Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 110 of 187
Found at i:32778052 original size:117 final size:116
Alignment explanation
Indices: 32777913--32778132 Score: 305
Period size: 117 Copynumber: 1.9 Consensus size: 116
32777903 TCATTTATCT
* * * * *
32777913 GAGATAGCAACAAAGGCATCCTTTTAACAGAGATAGCCACAAATGCATCCTTTTAACAAAGATTG
1 GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGCCACAAAGGCATCCTTTTAACAAAGATCG
** *
32777978 ACACAAAGACTTTTTTTTTAACAAAGATTGCCACAAAGGTTTCCTTTTAATA
66 ACACAAAGAC-TTCCTTTTAACAAAGATAGCCACAAAGGTTTCCTTTTAATA
* * *
32778030 GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGTCACAAAGGCATCCTTTTAATAGAGATCG
1 GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGCCACAAAGGCATCCTTTTAACAAAGATCG
* * *
32778095 CCACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGG
66 ACACAAAGACTTCCTTTTAACAAAGATAGCCACAAAGG
32778133 CATCCATTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
116 24 0.27
117 65 0.73
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (116 bp):
GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGCCACAAAGGCATCCTTTTAACAAAGATCG
ACACAAAGACTTCCTTTTAACAAAGATAGCCACAAAGGTTTCCTTTTAATA
Found at i:32801616 original size:15 final size:14
Alignment explanation
Indices: 32801591--32801622 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
32801581 AACGAATAAT
32801591 AATTTTAAAAATTA
1 AATTTTAAAAATTA
32801605 AATTTGTAAAAATTA
1 AATTT-TAAAAATTA
32801620 AAT
1 AAT
32801623 CGAATATCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTTTAAAAATTA
Found at i:32802727 original size:21 final size:22
Alignment explanation
Indices: 32802701--32802747 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
32802691 ATCAATAGAC
32802701 CATAATTTAAAATTTTCACTA-
1 CATAATTTAAAATTTTCACTAT
32802722 CATAATTTAAAATTTTCACTAT
1 CATAATTTAAAATTTTCACTAT
32802744 CATA
1 CATA
32802748 TTTCCTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (22 bp):
CATAATTTAAAATTTTCACTAT
Found at i:32808811 original size:29 final size:29
Alignment explanation
Indices: 32808719--32808813 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
32808709 GGTGTTAGGC
* * * *
32808719 ACTGGTGATTACAATTTTAGGTACTTTGT
1 ACTGGTGATTATAGTTTCAGGTACTATGT
* * *
32808748 AACT-GTG-TTATAGTTCCAGGCACTCTGT
1 -ACTGGTGATTATAGTTTCAGGTACTATGT
* *
32808776 GCCGGTGATTATAGTTTCAGGTACTATGT
1 ACTGGTGATTATAGTTTCAGGTACTATGT
32808805 ACTGGTGAT
1 ACTGGTGAT
32808814 AGATACCATA
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
27 1 0.02
28 18 0.36
29 28 0.56
30 3 0.06
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (29 bp):
ACTGGTGATTATAGTTTCAGGTACTATGT
Found at i:32813789 original size:19 final size:19
Alignment explanation
Indices: 32813767--32813804 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
32813757 CGATTTGGGT
32813767 TCTCAAG-CACAATTTTCAA
1 TCTCAAGTC-CAATTTTCAA
32813786 TCTCAAGTCCAATTTTCAA
1 TCTCAAGTCCAATTTTCAA
32813805 GTTCAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (19 bp):
TCTCAAGTCCAATTTTCAA
Found at i:32816112 original size:121 final size:121
Alignment explanation
Indices: 32815957--32816210 Score: 472
Period size: 121 Copynumber: 2.1 Consensus size: 121
32815947 AATTACATCA
* *
32815957 AATTGTAAAGAATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTACTAAAATCTCCATTTA
1 AATTGAAAAG-ATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTA
32816022 AAATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
65 AAATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
*
32816079 AATTTAAAAGATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTAA
1 AATTGAAAAGATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTAA
32816144 AATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
66 AATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
32816200 AATTGAAAAGA
1 AATTGAAAAGA
32816211 CCTTAATACA
Statistics
Matches: 128, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 120 0.94
122 8 0.06
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (121 bp):
AATTGAAAAGATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTAA
AATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
Found at i:32819318 original size:3 final size:3
Alignment explanation
Indices: 32819310--32819345 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
32819300 TTCATCTGCA
32819310 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32819346 AAAATAAAAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:32820650 original size:12 final size:11
Alignment explanation
Indices: 32820633--32820667 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
32820623 AACAAATCCT
32820633 CTCTCATATTTC
1 CTCTCA-ATTTC
32820645 CTCTCAA-TTC
1 CTCTCAATTTC
32820655 CTCTCAATTTC
1 CTCTCAATTTC
32820666 CT
1 CT
32820668 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:32820714 original size:51 final size:51
Alignment explanation
Indices: 32820648--32820758 Score: 197
Period size: 51 Copynumber: 2.2 Consensus size: 51
32820638 ATATTTCCTC
* *
32820648 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
32820698 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
32820749 TCAATTTCCT
1 TCAATTTCCT
32820759 TTTTTAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 4 0.07
51 54 0.93
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
Found at i:32821914 original size:7 final size:7
Alignment explanation
Indices: 32821902--32821926 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32821892 ATTTGATTGA
32821902 TATTTAG
1 TATTTAG
32821909 TATTTAG
1 TATTTAG
32821916 TATTTAG
1 TATTTAG
32821923 TATT
1 TATT
32821927 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:32822604 original size:18 final size:18
Alignment explanation
Indices: 32822578--32822612 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32822568 AGGTGCGTTT
*
32822578 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
32822596 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
32822613 TCCTTTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:32823117 original size:22 final size:22
Alignment explanation
Indices: 32823089--32823241 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
32823079 TGTTGATAGT
*
32823089 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
32823111 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
32823133 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
32823155 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
32823177 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
32823199 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
32823221 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
32823242 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:32823654 original size:23 final size:23
Alignment explanation
Indices: 32823624--32824032 Score: 446
Period size: 23 Copynumber: 17.3 Consensus size: 23
32823614 NTAAAACCCT
*
32823624 AACCCTAACCTAATTCAATTAAA
1 AACCCTAACCTAATTTAATTAAA
32823647 AACCCTAACCCTAACCTAATTCAATTAAA
1 AACCCTAA-CCTAA--T--TT-AATTAAA
32823676 AACCCTAACCCTTAA-TTAA--AAA
1 AACCCTAA-CC-TAATTTAATTAAA
32823698 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
32823721 AACCCTAGCCTAATTTAATT-AA
1 AACCCTAACCTAATTTAATTAAA
*
32823743 AACCCTAGCCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
32823766 AACCCAAAACCCTTAA-TTAA--AAA
1 AACCC-TAA-CC-TAATTTAATTAAA
32823789 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
* *
32823816 AACCCTAGCTTAATTTAATT-AA
1 AACCCTAACCTAATTTAATTAAA
32823838 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
32823861 AATCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
32823884 AACCCTAAACCCTTAA-TTAA--AAA
1 AACCCT-AA-CC-TAATTTAATTAAA
32823907 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
*
32823934 AACCCTAGCCTAATTTAATT-AA
1 AACCCTAACCTAATTTAATTAAA
32823956 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
32823979 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
32824002 AACCCTAGCCTAATTTATTTAAA
1 AACCCTAACCTAATTTAATTAAA
32824025 AACCCTAA
1 AACCCTAA
32824033 ACCCTTAACT
Statistics
Matches: 337, Mismatches: 16, Indels: 66
0.80 0.04 0.16
Matches are distributed among these distances:
20 3 0.01
21 6 0.02
22 74 0.22
23 162 0.48
24 16 0.05
25 26 0.08
26 11 0.03
27 17 0.05
28 1 0.00
29 18 0.05
30 3 0.01
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:32823656 original size:29 final size:29
Alignment explanation
Indices: 32823616--32823687 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
32823606 NNNNNNNNNT
32823616 AAAACCCTAACCCTAACCTAATTCAATTA
1 AAAACCCTAACCCTAACCTAATTCAATTA
32823645 AAAACCCTAACCCTAACCTAATTCAATTA
1 AAAACCCTAACCCTAACCTAATTCAATTA
32823674 AAAACCCTAACCCT
1 AAAACCCTAACCCT
32823688 TAATTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (29 bp):
AAAACCCTAACCCTAACCTAATTCAATTA
Found at i:32823706 original size:45 final size:46
Alignment explanation
Indices: 32823653--32824061 Score: 409
Period size: 45 Copynumber: 8.8 Consensus size: 46
32823643 TAAAAACCCT
*
32823653 AACCCTAACCTAATTCAATTAAAAACCCTAACCCTTAA-TTAA-AAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAA-CCTTAATTTAATAAA
* *
32823698 AACCCTAACCTAATTTAATTAAAAACCCTAGCC-TAATTTAATTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAATAAA
* *
32823743 AACCCTAGCCTAATTTAATTAAAAACCCAAAACCCTTAA-TTAA-AAA
1 AACCCTAACCTAATTTAATTAAAAACCC-TAA-CCTTAATTTAATAAA
* *
32823789 CCCTAACCCTAACCTAATTTAATTAAAAACCCT-AGCTTAATTTAATTAA
1 ----AACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAATAAA
*
32823838 AACCCTAACCTAATTTAATTAAAAATCCTAACC-TAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAA-TAAA
*
32823884 AACCCTAAACC---CTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCTAATTTAATTAAAAACCCTAA-CCT----TAATTTAA-TAAA
*
32823934 AACCCTAGCCTAATTTAATT-AAAACCCTAACC-TAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAA-TAAA
* *
32823979 AACCCTAACCTAATTTAATTAAAAACCCTAGCC-TAATTTATTTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTA-ATAAA
*
32824025 AACCCTAAACC---CTTAACTTTAAAAACCCTAACCTTAA
1 AACCCT-AACCTAATTTAA--TTAAAAACCCTAACCTTAA
32824062 CGTAATGTTA
Statistics
Matches: 312, Mismatches: 23, Indels: 56
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.01
44 26 0.08
45 128 0.41
46 56 0.18
47 22 0.07
48 8 0.03
49 5 0.02
50 48 0.15
51 10 0.03
52 6 0.02
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.29
Consensus pattern (46 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAATAAA
Found at i:32824007 original size:118 final size:118
Alignment explanation
Indices: 32823695--32824008 Score: 558
Period size: 118 Copynumber: 2.7 Consensus size: 118
32823685 CCTTAATTAA
* * *
32823695 AAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATT-AAAACCCTAGCCTAATTT
1 AAAAACCCTAGCCTAATTTAATT-AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTT
*
32823759 AATTAAAAACCCAAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
65 AATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
* *
32823813 AAAAACCCTAGCTTAATTTAATTAAAACCCTAACCTAATTTAATTAAAAATCCTAACCTAATTTA
1 AAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
32823878 ATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
66 ATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
32823931 AAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
1 AAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
32823996 ATTAAAAACCCTA
66 ATTAAAAACCCTA
32824009 GCCTAATTTA
Statistics
Matches: 187, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
117 21 0.11
118 166 0.89
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (118 bp):
AAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
ATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
Found at i:32824045 original size:23 final size:21
Alignment explanation
Indices: 32824019--32824062 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
32824009 GCCTAATTTA
32824019 TTTAAAAACCCTAAACCCTTAAC
1 TTTAAAAACCCT-AA-CCTTAAC
32824042 TTTAAAAACCCTAACCTTAAC
1 TTTAAAAACCCTAACCTTAAC
32824063 GTAATGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 12 0.57
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (21 bp):
TTTAAAAACCCTAACCTTAAC
Found at i:32824046 original size:118 final size:116
Alignment explanation
Indices: 32823624--32824008 Score: 530
Period size: 118 Copynumber: 3.3 Consensus size: 116
32823614 NTAAAACCCT
* * *
32823624 AACCCTAACCTAATTCAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAACCCTT
1 AACCCTAACCTAATTTAATTAAAAACCCT-A----AACC--CTT-AATTAAAAACCCTAACCCTA
* *
32823689 A--A-TTAA--AAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATT-AA
58 ACCATTTAATTAAAAACCCTAGCCTAATTTAATT-AAAACCCTAACCTAATTTAATTAAA
* *
32823743 AACCCTAGCCTAATTTAATTAAAAACCCAAAACCCTTAATTAAAAACCCTAACCCTAACCTAATT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACC--ATT
*
32823808 TAATTAAAAACCCTAGCTTAATTTAATTAAAACCCTAACCTAATTTAATTAAA
64 TAATTAAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAA
*
32823861 AATCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACC--ATT
32823926 TAATTAAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAA
64 TAATTAAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAA
32823979 AACCCTAACCTAATTTAATTAAAAACCCTA
1 AACCCTAACCTAATTTAATTAAAAACCCTA
32824009 GCCTAATTTA
Statistics
Matches: 245, Mismatches: 13, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
111 20 0.08
112 2 0.01
114 4 0.02
115 1 0.00
116 4 0.02
117 21 0.09
118 167 0.68
119 26 0.11
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (116 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCATTTA
ATTAAAAACCCTAGCCTAATTTAATTAAAACCCTAACCTAATTTAATTAAA
Found at i:32824193 original size:111 final size:111
Alignment explanation
Indices: 32824064--32824275 Score: 370
Period size: 111 Copynumber: 1.9 Consensus size: 111
32824054 AACCTTAACG
*
32824064 TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
32824129 ATTTTACTAACCATTAATACAATTTTTTAACTTAATTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTAACTTAATTACATTCACA
* * * *
32824175 TAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAATTAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
*
32824240 ATTTTACTAACCATTAATACAATTTTTTGACTTAAT
66 ATTTTACTAACCATTAATACAATTTTTTAACTTAAT
32824276 ACAATTTATT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 95 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (111 bp):
TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTAACTTAATTACATTCACA
Found at i:32827294 original size:124 final size:126
Alignment explanation
Indices: 32827122--32827473 Score: 518
Period size: 126 Copynumber: 2.8 Consensus size: 126
32827112 CCCAAACATG
32827122 CTACTGTAGCAAAAGCGCGTCCACGAGGACT-CGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGG-CTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
32827186 CTAGAAGCAATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AA-TATTTCTTAC-ATGAT
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTT-CTATGAC
* * *
32827246 CTACTGTAGCAAAAACGCG-CTGACGAGGCTGCAATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGCTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
32827310 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTATGAC
* *
32827372 CTACTGTAGCAAAAGCGCGTCCACGAGGGC-GCGATTTTACAAATTCTTCTCAAATACCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGA-GGCTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* **
32827436 CTAGAAGTGATTTTATATTATTTTATCAGAAACGTCAA
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
32827474 CTCGAAATTA
Statistics
Matches: 205, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
123 3 0.01
124 97 0.47
125 3 0.01
126 98 0.48
127 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGCTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTATGAC
Found at i:32827999 original size:12 final size:12
Alignment explanation
Indices: 32827978--32828013 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
32827968 ATATTTTTTT
32827978 AGCCATAGCCAA
1 AGCCATAGCCAA
*
32827990 AGCCAAAGCCAA
1 AGCCATAGCCAA
32828002 AGCCATAGCCAA
1 AGCCATAGCCAA
32828014 TAGCACAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.33, G:0.17, T:0.06
Consensus pattern (12 bp):
AGCCATAGCCAA
Found at i:32828005 original size:18 final size:18
Alignment explanation
Indices: 32827978--32828013 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32827968 ATATTTTTTT
*
32827978 AGCCATAGCCAAAGCCAA
1 AGCCAAAGCCAAAGCCAA
*
32827996 AGCCAAAGCCATAGCCAA
1 AGCCAAAGCCAAAGCCAA
32828014 TAGCACAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.33, G:0.17, T:0.06
Consensus pattern (18 bp):
AGCCAAAGCCAAAGCCAA
Found at i:32835168 original size:32 final size:32
Alignment explanation
Indices: 32835126--32835201 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
32835116 TGCATGTGTG
* * *
32835126 TAACTTTTCATCTTCAAGTCTCTTCGCATTAT
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
* **
32835158 TAACTCTTCATATTCAAGTCTTTTCACATTCG
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
*
32835190 TAACTTTTCATA
1 TAACTCTTCATA
32835202 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (32 bp):
TAACTCTTCATATTCAAGTCTCTTCACATTAT
Found at i:32839663 original size:32 final size:32
Alignment explanation
Indices: 32839621--32839696 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
32839611 TGCATGTGTG
* * *
32839621 TAACTTTTCATCTTCAAGTCTCTTCGCATTAT
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
* **
32839653 TAACTCTTCATATTCAAGTCTTTTCACATTCG
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
*
32839685 TAACTTTTCATA
1 TAACTCTTCATA
32839697 ATTTCTTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (32 bp):
TAACTCTTCATATTCAAGTCTCTTCACATTAT
Found at i:32846880 original size:33 final size:33
Alignment explanation
Indices: 32846838--32846904 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
32846828 CACACACTCA
32846838 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
1 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
32846871 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
1 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
32846904 T
1 T
32846905 AACGCTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (33 bp):
TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
Found at i:32849559 original size:39 final size:39
Alignment explanation
Indices: 32849481--32849559 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 39
32849471 CCTCATTTTT
* *
32849481 AGCAACTTCTTCTTTAGCAACAACTTCCTCTTCTGCAGC
1 AGCAACTTCTTCTTTAACAACAACTTCCTCTTATGCAGC
32849520 AGCAACTTCCTTC-TTAACAACAA-TGTCCTCTTGAT-CAGC
1 AGCAACTT-CTTCTTTAACAACAACT-TCCTCTT-ATGCAGC
32849559 A
1 A
32849560 AAAAGACCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 1 0.03
39 29 0.83
40 5 0.14
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (39 bp):
AGCAACTTCTTCTTTAACAACAACTTCCTCTTATGCAGC
Found at i:32860310 original size:41 final size:41
Alignment explanation
Indices: 32860262--32860353 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
32860252 GGCAGATGAG
***
32860262 ACGGGCGTGTGTCAGGTTGTGGGAGCCACACAGGCAAGCAC
1 ACGGGCGTGTGTCAGGCCATGGGAGCCACACAGGCAAGCAC
* * * *
32860303 ATGGGCGTATGTCAGGCCATTGGAGCCACACGGGCAAGCAC
1 ACGGGCGTGTGTCAGGCCATGGGAGCCACACAGGCAAGCAC
*
32860344 ACGGGTGTGT
1 ACGGGCGTGT
32860354 ACAAGGCCAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (41 bp):
ACGGGCGTGTGTCAGGCCATGGGAGCCACACAGGCAAGCAC
Found at i:32866565 original size:20 final size:20
Alignment explanation
Indices: 32866542--32866584 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
32866532 TTTTTCATTA
32866542 TTTTCTTCTTTCT-TTTCCTC
1 TTTTCTT-TTTCTGTTTCCTC
32866562 TTTTCTTTTTCTGTTTCCTC
1 TTTTCTTTTTCTGTTTCCTC
32866582 TTT
1 TTT
32866585 CAATTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTCTTTTTCTGTTTCCTC
Found at i:32875529 original size:48 final size:48
Alignment explanation
Indices: 32875458--32875549 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
32875448 TTGTTTTCTT
*
32875458 AAAAATGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAAACGC
1 AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAAACGC
* *
32875506 AAAAACGCCTAAGTCGGCCTAACTTGTAATGATAAAGGATTCAA
1 AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAA
32875550 CAAAATTCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAAACGC
Found at i:32875798 original size:19 final size:19
Alignment explanation
Indices: 32875774--32875827 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
32875764 AAAGCTGTAT
32875774 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
32875793 ACAATTAGAAGT-T--GTAT
1 ACAATTAGAACTCTAAG-AC
32875810 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
32875828 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 2 0.07
19 12 0.43
20 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:32875809 original size:36 final size:36
Alignment explanation
Indices: 32875757--32875827 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
32875747 ATCAAAGGCT
32875757 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
* *
32875793 ACAATTAGAAGTTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
32875828 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:32875815 original size:17 final size:17
Alignment explanation
Indices: 32875756--32875819 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
32875746 CATCAAAGGC
* *
32875756 TACAATTAAAAGCTGTA
1 TACAATTAGAAGTTGTA
*
32875773 TACAATTAGAACTCTAAG-A
1 TACAATTAGAAGT-T--GTA
*
32875792 CACAATTAGAAGTTGTA
1 TACAATTAGAAGTTGTA
32875809 TACAATTAGAA
1 TACAATTAGAA
32875820 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 2 0.05
19 12 0.32
20 1 0.03
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGTTGTA
Found at i:32880888 original size:17 final size:17
Alignment explanation
Indices: 32880866--32880929 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
32880856 CATCAAAGGC
*
32880866 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
32880883 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
32880902 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
32880919 TACAATTAGAA
1 TACAATTAGAA
32880930 CTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 21 0.55
19 11 0.29
20 3 0.08
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:32880908 original size:19 final size:19
Alignment explanation
Indices: 32880884--32880937 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
32880874 AAAGCTGTAT
32880884 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
32880903 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
32880920 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
32880938 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:32880915 original size:36 final size:36
Alignment explanation
Indices: 32880867--32880937 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
32880857 ATCAAAGGCT
32880867 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
32880903 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
32880938 TTACATAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:32893138 original size:35 final size:35
Alignment explanation
Indices: 32893087--32893154 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
32893077 GTGAATGAAC
32893087 AACTCAAAGACAAGTCGAGATGGACCTTGGAAAAA
1 AACTCAAAGACAAGTCGAGATGGACCTTGGAAAAA
*
32893122 AACTTAAAGACAAGTCGAGATGGACCTTGGAAA
1 AACTCAAAGACAAGTCGAGATGGACCTTGGAAA
32893155 TTTGAATCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (35 bp):
AACTCAAAGACAAGTCGAGATGGACCTTGGAAAAA
Found at i:32905042 original size:13 final size:13
Alignment explanation
Indices: 32905024--32905048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32905014 ATAATGACTC
32905024 TAAAAATATTTAA
1 TAAAAATATTTAA
32905037 TAAAAATATTTA
1 TAAAAATATTTA
32905049 CGACTTTATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAA
Found at i:32908910 original size:37 final size:37
Alignment explanation
Indices: 32908864--32908981 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
32908854 AGCTTTTCGG
32908864 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
1 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
* * *
32908901 AGCACCTGGCTTGTTATCAGGTGGATTAGCTCTTATA
1 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
* * *
32908938 AGCATTTGGTGTGTTATTAGGTGGATTAGATCTTATGA
1 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTAT-A
32908976 A-CATCT
1 AGCATCT
32908982 AGCATGTTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
37 68 0.97
38 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (37 bp):
AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
Found at i:32913555 original size:13 final size:13
Alignment explanation
Indices: 32913539--32913565 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32913529 GACAAGAAGA
32913539 ATTTGATGACTCC
1 ATTTGATGACTCC
32913552 ATTTGATGACTCC
1 ATTTGATGACTCC
32913565 A
1 A
32913566 ATAGAGGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTTGATGACTCC
Found at i:32914230 original size:28 final size:28
Alignment explanation
Indices: 32914194--32914275 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
32914184 TAATATTAAG
*
32914194 AATTTTATTAAATTATATATTTTTATTA
1 AATTATATTAAATTATATATTTTTATTA
* * *
32914222 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTAAATTATATATTTTTATTA
* * *
32914248 AAATATTATTAAACTATTTATTATTTAT
1 AATTA-TATTAAATTATATATT-TTTAT
32914276 ATTAATAATC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
26 7 0.17
27 13 0.32
28 17 0.43
29 2 0.05
30 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTAAATTATATATTTTTATTA
Found at i:32914484 original size:16 final size:16
Alignment explanation
Indices: 32914463--32914515 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
32914453 AGGATTACCT
32914463 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
32914479 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
32914495 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
32914511 ATTAC
1 ATTAC
32914516 AACGAACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:32926961 original size:22 final size:23
Alignment explanation
Indices: 32926920--32926963 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
32926910 CAACTTAGTA
32926920 AGTCATAAGCAATGAAAACATTT
1 AGTCATAAGCAATGAAAACATTT
32926943 AGTCATATA-CAA-GAAAACATT
1 AGTCATA-AGCAATGAAAACATT
32926964 AATCTATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 10 0.50
24 1 0.05
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (23 bp):
AGTCATAAGCAATGAAAACATTT
Found at i:32928026 original size:29 final size:28
Alignment explanation
Indices: 32927975--32928034 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
32927965 AAGTCCATAT
* *
32927975 ATTTCATTTATTTCACATTTTAGTCCCTCA
1 ATTTAATTTATTTCACAATTTAG-CCCT-A
*
32928005 ATTTAATTT-TTTTACAATTTAGCCCTA
1 ATTTAATTTATTTCACAATTTAGCCCTA
32928032 ATT
1 ATT
32928035 ACCCAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 11 0.41
30 8 0.30
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (28 bp):
ATTTAATTTATTTCACAATTTAGCCCTA
Found at i:32929035 original size:20 final size:20
Alignment explanation
Indices: 32929010--32929047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32929000 AATGCATAAC
*
32929010 AGAGGCTCCAAAGTGCAACT
1 AGAGGCACCAAAGTGCAACT
*
32929030 AGAGGCACCAAATTGCAA
1 AGAGGCACCAAAGTGCAA
32929048 TCTCATACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAACT
Found at i:32929835 original size:19 final size:20
Alignment explanation
Indices: 32929794--32929835 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
32929784 AGTCCTATTT
*
32929794 ATCTATCAAACTTATAAATC
1 ATCTATCAAACTTATAAAAC
32929814 ATCT-TCAAACTT-TGAAAAC
1 ATCTATCAAACTTAT-AAAAC
32929833 ATC
1 ATC
32929836 ACAAATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.75
20 4 0.20
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.33
Consensus pattern (20 bp):
ATCTATCAAACTTATAAAAC
Found at i:32932863 original size:171 final size:171
Alignment explanation
Indices: 32932572--32932915 Score: 643
Period size: 171 Copynumber: 2.0 Consensus size: 171
32932562 AAGAGATGAT
*
32932572 GGTAACAAAAAACAAGACATTGAATAGGTAGGTCTTGCTTGCAAAACACTTTTAATAAAAACTTC
1 GGTAACAAAAAACAAGACATTGAATAGGTAGGTATTGCTTGCAAAACACTTTTAATAAAAACTTC
*
32932637 TTTCCCTCCTTGGAAGAGTGGTTTAATACACCAAATATCTATTCGGCTATTCATACGATCTTTTA
66 TTTCCCGCCTTGGAAGAGTGGTTTAATACACCAAATATCTATTCGGCTATTCATACGATCTTTTA
32932702 ATAATTGGAAAGCCTACCTTTTGTTTTGACCCACAAAATAA
131 ATAATTGGAAAGCCTACCTTTTGTTTTGACCCACAAAATAA
*
32932743 GGTAGCAAAAAACAAGACATTGAATAGGTAGGTATTGCTTGCAAAACACTTTTAATAAAAACTTC
1 GGTAACAAAAAACAAGACATTGAATAGGTAGGTATTGCTTGCAAAACACTTTTAATAAAAACTTC
* *
32932808 TTTCCCGCCTTGGAAGAGTGGTTTAATACACGAAATATCTATTCGGCTGTTCATACGATCTTTTA
66 TTTCCCGCCTTGGAAGAGTGGTTTAATACACCAAATATCTATTCGGCTATTCATACGATCTTTTA
32932873 ATAATTGGAAAGCCTACCTTTTGTTTTGACCCACAAAATAA
131 ATAATTGGAAAGCCTACCTTTTGTTTTGACCCACAAAATAA
32932914 GG
1 GG
32932916 GAGCCCCAAA
Statistics
Matches: 168, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
171 168 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (171 bp):
GGTAACAAAAAACAAGACATTGAATAGGTAGGTATTGCTTGCAAAACACTTTTAATAAAAACTTC
TTTCCCGCCTTGGAAGAGTGGTTTAATACACCAAATATCTATTCGGCTATTCATACGATCTTTTA
ATAATTGGAAAGCCTACCTTTTGTTTTGACCCACAAAATAA
Found at i:32934926 original size:14 final size:14
Alignment explanation
Indices: 32934907--32934959 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
32934897 AAGTTATTAT
32934907 CCCAAAATTTTCTC
1 CCCAAAATTTTCTC
* * *
32934921 CCCAAAAATTACTT
1 CCCAAAATTTTCTC
32934935 CCCAAAA-TTTCTGC
1 CCCAAAATTTTCT-C
*
32934949 CCTAAAATTTT
1 CCCAAAATTTT
32934960 GTCTCCCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 24 0.77
15 3 0.10
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (14 bp):
CCCAAAATTTTCTC
Found at i:32935633 original size:24 final size:24
Alignment explanation
Indices: 32935606--32935659 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
32935596 AAATAAAATA
32935606 CAAAAAAA-AGGAAAACATCATATT
1 CAAAAAAATAGG-AAACATCATATT
* **
32935630 CAAAAAAATAGGTAATTTCATATT
1 CAAAAAAATAGGAAACATCATATT
32935654 CAAAAA
1 CAAAAA
32935660 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (24 bp):
CAAAAAAATAGGAAACATCATATT
Found at i:32939293 original size:26 final size:26
Alignment explanation
Indices: 32939263--32939337 Score: 114
Period size: 26 Copynumber: 2.9 Consensus size: 26
32939253 TGGAGGAAGT
* *
32939263 ATACTGTTACTGGCAACTTTGTTGCG
1 ATACTGCTACTGGCAACTTTGCTGCG
*
32939289 ATACTGCTACTGGCAACTTTGCTGTG
1 ATACTGCTACTGGCAACTTTGCTGCG
*
32939315 ATACTGCTACTGGCAGCTTTGCT
1 ATACTGCTACTGGCAACTTTGCT
32939338 ACGGTATTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
ATACTGCTACTGGCAACTTTGCTGCG
Found at i:32939513 original size:33 final size:33
Alignment explanation
Indices: 32939440--32939531 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 33
32939430 TGTATTATTG
* *
32939440 CACTGTACTGATATTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
32939473 CA---T--TGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
* * *
32939501 CACTGTACTGTTACTGAATAGGGCTCAGGCC
1 CACTGTACTGTTACTGTATTGGGCTAAGGCC
32939532 TAAACTGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
28 25 0.51
30 1 0.02
31 1 0.02
33 22 0.45
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:32939539 original size:33 final size:34
Alignment explanation
Indices: 32939476--32939544 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
32939466 AGGCCCACAT
* * *
32939476 TGTTACTGTATTGGGCTAAGGCCCACACTG-TAC
1 TGTTACTGAATAGGGCTAAGGCCCAAACTGTTAC
* *
32939509 TGTTACTGAATAGGGCTCAGGCCTAAACTGTTAC
1 TGTTACTGAATAGGGCTAAGGCCCAAACTGTTAC
32939543 TG
1 TG
32939545 CATGTTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (34 bp):
TGTTACTGAATAGGGCTAAGGCCCAAACTGTTAC
Found at i:32947945 original size:26 final size:26
Alignment explanation
Indices: 32947911--32948017 Score: 106
Period size: 26 Copynumber: 4.1 Consensus size: 26
32947901 TGGAGGAAGT
* * *
32947911 ATACTGTTACTGGCAACTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTACTGCA
* * * * * **
32947937 ATATTGTTATTGCCAGCTCTACCGTG
1 ATACTGTTACTGGCAGCTTTACTGCA
*
32947963 ATACTGTTACTGGCAGCTTTGCTGCA
1 ATACTGTTACTGGCAGCTTTACTGCA
*
32947989 ATACTATTACTGGCAGCTTTACTGCA
1 ATACTGTTACTGGCAGCTTTACTGCA
32948015 ATA
1 ATA
32948018 TTGGTGTGTT
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTACTGCA
Found at i:32961783 original size:31 final size:31
Alignment explanation
Indices: 32961738--32961796 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
32961728 CAATCACATT
32961738 TTAACCATTTATCCTTTTCCAATCACATAAA
1 TTAACCATTTATCCTTTTCCAATCACATAAA
32961769 TTAACC-TTTCATCCTTTTCCAATCACAT
1 TTAACCATTT-ATCCTTTTCCAATCACAT
32961797 CAATGTCGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.41
Consensus pattern (31 bp):
TTAACCATTTATCCTTTTCCAATCACATAAA
Found at i:32978978 original size:94 final size:94
Alignment explanation
Indices: 32978816--32978995 Score: 288
Period size: 94 Copynumber: 1.9 Consensus size: 94
32978806 TTTAATTAGA
** * *
32978816 ACTTGAACTCGAACCTGAATAATCAGGTTTAAAATTGAGCATGATTATTTTTACGGGATATGACG
1 ACTTGAACTCGAACCTGAATAATCACATTTAAAATCGAGCATGATTATTTTTACGGCATATGACG
*
32978881 TATTAGATCCTCCGGATACATGAAACTTG
66 TATTAGATCCTCCGAATACATGAAACTTG
* **
32978910 ACTTGAACTCGAACTTGAATAATCACATTTAAAATCGAGCATGATTATTTTTACGGCATATGGTG
1 ACTTGAACTCGAACCTGAATAATCACATTTAAAATCGAGCATGATTATTTTTACGGCATATGACG
32978975 TATTAGATCCTCCGAATACAT
66 TATTAGATCCTCCGAATACAT
32978996 TATATATGTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (94 bp):
ACTTGAACTCGAACCTGAATAATCACATTTAAAATCGAGCATGATTATTTTTACGGCATATGACG
TATTAGATCCTCCGAATACATGAAACTTG
Found at i:32987540 original size:7 final size:7
Alignment explanation
Indices: 32987525--32987563 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
32987515 GAGTCTTGAT
32987525 TTTAGGG
1 TTTAGGG
*
32987532 TTTATGG
1 TTTAGGG
*
32987539 TTTAGAG
1 TTTAGGG
32987546 TTTAGGG
1 TTTAGGG
*
32987553 TTTGGGG
1 TTTAGGG
32987560 TTTA
1 TTTA
32987564 TTATTTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:32987742 original size:7 final size:7
Alignment explanation
Indices: 32987730--32987914 Score: 131
Period size: 7 Copynumber: 26.6 Consensus size: 7
32987720 AATATATATA
32987730 TTTAGGG
1 TTTAGGG
32987737 TTTAGGG
1 TTTAGGG
*
32987744 TGTA-GG
1 TTTAGGG
*
32987750 TTTATGG
1 TTTAGGG
32987757 TTTAGGG
1 TTTAGGG
*
32987764 TTTAAGG
1 TTTAGGG
32987771 TTTAGGG
1 TTTAGGG
* *
32987778 TTTATGA
1 TTTAGGG
*
32987785 TTTAGTG
1 TTTAGGG
* **
32987792 TTAACAG
1 TTTAGGG
*
32987799 TTTAGTG
1 TTTAGGG
*
32987806 TTTACGG
1 TTTAGGG
32987813 TTTAGGG
1 TTTAGGG
* *
32987820 TGTA-TG
1 TTTAGGG
*
32987826 TTTATGG
1 TTTAGGG
*
32987833 TTTAGTG
1 TTTAGGG
* *
32987840 TTTATGA
1 TTTAGGG
32987847 TTTAGGG
1 TTTAGGG
*
32987854 TTTAGGC
1 TTTAGGG
*
32987861 TTTAGTG
1 TTTAGGG
*
32987868 TTTATGG
1 TTTAGGG
32987875 TTTAGGGG
1 TTTA-GGG
*
32987883 TTAAGGG
1 TTTAGGG
* *
32987890 ATTATGG
1 TTTAGGG
*
32987897 TTTAGGA
1 TTTAGGG
32987904 TTTAGGG
1 TTTAGGG
32987911 TTTA
1 TTTA
32987915 AGGTGTAACA
Statistics
Matches: 131, Mismatches: 44, Indels: 6
0.72 0.24 0.03
Matches are distributed among these distances:
6 9 0.07
7 117 0.89
8 5 0.04
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:32987829 original size:62 final size:62
Alignment explanation
Indices: 32987763--32987881 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
32987753 ATGGTTTAGG
*
32987763 GTTTAAGGTTTAGGGTTTATGATTTAGTGTTAACAG-TTTAGTGTTTACGGTTTAGGGTGTAT
1 GTTTAAGGTTTAGGGTTTATGATTTAGGGTTAA-AGCTTTAGTGTTTACGGTTTAGGGTGTAT
* * * * *
32987825 GTTTATGGTTTAGTGTTTATGATTTAGGGTTTAGGCTTTAGTGTTTATGGTTTAGGG
1 GTTTAAGGTTTAGGGTTTATGATTTAGGGTTAAAGCTTTAGTGTTTACGGTTTAGGG
32987882 GTTAAGGGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
61 1 0.02
62 49 0.98
ACGTcount: A:0.18, C:0.03, G:0.30, T:0.49
Consensus pattern (62 bp):
GTTTAAGGTTTAGGGTTTATGATTTAGGGTTAAAGCTTTAGTGTTTACGGTTTAGGGTGTAT
Found at i:32988972 original size:18 final size:18
Alignment explanation
Indices: 32988949--32988995 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
32988939 ATAGTGTGAA
32988949 ACGATCTCC-GACATCCTT
1 ACGATC-CCTGACATCCTT
32988967 ACGATCCCTGACATCCTT
1 ACGATCCCTGACATCCTT
32988985 ACGATCCCTGA
1 ACGATCCCTGA
32988996 ATTTGCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (18 bp):
ACGATCCCTGACATCCTT
Found at i:32989165 original size:20 final size:20
Alignment explanation
Indices: 32989140--32989178 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
32989130 TCGCTTCTTT
32989140 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
32989160 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
32989179 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:32993538 original size:161 final size:159
Alignment explanation
Indices: 32993337--32993660 Score: 567
Period size: 161 Copynumber: 2.0 Consensus size: 159
32993327 AAGGTAGTGT
*
32993337 AGAGGATTTTTATAGAAAGTTTGCGGCTTTTGAGAAGCAATATGGAGAAAAGGAAGGGATTGAGG
1 AGAGGATTGTTATAGAAAGTTTGCGGCTTTTGAGAAGCAATATGGAGAAAAGGAAGGGATTGAGG
* *
32993402 ATGCCATTGTGGGGAAGAGGAGGTTTCAGTATGAGGATGAAGTCAGGAAGAATCCATTGAATTAT
66 ATGCCATTGTAGGGAAGAAGAGGTTTCAGTATGAGGATGAAGTCAGGAAGAATCCATTGAATTAT
32993467 GATGCTTGGTTTGATTATATAAGGTTGGA
131 GATGCTTGGTTTGATTATATAAGGTTGGA
* * *
32993496 AGAGGATTGTTATAGAAACTTTTTGTGGCTTTTGAGAAGCAATATGGAGATAAGGAAGGGATTGA
1 AGAGGATTGTTATAGAAA--GTTTGCGGCTTTTGAGAAGCAATATGGAGAAAAGGAAGGGATTGA
*
32993561 GGATGCCATTGTAGGGAAGAAGAGGTTTTAGTATGAGGATGAAGTCAGGAAGAATCCATTGAATT
64 GGATGCCATTGTAGGGAAGAAGAGGTTTCAGTATGAGGATGAAGTCAGGAAGAATCCATTGAATT
32993626 ATGATGCTTGGTTTGATTATATAAGGTTGGA
129 ATGATGCTTGGTTTGATTATATAAGGTTGGA
32993657 AGAG
1 AGAG
32993661 AGTGTAGGCA
Statistics
Matches: 156, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
159 17 0.11
161 139 0.89
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (159 bp):
AGAGGATTGTTATAGAAAGTTTGCGGCTTTTGAGAAGCAATATGGAGAAAAGGAAGGGATTGAGG
ATGCCATTGTAGGGAAGAAGAGGTTTCAGTATGAGGATGAAGTCAGGAAGAATCCATTGAATTAT
GATGCTTGGTTTGATTATATAAGGTTGGA
Found at i:32995298 original size:34 final size:34
Alignment explanation
Indices: 32995238--32995302 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
32995228 TCTACCAAAG
* * *
32995238 TTAGTGGCGTTTTCCCATAAATGCCACTAAAGAA
1 TTAGTGGCGTTTTCCAAAAAAAGCCACTAAAGAA
32995272 TTAGTGGCGTTTGT-CAAAAAAAGCCACTAAA
1 TTAGTGGCGTTT-TCCAAAAAAAGCCACTAAA
32995303 AGTCATTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (34 bp):
TTAGTGGCGTTTTCCAAAAAAAGCCACTAAAGAA
Found at i:32995368 original size:43 final size:43
Alignment explanation
Indices: 32995315--32995404 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
32995305 TCATTCTCTA
* * *
32995315 TAGCGACATTTGT-GATAAAAGCGCCAGTAAAGATCATGTTCTT
1 TAGCAACATTTGTGGAT-AAAGCACCACTAAAGATCATGTTCTT
* * *
32995358 TAGCAACATTTGTGGGTAAAGCACCCCTAAAGGTCATGTTCTT
1 TAGCAACATTTGTGGATAAAGCACCACTAAAGATCATGTTCTT
32995401 TAGC
1 TAGC
32995405 GATGTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 38 0.95
44 2 0.05
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (43 bp):
TAGCAACATTTGTGGATAAAGCACCACTAAAGATCATGTTCTT
Found at i:33004671 original size:56 final size:51
Alignment explanation
Indices: 33004500--33004755 Score: 309
Period size: 56 Copynumber: 4.8 Consensus size: 51
33004490 ATAATAACAA
* **
33004500 GCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTC-ATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCGGT
* * *
33004550 GCCAACGCAATGTCTCAGACATGGTCTTATGACATGGGACCTCTCG-TCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTC-T-T-ACATGGGACCTCTCGATCTCGGT
33004603 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--GATCTC--GG-T
33004659 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--GATCTC--GG-T
* *
33004715 GCCAATGCCATGTCCCAGACAGGGTCTTACATGGGATCTCT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
33004756 TTACGAAAAT
Statistics
Matches: 186, Mismatches: 10, Indels: 14
0.89 0.05 0.07
Matches are distributed among these distances:
50 37 0.20
51 2 0.01
52 3 0.02
53 46 0.25
55 2 0.01
56 96 0.52
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (51 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCGGT
Found at i:33008436 original size:17 final size:17
Alignment explanation
Indices: 33008414--33008448 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
33008404 TCTTTTACCA
33008414 GTAACTAGTAATAACCC
1 GTAACTAGTAATAACCC
*
33008431 GTAACTGGTAATAACCC
1 GTAACTAGTAATAACCC
33008448 G
1 G
33008449 ATCGGAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (17 bp):
GTAACTAGTAATAACCC
Found at i:33012200 original size:50 final size:50
Alignment explanation
Indices: 33012079--33012368 Score: 269
Period size: 50 Copynumber: 5.7 Consensus size: 50
33012069 ACATGCCTAA
* ** * * * *
33012079 GCCATGTCCGAGACATGGTCTTACATGGGATGTTTCGTGTAC--TTCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAAT
* * * ** *
33012128 GCCATATCCAAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * *
33012178 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * ** * * *
33012228 GCCATGTCTTAGATATGGTCTTACATGGGACCTCTTGTCTTGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
33012278 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG-TGCCAAT
*
33012334 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
33012369 TTACCCAAAT
Statistics
Matches: 196, Mismatches: 37, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 32 0.16
50 120 0.61
53 1 0.01
55 2 0.01
56 40 0.20
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
Found at i:33025633 original size:33 final size:33
Alignment explanation
Indices: 33025458--33025633 Score: 142
Period size: 33 Copynumber: 5.3 Consensus size: 33
33025448 TGTATAAATG
* *
33025458 TAAGACCATAGCTAGGCTATGGCATACTGATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
*
33025491 TAAGACCATAGCTGGTCTATGGCATTCTGATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
* * ** * * * *
33025524 TAAGACCGTAAC-AAGTTACGGCATTATGGACG-
1 TAAGACCATAGCTGGGCTATGGCATTCT-GATGA
* * * * *
33025556 TAAGACCATGGTTGGGCCATGGCAGTGTATACATG-
1 TAAGACCATAGCTGGGCTATGGCA-T-TCT-GATGA
*
33025591 TAAGACCATAGCTGGGCTATGGCGTTCTGATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
33025624 TAAGACCATA
1 TAAGACCATA
33025634 AATGGGTTAT
Statistics
Matches: 108, Mismatches: 30, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
32 20 0.19
33 61 0.56
34 2 0.02
35 25 0.23
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGGCATTCTGATGA
Found at i:33025661 original size:133 final size:133
Alignment explanation
Indices: 33025419--33025663 Score: 350
Period size: 133 Copynumber: 1.8 Consensus size: 133
33025409 CAACTATTCA
33025419 GACGTAAGACCATAGTTGGACCATGGCAGTGTATAAATGTAAGACCATAGCTAGGCTATGGCATA
1 GACGTAAGACCATAGTTGGACCATGGCAGTGTATAAATGTAAGACCATAGCTAGGCTATGGCATA
** * * *
33025484 CTGATGATAAGACCATAGCTGGTCTATGGCATTCTGATGATAAGACCGTAACAAGTTACGGCATT
66 CTGATGATAAGACCATAAATGGTCTATGACATTCTAACGATAAGACCGTAACAAGTTACGGCATT
33025549 ATG
131 ATG
* * * * * *
33025552 GACGTAAGACCATGGTTGGGCCATGGCAGTGTATACATGTAAGACCATAGCTGGGCTATGGCGTT
1 GACGTAAGACCATAGTTGGACCATGGCAGTGTATAAATGTAAGACCATAGCTAGGCTATGGCATA
*
33025617 CTGATGATAAGACCATAAATGGGT-TATGACATTATTAACG-TAAGACC
66 CTGATGATAAGACCATAAAT-GGTCTATGACATT-CTAACGATAAGACC
33025664 ATGGCAGAGC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
133 92 0.94
134 6 0.06
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (133 bp):
GACGTAAGACCATAGTTGGACCATGGCAGTGTATAAATGTAAGACCATAGCTAGGCTATGGCATA
CTGATGATAAGACCATAAATGGTCTATGACATTCTAACGATAAGACCGTAACAAGTTACGGCATT
ATG
Found at i:33041040 original size:58 final size:57
Alignment explanation
Indices: 33040978--33041100 Score: 167
Period size: 57 Copynumber: 2.1 Consensus size: 57
33040968 ATAGAAATGG
* * *
33040978 TGAAAATGGAGAAATGAGAAA-CATTTGGAAATGATTATGATTTTTTTCAAAATGAAAA
1 TGAAAATGGAGAAA--AGAAATCATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
** *
33041036 TGAAAATATAGAAAAGAAATCATTTGGAAATGAATGTGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAAAGAAATCATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
33041093 TGAAAATG
1 TGAAAATG
33041101 ACCTAAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
56 5 0.09
57 40 0.70
58 12 0.21
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (57 bp):
TGAAAATGGAGAAAAGAAATCATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
Found at i:33045435 original size:18 final size:19
Alignment explanation
Indices: 33045398--33045435 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
33045388 GACTCTCATG
*
33045398 GAGTAAGTTTCTTTTAAACT
1 GAGTAAGTTTC-TATAAACT
33045418 GAGTAAGTTTC-ATAAACT
1 GAGTAAGTTTCTATAAACT
33045436 ACTCCTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (19 bp):
GAGTAAGTTTCTATAAACT
Found at i:33058803 original size:14 final size:14
Alignment explanation
Indices: 33058784--33058810 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33058774 GTGGTCCAGT
33058784 TGAACTGAACCGAG
1 TGAACTGAACCGAG
33058798 TGAACTGAACCGA
1 TGAACTGAACCGA
33058811 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:33065010 original size:27 final size:27
Alignment explanation
Indices: 33064980--33065033 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
33064970 CTAATAAACC
* * * *
33064980 ATAAAATAGATTAATGAGATAAATAAA
1 ATAAAATAAATAAATAAGAAAAATAAA
33065007 ATAAAATAAATAAATAAGAAAAATAAA
1 ATAAAATAAATAAATAAGAAAAATAAA
33065034 CAAAGAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (27 bp):
ATAAAATAAATAAATAAGAAAAATAAA
Found at i:33065031 original size:17 final size:17
Alignment explanation
Indices: 33064998--33065054 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
33064988 GATTAATGAG
33064998 ATAAATAAAATAAAATAA
1 ATAAATAAAA-AAAATAA
*
33065016 ATAAATAAGAAAAATAA
1 ATAAATAAAAAAAATAA
* * * *
33065033 ACAAAGAATAAAAATTA
1 ATAAATAAAAAAAATAA
33065050 ATAAA
1 ATAAA
33065055 CTAATCAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (17 bp):
ATAAATAAAAAAAATAA
Found at i:33067470 original size:32 final size:34
Alignment explanation
Indices: 33067407--33067470 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 34
33067397 TTGTAAAGAC
*
33067407 ATAACTTTTGTATGTAAAGTTGTCTTATAAAAAT
1 ATAACTTTTGTATGTAAAGTTATCTTATAAAAAT
* * *
33067441 ATAAC-TTT-TATGTAAGGTTATTTTTTAAAA
1 ATAACTTTTGTATGTAAAGTTATCTTATAAAA
33067471 TAACACAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 18 0.69
33 3 0.12
34 5 0.19
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (34 bp):
ATAACTTTTGTATGTAAAGTTATCTTATAAAAAT
Found at i:33071940 original size:25 final size:25
Alignment explanation
Indices: 33071912--33071959 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33071902 CAAATGTTTC
*
33071912 ATTTGAAAATTTTAAAACTTTTCTT
1 ATTTGAAAATTATAAAACTTTTCTT
* *
33071937 ATTTGATAATTATAATACTTTTC
1 ATTTGAAAATTATAAAACTTTTC
33071960 AGAAATCGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTTGAAAATTATAAAACTTTTCTT
Found at i:33075025 original size:2 final size:2
Alignment explanation
Indices: 33075018--33075049 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33075008 TTATAAAATA
33075018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33075050 GAAATAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33075108 original size:24 final size:24
Alignment explanation
Indices: 33075044--33075114 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 24
33075034 ATATATATAT
*
33075044 ATATAT-GAAATAGAATGAAAATA
1 ATATATGGAAATAAAATGAAAATA
*
33075067 GTATATGGAAAATCAAAATGAAAAGTA
1 ATATATGG-AAAT-AAAATGAAAA-TA
33075094 ATA-ATGGAAATAAAAT-AAAAT
1 ATATATGGAAATAAAATGAAAAT
33075115 TTTAAAGGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.02
23 9 0.22
24 6 0.15
25 8 0.20
26 13 0.32
27 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.14, T:0.24
Consensus pattern (24 bp):
ATATATGGAAATAAAATGAAAATA
Found at i:33075902 original size:19 final size:21
Alignment explanation
Indices: 33075880--33075928 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
33075870 ATTATATAAA
33075880 TGTTTATATTTTA-ATTT-AT
1 TGTTTATATTTTAGATTTGAT
* *
33075899 TGTTAATA-GTTAGATTTGAT
1 TGTTTATATTTTAGATTTGAT
33075919 T-TTTATATTT
1 TGTTTATATTT
33075929 AATATTTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (21 bp):
TGTTTATATTTTAGATTTGAT
Found at i:33078545 original size:2 final size:2
Alignment explanation
Indices: 33078532--33078562 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
33078522 CGCATTGAAG
33078532 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
33078563 TAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33084905 original size:26 final size:26
Alignment explanation
Indices: 33084874--33084937 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
33084864 TGACCTGCAA
*
33084874 CTCGTGTGAGCAG-GCTCATTTCACAG
1 CTCGTGTGAGCAGACCT-ATTTCACAG
*
33084900 CTCGTGTGAGCATACCTATTTCACAG
1 CTCGTGTGAGCAGACCTATTTCACAG
*
33084926 CTCGTATGAGCA
1 CTCGTGTGAGCA
33084938 ACTATGTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 32 0.94
27 2 0.06
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (26 bp):
CTCGTGTGAGCAGACCTATTTCACAG
Found at i:33095728 original size:20 final size:20
Alignment explanation
Indices: 33095703--33095741 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
33095693 TACTTTCTTC
33095703 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
33095723 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
33095742 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:33097538 original size:51 final size:50
Alignment explanation
Indices: 33097480--33097704 Score: 249
Period size: 51 Copynumber: 4.4 Consensus size: 50
33097470 TTTGGGGGTT
* * * * * *
33097480 TTCACATAGTACCACCCATGTTACTATTATCATTCGATACACGTAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTAT-TTTCGATACACGTAGTAGCC
* * *
33097531 TTCACATAGTACTACACACGTTACCA--AGTTTTACGGTTCACGTAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTA-TTTT-CGATACACGTAGTAGCC
* * *
33097581 TCCACATAGTACTACACACGTGACCA-GAGCTTTTCGATACACATAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTA--TTTTCGATACACGTAGTAGCC
* *
33097632 TTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAGTAGCC
1 TTCACATAGTACTACACACGTGACCATTATTT-TCGATACACGTAGTAGCC
33097683 TTCACATAGTACTACACACGTG
1 TTCACATAGTACTACACACGTG
33097705 TTCATCAATA
Statistics
Matches: 148, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.02
50 43 0.29
51 97 0.66
52 5 0.03
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (50 bp):
TTCACATAGTACTACACACGTGACCATTATTTTCGATACACGTAGTAGCC
Found at i:33099528 original size:5 final size:5
Alignment explanation
Indices: 33099520--33099545 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33099510 GAGATGGAAT
33099520 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
33099546 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:33099545 original size:26 final size:26
Alignment explanation
Indices: 33099494--33099545 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
33099484 TGAAGTTTTC
* * *
33099494 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
33099520 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
33099546 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:33100243 original size:31 final size:31
Alignment explanation
Indices: 33100186--33100245 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
33100176 AGAGGTGGGA
*
33100186 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
33100217 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
33100246 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:33100564 original size:9 final size:9
Alignment explanation
Indices: 33100547--33100577 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33100537 TCAGGTTGAT
33100547 TCGAATAAC
1 TCGAATAAC
*
33100556 TCGATTAAC
1 TCGAATAAC
33100565 TCGAATAAC
1 TCGAATAAC
33100574 TCGA
1 TCGA
33100578 TTCGTTTAAC
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:33103675 original size:26 final size:26
Alignment explanation
Indices: 33103646--33103716 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
33103636 ATAAAATGAC
33103646 GCTTTTGTGGCTACCTC-GAAAAGGAT
1 GCTTTTGTGGCTACCTCTG-AAAGGAT
* * *
33103672 GCTTTTATGGTTATCTCTGAAAGGAT
1 GCTTTTGTGGCTACCTCTGAAAGGAT
* *
33103698 GCATTTGTGGCTATCTCTG
1 GCTTTTGTGGCTACCTCTG
33103717 TTAAAAATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 37 0.97
27 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (26 bp):
GCTTTTGTGGCTACCTCTGAAAGGAT
Found at i:33103898 original size:29 final size:28
Alignment explanation
Indices: 33103862--33103982 Score: 93
Period size: 28 Copynumber: 4.3 Consensus size: 28
33103852 TTCCATAAGA
*
33103862 AAGCCTTTGTGGCGATCTCTGTTAAAAGG
1 AAGCCTTTGTGGCAATCTCTG-TAAAAGG
* * * *
33103891 AAGCCTTTATAGCAATCTCTGTCAAATG
1 AAGCCTTTGTGGCAATCTCTGTAAAAGG
* ** *
33103919 ATGCCTTTGTGGCAATCTCCATCAAAGG
1 AAGCCTTTGTGGCAATCTCTGTAAAAGG
* * *
33103947 ACGCTTTTGTGGCAAGACTC--TAAAAGG
1 AAGCCTTTGTGGCAA-TCTCTGTAAAAGG
33103974 AAAGCCTTT
1 -AAGCCTTT
33103983 TTGCTATCTT
Statistics
Matches: 73, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
27 6 0.08
28 46 0.63
29 21 0.29
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (28 bp):
AAGCCTTTGTGGCAATCTCTGTAAAAGG
Found at i:33103933 original size:28 final size:28
Alignment explanation
Indices: 33103862--33103961 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
33103852 TTCCATAAGA
* *
33103862 AAGCCTTTGTGGCGATCTCTGTTAAAAGG
1 AAGCCTTTGTGGCAATCTCTG-TCAAAGG
* * *
33103891 AAGCCTTTATAGCAATCTCTGTCAAATG
1 AAGCCTTTGTGGCAATCTCTGTCAAAGG
* **
33103919 ATGCCTTTGTGGCAATCTCCATCAAAGG
1 AAGCCTTTGTGGCAATCTCTGTCAAAGG
* *
33103947 ACGCTTTTGTGGCAA
1 AAGCCTTTGTGGCAA
33103962 GACTCTAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 40 0.69
29 18 0.31
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (28 bp):
AAGCCTTTGTGGCAATCTCTGTCAAAGG
Found at i:33105875 original size:23 final size:24
Alignment explanation
Indices: 33105849--33105894 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
33105839 GGGTGGAAAT
33105849 AAGGAGGGTTTAAG-GGTAAAAAC
1 AAGGAGGGTTTAAGAGGTAAAAAC
** *
33105872 AAGGATTGTTTAAGAGGTTAAAA
1 AAGGAGGGTTTAAGAGGTAAAAA
33105895 TGCTCAGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.24
Consensus pattern (24 bp):
AAGGAGGGTTTAAGAGGTAAAAAC
Found at i:33111337 original size:12 final size:12
Alignment explanation
Indices: 33111320--33111346 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33111310 AAATTGAATC
33111320 TAGATAAATGTA
1 TAGATAAATGTA
33111332 TAGATAAATGTA
1 TAGATAAATGTA
33111344 TAG
1 TAG
33111347 GAGTGAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (12 bp):
TAGATAAATGTA
Found at i:33114782 original size:97 final size:91
Alignment explanation
Indices: 33114668--33114849 Score: 242
Period size: 92 Copynumber: 1.9 Consensus size: 91
33114658 TTCCAGAAAT
* *
33114668 CGCCGCAAAAAACCTAAGCCCAATGACGCCGTTTTCCT-AGCTTTCGGGGATTTAGCGACG-TTT
1 CGCCGCAAAAAACCTAAGCCCAACGACG-C----T-CTGAGCTTTAGGGGATTTAGCGACGCTTT
33114731 TTAAGAAAGCGCCGCTAATGCTCAGGGCAAAAA
60 TTAA-AAAGCGCCGCTAATGCTCAGGGCAAAAA
* *
33114764 CGCCGCAAAAAAACCTAAGCCCAACGACGCTCTGAGCTTTAGGGGATTTAGCGGCGCTTTTTTAA
1 CGCCGC-AAAAAACCTAAGCCCAACGACGCTCTGAGCTTTAGGGGATTTAGCGACGCTTTTTAAA
33114829 AAGCGCCGCTAATGCTCAGGG
65 AAGCGCCGCTAATGCTCAGGG
33114850 ATTTAGCGGC
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
91 2 0.03
92 43 0.54
93 6 0.08
96 7 0.09
97 21 0.27
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.21
Consensus pattern (91 bp):
CGCCGCAAAAAACCTAAGCCCAACGACGCTCTGAGCTTTAGGGGATTTAGCGACGCTTTTTAAAA
AGCGCCGCTAATGCTCAGGGCAAAAA
Found at i:33114952 original size:106 final size:106
Alignment explanation
Indices: 33114799--33114991 Score: 298
Period size: 106 Copynumber: 1.8 Consensus size: 106
33114789 GACGCTCTGA
* * * *
33114799 GCTTTAGGGGATTTAGCGGCGCTTTTTTAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTT
1 GCTTTAGGGGATTTAGCGGCGATTTTTAAAAAGCGCCGCTAATGCTCAAGGATTTAGCGACGTTT
33114864 TTGAGAAAGCGCCGCAAAAAAAAAACTTAAGCCCAATTAAT
66 TTGAGAAAGCGCCGCAAAAAAAAAACTTAAGCCCAATTAAT
* * *
33114905 GCTTTCGGGGATTTAGCGGC-ATTTTTAAGAAAGCGTCGCTAATGCTCAAGGCTTTAGCGACGTT
1 GCTTTAGGGGATTTAGCGGCGATTTTTAA-AAAGCGCCGCTAATGCTCAAGGATTTAGCGACGTT
*
33114969 TTTGGGAAAGCGCCGCAAAAAAA
65 TTTGAGAAAGCGCCGCAAAAAAA
33114992 CCTAAGCCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 6 0.08
106 72 0.92
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (106 bp):
GCTTTAGGGGATTTAGCGGCGATTTTTAAAAAGCGCCGCTAATGCTCAAGGATTTAGCGACGTTT
TTGAGAAAGCGCCGCAAAAAAAAAACTTAAGCCCAATTAAT
Found at i:33115078 original size:74 final size:73
Alignment explanation
Indices: 33114957--33115120 Score: 274
Period size: 74 Copynumber: 2.2 Consensus size: 73
33114947 TGCTCAAGGC
* ** *
33114957 TTTAGCGACGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
33115022 TTCGGGTGA
66 TTCGGG-GA
*
33115031 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAATAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
33115096 TTCGGGGA
66 TTCGGGGA
33115104 TTTAGCGGCGTTTTTAA
1 TTTAGCGGCGTTTTTAA
33115121 TAATTTGTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 19 0.22
74 66 0.78
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGA
Found at i:33115139 original size:13 final size:13
Alignment explanation
Indices: 33115121--33115209 Score: 98
Period size: 13 Copynumber: 7.2 Consensus size: 13
33115111 GCGTTTTTAA
33115121 TAATTTGTCTATT
1 TAATTTGTCTATT
33115134 TAA--T-T-TATT
1 TAATTTGTCTATT
*
33115143 TAATTTGTTTATT
1 TAATTTGTCTATT
* *
33115156 T-ATTTAATTTATT
1 TAATTT-GTCTATT
33115169 TAATTTGTCTATT
1 TAATTTGTCTATT
33115182 TAATTTGTCTATT
1 TAATTTGTCTATT
*
33115195 TAATTTGTTTATT
1 TAATTTGTCTATT
33115208 TA
1 TA
33115210 TATTAATTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
9 7 0.11
10 1 0.02
11 2 0.03
12 5 0.08
13 47 0.71
14 4 0.06
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (13 bp):
TAATTTGTCTATT
Found at i:33115144 original size:9 final size:9
Alignment explanation
Indices: 33115130--33115217 Score: 76
Period size: 9 Copynumber: 10.0 Consensus size: 9
33115120 ATAATTTGTC
33115130 TATTTAATT
1 TATTTAATT
33115139 TATTTAATT
1 TATTTAATT
*
33115148 TGTTT-ATT
1 TATTTAATT
33115156 TATTTAATT
1 TATTTAATT
33115165 TATTTAATT
1 TATTTAATT
* *
33115174 TGTCT-ATT
1 TATTTAATT
* *
33115182 TAATTT-GTC
1 T-ATTTAATT
33115191 TATTTAATT
1 TATTTAATT
*
33115200 TGTTT-ATT
1 TATTTAATT
33115208 TATATTAATT
1 TAT-TTAATT
33115218 AAAATTCAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
8 20 0.32
9 39 0.63
10 3 0.05
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:33115161 original size:26 final size:26
Alignment explanation
Indices: 33115130--33115217 Score: 124
Period size: 26 Copynumber: 3.3 Consensus size: 26
33115120 ATAATTTGTC
33115130 TATTTAATTTATTTAATTTGTTTATT
1 TATTTAATTTATTTAATTTGTTTATT
*
33115156 TATTTAATTTATTTAATTTGTCTATT
1 TATTTAATTTATTTAATTTGTTTATT
* *
33115182 TAATTT-GTCTATTTAATTTGTTTATT
1 T-ATTTAATTTATTTAATTTGTTTATT
33115208 TATATTAATT
1 TAT-TTAATT
33115218 AAAATTCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
25 2 0.04
26 46 0.87
27 5 0.09
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (26 bp):
TATTTAATTTATTTAATTTGTTTATT
Found at i:33115176 original size:48 final size:52
Alignment explanation
Indices: 33115121--33115217 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
33115111 GCGTTTTTAA
33115121 TAATTTGTCTATTTAA-T-T-TATTTAATTTGTTTATTTAT-TTAATTTATT
1 TAATTTGTCTATTTAATTGTCTATTTAATTTGTTTATTTATATTAATTTATT
33115169 TAATTTGTCTATTTAATTTGTCTATTTAATTTGTTTATTTATATTAATT
1 TAATTTGTCTATTTAA-TTGTCTATTTAATTTGTTTATTTATATTAATT
33115218 AAAATTCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
48 16 0.36
50 1 0.02
51 1 0.02
52 20 0.45
53 6 0.14
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (52 bp):
TAATTTGTCTATTTAATTGTCTATTTAATTTGTTTATTTATATTAATTTATT
Found at i:33115219 original size:22 final size:21
Alignment explanation
Indices: 33115116--33115169 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
33115106 TAGCGGCGTT
33115116 TTTAA-TAATTTGTCTATTTAA
1 TTTAATTAATTTGTCTATTT-A
* *
33115137 TTTATTTAATTTGTTTATTTA
1 TTTAATTAATTTGTCTATTTA
*
33115158 TTTAATTTATTT
1 TTTAATTAATTT
33115170 AATTTGTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTAATTAATTTGTCTATTTA
Found at i:33115594 original size:14 final size:15
Alignment explanation
Indices: 33115565--33115598 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
33115555 TAAGGTTTAT
33115565 AGATTATGGAATTAG
1 AGATTATGGAATTAG
33115580 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
33115594 AGATT
1 AGATT
33115599 CTGGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:33120025 original size:43 final size:43
Alignment explanation
Indices: 33119964--33120099 Score: 130
Period size: 43 Copynumber: 3.2 Consensus size: 43
33119954 TGTTTTTAGT
* * * * * *
33119964 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGTCTTGATCTTTAGT
1 GGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGATCTATAGC
* * *** *
33120007 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCCAACCTATAGC
1 GGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGATCTATAGC
* *
33120050 GGCGTTTGTGAAAAAAGCAAT-GCTAAAGGTCATGATCTATAGC
1 GGCGTTTGTGAGAAAAGC-GTCGCTAAAGGTCATGATCTATAGC
33120093 GGCGTTT
1 GGCGTTT
33120100 ATTTCTAAAA
Statistics
Matches: 74, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGATCTATAGC
Found at i:33120808 original size:19 final size:20
Alignment explanation
Indices: 33120763--33120808 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
33120753 CTGAAAACTC
33120763 ATATTTAATAATAAGTTTTA
1 ATATTTAATAATAAGTTTTA
* *
33120783 ACA-TTAATAAT-ATTTTTA
1 ATATTTAATAATAAGTTTTA
33120801 ATATTTAA
1 ATATTTAA
33120809 AAAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 8 0.36
19 12 0.55
20 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTTAATAATAAGTTTTA
Found at i:33121845 original size:23 final size:23
Alignment explanation
Indices: 33121819--33121867 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
33121809 ATTCAGATAC
33121819 AATAAAATACCATCT-TTTCTAAA
1 AATAAAAT-CCATCTATTTCTAAA
* *
33121842 AATAAAATTCATCTATTTTTAAA
1 AATAAAATCCATCTATTTCTAAA
33121865 AAT
1 AAT
33121868 TCTTTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAAAATCCATCTATTTCTAAA
Found at i:33122191 original size:22 final size:24
Alignment explanation
Indices: 33122166--33122219 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
33122156 ACCATTTTCT
33122166 ATATTTATTTTTTAATTTTT-TAA
1 ATATTTATTTTTTAATTTTTATAA
*
33122189 TATATATATTTTTTAATTTTTATAA
1 -ATATTTATTTTTTAATTTTTATAA
33122214 ATATTT
1 ATATTT
33122220 TGAATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATATTTATTTTTTAATTTTTATAA
Found at i:33122212 original size:16 final size:16
Alignment explanation
Indices: 33122169--33122212 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
33122159 ATTTTCTATA
*
33122169 TTTATTTTTTA-ATTT
1 TTTAATTTTTATATTT
* *
33122184 TTTAATATATATATTT
1 TTTAATTTTTATATTT
33122200 TTTAATTTTTATA
1 TTTAATTTTTATA
33122213 AATATTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAATTTTTATATTT
Found at i:33122246 original size:19 final size:18
Alignment explanation
Indices: 33122199--33122246 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
33122189 TATATATATT
33122199 TTTTAATTTTTATAAATA
1 TTTTAATTTTTATAAATA
33122217 TTTTGAA-TTTTA-AAATTTA
1 TTTT-AATTTTTATAAA--TA
33122236 TTTTAATTTTT
1 TTTTAATTTTT
33122247 TTATTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.12
18 11 0.42
19 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTAATTTTTATAAATA
Found at i:33122252 original size:18 final size:18
Alignment explanation
Indices: 33122199--33122252 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
33122189 TATATATATT
**
33122199 TTTTAATTTTTATAAATA
1 TTTTAATTTTTATATTTA
* *
33122217 TTTTGAATTTTAAAATTTA
1 TTTT-AATTTTTATATTTA
*
33122236 TTTTAATTTTTTTATTT
1 TTTTAATTTTTATATTT
33122253 GTTGTTGAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTAATTTTTATATTTA
Found at i:33123923 original size:29 final size:30
Alignment explanation
Indices: 33123891--33124077 Score: 114
Period size: 30 Copynumber: 6.3 Consensus size: 30
33123881 TCGATTATGG
*
33123891 AAAGGGATGGTGACTACCATC-AACAATGA
1 AAAGGGATGGTGACGACCATCAAACAATGA
*
33123920 AAAGGGATAGTGACGACCATCAAACAATGA
1 AAAGGGATGGTGACGACCATCAAACAATGA
* * * * ***
33123950 AAAGAGATGGCT-TC-AGCTATCGATTTATGA
1 AAAGGGATGG-TGACGA-CCATCAAACAATGA
* * * ** **
33123980 AAAGGGATAGCT-TCGACTATCAAATTACAA
1 AAAGGGAT-GGTGACGACCATCAAACAATGA
* *
33124010 AAAGGGATGGTGACGACCACCGAACAATGA
1 AAAGGGATGGTGACGACCATCAAACAATGA
* * *
33124040 AAAGGGTTGGTGATGACCATC-AACTTATGA
1 AAAGGGATGGTGACGACCATCAAAC-AATGA
33124070 AAAGGGAT
1 AAAGGGAT
33124078 AGTTTCGGCT
Statistics
Matches: 121, Mismatches: 30, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
29 25 0.21
30 93 0.77
31 3 0.02
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.20
Consensus pattern (30 bp):
AAAGGGATGGTGACGACCATCAAACAATGA
Found at i:33124040 original size:60 final size:59
Alignment explanation
Indices: 33123858--33124045 Score: 168
Period size: 60 Copynumber: 3.2 Consensus size: 59
33123848 GCTAACGAAT
* *
33123858 ATGAAAAGGGATAGCTTCGACTATC-GATTATGGAAAGGGATGGTGACTACCATC-AACA
1 ATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGAC-ACCATCGAACA
* * ** * * * ***
33123916 ATGAAAAGGGATAG-TGACGACCATCAAACAATGAAAAGAGATGGCT-TCAGCTATCGATTT
1 ATGAAAAGGGATAGCT-TCGACTATCAAATTATGAAAAGGGATGG-TGACA-CCATCGAACA
** *
33123976 ATGAAAAGGGATAGCTTCGACTATCAAATTACAAAAAGGGATGGTGACGACCACCGAACA
1 ATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGAC-ACCATCGAACA
33124036 ATGAAAAGGG
1 ATGAAAAGGG
33124046 TTGGTGATGA
Statistics
Matches: 97, Mismatches: 25, Indels: 14
0.71 0.18 0.10
Matches are distributed among these distances:
57 1 0.01
58 22 0.23
59 19 0.20
60 53 0.55
61 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (59 bp):
ATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACACCATCGAACA
Found at i:33125168 original size:12 final size:12
Alignment explanation
Indices: 33125151--33125180 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33125141 TCAAGCAATT
33125151 ACACGGCCTAGC
1 ACACGGCCTAGC
*
33125163 ACACGGCCTGGC
1 ACACGGCCTAGC
33125175 ACACGG
1 ACACGG
33125181 GTGTGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:33131610 original size:30 final size:29
Alignment explanation
Indices: 33131537--33131611 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
33131527 GGCTATCGAT
*
33131537 TATGAAAAGGGATGGTGATGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* *
33131566 AAAGAAAAGGGATGGTGACGACCATCAAAC
1 TATGAAAAGGGATGGTGACGACCATC-AAC
*
33131596 TATGAAAAGAGATGGT
1 TATGAAAAGGGATGGT
33131612 TTCGGCTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.43, C:0.12, G:0.28, T:0.17
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:33131698 original size:31 final size:30
Alignment explanation
Indices: 33131584--33131699 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 30
33131574 GGGATGGTGA
* * * * *
33131584 CGACCATCAAACTATGAAAAGAGATGGTTT
1 CGACTATCGAACTATGAAAAGGGATAGCTT
* * ** *
33131614 CGGCTATTGATTTATTAAAAGGGATAGCTT
1 CGACTATCGAACTATGAAAAGGGATAGCTT
* *
33131644 CGACTATCGAATTTTGAAAAGGGATAGCTT
1 CGACTATCGAACTATGAAAAGGGATAGCTT
*
33131674 C-ATCTGTCGAACTATGAAAAAGGGAT
1 CGA-CTATCGAACTATG-AAAAGGGAT
33131700 TATGATCTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 56 0.85
31 9 0.14
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (30 bp):
CGACTATCGAACTATGAAAAGGGATAGCTT
Found at i:33139768 original size:7 final size:7
Alignment explanation
Indices: 33139756--33139786 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
33139746 TTTGGTTGTA
33139756 ATTGGAC
1 ATTGGAC
33139763 ATTGGAC
1 ATTGGAC
33139770 ATTGGAC
1 ATTGGAC
33139777 ATTGGAC
1 ATTGGAC
33139784 ATT
1 ATT
33139787 TTATTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (7 bp):
ATTGGAC
Found at i:33142316 original size:25 final size:26
Alignment explanation
Indices: 33142266--33142318 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
33142256 AAAAGACACT
33142266 GTCTCACTTAAATACTAAAACGCATC
1 GTCTCACTTAAATACTAAAACGCATC
* * *
33142292 GTCTTACTTAAGTA-TAAAACTCATC
1 GTCTCACTTAAATACTAAAACGCATC
33142317 GT
1 GT
33142319 TTTAATAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (26 bp):
GTCTCACTTAAATACTAAAACGCATC
Found at i:33146442 original size:18 final size:19
Alignment explanation
Indices: 33146405--33146447 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
33146395 AAGTTCCATA
* *
33146405 TCTCAATTCATATTTCATT
1 TCTCATTTCATATATCATT
33146424 TCTCATTTCATA-ATCATT
1 TCTCATTTCATATATCATT
33146442 TCTCAT
1 TCTCAT
33146448 GTTTTCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (19 bp):
TCTCATTTCATATATCATT
Found at i:33146478 original size:43 final size:43
Alignment explanation
Indices: 33146422--33146507 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
33146412 TCATATTTCA
* * * *
33146422 TTTCTCATTTCATAATCATTTCTCATGTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATCTTTGCCATTTCAATAT
*
33146465 TTTCTCATCTCATATTCATTTATCATCTTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATCTTTGCCATTTCAATAT
33146508 CAATCACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTATCATCTTTGCCATTTCAATAT
Found at i:33146939 original size:25 final size:27
Alignment explanation
Indices: 33146901--33146951 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
33146891 CTCAATACAC
*
33146901 ATATATACATAATCAATATATTTCATA
1 ATATATACATAATCAATACATTTCATA
*
33146928 ATATATA-A-AATCAATCCATTTCAT
1 ATATATACATAATCAATACATTTCAT
33146952 TTCAATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 1 0.05
27 7 0.32
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATATACATAATCAATACATTTCATA
Found at i:33150257 original size:17 final size:18
Alignment explanation
Indices: 33150231--33150281 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
33150221 CTTCCATATC
33150231 AAAAAA-GAAAAAGAAAT
1 AAAAAAGGAAAAAGAAAT
33150248 -AAAAAGG-AAAAGAAAAT
1 AAAAAAGGAAAAAG-AAAT
*
33150265 AAAGAAAGTAAAAAGAA
1 AAA-AAAGGAAAAAGAA
33150282 CAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 10 0.36
17 5 0.18
18 2 0.07
19 6 0.21
20 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (18 bp):
AAAAAAGGAAAAAGAAAT
Found at i:33150286 original size:7 final size:6
Alignment explanation
Indices: 33150232--33150296 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
33150222 TTCCATATCA
* *
33150232 AAAAAG AAAAAG --AAAT AAAAAG GAAAAG AAAATA- AAGAAAG TAAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AA-AAAG -AAAAAG
33150280 AACAAAG AAAAAG AAAA
1 AA-AAAG AAAAAG AAAA
33150297 TAAAGAAAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
4 3 0.06
6 30 0.62
7 13 0.27
8 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:33150312 original size:18 final size:17
Alignment explanation
Indices: 33150257--33150312 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
33150247 TAAAAAGGAA
33150257 AAGAAAATAAAGAAAGT
1 AAGAAAATAAAGAAAGT
* *
33150274 AAAAAGAACAAAGAAA--
1 AAGAA-AATAAAGAAAGT
33150290 AAGAAAATAAAGAAAGT
1 AAGAAAATAAAGAAAGT
33150307 ATAGAA
1 A-AGAA
33150313 GGAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
17 5 0.16
18 13 0.42
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (17 bp):
AAGAAAATAAAGAAAGT
Found at i:33150723 original size:9 final size:9
Alignment explanation
Indices: 33150689--33150719 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
33150679 AATTCTGCCT
33150689 TTTTTATAA
1 TTTTTATAA
33150698 TTTTTATAA
1 TTTTTATAA
33150707 TTTTTA-AA
1 TTTTTATAA
33150715 TTTTT
1 TTTTT
33150720 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTATAA
Done.