Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 44 of 199
Found at i:17551970 original size:23 final size:22
Alignment explanation
Indices: 17551923--17551977 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
17551913 TAATTTTATC
17551923 AAAAACTTT--TAAATATTACT
1 AAAAACTTTAATAAATATTACT
* *
17551943 TAAAACTTTAATAATTATTTACT
1 AAAAACTTTAATAAATA-TTACT
*
17551966 AAAAATTTTAAT
1 AAAAACTTTAAT
17551978 GAAAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
22 5 0.18
23 15 0.54
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAACTTTAATAAATATTACT
Found at i:17553086 original size:38 final size:38
Alignment explanation
Indices: 17553039--17553192 Score: 188
Period size: 38 Copynumber: 4.4 Consensus size: 38
17553029 ACTTAGATAA
* *
17553039 TCCTGTCATTTATCTGGTTTGTTTGAATAATTTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAAATTCAACT
*
17553077 TCCAGTCATTTATCCGGTTTGTTTGAATAAATTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAAATTCAACT
17553115 TCCTG-------T-C----TGTTTGAATAAATTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAAATTCAACT
*
17553141 TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAAATTCAACT
17553179 TCCTGTCATTTATC
1 TCCTGTCATTTATC
17553193 ATTACAAATT
Statistics
Matches: 99, Mismatches: 5, Indels: 24
0.77 0.04 0.19
Matches are distributed among these distances:
26 24 0.24
30 1 0.01
31 1 0.01
33 1 0.01
34 1 0.01
38 71 0.72
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (38 bp):
TCCTGTCATTTATCCGGTTTGTTTGAATAAATTCAACT
Found at i:17553132 original size:26 final size:26
Alignment explanation
Indices: 17553096--17553147 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17553086 TTATCCGGTT
17553096 TGTTTGAATAAATTCAACTTCCTGTC
1 TGTTTGAATAAATTCAACTTCCTGTC
17553122 TGTTTGAATAAATTCAACTTCCTGTC
1 TGTTTGAATAAATTCAACTTCCTGTC
17553148 ATTTATCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (26 bp):
TGTTTGAATAAATTCAACTTCCTGTC
Found at i:17553159 original size:64 final size:64
Alignment explanation
Indices: 17553058--17553185 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
17553048 TTATCTGGTT
*
17553058 TGTTTGAATAATTTCAACTTCCAGTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCCTGTC
1 TGTTTGAATAAATTCAACTTCCAGTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCCTGTC
* *
17553122 TGTTTGAATAAATTCAACTTCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCTGTC
1 TGTTTGAATAAATTCAACTTCCAGTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCCTGTC
17553186 ATTTATCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (64 bp):
TGTTTGAATAAATTCAACTTCCAGTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCCTGTC
Found at i:17553606 original size:33 final size:34
Alignment explanation
Indices: 17553548--17553611 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
17553538 GATCTTTAAG
**
17553548 TTGGTTATATTTTTTTTTGTATAGTTTAATTTTT
1 TTGGTTATATTTTTAGTTGTATAGTTTAATTTTT
17553582 TTGGTTATA-TTTTAGTTGTATAGTTTAATT
1 TTGGTTATATTTTTAGTTGTATAGTTTAATT
17553612 ATTATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (34 bp):
TTGGTTATATTTTTAGTTGTATAGTTTAATTTTT
Found at i:17554430 original size:16 final size:16
Alignment explanation
Indices: 17554409--17554442 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17554399 AATCATGTAG
*
17554409 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAAAT
17554425 AAATAAGTTTGAAAAT
1 AAATAAGTTTGAAAAT
17554441 AA
1 AA
17554443 TGAAAATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (16 bp):
AAATAAGTTTGAAAAT
Found at i:17554513 original size:18 final size:16
Alignment explanation
Indices: 17554471--17554503 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17554461 AAACTTGTAG
17554471 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAGAT
17554487 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAGAT
17554503 A
1 A
17554504 TAATTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (16 bp):
AAATAAGTTTGAAGAT
Found at i:17554579 original size:9 final size:9
Alignment explanation
Indices: 17554567--17554663 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 9
17554557 TTAAAATAGT
17554567 TAACTTACA
1 TAACTTACA
17554576 TAACTTA-A
1 TAACTTACA
17554584 TTAA-TTA-A
1 -TAACTTACA
* *
17554592 T-ATTATATA
1 TAACT-TACA
17554601 TAACTTACA
1 TAACTTACA
17554610 TAACTTAC-
1 TAACTTACA
17554618 -AACTTACA
1 TAACTTACA
17554626 TAACTTACA
1 TAACTTACA
*
17554635 TTAATATTATACA
1 -T-A-ACT-TACA
*
17554648 TAAATTACA
1 TAACTTACA
17554657 TAACTTA
1 TAACTTA
17554664 ATTAATTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
6 1 0.01
7 9 0.12
8 7 0.10
9 41 0.57
10 5 0.07
11 2 0.03
12 3 0.04
13 4 0.06
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (9 bp):
TAACTTACA
Found at i:17554605 original size:34 final size:34
Alignment explanation
Indices: 17554571--17554790 Score: 175
Period size: 34 Copynumber: 6.2 Consensus size: 34
17554561 AATAGTTAAC
* *
17554571 TTACATAACTTAATTAATTAATATTATATATAAC
1 TTACATAACTTAATTAATTAATATTATACATAAA
*
17554605 TTACATAACTTACAACTTACA-TAACTTACATTAATATTATACATA
1 TTACATAACTT--AA-TTA-ATTAA--T--ATT-ATA-CATA-A-A
* **
17554650 AATTACATAACTTAATTAATTAA-A--ACACAGGAA
1 --TTACATAACTTAATTAATTAATATTATACATAAA
*
17554683 TTACATAACTT-A--CATTAATATTATACATAAA
1 TTACATAACTTAATTAATTAATATTATACATAAA
*
17554714 TTACATTAATATTAATTAATTAATATTATACATAAA
1 TTACA-TAA-CTTAATTAATTAATATTATACATAAA
17554750 TTACATAACTTAATTAATTAATATTATACATAAA
1 TTACATAACTTAATTAATTAATATTATACATAAA
17554784 TTACATA
1 TTACATA
17554791 GCTTGCATTA
Statistics
Matches: 151, Mismatches: 12, Indels: 46
0.72 0.06 0.22
Matches are distributed among these distances:
28 5 0.03
29 1 0.01
30 1 0.01
31 22 0.15
32 3 0.02
33 3 0.02
34 45 0.30
35 4 0.03
36 27 0.18
37 6 0.04
38 1 0.01
39 2 0.01
41 3 0.02
42 3 0.02
43 5 0.03
44 7 0.05
45 2 0.01
47 11 0.07
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (34 bp):
TTACATAACTTAATTAATTAATATTATACATAAA
Found at i:17554623 original size:16 final size:16
Alignment explanation
Indices: 17554602--17554634 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17554592 TATTATATAT
17554602 AACTTACATAACTTAC
1 AACTTACATAACTTAC
17554618 AACTTACATAACTTAC
1 AACTTACATAACTTAC
17554634 A
1 A
17554635 TTAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:17554656 original size:31 final size:31
Alignment explanation
Indices: 17554621--17554813 Score: 210
Period size: 31 Copynumber: 6.0 Consensus size: 31
17554611 AACTTACAAC
17554621 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATACATAAA
* * *
17554652 TTACATAACTTA-ATTAAT-TAAAACACAGGAA
1 TTACATAACTTACATTAATATTATACATA--AA
17554683 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATACATAAA
* *
17554714 TTACATTAATATTAATTAATTAATATTATACATAAA
1 TTACA-TAA-CTT-A--CATTAATATTATACATAAA
*
17554750 TTACATAACTTAATTAATTAATATTATACATAAA
1 TTACATAACTT-A--CATTAATATTATACATAAA
* *
17554784 TTACATAGCTTGCATTAATATTATACATAA
1 TTACATAACTTACATTAATATTATACATAA
17554814 CTTGCATTAA
Statistics
Matches: 141, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
29 6 0.04
30 6 0.04
31 50 0.35
32 9 0.06
33 8 0.06
34 36 0.26
35 3 0.02
36 23 0.16
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (31 bp):
TTACATAACTTACATTAATATTATACATAAA
Found at i:17554656 original size:47 final size:49
Alignment explanation
Indices: 17554568--17554663 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 49
17554558 TAAAATAGTT
* *
17554568 AACTTACATAACTTAATTAATTAATATTATATATAACTTACATAACTTAC
1 AACTTACATAACTTAA-TAATTAATATTATACATAAATTACATAACTTAC
*
17554618 AACTTACATAACTT-A-CATTAATATTATACATAAATTACATAACTTA
1 AACTTACATAACTTAATAATTAATATTATACATAAATTACATAACTTA
17554664 ATTAATTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 28 0.65
49 1 0.02
50 14 0.33
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (49 bp):
AACTTACATAACTTAATAATTAATATTATACATAAATTACATAACTTAC
Found at i:17554709 original size:22 final size:22
Alignment explanation
Indices: 17554684--17554727 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17554674 ACACAGGAAT
*
17554684 TACATAACTTACATTAATATTA
1 TACATAAATTACATTAATATTA
17554706 TACATAAATTACATTAATATTA
1 TACATAAATTACATTAATATTA
17554728 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAAATTACATTAATATTA
Found at i:17554737 original size:14 final size:15
Alignment explanation
Indices: 17554712--17554772 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 15
17554702 ATTATACATA
17554712 AATTACATTAATA-TT
1 AATTA-ATTAATACTT
*
17554727 AATTAATTAATATTAT
1 AATTAATTAATACT-T
*
17554743 ACATAAATTACATAACTT
1 A-ATTAATTA-AT-ACTT
17554761 AATTAATTAATA
1 AATTAATTAATA
17554773 TTATACATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 7 0.18
15 7 0.18
16 4 0.11
17 14 0.37
18 4 0.11
19 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAATTAATACTT
Found at i:17554756 original size:9 final size:9
Alignment explanation
Indices: 17554681--17554790 Score: 52
Period size: 9 Copynumber: 12.0 Consensus size: 9
17554671 AAAACACAGG
17554681 AATTACATA
1 AATTACATA
*
17554690 ACTTACATTA
1 AATTACA-TA
17554700 ATATTATACATA
1 A-A-T-TACATA
17554712 AATTACATTA
1 AATTACA-TA
*
17554722 ATATTA-ATT
1 A-ATTACATA
17554731 AATTA-AT-
1 AATTACATA
*
17554738 ATTATACATA
1 AAT-TACATA
17554748 AATTACATA
1 AATTACATA
* *
17554757 ACTTA-ATT
1 AATTACATA
17554765 AATTA-AT-
1 AATTACATA
*
17554772 ATTATACATA
1 AAT-TACATA
17554782 AATTACATA
1 AATTACATA
17554791 GCTTGCATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
7 4 0.05
8 18 0.23
9 32 0.41
10 12 0.15
11 5 0.06
12 4 0.05
13 4 0.05
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTACATA
Found at i:17557956 original size:66 final size:65
Alignment explanation
Indices: 17557848--17558017 Score: 175
Period size: 66 Copynumber: 2.6 Consensus size: 65
17557838 GAGCAAATTA
* * * *
17557848 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTAAAGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGAAGCAGCAGCGAGAGAAGCTAAAGTTCAACAAAAG-TATGAAGAACTCCA
17557912 G
65 G
* * * * * *
17557913 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTTCA
1 C-ACAACTTAAAGCAGAAGCAGCAGCGAGAGAAGCTAAAGTTCAACAAAAGTATGAAGAACTCCA
17557978 G
65 G
* *
17557979 CAGCAGCTTAAAGCAGAAG-AGACAGCAAGAGAAGC-AAAG
1 CA-CAACTTAAAGCAGAAGCAG-CAGCGAGAGAAGCTAAAG
17558018 GCGGCAGCGA
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
65 6 0.07
66 76 0.88
67 4 0.05
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.12
Consensus pattern (65 bp):
CACAACTTAAAGCAGAAGCAGCAGCGAGAGAAGCTAAAGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:17558025 original size:21 final size:21
Alignment explanation
Indices: 17557999--17558077 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 21
17557989 AAGCAGAAGA
*
17557999 GACAGCAAGAGAAGCAAAGGC
1 GACAGCGAGAGAAGCAAAGGC
* * *
17558020 GGCAGCGAGAGAAGTACAGGC
1 GACAGCGAGAGAAGCAAAGGC
* *
17558041 TACAGCGAGGGAAGCAAAGGC
1 GACAGCGAGAGAAGCAAAGGC
* *
17558062 TACAGCGAGGGAAGCA
1 GACAGCGAGAGAAGCA
17558078 GAGCAGCGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.39, C:0.19, G:0.38, T:0.04
Consensus pattern (21 bp):
GACAGCGAGAGAAGCAAAGGC
Found at i:17558478 original size:43 final size:43
Alignment explanation
Indices: 17558431--17558606 Score: 194
Period size: 43 Copynumber: 4.1 Consensus size: 43
17558421 AGGTGTTGGC
* * **
17558431 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
* * ** *
17558474 CTTTAGCAGTGTTTGTGGAAAAAGCGCCACTAAAGATCAA-GGT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGAT-AAGGGT
* *
17558517 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
* * *
17558560 CTATT-GCGGCGTTTGAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
17558603 CTTT
1 CTTT
17558607 CATGGCGTTT
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
42 3 0.03
43 105 0.94
44 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
Found at i:17558614 original size:43 final size:41
Alignment explanation
Indices: 17558451--17558638 Score: 153
Period size: 43 Copynumber: 4.4 Consensus size: 41
17558441 GTTTTTGGTC
* * *
17558451 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCAGTGTTTGTGGAA
1 AAAGCGCCGCTAAAGATAAGGGTCTTTAG--GCGTTTGAGGGA
* * *
17558494 AAAGCGCCACTAAAGATCAA-GGTCTTTAGCGGCGTTTGTGGGG
1 AAAGCGCCGCTAAAGAT-AAGGGTCTTTA--GGCGTTTGAGGGA
* * * *
17558537 AAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGG
1 AAAGCGCCGCTAAAGATAAGGGTCT-TT-AGGCGTTTGAGGGA
* * *
17558580 AAAGCGCCGCTAAAGATTAGGTTCTTTCATGGCGTTTGAGAGA
1 AAAGCGCCGCTAAAGATAAGGGTCTTT-A-GGCGTTTGAGGGA
* *
17558623 AAAACGCCTCTAAAGA
1 AAAGCGCCGCTAAAGA
17558639 CCCTGATCTT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
42 3 0.03
43 112 0.93
44 4 0.03
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGATAAGGGTCTTTAGGCGTTTGAGGGA
Found at i:17559337 original size:27 final size:26
Alignment explanation
Indices: 17559293--17559346 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
17559283 AATTTAGATT
*
17559293 AATATTTTAATAATAAATATAATTTATA
1 AATATTTTAATAACAAATAT--TTTATA
*
17559321 AATA-TTTAGTAACAAATATTTTATA
1 AATATTTTAATAACAAATATTTTATA
17559346 A
1 A
17559347 CATAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
27 13 0.54
28 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATTTTAATAACAAATATTTTATA
Found at i:17562712 original size:22 final size:23
Alignment explanation
Indices: 17562677--17562719 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
17562667 AGATATTACT
*
17562677 AAAAATTAAGATAAAAGCAAAAC
1 AAAAATTAAAATAAAAGCAAAAC
17562700 AAAAA-TAAAATAAAAGCAAA
1 AAAAATTAAAATAAAAGCAAA
17562720 CGAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (23 bp):
AAAAATTAAAATAAAAGCAAAAC
Found at i:17569189 original size:18 final size:17
Alignment explanation
Indices: 17569156--17569194 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
17569146 TTTTATAAAT
17569156 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
17569174 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
17569191 TGTG
1 TGTG
17569195 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:17569446 original size:23 final size:23
Alignment explanation
Indices: 17569420--17569489 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
17569410 AGTGTTATTG
17569420 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
*
17569443 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGT
17569466 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
17569489 A
1 A
17569490 GCTTCGGCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACGT
Found at i:17569473 original size:46 final size:46
Alignment explanation
Indices: 17569420--17569624 Score: 320
Period size: 46 Copynumber: 4.7 Consensus size: 46
17569410 AGTGTTATTG
17569420 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
*
17569466 ATCAGTGGTAGCTTCGG---C-TA-C----GTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
17569503 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
*
17569549 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
*
17569595 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTG
17569625 TGGCACTTAT
Statistics
Matches: 146, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
37 32 0.22
40 1 0.01
41 3 0.02
42 3 0.02
43 1 0.01
46 106 0.73
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
Found at i:17569492 original size:14 final size:14
Alignment explanation
Indices: 17569473--17569503 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17569463 CATATCAGTG
17569473 GTAGCTTCGGCTAC
1 GTAGCTTCGGCTAC
17569487 GTAGCTTCGGCTAC
1 GTAGCTTCGGCTAC
17569501 GTA
1 GTA
17569504 TCAGTGGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (14 bp):
GTAGCTTCGGCTAC
Found at i:17569500 original size:37 final size:37
Alignment explanation
Indices: 17569450--17569572 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 37
17569440 CGTATCAGTG
17569450 GTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
1 GTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
*
17569487 GTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACGTATC
1 GTAGCTTCGGCTACATATCAGTGGTAGCTTCGG---C-TA-C
17569529 AGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
1 ----GTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
17569570 GTA
1 GTA
17569573 TCAGTGGTAG
Statistics
Matches: 75, Mismatches: 2, Indels: 18
0.79 0.02 0.19
Matches are distributed among these distances:
37 35 0.47
40 1 0.01
41 3 0.04
42 3 0.04
43 1 0.01
46 32 0.43
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (37 bp):
GTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
Found at i:17569517 original size:23 final size:23
Alignment explanation
Indices: 17569487--17569624 Score: 258
Period size: 23 Copynumber: 6.0 Consensus size: 23
17569477 CTTCGGCTAC
17569487 GTAGCTTCGGCTACGTATCAGTG
1 GTAGCTTCGGCTACGTATCAGTG
17569510 GTAGCTTCGGCTACGTATCAGTG
1 GTAGCTTCGGCTACGTATCAGTG
*
17569533 GTAGCTTCGGCTACATATCAGTG
1 GTAGCTTCGGCTACGTATCAGTG
17569556 GTAGCTTCGGCTACGTATCAGTG
1 GTAGCTTCGGCTACGTATCAGTG
17569579 GTAGCTTCGGCTACGTATCAGTG
1 GTAGCTTCGGCTACGTATCAGTG
*
17569602 GTAGCTTCGGCTACATATCAGTG
1 GTAGCTTCGGCTACGTATCAGTG
17569625 TGGCACTTAT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 112 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (23 bp):
GTAGCTTCGGCTACGTATCAGTG
Found at i:17569559 original size:83 final size:87
Alignment explanation
Indices: 17569420--17569624 Score: 328
Period size: 83 Copynumber: 2.3 Consensus size: 87
17569410 AGTGTTATTG
17569420 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGG-C
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGAC
17569484 -TA-C-GTAGCTTCGGCTACGT
66 GTATCGGTAGCTTCGGCTACGT
17569503 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGG--
17569568 ACGTATCAGTGGTAGCTTCGGCTACGT
64 ACGTATC---GGTAGCTTCGGCTACGT
*
17569595 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTG
17569625 TGGCACTTAT
Statistics
Matches: 112, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
83 63 0.56
86 1 0.01
87 2 0.02
88 1 0.01
92 45 0.40
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (87 bp):
ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGAC
GTATCGGTAGCTTCGGCTACGT
Found at i:17585053 original size:84 final size:86
Alignment explanation
Indices: 17584878--17585053 Score: 196
Period size: 86 Copynumber: 2.1 Consensus size: 86
17584868 TTTTTTAAAT
* * *
17584878 AAAATATATTTAAGATAATGATAAATATAAAAATATATATTATATAATTATTATTTTATTTATAT
1 AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
* *
17584943 AAATAAAGTAGTTGTTAATTT
66 AAATAAAATAGTTGTTAATTA
* * * * * ** *
17584964 CAAATATTTTTAACATAATGATATATTTTATTATATA-ATTACATATTTATTATTTGATTT-TAT
1 AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
*
17585027 AAATAAAATATTTAG-TAATTA
66 AAATAAAATAGTT-GTTAATTA
17585048 AAAATA
1 AAAATA
17585054 AAAAATTTGA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 24 0.32
85 21 0.28
86 29 0.39
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (86 bp):
AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
AAATAAAATAGTTGTTAATTA
Found at i:17589437 original size:2 final size:2
Alignment explanation
Indices: 17589430--17589462 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17589420 GATCCTGCGA
17589430 AT AT 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 AT AT A
17589463 AGTCAATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17589845 original size:46 final size:46
Alignment explanation
Indices: 17589778--17589963 Score: 327
Period size: 46 Copynumber: 4.0 Consensus size: 46
17589768 ACAATGCTAT
* *
17589778 AACTCAGTATGGTTTCCTTCACTGAAACAACATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
17589824 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
17589870 AACTCAGTATGATTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
17589916 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTATTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
17589962 AA
1 AA
17589964 TTTGCCATGG
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:17591234 original size:16 final size:17
Alignment explanation
Indices: 17591188--17591235 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
17591178 AAATTCTTTT
*
17591188 TAAATCGCAAAATTCAC
1 TAAATCACAAAATTCAC
*
17591205 TAAATCACAAAATTTAC
1 TAAATCACAAAATTCAC
*
17591222 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
17591236 TTATAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:17591366 original size:42 final size:42
Alignment explanation
Indices: 17591314--17591393 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
17591304 GATCTCGAAT
*
17591314 CACTGTTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
1 CACTATTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
* *
17591356 CACTATTTCCGACGCCACTGAAAATTGGGCTGTTACAT
1 CACTATTTCCGACACCACTGAAAATTAGGCTGTTACAT
17591394 TTACTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
CACTATTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
Found at i:17599774 original size:20 final size:20
Alignment explanation
Indices: 17599733--17599783 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
17599723 AAACTTGGGG
17599733 TTTTATAGGAAATTAACTGAT
1 TTTTATAGGAAATTAAC-GAT
*
17599754 TTTTATAGGAAAATTTA-GAT
1 TTTTATAGG-AAATTAACGAT
17599774 TTTTACTAGG
1 TTTTA-TAGG
17599784 GTTGTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 13 0.48
22 6 0.22
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (20 bp):
TTTTATAGGAAATTAACGAT
Found at i:17603022 original size:16 final size:16
Alignment explanation
Indices: 17603001--17603048 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
17602991 TTTTACATGG
17603001 AATTGTTATTAAAATT
1 AATTGTTATTAAAATT
*
17603017 AATTGTTATCAAAATT
1 AATTGTTATTAAAATT
17603033 AATTGTTATTAAAATT
1 AATTGTTATTAAAATT
17603049 GTATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (16 bp):
AATTGTTATTAAAATT
Found at i:17603203 original size:93 final size:93
Alignment explanation
Indices: 17603094--17603277 Score: 332
Period size: 93 Copynumber: 2.0 Consensus size: 93
17603084 TTTGTAAAAT
* *
17603094 CTAACATTTTGCTAGTAAAATTATTAATTGTTACTTGTATTAATTGTTATTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
17603159 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
*
17603187 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
*
17603252 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
17603278 ATTAATTGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (93 bp):
CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:17606133 original size:18 final size:18
Alignment explanation
Indices: 17606087--17606133 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
17606077 GCTTACTTAA
*
17606087 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
17606104 TATTTTAGTTATTTATTT
1 TATTTTATTTATTTATTT
17606122 TAATTTT-TTTAT
1 T-ATTTTATTTAT
17606134 CTGACTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:17608227 original size:40 final size:39
Alignment explanation
Indices: 17608165--17608281 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
17608155 TTGGCACCTA
* *
17608165 GTGCCTCATCTGATAATTCGAAGTAATAATTTGACACCCG
1 GTGCCTCATCGGATAATCCGAAGTAATAA-TTGACACCCG
* * * *
17608205 GTGCCTCATCGGCTAAACCGAAGT-A-AATTGGCACCCT
1 GTGCCTCATCGGATAATCCGAAGTAATAATTGACACCCG
* *
17608242 GTGCCTCATTGAATTAATCCGAAGTAATGAATTGACACCC
1 GTGCCTCATCGGA-TAATCCGAAGTAAT-AATTGACACCC
17608282 AGTGTCTTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
37 18 0.29
38 12 0.19
39 2 0.03
40 20 0.32
41 10 0.16
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (39 bp):
GTGCCTCATCGGATAATCCGAAGTAATAATTGACACCCG
Found at i:17608454 original size:17 final size:16
Alignment explanation
Indices: 17608416--17608473 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
17608406 TATTCATTTC
17608416 AATTCAA-ATAATCAATA
1 AATTCAATATAAT--ATA
*
17608433 TATTCAATAT-ATATA
1 AATTCAATATAATATA
17608448 CCAATTCAAT-TAATATA
1 --AATTCAATATAATATA
17608465 AATTCAATA
1 AATTCAATA
17608474 AATTCATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
15 11 0.32
16 1 0.03
17 20 0.59
18 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTCAATATAATATA
Found at i:17609314 original size:21 final size:21
Alignment explanation
Indices: 17609275--17609316 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17609265 AATACATATT
*
17609275 TTATTATTAAATATATATTTA
1 TTATTATTAAACATATATTTA
* *
17609296 TTATTATTACACATGTATTTA
1 TTATTATTAAACATATATTTA
17609317 CCAACACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATTATTAAACATATATTTA
Found at i:17614700 original size:31 final size:32
Alignment explanation
Indices: 17614665--17614727 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
17614655 TTAGCATTTC
17614665 ATTAATGATTTAACAA-ATAAATGACTAAAAT
1 ATTAATGATTTAACAATATAAATGACTAAAAT
** * *
17614696 ATTAATTTTTTAATAATATTAATGACTAAAAT
1 ATTAATGATTTAACAATATAAATGACTAAAAT
17614728 TGCCAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTAATGATTTAACAATATAAATGACTAAAAT
Found at i:17614864 original size:54 final size:54
Alignment explanation
Indices: 17614792--17614896 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
17614782 GCTAAAACAA
* **
17614792 TTTTGGGCACAGTGAAGTTTCGTCCGTTCCAAACTTGCCGCAGCCTAACACGAC
1 TTTTGGGCACAGTCAAGTTTCACCCGTTCCAAACTTGCCGCAGCCTAACACGAC
* **
17614846 TTTTGGGCAGAGTCAAGTTTCACCCGTTCCAATTTTGCCGCAGCCTAACAC
1 TTTTGGGCACAGTCAAGTTTCACCCGTTCCAAACTTGCCGCAGCCTAACAC
17614897 TGAATTCTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (54 bp):
TTTTGGGCACAGTCAAGTTTCACCCGTTCCAAACTTGCCGCAGCCTAACACGAC
Found at i:17615298 original size:7 final size:7
Alignment explanation
Indices: 17615286--17615311 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17615276 CTCATCTTTC
17615286 AAATTTT
1 AAATTTT
17615293 AAATTTT
1 AAATTTT
17615300 AAATTTT
1 AAATTTT
17615307 AAATT
1 AAATT
17615312 ATATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:17617313 original size:88 final size:88
Alignment explanation
Indices: 17617164--17617335 Score: 299
Period size: 88 Copynumber: 2.0 Consensus size: 88
17617154 AATTCAGATG
**
17617164 CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTATTCCAACTCCAAACTTTCACCAT
1 CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
17617229 CCAACAAAGCACAACCATGAACA
66 CCAACAAAGCACAACCATGAACA
* *
17617252 CTTCCAATTATACTCAGCATTGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
1 CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
*
17617317 CCAACAAAGGACAACCATG
66 CCAACAAAGCACAACCATG
17617336 GACAATCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (88 bp):
CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
CCAACAAAGCACAACCATGAACA
Found at i:17622277 original size:40 final size:41
Alignment explanation
Indices: 17622221--17622300 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
17622211 TATAAAAGAA
17622221 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
*
17622262 AGAAAG-AAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
17622301 AAGGAAGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 32 0.84
41 6 0.16
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (41 bp):
AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
Found at i:17630386 original size:16 final size:17
Alignment explanation
Indices: 17630355--17630389 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17630345 TAAAAAAATC
*
17630355 CAATTATCATATTTACA
1 CAATTATCACATTTACA
17630372 CAATT-TCACATTTACA
1 CAATTATCACATTTACA
17630388 CA
1 CA
17630390 CACATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATTATCACATTTACA
Found at i:17631189 original size:16 final size:17
Alignment explanation
Indices: 17631162--17631193 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17631152 CGTTTTAAGC
17631162 TTTCTGTTTCTTTCTTA
1 TTTCTGTTTCTTTCTTA
17631179 TTTCT-TTTCTTTCTT
1 TTTCTGTTTCTTTCTT
17631194 TTGTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTCTGTTTCTTTCTTA
Found at i:17632838 original size:23 final size:24
Alignment explanation
Indices: 17632802--17632870 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 24
17632792 GGACTCACCA
*
17632802 CAGCTCGTATGAGCTTACCGTT-T
1 CAGCTCGAATGAGCTTACCGTTAT
*
17632825 CAGCTC-AATAGAGCTTACCATTTAT
1 CAGCTCGAAT-GAGCTTACC-GTTAT
17632850 CAGCTCGGAATGAGCTTACCG
1 CAGCTC-GAATGAGCTTACCG
17632871 ATCATGGCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.05
23 15 0.39
24 2 0.05
25 7 0.18
26 9 0.24
27 3 0.08
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (24 bp):
CAGCTCGAATGAGCTTACCGTTAT
Found at i:17633729 original size:7 final size:7
Alignment explanation
Indices: 17633712--17633740 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
17633702 AATTTTTAAA
17633712 AAAAAAG
1 AAAAAAG
17633719 -AAAAAG
1 AAAAAAG
17633725 AAAAAAG
1 AAAAAAG
17633732 AAAAAAG
1 AAAAAAG
17633739 AA
1 AA
17633741 TGAAGTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17633730 original size:13 final size:13
Alignment explanation
Indices: 17633712--17633736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17633702 AATTTTTAAA
17633712 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
17633725 AAAAAAGAAAAA
1 AAAAAAGAAAAA
17633737 AGAATGAAGT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:17647179 original size:9 final size:9
Alignment explanation
Indices: 17647165--17647194 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
17647155 TAACAATTTC
17647165 GAAATGGTG
1 GAAATGGTG
17647174 GAAATGGTG
1 GAAATGGTG
17647183 GAAATGGTG
1 GAAATGGTG
17647192 GAA
1 GAA
17647195 GAGGAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (9 bp):
GAAATGGTG
Found at i:17653399 original size:7 final size:7
Alignment explanation
Indices: 17653384--17653432 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
17653374 TAAAGCTACT
17653384 ACTTATC
1 ACTTATC
*
17653391 ACTTGTC
1 ACTTATC
17653398 ACTTATC
1 ACTTATC
*
17653405 AC-TACC
1 ACTTATC
17653411 ACTTATC
1 ACTTATC
*
17653418 ACTTGTC
1 ACTTATC
*
17653425 ACTGATC
1 ACTTATC
17653432 A
1 A
17653433 AAAGTACTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.37
Consensus pattern (7 bp):
ACTTATC
Found at i:17653403 original size:14 final size:14
Alignment explanation
Indices: 17653384--17653432 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
17653374 TAAAGCTACT
17653384 ACTTATCACTTGTC
1 ACTTATCACTTGTC
**
17653398 ACTTATCAC-TACC
1 ACTTATCACTTGTC
17653411 ACTTATCACTTGTC
1 ACTTATCACTTGTC
*
17653425 ACTGATCA
1 ACTTATCA
17653433 AAAGTACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.37
Consensus pattern (14 bp):
ACTTATCACTTGTC
Found at i:17653416 original size:27 final size:27
Alignment explanation
Indices: 17653379--17653432 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
17653369 GTAGCTAAAG
* *
17653379 CTACTACTTATCACTTGTCACTTATCA
1 CTACCACTTATCACTTGTCACTGATCA
17653406 CTACCACTTATCACTTGTCACTGATCA
1 CTACCACTTATCACTTGTCACTGATCA
17653433 AAAGTACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.37
Consensus pattern (27 bp):
CTACCACTTATCACTTGTCACTGATCA
Found at i:17653419 original size:20 final size:20
Alignment explanation
Indices: 17653390--17653427 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17653380 TACTACTTAT
*
17653390 CACTTGTCACTTATCACTAC
1 CACTTATCACTTATCACTAC
*
17653410 CACTTATCACTTGTCACT
1 CACTTATCACTTATCACT
17653428 GATCAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.05, T:0.37
Consensus pattern (20 bp):
CACTTATCACTTATCACTAC
Found at i:17656739 original size:2 final size:2
Alignment explanation
Indices: 17656732--17656756 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17656722 CTCCTTGTAA
17656732 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17656757 ATAGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17657969 original size:9 final size:9
Alignment explanation
Indices: 17657929--17658023 Score: 68
Period size: 9 Copynumber: 10.4 Consensus size: 9
17657919 GTAAATATAT
*
17657929 TAAAAATAA
1 TAAAAATTA
* *
17657938 AAAAAAATA
1 TAAAAATTA
17657947 -AAAAATTA
1 TAAAAATTA
*
17657955 T-TAAATTA
1 TAAAAATTA
*
17657963 TAAAAATGA
1 TAAAAATTA
*
17657972 TAAAAATGA
1 TAAAAATTA
*
17657981 TAAAAAAATA
1 T-AAAAATTA
* *
17657991 TAATAATTTT
1 TAA-AAATTA
17658001 TAATAAATTA
1 TAA-AAATTA
17658011 TAAAAATTA
1 TAAAAATTA
17658020 TAAA
1 TAAA
17658024 TGTAATAAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
8 14 0.21
9 33 0.49
10 21 0.31
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:17662608 original size:19 final size:18
Alignment explanation
Indices: 17662584--17662622 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
17662574 AGTCTAATAA
17662584 TTTC-TTTCTTTCTTTCCTT
1 TTTCTTTTCTTT-TTT-CTT
17662603 TTTCTTTTCTTTTTTCTT
1 TTTCTTTTCTTTTTTCTT
17662621 TT
1 TT
17662623 AAATTTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTCTT
Found at i:17664305 original size:31 final size:29
Alignment explanation
Indices: 17664270--17664346 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
17664260 TTAATAGCTC
*
17664270 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
17664301 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
17664330 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
17664347 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:17668711 original size:2 final size:2
Alignment explanation
Indices: 17668704--17668740 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17668694 TCTTTTCCCT
17668704 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17668741 TGGGGTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17690158 original size:13 final size:12
Alignment explanation
Indices: 17690116--17690158 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
17690106 ATTCTTAGTT
17690116 TTTTTTATATTAA
1 TTTTTTAT-TTAA
17690129 TTTTTTATTTAAA
1 TTTTTTATTT-AA
17690142 TTTTTTGATTT-A
1 TTTTTT-ATTTAA
17690154 TTTTT
1 TTTTT
17690159 ACAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.29
13 16 0.57
14 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:17706459 original size:31 final size:31
Alignment explanation
Indices: 17706401--17706460 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
17706391 TGTGTCAATA
* *
17706401 ATTTATAAAATTTAAATCAAACCAAATTTTC
1 ATTTATAAAATTTAAATAAAACAAAATTTTC
*
17706432 ATTTATAAAA-TTATATAAAATCAAAATTT
1 ATTTATAAAATTTAAATAAAA-CAAAATTT
17706461 ATGTATGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTATAAAATTTAAATAAAACAAAATTTTC
Found at i:17715593 original size:56 final size:59
Alignment explanation
Indices: 17715484--17715630 Score: 194
Period size: 56 Copynumber: 2.5 Consensus size: 59
17715474 AATTGACAAT
*
17715484 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCTGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
17715547 AAAAAGATCTAG-CCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* *
17715602 AAAATAGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
17715631 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
55 5 0.06
56 33 0.42
57 12 0.15
58 2 0.03
60 1 0.01
61 13 0.17
62 7 0.09
63 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:17715859 original size:66 final size:66
Alignment explanation
Indices: 17715752--17715877 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
17715742 GTTTATATTA
*
17715752 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCGGGAGTGTGCTATCTT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCAGGAGTGTGCTATCTT
17715817 G
66 G
*
17715818 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCAGGAGTGTGCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCAGGAGTGTGCT
17715878 CTCTGAAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (66 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCAGGAGTGTGCTATCTT
G
Found at i:17718459 original size:7 final size:7
Alignment explanation
Indices: 17718435--17718483 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
17718425 AAAAATAATA
*
17718435 ATTGAGG
1 ATTGAGT
* *
17718442 ATTTAGG
1 ATTGAGT
17718449 ATTGAGT
1 ATTGAGT
*
17718456 ATTGAAT
1 ATTGAGT
17718463 ATTGAGT
1 ATTGAGT
17718470 ATTGAGT
1 ATTGAGT
17718477 ATTGAGT
1 ATTGAGT
17718484 TGAAAAGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.41
Consensus pattern (7 bp):
ATTGAGT
Found at i:17718938 original size:15 final size:15
Alignment explanation
Indices: 17718918--17718953 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17718908 ATTAAAAAAA
*
17718918 TTAAAAATTTAAACT
1 TTAAAAATTCAAACT
17718933 TTAAAAATTCAAACT
1 TTAAAAATTCAAACT
*
17718948 CTAAAA
1 TTAAAA
17718954 GGCTCGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATTCAAACT
Found at i:17718964 original size:31 final size:31
Alignment explanation
Indices: 17718929--17719001 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
17718919 TAAAAATTTA
* * **
17718929 AACTTTAAAAAT-TCAAACTCTAAAAGGCTCG
1 AACTTAAAAAATAT-AAACTCGAAAAAACTCG
17718960 AACTTAAAAAATATAAACTCGAAAAAACTCG
1 AACTTAAAAAATATAAACTCGAAAAAACTCG
17718991 AACTTAAAAAA
1 AACTTAAAAAA
17719002 AATCGAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (31 bp):
AACTTAAAAAATATAAACTCGAAAAAACTCG
Found at i:17719011 original size:16 final size:16
Alignment explanation
Indices: 17718957--17719011 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
17718947 TCTAAAAGGC
*
17718957 TCGAACTTAAAAAATA
1 TCGAACTTAAAAAAAA
* ** *
17718973 T-AAACTCGAAAAAAC
1 TCGAACTTAAAAAAAA
17718988 TCGAACTTAAAAAAAA
1 TCGAACTTAAAAAAAA
17719004 TCGAACTT
1 TCGAACTT
17719012 GAGACTGACC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (16 bp):
TCGAACTTAAAAAAAA
Found at i:17720015 original size:25 final size:21
Alignment explanation
Indices: 17719976--17720027 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 21
17719966 AACAAATTTT
17719976 AATT-TTAATTAAAATATAATTAA
1 AATTATTAATTAAAATA-AA--AA
17719999 AATTATTATATTAAAATAAAAA
1 AATTATTA-ATTAAAATAAAAA
17720021 AATTATT
1 AATTATT
17720028 TAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 9 0.33
23 4 0.15
24 5 0.19
25 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATTAATTAAAATAAAAA
Found at i:17720025 original size:19 final size:20
Alignment explanation
Indices: 17720003--17720046 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
17719993 AATTAAAATT
17720003 ATTATATTAAAATA-AAAAA
1 ATTATATTAAAATATAAAAA
*
17720022 ATTAT-TTAAAATATAATAA
1 ATTATATTAAAATATAAAAA
17720041 ATTATA
1 ATTATA
17720047 AATTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATATTAAAATATAAAAA
Found at i:17720039 original size:23 final size:22
Alignment explanation
Indices: 17719983--17720041 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
17719973 TTTAATTTTA
*
17719983 ATTAAAATATAAT--TAAAATT
1 ATTAAAATATAATAAAAAAATT
* * *
17720003 ATTATATTAAAATAAAAAAATT
1 ATTAAAATATAATAAAAAAATT
17720025 ATTTAAAATATAATAAA
1 A-TTAAAATATAATAAA
17720042 TTATAAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 10 0.34
22 7 0.24
23 12 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTAAAATATAATAAAAAAATT
Found at i:17721830 original size:28 final size:28
Alignment explanation
Indices: 17721797--17721851 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
17721787 TCTAATTTGA
17721797 AATTTCAAATCAAATTGATAATACTATG
1 AATTTCAAATCAAATTGATAATACTATG
*
17721825 AATTTCAAATGAAATTGATAATACTAT
1 AATTTCAAATCAAATTGATAATACTAT
17721852 TAAATAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (28 bp):
AATTTCAAATCAAATTGATAATACTATG
Found at i:17729470 original size:9 final size:9
Alignment explanation
Indices: 17729453--17729489 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17729443 TATAGTTTGA
*
17729453 TATTTGAAT
1 TATTCGAAT
17729462 TATTCGAAT
1 TATTCGAAT
*
17729471 TATTCGAGT
1 TATTCGAAT
17729480 TATTCGAAT
1 TATTCGAAT
17729489 T
1 T
17729490 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17729880 original size:9 final size:9
Alignment explanation
Indices: 17729868--17729922 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
17729858 TATTTAGGAA
17729868 TTTTAAAAC
1 TTTTAAAAC
17729877 TTTTAAAA-
1 TTTTAAAAC
17729885 TTTTAAATTAGGAC
1 TTTT-AA--A--AC
17729899 TTTTAAAAC
1 TTTTAAAAC
17729908 TTTTAAAA-
1 TTTTAAAAC
17729916 TTTTAAA
1 TTTTAAA
17729923 TTAATAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 11 0.28
9 20 0.50
11 2 0.05
13 3 0.08
14 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (9 bp):
TTTTAAAAC
Found at i:17729897 original size:31 final size:31
Alignment explanation
Indices: 17729861--17729925 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
17729851 TTTTTCTTAT
17729861 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
1 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
*
17729892 TTAGGACTTTTAAAACTTTTAAAATTTTAAA
1 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
17729923 TTA
1 TTA
17729926 ATAATGATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAGGAATTTTAAAACTTTTAAAATTTTAAA
Found at i:17730265 original size:12 final size:12
Alignment explanation
Indices: 17730248--17730290 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
17730238 AACTAATCCT
17730248 CTCTCAAATTTC
1 CTCTCAAATTTC
17730260 CTCTCAAA-TTC
1 CTCTCAAATTTC
17730271 CT-TCAAAATTT-
1 CTCTC-AAATTTC
17730282 CTCTCAAAT
1 CTCTCAAAT
17730291 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 12 0.43
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:17730363 original size:10 final size:10
Alignment explanation
Indices: 17730348--17730372 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17730338 AAATCTCTAT
17730348 TTTTAAATAA
1 TTTTAAATAA
17730358 TTTTAAATAA
1 TTTTAAATAA
17730368 TTTTA
1 TTTTA
17730373 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:17731166 original size:7 final size:7
Alignment explanation
Indices: 17731154--17731179 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17731144 TAGTCGATTG
17731154 GTATTTA
1 GTATTTA
17731161 GTATTTA
1 GTATTTA
17731168 GTATTTA
1 GTATTTA
17731175 GTATT
1 GTATT
17731180 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:17734804 original size:52 final size:49
Alignment explanation
Indices: 17734720--17735085 Score: 431
Period size: 46 Copynumber: 7.6 Consensus size: 49
17734710 TTTGAGTACT
* **
17734720 TCTGATCAAGTG---ATAAAGTGAT-AGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
17734765 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
17734817 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
17734863 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
17734909 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
17734961 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
17735013 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
17735059 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
17735086 GCTACACTTA
Statistics
Matches: 291, Mismatches: 15, Indels: 29
0.87 0.04 0.09
Matches are distributed among these distances:
45 12 0.04
46 143 0.49
48 2 0.01
49 2 0.01
51 8 0.03
52 124 0.43
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:17735060 original size:196 final size:195
Alignment explanation
Indices: 17734734--17735085 Score: 596
Period size: 196 Copynumber: 1.8 Consensus size: 195
17734724 ATCAAGTGAT
* * *
17734734 AAAGTGATAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAA
1 AAAGTGATAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAA
* * * *
17734799 TAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTAT
66 TAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTAT
*
17734864 CTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
131 CTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
17734929 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGAT-AGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
17734994 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
65 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
17735059 TCTGATCAAGAGACAAAGTGATAAGTG
130 TCTGATCAAGAGACAAAGTGATAAGTG
17735086 GCTACACTTA
Statistics
Matches: 145, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
195 8 0.06
196 137 0.94
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (195 bp):
AAAGTGATAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAA
TAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTAT
CTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:17735093 original size:37 final size:37
Alignment explanation
Indices: 17735049--17735194 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
17735039 GATAGCTTTA
*
17735049 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
17735086 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
17735123 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
17735160 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
17735195 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:17735122 original size:150 final size:149
Alignment explanation
Indices: 17734720--17735074 Score: 458
Period size: 150 Copynumber: 2.4 Consensus size: 149
17734710 TTTGAGTACT
* * * * *
17734720 TCTGATCAAGTGATAAAGTGAT-AGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * *
17734784 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
17734842 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
17734863 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * * *
17734928 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
17734992 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
17735013 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
17735075 AGTGATAAGT
Statistics
Matches: 191, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
143 21 0.11
144 61 0.32
145 1 0.01
149 7 0.04
150 91 0.48
151 7 0.04
152 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:17736535 original size:125 final size:124
Alignment explanation
Indices: 17736238--17736614 Score: 612
Period size: 125 Copynumber: 3.0 Consensus size: 124
17736228 CCCAAACATG
* * *
17736238 CTACAGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCCT-G
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCAT-CTAG
17736302 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* *
17736362 CTACTGTAGCAAAAACGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
*
17736427 TAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAAAAAAAATTTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAA-TTATTTCTTCCATGAC
*
17736487 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
* *** *
17736552 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
17736612 CTA
1 CTA
17736615 AAAACCCTAA
Statistics
Matches: 235, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
123 2 0.01
124 99 0.42
125 131 0.56
126 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:17742447 original size:24 final size:24
Alignment explanation
Indices: 17742415--17742487 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 24
17742405 TAAGTGATCA
17742415 TTATTTCTCATGTTCTTTTACCTT
1 TTATTTCTCATGTTCTTTTACCTT
* *
17742439 TTATTTCTCATCCTTTGCCCTTTACCTT
1 TTATTTCTCAT--GTT--CTTTTACCTT
17742467 TTATTTCTCATGTTCTTTTAC
1 TTATTTCTCATGTTCTTTTAC
17742488 TCTCTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 17 0.41
26 4 0.10
28 20 0.49
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59
Consensus pattern (24 bp):
TTATTTCTCATGTTCTTTTACCTT
Found at i:17750702 original size:33 final size:33
Alignment explanation
Indices: 17750665--17750732 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
17750655 AAACTGTAAC
17750665 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
1 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
*
17750698 ATGTGTTTTAGCTAAAATTTCTATGGATTATTG
1 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
17750731 AT
1 AT
17750733 TTTGGATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (33 bp):
ATGTGTTTTAGCTAAAATATCTATGGATTATTG
Found at i:17752236 original size:66 final size:66
Alignment explanation
Indices: 17752130--17752262 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
17752120 CTATCCTCAA
17752130 GCTCTAACCTTTGATATAAATATCTTTGCCAACTTTTAGTCATGGTTAGACTTTTATTTATCATG
1 GCTCTAACCTTTGATATAAATATCTTTGCCAACTTTTAGTCATGGTTAGACTTTTATTTATCATG
17752195 G
66 G
17752196 GCTCTAACCTTTGATATAAATATCTTTGCCAACTTTTAGTCATGGTTAGACTTTTATTTATCATG
1 GCTCTAACCTTTGATATAAATATCTTTGCCAACTTTTAGTCATGGTTAGACTTTTATTTATCATG
17752261 G
66 G
17752262 G
1 G
17752263 GAGGTTGATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (66 bp):
GCTCTAACCTTTGATATAAATATCTTTGCCAACTTTTAGTCATGGTTAGACTTTTATTTATCATG
G
Found at i:17756257 original size:14 final size:13
Alignment explanation
Indices: 17756235--17756265 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
17756225 CTCACCATCC
17756235 AGCATATATAT-T
1 AGCATATATATAT
17756247 AGCATATATATAT
1 AGCATATATATAT
17756260 AGCATA
1 AGCATA
17756266 CAAAATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (13 bp):
AGCATATATATAT
Found at i:17758036 original size:20 final size:20
Alignment explanation
Indices: 17757995--17758041 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17757985 TTTTAATATA
* *
17757995 TTAAAATATTTTTATACTTT
1 TTAAATTATTTTTATACATT
17758015 TTAAATTATTTTTA-ACGATT
1 TTAAATTATTTTTATAC-ATT
*
17758035 TTTAATT
1 TTAAATT
17758042 TTGAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAAATTATTTTTATACATT
Found at i:17758159 original size:148 final size:147
Alignment explanation
Indices: 17757945--17758250 Score: 535
Period size: 148 Copynumber: 2.1 Consensus size: 147
17757935 ATGGTAACAT
******
17757945 TTAATT-AAT-TTTTTAAAATTTTAAAAATATTCAAATTTTTTTTTAATATATTAAAATATTTTT
1 TTAATTAAATGTTTTTAAAATTTTAAAAATATTCAAAAAAAAATTTAATATATTAAAATATTTTT
17758008 ATACTTTTTAAATTATTTTTAACGATTTTTAATTTTGAAAAATAATTTTTATATATTTTTTTAAT
66 ATACTTTTTAAATTATTTTTAACGATTTTTAATTTTGAAAAATAATTTTTATATATTTTTTTAAT
17758073 TTTTAAATTTTAAAAAA
131 TTTTAAATTTTAAAAAA
17758090 TTAATTAAATGTTTTTAAAATTTTAAAAATATTCAAAAAAAAAATTTAATATATTAAAATATTTT
1 TTAATTAAATGTTTTTAAAATTTTAAAAATATTC-AAAAAAAAATTTAATATATTAAAATATTTT
17758155 TATACTTTTTAAATTATTTTTAACGATTTTTAATTTTGAAAAATAATTTTTATATATTTTTTTAA
65 TATACTTTTTAAATTATTTTTAACGATTTTTAATTTTGAAAAATAATTTTTATATATTTTTTTAA
17758220 TTTTTAAATTTTAAAAAA
130 TTTTTAAATTTTAAAAAA
17758238 TTAATTAAATGTT
1 TTAATTAAATGTT
17758251 GATGTGTCAT
Statistics
Matches: 152, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
145 6 0.04
146 3 0.02
147 23 0.15
148 120 0.79
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (147 bp):
TTAATTAAATGTTTTTAAAATTTTAAAAATATTCAAAAAAAAATTTAATATATTAAAATATTTTT
ATACTTTTTAAATTATTTTTAACGATTTTTAATTTTGAAAAATAATTTTTATATATTTTTTTAAT
TTTTAAATTTTAAAAAA
Found at i:17758184 original size:20 final size:20
Alignment explanation
Indices: 17758143--17758189 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17758133 ATTTAATATA
* *
17758143 TTAAAATATTTTTATACTTT
1 TTAAATTATTTTTATACATT
17758163 TTAAATTATTTTTA-ACGATT
1 TTAAATTATTTTTATAC-ATT
*
17758183 TTTAATT
1 TTAAATT
17758190 TTGAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAAATTATTTTTATACATT
Found at i:17764254 original size:16 final size:17
Alignment explanation
Indices: 17764219--17764256 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17764209 CTTAAATTTT
* *
17764219 TTTTAATATGTTTAATA
1 TTTTAATATGATTAAAA
17764236 TTTTAATAT-ATTAAAA
1 TTTTAATATGATTAAAA
17764252 TTTTA
1 TTTTA
17764257 GAATTAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAATATGATTAAAA
Found at i:17764317 original size:17 final size:17
Alignment explanation
Indices: 17764281--17764316 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
17764271 CAACATTTTC
17764281 TTTAACATATTTAGAAT
1 TTTAACATATTTAGAAT
*
17764298 TTTAATATATTTA-AAT
1 TTTAACATATTTAGAAT
17764314 TTT
1 TTT
17764317 TTAAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAACATATTTAGAAT
Found at i:17764581 original size:17 final size:18
Alignment explanation
Indices: 17764520--17764597 Score: 95
Period size: 18 Copynumber: 4.3 Consensus size: 18
17764510 TAAAATTGGT
* *
17764520 TATACTTAACATTTTTTAA
1 TATATTTAA-ATTTTTAAA
*
17764539 TATATTTAATTTTTTAAA
1 TATATTTAAATTTTTAAA
17764557 TATATTTAAATTTTTAAA
1 TATATTTAAATTTTTAAA
* *
17764575 T-TTTTTAAAGTTTTAAA
1 TATATTTAAATTTTTAAA
17764592 TATATT
1 TATATT
17764598 AAGAAAATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 15 0.29
18 28 0.55
19 8 0.16
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (18 bp):
TATATTTAAATTTTTAAA
Found at i:17764583 original size:70 final size:70
Alignment explanation
Indices: 17764409--17764567 Score: 241
Period size: 70 Copynumber: 2.3 Consensus size: 70
17764399 TTAAAATATA
* * **
17764409 TTTTAAAAATATATTGAATATATTGAA-ATTTTAAAATTGATTATACTTAGTATTTTTTAATATA
1 TTTTTAAAATATATTAAATATATT-AACATTTTAAAATTGATTATACTTAACATTTTTTAATATA
17764473 TTTAAT
65 TTTAAT
*
17764479 TTTTTAAAATATATTAAATATATTAACATTTTAAAATTGGTTATACTTAACATTTTTTAATATAT
1 TTTTTAAAATATATTAAATATATTAACATTTTAAAATTGATTATACTTAACATTTTTTAATATAT
17764544 TTAAT
66 TTAAT
17764549 TTTTT-AAATATATTTAAAT
1 TTTTTAAAATATA-TTAAAT
17764568 TTTTAAATTT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
69 9 0.11
70 73 0.89
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (70 bp):
TTTTTAAAATATATTAAATATATTAACATTTTAAAATTGATTATACTTAACATTTTTTAATATAT
TTAAT
Found at i:17764599 original size:17 final size:17
Alignment explanation
Indices: 17764550--17764599 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
17764540 ATATTTAATT
*
17764550 TTTTAAATATATTTAAAT
1 TTTTAAATATA-TTAAAG
* *
17764568 TTTTAAATTTTTTAAAG
1 TTTTAAATATATTAAAG
17764585 TTTTAAATATATTAA
1 TTTTAAATATATTAA
17764600 GAAAATCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTAAATATATTAAAG
Found at i:17764692 original size:19 final size:20
Alignment explanation
Indices: 17764660--17764698 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
17764650 AATTTTAAAA
*
17764660 TTAATTATACTTAACATTTT
1 TTAATTATACTTAAAATTTT
*
17764680 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
17764699 AAAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTATACTTAAAATTTT
Found at i:17768003 original size:14 final size:13
Alignment explanation
Indices: 17767981--17768011 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
17767971 CTCACCATCC
17767981 AGCATATATAT-T
1 AGCATATATATAT
17767993 AGCATATATATAT
1 AGCATATATATAT
17768006 AGCATA
1 AGCATA
17768012 CAAAATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (13 bp):
AGCATATATATAT
Found at i:17773935 original size:16 final size:18
Alignment explanation
Indices: 17773914--17773952 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
17773904 ATAATCTATA
17773914 ATATAATAATAGT-TA-T
1 ATATAATAATAGTATATT
*
17773930 ATATAATAGTAGTATATT
1 ATATAATAATAGTATATT
17773948 ATATA
1 ATATA
17773953 TAAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATAATAATAGTATATT
Found at i:17774209 original size:22 final size:21
Alignment explanation
Indices: 17774158--17774219 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
17774148 TCTATCTTTT
*
17774158 ATTATAATCTATAATA-TAATA
1 ATTAT-ATATATAATATTAATA
*
17774179 ATATTTATATATAATATTAATA
1 AT-TATATATATAATATTAATA
17774201 CATTATATAT-TACATATTA
1 -ATTATATATATA-ATATTA
17774220 TTATATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 13 0.38
22 19 0.56
23 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATATATATAATATTAATA
Found at i:17774443 original size:254 final size:252
Alignment explanation
Indices: 17773873--17774695 Score: 939
Period size: 254 Copynumber: 3.2 Consensus size: 252
17773863 TACTATATTA
*
17773873 TATAATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * * ** *
17773938 GTAGTATATTATATA-TA-A-ATTATTATACATTATTGTTTATTATTACACAAGGTTGAAATATG
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATA-GTGGTTAAAATATG
* * * *
17774000 CTCCAAGTCCCTATACTTTTTGTACATTTAAAAGTTAACCCTCCTACTATATTATATATATATAT
130 CTCTAAGTCTCTAT-CTTTTTGTACATTTGAAAGTTAGCCCTCCTACTATATTATATA-ATA-AT
* *
17774065 ATAATGCTATATCATATAGAATATAATATATTAATA-ATT-T-TATACATGCATCAATGATTGAA
192 AT-AT-C-ATATCATAT---AT-TAATATATTAATATATTATATATATATGCATCAATGATTAAA
17774127 CAT
250 CAT
* * ** * *
17774130 TAAAATATTATGTAATTTTCTATCTTTTATTATAATCTATAATATAATAATATTTATATATAATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * *
17774195 TTAATACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATTTGC
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATATGC
* * * * **
17774260 TCTAAGTTTCTATGCTTTTTATGCATTTGAAAGTTAGCCTTCCTACTATATTATATAATGCTATA
131 TCTAAGTCTCTAT-CTTTTTGTACATTTGAAAGTTAGCCCTCCTACTATATTATATAATAATATA
* * *
17774325 TCATATCATATATTAATATTTTATATATATGTATATATATATGCATAAATGATT-AATAT
195 TCATATCATATATTAATATATTA-ATATAT-TATATATATATGCATCAATGATTAAACAT
* *
17774384 TATAATATCATGTAATACTATATTTTTTATTATAATCTATATTATAATAATAGTTATATATAATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * * * *
17774449 GTAGTACACTATATATTACTTATTATTGTATATTATTGTTTATTGTTATAGTAGTTAAAATATGC
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATATGC
* * ** *
17774514 TTTAAGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTATTACTATATTATATAATATTATA
131 TCTAAGTCTCTATCTTTTT-GTACATTTGAAAGTTAGCCCTCCTACTATATTATATAATAATATA
* * * * *
17774579 TCATATCATA-A--AATATATTAATGGTTTATATATATATATGTATCGATAATTAAACAT
195 TCATATCATATATTAATATATTAAT-ATAT-TATATATATATGCATCAATGATTAAACAT
* ** *
17774636 TACAATATCATGTAATTTTATATCTTTTATTATAATCTAT-ATAAAAATAATAGTTATATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAAT-ATAATAATAGTTATATA
17774696 CGTGTTAATA
Statistics
Matches: 482, Mismatches: 72, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
250 11 0.02
251 35 0.07
252 58 0.12
253 7 0.01
254 187 0.39
255 18 0.04
256 2 0.00
257 73 0.15
258 4 0.01
259 60 0.12
260 27 0.06
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (252 bp):
TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATATGC
TCTAAGTCTCTATCTTTTTGTACATTTGAAAGTTAGCCCTCCTACTATATTATATAATAATATAT
CATATCATATATTAATATATTAATATATTATATATATATGCATCAATGATTAAACAT
Found at i:17774447 original size:16 final size:17
Alignment explanation
Indices: 17774421--17774453 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17774411 TATTATAATC
17774421 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
17774438 TATA-TATAATAGTAGT
1 TATATTATAATAATAGT
17774454 ACACTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:17777806 original size:16 final size:16
Alignment explanation
Indices: 17777773--17777806 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17777763 CATATATGTT
* *
17777773 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
17777789 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
17777805 AA
1 AA
17777807 TAAAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:17780633 original size:21 final size:21
Alignment explanation
Indices: 17780607--17780647 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17780597 AGACGAGCAA
* *
17780607 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17780628 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17780648 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:17783238 original size:29 final size:27
Alignment explanation
Indices: 17783174--17783238 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
17783164 AATTTTTGCA
*
17783174 AAATTTTAATTTTTTTAAATTTTCATT
1 AAATTTTAATTTTTTTAAATTTTAATT
*
17783201 ATACCTTTTAATTTTTTTAAATATTTTAATT
1 A-A-ATTTTAATTTTTTT-AA-ATTTTAATT
17783232 AAATTTT
1 AAATTTT
17783239 CTTAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 17 0.55
30 3 0.10
31 9 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (27 bp):
AAATTTTAATTTTTTTAAATTTTAATT
Found at i:17787021 original size:251 final size:249
Alignment explanation
Indices: 17786566--17787068 Score: 943
Period size: 251 Copynumber: 2.0 Consensus size: 249
17786556 AATTCATGGC
*
17786566 TTTGTAACCCCCCTCTGTCACCCCCTTCCCAGAAATGTATGTAAAATGTGTCAAAGATATTTTGA
1 TTTGTAACCCCCCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTTGA
* *
17786631 GTATATAAGAGTTAATAGATATTGTAATGGCTCGAATTATCAATGTAGGTTATTAAATATTATAC
66 GTATATAAGAGTTAATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTATAC
17786696 TAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGGCT
131 TAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGGCT
17786761 TATTTTTTCCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
196 TATTTTTTCCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
17786815 TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
1 TTTGTAA-CCCCC-CTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
*
17786880 GAGTATATAAGAGTTGATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTAT
64 GAGTATATAAGAGTTAATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTAT
17786945 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
129 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
*
17787010 CTTATTTTTTCCGTTTCAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
194 CTTATTTTTTCCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
17787066 TTT
1 TTT
17787069 TTGTTACTGT
Statistics
Matches: 247, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
249 7 0.03
250 5 0.02
251 235 0.95
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (249 bp):
TTTGTAACCCCCCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTTGA
GTATATAAGAGTTAATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTATAC
TAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGGCT
TATTTTTTCCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
Found at i:17790446 original size:20 final size:21
Alignment explanation
Indices: 17790399--17790449 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
17790389 TTATATATTT
17790399 TTTATAAAA-TTAATAAAACA
1 TTTATAAAATTTAATAAAACA
*
17790419 TATT-TAAAATTTTATAAAA-A
1 T-TTATAAAATTTAATAAAACA
17790439 TTTATAAAATT
1 TTTATAAAATT
17790450 CAAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 10 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTATAAAATTTAATAAAACA
Found at i:17790482 original size:20 final size:19
Alignment explanation
Indices: 17790424--17790486 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
17790414 AAACATATTT
*
17790424 AAAATTTTATAAAAATT-TA
1 AAAATTCTA-AAAAATTATA
*
17790443 TAAAATTC-AAAAATAATATA
1 -AAAATTCTAAAAA-ATTATA
17790463 ATAAATTCTAAAAAATTATA
1 A-AAATTCTAAAAAATTATA
17790483 AAAA
1 AAAA
17790487 AAGTCAACTC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 20 0.56
21 5 0.14
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTCTAAAAAATTATA
Found at i:17792899 original size:103 final size:104
Alignment explanation
Indices: 17792606--17792970 Score: 598
Period size: 102 Copynumber: 3.5 Consensus size: 104
17792596 GTATATAAAA
** *
17792606 GGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
17792671 AAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
66 AAATGTGAAAAGGGGGTTGCTATGTGCTGATT-CCCCGAG
*
17792711 GGGTTGCTAAGTGCTGATTCCCCGATTC-TTGGTGGTGCTATGTGCGTGATCCACCATATCTTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
17792775 AAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCGAG
66 AAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCGAG
*
17792813 GGGTTGCTAAGTGCTGATT-CCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCTTT
*
17792876 GAAATGTGAAAAGGGGGTGGCTATGTGCTGATTCCCCGAG
65 GAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCGAG
* *
17792916 GGGTTGCTAAGTGCTGA-T-CCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCA
17792971 ATAACGGTTA
Statistics
Matches: 248, Mismatches: 8, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
101 7 0.03
102 100 0.40
103 72 0.29
104 43 0.17
105 26 0.10
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.31
Consensus pattern (104 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
AAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCGAG
Found at i:17800284 original size:26 final size:26
Alignment explanation
Indices: 17800249--17800300 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
17800239 AATGTGAAAG
*
17800249 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
17800275 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
17800301 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:17800394 original size:103 final size:104
Alignment explanation
Indices: 17800172--17800538 Score: 627
Period size: 103 Copynumber: 3.6 Consensus size: 104
17800162 TGTATATAAA
** *
17800172 AGGGGTTGCTGTGTGCTGATTCCCCGATTCA-TGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
17800235 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
17800274 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
17800338 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
17800377 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
17800442 TGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
17800480 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
17800539 ATAACGGTTA
Statistics
Matches: 254, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
102 76 0.30
103 156 0.61
104 22 0.09
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:17804699 original size:9 final size:9
Alignment explanation
Indices: 17804685--17804715 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17804675 GTTAAACGAA
17804685 TCGAGTTAT
1 TCGAGTTAT
*
17804694 TCGAGTTAA
1 TCGAGTTAT
17804703 TCGAGTTAT
1 TCGAGTTAT
17804712 TCGA
1 TCGA
17804716 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:17810748 original size:26 final size:25
Alignment explanation
Indices: 17810719--17810777 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
17810709 CTTCGTAAGT
*
17810719 TTCCCGATTAAAGGCTCTTTATGAGC
1 TTCCCGATTAAAGGCTCTCTA-GAGC
* *
17810745 TTCCTGATTAATGGCTCTCTAGAGC
1 TTCCCGATTAAAGGCTCTCTAGAGC
17810770 TTCCCGAT
1 TTCCCGAT
17810778 ATGGCTCGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (25 bp):
TTCCCGATTAAAGGCTCTCTAGAGC
Found at i:17810795 original size:23 final size:23
Alignment explanation
Indices: 17810755--17810802 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
17810745 TTCCTGATTA
* *
17810755 ATGGCTCTCTAGAGCTTCCCGAT
1 ATGGCTCGCTAGAACTTCCCGAT
*
17810778 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCTAGAACTTCCCGAT
17810801 AT
1 AT
17810803 ATGGCTATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (23 bp):
ATGGCTCGCTAGAACTTCCCGAT
Found at i:17810970 original size:25 final size:25
Alignment explanation
Indices: 17810909--17810973 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
17810899 TACAACCCGG
* *
17810909 ATAAGCTTCCCATTACAAGATTCAC
1 ATAAGCTTCCCGTTACAAGACTCAC
*
17810934 ATAAGCTTCCCGTTACACGACTCAC
1 ATAAGCTTCCCGTTACAAGACTCAC
17810959 ATAAGCTTCCCGTTA
1 ATAAGCTTCCCGTTA
17810974 TATGGCTCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.28
Consensus pattern (25 bp):
ATAAGCTTCCCGTTACAAGACTCAC
Found at i:17813104 original size:10 final size:9
Alignment explanation
Indices: 17813087--17813231 Score: 77
Period size: 9 Copynumber: 15.7 Consensus size: 9
17813077 TTATTAAAAA
17813087 TTAT-ATTT
1 TTATAATTT
17813095 TTAATAATTT
1 TT-ATAATTT
* *
17813105 ATTAGAACTTA
1 -TTATAA-TTT
17813116 TTATGAATTT
1 TTAT-AATTT
17813126 TTATAA-TT
1 TTATAATTT
17813134 TTATAATTAT
1 TTATAATT-T
*
17813144 TGATAA-TT
1 TTATAATTT
17813152 TTATAA-TT
1 TTATAATTT
17813160 TTAT-ATTT
1 TTATAATTT
*
17813168 TATTTGAATTT
1 T-TAT-AATTT
17813179 TT-TATATGTT
1 TTATA-AT-TT
*
17813189 CTTATAATGT
1 -TTATAATTT
*
17813199 TTATTATTT
1 TTATAATTT
*
17813208 TTATAATAT
1 TTATAATTT
* *
17813217 TTACAAATT
1 TTATAATTT
17813226 TTATAA
1 TTATAA
17813232 GTTCACAGAA
Statistics
Matches: 106, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
7 1 0.01
8 26 0.25
9 36 0.34
10 26 0.25
11 15 0.14
12 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:17813137 original size:8 final size:8
Alignment explanation
Indices: 17813124--17813170 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
17813114 TATTATGAAT
17813124 TTTTATAA
1 TTTTATAA
17813132 TTTTATAA
1 TTTTATAA
17813140 TTATTGATAA
1 TT-TT-ATAA
17813150 TTTTATAA
1 TTTTATAA
17813158 TTTTAT-A
1 TTTTATAA
17813165 TTTTAT
1 TTTTAT
17813171 TTGAATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.19
8 20 0.54
9 4 0.11
10 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:17813177 original size:26 final size:25
Alignment explanation
Indices: 17813113--17813179 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 25
17813103 TTATTAGAAC
17813113 TTATTATGAATTTTTATAATTTTATAA
1 TTATT-TGAA-TTTTATAATTTTATAA
*
17813140 TTA-TTGATAATTTTATAATTTTATATT
1 TTATTTG--AATTTTATAATTTTATA-A
17813167 TTATTTGAATTTT
1 TTATTTGAATTTT
17813180 TTATATGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
27 8 0.23
28 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
TTATTTGAATTTTATAATTTTATAA
Found at i:17813319 original size:19 final size:20
Alignment explanation
Indices: 17813277--17813327 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
17813267 TATTTTTATT
*
17813277 TTTTTATAATTAATTAGAAT
1 TTTTTATAATTAATTAGAAA
* *
17813297 TTTTTATAA-TATTTATAAA
1 TTTTTATAATTAATTAGAAA
17813316 TTTTTATGAATT
1 TTTTTAT-AATT
17813328 TTTTATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 14 0.54
20 11 0.42
21 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTTATAATTAATTAGAAA
Found at i:17813327 original size:10 final size:9
Alignment explanation
Indices: 17813268--17813414 Score: 52
Period size: 10 Copynumber: 15.9 Consensus size: 9
17813258 AACATGTTTT
17813268 ATTTTTAT-
1 ATTTTTATA
*
17813276 TTTTTTATA
1 ATTTTTATA
* *
17813285 ATTAATTAGA
1 ATT-TTTATA
17813295 ATTTTTTATA
1 A-TTTTTATA
*
17813305 ATATTTATAA
1 ATTTTTAT-A
17813315 ATTTTTATGA
1 ATTTTTAT-A
17813325 ATTTTTTATTA
1 A-TTTTTA-TA
*
17813336 GTTTTGTA-A
1 ATTTT-TATA
*
17813345 AATTTTATA
1 ATTTTTATA
*
17813354 A-TATTATA
1 ATTTTTATA
*
17813362 AGTTTATATA
1 A-TTTTTATA
* *
17813372 A-ATTTGTA
1 ATTTTTATA
17813380 ATATTTTAT-
1 AT-TTTTATA
*
17813389 TTTTTTATA
1 ATTTTTATA
* * *
17813398 ATTCTAATG
1 ATTTTTATA
17813407 ATTTTTAT
1 ATTTTTAT
17813415 GGAAAAATAT
Statistics
Matches: 99, Mismatches: 27, Indels: 25
0.66 0.18 0.17
Matches are distributed among these distances:
8 27 0.27
9 26 0.26
10 34 0.34
11 11 0.11
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:17813351 original size:30 final size:30
Alignment explanation
Indices: 17813293--17813352 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17813283 TAATTAATTA
*
17813293 GAATTTTTTATAATATTTATAAATTTTTAT
1 GAATTTTTTATAATATTTATAAAATTTTAT
* *
17813323 GAATTTTTTATTAGT-TTTGTAAAATTTTAT
1 GAATTTTTTA-TAATATTTATAAAATTTTAT
17813353 AATATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (30 bp):
GAATTTTTTATAATATTTATAAAATTTTAT
Done.