224329 AATTATATTCTTTCCAAAAGAATA-CTAATTTTCATGTCTTTCATATTTTGAGTGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATC-AATTTCCATGTCTTTCATATTTTGACTGAAATTAATTA
* * *
19224393 ATATAACTATTTATATTAATAAATTCGGTAATATATATA-AATTAATATTTTGTATGAATTAAAT
65 ATATAATTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAAAT
19224457 TCATATATT
130 TCATATATT
* * * * * *
19224466 AATTATATTCTTTCCAAAAGAATATTAA-TACTCATTTCTTTTACATTTTGACTGAAATTAATCA
1 AATTATATTCTTTCCAAAAGAATATCAATTTC-CATGTCTTTCATATTTTGACTGAAATTAATTA
* *
19224530 ATATAATTATTTATATTAATAAATTCAGTAAAATATATATAATTGATATTTTGTATGAATCAAAT
65 ATATAATTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAAAT
19224595 TCATATATT
130 TCATATATT
* * * *
19224604 AATTATATTCCTTT-CAAAAGAATATCAACTTCCATGTCGTTT-GTATTTTAATTGAAATTAATT
1 AATTATATT-CTTTCCAAAAGAATATCAATTTCCATGTC-TTTCATATTTTGACTGAAATTAATT
*
19224667 AATATAATTGTTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAAA
64 AATATAATTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAAA
19224732 TTCATATATT
129 TTCATATATT
19224742 AATTATA
1 AATTATA
19224749 CCTATGCTCT
Statistics
Matches: 377, Mismatches: 36, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
136 1 0.00
137 120 0.32
138 247 0.66
139 9 0.02
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATCAATTTCCATGTCTTTCATATTTTGACTGAAATTAATTAA
TATAATTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:19224683 original size:275 final size:276
Alignment explanation
Indices: 19224191--19224748 Score: 820
Period size: 275 Copynumber: 2.0 Consensus size: 276
19224181 TAGAAGAATG
** * *
19224191 AATTATATTCTTTCCAAAAGAAAATTAATTTTCATGTATTTCATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAAAATTAATACTCATGTATTTCACATTTTGACCGAAATTAATCAA
*
19224256 TATAAATGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATAAATAAAATC
66 TATAAATATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATAAATAAAATC
* * *
19224321 CATATATTAATTATATTCTTTCCAAAAGAATACTAATTTTCATGTCTTTCATATTTTGAGTGAAA
131 CATATATTAATTATATTCTTTCCAAAAGAATACTAACTTCCATGTCTTTCATATTTTAAGTGAAA
*
19224386 TTAATTAATATAACTATTTATATTAATAAATTCGGTAATATATATA-AATTAATATTTTGTATGA
196 TTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGA
*
19224450 ATTAAATTCATATATT
261 ATCAAATTCATATATT
* * * * *
19224466 AATTATATTCTTTCCAAAAGAATATTAATACTCATTTCTTTTACATTTTGACTGAAATTAATCAA
1 AATTATATTCTTTCCAAAAGAAAATTAATACTCATGTATTTCACATTTTGACCGAAATTAATCAA
* * * * *
19224531 TATAATTATTTATATTAATAAATTC-AGTAAAATATATATAATTGATATTTTGTATGAATCAAAT
66 TATAAATATTTATATTAATAAATTCGA-TAAAATATATACAATTAATATTTTGTATAAATAAAAT
* * *
19224595 TCATATATTAATTATATTCCTTT-CAAAAGAATA-TCAACTTCCATGTCGTTT-GTATTTTAATT
130 CCATATATTAATTATATT-CTTTCCAAAAGAATACT-AACTTCCATGTC-TTTCATATTTTAAGT
* *
19224657 GAAATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGT
192 GAAATTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGT
19224722 ATGAATCAAATTCATATATT
257 ATGAATCAAATTCATATATT
19224742 AATTATA
1 AATTATA
19224749 CCTATGCTCT
Statistics
Matches: 253, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
274 2 0.01
275 204 0.81
276 47 0.19
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (276 bp):
AATTATATTCTTTCCAAAAGAAAATTAATACTCATGTATTTCACATTTTGACCGAAATTAATCAA
TATAAATATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATAAATAAAATC
CATATATTAATTATATTCTTTCCAAAAGAATACTAACTTCCATGTCTTTCATATTTTAAGTGAAA
TTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGA
ATCAAATTCATATATT
Found at i:19229944 original size:17 final size:17
Alignment explanation
Indices: 19229920--19229978 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
19229910 ATATATATGG
*
19229920 AAATGCAATGACAATGA
1 AAATGCAATGACAATAA
* *
19229937 AGATGCAACGACAATAA
1 AAATGCAATGACAATAA
*
19229954 AAATGCAGTGACAATAA
1 AAATGCAATGACAATAA
19229971 AAATGCAA
1 AAATGCAA
19229979 GGATAATCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:19233627 original size:19 final size:19
Alignment explanation
Indices: 19233574--19233635 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
19233564 GAGGAATTGT
*
19233574 AGTGCAAATAGAGGCA-CA
1 AGTGCTAATAGAGGCACCA
* *
19233592 AATGTTCAATCAGAGGCACCA
1 AGTGCT-AAT-AGAGGCACCA
19233613 AGTGCTAATAGAGGCACCGA
1 AGTGCTAATAGAGGCACC-A
19233633 AGT
1 AGT
19233636 ACAGTTAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 3 0.09
19 12 0.34
20 14 0.40
21 6 0.17
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (19 bp):
AGTGCTAATAGAGGCACCA
Found at i:19233644 original size:20 final size:20
Alignment explanation
Indices: 19233621--19233675 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
19233611 CAAGTGCTAA
*
19233621 TAGAGGCACCGAAGTACAGT
1 TAGAGGCACCAAAGTACAGT
*
19233641 TAGAGACACCAAAGTACAGT
1 TAGAGGCACCAAAGTACAGT
* *
19233661 CAAAGGCACCAAAGT
1 TAGAGGCACCAAAGT
19233676 GCAAACAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (20 bp):
TAGAGGCACCAAAGTACAGT
Found at i:19233690 original size:20 final size:20
Alignment explanation
Indices: 19233642--19233696 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
19233632 AAGTACAGTT
* **
19233642 AGAGACACCAAAGTACAGTC
1 AGAGACACCAAAGTGCAAAC
* *
19233662 AAAGGCACCAAAGTGCAAAC
1 AGAGACACCAAAGTGCAAAC
*
19233682 AGAGACACCGAAGTG
1 AGAGACACCAAAGTG
19233697 AAATCATGTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.24, T:0.07
Consensus pattern (20 bp):
AGAGACACCAAAGTGCAAAC
Found at i:19241998 original size:25 final size:25
Alignment explanation
Indices: 19241964--19242013 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
19241954 TAAGTAGGCT
19241964 GTAAGATTGCATAAGTCTATGAGTA
1 GTAAGATTGCATAAGTCTATGAGTA
19241989 GTAAGATTGCATAAGTCTATGAGTA
1 GTAAGATTGCATAAGTCTATGAGTA
19242014 TCCACCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (25 bp):
GTAAGATTGCATAAGTCTATGAGTA
Found at i:19248341 original size:15 final size:15
Alignment explanation
Indices: 19248321--19248424 Score: 118
Period size: 15 Copynumber: 6.9 Consensus size: 15
19248311 GTTTGTATAA
*
19248321 GTGAGTTCACCATAG
1 GTGAGTTCGCCATAG
*
19248336 GTGAGTTCGCCATAA
1 GTGAGTTCGCCATAG
*
19248351 GTGAGTTTGCCATAG
1 GTGAGTTCGCCATAG
*
19248366 GTGAGTTCTCCATAG
1 GTGAGTTCGCCATAG
* *
19248381 GAGAGTTCGCCAAAG
1 GTGAGTTCGCCATAG
* * *
19248396 GTGAGTTCACTATCG
1 GTGAGTTCGCCATAG
*
19248411 GAGAGTTCGCCATA
1 GTGAGTTCGCCATA
19248425 CGATAACGCC
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 71 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (15 bp):
GTGAGTTCGCCATAG
Found at i:19249377 original size:3 final size:3
Alignment explanation
Indices: 19249369--19249414 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
19249359 AACCAGAGAA
* *
19249369 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAG AAT AAT AAG AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19249415 GAAAAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:19269526 original size:20 final size:21
Alignment explanation
Indices: 19269501--19269546 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
19269491 TTAAATCAAG
19269501 AAAAAAC-ACAAAAAGAGAA-A
1 AAAAAACAACAAAAA-AGAAGA
19269521 AAAAAACAACAAAAAAGAAGA
1 AAAAAACAACAAAAAAGAAGA
19269542 AAAAA
1 AAAAA
19269547 TAGAGAGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (21 bp):
AAAAAACAACAAAAAAGAAGA
Found at i:19269536 original size:23 final size:22
Alignment explanation
Indices: 19269501--19269546 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
19269491 TTAAATCAAG
19269501 AAAAAACACAAAAAG-AGAAAAA
1 AAAAAACA-AAAAAGAAGAAAAA
19269523 AAAACAACAAAAAAGAAGAAAAA
1 AAAA-AACAAAAAAGAAGAAAAA
19269546 A
1 A
19269547 TAGAGAGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAAACAAAAAAGAAGAAAAA
Found at i:19270001 original size:42 final size:42
Alignment explanation
Indices: 19269942--19270503 Score: 696
Period size: 42 Copynumber: 13.2 Consensus size: 42
19269932 AAGGGAAGCA
* *
19269942 TTCATTGCATTTAGAGGCCTAAGTGTTGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
19269984 TTCATTGCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * * * * *
19270026 TTCAATGCATTCAAAGGCATAGATATGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
19270068 TTCATTGCATTTAGAGGCATAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
19270110 TTCATTGC-TCTTAGAGGTCC-AGGTGTGGAGGTCCATTTACTT
1 TTCATTGCAT-TTAGAGG-CCTAGGTGTGGAGGTCCATTTACTT
**
19270152 TTCATTGCATTTAGAGGTATAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
19270194 TTCATTGCATTTAGAGGGCTAAGTGTGGAGTTCCATTTACTTGTCATTGT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTA-----C--T-T
19270244 TGTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 T-TCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
19270287 TTCATTACATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
19270329 TTTATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
19270371 TTCATCGCATTTAGAGGCCTAGGTGTGGAGTTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
19270413 TTCATTACATTTAAAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * **
19270455 TTTATTGCATTTAGAAGCCTAGGTGTTGAGGTTTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
19270497 TTCATTG
1 TTCATTG
19270504 TGAATTACCT
Statistics
Matches: 451, Mismatches: 56, Indels: 26
0.85 0.11 0.05
Matches are distributed among these distances:
41 1 0.00
42 405 0.90
43 4 0.01
44 1 0.00
46 1 0.00
47 1 0.00
49 1 0.00
50 2 0.00
51 35 0.08
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:19270271 original size:51 final size:51
Alignment explanation
Indices: 19270195--19270292 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
19270185 CATTTACTTT
* *
19270195 TCATTGCATTTAGAGGGCTAAGTGTGGAGTTCCATTTACTTGTCATTGTTG
1 TCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTTGTCATTGTTG
* *
19270246 TCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATT
1 TCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTTGTCATT
19270293 ACATTTAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.41
Consensus pattern (51 bp):
TCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTTGTCATTGTTG
Found at i:19284844 original size:15 final size:15
Alignment explanation
Indices: 19284826--19284869 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
19284816 AAGATACAAG
19284826 CACTCATGTTGCGAA
1 CACTCATGTTGCGAA
*
19284841 CACT-AGAGTTGCGAA
1 CACTCA-TGTTGCGAA
19284856 CACTCATGTTGCGA
1 CACTCATGTTGCGA
19284870 GCACACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (15 bp):
CACTCATGTTGCGAA
Found at i:19286254 original size:10 final size:9
Alignment explanation
Indices: 19286229--19286253 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19286219 ATTAGCATTC
19286229 AAAAAAATT
1 AAAAAAATT
19286238 AAAAAAATT
1 AAAAAAATT
19286247 AAAAAAA
1 AAAAAAA
19286254 AGTACAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:19287142 original size:16 final size:16
Alignment explanation
Indices: 19287121--19287164 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
19287111 AAAGAATGAG
* *
19287121 AGAAAAGGAAGCTAAA
1 AGAAAAGAAAGATAAA
19287137 AGAAAAGAAAGATAAA
1 AGAAAAGAAAGATAAA
19287153 AGAAAAGAAAGA
1 AGAAAAGAAAGA
19287165 CAAGAGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (16 bp):
AGAAAAGAAAGATAAA
Found at i:19287250 original size:21 final size:21
Alignment explanation
Indices: 19287204--19287266 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 21
19287194 AAAAATAAAA
**
19287204 GAAATAGAGAGAAGAAA-AAAAA
1 GAAA-AGAGAGAA-AAAGAAATT
19287226 GAAAAGAGAGAAAAAGAAATT
1 GAAAAGAGAGAAAAAGAAATT
*
19287247 G--AA-AGAGAAAAAGAACTT
1 GAAAAGAGAGAAAAAGAAATT
19287265 GA
1 GA
19287267 GAGAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 15 0.42
19 2 0.06
20 3 0.08
21 12 0.33
22 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.08
Consensus pattern (21 bp):
GAAAAGAGAGAAAAAGAAATT
Found at i:19287271 original size:16 final size:16
Alignment explanation
Indices: 19287221--19287274 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 16
19287211 AGAGAAGAAA
*
19287221 AAAAAGAAA-AGAGAG
1 AAAAAGAAATTGAGAG
19287236 AAAAAGAAATTGAAAGAG
1 AAAAAGAAATTG--AGAG
*
19287254 AAAAAGAACTTGAGAG
1 AAAAAGAAATTGAGAG
19287270 AAAAA
1 AAAAA
19287275 AAAGAGAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.26
16 10 0.29
18 15 0.44
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.07
Consensus pattern (16 bp):
AAAAAGAAATTGAGAG
Found at i:19287276 original size:18 final size:18
Alignment explanation
Indices: 19287230--19287275 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
19287220 AAAAAAGAAA
19287230 AGAGAGAAAAAGAAATTG
1 AGAGAGAAAAAGAAATTG
* *
19287248 AAAGAGAAAAAGAACTTG
1 AGAGAGAAAAAGAAATTG
19287266 AGAGA-AAAAA
1 AGAGAGAAAAA
19287276 AAGAGAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.24, T:0.09
Consensus pattern (18 bp):
AGAGAGAAAAAGAAATTG
Found at i:19287287 original size:34 final size:33
Alignment explanation
Indices: 19287200--19287287 Score: 79
Period size: 34 Copynumber: 2.5 Consensus size: 33
19287190 AGCAAAAAAT
*
19287200 AAAAGAAATAGAGAGAAGAAAAAAAAGAAAAGAGAG
1 AAAA-AAA-AGAGAGAAG-AGAAAAAGAAAAGAGAG
** **
19287236 AAAAAGAAATTGA-AAGAGAAAAAGAACTTGAGAG
1 AAAAA-AAAGAGAGAAGAGAAAAAGAA-AAGAGAG
19287270 AAAAAAAAGAGAGAAGAG
1 AAAAAAAAGAGAGAAGAG
19287288 TTGTTGATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
33 14 0.33
34 18 0.43
35 4 0.10
36 6 0.14
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.06
Consensus pattern (33 bp):
AAAAAAAAGAGAGAAGAGAAAAAGAAAAGAGAG
Found at i:19289766 original size:18 final size:18
Alignment explanation
Indices: 19289743--19289786 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19289733 TCATGCATTC
19289743 CATGCATTTCATT-CAACT
1 CATGCATTTC-TTGCAACT
* *
19289761 CGTGCACTTCTTGCAACT
1 CATGCATTTCTTGCAACT
19289779 CATGCATT
1 CATGCATT
19289787 CCATGCAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (18 bp):
CATGCATTTCTTGCAACT
Found at i:19289793 original size:18 final size:17
Alignment explanation
Indices: 19289743--19289794 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
19289733 TCATGCATTC
*
19289743 CATGCATTTCATTCAACT
1 CATGCA-TTCATGCAACT
* *
19289761 CGTGCACTTCTTGCAACT
1 CATGCA-TTCATGCAACT
19289779 CATGCATTCCATGCAA
1 CATGCATT-CATGCAA
19289795 TGTGCAGCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.33
Consensus pattern (17 bp):
CATGCATTCATGCAACT
Found at i:19294247 original size:16 final size:16
Alignment explanation
Indices: 19294219--19294251 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19294209 AGATGATTAT
19294219 ATAAAAAATTTTAATAA
1 ATAAAAAATTTT-ATAA
19294236 ATAAAAAA-TTTATAA
1 ATAAAAAATTTTATAA
19294251 A
1 A
19294252 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 3 0.19
17 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAAATTTTATAA
Found at i:19310957 original size:18 final size:18
Alignment explanation
Indices: 19310905--19311013 Score: 159
Period size: 18 Copynumber: 6.2 Consensus size: 18
19310895 AAATGAATAT
19310905 CATACTGGCTCGTTTGAG
1 CATACTGGCTCGTTTGAG
19310923 CATAC-GGCTCG-TTGAG
1 CATACTGGCTCGTTTGAG
19310939 CATACTGGCTCGTTTGAG
1 CATACTGGCTCGTTTGAG
*
19310957 CATACTAGCTCGTTTGAG
1 CATACTGGCTCGTTTGAG
*
19310975 CATACTAGCTCGTTTGAG
1 CATACTGGCTCGTTTGAG
** *
19310993 CATGTTGGCTCATTTGAG
1 CATACTGGCTCGTTTGAG
19311011 CAT
1 CAT
19311014 TTCTGGATCG
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
16 10 0.12
17 12 0.14
18 62 0.74
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (18 bp):
CATACTGGCTCGTTTGAG
Found at i:19316548 original size:30 final size:30
Alignment explanation
Indices: 19316503--19316585 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
19316493 CAGCACTAAT
* *
19316503 GCTGCGAGCACTAATGTTGTGAGAACTGAA
1 GCTGCAAGCAATAATGTTGTGAGAACTGAA
*
19316533 GCTGCAAGCAATAATGTTGTGAGCACTGAA
1 GCTGCAAGCAATAATGTTGTGAGAACTGAA
* *
19316563 GTTGCAAGAAATAATGTTGTGAG
1 GCTGCAAGCAATAATGTTGTGAG
19316586 CACTAATCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (30 bp):
GCTGCAAGCAATAATGTTGTGAGAACTGAA
Found at i:19316566 original size:15 final size:15
Alignment explanation
Indices: 19316494--19316592 Score: 67
Period size: 15 Copynumber: 6.6 Consensus size: 15
19316484 TGAAGGTTGC
* *
19316494 AGCACTAATGCTGCG
1 AGCACTAATGTTGTG
19316509 AGCACTAATGTTGTG
1 AGCACTAATGTTGTG
* * **
19316524 AGAACTGAA-GCTGCA
1 AGCACT-AATGTTGTG
*
19316539 AGCAATAATGTTGTG
1 AGCACTAATGTTGTG
**
19316554 AGCACTGAA-GTTGCA
1 AGCACT-AATGTTGTG
* *
19316569 AGAAATAATGTTGTG
1 AGCACTAATGTTGTG
19316584 AGCACTAAT
1 AGCACTAAT
19316593 CTTACTAGCA
Statistics
Matches: 60, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
14 4 0.07
15 52 0.87
16 4 0.07
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (15 bp):
AGCACTAATGTTGTG
Found at i:19316586 original size:30 final size:30
Alignment explanation
Indices: 19316514--19316589 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
19316504 CTGCGAGCAC
* *
19316514 TAATGTTGTGAGAACTGAAGCTGCAAGCAA
1 TAATGTTGTGAGCACTGAAGCTGCAAGAAA
*
19316544 TAATGTTGTGAGCACTGAAGTTGCAAGAAA
1 TAATGTTGTGAGCACTGAAGCTGCAAGAAA
19316574 TAATGTTGTGAGCACT
1 TAATGTTGTGAGCACT
19316590 AATCTTACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (30 bp):
TAATGTTGTGAGCACTGAAGCTGCAAGAAA
Found at i:19321961 original size:18 final size:18
Alignment explanation
Indices: 19321940--19321983 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19321930 CATTGCATGG
19321940 AATGCATGAGTTGCAAT-A
1 AATGCATGAGTTG-AATGA
* *
19321958 AATGCACGAGTTGTATGA
1 AATGCATGAGTTGAATGA
19321976 AATGCATG
1 AATGCATG
19321984 GAATGCATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (18 bp):
AATGCATGAGTTGAATGA
Found at i:19322179 original size:45 final size:45
Alignment explanation
Indices: 19322115--19322221 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
19322105 CCTTCGTTCA
* ***
19322115 TGCTCGCAACGCGAGTGTTCACAACAT-CAGTGTTCTCATTTTGAG
1 TGCTCGCAACACGAGTGTTCACAAC-TCCAGTGTTCTCAACATGAG
* * *
19322160 TGCTCGCAACATGAGTGTTCCCAGCTCCAGTGTTCTCAACATGAG
1 TGCTCGCAACACGAGTGTTCACAACTCCAGTGTTCTCAACATGAG
* *
19322205 TGCTCACAACACCAGTG
1 TGCTCGCAACACGAGTG
19322222 CTCGCATCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 50 0.98
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (45 bp):
TGCTCGCAACACGAGTGTTCACAACTCCAGTGTTCTCAACATGAG
Found at i:19324632 original size:22 final size:24
Alignment explanation
Indices: 19324589--19324635 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19324579 AATCTTCTCT
*
19324589 TTTTTTTCTCTCAAGTTCTTTTTC
1 TTTTTCTCTCTCAAGTTCTTTTTC
*
19324613 TTTTTCTCTTTCAA-TT-TTTTTC
1 TTTTTCTCTCTCAAGTTCTTTTTC
19324635 T
1 T
19324636 CTCATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 2 0.10
24 12 0.57
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTTCTCTCTCAAGTTCTTTTTC
Found at i:19324648 original size:18 final size:19
Alignment explanation
Indices: 19324588--19324683 Score: 72
Period size: 20 Copynumber: 4.9 Consensus size: 19
19324578 AAATCTTCTC
* *
19324588 TTTTTTTTCTCTCAAGTTCT
1 TTTTTTTTCTCTC-ATTTAT
19324608 TTTTCTTTT-TCTC-TTTCA-
1 TTTT-TTTTCTCTCATTT-AT
*
19324626 ATTTTTTTCTCTCATTTAT
1 TTTTTTTTCTCTCATTTAT
*
19324645 TTTTTTCTTCTCCCTATTTAT
1 TTTTTT-TTCTCTC-ATTTAT
*
19324666 TTTATTTTTCACTCATTT
1 TTT-TTTTTCTCTCATTT
19324684 TCACTCATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
17 4 0.07
18 10 0.16
19 8 0.13
20 18 0.30
21 18 0.30
22 3 0.05
ACGTcount: A:0.11, C:0.20, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTTTTTCTCTCATTTAT
Found at i:19324650 original size:20 final size:20
Alignment explanation
Indices: 19324627--19324683 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
19324617 TCTCTTTCAA
19324627 TTTTTTTCTCTCATTTATTT
1 TTTTTTTCTCTCATTTATTT
* *
19324647 TTTTCTTCTCCCTATTTATTT
1 TTTTTTTCTCTC-ATTTATTT
* *
19324668 TATTTTTCACTCATTT
1 TTTTTTTCTCTCATTT
19324684 TCACTCATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTTCTCTCATTTATTT
Found at i:19326723 original size:22 final size:22
Alignment explanation
Indices: 19326698--19326740 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
19326688 AAAATATTTC
*
19326698 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
19326720 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
19326741 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:19351478 original size:17 final size:18
Alignment explanation
Indices: 19351458--19351491 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19351448 AAGGAAAATG
19351458 AGAAAAAAG-AAAGAAAA
1 AGAAAAAAGAAAAGAAAA
*
19351475 AGAAAAGAGAAAAGAAA
1 AGAAAAAAGAAAAGAAA
19351492 TGGAAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAAAGAAAAGAAAA
Found at i:19359496 original size:43 final size:43
Alignment explanation
Indices: 19359442--19359540 Score: 171
Period size: 43 Copynumber: 2.3 Consensus size: 43
19359432 ATCGCCGTTG
* *
19359442 CACCATCCTTGCCGTTGCAAGGTTGTCATCGTAGCAAGTCCTTA
1 CACCA-CCTTGCCGTCGCAAGGTTGTCATCGTAGCAAGTCCCTA
19359486 CACCACCTTGCCGTCGCAAGGTTGTCATCGTAGCAAGTCCCTA
1 CACCACCTTGCCGTCGCAAGGTTGTCATCGTAGCAAGTCCCTA
19359529 CACCACCTTGCC
1 CACCACCTTGCC
19359541 AATTTCTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 48 0.91
44 5 0.09
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (43 bp):
CACCACCTTGCCGTCGCAAGGTTGTCATCGTAGCAAGTCCCTA
Found at i:19367280 original size:16 final size:16
Alignment explanation
Indices: 19367259--19367312 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 16
19367249 CTTTCTTTTT
*
19367259 TTTTTCTCTCAAGTTC
1 TTTTTCTCTCAATTTC
*
19367275 TTTTTCTCTTTCAATTTA
1 TTTTTCTC--TCAATTTC
19367293 TTTTTCTCTC-ATTTC
1 TTTTTCTCTCAATTTC
19367308 TTTTT
1 TTTTT
19367313 TTCTTCTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 9 0.27
16 10 0.30
18 14 0.42
ACGTcount: A:0.11, C:0.20, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTCTCTCAATTTC
Found at i:19369371 original size:18 final size:18
Alignment explanation
Indices: 19369330--19369371 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19369320 CATTGCATGG
*
19369330 AATGCATGAGTTGTAAGA
1 AATGCACGAGTTGTAAGA
* *
19369348 AGTGCACGAGTTGTATGA
1 AATGCACGAGTTGTAAGA
19369366 AATGCA
1 AATGCA
19369372 TGGAATGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.26
Consensus pattern (18 bp):
AATGCACGAGTTGTAAGA
Found at i:19369566 original size:15 final size:15
Alignment explanation
Indices: 19369546--19369618 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
19369536 TATTCTCATT
19369546 ATGAGTGCTCGCAAC
1 ATGAGTGCTCGCAAC
* *
19369561 ATGAGTGTTCGCAGC
1 ATGAGTGCTCGCAAC
* *
19369576 -TCCAGTGTTCGCAAC
1 AT-GAGTGCTCGCAAC
*
19369591 ATGAGTGCTCACAAC
1 ATGAGTGCTCGCAAC
**
19369606 ACCAGTGCTCGCA
1 ATGAGTGCTCGCA
19369619 TCTTCCAAGC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
14 1 0.02
15 44 0.96
16 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (15 bp):
ATGAGTGCTCGCAAC
Found at i:19369611 original size:30 final size:30
Alignment explanation
Indices: 19369549--19369618 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
19369539 TCTCATTATG
* * * *
19369549 AGTGCTCGCAACATGAGTGTTCGCAGCTCC
1 AGTGCTCGCAACATGAGTGCTCACAACACC
*
19369579 AGTGTTCGCAACATGAGTGCTCACAACACC
1 AGTGCTCGCAACATGAGTGCTCACAACACC
19369609 AGTGCTCGCA
1 AGTGCTCGCA
19369619 TCTTCCAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.21
Consensus pattern (30 bp):
AGTGCTCGCAACATGAGTGCTCACAACACC
Found at i:19382679 original size:50 final size:51
Alignment explanation
Indices: 19382568--19382742 Score: 253
Period size: 51 Copynumber: 3.5 Consensus size: 51
19382558 GAAAGGGTTC
* *
19382568 GATGACTAAGTGTCATCGTGAGTGAATGAATCATTTATGGATTAATTGTCT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGGATTAATGGTCT
* * * *
19382619 GATGATTAAGTGTCATCATGAGTAAATGAATC-CTTATGGATTAATGGTAT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGGATTAATGGTCT
* * *
19382669 GATGACTAAGTGTCATCGTGAGTAAATGAATCTTTTATGGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGGATTAATGGTCT
*
19382720 GATGACTAAGTGTCATTGTGAGT
1 GATGACTAAGTGTCATCGTGAGT
19382743 TTATGGATTC
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 45 0.41
51 65 0.59
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (51 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGGATTAATGGTCT
Found at i:19384560 original size:3 final size:3
Alignment explanation
Indices: 19384552--19384591 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
19384542 CAAGACCCAA
* *
19384552 ATT ATT ATT ATC ATT ACT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19384592 GGGTTTCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:19385457 original size:150 final size:150
Alignment explanation
Indices: 19385006--19385959 Score: 1290
Period size: 150 Copynumber: 6.4 Consensus size: 150
19384996 GATTTTGAGA
* * * * * *
19385006 AAAGTTTTGGTTTTTTTAAACAATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATTT
** *
19385071 TTTTTAAAAAAA-AGAAAGTTTAGATTTTTAAAAATAAAAATCT-G-----T--TT-TTTT--AG
65 TCATTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTAAAG
*
19385124 -AAAAGTTTAAATTTTTAAAC
130 AAAAAGTTTAAATTTTTAAAT
19385144 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTT-GTATTTTTAAGAAAGTAGTGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAG-ATTTTTAAGAAAGTAGTGATTT
* *
19385208 TCATTAAAAAAAAAGGAGAAATTTTATATTTTTAAAAATGAAAATCT-GTTTTTTAGTTATTTTA
65 TCATT--AAAAAAA-GAGAAAGTTTATATTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTA
19385272 AAGAAAAAGTTTAAATTTTTAAAT
127 AAGAAAAAGTTTAAATTTTTAAAT
* * *
19385296 AAAATTTTGA-TTTTTTTAACTATTTCGAAATAAAAATTTAAATTTTTAAGAAAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTT
** * * *
19385360 CATTAAAAAGGGATAAAGTTTATATTTTTTAAAAATAAAAAACTATTTTTTTAGTTATTTTAAAG
66 CATTAAAAAAAGAGAAAGTTTATA-TTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTAAAG
19385425 AAAAAGTTTAAATTTTTAAAT
130 AAAAAGTTTAAATTTTTAAAT
* * *
19385446 AAATTTTTGA-TTTTTTTAACTATTTCGAAGTAAAAGTTTAAATTTTTAAGAAAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTT
* *
19385510 TATTAAAAAAAAGAGAGAAAGTTTATA-TTTTAAAAATAAAAATCTA-TTTTTTAATTATTTT-A
66 CATT--AAAAAA-AGAGAAAGTTTATATTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTAA
19385572 A-AAAAAGTTTAAATTTTTAAAT
128 AGAAAAAGTTTAAATTTTTAAAT
* *
19385594 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAGGTTTAGTTTTTTAAGAAAGTAGTGATTT
1 AAAGTTTTGA-TTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTT
* *
19385659 TCATT-AAAAATGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTTAGTTATTTTAAAG
65 TCATTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTAAAG
*
19385723 AAAAATTTTAAATTTTTAAAT
130 AAAAAGTTTAAATTTTTAAAT
* * *
19385744 AAAGTTTTGA-TTTTTTTAACCATTTTGAAATAAAAGTTCAGATTTTTAAGAAAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTT
* *
19385808 CATTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCT-GTTTTTTAATGATTTTAAAGA
66 CATTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTAAAGA
19385872 AAAAGTTTAAATTTTTAAAT
131 AAAAGTTTAAATTTTTAAAT
* *
19385892 AAAGTTTTGATTTTTTTTTAAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGAT
1 AAAGTTTTGA-TTTTTTTT-AACTATTTCGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGAT
19385957 TTT
63 TTT
19385960 GTTTAATCAA
Statistics
Matches: 729, Mismatches: 54, Indels: 52
0.87 0.06 0.06
Matches are distributed among these distances:
137 16 0.02
138 45 0.06
139 7 0.01
141 29 0.04
146 14 0.02
147 24 0.03
148 157 0.22
149 67 0.09
150 208 0.29
151 103 0.14
152 47 0.06
153 12 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (150 bp):
AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTT
CATTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTAGTTTTTTAGTTATTTTAAAGA
AAAAGTTTAAATTTTTAAAT
Found at i:19385745 original size:298 final size:300
Alignment explanation
Indices: 19385006--19385959 Score: 1356
Period size: 298 Copynumber: 3.2 Consensus size: 300
19384996 GATTTTGAGA
* * * * *
19385006 AAAGTTTTG-GTTTTTTTAAACAATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATT
** * * *
19385070 TTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTTAG--A----AAAG
66 TTCATTAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTTAGTTATTTTAAAG
* **
19385129 -----TTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGTATT
131 AAAAATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTAAATT
* *
19385189 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAAAGGAGAAATTTTATATTTTTAAAAATGAAAATC
195 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAAA-GAGAAAGTTTATATTTTTAAAAATAAAAATC
*
19385254 TGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAAT
259 TGTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAT
* *
19385296 AAAATTTTGA--TTTTTTTAACTATTTCGAAATAAAAATTTAAATTTTTAAG-AAAGTAGTGATT
1 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATT
* * *
19385358 TTCATTAAAAAGGGATAAAGTTTATATTTTTTAAAAATAAAAAACTATTTTTTTAGTTATTTTAA
66 TTCATTAAAAA-AGAGAAAGTTTATA-TTTTTAAAAATAAAAATCTATTTTTTTAGTTATTTTAA
* *
19385423 AGAAAAAGTTTAAATTTTTAAATAAATTTTTGATTTTTTTAACTATTTCGAAGTAAAAGTTTAAA
129 AGAAAAA-TTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAAA
*
19385488 TTTTTAAGAAAGTAGTGATTTTTATTAAAAAAAAGAGAGAAAGTTTATA-TTTTAAAAATAAAAA
193 TTTTTAAGAAAGTAGTGATTTTCATTAAAAAAAA-AGAGAAAGTTTATATTTTTAAAAATAAAAA
*
19385552 TCTATTTTTTAATTATTTT-AA-AAAAAGTTTAAATTTTTAAAT
257 TCTGTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAT
** *
19385594 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAGGTTTAGTTTTTTAAG-AAAGTAGTGATT
1 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATT
*
19385658 TTCATTAAAAATGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTTAGTTATTTTAAAG
66 TTCATTAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTTAGTTATTTTAAAG
* * * *
19385723 AAAAATTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACCATTTTGAAATAAAAGTTCAGATT
131 AAAAA-TTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAAATT
19385788 TTTAAGAAAGTAGTGATTTTCATT--AAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCT
195 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCT
*
19385851 GTTTTTTAATGATTTTAAAGAAAAAGTTTAAATTTTTAAAT
260 GTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAT
* * *
19385892 AAAGTTTTGATTTTTTTTTAAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGAT
1 AAAGTTTTGATTTTTTTTT-AACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGAT
19385957 TTT
65 TTT
19385960 GTTTAATCAA
Statistics
Matches: 595, Mismatches: 46, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
288 20 0.03
289 46 0.08
290 35 0.06
292 1 0.00
295 14 0.02
296 42 0.07
297 2 0.00
298 190 0.32
299 43 0.07
300 104 0.17
301 74 0.12
302 24 0.04
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (300 bp):
AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATT
TTCATTAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTTAGTTATTTTAAAG
AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAAATTT
TTAAGAAAGTAGTGATTTTCATTAAAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTG
TTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAT
Found at i:19386563 original size:21 final size:20
Alignment explanation
Indices: 19386539--19386578 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
19386529 ATAATTTTTA
19386539 TTTATTATT-ATTTCATATTTG
1 TTTATT-TTCATTTC-TATTTG
19386560 TTTATTTTCATTTCTATTT
1 TTTATTTTCATTTCTATTT
19386579 ATATGTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTATTTTCATTTCTATTTG
Found at i:19408624 original size:14 final size:14
Alignment explanation
Indices: 19408607--19408636 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19408597 TATTGCAATA
19408607 TATTTCTCTTTTTT
1 TATTTCTCTTTTTT
19408621 TATTTCTCTTTTTT
1 TATTTCTCTTTTTT
19408635 TA
1 TA
19408637 ATAAGTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTCTCTTTTTT
Found at i:19409245 original size:34 final size:34
Alignment explanation
Indices: 19409181--19409246 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
19409171 ATATATATGG
* *
19409181 AAATGCAATGACAATGTAGATTCAGCGACAATAA
1 AAATGCAATGACAATATAGATGCAGCGACAATAA
* *
19409215 AAATGCAATGACATTAATA-ATGCAGGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAGCGACAAT
19409247 TATACTACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAGCGACAATAA
Found at i:19418221 original size:42 final size:42
Alignment explanation
Indices: 19418155--19418402 Score: 340
Period size: 42 Copynumber: 5.9 Consensus size: 42
19418145 AAGTAAAGCA
* *
19418155 TTCATTGCATTTAGAGGCGCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
* * * *
19418197 TTCATCT-CATTCAAAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCAT-TGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
* * *
19418239 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
*
19418281 TTCATTGCATTTAGAGGCCCAAGTGTAGAGG-CTCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTC-CATTTACTT
*
19418322 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
* *
19418364 TTCATTGCATTTAGAGGCCTAGGCGTAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTA
19418403 TTTATTTTTT
Statistics
Matches: 186, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
41 40 0.22
42 145 0.78
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
Found at i:19418369 original size:83 final size:84
Alignment explanation
Indices: 19418155--19418402 Score: 347
Period size: 83 Copynumber: 3.0 Consensus size: 84
19418145 AAGTAAAGCA
* * * *
19418155 TTCATTGCATTTAGAGGCGCAGGTGTGGAGGTCCATTTACTTTTCATCT-CATTCAAAGGCCCAG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCAT-TGCATTTAGAGGCCCAA
*
19418219 GTGTGGAGGCCCATTTACTT
65 GTGTAGAGGCCCATTTACTT
* *
19418239 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
*
19418304 TGTAGAGGCTCATTTAC-T
66 TGTAGAGGCCCATTTACTT
* * * *
19418322 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
* *
19418387 CGTAGAGGTCCATTTA
66 TGTAGAGGCCCATTTA
19418403 TTTATTTTTT
Statistics
Matches: 146, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
83 74 0.51
84 72 0.49
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (84 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
TGTAGAGGCCCATTTACTT
Found at i:19418378 original size:125 final size:126
Alignment explanation
Indices: 19418155--19418402 Score: 376
Period size: 125 Copynumber: 2.0 Consensus size: 126
19418145 AAGTAAAGCA
* * *
19418155 TTCATTGCATTTAGAGGCGCAGGTGTGGAGGTCCATTTACTTTTCATCTCATTCAAAGGCCCAGG
1 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCATCTCATTCAAAGGCCCAGG
* * *
19418220 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
66 TGTAGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAAGCGTAGAGGTCCATTTACTT
* *
19418281 TTCATTGCATTTAGAGGCCCAAGTGTAGAGG-CTCATTTAC-TTTCAT-TGCATTTAGAGGCCCA
1 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTC-CATTTACTTTTCATCT-CATTCAAAGGCCCA
*
19418343 GGTGTAGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAGGCGTAGAGGTCCATTTA
64 GGTGTAGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAAGCGTAGAGGTCCATTTA
19418403 TTTATTTTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
124 1 0.01
125 75 0.68
126 35 0.32
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCATCTCATTCAAAGGCCCAGG
TGTAGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAAGCGTAGAGGTCCATTTACTT
Found at i:19418868 original size:3 final size:3
Alignment explanation
Indices: 19418849--19418903 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
19418839 AAAGGCCCAA
*
19418849 ATT A-T ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
19418894 ATT ATT ATT A
1 ATT ATT ATT A
19418904 GGGTTTCATG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:19419437 original size:19 final size:18
Alignment explanation
Indices: 19419397--19419437 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19419387 TAAAAAAGAG
* *
19419397 AAAGTTTAAATTTTTAGA
1 AAAGCTTAAATTTTTAAA
19419415 AAAGCTTAAATTTTTAAA
1 AAAGCTTAAATTTTTAAA
19419433 CAAAG
1 -AAAG
19419438 TTTTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (18 bp):
AAAGCTTAAATTTTTAAA
Found at i:19419531 original size:114 final size:115
Alignment explanation
Indices: 19419309--19419519 Score: 311
Period size: 116 Copynumber: 1.8 Consensus size: 115
19419299 AAATAGCTTG
*
19419309 ATTTTGAAAAAAGTTTTGGTTTTTTTAAACAATTTCAAAATAACAGTTTTGATTTTTAAGTAAAA
1 ATTTTGAAAAAAGTTTTGATTTTTTTAAACAATTTCAAAATAACAGTTTTGATTTTTAAGTAAAA
*
19419374 TAGTGATTTTCTTTAAAAAAGAGAAAGTTTAAATTTTTAGAAAAGCTTAA
66 TAGTGATTTTCATTAAAAAAGAGAAAGTTTAAATTTTTAGAAAAGCTTAA
* * *
19419424 ATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAA-A-TTTTGTATTTTTAAG-AA
1 ATTTTGAAA-AAAGTTTTGATTTTTTTAAACAATTTCAAAATAACAGTTTTG-ATTTTTAAGTAA
* *
19419486 AGTAGTGATTTTCATTAAAAAAGGATAAAGTTTA
64 AATAGTGATTTTCATTAAAAAA-GAGAAAGTTTA
19419520 TTTTTTTGAA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
114 27 0.31
115 28 0.33
116 31 0.36
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (115 bp):
ATTTTGAAAAAAGTTTTGATTTTTTTAAACAATTTCAAAATAACAGTTTTGATTTTTAAGTAAAA
TAGTGATTTTCATTAAAAAAGAGAAAGTTTAAATTTTTAGAAAAGCTTAA
Found at i:19419871 original size:299 final size:297
Alignment explanation
Indices: 19419414--19420236 Score: 1098
Period size: 299 Copynumber: 2.8 Consensus size: 297
19419404 AAATTTTTAG
* * * *
19419414 AAAAGCTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAAT-AAA-TTTTGTAT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAG-AT
* * * *
19419477 TTTTAAGAAAGTAGTGATTTTCATTAAAAAAGGATAAAGTTTATTTTTTTGAAAATGAAAATTTA
65 TTTTAAGAAAGTAGTGATTTTCATTAAAAAAGGA-AAAATTTATATTTTTAAAAATAAAAATTTA
* * *
19419542 TTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGGTTTTCTTAACCATTT
129 TTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTT
* * *
19419607 CGAAATAAAAGTTTTAATTTTTTATAAAATAGTGATTTTCAAT-AAAAATG-AGAAAGTTTATAT
194 CGAAATAAAAGTTTTAATTTTTAATAAAGTAGTGATTTTCAATAAAAAAAGAAGAAAGTTT-TAT
* *
19419670 TTTTAAAAATAAAAATATTTTTTTTTACTTATTTTAAAGA
258 TTTTAAAAATAAAAATATGTCTTTTTACTTATTTTAAAGA
* * * *
19419710 GAAAGTTTAAATTTTTAAATAAATTTTTGATTTTTTTTAATTATTTCGAAGTAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* *
19419775 TTCAAGAAAGTAATGATTTTCATTAAAAAAAGGAGAAAATTTATATTTTTAAAAAATAAAAATTT
66 TTTAAGAAAGTAGTGATTTTCATT-AAAAAAGGA-AAAATTTATATTTTT-AAAAATAAAAATTT
* *
19419840 ATTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAATTATT
128 ATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATT
* * *
19419905 TCTAAATAAAAG-TTTAGATTTTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTTA
193 TCGAAATAAAAGTTTTA-ATTTTTAATAAAGTAGTGATTTTCAATAAAAAAAGAAGAAAGTTTTA
* *
19419969 TTTTTAAAAATAAAAATCTGTCTTTTTAGTTATTTTAAAGA
257 TTTTTAAAAATAAAAATATGTCTTTTTACTTATTTTAAAGA
* *
19420010 AAAAATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTTGAAATAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* *
19420074 TTTAAGAAGGTAGTGATTTTCATTAAAAAAGGAAAAAGTTTATATTTTTTAAAA-AAAAA---A-
66 TTTAAGAAAGTAGTGATTTTCATTAAAAAAGGAAAAA-TTTATATTTTTAAAAATAAAAATTTAT
* * * *
19420134 ---TTAGTGATTTTAAAGAAAAATTTTAAATTTTTAAACAAAATTTTGATTTTTTTTAAACTATT
130 TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTT-AACTATT
* *
19420196 TCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGATTTT
193 TCGAAATAAAAGTTTTAATTTTTAA-TAAAGTAGTGATTTT
19420237 GTTTTAACCA
Statistics
Matches: 465, Mismatches: 50, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
289 41 0.09
290 7 0.02
291 24 0.05
292 17 0.04
293 1 0.00
296 50 0.11
297 36 0.08
298 50 0.11
299 158 0.34
300 72 0.15
301 9 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (297 bp):
AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
TTTAAGAAAGTAGTGATTTTCATTAAAAAAGGAAAAATTTATATTTTTAAAAATAAAAATTTATT
TTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCG
AAATAAAAGTTTTAATTTTTAATAAAGTAGTGATTTTCAATAAAAAAAGAAGAAAGTTTTATTTT
TAAAAATAAAAATATGTCTTTTTACTTATTTTAAAGA
Found at i:19419942 original size:50 final size:51
Alignment explanation
Indices: 19419689--19420093 Score: 193
Period size: 51 Copynumber: 8.1 Consensus size: 51
19419679 TAAAAATATT
* * * * **
19419689 TTTTTTTACTTATTTTAAAGAGAAAGTTTAAATTTTTAAATAAATTTTTGA
1 TTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
** * * * *
19419740 TTTTTTTTAATTATTTCGAAGTAAAAGTTTAGA-TTTTCAAGAAAGTAATGA
1 -TTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
* * * ***
19419791 TTTTCATTAA--A---AAAAGGAGAAAA-TTTATATTTTTAAA-AAA-TAAAAA
1 TTTT-TTTAATTATTTTAAA-GA-AAAAGTTTAAATTTTTAAAGAAAGTAGTGA
* **
19419837 TTTATTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGA
1 --T-TTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
* *
19419891 TTTTTTTAATTATTTCTAAA-TAAAAGTTTAGATTTTT-AAGAAAGTAGTGA
1 TTTTTTTAATTATTT-TAAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
* * * * ** *
19419941 TTTTCATTAA--A---AAAAGAAGAAAGTTT-TATTTTTAAAAATAAAAATCTG-
1 TTTT-TTTAATTATTTTAAAGAA-AAAGTTTAAATTTTTAAAGA-AAGTA-GTGA
* * * * **
19419989 TCTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAAATAAAGTTTTGA
1 TTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
* * * *
19420040 TTTTTTTAACTATTTTGAAA-TAAAAGTTTAGATTTTT-AAGAAGGTAGTGA
1 TTTTTTTAATTATTTT-AAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
19420090 TTTT
1 TTTT
19420094 CATTAAAAAA
Statistics
Matches: 263, Mismatches: 60, Indels: 62
0.68 0.16 0.16
Matches are distributed among these distances:
45 3 0.01
46 13 0.05
47 22 0.08
48 21 0.08
49 8 0.03
50 34 0.13
51 89 0.34
52 65 0.25
53 6 0.02
54 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (51 bp):
TTTTTTTAATTATTTTAAAGAAAAAGTTTAAATTTTTAAAGAAAGTAGTGA
Found at i:19420032 original size:149 final size:150
Alignment explanation
Indices: 19419414--19420236 Score: 1063
Period size: 149 Copynumber: 5.6 Consensus size: 150
19419404 AAATTTTTAG
* * * *
19419414 AAAAGCTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAAT-AAA-TTTTGTAT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAG-AT
* * * * *
19419477 TTTTAAGAAAGTAGTGATTTTCATT-AAAAAAGGATAAAGTTTATTTTTTTGAAAATGAAAATTT
65 TTTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATTT
19419541 ATTTTTTAGTTATTTTAAAGA
130 ATTTTTTAGTTATTTTAAAGA
* * *
19419562 AAAAGTTTAAATTTTTAAATAAAGTTTTG-GTTTTCTTAACCATTTCGAAATAAAAGTTTTA-AT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAG-TTTAGAT
* * * * *
19419625 TTTTTATAAAATAGTGATTTTCAAT-AAAAATG-AGAAAGTTTATATTTTTAAAAATAAAAATAT
65 TTTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAAT-T
* *
19419688 TTTTTTTTACTTATTTTAAAGA
129 TATTTTTTAGTTATTTTAAAGA
* * * *
19419710 GAAAGTTTAAATTTTTAAATAAATTTTTGATTTTTTTTAATTATTTCGAAGTAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* * * *
19419775 TTCAAGAAAGTAATGATTTTCATTAAAAAAAGGAGAAAATTTATATTTTTAAAAAATAAAAATTT
66 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTATATTTTT-AAAAATAAAAATTT
*
19419840 ATTTTTTAATTATTTTAAAGA
130 ATTTTTTAGTTATTTTAAAGA
* *
19419861 AAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAATTATTTCTAAATAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* *
19419925 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTT-TATTTTTAAAAATAAAAATCTG
66 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATTTA
19419989 TCTTTTTAGTTATTTTAAAGA
131 T-TTTTTAGTTATTTTAAAGA
* *
19420010 AAAAATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTTGAAATAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* * *
19420074 TTTAAGAAGGTAGTGATTTTCATTAAAAAAGGAA-AAAGTTTATATTTTTTAAAA-AAAAA---A
66 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATTTA
*
19420134 ----TTAGTGATTTTAAAGA
131 TTTTTTAGTTATTTTAAAGA
* * * *
19420150 AAAATTTTAAATTTTTAAACAAAATTTTGATTTTTTTTAAACTATTTCGAAATAAAAGTTTTGAT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTT-AACTATTTCGAAATAAAAGTTTAGAT
*
19420215 TTTGAAGTAAAGTAGTGATTTT
65 TTTTAAG-AAAGTAGTGATTTT
19420237 GTTTTAACCA
Statistics
Matches: 599, Mismatches: 62, Indels: 33
0.86 0.09 0.05
Matches are distributed among these distances:
140 42 0.07
141 7 0.01
142 30 0.05
143 13 0.02
147 43 0.07
148 137 0.23
149 171 0.29
150 79 0.13
151 65 0.11
152 12 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (150 bp):
AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
TTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATTTA
TTTTTTAGTTATTTTAAAGA
Found at i:19421239 original size:196 final size:196
Alignment explanation
Indices: 19420891--19421290 Score: 728
Period size: 196 Copynumber: 2.0 Consensus size: 196
19420881 TTAGGTTAGT
* *
19420891 TTTTAAGAGCTTGTTTATCATTTACCCTAAAAAAATTATAAATAATATGTAGGATTTTTTTTAAG
1 TTTT-AGAGATTGTTTATCATTTACCCTAAAAAAATTATAAATAATATGTAAGATTTTTTTTAAG
19420956 ATTTTAAACTAATTTTAAATATCATATAGGATAATTAATATGTAAATATTATTTAAGACTTTGTT
65 ATTTTAAACTAATTTTAAATATCATATAGGATAATTAATATGTAAATATTATTTAAGACTTTGTT
*
19421021 TAAGATTAAAATTAAGGATTGTTGTAGGTGAATTGTAAATCATGAGTAAGCCTCTTTAAGTATTT
130 TAAGATTAAAACTAAGGATTGTTGTAGGTGAATTGTAAATCATGAGTAAGCCTCTTTAAGTATTT
19421086 TA
195 TA
19421088 TTTTAGAGATTGTTTATCATTTACCCTAAAAAAATTATAAATAATATGTAAGATTTTTTTTAAGA
1 TTTTAGAGATTGTTTATCATTTACCCTAAAAAAATTATAAATAATATGTAAGATTTTTTTTAAGA
* *
19421153 TTTTAAACTAATTTTAAATATTATATAGGATAATTAATATGTAAATATTATTTAGGACTTTGTTT
66 TTTTAAACTAATTTTAAATATCATATAGGATAATTAATATGTAAATATTATTTAAGACTTTGTTT
* *
19421218 AAGATTAAAACTAATGATTGTTGTAGGTGAATTGTAAATCATGAGTAAGCCTTTTTAAGTATTTT
131 AAGATTAAAACTAAGGATTGTTGTAGGTGAATTGTAAATCATGAGTAAGCCTCTTTAAGTATTTT
19421283 A
196 A
19421284 TTTTAGA
1 TTTTAGA
19421291 TACTCTTTAA
Statistics
Matches: 196, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
196 192 0.98
197 4 0.02
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (196 bp):
TTTTAGAGATTGTTTATCATTTACCCTAAAAAAATTATAAATAATATGTAAGATTTTTTTTAAGA
TTTTAAACTAATTTTAAATATCATATAGGATAATTAATATGTAAATATTATTTAAGACTTTGTTT
AAGATTAAAACTAAGGATTGTTGTAGGTGAATTGTAAATCATGAGTAAGCCTCTTTAAGTATTTT
A
Found at i:19422520 original size:27 final size:27
Alignment explanation
Indices: 19422467--19422586 Score: 152
Period size: 27 Copynumber: 4.4 Consensus size: 27
19422457 TTAGAGTACA
* * *
19422467 CCACAAAGACAGTCCATTT-AGAGTACG
1 CCACAAAGGCATTCC-TTTCAGATTACG
* * * *
19422494 CTACTAAGACATTCTTTTCAGATTACG
1 CCACAAAGGCATTCCTTTCAGATTACG
*
19422521 CCACAAAGGCATTCCTTTCAGATAACG
1 CCACAAAGGCATTCCTTTCAGATTACG
19422548 CCACAAAGGCATTCCTTTCAGATTACG
1 CCACAAAGGCATTCCTTTCAGATTACG
19422575 CCACAAAGGCAT
1 CCACAAAGGCAT
19422587 AACAGAGTAC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 3 0.04
27 78 0.96
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (27 bp):
CCACAAAGGCATTCCTTTCAGATTACG
Found at i:19422597 original size:23 final size:22
Alignment explanation
Indices: 19422566--19422612 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
19422556 GCATTCCTTT
*
19422566 CAGATTACGCCACAAAGGCATAA
1 CAGAGTACGCCACAAAGGC-TAA
*
19422589 CAGAGTACGCCATAAAGGCTAA
1 CAGAGTACGCCACAAAGGCTAA
19422611 CA
1 CA
19422613 AGATGCCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (22 bp):
CAGAGTACGCCACAAAGGCTAA
Found at i:19430829 original size:244 final size:243
Alignment explanation
Indices: 19430401--19430883 Score: 921
Period size: 244 Copynumber: 2.0 Consensus size: 243
19430391 ACATGACACA
19430401 AATTCCACACACCTTTGCTGGGTTTTTTATCTACAAGCAAACTCTGCACAATATTAATAAGTTTA
1 AATTCCACACACCTTTGCTGGGTTTTTTATCTACAAGCAAACTCTGCACAATATTAATAAGTTTA
19430466 TCTATTTTATTTTTTAAGGTTAGAGAACTTAACCCATGAACCTATCTCGTAGGTTCTGTAGCTGG
66 TCTATTTTATTTTTTAAGGTTAGAGAACTTAACCCATGAACCTATCTCGTAGGTTCTGTAGCTGG
*
19430531 TCAGAATTGTTGACAGTTCATAGCCATTGTTGAAATCAACTCCCTTACTCTTTGGGGAGTCATGT
131 TCAGAATTGTTGACAGTTCATAACCATTGTTGAAATCAACTCCCTTACTCTTTGGGGAGTCATGT
19430596 TAACAATTACCCCTCCACTAGCAGCATCAATCATCTTCATCTCCGCAC
196 TAACAATTACCCCTCCACTAGCAGCATCAATCATCTTCATCTCCGCAC
19430644 AATTCCACACACCTTTGCTGGGTTTTTTTATCTACAAGCAAACTCTGCACAATATTAATAAGTTT
1 AATTCCACACACCTTTGCTGGG-TTTTTTATCTACAAGCAAACTCTGCACAATATTAATAAGTTT
*
19430709 ATCTATTTTATTTTTTAAGGTTAGAGAACTTAACCCATGAACCTGTCTCGTAGGTTCTGTAGCTG
65 ATCTATTTTATTTTTTAAGGTTAGAGAACTTAACCCATGAACCTATCTCGTAGGTTCTGTAGCTG
* *
19430774 GTCGGAATTGTTGACAGTTCGTAACCATTGTTGAAATCAACTCCCTTACTCTTTGGGGAGTCATG
130 GTCAGAATTGTTGACAGTTCATAACCATTGTTGAAATCAACTCCCTTACTCTTTGGGGAGTCATG
19430839 TTAACAATTACCCCTCCACTAGCAGCATCAATCATCTTCATCTCC
195 TTAACAATTACCCCTCCACTAGCAGCATCAATCATCTTCATCTCC
19430884 ATAGGGGCCC
Statistics
Matches: 235, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
243 22 0.09
244 213 0.91
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (243 bp):
AATTCCACACACCTTTGCTGGGTTTTTTATCTACAAGCAAACTCTGCACAATATTAATAAGTTTA
TCTATTTTATTTTTTAAGGTTAGAGAACTTAACCCATGAACCTATCTCGTAGGTTCTGTAGCTGG
TCAGAATTGTTGACAGTTCATAACCATTGTTGAAATCAACTCCCTTACTCTTTGGGGAGTCATGT
TAACAATTACCCCTCCACTAGCAGCATCAATCATCTTCATCTCCGCAC
Found at i:19443353 original size:24 final size:25
Alignment explanation
Indices: 19443308--19443354 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
19443298 ATTTTAACAT
* *
19443308 AGATAATATATATTTATTATAATTA
1 AGATAATATATATTGATAATAATTA
*
19443333 AGATATTAT-TATTGATAATAAT
1 AGATAATATATATTGATAATAAT
19443355 GATTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
AGATAATATATATTGATAATAATTA
Found at i:19451015 original size:40 final size:40
Alignment explanation
Indices: 19450971--19451100 Score: 140
Period size: 40 Copynumber: 3.2 Consensus size: 40
19450961 GCCGTGGCCC
*
19450971 GAATCATATCACTGGCTCATAGCCTGTTAGACCGTACCTT
1 GAATCATATCACTGGCTCAAAGCCTGTTAGACCGTACCTT
* * ** *
19451011 GAATCACATCACTAGCTCAAAGCCTACTA-AGTCGTACCTT
1 GAATCATATCACTGGCTCAAAGCCTGTTAGA-CCGTACCTT
* *
19451051 GAATCAAATCA-TCGGCTCAAAGCCTGTTAGACCGTAGCC-C
1 GAATCATATCACT-GGCTCAAAGCCTGTTAGACCGTA-CCTT
19451091 GAATCATATC
1 GAATCATATC
19451101 TCCAGCTCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
39 2 0.03
40 68 0.93
41 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (40 bp):
GAATCATATCACTGGCTCAAAGCCTGTTAGACCGTACCTT
Found at i:19451109 original size:40 final size:40
Alignment explanation
Indices: 19450954--19451137 Score: 124
Period size: 40 Copynumber: 4.6 Consensus size: 40
19450944 CGGCTATAGT
* * ** *
19450954 CTGCTAGGCCGTGGCCCGAATCATATCACTGGCTCATAGC
1 CTGCTAGACCGTAGCCCGAATCATATCACCAGCTCAAAGC
* * * *
19450994 CTGTTAGACCGTA-CCTTGAATCACATCACTAGCTCAAAGC
1 CTGCTAGACCGTAGCC-CGAATCATATCACCAGCTCAAAGC
* * * * * *
19451034 CTACTA-AGTCGTA-CCTTGAATCAAATCATCGGCTCAAAGC
1 CTGCTAGA-CCGTAGCC-CGAATCATATCACCAGCTCAAAGC
* *
19451074 CTGTTAGACCGTAGCCCGAATCATATCTCCAGCTCAAA-C
1 CTGCTAGACCGTAGCCCGAATCATATCACCAGCTCAAAGC
***
19451113 TCTGCTAGGTTGTAGCCCGAATCAT
1 -CTGCTAGACCGTAGCCCGAATCAT
19451138 TTCTAGTATT
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
39 4 0.04
40 106 0.94
41 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (40 bp):
CTGCTAGACCGTAGCCCGAATCATATCACCAGCTCAAAGC
Found at i:19451135 original size:80 final size:81
Alignment explanation
Indices: 19450937--19451136 Score: 198
Period size: 80 Copynumber: 2.5 Consensus size: 81
19450927 CCATTTTACG
* * * * * *
19450937 ACATCACCGGCT-ATAG-TCTGCTAGGCCGTGGCCCGAATCATATCACTGGCTCATAGCCTGTTA
1 ACATCACCAGCTCAAAGCTCTGCTAGGTCGTAGCCCGAATCAAATCACTGGCTCAAAGCCTGTTA
*
19451000 GACCGTACCTTGAATC
66 GACCGTACCTCGAATC
* * * *
19451016 ACATCACTAGCTCAAAGC-CTACTAAGTCGTA-CCTTGAATCAAATCA-TCGGCTCAAAGCCTGT
1 ACATCACCAGCTCAAAGCTCTGCTAGGTCGTAGCC-CGAATCAAATCACT-GGCTCAAAGCCTGT
19451078 TAGACCGTAGCC-CGAATC
64 TAGACCGTA-CCTCGAATC
* * *
19451096 ATATCTCCAGCTCAAA-CTCTGCTAGGTTGTAGCCCGAATCA
1 ACATCACCAGCTCAAAGCTCTGCTAGGTCGTAGCCCGAATCA
19451137 TTTCTAGTAT
Statistics
Matches: 96, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
79 14 0.15
80 78 0.81
81 4 0.04
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (81 bp):
ACATCACCAGCTCAAAGCTCTGCTAGGTCGTAGCCCGAATCAAATCACTGGCTCAAAGCCTGTTA
GACCGTACCTCGAATC
Found at i:19453641 original size:21 final size:21
Alignment explanation
Indices: 19453617--19453663 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
19453607 CAACTAGGAG
* *
19453617 TTCTACCGGTACACTTCT-AAC
1 TTCTACCGATACA-TCCTAAAC
19453638 TTCTACCGATACATCCTAAAC
1 TTCTACCGATACATCCTAAAC
19453659 TTCTA
1 TTCTA
19453664 TTGAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.28, C:0.32, G:0.06, T:0.34
Consensus pattern (21 bp):
TTCTACCGATACATCCTAAAC
Found at i:19456121 original size:20 final size:20
Alignment explanation
Indices: 19456098--19456147 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
19456088 GGGGCACAAT
*
19456098 AGTGCAAACAGGGGCACTGA
1 AGTGCAAACAGAGGCACTGA
*
19456118 AGTGCAAATAGAGGCACTGA
1 AGTGCAAACAGAGGCACTGA
*
19456138 AGTACAAACA
1 AGTGCAAACA
19456148 TAGTGATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (20 bp):
AGTGCAAACAGAGGCACTGA
Found at i:19456719 original size:13 final size:13
Alignment explanation
Indices: 19456701--19456730 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19456691 AGAAAAATCT
19456701 AAAGAAATGAAGA
1 AAAGAAATGAAGA
*
19456714 AAAGAAATGATGA
1 AAAGAAATGAAGA
19456727 AAAG
1 AAAG
19456731 GCTATAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (13 bp):
AAAGAAATGAAGA
Found at i:19459519 original size:2 final size:2
Alignment explanation
Indices: 19459512--19459536 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19459502 AAATCAAAAG
19459512 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19459537 TTACTCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19463530 original size:3 final size:3
Alignment explanation
Indices: 19463484--19463519 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
19463474 CTATGCTTTA
19463484 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19463520 GTTGATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19466839 original size:8 final size:9
Alignment explanation
Indices: 19466814--19466838 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19466804 TTATCACTCG
19466814 AAAAAAAAT
1 AAAAAAAAT
19466823 AAAAAAAAT
1 AAAAAAAAT
19466832 AAAAAAA
1 AAAAAAA
19466839 TGCAGTGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:19479328 original size:30 final size:29
Alignment explanation
Indices: 19479294--19479653 Score: 131
Period size: 30 Copynumber: 12.3 Consensus size: 29
19479284 AAAATCGAAC
19479294 TTTTGGAAAATTTGAGGTCGAAAATGTGAT
1 TTTTGGAAAATTTGAGGT-GAAAATGTGAT
** *
19479324 TTTTGG-AAATTTGAGGACAAAATGGTAAT
1 TTTTGGAAAATTTGAGGTGAAAAT-GTGAT
* * *
19479353 TTTT----AATTTTAGGGGCAAAATGGTAAT
1 TTTTGGAAAATTTGAGGTG-AAAAT-GTGAT
** * *
19479380 TTTT-GAATGTTT-AGGGGCAAAATGGTAAT
1 TTTTGGAAAATTTGAGGTG-AAAAT-GTGAT
* ** * *
19479409 TTTTAG-ATGTTCGAGGTTAAAATGTGAT
1 TTTTGGAAAATTTGAGGTGAAAATGTGAT
* * *
19479437 TTTT-GAGAAGTTTGGGGGTTAAAATGT-ATT
1 TTTTGGA-AAATTT-GAGGTGAAAATGTGA-T
*
19479467 TTTTGCAAAATTT-AGGGTGAAAATGTGA-
1 TTTTGGAAAATTTGA-GGTGAAAATGTGAT
* * *
19479495 TTTTAGAAAGGTTTGGAGGTGAAAATGT-AA
1 TTTTGGAAA-ATTT-GAGGTGAAAATGTGAT
*
19479525 TTTTGGAAAAGTTTGGGGTGAAAATGTGA-
1 TTTTGGAAAA-TTTGAGGTGAAAATGTGAT
* *
19479554 TTTTGGAAAAGTTTGAGGGTTAAAATGT-AA
1 TTTTGGAAAA-TTTGA-GGTGAAAATGTGAT
* * * * * *
19479584 TTTTAGAGAAGTTTAGGGGTTAAAATAT-AA
1 TTTTGGA-AAATTT-GAGGTGAAAATGTGAT
* * *
19479614 TTTTGGAAAAGTTTTGGGGTTAAAATATGAT
1 TTTTGGAAAA--TTTGAGGTGAAAATGTGAT
19479645 TTTTGGAAA
1 TTTTGGAAA
19479654 GTTCAGGGAC
Statistics
Matches: 269, Mismatches: 34, Indels: 53
0.76 0.10 0.15
Matches are distributed among these distances:
26 8 0.03
27 16 0.06
28 20 0.07
29 98 0.36
30 109 0.41
31 18 0.07
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
TTTTGGAAAATTTGAGGTGAAAATGTGAT
Found at i:19479354 original size:29 final size:28
Alignment explanation
Indices: 19479314--19479412 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 28
19479304 TTTGAGGTCG
* *
19479314 AAAAT-GTGATTTTTGGAAATTTGA-GGAC
1 AAAATGGTAATTTTT-G-AATTTGAGGGGC
*
19479342 AAAATGGTAATTTTT-AATTTTAGGGGC
1 AAAATGGTAATTTTTGAATTTGAGGGGC
*
19479369 AAAATGGTAATTTTTGAATGTTTAGGGGC
1 AAAATGGTAATTTTTGAAT-TTGAGGGGC
19479398 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
19479413 AGATGTTCGA
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
26 6 0.09
27 18 0.28
28 8 0.12
29 32 0.50
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.39
Consensus pattern (28 bp):
AAAATGGTAATTTTTGAATTTGAGGGGC
Found at i:19479418 original size:29 final size:29
Alignment explanation
Indices: 19479341--19479419 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
19479331 AATTTGAGGA
19479341 CAAAATGGTAATTTTTA-AT-TTTAGGGG
1 CAAAATGGTAATTTTTAGATGTTTAGGGG
19479368 CAAAATGGTAATTTTT-GAATGTTTAGGGG
1 CAAAATGGTAATTTTTAG-ATGTTTAGGGG
19479397 CAAAATGGTAATTTTTAGATGTT
1 CAAAATGGTAATTTTTAGATGTT
19479420 CGAGGTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
27 16 0.33
28 2 0.04
29 29 0.60
30 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.41
Consensus pattern (29 bp):
CAAAATGGTAATTTTTAGATGTTTAGGGG
Found at i:19479432 original size:29 final size:28
Alignment explanation
Indices: 19479334--19479424 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
19479324 TTTTGGAAAT
*
19479334 TTGAGGACAAAATGGTAATTTTTA-AT-
1 TTGAGGGCAAAATGGTAATTTTTAGATG
*
19479360 TTTAGGGGCAAAATGGTAATTTTT-GAATG
1 TTGA-GGGCAAAATGGTAATTTTTAG-ATG
*
19479389 TTTAGGGGCAAAATGGTAATTTTTAGATG
1 TTGA-GGGCAAAATGGTAATTTTTAGATG
19479418 TTCGAGG
1 TT-GAGG
19479425 TTAAAATGTG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
26 3 0.05
27 18 0.32
28 2 0.04
29 31 0.55
30 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
TTGAGGGCAAAATGGTAATTTTTAGATG
Found at i:19479493 original size:59 final size:58
Alignment explanation
Indices: 19479427--19479653 Score: 238
Period size: 59 Copynumber: 3.8 Consensus size: 58
19479417 GTTCGAGGTT
* *
19479427 AAAATGTGATTTTTGAGAAGTTTGGGGGTTAAAATGTATTTTTTGCAAAATTTAGGGTG
1 AAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGTATTTTTTG-AAAATTTAGGGTG
* * * * * * *
19479486 AAAATGTGATTTTAGAAAGGTTTGGAGGTGAAAATGTAATTTTGGAAAAGTTTGGGGTG
1 AAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGTATTTTTTGAAAA-TTTAGGGTG
* * * * *
19479545 AAAATGTGATTTTGGAAAAGTTTGAGGGTTAAAATGTAATTTTAGAGAAGTTTAGGGGTT
1 AAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGTATTTTTTGA-AAATTTA-GGGTG
* * * * *
19479605 AAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATATGATTTTTGGAAA
1 AAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGT-ATTTTTTGAAA
19479654 GTTCAGGGAC
Statistics
Matches: 140, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
58 4 0.03
59 89 0.64
60 40 0.29
61 7 0.05
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.37
Consensus pattern (58 bp):
AAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGTATTTTTTGAAAATTTAGGGTG
Found at i:19479539 original size:89 final size:92
Alignment explanation
Indices: 19479421--19479648 Score: 283
Period size: 89 Copynumber: 2.5 Consensus size: 92
19479411 TTAGATGTTC
* * *
19479421 GAGGTTAAAATGTGATTTTTGAGAAGTTTGGGGGTTAAAATGT-ATTTTTTGCAAAA-TTT-AGG
1 GAGGTTAAAATGTAATTTTGGAAAAGTTT-GGGGTTAAAATGTGATTTTTTGCAAAAGTTTGAGG
*
19479483 GTGAAAATGTGATTTTAGA-AAGGTTT-G
65 GTGAAAATGTAATTTTAGAGAA-GTTTAG
* * *
19479510 GAGGTGAAAATGTAATTTTGGAAAAGTTTGGGGTGAAAATGTGA--TTTTGGAAAAGTTTGAGGG
1 GAGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTGATTTTTTGCAAAAGTTTGAGGG
*
19479573 TTAAAATGTAATTTTAGAGAAGTTTAG
66 TGAAAATGTAATTTTAGAGAAGTTTAG
* *
19479600 G-GGTTAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATATGATTTTT
1 GAGGTTAAAATGTAATTTTGGAAAAG-TTTGGGGTTAAAATGTGATTTTT
19479649 GGAAAGTTCA
Statistics
Matches: 119, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
87 9 0.08
88 15 0.13
89 72 0.61
90 20 0.17
92 3 0.03
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (92 bp):
GAGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTGATTTTTTGCAAAAGTTTGAGGG
TGAAAATGTAATTTTAGAGAAGTTTAG
Found at i:19479655 original size:30 final size:29
Alignment explanation
Indices: 19479423--19479656 Score: 195
Period size: 30 Copynumber: 7.9 Consensus size: 29
19479413 AGATGTTCGA
* * *
19479423 GGTTAAAATGTGATTTTTGAGAAGTTTGGG
1 GGTTAAAATGTAATTTTGGA-AAGTTTTGG
* * * *
19479453 GGTTAAAATGTATTTTTTGCAAA-ATTTAG
1 GGTTAAAATGTA-ATTTTGGAAAGTTTTGG
* * * *
19479482 GGTGAAAATGTGATTTTAGAAAGGTTTGG
1 GGTTAAAATGTAATTTTGGAAAGTTTTGG
*
19479511 AGGTGAAAATGTAATTTTGGAAAAG-TTTGG
1 -GGTTAAAATGTAATTTTGG-AAAGTTTTGG
* *
19479541 GGTGAAAATGTGATTTTGGAAAAG-TTTGAG
1 GGTTAAAATGTAATTTTGG-AAAGTTTTG-G
* *
19479571 GGTTAAAATGTAATTTTAGAGAAGTTTAGG
1 GGTTAAAATGTAATTTTGGA-AAGTTTTGG
*
19479601 GGTTAAAATATAATTTTGGAAAAGTTTTGG
1 GGTTAAAATGTAATTTTGG-AAAGTTTTGG
* *
19479631 GGTTAAAATATGATTTTTGGAAAGTT
1 GGTTAAAATGT-AATTTTGGAAAGTT
19479657 CAGGGACCTT
Statistics
Matches: 170, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.04
29 45 0.26
30 98 0.58
31 20 0.12
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTGGAAAGTTTTGG
Found at i:19481969 original size:49 final size:49
Alignment explanation
Indices: 19481884--19482375 Score: 385
Period size: 49 Copynumber: 10.0 Consensus size: 49
19481874 AGGTGCTAGG
* * * * *
19481884 TTCGTCGTTGCGGCCTAAACATTTCCCATTATATCTTCATGGTATCGGA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGA
* * * *
19481933 TTTGCCATTGCGACCTCAATCC-TTCCCATCACATCTTCTAAGGTATC-GA
1 TTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTATCGGA
* * * * *
19481982 GTTCGCCGTCGCGGCCTCAATCTTTCCCTTTATC-TCTTCATGGTAAT-GGG
1 -TTCGCCGTTGCGGCCTCAACCTTTCCCATCA-CATCTTCATGGT-ATCGGA
* ** * *
19482032 TTCGCCGTTGCGGCCTCAACCTTTCCCTTCGTATCTTCATGGTACCGGG
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGA
* * * * *
19482081 TTCACCATTGCGGCCTCAACCTTTCCCATTACATCTTCTTAGGTACCGGA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT-GGTATCGGA
* * * *
19482131 TTCACCGTCGCGGCCTCAATCC-TTCCCTTCATC-TCTTCATGGTACTAGG-
1 TTCGCCGTTGCGGCCTCAA-CCTTTCCCATCA-CATCTTCATGGTA-TCGGA
* * ** * **
19482180 TTCGCCATTGCGGCCTCAACCTTTCCCTTCGTATCTTCTTGGTATCAAA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGA
* * * *
19482229 TTCGCCATTGCAGCCTCAGCCTTTCCCATCACATCTTCTTAGGTA-CTGGA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT-GGTATC-GGA
* * * * *
19482279 TTTGCCGTCGCGGCCTCAATCC-TTCCCTTCATC-TCTTCATGGTATTGGG
1 TTCGCCGTTGCGGCCTCAA-CCTTTCCCATCA-CATCTTCATGGTATCGGA
*
19482328 TTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTA-CGGA
1 TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGA
19482376 GCACTATTTA
Statistics
Matches: 350, Mismatches: 70, Indels: 47
0.75 0.15 0.10
Matches are distributed among these distances:
48 9 0.03
49 223 0.64
50 111 0.32
51 7 0.02
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (49 bp):
TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGA
Found at i:19482008 original size:99 final size:97
Alignment explanation
Indices: 19481883--19482371 Score: 407
Period size: 99 Copynumber: 5.0 Consensus size: 97
19481873 AAGGTGCTAG
* * * * * *
19481883 GTTCGTCGTTGCGGCCTAAACATTTCCCATTATATCTTCATGGTATCGGATTTGCCATTGCGACC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCC-TTATATCTTCATGGTATCGGATTCGCCGTTGCGGCC
19481948 TCAATCC-TTCCCATCACATCTTCTAAGGTATCGA
65 TCAA-CCTTTCCCATCACATCTTC-AAGGTATCGA
* * * *
19481982 GTTCGCCGTCGCGGCCTCAATCTTTCCCTTTATCTCTTCATGGTAAT-GGGTTCGCCGTTGCGGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCC-TTATATCTTCATGGT-ATCGGATTCGCCGTTGCGGC
* ** * * *
19482046 CTCAACCTTTCCCTTCGTATCTTCATGGTACCGG
64 CTCAACCTTTCCCATCACATCTTCAAGGTATCGA
* * * * * * *
19482080 GTTCACCATTGCGGCCTCAACCTTTCCCATTACATCTTCTTAGGTACCGGATTCACCGTCGCGGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCC-TTATATCTTCAT-GGTATCGGATTCGCCGTTGCGGC
* * *
19482145 CTCAATCC-TTCCCTTCATC-TCTTCATGGTA-CTA
64 CTCAA-CCTTTCCCATCA-CATCTTCAAGGTATCGA
* * * ** * *
19482178 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCGTATCTTCTTGGTATCAAATTCGCCATTGCAGC
1 -GTTCGCCGTTGCGGCCTCAACCTTTCCCTT-ATATCTTCATGGTATCGGATTCGCCGTTGCGGC
* * *
19482243 CTCAGCCTTTCCCATCACATCTTCTTAGGTACTGGA
64 CTCAACCTTTCCCATCACATCTTC-AAGGTA-TCGA
* * * * * *
19482279 -TTTGCCGTCGCGGCCTCAATCC-TTCCCTTCATCTCTTCATGGTATTGGGTTCACCGTTGCGGC
1 GTTCGCCGTTGCGGCCTCAA-CCTTTCCCTT-ATATCTTCATGGTATCGGATTCGCCGTTGCGGC
*
19482342 CTCAACCTTTCCCATCACATCTTCATGGTA
64 CTCAACCTTTCCCATCACATCTTCAAGGTA
19482372 CGGAGCACTA
Statistics
Matches: 311, Mismatches: 65, Indels: 29
0.77 0.16 0.07
Matches are distributed among these distances:
97 3 0.01
98 83 0.27
99 218 0.70
100 6 0.02
101 1 0.00
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (97 bp):
GTTCGCCGTTGCGGCCTCAACCTTTCCCTTATATCTTCATGGTATCGGATTCGCCGTTGCGGCCT
CAACCTTTCCCATCACATCTTCAAGGTATCGA
Found at i:19482098 original size:148 final size:148
Alignment explanation
Indices: 19481882--19482372 Score: 639
Period size: 148 Copynumber: 3.3 Consensus size: 148
19481872 TAAGGTGCTA
* * * * * *
19481882 GGTTCGTCGTTGCGGCCTAAACATTTCCCATT-ATATCTTCATGGTATCGGATTTGCCATTGCGA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCC-TTCATATCTTCATGGTACCGGATTCGCCATTGCGG
* *
19481946 CCTCAATCC-TTCCCATCACATCTTCTAAGGTATCGAGTTCGCCGTCGCGGCCTCAATCTTTCCC
65 CCTCAA-CCTTTCCCATCACATCTTCTTAGGTATCGAGTTCGCCGTCGCGGCCTCAATCCTTCCC
*
19482010 TTTATCTCTTCATGGTAATG
129 TTCATCTCTTCATGGTAATG
* * *
19482030 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCGTATCTTCATGGTACCGGGTTCACCATTGCGGC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCATTGCGGC
* * *
19482095 CTCAACCTTTCCCATTACATCTTCTTAGGTACCG-GATTCACCGTCGCGGCCTCAATCCTTCCCT
66 CTCAACCTTTCCCATCACATCTTCTTAGGTATCGAG-TTCGCCGTCGCGGCCTCAATCCTTCCCT
* *
19482159 TCATCTCTTCATGGTACTA
130 TCATCTCTTCATGGTAATG
* * * * ** *
19482178 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCGTATCTTCTTGGTATCAAATTCGCCATTGCAGC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCATTGCGGC
* * *
19482243 CTCAGCCTTTCCCATCACATCTTCTTAGGTACTGGA-TTTGCCGTCGCGGCCTCAATCCTTCCCT
66 CTCAACCTTTCCCATCACATCTTCTTAGGTA-TCGAGTTCGCCGTCGCGGCCTCAATCCTTCCCT
*
19482307 TCATCTCTTCATGGTATTG
130 TCATCTCTTCATGGTAATG
* * *
19482326 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTAC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTAC
19482373 GGAGCACTAT
Statistics
Matches: 298, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
147 5 0.02
148 292 0.98
149 1 0.00
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (148 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCATTGCGGC
CTCAACCTTTCCCATCACATCTTCTTAGGTATCGAGTTCGCCGTCGCGGCCTCAATCCTTCCCTT
CATCTCTTCATGGTAATG
Found at i:19500968 original size:13 final size:13
Alignment explanation
Indices: 19500939--19500970 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
19500929 TAAAATTTAA
19500939 AAAATAAAAAATT
1 AAAATAAAAAATT
19500952 -AAATAAAAAATT
1 AAAATAAAAAATT
19500964 AAAATAA
1 AAAATAA
19500971 TTTTTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:19506163 original size:127 final size:129
Alignment explanation
Indices: 19506032--19506285 Score: 415
Period size: 127 Copynumber: 2.0 Consensus size: 129
19506022 TATAAATTAT
*
19506032 CAAATTTTAGTAGAGGGACTAAACATGCAAAAAAAACATAAAATAGGGACCTCTAAAATTAGACC
1 CAAATTATAGTAGAGGGACTAAACATGC-AAAAAAACATAAAATAGGGACCTCTAAAATTAGACC
* *
19506097 TATTGAT-TGTAAAAAAAGATGATAATTCCT-AA-AAGTACGCTCCCCAACTAGTAGAATATAGC
65 TACTGATAAGTAAAAAAAGATGATAATTCCTAAAGAAGTACGCTCCCCAACTAGTAGAATATAGC
19506159 CAAATTATAGTAGAGGGACTAAACATGCAAAAAAACATAAAATAGGGACCTCTAAAATTAGACCT
1 CAAATTATAGTAGAGGGACTAAACATGCAAAAAAACATAAAATAGGGACCTCTAAAATTAGACCT
* * *
19506224 ACTGATAAGTCAAAAAAGATGATAATTCCTAAAAGAAGTATGCTGCCCAACTAGTAGAATAT
66 ACTGATAAGTAAAAAAAGATGATAATTCCT-AAAGAAGTACGCTCCCCAACTAGTAGAATAT
19506286 GGTCATGGTT
Statistics
Matches: 117, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
126 42 0.36
127 48 0.41
129 2 0.02
130 25 0.21
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (129 bp):
CAAATTATAGTAGAGGGACTAAACATGCAAAAAAACATAAAATAGGGACCTCTAAAATTAGACCT
ACTGATAAGTAAAAAAAGATGATAATTCCTAAAGAAGTACGCTCCCCAACTAGTAGAATATAGC
Found at i:19509516 original size:30 final size:29
Alignment explanation
Indices: 19509474--19509553 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 29
19509464 ATTGAAAATT
19509474 AAAATAATATAATATTTTTATATTTCAAA
1 AAAATAATATAATATTTTTATATTTCAAA
19509503 AAAATATATATAAT-TATTTTATATTTCAAA
1 AAAATA-ATATAATAT-TTTTATATTTCAAA
* *
19509533 AAAATAAATTTAATAATTTTA
1 AAAAT-AATATAATATTTTTA
19509554 AAATTATTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 7 0.16
30 37 0.82
31 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATAATATAATATTTTTATATTTCAAA
Found at i:19512697 original size:10 final size:10
Alignment explanation
Indices: 19512682--19512717 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
19512672 GTTAATCTAA
19512682 AAATAAAATG
1 AAATAAAATG
19512692 AAATAAAAT-
1 AAATAAAATG
*
19512701 AAATAAAGTG
1 AAATAAAATG
19512711 AAATAAA
1 AAATAAA
19512718 TCTGGTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (10 bp):
AAATAAAATG
Found at i:19520064 original size:18 final size:18
Alignment explanation
Indices: 19520043--19520078 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19520033 CTATTGCAGT
19520043 TCTAAAGGATGATGCAAA
1 TCTAAAGGATGATGCAAA
19520061 TCTAAAGGATGATGCAAA
1 TCTAAAGGATGATGCAAA
19520079 GACAGTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
TCTAAAGGATGATGCAAA
Found at i:19524514 original size:24 final size:24
Alignment explanation
Indices: 19524486--19524560 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
19524476 ATATACTGGT
19524486 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
*
19524510 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
*
19524534 TAACCA-TCTTGGGCTCATGAGAGC
1 TAACCATTC-TGGGCTCATAAGAGC
19524558 TAA
1 TAA
19524561 TGTTGTCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 2 0.04
24 45 0.96
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:19532862 original size:2 final size:2
Alignment explanation
Indices: 19532855--19532881 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19532845 ATAGTAGTAT
19532855 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
19532882 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19532886 original size:2 final size:2
Alignment explanation
Indices: 19532881--19532909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19532871 ACACACACAC
19532881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19532910 GATTCTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19533551 original size:17 final size:17
Alignment explanation
Indices: 19533496--19533543 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
19533486 ATATATATGG
*
19533496 AAATGCAATGACAATAA
1 AAATGCAATGACAAGAA
* * *
19533513 AGATGTAGTGACAAGAA
1 AAATGCAATGACAAGAA
19533530 AAATGCAATGACAA
1 AAATGCAATGACAA
19533544 ACAAAATGTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (17 bp):
AAATGCAATGACAAGAA
Found at i:19533559 original size:34 final size:34
Alignment explanation
Indices: 19533496--19533560 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
19533486 ATATATATGG
*
19533496 AAATGCAATGACAATAAAGATGTAGTGACAAGAA
1 AAATGCAATGACAATAAAAATGTAGTGACAAGAA
19533530 AAATGCAATGACAA-ACAAAATGT-GATGACAA
1 AAATGCAATGACAATA-AAAATGTAG-TGACAA
19533561 CTACATGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (34 bp):
AAATGCAATGACAATAAAAATGTAGTGACAAGAA
Found at i:19555984 original size:649 final size:649
Alignment explanation
Indices: 19554747--19556045 Score: 2508
Period size: 649 Copynumber: 2.0 Consensus size: 649
19554737 TTAGGCTAAG
*
19554747 CTTCATTAAGTTAGAAAATGTAATAACTAAGTTAAAAATACTAAAAGTGTATGCTAAAGATGATC
1 CTTCATTAAGTTAGAAAATGTAATAACTAAGTTAAAAATACTAAAAATGTATGCTAAAGATGATC
**
19554812 AAATGGGAACAAATTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGTTATCAATGTT
66 AAATGGGAACAAATTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGTTATCAACATT
19554877 TTACTCGGTTCGACAATGGTTGCTCATTTCGGTTTGACGATTCCGCTTCCTCATGATACGAGGTG
131 TTACTCGGTTCGACAATGGTTGCTCATTTCGGTTTGACGATTCCGCTTCCTCATGATACGAGGTG
19554942 CTAGTCCCATCCGAATGATCTGCATGAAACGTTAGTAGTGGTAAAACATAACGAGAAGTTGAAGT
196 CTAGTCCCATCCGAATGATCTGCATGAAACGTTAGTAGTGGTAAAACATAACGAGAAGTTGAAGT
* *
19555007 GTTATATCTTATCTCGTCGGCAGCATCTGATTGAGTTTTTCCTCTAGTTCAATCGGAGTTGGGCT
261 GTTATATCTTATCTCGTCGGCAGCATCCGATTGAGTTTTTCCTCTAGTTCAATCAGAGTTGGGCT
*
19555072 CCTACGACATCGACGTCGATTCGATTTAGTGGTACGTACTGGTGGTGAAGGTGAGGGCATGTCAG
326 CCTACAACATCGACGTCGATTCGATTTAGTGGTACGTACTGGTGGTGAAGGTGAGGGCATGTCAG
*
19555137 AATCGTCATCATTGACGTCGATGACCGGTGGAGCTGTAAAATGATTACCTTGACGGTTAAGAGTT
391 AATCGTCATCATTGACGTCGATGACCGGTGGAGCTGTAAAATGATTACCTCGACGGTTAAGAGTT
19555202 GTTGGAAATCAATCAGCTAAATGGATTTGTGTGCGAACCATGCTATGATTTTTTCGTATTTCGTT
456 GTTGGAAATCAATCAGCTAAATGGATTTGTGTGCGAACCATGCTATGATTTTTTCGTATTTCGTT
19555267 CGTTATGGTGGTACACGGCAGTAGACGACAGTGGGTGCGGCAACGAACAGTAGTCGGATAGTGGC
521 CGTTATGGTGGTACACGGCAGTAGACGACAGTGGGTGCGGCAACGAACAGTAGTCGGATAGTGGC
19555332 GTGAAAGGTAATGGTGAAAGAAATTAAGTTGGAATGGTGGCCATGATATGTGGATGCGTGTGGT
586 GTGAAAGGTAATGGTGAAAGAAATTAAGTTGGAATGGTGGCCATGATATGTGGATGCGTGTGGT
19555396 CTTCATTAAGTTAGAAAATGTAATAACTAAGTTAAAAATACTAAAAATGTATGCTAAAGATGATC
1 CTTCATTAAGTTAGAAAATGTAATAACTAAGTTAAAAATACTAAAAATGTATGCTAAAGATGATC
19555461 AAATGGGAACAAATTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGTTATCAACATT
66 AAATGGGAACAAATTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGTTATCAACATT
*
19555526 TTACTCGGTTCGACAATGGTTGCTCATTTCGGTTTGACGGTTCCGCTTCCTCATGATACGAGGTG
131 TTACTCGGTTCGACAATGGTTGCTCATTTCGGTTTGACGATTCCGCTTCCTCATGATACGAGGTG
19555591 CTAGTCCCATCCGAATGATCTGCATGAAACGTTAGTAGTGGTAAAACATAACGAGAAGTTGAAGT
196 CTAGTCCCATCCGAATGATCTGCATGAAACGTTAGTAGTGGTAAAACATAACGAGAAGTTGAAGT
19555656 GTTATATCTTATCTCGTCGGCAGCATCCGATTGAGTTTTTCCTCTAGTTCAATCAGAGTTGGGCT
261 GTTATATCTTATCTCGTCGGCAGCATCCGATTGAGTTTTTCCTCTAGTTCAATCAGAGTTGGGCT
*
19555721 CCTACAACATCGACGTCGATTCGATTTAGTGGTACGTACTGGTGGTGAAGGTGAGGGCGTGTCAG
326 CCTACAACATCGACGTCGATTCGATTTAGTGGTACGTACTGGTGGTGAAGGTGAGGGCATGTCAG
19555786 AATCGTCATCATTGACGTCGATGACCGGTGGAGCTGTAAAATGATTACCTCGACGGTTAAGAGTT
391 AATCGTCATCATTGACGTCGATGACCGGTGGAGCTGTAAAATGATTACCTCGACGGTTAAGAGTT
19555851 GTTGGAAATCAATCAGCTAAATGGATTTGTGTGCGAACCATGCTATGATTTTTTCGTATTTCGTT
456 GTTGGAAATCAATCAGCTAAATGGATTTGTGTGCGAACCATGCTATGATTTTTTCGTATTTCGTT
*
19555916 CGTTATGGTGGTACACGGCAGTAGACGACAGTGGGTGCGGCAACGAATAGTAGTCGGATAGTGGC
521 CGTTATGGTGGTACACGGCAGTAGACGACAGTGGGTGCGGCAACGAACAGTAGTCGGATAGTGGC
19555981 GTGAAAGGTAATGGTGAAAGAAATTAAGTTGGAATGGTGGCCATGATATGTGGATGCGTGTGGT
586 GTGAAAGGTAATGGTGAAAGAAATTAAGTTGGAATGGTGGCCATGATATGTGGATGCGTGTGGT
19556045 C
1 C
19556046 AGGAATGGTG
Statistics
Matches: 640, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
649 640 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (649 bp):
CTTCATTAAGTTAGAAAATGTAATAACTAAGTTAAAAATACTAAAAATGTATGCTAAAGATGATC
AAATGGGAACAAATTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGTTATCAACATT
TTACTCGGTTCGACAATGGTTGCTCATTTCGGTTTGACGATTCCGCTTCCTCATGATACGAGGTG
CTAGTCCCATCCGAATGATCTGCATGAAACGTTAGTAGTGGTAAAACATAACGAGAAGTTGAAGT
GTTATATCTTATCTCGTCGGCAGCATCCGATTGAGTTTTTCCTCTAGTTCAATCAGAGTTGGGCT
CCTACAACATCGACGTCGATTCGATTTAGTGGTACGTACTGGTGGTGAAGGTGAGGGCATGTCAG
AATCGTCATCATTGACGTCGATGACCGGTGGAGCTGTAAAATGATTACCTCGACGGTTAAGAGTT
GTTGGAAATCAATCAGCTAAATGGATTTGTGTGCGAACCATGCTATGATTTTTTCGTATTTCGTT
CGTTATGGTGGTACACGGCAGTAGACGACAGTGGGTGCGGCAACGAACAGTAGTCGGATAGTGGC
GTGAAAGGTAATGGTGAAAGAAATTAAGTTGGAATGGTGGCCATGATATGTGGATGCGTGTGGT
Found at i:19558180 original size:3 final size:3
Alignment explanation
Indices: 19558172--19558201 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19558162 TATATCCCAA
19558172 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19558202 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:19559253 original size:13 final size:13
Alignment explanation
Indices: 19559235--19559315 Score: 99
Period size: 13 Copynumber: 6.2 Consensus size: 13
19559225 TTTTTCGAAA
19559235 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
19559248 AAAGTCAACGATC
1 AAAGTCAACGGTC
*
19559261 AAAGTCAACGTTC
1 AAAGTCAACGGTC
19559274 AAAGTCAACGGTC
1 AAAGTCAACGGTC
** *
19559287 AGCGATCAGCGGTC
1 AAAG-TCAACGGTC
*
19559301 AAAGTCAACGATC
1 AAAGTCAACGGTC
19559314 AA
1 AA
19559316 CGGTCAGTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
13 47 0.82
14 10 0.18
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:19559310 original size:27 final size:26
Alignment explanation
Indices: 19559238--19559329 Score: 103
Period size: 27 Copynumber: 3.5 Consensus size: 26
19559228 TTCGAAAAAA
* *
19559238 GTCAACGGTCAAAGTCAACGATCAAA
1 GTCAGCGGTCAAAGTCAACGATCAAC
* * * *
19559264 GTCAACGTTCAAAGTCAACGGTCAGC
1 GTCAGCGGTCAAAGTCAACGATCAAC
19559290 GATCAGCGGTCAAAGTCAACGATCAAC
1 G-TCAGCGGTCAAAGTCAACGATCAAC
*
19559317 GGTCAGTGGTCAA
1 -GTCAGCGGTCAA
19559330 CGTCGGTCAA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
26 23 0.42
27 31 0.56
28 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (26 bp):
GTCAGCGGTCAAAGTCAACGATCAAC
Found at i:19559319 original size:20 final size:20
Alignment explanation
Indices: 19559252--19559321 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
19559242 ACGGTCAAAG
* *
19559252 TCAACGATCAAAGTCAACGT
1 TCAACGGTCAAAGTCAACGA
* * *
19559272 TCAA-AGTCAACGGTCAGCGA
1 TCAACGGTCAA-AGTCAACGA
*
19559292 TCAGCGGTCAAAGTCAACGA
1 TCAACGGTCAAAGTCAACGA
19559312 TCAACGGTCA
1 TCAACGGTCA
19559322 GTGGTCAACG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 4 0.11
20 29 0.76
21 5 0.13
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
TCAACGGTCAAAGTCAACGA
Found at i:19559394 original size:14 final size:15
Alignment explanation
Indices: 19559375--19559409 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19559365 TGGGTTGGAC
*
19559375 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
19559389 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
19559404 TTGGTT
1 TTGGTT
19559410 AGGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:19559422 original size:21 final size:20
Alignment explanation
Indices: 19559384--19559490 Score: 142
Period size: 20 Copynumber: 5.2 Consensus size: 20
19559374 CTTGGTTCAA
*
19559384 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
*
19559404 TTGGTTAGGTTTTAAATGGGT
1 TTGGTTTGG-TTTAAATGGGT
19559425 TTGGTTTGGTTTAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
**
19559445 TTGGTTTGGTTTAAATGAAT
1 TTGGTTTGGTTTAAATGGGT
*
19559465 GTGGGTTTGGTTTAAATGGGAT
1 -TTGGTTTGGTTTAAATGGG-T
19559487 TTGG
1 TTGG
19559491 GCTTGATGGG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 37 0.49
21 37 0.49
22 1 0.01
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.47
Consensus pattern (20 bp):
TTGGTTTGGTTTAAATGGGT
Found at i:19559441 original size:41 final size:41
Alignment explanation
Indices: 19559384--19559490 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 41
19559374 CTTGGTTCAA
* **
19559384 TTGGTTTGGTTCAAATGGGTTTGGTTAGGTTTTAAATGGGT-
1 TTGGTTTGGTTTAAATGGGTTTGGTTAGG-TTTAAATGAATG
*
19559425 TTGGTTTGGTTTAAATGGGTTTGGTTTGGTTTAAATGAATG
1 TTGGTTTGGTTTAAATGGGTTTGGTTAGGTTTAAATGAATG
*
19559466 TGGGTTTGGTTTAAATGGGATTTGG
1 TTGGTTTGGTTTAAATGGG-TTTGG
19559491 GCTTGATGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
40 9 0.15
41 45 0.76
42 5 0.08
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.47
Consensus pattern (41 bp):
TTGGTTTGGTTTAAATGGGTTTGGTTAGGTTTAAATGAATG
Found at i:19565412 original size:3 final size:3
Alignment explanation
Indices: 19565404--19565433 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19565394 TATATCCCAA
19565404 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19565434 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:19566485 original size:13 final size:13
Alignment explanation
Indices: 19566467--19566534 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
19566457 TTTTTCGAAA
19566467 AAAGTCAACGGTC
1 AAAGTCAACGGTC
19566480 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
19566493 AAAGTCAGCGGTC
1 AAAGTCAACGGTC
**
19566506 AGCGGTCAACGGTC
1 A-AAGTCAACGGTC
*
19566520 AAAGTCAATGGTC
1 AAAGTCAACGGTC
19566533 AA
1 AA
19566535 CGGTCAATGG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
13 37 0.79
14 10 0.21
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.16
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:19566493 original size:7 final size:7
Alignment explanation
Indices: 19566470--19566557 Score: 74
Period size: 7 Copynumber: 13.0 Consensus size: 7
19566460 TTCGAAAAAA
19566470 GTCAACG
1 GTCAACG
*
19566477 GTCAA-A
1 GTCAACG
19566483 GTCAACG
1 GTCAACG
*
19566490 GTCAA-A
1 GTCAACG
*
19566496 GTCAGCG
1 GTCAACG
*
19566503 GTCAGCG
1 GTCAACG
19566510 GTCAACG
1 GTCAACG
*
19566517 GTCAA-A
1 GTCAACG
*
19566523 GTCAATG
1 GTCAACG
19566530 GTCAACG
1 GTCAACG
*
19566537 GTCAATG
1 GTCAACG
**
19566544 GTCAGTG
1 GTCAACG
19566551 GTCAACG
1 GTCAACG
19566558 CCGGTCAACG
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
6 14 0.22
7 51 0.78
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:19566521 original size:27 final size:27
Alignment explanation
Indices: 19566467--19566547 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
19566457 TTTTTCGAAA
*
19566467 AAAGTCAACGGTCAA-AGTCAACGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
* *
19566493 AAAGTCAGCGGTCAGCGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
* *
19566520 AAAGTCAATGGTCAACGGTCAATGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
19566547 A
1 A
19566548 GTGGTCAACG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 13 0.28
27 34 0.72
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.17
Consensus pattern (27 bp):
AAAGTCAACGGTCAACGGTCAACGGTC
Found at i:19566565 original size:10 final size:10
Alignment explanation
Indices: 19566550--19566577 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
19566540 AATGGTCAGT
19566550 GGTCAACGCC
1 GGTCAACGCC
19566560 GGTCAACGCC
1 GGTCAACGCC
19566570 GGTCAACG
1 GGTCAACG
19566578 GTTTGACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.32, T:0.11
Consensus pattern (10 bp):
GGTCAACGCC
Found at i:19566620 original size:14 final size:15
Alignment explanation
Indices: 19566601--19566635 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19566591 TGGGTTGGAC
*
19566601 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
19566615 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
19566630 TTGGTT
1 TTGGTT
19566636 AGGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:19566633 original size:20 final size:20
Alignment explanation
Indices: 19566610--19566677 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
19566600 CTTGGTTCAA
*
19566610 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
*
19566630 TTGGTTAGGTTTTAAATGGGT
1 TTGGTTTGG-TTTAAATGGGT
19566651 TTGGTTTGGTTTAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
19566671 TTGGTTT
1 TTGGTTT
19566678 AAATGAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 26 0.59
21 18 0.41
ACGTcount: A:0.15, C:0.01, G:0.34, T:0.50
Consensus pattern (20 bp):
TTGGTTTGGTTTAAATGGGT
Found at i:19566673 original size:15 final size:15
Alignment explanation
Indices: 19566653--19566682 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19566643 AAATGGGTTT
19566653 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
19566668 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
19566683 AATGTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTGGTTTAAATG
Found at i:19570218 original size:48 final size:48
Alignment explanation
Indices: 19570166--19570262 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
19570156 CATGGCTTTC
19570166 TTTATGCCAACATTACCTATTTTGCAAGAAATTGAGAACATACCTTGG
1 TTTATGCCAACATTACCTATTTTGCAAGAAATTGAGAACATACCTTGG
19570214 TTTATGCCAACATTACCTATTTTGCAAGAAATTGAGAACATACCTTGG
1 TTTATGCCAACATTACCTATTTTGCAAGAAATTGAGAACATACCTTGG
19570262 T
1 T
19570263 CCTTACACTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (48 bp):
TTTATGCCAACATTACCTATTTTGCAAGAAATTGAGAACATACCTTGG
Found at i:19573865 original size:23 final size:23
Alignment explanation
Indices: 19573835--19573884 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
19573825 TTACTTGATC
19573835 ACATTGAAAAAGAATTTGCACAA
1 ACATTGAAAAAGAATTTGCACAA
* *
19573858 ACATTGAAATAGAATTTGCACAG
1 ACATTGAAAAAGAATTTGCACAA
19573881 ACAT
1 ACAT
19573885 ATGATGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (23 bp):
ACATTGAAAAAGAATTTGCACAA
Found at i:19577887 original size:21 final size:21
Alignment explanation
Indices: 19577863--19577902 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19577853 TACCCTGTAC
*
19577863 TTCTACCGAAACATGTATGGG
1 TTCTACCGAAACAAGTATGGG
19577884 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
19577903 CAGAATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Found at i:19586953 original size:96 final size:99
Alignment explanation
Indices: 19586781--19586969 Score: 303
Period size: 96 Copynumber: 1.9 Consensus size: 99
19586771 GGGTGTTACA
*
19586781 GCTACTTCTCCACTTGGGATTCTAAACCAAACCATGGCTTCTTCTTCTTCCATCAATCTCCCAAC
1 GCTACTTCTCCACTTGGGATTCTAAACCAAACCATGGCTTCTTCTACTT-CATCAATCTCCCAAC
*
19586846 GCTTCAAGGTTCTCTATTTCAATCTCATAACCATG
65 CCTTCAAGGTTCTCTATTTCAATCTCATAACCATG
* * *
19586881 GCTACTTCTCTACTT-GGATTCTAAATCAAACCATGGCTTCTTCTAC-T-ATCATTCTCCCAACC
1 GCTACTTCTCCACTTGGGATTCTAAACCAAACCATGGCTTCTTCTACTTCATCAATCTCCCAACC
19586943 CTTCAAGGTTCTCTATTTCAATCTCAT
66 CTTCAAGGTTCTCTATTTCAATCTCAT
19586970 TTCTTGGAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
96 40 0.48
98 1 0.01
99 29 0.35
100 14 0.17
ACGTcount: A:0.24, C:0.31, G:0.09, T:0.36
Consensus pattern (99 bp):
GCTACTTCTCCACTTGGGATTCTAAACCAAACCATGGCTTCTTCTACTTCATCAATCTCCCAACC
CTTCAAGGTTCTCTATTTCAATCTCATAACCATG
Found at i:19587589 original size:40 final size:41
Alignment explanation
Indices: 19587543--19587636 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 41
19587533 GATTAAAATA
*
19587543 TTAAAATAATTTTAATAATTTTATATTTTAAAAA-ATAATT
1 TTAAAATAATTTTAATAAATTTATATTTTAAAAAGATAATT
19587583 TTAAAATAATTTTAATAAATTTATATTTTAAAAAGATAATT
1 TTAAAATAATTTTAATAAATTTATATTTTAAAAAGATAATT
19587624 TT--AATAATTTTAA
1 TTAAAATAATTTTAA
19587637 AATCATTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
39 11 0.21
40 33 0.63
41 8 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (41 bp):
TTAAAATAATTTTAATAAATTTATATTTTAAAAAGATAATT
Found at i:19587621 original size:21 final size:23
Alignment explanation
Indices: 19587597--19587638 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19587587 AATAATTTTA
19587597 ATAAATTT-AT-ATTTTAAAAAG
1 ATAAATTTAATAATTTTAAAAAG
*
19587618 ATAATTTTAATAATTTTAAAA
1 ATAAATTTAATAATTTTAAAA
19587639 TCATTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAATTTAATAATTTTAAAAAG
Done.