Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010993.1 Corchorus capsularis cultivar CVL-1 contig11014, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 322808
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
File 1 of 2
Found at i:131 original size:14 final size:15
Alignment explanation
Indices: 103--131 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
93 GTGTGAATTC
103 AAATTGATCTTTTGA
1 AAATTGATCTTTTGA
118 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
132 TTAACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (15 bp):
AAATTGATCTTTTGA
Found at i:1229 original size:14 final size:15
Alignment explanation
Indices: 1201--1229 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1191 GTGTGAATTC
1201 AAATTGATCTTTTGA
1 AAATTGATCTTTTGA
1216 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
1230 TTAACTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (15 bp):
AAATTGATCTTTTGA
Found at i:6840 original size:21 final size:19
Alignment explanation
Indices: 6815--6853 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
6805 TATGACTCAT
6815 ATGCTATGAATGCTATGATTG
1 ATGCTATGAAT-CT-TGATTG
*
6836 ATGCTTTGAATCTTGATT
1 ATGCTATGAATCTTGATT
6854 TGCTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
ATGCTATGAATCTTGATTG
Found at i:9740 original size:57 final size:57
Alignment explanation
Indices: 9652--9765 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
9642 GTCATAGTTA
9652 ACAATCATTGCACGTACTACCAAAGGGTCATTGCTAGAGTCTTCGTAGATGTTCATG
1 ACAATCATTGCACGTACTACCAAAGGGTCATTGCTAGAGTCTTCGTAGATGTTCATG
9709 ACAATCATTGCACGTACTACCAAAGGGTCATTGCTAGAGTCTTCGTAGATGTTCATG
1 ACAATCATTGCACGTACTACCAAAGGGTCATTGCTAGAGTCTTCGTAGATGTTCATG
9766 TCCTCCTTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (57 bp):
ACAATCATTGCACGTACTACCAAAGGGTCATTGCTAGAGTCTTCGTAGATGTTCATG
Found at i:15754 original size:15 final size:15
Alignment explanation
Indices: 15730--15763 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
15720 TTATATATAG
*
15730 TAGTAGTAATAGTAA
1 TAGTAATAATAGTAA
15745 TAGTAATAATAGTAA
1 TAGTAATAATAGTAA
15760 TAGT
1 TAGT
15764 GATCGGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (15 bp):
TAGTAATAATAGTAA
Found at i:16136 original size:21 final size:21
Alignment explanation
Indices: 16110--16158 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
16100 GCACTGGAGT
* * *
16110 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
16131 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
16152 ACATGGG
1 ACATGGG
16159 CCCCTAGCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:18486 original size:17 final size:17
Alignment explanation
Indices: 18460--18496 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18450 TCCCTCTCAT
18460 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
*
18477 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATGA
18494 GGT
1 GGT
18497 TCTGGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.38, T:0.22
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:19086 original size:156 final size:154
Alignment explanation
Indices: 18823--19210 Score: 442
Period size: 156 Copynumber: 2.5 Consensus size: 154
18813 TTCAAGCCTT
* * *
18823 CCTTCATGGTGAACTAGGTTTCACACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
1 CCTTGATGGTGAACTAGGTTTCTCACCCCAAACTGTCCTT-AATGAAAAACTAGCATAAGTTTTT
* * * *
18888 CATTCTAAGTCTGAATGAGATGAAACTTTGCCACGAGACTTAGACTGTCTCCATAAGACTATTGA
65 CATTCTAAGTCTCAATAAGATG-AACTTTGCCACGAGACTTAGACTATCTCCATAAGACTATGGA
18953 AAAAATTCCAAGTAAAACCGACCTCC
129 AAAAATTCCAAGTAAAACCGACCTCC
* *
18979 CCTTGATGGTGAACTTGGTTTCTCTCCCCAAACTGTCCTTGAATGAAAAACTAGCATAAGTTTTT
1 CCTTGATGGTGAACTAGGTTTCTCACCCCAAACTGTCCTT-AATGAAAAACTAGCATAAGTTTTT
* * * * *
19044 CATTCTAAGTC-CAATAAGGCTG-A-TTTTCCACCAGTAGGCTTAGATTATTTCCATAAGACTAT
65 CATTCTAAGTCTCAATAA-GATGAACTTTGCCA-C-G-AGACTTAGACTATCTCCATAAGACTAT
* * * *
19106 GGAAAAGATTCTAAGTAAAACCGAGCTCT
126 GGAAAAAATTCCAAGTAAAACCGACCTCC
** * ** * *
19135 CCTTGATAATGAAC-CGACTTCTCACCTCAAACTGTCCTTAACTGAAAAACTAACATAAGTTTTT
1 CCTTGATGGTGAACTAGGTTTCTCACCCCAAACTGTCCTTAA-TGAAAAACTAGCATAAGTTTTT
*
19199 CATACTAAGTCT
65 CATTCTAAGTCT
19211 GCTTGAGATG
Statistics
Matches: 198, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
153 6 0.03
154 4 0.02
155 56 0.28
156 132 0.67
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (154 bp):
CCTTGATGGTGAACTAGGTTTCTCACCCCAAACTGTCCTTAATGAAAAACTAGCATAAGTTTTTC
ATTCTAAGTCTCAATAAGATGAACTTTGCCACGAGACTTAGACTATCTCCATAAGACTATGGAAA
AAATTCCAAGTAAAACCGACCTCC
Found at i:24768 original size:162 final size:162
Alignment explanation
Indices: 24489--24966 Score: 733
Period size: 162 Copynumber: 3.0 Consensus size: 162
24479 AAGATGATAA
** * * *
24489 TCAGATGAAGGCTTCATCAAGCAAAGATGCGGAGCAGCACTCTCCCTCAAATTTCACGCACTGTG
1 TCAGATGAAGGCTTCATCAAGCAAAGATGAAGAGGAGCACTCTCCCTCAAGTTTCACGCACAGTG
* * * * * *
24554 ACGATAATCAGAGGGTTTTGTCAATTGAAGATGAAAACGAGCAG-CTTTCCTCAGCGAGTACAAC
66 ATGATAATCAGAGGGCTTTGTCAACTGAAGATGAAAACAAGCCGTC-TTCCTCAGTGAGTACAAC
24618 ACATCAAGAGCAGTTGCCAATTGACAATTGTAC
130 ACATCAAGAGCAGTTGCCAATTGACAATTGTAC
* * *
24651 TCAGATGAAGGCCTCATCAAGCAAAGATGAAGAGGAGCACTGTCCCTCAAGTTTCACGCAAAGTG
1 TCAGATGAAGGCTTCATCAAGCAAAGATGAAGAGGAGCACTCTCCCTCAAGTTTCACGCACAGTG
24716 ATGATAATCAGAGGGCTTTGTCAACTGAAGATGAAAACAAGCCGTCTTCCTCAGTGAGTACAACA
66 ATGATAATCAGAGGGCTTTGTCAACTGAAGATGAAAACAAGCCGTCTTCCTCAGTGAGTACAACA
* * *
24781 CATCAAGAGCAGTTGCCAGTTGACAATTTTAT
131 CATCAAGAGCAGTTGCCAATTGACAATTGTAC
* *
24813 TCAGATGAAGGCTTCATCAAGCAAAGATGAAAAGGAGCACTCTCCCTCAAGTTTCTCGCACAGTG
1 TCAGATGAAGGCTTCATCAAGCAAAGATGAAGAGGAGCACTCTCCCTCAAGTTTCACGCACAGTG
* * * *
24878 ATGATAATCAGAAGGCTTTTTCAACTGAAGATGAAAACAAACCGTCTTCCTCGGTGAGTACAACA
66 ATGATAATCAGAGGGCTTTGTCAACTGAAGATGAAAACAAGCCGTCTTCCTCAGTGAGTACAACA
24943 CATCAAGAGCAGTTGCCAATTGAC
131 CATCAAGAGCAGTTGCCAATTGAC
24967 TCGCACAGCC
Statistics
Matches: 288, Mismatches: 27, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
162 287 1.00
163 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (162 bp):
TCAGATGAAGGCTTCATCAAGCAAAGATGAAGAGGAGCACTCTCCCTCAAGTTTCACGCACAGTG
ATGATAATCAGAGGGCTTTGTCAACTGAAGATGAAAACAAGCCGTCTTCCTCAGTGAGTACAACA
CATCAAGAGCAGTTGCCAATTGACAATTGTAC
Found at i:27677 original size:1 final size:1
Alignment explanation
Indices: 27671--27702 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
27661 TGTGTGTCGG
27671 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27703 AAATCCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29929 original size:20 final size:21
Alignment explanation
Indices: 29894--29939 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
29884 AAATATTATA
*
29894 TTTATCCTATAATGGGTAATT
1 TTTATCCTAAAATGGGTAATT
*
29915 TTTAT-CTAAAATGGGTAGTT
1 TTTATCCTAAAATGGGTAATT
29935 TTTAT
1 TTTAT
29940 TTTATTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTATCCTAAAATGGGTAATT
Found at i:30849 original size:18 final size:18
Alignment explanation
Indices: 30826--30860 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30816 ACCGACCGCC
*
30826 ATCGGTTCGGTCGGTTAT
1 ATCGGTTCAGTCGGTTAT
*
30844 ATCGGTTTAGTCGGTTA
1 ATCGGTTCAGTCGGTTA
30861 AACAGTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (18 bp):
ATCGGTTCAGTCGGTTAT
Found at i:32738 original size:22 final size:22
Alignment explanation
Indices: 32696--32738 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
32686 ATGCTTTGCT
* *
32696 GCAGCCCAATCTTGTTTAGTTG
1 GCAGCCCAATCATGTTGAGTTG
32718 GCAGCCC-ATCATGTCTGAGTT
1 GCAGCCCAATCATGT-TGAGTT
32739 CATATCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (22 bp):
GCAGCCCAATCATGTTGAGTTG
Found at i:39504 original size:49 final size:49
Alignment explanation
Indices: 39414--39680 Score: 239
Period size: 49 Copynumber: 5.5 Consensus size: 49
39404 CAATTTTCAG
* * ** *
39414 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGTTGGAAGACATTTA
1 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTA
* * * * * **
39463 TTTTTACCTGCCATTTCCCAAAATGACCTTCCCGGACGGAAGGTACTTA
1 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTA
* * * * **
39512 -TTTTACTTGTTTTTTTCCAAAACGCCCTTCTCAGACGGAAGACACAAA
1 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTA
* * **
39560 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACCAA
1 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTA
* ** * * * *
39609 TTTTTACTTGCTTTTTCTTAAAACGCCCTTCCCGGACGGAAGGCGCTAA
1 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTA
* * *
39658 TTTTTACTCGCTTTTTCTCAAAA
1 TTTTTACTTGCTATTTCCCAAAA
39681 TGCGCTTTCA
Statistics
Matches: 180, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
48 35 0.19
49 145 0.81
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.34
Consensus pattern (49 bp):
TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTA
Found at i:39590 original size:97 final size:98
Alignment explanation
Indices: 39414--39680 Score: 270
Period size: 97 Copynumber: 2.7 Consensus size: 98
39404 CAATTTTCAG
* * ** * ** *** * *
39414 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGTTGGAAGACATTTATTTTTACCTGCCATTT
1 TTTTTACTTGCTTTTTCTTAAAACGCCCTTCCCAGACGGAAGACACAAATTTTTACTTGCTATTT
* * **
39479 CCCAAAATGACCTTCCCGGACGGAAGGTACTTA
66 CCCAAAACGACCTTCCCGGACGGAAGGCACCAA
*
39512 -TTTTACTTG-TTTTT-TTCCAAAACGCCCTTCTCAGACGGAAGACACAAATTTTTACTTGCTAT
1 TTTTTACTTGCTTTTTCTT--AAAACGCCCTTCCCAGACGGAAGACACAAATTTTTACTTGCTAT
*
39574 TTCCCAAAACGCCCTTCCCGGACGGAAGGCACCAA
64 TTCCCAAAACGACCTTCCCGGACGGAAGGCACCAA
* * * * * *
39609 TTTTTACTTGCTTTTTCTTAAAACGCCCTTCCCGGACGGAAGGCGCTAATTTTTACTCGCTTTTT
1 TTTTTACTTGCTTTTTCTTAAAACGCCCTTCCCAGACGGAAGACACAAATTTTTACTTGCTATTT
*
39674 CTCAAAA
66 CCCAAAA
39681 TGCGCTTTCA
Statistics
Matches: 138, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
96 4 0.03
97 73 0.53
98 54 0.39
99 5 0.04
100 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.34
Consensus pattern (98 bp):
TTTTTACTTGCTTTTTCTTAAAACGCCCTTCCCAGACGGAAGACACAAATTTTTACTTGCTATTT
CCCAAAACGACCTTCCCGGACGGAAGGCACCAA
Found at i:39692 original size:146 final size:146
Alignment explanation
Indices: 39414--39693 Score: 321
Period size: 146 Copynumber: 1.9 Consensus size: 146
39404 CAATTTTCAG
* ** ***
39414 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGTTGGAAGACATTTATTTTTACCTGCCATTT
1 TTTTCACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACCAATTTTTACCTGCCATTT
* * * * *
39479 CCCAAAATGACCTTCCCGGACGGAAGGTACTTATTTTACTTGTTTTTTTCCAAAACGCCCTTCTC
66 CCCAAAACGACCTTCCCGGACGGAAGGCACTAATTTTACTCGTTTTTCTCCAAAACGCCCTTCTC
39544 AGACGGAAGACACAAA
131 AGACGGAAGACACAAA
* * * * **
39560 TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACCAATTTTTACTTGCTTTTT
1 TTTTCACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACCAATTTTTACCTGCCATTT
** * * * *
39625 CTTAAAACGCCCTTCCCGGACGGAAGGCGCTAATTTTTACTCGCTTTTTCT-CAAAATGCGCTT-
66 CCCAAAACGACCTTCCCGGACGGAAGGCACTAA-TTTTACTCG-TTTTTCTCCAAAACGCCCTTC
39688 TCAGAC
129 TCAGAC
39694 AAAGGGCTAA
Statistics
Matches: 109, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
146 85 0.78
147 18 0.17
148 6 0.06
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (146 bp):
TTTTCACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGACACCAATTTTTACCTGCCATTT
CCCAAAACGACCTTCCCGGACGGAAGGCACTAATTTTACTCGTTTTTCTCCAAAACGCCCTTCTC
AGACGGAAGACACAAA
Found at i:39958 original size:62 final size:63
Alignment explanation
Indices: 39741--39965 Score: 262
Period size: 63 Copynumber: 3.6 Consensus size: 63
39731 AGTACTTTCG
* ** * *
39741 ATTCCCAAAAATACCCTTTCGGACAAAGGGTTGGTTT-TGTCACCTTCTTGCATTTAAGTTTAGT
1 ATTCCC-AAAATACCCTTTCAGACAAAGGGTCAGTTTCT-TCACATTCCTGCATTTAAGTTTAGT
* * **
39805 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCGTCAAATTCCAACATTTAAGTTTAGT
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTAAGTTTAGT
* *
39868 ATTCCCAAAATACCCATTT-AGACAAAGGGTCAGTTTCTTCACATTCCTGCACTT-AGATCCTA-
1 ATTCCCAAAATACCC-TTTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTAAG-T-TTAG
39930 T
63 T
*
39931 -TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTT
39966 AGCCATGTTT
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
61 3 0.02
62 32 0.23
63 94 0.67
64 11 0.08
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (63 bp):
ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTAAGTTTAGT
Found at i:43881 original size:14 final size:13
Alignment explanation
Indices: 43844--43893 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
43834 TTTTTCAAAA
43844 AAAATGGTTTTCAAG
1 AAAATGGTTTTC--G
43859 AAAA-GGTTTTCG
1 AAAATGGTTTTCG
43871 AAAATGAGTTTTC-
1 AAAATG-GTTTTCG
43884 AAAA-GGTTTT
1 AAAATGGTTTT
43894 TAGTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.15
12 6 0.18
13 5 0.15
14 13 0.39
15 4 0.12
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (13 bp):
AAAATGGTTTTCG
Found at i:45695 original size:38 final size:36
Alignment explanation
Indices: 45642--45969 Score: 181
Period size: 38 Copynumber: 9.5 Consensus size: 36
45632 AAGTTAACTG
*
45642 GAAACAGGTCATCTTTCAACACTTATCAAGATTGACT
1 GAAACAGGTCATCTTTCAACA-TTATCAAGATCGACT
*
45679 AGAAACAGGTCGTCTTTCAACAGTTATCAAGATCGACT
1 -GAAACAGGTCATCTTTCAACA-TTATCAAGATCGACT
45717 GTAAACAGGTCATCTTTCAA-ATTATC-AGA--G---
1 G-AAACAGGTCATCTTTCAACATTATCAAGATCGACT
** ** *
45747 G--TTA--TC-T-TTCAACA-ATTACCAAGATCGACT
1 GAAACAGGTCATCTTTCA-ACATTATCAAGATCGACT
45777 GGAAACAGGTCATCTTTCAACAATTATCAAGATCGACT
1 -GAAACAGGTCATCTTTCAAC-ATTATCAAGATCGACT
*
45815 GGAAACAGGTCATCTTTCAA-ACTATC-AGA--G---
1 -GAAACAGGTCATCTTTCAACATTATCAAGATCGACT
** ** *
45845 G--TTA--TC-T-TTCAACA-ATTATCAAGATTGACT
1 GAAACAGGTCATCTTTCA-ACATTATCAAGATCGACT
* * *
45875 AGAAACAGGTCATCTTTCAGCACTTGTCAAGTTCGACT
1 -GAAACAGGTCATCTTTCAACA-TTATCAAGATCGACT
*
45913 GGAAACAGGTCATCTTTCAACAGTTATCAAGATCAACT
1 -GAAACAGGTCATCTTTCAACA-TTATCAAGATCGACT
45951 GGAAACAGGTCATCTTTCA
1 -GAAACAGGTCATCTTTCA
45970 GCAGTTTTCG
Statistics
Matches: 223, Mismatches: 34, Indels: 66
0.69 0.11 0.20
Matches are distributed among these distances:
23 6 0.03
24 14 0.06
25 10 0.04
27 4 0.02
29 1 0.00
30 1 0.00
31 2 0.01
33 4 0.02
35 10 0.04
36 13 0.06
37 9 0.04
38 149 0.67
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (36 bp):
GAAACAGGTCATCTTTCAACATTATCAAGATCGACT
Found at i:45784 original size:60 final size:62
Alignment explanation
Indices: 45691--45805 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 62
45681 AAACAGGTCG
* * *
45691 TCTTTCAACAGTTATCAAGATCGACTGTAAACAGGTCATCTTTC-A-AATTATCAGAGGTTA
1 TCTTTCAACAATTACCAAGATCGACTGGAAACAGGTCATCTTTCAACAATTATCAGAGGTTA
45751 TCTTTCAACAATTACCAAGATCGACTGGAAACAGGTCATCTTTCAACAATTATCA
1 TCTTTCAACAATTACCAAGATCGACTGGAAACAGGTCATCTTTCAACAATTATCA
45806 AGATCGACTG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 41 0.82
61 1 0.02
62 8 0.16
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (62 bp):
TCTTTCAACAATTACCAAGATCGACTGGAAACAGGTCATCTTTCAACAATTATCAGAGGTTA
Found at i:45821 original size:98 final size:98
Alignment explanation
Indices: 45647--45941 Score: 455
Period size: 98 Copynumber: 3.0 Consensus size: 98
45637 AACTGGAAAC
* * * *
45647 AGGTCATCTTTCAACACTTATCAAGATTGACTAGAAACAGGTCGTCTTTCAACAGTTATCAAGAT
1 AGGTTATCTTTCAACAATTATCAAGATTGACTAGAAACAGGTCATCTTTCAACAATTATCAAGAT
*
45712 CGACTGTAAACAGGTCATCTTTCAAATTATCAG
66 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
* * *
45745 AGGTTATCTTTCAACAATTACCAAGATCGACTGGAAACAGGTCATCTTTCAACAATTATCAAGAT
1 AGGTTATCTTTCAACAATTATCAAGATTGACTAGAAACAGGTCATCTTTCAACAATTATCAAGAT
*
45810 CGACTGGAAACAGGTCATCTTTCAAACTATCAG
66 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
* * * *
45843 AGGTTATCTTTCAACAATTATCAAGATTGACTAGAAACAGGTCATCTTTCAGCACTTGTCAAGTT
1 AGGTTATCTTTCAACAATTATCAAGATTGACTAGAAACAGGTCATCTTTCAACAATTATCAAGAT
45908 CGACTGGAAACAGGTCATCTTTCAACAGTTATCA
66 CGACTGGAAACAGGTCATCTTTCAA-A-TTATCA
45942 AGATCAACTG
Statistics
Matches: 178, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
98 172 0.97
99 1 0.01
100 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (98 bp):
AGGTTATCTTTCAACAATTATCAAGATTGACTAGAAACAGGTCATCTTTCAACAATTATCAAGAT
CGACTGGAAACAGGTCATCTTTCAAATTATCAG
Found at i:47827 original size:49 final size:49
Alignment explanation
Indices: 47762--48036 Score: 311
Period size: 49 Copynumber: 5.6 Consensus size: 49
47752 CAATTTTCAG
* * * *
47762 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACGGAAGGCATTTA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* * *
47811 TTTTTACTTG-TCATTTCCCAAAATGACCTTCCCGGACGGAAGGTACTTA
1 TTTTTACTTGCT-ATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* * * * * *
47860 -TTTTACTTGTTTTTTTTCCAAAACGCCCTTCTCGGACGGAAGGCACAAA
1 TTTTTACTTG-CTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* *
47909 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGACACCAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* * * * *
47958 TTTTTACTTGCTTTTTCCTAAAACGCCGTTCCCGGACGGAAGGCGCTAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* * *
48007 TTTTTACTCGCTTTTTCTCAAAATGCCCTT
1 TTTTTACTTGCTATTTCCCAAAATGCCCTT
48037 TCAGACAAAG
Statistics
Matches: 190, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
48 10 0.05
49 170 0.89
50 10 0.05
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (49 bp):
TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
Found at i:48035 original size:147 final size:147
Alignment explanation
Indices: 47762--48036 Score: 358
Period size: 147 Copynumber: 1.9 Consensus size: 147
47752 CAATTTTCAG
* ***
47762 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACGGAAGGCATTTATTTTTACTTGTCATTT
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACGGAAGACACCAATTTTTACTTGTCATTT
* * * * * *
47827 CCCAAAATGACCTTCCCGGACGGAAGGTACTTATTTTACTTGTTTTTTTTCCAAAACGCCCTTCT
66 CCCAAAACGACCTTCCCGGACGGAAGGCACTAATTTTACTCGCTTTTTCTCCAAAACGCCCTTCT
47892 CGGACGGAAGGCACAAA
131 CGGACGGAAGGCACAAA
* * *
47909 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGACACCAATTTTTACTTG-CTTTT
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACGGAAGACACCAATTTTTACTTGTC-ATT
* * *
47973 TCCTAAAACG-CCGTTCCCGGACGGAAGGCGCTAATTTTTACTCGCTTTTTCT-CAAAATGCCCT
65 TCCCAAAACGACC-TTCCCGGACGGAAGGCACTAA-TTTTACTCGCTTTTTCTCCAAAACGCCCT
48036 T
128 T
48037 TCAGACAAAG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
146 3 0.03
147 92 0.84
148 14 0.13
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (147 bp):
TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACGGAAGACACCAATTTTTACTTGTCATTT
CCCAAAACGACCTTCCCGGACGGAAGGCACTAATTTTACTCGCTTTTTCTCCAAAACGCCCTTCT
CGGACGGAAGGCACAAA
Found at i:48304 original size:62 final size:62
Alignment explanation
Indices: 48090--48311 Score: 240
Period size: 62 Copynumber: 3.6 Consensus size: 62
48080 AGTACTTTCG
* ** * *
48090 ATTCCCAAAAATACCCTTTCGGACAAAGGGTTGGTTT-TGTCACCTTCTTGCATTTA-AGTTTAG
1 ATTCCC-AAAATACCCTTTCAGACAAAGGGTCAGTTTCT-TCACATTCCTGCA-TTAGA-TTTAG
48153 T
62 T
* * *
48154 ATTCCCAAAATACCCTTTCAGAC-AAGGTTCAGTTTCGTCACATTCCTACATTAG-TTTAGT
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCATTAGATTTAGT
* *
48214 ATTCCCAAAATACCCATTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCACTTAGATCCTA-T
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCA-TTAGAT-TTAGT
* *
48277 -TTCCTAAAATACCCTTTCGGACAAAGGGTCAGTTT
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTT
48312 AGCCATGTTT
Statistics
Matches: 136, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
60 28 0.21
61 27 0.20
62 55 0.40
63 18 0.13
64 8 0.06
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (62 bp):
ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCTTCACATTCCTGCATTAGATTTAGT
Found at i:57283 original size:18 final size:19
Alignment explanation
Indices: 57262--57301 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
57252 TATTAATTAA
57262 TTTTATGCACTTTATAT-T
1 TTTTATGCACTTTATATAT
57280 TTTTATGCACTTTATATAT
1 TTTTATGCACTTTATATAT
57299 TTT
1 TTT
57302 GCCTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTATGCACTTTATATAT
Found at i:57554 original size:4 final size:4
Alignment explanation
Indices: 57547--57573 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
57537 ATAACTTACT
57547 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
57574 TAATTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:58940 original size:29 final size:31
Alignment explanation
Indices: 58867--58947 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 31
58857 GGGCTAAATA
* **
58867 ACCAATTCAGGATATAACGTTTACTATTACG
1 ACCATTTCAGGATATAACGTTTACTAAAACG
* *
58898 ATCAATTT-GGGATATAACGTTT-C-AAAACG
1 A-CCATTTCAGGATATAACGTTTACTAAAACG
58927 ACCATTTCAGGATATAACGTT
1 ACCATTTCAGGATATAACGTT
58948 ACCCAATCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 5 0.12
29 17 0.41
30 1 0.02
31 14 0.34
32 4 0.10
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (31 bp):
ACCATTTCAGGATATAACGTTTACTAAAACG
Found at i:59947 original size:12 final size:12
Alignment explanation
Indices: 59930--59954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59920 GATATAGCCT
59930 CCATTGAAGAAG
1 CCATTGAAGAAG
59942 CCATTGAAGAAG
1 CCATTGAAGAAG
59954 C
1 C
59955 TTTTGGAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CCATTGAAGAAG
Found at i:61141 original size:19 final size:19
Alignment explanation
Indices: 61117--61176 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
61107 TTATTTACTT
61117 AATTACACCGAATTAATCC
1 AATTACACCGAATTAATCC
* * **
61136 AATT--ACTG-ATTTATTT
1 AATTACACCGAATTAATCC
*
61152 AATTACACCGAATTAAGCC
1 AATTACACCGAATTAATCC
61171 AATTAC
1 AATTAC
61177 TGATTTACTT
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
16 9 0.31
17 3 0.10
18 3 0.10
19 14 0.48
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (19 bp):
AATTACACCGAATTAATCC
Found at i:61148 original size:35 final size:35
Alignment explanation
Indices: 61109--61615 Score: 415
Period size: 35 Copynumber: 14.1 Consensus size: 35
61099 TAAGCCATTT
* *
61109 ATTTACTTAATTACACCGAATTAA-TCCAATTACTG
1 ATTTACTTAATTACACCGAATTAAGT-TAATTACTA
* ** *
61144 ATTTATTTAATTACACCGAATTAAGCCAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* * *
61179 ATTTACTTAATTACATCGAATTAAGTTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
*
61214 ATTTACTTAATTACACCGAATTAAGTTAATTACAA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* *
61249 ATTTACTTAATTACACCTAATTAAGTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
** *
61284 ATTTACTTAATTACACCGAATTAAGTGGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* *
61319 ATTTACTTAATTACACCGAATTAAG-TGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* * * * * *
61353 ATTTGCTTAATCACACTGAATTAAGTTGACTACCAAA
1 ATTTACTTAATTACACCGAATTAAGTTAATTA-C-TA
* *** * * * *
61390 CTATTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
1 --ATTT-ACTTAATTA-C-ACCGAATTAAGTTAATTACTA
* * *
61430 ATTTACTTAATTGCACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* * *
61465 AATTACTTAATTACACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* * * * * *
61500 AATTACTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
1 ATTTACTTAA-TT-A-CACCGA---A-TTAAGTTAATTACTA
* * *
61542 ATTTACTTAATTGCACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
* * * *
61577 AATTACTTAATTACACCGAATTAAATTGATTACAA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTA
61612 ATTT
1 ATTT
61616 GCTTTTTCTT
Statistics
Matches: 395, Mismatches: 61, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
34 30 0.08
35 291 0.74
36 5 0.01
37 9 0.02
38 8 0.02
39 8 0.02
40 7 0.02
41 5 0.01
42 32 0.08
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACTA
Found at i:61192 original size:16 final size:16
Alignment explanation
Indices: 61171--61227 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
61161 GAATTAAGCC
61171 AATTACTGATTTACTT
1 AATTACTGATTTACTT
* *
61187 AATTACATCGAATTAAGTT
1 AATTAC-T-G-ATTTACTT
*
61206 GATTACTGATTTACTT
1 AATTACTGATTTACTT
61222 AATTAC
1 AATTAC
61228 ACCGAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 17 0.53
17 2 0.06
18 2 0.06
19 11 0.34
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTACTGATTTACTT
Found at i:61258 original size:16 final size:17
Alignment explanation
Indices: 61214--61334 Score: 95
Period size: 16 Copynumber: 6.9 Consensus size: 17
61204 TTGATTACTG
61214 ATTTACTTAATTACACCGA
1 ATTTACTTAATTACA-C-A
* *
61233 ATTAAGTTAATTACA-A
1 ATTTACTTAATTACACA
61249 ATTTACTTAATTACACCTA
1 ATTTACTTAATTACA-C-A
* *
61268 ATTAAGTTAATTAC-CA
1 ATTTACTTAATTACACA
61284 ATTTACTTAATTACACCGA
1 ATTTACTTAATTACA-C-A
* * **
61303 ATTAAGTGGATTAC-CA
1 ATTTACTTAATTACACA
61319 ATTTACTTAATTACAC
1 ATTTACTTAATTACAC
61335 CGAATTAAGT
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
16 38 0.48
17 3 0.04
18 1 0.01
19 37 0.47
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTTACTTAATTACACA
Found at i:61407 original size:21 final size:21
Alignment explanation
Indices: 61383--61441 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
61373 TTAAGTTGAC
*
61383 TACCAAACTATTTAATTTAAT
1 TACCAAACTACTTAATTTAAT
**
61404 TACCAATTTACTTAATTTAAT
1 TACCAAACTACTTAATTTAAT
* **
61425 TTCCAATTTACTTAATT
1 TACCAAACTACTTAATT
61442 GCACCGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.47
Consensus pattern (21 bp):
TACCAAACTACTTAATTTAAT
Found at i:61512 original size:112 final size:112
Alignment explanation
Indices: 61214--61614 Score: 543
Period size: 112 Copynumber: 3.7 Consensus size: 112
61204 TTGATTACTG
* * *
61214 ATTTACTTAATTACACCGAATTAAGTTAATTA-CAAATTTACTTAATTACACCTAATTAAGTTAA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCAAA-TTACTTAATTACACCGAATTAAGTTGA
* * * * ** *
61278 TTACCAATTTACTTAA-TT-A-CACCGA---A-TTAAGTGGATTACCA
65 TTACCAAATTACTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
* * * * *
61319 ATTTACTTAATTACACCGAATTAAG-TGATTACCAATTTGCTTAATCACACTGAATTAAGTTGAC
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
* *
61383 TACCAAACTATTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
66 TACCAAATTACTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
*
61430 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
61495 TACCAAATTACTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
66 TACCAAATTACTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
* *
61542 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAATTGAT
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
61607 TA-CAAATT
66 TACCAAATT
61615 TGCTTTTTCT
Statistics
Matches: 261, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
104 39 0.15
105 30 0.11
106 1 0.00
107 4 0.02
110 1 0.00
111 41 0.16
112 145 0.56
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (112 bp):
ATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
TACCAAATTACTTAATTTAATTACCAATTTACTTAATTTAATTTCCA
Found at i:61517 original size:21 final size:21
Alignment explanation
Indices: 61493--61553 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
61483 AATTAAGTTG
*
61493 ATTACCAAATTACTTAATTTA
1 ATTACCAATTTACTTAATTTA
61514 ATTACCAATTTACTTAATTTA
1 ATTACCAATTTACTTAATTTA
*
61535 ATTTCCAATTTACTTAATT
1 ATTACCAATTTACTTAATT
61554 GCACCGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTACCAATTTACTTAATTTA
Found at i:61615 original size:77 final size:77
Alignment explanation
Indices: 61462--61608 Score: 201
Period size: 77 Copynumber: 1.9 Consensus size: 77
61452 AAGTTGATTA
* * *
61462 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCAATTTAC
1 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATCACCAATTAAA
*
61527 TTAATTTAATTT
66 TTAATTAAATTT
* *
61539 CCAATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAA-TT-A-CACCGAATTAA
1 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATCACC-AATTAA
*
61601 ATTGATTA
65 ATTAATTA
61609 CAAATTTGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
74 3 0.05
75 11 0.18
76 2 0.03
77 46 0.74
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (77 bp):
CCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATCACCAATTAAA
TTAATTAAATTT
Found at i:65270 original size:20 final size:20
Alignment explanation
Indices: 65245--65283 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65235 AAATATACAT
*
65245 GTGGCATCAATGTGGCACAG
1 GTGGCATCAACGTGGCACAG
*
65265 GTGGCATCCACGTGGCACA
1 GTGGCATCAACGTGGCACA
65284 ATTAACCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.18
Consensus pattern (20 bp):
GTGGCATCAACGTGGCACAG
Found at i:68396 original size:69 final size:69
Alignment explanation
Indices: 68274--68402 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
68264 GAGTTGCCCG
* * ** * *
68274 ATTCAATTGGTGACTTAAGACAGCTAGGCTACTTGGACCTTTCTGGCACAAAGATTGCTTCTTTT
1 ATTCAATTGGCGACTTAACACAGCTAGGCTACTTGGACCTTTCAAGCAAAAAGATAGCTTCTTTT
68339 CCCA
66 CCCA
*
68343 ATTCAATTGGCGGCTTAACACAGCTAGGCTACTTGGACCTTTCAAGCAAAAAGATAGCTT
1 ATTCAATTGGCGACTTAACACAGCTAGGCTACTTGGACCTTTCAAGCAAAAAGATAGCTT
68403 TTAATTTGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (69 bp):
ATTCAATTGGCGACTTAACACAGCTAGGCTACTTGGACCTTTCAAGCAAAAAGATAGCTTCTTTT
CCCA
Found at i:71008 original size:13 final size:13
Alignment explanation
Indices: 70990--71016 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70980 GTCAAACAAA
70990 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
71003 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
71016 T
1 T
71017 TCAGTTGTTT
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:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:76359 original size:10 final size:10
Alignment explanation
Indices: 76344--76383 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
76334 TAATTTAGAA
76344 ATCTATCTAT
1 ATCTATCTAT
76354 ATCTATCTAT
1 ATCTATCTAT
76364 ATCTATCTAT
1 ATCTATCTAT
*
76374 A-CTATATAT
1 ATCTATCTAT
76383 A
1 A
76384 AAGTACGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.47
Consensus pattern (10 bp):
ATCTATCTAT
Found at i:81375 original size:32 final size:32
Alignment explanation
Indices: 81287--81376 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
81277 ATTAAAGATG
** *
81287 GCGGCGTCTTGGGGTTCAGACGCCACCATTTA
1 GCGGCGTCTAAGGGTTCAGACGCCGCCATTTA
*
81319 GCGGTGTCTAAGGGTTCAGACGCCGCCATTTA
1 GCGGCGTCTAAGGGTTCAGACGCCGCCATTTA
81351 GCGGCGTCTAAGGGTTCAGACGCCGC
1 GCGGCGTCTAAGGGTTCAGACGCCGC
81377 TATATTTTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (32 bp):
GCGGCGTCTAAGGGTTCAGACGCCGCCATTTA
Found at i:81755 original size:114 final size:114
Alignment explanation
Indices: 81398--81802 Score: 552
Period size: 114 Copynumber: 3.6 Consensus size: 114
81388 CTTCATTTGC
* * * **
81398 CTTTCTCGGAGAGAAATTAAAGATGGTGGCATCTTGGGGTTCATTCGCCTCCATTTAGCGGCGTC
1 CTTTCTCGGAGAAAAATTAAAGATGGCGGCGTCTTGGGGTTCAGACGCCTCCATTTAGCGGCGTC
* * *
81463 TGAGCCCAAGACGCCGCTATATTTTAGCCTTCTTTTTCACCCACTTTAA
66 TGGGCCCAAGACGCCGCTATATTTTAGCCTTATTTTTCACCCAATTTAA
* *
81512 CTTTCTCGGAGAAAAATTAAAGATAGC-G-G---TGTGGTTCAGACGCCTCCATTTAGCGGCGTC
1 CTTTCTCGGAGAAAAATTAAAGATGGCGGCGTCTTGGGGTTCAGACGCCTCCATTTAGCGGCGTC
* * *
81572 TCGGGGTCC-AGACACCGCTATATTTTAGCCTTTTTTTTTCACCCAATTTAA
66 T--GGGCCCAAGACGCCGCTATATTTTAGCC-TTATTTTTCACCCAATTTAA
* * * *
81623 CTTTCTCAGAGAAAAATTAAAGATGGCGACGTCTTGGGGTTCATACACCTCCATTTAGCGGCGTC
1 CTTTCTCGGAGAAAAATTAAAGATGGCGGCGTCTTGGGGTTCAGACGCCTCCATTTAGCGGCGTC
* *
81688 TGGGCCCAAGACGCCGCTATATTTTAGGCTAATTTTTCACCCAATTTAA
66 TGGGCCCAAGACGCCGCTATATTTTAGCCTTATTTTTCACCCAATTTAA
* *
81737 CTTTCTCGGAGATAAATTAAAGATGGCGGCGTCTAGGGGTTCAGACGCCTCCATTTAGCGGCGTC
1 CTTTCTCGGAGAAAAATTAAAGATGGCGGCGTCTTGGGGTTCAGACGCCTCCATTTAGCGGCGTC
81802 T
66 T
81803 TGTGATTTCT
Statistics
Matches: 253, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
109 29 0.11
110 20 0.08
111 47 0.19
113 2 0.01
114 107 0.42
115 19 0.08
116 29 0.11
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (114 bp):
CTTTCTCGGAGAAAAATTAAAGATGGCGGCGTCTTGGGGTTCAGACGCCTCCATTTAGCGGCGTC
TGGGCCCAAGACGCCGCTATATTTTAGCCTTATTTTTCACCCAATTTAA
Found at i:81851 original size:70 final size:70
Alignment explanation
Indices: 81738--81873 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
81728 CCAATTTAAC
* *
81738 TTTCTCGGAGATAAATTAAAGATGGCGGCGTCTAGGGGTTCAGACGCCTCCATTTAGCGGCGTCT
1 TTTCTCGGAGATAAATTAAAGATGGCGGCGTCTAGGGATTCAGACGCCTCCATTTAGCAGCGTCT
81803 TGTGA
66 TGTGA
81808 TTTCTCGGAGATAAATTAAAGATGGCGGCGTCTAGGGATTCAGACGCCTCCATTTAGCAGCGTCT
1 TTTCTCGGAGATAAATTAAAGATGGCGGCGTCTAGGGATTCAGACGCCTCCATTTAGCAGCGTCT
81873 T
66 T
81874 AATCCAAAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (70 bp):
TTTCTCGGAGATAAATTAAAGATGGCGGCGTCTAGGGATTCAGACGCCTCCATTTAGCAGCGTCT
TGTGA
Found at i:84874 original size:62 final size:63
Alignment explanation
Indices: 84775--84897 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 63
84765 GTTCATTTTT
*
84775 TTTTTTTGGTGCTATAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGACTC
1 TTTTTTT-GTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGACTC
* *
84839 TTTTTTT-TGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGA
1 TTTTTTTGTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGA
84898 ATTTTCTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 49 0.88
64 7 0.12
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (63 bp):
TTTTTTTGTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGACTC
Found at i:84915 original size:6 final size:6
Alignment explanation
Indices: 84904--84930 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
84894 GAGAATTTTC
84904 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
84931 TTGCTCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:85003 original size:85 final size:86
Alignment explanation
Indices: 84840--85004 Score: 242
Period size: 85 Copynumber: 1.9 Consensus size: 86
84830 GCGAGACTCT
* *
84840 TTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGAATTTTCT
1 TTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTACAGGATTTTCAACTTAGCCAGAATTTTCT
84905 TTCTTTTTCTTTTTCTTTTTC
66 TTCTTTTTCTTTTTCTTTTTC
* * ** *
84926 TTTTTTTGCTCTAACTTTT-CCTAAGCTTTTCTTTACAGGATTTTCAACTTAGCCAGCTTTTTTT
1 TTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTACAGGATTTTCAACTTAGCCAGAATTTTCT
*
84990 TTCATTTTTTTTTTT
66 TTC-TTTTTCTTTTT
85005 TTGGTGTGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
85 41 0.59
86 29 0.41
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.57
Consensus pattern (86 bp):
TTTTTTTGCTCTAACTTTTGCCTAAGCTGTCCTTTACAGGATTTTCAACTTAGCCAGAATTTTCT
TTCTTTTTCTTTTTCTTTTTC
Found at i:86756 original size:41 final size:40
Alignment explanation
Indices: 86705--86852 Score: 172
Period size: 41 Copynumber: 3.6 Consensus size: 40
86695 ATTTGATTTG
* * *
86705 ATTTGATTCAAAGGG-TCGAATGATTTGGTCTTGAATTGATA
1 ATTTAATTC-AAGGGTTCG-ATGACTTGATCTTGAATTGATA
* *
86746 ATTTAATTCAAGGGTTTCGATAACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGG-TTCGATGACTTGATCTTGAATTGATA
* **
86787 ATTTAATCCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGT-TCGATGACTTGATCTTGAATTGATA
86828 ATTTAATTCAAGGGTCTCGATGACT
1 ATTTAATTCAAGGGT-TCGATGACT
86853 CAGTCTTGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
40 6 0.06
41 85 0.90
42 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGGGTTCGATGACTTGATCTTGAATTGATA
Found at i:86853 original size:41 final size:41
Alignment explanation
Indices: 86733--86862 Score: 197
Period size: 41 Copynumber: 3.2 Consensus size: 41
86723 AATGATTTGG
* * ***
86733 TCTTGAATTGATAATTTAATTCAAGGGTTTCGATAACTTGT
1 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
*
86774 TCTTGAATTGATAATTTAATCCAAGGGTCTCGATGACTCAA
1 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
*
86815 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAG
1 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
86856 TCTTGAA
1 TCTTGAA
86863 CAAACGAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (41 bp):
TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
Found at i:91739 original size:43 final size:44
Alignment explanation
Indices: 91691--91780 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
91681 TATCTATTGT
* *
91691 ATCCTTCTCCCTCTGTTCT-CCCTCAGGTATTTTTGTTTAACAA
1 ATCCTTCTCCCTCTGTTCTCCCCTCAGGGATTTTTGCTTAACAA
*
91734 ATCCTTCTCCCTCTGTTCTCCCCCTCAGGGATTTTTGCTTCACAA
1 ATCCTTCTCCCTCTGTTCT-CCCCTCAGGGATTTTTGCTTAACAA
91779 AT
1 AT
91781 TTATGAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 19 0.45
45 23 0.55
ACGTcount: A:0.16, C:0.33, G:0.10, T:0.41
Consensus pattern (44 bp):
ATCCTTCTCCCTCTGTTCTCCCCTCAGGGATTTTTGCTTAACAA
Found at i:92472 original size:26 final size:28
Alignment explanation
Indices: 92429--92481 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
92419 TTTTCCTGGC
* *
92429 AGGCTTGTTCAAATCCTTT-TTCTTTGT
1 AGGCTTCTCCAAATCCTTTCTTCTTTGT
92456 AGGCTTCTCCAAA-CCTTTCTTCTTTG
1 AGGCTTCTCCAAATCCTTTCTTCTTTG
92482 AAGTCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.15, C:0.25, G:0.13, T:0.47
Consensus pattern (28 bp):
AGGCTTCTCCAAATCCTTTCTTCTTTGT
Found at i:96092 original size:31 final size:31
Alignment explanation
Indices: 95997--96233 Score: 199
Period size: 31 Copynumber: 7.1 Consensus size: 31
95987 AGTACTAAGA
*
95997 AACTTAATTCAGGGTAATTAAGTAAGTCAGTGAAT
1 AACTTAATTCAGGGTAATTAAGTAAGT---T-AGT
96032 AACTTAATTCAGGGTAATTAAGTAAGTAAGTTAGT
1 AACTTAATTCAGGGTAA-T---TAAGTAAGTTAGT
* *
96067 AACTTGATTCAAGGTAATTAAGTAAGTAATATGT
1 AACTTAATTCAGGGTAATTAAGTAAGT--TA-GT
* *
96101 AAATTAATTCAGGGTAATTAAGTGAA-TAAGT
1 AACTTAATTCAGGGTAATTAAGT-AAGTTAGT
*
96132 AGCTTAATTCAGGGTGATTATGTAAGTAAGTAATATGT
1 AACTTAATTCAGGGT-A--AT-TAAGTAAGT--TA-GT
*
96170 AACTTAATTCAGGGTAATTAAGTGAA-TAAGT
1 AACTTAATTCAGGGTAATTAAGT-AAGTTAGT
**
96201 TGCTTAATTCAGGGTAATTAAGTAAGTTAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTTAGT
96232 AA
1 AA
96234 GTCAGTAACT
Statistics
Matches: 167, Mismatches: 17, Indels: 40
0.75 0.08 0.18
Matches are distributed among these distances:
30 2 0.01
31 51 0.31
32 3 0.02
33 2 0.01
34 34 0.20
35 46 0.28
36 2 0.01
37 2 0.01
38 16 0.10
39 9 0.05
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (31 bp):
AACTTAATTCAGGGTAATTAAGTAAGTTAGT
Found at i:96131 original size:69 final size:67
Alignment explanation
Indices: 95999--96262 Score: 308
Period size: 69 Copynumber: 3.8 Consensus size: 67
95989 TACTAAGAAA
*
95999 CTTAATTCAGGGTAATTAAGTAAGTCAGTGAA--TAACTTAATTCAGGGTAATTAAGT-AAGTAA
1 CTTAATTCAGGGTAATTAAGTAAGT-AAT-AATGTAACTTAATTCAGGGTAATTAAGTGAA-TAA
96061 GTTAG
63 GTTAG
* * *
96066 TAACTTGATTCAAGGTAATTAAGTAAGTAAT-ATGTAAATTAATTCAGGGTAATTAAGTGAATAA
1 ---CTTAATTCAGGGTAATTAAGTAAGTAATAATGTAACTTAATTCAGGGTAATTAAGTGAATAA
96130 G-TAG
63 GTTAG
96134 CTTAATTCAGGGTGATTATGTAAGTAAGTAAT-ATGTAACTTAATTCAGGGTAATTAAGTGAATA
1 CTTAATTCAGGGT-A--AT-TAAGTAAGTAATAATGTAACTTAATTCAGGGTAATTAAGTGAATA
96198 AGTT-G
62 AGTTAG
*
96203 CTTAATTCAGGGTAATTAAGTAAGTTAGTAAGTCAGTAACTTAATTCAGGGTAATTAAGT
1 CTTAATTCAGGGTAATTAAGTAAG-TAATAA-T--GTAACTTAATTCAGGGTAATTAAGT
96263 TTAGTAAGGA
Statistics
Matches: 173, Mismatches: 8, Indels: 26
0.84 0.04 0.13
Matches are distributed among these distances:
65 19 0.11
66 6 0.03
67 2 0.01
68 7 0.04
69 88 0.51
70 51 0.29
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (67 bp):
CTTAATTCAGGGTAATTAAGTAAGTAATAATGTAACTTAATTCAGGGTAATTAAGTGAATAAGTT
AG
Found at i:96157 original size:100 final size:99
Alignment explanation
Indices: 96034--96223 Score: 258
Period size: 100 Copynumber: 1.9 Consensus size: 99
96024 CAGTGAATAA
*
96034 CTTAATTCAGGGTAATTAAGTAAGTAAGT-TA-GTAACTTGATTCAAGGTAATTAAGTAAGTAAT
1 CTTAATTCAGGGTAATTAAGTAAGTAAGTATATGTAACTTAATTCAAGGTAATTAAGT--G-AAT
*
96097 ATGTAAATTAATTCAGGGTAATTAAGTGAATAAGTAG
63 AAGTAAATTAATTCAGGGTAATTAAGTGAATAAGTAG
* * *
96134 CTTAATTCAGGGTGATTATGTAAGTAAGTAATATGTAACTTAATTCAGGGTAATTAAGTGAATAA
1 CTTAATTCAGGGTAATTAAGTAAGTAAGT-ATATGTAACTTAATTCAAGGTAATTAAGTGAATAA
***
96199 GTTGCTTAATTCAGGGTAATTAAGT
65 GTAAATTAATTCAGGGTAATTAAGT
96224 AAGTTAGTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
100 53 0.67
101 1 0.01
102 2 0.03
103 23 0.29
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (99 bp):
CTTAATTCAGGGTAATTAAGTAAGTAAGTATATGTAACTTAATTCAAGGTAATTAAGTGAATAAG
TAAATTAATTCAGGGTAATTAAGTGAATAAGTAG
Found at i:96263 original size:35 final size:35
Alignment explanation
Indices: 95992--96262 Score: 283
Period size: 35 Copynumber: 7.8 Consensus size: 35
95982 GAATCAGTAC
* *
95992 TAAGAAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTAAG
96027 TGAA-TAACTTAATTCAGGGTAATTAAGTAAGTAAG
1 T-AAGTAACTTAATTCAGGGTAATTAAGTAAGTAAG
* * *
96062 TTAGTAACTTGATTCAAGGTAATTAAGTAAGTAA-
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTAAG
* *
96096 TATGTAAATTAATTCAGGGTAATTAAGT--G-AA-
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTAAG
* * *
96127 TAAGTAGCTTAATTCAGGGTGATTATGTAAGTAAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTAAG
96162 TAATATGTAACTTAATTCAGGGTAATTAAGT--G-AA-
1 T-A-A-GTAACTTAATTCAGGGTAATTAAGTAAGTAAG
**
96196 TAAGTTGCTTAATTCAGGGTAATTAAGTAAGTTAGTAAG
1 TAAGTAACTTAATTCAGGGTAATTAAGT-A---AGTAAG
*
96235 TCAGTAACTTAATTCAGGGTAATTAAGT
1 TAAGTAACTTAATTCAGGGTAATTAAGT
96263 TTAGTAAGGA
Statistics
Matches: 196, Mismatches: 23, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
31 48 0.24
32 2 0.01
33 2 0.01
34 27 0.14
35 62 0.32
36 4 0.02
37 2 0.01
38 24 0.12
39 25 0.13
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (35 bp):
TAAGTAACTTAATTCAGGGTAATTAAGTAAGTAAG
Found at i:109504 original size:20 final size:20
Alignment explanation
Indices: 109479--109517 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
109469 CATATAAAAT
*
109479 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
109499 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
109518 TTTTAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:109593 original size:33 final size:33
Alignment explanation
Indices: 109556--109640 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
109546 AACAGGTCTC
* *
109556 GTCGCGTGCGGATCGCGACGGAGCCATGGCTTG
1 GTCGCGCGCCGATCGCGACGGAGCCATGGCTTG
*
109589 GTCGCGCGCCGCTCGCGACGGAGCCATGGCTTG
1 GTCGCGCGCCGATCGCGACGGAGCCATGGCTTG
* *
109622 GTCCCGCGCCGCTCGCGAC
1 GTCGCGCGCCGATCGCGAC
109641 CAAGCCGCGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.09, C:0.36, G:0.39, T:0.15
Consensus pattern (33 bp):
GTCGCGCGCCGATCGCGACGGAGCCATGGCTTG
Found at i:110879 original size:3 final size:3
Alignment explanation
Indices: 110871--110912 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
110861 AACATCTATG
110871 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
110913 TTGGTGAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:111813 original size:27 final size:25
Alignment explanation
Indices: 111757--111814 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
111747 TCACTTGTTT
* *
111757 TCTTCAACTGTAAGAATCTCAAGTC
1 TCTTCAACTGTAAGAAGCTCAAATC
* *
111782 ACTTCAACTGATACGAAGCGTCAAATC
1 TCTTCAACTG-TAAGAAGC-TCAAATC
111809 TCTTCA
1 TCTTCA
111815 GTCACTGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 9 0.35
26 6 0.23
27 11 0.42
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (25 bp):
TCTTCAACTGTAAGAAGCTCAAATC
Found at i:123579 original size:22 final size:23
Alignment explanation
Indices: 123531--123586 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
123521 TGATAAGCAA
*
123531 ATTATGAAAATT-TGATAATCTTC
1 ATTATG-AAATTATGATAAACTTC
123554 -TTATGAAATTATGATAAAC-TC
1 ATTATGAAATTATGATAAACTTC
*
123575 ATTATAAAATTA
1 ATTATGAAATTA
123587 AAAATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (23 bp):
ATTATGAAATTATGATAAACTTC
Found at i:123579 original size:44 final size:43
Alignment explanation
Indices: 123488--123585 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 43
123478 TTGTTATCTT
*
123488 TTATAAAATTTTGATAATCTCCCTATAATATCATGATAAGCAAA
1 TTATAAAA-TTTGATAATCTCCCTATAATATCATGATAAACAAA
* * * **
123532 TTATGAAAATTTGATAATCTTCTTATGAA-ATTATGATAAACTCA
1 TTAT-AAAATTTGATAATCTCCCTAT-AATATCATGATAAACAAA
123576 TTATAAAATT
1 TTATAAAATT
123586 AAAAATTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
43 6 0.13
44 34 0.74
45 6 0.13
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (43 bp):
TTATAAAATTTGATAATCTCCCTATAATATCATGATAAACAAA
Found at i:123613 original size:22 final size:22
Alignment explanation
Indices: 123588--123644 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
123578 ATAAAATTAA
123588 AAATTTTGATAACATA-ACTATG
1 AAATTTTGATAACATACA-TATG
* *
123610 AAATTTTGATAAACGTTCATATG
1 AAATTTTGAT-AACATACATATG
123633 AAATTTTGATAA
1 AAATTTTGATAA
123645 TCTCGTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.39
23 18 0.58
24 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACATACATATG
Found at i:123718 original size:22 final size:21
Alignment explanation
Indices: 123607--123719 Score: 65
Period size: 22 Copynumber: 5.2 Consensus size: 21
123597 TAACATAACT
*
123607 ATGAAATTTTGATAAACGT-TCA
1 ATGAAATTTTGATAATC-TCT-A
*
123629 TATGAAATTTTGATAATCTCGTT
1 -ATGAAATTTTGATAATCTC-TA
* *
123652 ATTACATTTTGATAATCTCT-
1 ATGAAATTTTGATAATCTCTA
* *
123672 AT-AAATCTTCGAT-A-CTATAA
1 ATGAAAT-TTTGATAATCTCT-A
123692 TATGAAATTTTGATAATCTCTCA
1 -ATGAAATTTTGATAATCTCT-A
123715 ATGAA
1 ATGAA
123720 GTTATATACT
Statistics
Matches: 71, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
18 3 0.04
19 4 0.06
20 7 0.10
21 8 0.11
22 28 0.39
23 20 0.28
24 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (21 bp):
ATGAAATTTTGATAATCTCTA
Found at i:130562 original size:36 final size:36
Alignment explanation
Indices: 130522--131648 Score: 241
Period size: 36 Copynumber: 31.6 Consensus size: 36
130512 TAAGAAGCCA
*
130522 TACAAGTACAAATCTCCTCCTCCTCCTCCCCCAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* **
130558 TACAAGTACAAGTCTCCACCACCTCCAATGCATTCTCCCCCTCCACCT
1 TACAAGTACAAGTCT---CCTCCTCC--T-C---CT--CCC-CCAGTT
* * * * *
130606 TACAAATATAAGTCTCCTCCTCCACCACCACCAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * **** *
130642 TACAAGTACAAATCCCCTCCTCCTCCT-AAGGAGGTA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCA-GTT
*
130678 TACAAGTACAAG-----T-CTCCTCCTCCCCCAGTA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* ** **
130708 TACAAGTACAAGTCGCCTCCTCCTCC-CCCAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCC--CCAG-TT
* * *
130746 TACAAGTACAAGTCTCCTCCACCACCACCCCCAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* *
130782 TACAAATACAAG--T-CTCCTCCACCT---CCAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * ** **
130812 TACAAGTACAAATCCCCTCCTCCTCCTCCCAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCC--CCAG-TT
**** **
130851 TACAAGTACAAGTCTCCTCCTCCTCCT-AAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAG-TT
* * * *
130887 TACAAGTACAAGTCTCCTCCACCACCACCCCTAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * *
130923 TACAAATACAAG--T-CTCCTCCACCT---CCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * *** **
130953 TATAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCC--CCCAG-TT
* * * * *
130992 CACAAGTACAAGTCTCCTCCACCACCACCCCCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * *
131028 TATAAGTACAAG--T-CTCCTCCACCT---CCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* *** **
131058 TACAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCC--CCCAG-TT
* * * *
131097 TACAAGTACAAG--T-CTCCACCACCACCCTCAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * * *
131130 TACAAATACAA--AT-CTCCTCCACCT---CCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* ** **
131160 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCC--CCAG-TT
* * * * * *
131199 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * * * *
131235 TATAAGTACAAGTCTCCTCCACCACCACCCCTAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * *
131271 TACAAATACAAG--T-CTCCTCCACCT---CCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * ** **
131301 TATAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCC--CCAG-TT
* *** * *
131340 TACAAGTACAAGTCTCCTCCTCCACCTAAGGTGCTAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCT---CCCCCAGTT
* * * *** **
131379 TATAAGTACAAGTCTCCTCCACCACC-CCAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCC-CCCAG-TT
* * **
131416 TACAAGTACAAGTCTCCTCCACCACCAACCCCAGTT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* * *
131452 TACAAATACAAG--T-CTCCTCCACCT---CCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* ** **
131482 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCA
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCC--CCAG-TT
* * * * * *
131521 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
* **** *
131557 TATAAGTACAAGTCTCCTCCTCCTCCT-AAGGAGCAT
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAG-TT
* * *
131593 TACAAGTATAAGTCTCCCCCTCCTCC-CCCTCCAGTC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCC-CCAGTT
*
131629 TACAAGTACAAATCTCCTCC
1 TACAAGTACAAGTCTCCTCC
131649 ACCACCATCA
Statistics
Matches: 785, Mismatches: 217, Indels: 178
0.67 0.18 0.15
Matches are distributed among these distances:
30 114 0.15
31 2 0.00
33 125 0.16
34 7 0.01
35 8 0.01
36 248 0.32
37 43 0.05
38 37 0.05
39 167 0.21
40 2 0.00
41 1 0.00
42 2 0.00
45 9 0.01
47 3 0.00
48 17 0.02
ACGTcount: A:0.28, C:0.41, G:0.10, T:0.22
Consensus pattern (36 bp):
TACAAGTACAAGTCTCCTCCTCCTCCTCCCCCAGTT
Found at i:130926 original size:141 final size:142
Alignment explanation
Indices: 130707--131011 Score: 522
Period size: 141 Copynumber: 2.1 Consensus size: 142
130697 CTCCCCCAGT
*
130707 ATACAAGTACAAGTCGCCTCCTCCTCCCCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCACC
1 ATACAAGTACAAGTCTCCTCCTCCT-CCCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCACC
*
130772 ACCCCCAGTTTACAAATACAAGTCTCCTCCACCTCCAGTTTACAAGTACAAATCCCCTCCTCCTC
65 ACCCCCAGTTTACAAATACAAGTCTCCTCCACCTCCAGTCTACAAGTACAAATCCCCTCCTCCTC
130837 CTCCCAAGGAGCC
130 CTCCCAAGGAGCC
*
130850 ATACAAGTACAAGTCTCCTCCTCCT-CCTAAGGAGCCATACAAGTACAAGTCTCCTCCACCACCA
1 ATACAAGTACAAGTCTCCTCCTCCTCCCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCACCA
* * *
130914 CCCCTAGTTTACAAATACAAGTCTCCTCCACCTCCAGTCTATAAGTACAAGTCCCCTCCTCCTCC
66 CCCCCAGTTTACAAATACAAGTCTCCTCCACCTCCAGTCTACAAGTACAAATCCCCTCCTCCTCC
*
130979 TCCTAAGGAGCC
131 TCCCAAGGAGCC
*
130991 ACACAAGTACAAGTCTCCTCC
1 ATACAAGTACAAGTCTCCTCC
131012 ACCACCACCC
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 130 0.84
143 24 0.16
ACGTcount: A:0.28, C:0.40, G:0.10, T:0.21
Consensus pattern (142 bp):
ATACAAGTACAAGTCTCCTCCTCCTCCCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCACCA
CCCCCAGTTTACAAATACAAGTCTCCTCCACCTCCAGTCTACAAGTACAAATCCCCTCCTCCTCC
TCCCAAGGAGCC
Found at i:131035 original size:141 final size:141
Alignment explanation
Indices: 130741--131050 Score: 471
Period size: 141 Copynumber: 2.2 Consensus size: 141
130731 TCCCCCAAGG
130741 AGCCATACAAGTACAAGTCTCCTCCACCACCACCCCCAGTTTACAAATACAAGTCTCCTCCACCT
1 AGCCATACAAGTACAAGTCTCCTCCACCACCACCCCCAGTTTACAAATACAAGTCTCCTCCACCT
* *
130806 CCAGTTTACAAGTACAAATCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCTCC
66 CCAGTCTACAAGTACAAATCCCCTCCTCCTCCTCCCAAGGAGCCACACAAGTACAAGTCTCCTCC
* * **
130871 TCCTCCTAAGG
131 ACCACCTAACC
*
130882 AGCCATACAAGTACAAGTCTCCTCCACCACCACCCCTAGTTTACAAATACAAGTCTCCTCCACCT
1 AGCCATACAAGTACAAGTCTCCTCCACCACCACCCCCAGTTTACAAATACAAGTCTCCTCCACCT
* * *
130947 CCAGTCTATAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGCCACACAAGTACAAGTCTCCTCC
66 CCAGTCTACAAGTACAAATCCCCTCCTCCTCCTCCCAAGGAGCCACACAAGTACAAGTCTCCTCC
*
131012 ACCACC-ACCCCC
131 ACCACCTA--ACC
* *
131024 AGTC-TATAAGTACAAGTCTCCTCCACC
1 AGCCATACAAGTACAAGTCTCCTCCACC
131051 TCCAGTCTAC
Statistics
Matches: 154, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
140 1 0.01
141 150 0.97
142 3 0.02
ACGTcount: A:0.28, C:0.41, G:0.10, T:0.21
Consensus pattern (141 bp):
AGCCATACAAGTACAAGTCTCCTCCACCACCACCCCCAGTTTACAAATACAAGTCTCCTCCACCT
CCAGTCTACAAGTACAAATCCCCTCCTCCTCCTCCCAAGGAGCCACACAAGTACAAGTCTCCTCC
ACCACCTAACC
Found at i:131081 original size:141 final size:138
Alignment explanation
Indices: 130795--131507 Score: 378
Period size: 141 Copynumber: 5.1 Consensus size: 138
130785 AAATACAAGT
* * * * * * *
130795 CTCCTCCACCTCCAGTTTACAAGTACAAATCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTAC
1 CTCCTCCACCTCCAGTCTATAAGTACAAGTCTCCTCCACCTCC-CCTAAGGAGCCACACAAGTAC
*** * * * *
130860 AAGTCTCCTCCTCCTCCTA--AGGAGCCATACAAGTACAAGTCTCCTCCACCACCA-CC-CCTAG
65 AAGTCTCCTCC-CC-CC-ACCCCCAGTC-TACAAGTACAAGTCTCCTCCACCTCCAGCCTACAAG
* ***
130921 TTTACAAATACAAGT-
126 --TACAAGT-CCCCTC
* *
130936 CTCCTCCACCTCCAGTCTATAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGCCACACAAGTAC
1 CTCCTCCACCTCCAGTCTATAAGTACAAGTCTCCTCCACCTCC-CCTAAGGAGCCACACAAGTAC
* *
131001 AAGTCTCCTCCACCACCACCCCCAGTCTATAAGTACAAGTCTCCTCCACCTCCAGTCTACAAGTA
65 AAGTCTCCTCC-CC-CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCTCCAGCCTACAAGTA
131066 CAAGTCCCCTC
128 CAAGTCCCCTC
* ** * * * * * ***
131077 CTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCACCACC-ACCCTCA-G-TTTACA-AA-T
1 CTCCTCCACCT--CCAGTC-TATAAGTACAAGTCTCCTCCACCTCCCCTAAGGAGCCACACAAGT
* * *
131137 ACAAATCTCCT----CCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCC
63 ACAAGTCTCCTCCCCCCACCCCCAGTCTACAAGTACAAGT---CTCCTCCACCT-CC----AGCC
131198 ATACAAGTACAAGTCTCCC-C
120 -TACAAGTACAAGTC-CCCTC
* * * ***
131218 CACCACCACCTCCAGTCTATAAGTACAAGTCTCCTCCACCACCACCCCT-A-G-TTTACA-AA-T
1 CTCCTCCACCTCCAGTCTATAAGTACAAGTCTCCT---CCACCTCCCCTAAGGAGCCACACAAGT
* * *
131278 ACAAGTCTCCT----CCACCTCCAGTCTATAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCC
63 ACAAGTCTCCTCCCCCCACCCCCAGTCTACAAGTACAAGT---CTCCTCCACCT-CC----AGCC
*
131339 ATACAAGTACAAGTCTCCTC
120 -TACAAGTACAAGTCCCCTC
* ** * * *
131359 CTCCACCTAAGGTGCTAGTCTATAAGTACAAGTCTCCTCCACCACCCC-AAGGAGCCATACAAGT
1 CTCCTCC--ACCT-CCAGTCTATAAGTACAAGTCTCCTCCACCTCCCCTAAGGAGCCACACAAGT
* * * *
131423 ACAAGTCTCCTCCACCACCAACCCCAGTTTACAAATACAAGTCTCCTCCACCTCCAGTCTACAAG
63 ACAAGTCTCCTCC-CC-CCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCTCCAGCCTACAAG
131488 TACAAGTCCCCTC
126 TACAAGTCCCCTC
131501 CTCCTCC
1 CTCCTCC
131508 TCCCAAGGAG
Statistics
Matches: 468, Mismatches: 67, Indels: 73
0.77 0.11 0.12
Matches are distributed among these distances:
132 23 0.05
135 10 0.02
136 2 0.00
138 27 0.06
139 5 0.01
140 11 0.02
141 248 0.53
142 40 0.09
143 14 0.03
144 44 0.09
145 12 0.03
147 2 0.00
148 10 0.02
151 20 0.04
ACGTcount: A:0.28, C:0.41, G:0.10, T:0.21
Consensus pattern (138 bp):
CTCCTCCACCTCCAGTCTATAAGTACAAGTCTCCTCCACCTCCCCTAAGGAGCCACACAAGTACA
AGTCTCCTCCCCCCACCCCCAGTCTACAAGTACAAGTCTCCTCCACCTCCAGCCTACAAGTACAA
GTCCCCTC
Found at i:131185 original size:30 final size:30
Alignment explanation
Indices: 131097--131326 Score: 84
Period size: 30 Copynumber: 6.9 Consensus size: 30
131087 TAAGGAGCCA
* *
131097 TACAAGTACAAGTCTCCACCACCACC-CTCAGTT
1 TACAAGTACAAG--TCC-CCTCCACCTC-CAGTC
* * *
131130 TACAAATACAAATCTCCTCCACCTCCAGTC
1 TACAAGTACAAGTCCCCTCCACCTCCAGTC
* *
131160 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCC
1 TACAAGTACAAGT--CC-CCTCCACCT-CC----AGTC
*
131198 ATACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
1 -TACAAGTACAAG--T---CC-CCTCCACCTCCAGTC
* * * *
131235 TATAAGTACAAGTCTCCTCCACCACCACCCCTAGTT
1 TACAAGTACAAG--TCC-CCTCCA-C-CTCC-AGTC
* *
131271 TACAAATACAAGTCTCCTCCACCTCCAGTC
1 TACAAGTACAAGTCCCCTCCACCTCCAGTC
* *
131301 TATAAGTACAAGTCCCCTCCTCCTCC
1 TACAAGTACAAGTCCCCTCCACCTCC
131327 TCCCAAGGAG
Statistics
Matches: 153, Mismatches: 28, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
30 47 0.31
31 6 0.04
32 2 0.01
33 31 0.20
34 5 0.03
35 3 0.02
36 27 0.18
37 3 0.02
38 3 0.02
39 12 0.08
41 3 0.02
42 11 0.07
ACGTcount: A:0.28, C:0.42, G:0.08, T:0.22
Consensus pattern (30 bp):
TACAAGTACAAGTCCCCTCCACCTCCAGTC
Found at i:131480 original size:30 final size:30
Alignment explanation
Indices: 131446--131507 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
131436 ACCACCAACC
* *
131446 CCAGTTTACAAATACAAGTCTCCTCCACCT
1 CCAGTCTACAAATACAAGTCCCCTCCACCT
* *
131476 CCAGTCTACAAGTACAAGTCCCCTCCTCCT
1 CCAGTCTACAAATACAAGTCCCCTCCACCT
131506 CC
1 CC
131508 TCCCAAGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.42, G:0.08, T:0.24
Consensus pattern (30 bp):
CCAGTCTACAAATACAAGTCCCCTCCACCT
Found at i:131544 original size:105 final size:104
Alignment explanation
Indices: 130851--131582 Score: 789
Period size: 105 Copynumber: 7.0 Consensus size: 104
130841 CAAGGAGCCA
* *
130851 TACAAGTACAAGT---CTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCTCCACCACC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
* *
130913 ACCCCTAGTTTACAAATACAAGTCTCCTCCACCTCCAGTC
66 ACCCC-AGTCTACAAGTACAAGTCTCCTCCACCTCCAGTC
* * * *
130953 TATAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGCCACACAAGTACAAGTCTCCTCCACCACC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
*
131018 ACCCCCAGTCTATAAGTACAAGTCTCCTCCACCTCCAGTC
66 A-CCCCAGTCTACAAGTACAAGTCTCCTCCACCTCCAGTC
*
131058 TACAAGTACAAGTCCCCTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCT---CCACCACC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
* * *
131120 ACCCTCAGTTTACAAATACAAATCTCCTCCACCTCCAGTC
66 ACCC-CAGTCTACAAGTACAAGTCTCCTCCACCTCCAGTC
131160 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
* * *
131225 ACCTCCAGTCTATAAGTACAAGTCTCCTCCACCACCACCCCTAGTT
66 ACC-CCAGTCTACAAGTACAAGTCTCCT---CCA-C-CTCC-AGTC
* * * * * *
131271 TACAAATACAAGT---CTCCTCCACCT-CC----AGTC-TATAAGTACAAGTC-CCCTCCTCCTC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCC-CCACCAC
* * * *
131326 CTCCCAAGGAGCCATACAAGTACAAGTCTCCTCCTCCACCTAAGGTGCTAGTC
65 CACCC---CAGTC-TACAAGTACAAG--T-CTCCTCCACC-----T-CCAGTC
* * * * *
131379 TATAAGTACAAGTCTCCTCCACC-AC-CCCAAGGAGCCATACAAGTACAAGTCTCCTCCACCACC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
* *
131442 AACCCCAGTTTACAAATACAAGTCTCCTCCACCTCCAGTC
66 -ACCCCAGTCTACAAGTACAAGTCTCCTCCACCTCCAGTC
131482 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
1 TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
* *
131547 ACCTCCAGTCTATAAGTACAAGTCTCCTCCTCCTCC
66 ACC-CCAGTCTACAAGTACAAGTCTCCTCCACCTCC
131583 TAAGGAGCAT
Statistics
Matches: 532, Mismatches: 55, Indels: 83
0.79 0.08 0.12
Matches are distributed among these distances:
101 7 0.01
102 126 0.24
103 29 0.05
104 9 0.02
105 241 0.45
106 5 0.01
107 3 0.01
108 32 0.06
109 12 0.02
110 7 0.01
111 21 0.04
112 11 0.02
113 2 0.00
114 3 0.01
115 19 0.04
116 5 0.01
ACGTcount: A:0.28, C:0.41, G:0.10, T:0.21
Consensus pattern (104 bp):
TACAAGTACAAGTCCCCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCCCCCACCACC
ACCCCAGTCTACAAGTACAAGTCTCCTCCACCTCCAGTC
Found at i:131610 original size:72 final size:72
Alignment explanation
Indices: 130606--131648 Score: 345
Period size: 69 Copynumber: 14.8 Consensus size: 72
130596 CCCTCCACCT
* * * * * * * * *
130606 TACAAATATAAGTCTCCTCCTCCACCACCACCAGTTTACAAGTACAAATCCCCTCCTCCTCCTAA
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAA
**
130671 GGAGGTA
66 GGAGCCA
* * * *
130678 TACAAGTACAAGTCT---CCTCC-TC-CC-CCAGTATACAAGTACAAGTCGCCTCCTCCTCCCCC
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCT--CCC
130737 AAGGAGCCA
64 AAGGAGCCA
* * * * *
130746 TACAAGTACAAGTCTCCTCCACCACCACCCCCAGTTTACAAATACAAGTCTCCTCCACCT-CC--
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAA
**
130808 --AG-TT
66 GGAGCCA
* * * * * *
130812 TACAAGTACAAATC-CCCTCCTCCTCCTCC-CAAGGAGCCATACAAGTACAAGTCTCCTCCTCCT
1 TACAAGTACAAGTCTCCC-CCACCACCACCTC---CAGTC-TACAAGTACAAGTCTCCTCCTCCT
*
130875 CCTAAGGAGCCA
61 CCCAAGGAGCCA
* * * *
130887 TACAAGTACAAGTCTCCTCCACCACCACC-CCTAGTTTACAAATACAAGTCTCCTCCACCT-CC-
1 TACAAGTACAAGTCTCCCCCACCACCACCTCC-AGTCTACAAGTACAAGTCTCCTCCTCCTCCCA
*
130949 ---AGTC-
65 AGGAGCCA
* * * * ** * * * *
130953 TATAAGTACAAGTC-CCCTCCTCCTCCTCCTAAGGAGCCACACAAGTACAAGTCTCCTCCACCAC
1 TACAAGTACAAGTCTCCC-CCACCACCACCT--CCAGTC-TACAAGTACAAGTCTCCTCCTCCTC
**** *
131017 CACCCCCAGTC-
62 C-CAAGGAGCCA
* *
131028 TATAAGTACAAGTCT------CCTCCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCCTCC
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGT---CTCCTCCTCCTCC
*
131087 TAAGGAGCCA
63 CAAGGAGCCA
* * * * *
131097 TACAAGTACAAGTCTCCACCACCA-C-CCT-CAGTTTACAAATACAAATCTCCTCCACCT-CC--
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAA
*
131156 --AGTC-
66 GGAGCCA
* * * * * * * *
131160 TACAAGTACAAGTC-CCCTCCTCCTCCTCC-CAAGGAGCCATACAAGTACAAGTCTCCCCCACCA
1 TACAAGTACAAGTCTCCC-CCACCACCACCTC---CAGTC-TACAAGTACAAGTCTCCTCCTCCT
**** *
131223 CCACCTCCAGTC-
61 CC-CAAGGAGCCA
* * * * *
131235 TATAAGTACAAGTCTCCTCCACCACCACC-CCTAGTTTACAAATACAAGTCTCCTCCACCT-CC-
1 TACAAGTACAAGTCTCCCCCACCACCACCTCC-AGTCTACAAGTACAAGTCTCCTCCTCCTCCCA
*
131297 ---AGTC-
65 AGGAGCCA
* * * * * * *
131301 TATAAGTACAAGTC-CCCTCCTCCTCCTCC-CAAGGAGCCATACAAGTACAAGTCTCCTCCTCCA
1 TACAAGTACAAGTCTCCC-CCACCACCACCTC---CAGTC-TACAAGTACAAGTCTCCTCCTCCT
* * *
131364 CCTAAGGTGCTA
61 CCCAAGGAGCCA
* * *** * *
131376 GTCTATAAGTACAAGTCTCCTCCACCACC-CCAAGGAGCCATACAAGTACAAGTCTCCTCCACC-
1 ---TACAAGTACAAGTCTCCCCCACCACCACC-TCCAGTC-TACAAGTACAAGTCTCCTCCTCCT
* **
131439 ACCAA--CCCCA
61 CCCAAGGAGCCA
* *
131449 GTTTACAAATACAAGTCT------CCTCCACCTCCAGTCTACAAGTACAAGTCCCCTCCTCCTCC
1 ---TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGT---CTCCTCCTCC
131508 TCCCAAGGAGCCA
60 TCCCAAGGAGCCA
* *
131521 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTATAAGTACAAGTCTCCTCCTCCTCCTAA
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAA
131586 GGAG-CA
66 GGAGCCA
* * * * *
131592 TTACAAGTATAAGTCTCCCCCTCCTCCCCCTCCAGTCTACAAGTACAAATCTCCTCC
1 -TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCC
131649 ACCACCATCA
Statistics
Matches: 739, Mismatches: 142, Indels: 180
0.70 0.13 0.17
Matches are distributed among these distances:
62 2 0.00
63 18 0.02
64 4 0.01
65 9 0.01
66 121 0.16
67 17 0.02
68 39 0.05
69 155 0.21
70 9 0.01
71 12 0.02
72 144 0.19
73 26 0.04
74 30 0.04
75 97 0.13
76 32 0.04
77 2 0.00
78 20 0.03
79 2 0.00
ACGTcount: A:0.28, C:0.40, G:0.10, T:0.21
Consensus pattern (72 bp):
TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTCTACAAGTACAAGTCTCCTCCTCCTCCCAA
GGAGCCA
Found at i:134423 original size:16 final size:16
Alignment explanation
Indices: 134392--134426 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
134382 ACAATTCAGA
*
134392 AAGCAGAAAAATTCTG
1 AAGCAGAAAAACTCTG
*
134408 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAACTCTG
134424 AAG
1 AAG
134427 TATTTCAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (16 bp):
AAGCAGAAAAACTCTG
Found at i:138179 original size:2 final size:2
Alignment explanation
Indices: 138174--138205 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
138164 ACAGAGAGAG
138174 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
138206 GTTATATCTG
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:139290 original size:29 final size:29
Alignment explanation
Indices: 139257--139326 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
139247 ATCCAAACTT
* * *
139257 TTAGGCTTAATTAGATTCAATTTAAAGAA
1 TTAGGCCTAATTAGACTCAATCTAAAGAA
139286 TTAGGCCTAATTAGACTCAATCTAAAGAA
1 TTAGGCCTAATTAGACTCAATCTAAAGAA
139315 TTAGGCCTAATT
1 TTAGGCCTAATT
139327 TGAGCAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (29 bp):
TTAGGCCTAATTAGACTCAATCTAAAGAA
Found at i:149264 original size:21 final size:21
Alignment explanation
Indices: 149240--149282 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
149230 TCTTCTGTAA
149240 ATAAAAGAAAAGGACAAGTGT
1 ATAAAAGAAAAGGACAAGTGT
149261 ATAAAAGAAAAGGACAAGTGT
1 ATAAAAGAAAAGGACAAGTGT
149282 A
1 A
149283 GGGAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.05, G:0.23, T:0.14
Consensus pattern (21 bp):
ATAAAAGAAAAGGACAAGTGT
Found at i:153948 original size:9 final size:9
Alignment explanation
Indices: 153934--153996 Score: 57
Period size: 9 Copynumber: 7.7 Consensus size: 9
153924 GACGAACCCG
153934 TGACCCGAA
1 TGACCCGAA
153943 TGACCCG--
1 TGACCCGAA
* *
153950 TAACCCAAA
1 TGACCCGAA
153959 TGACCCGAA
1 TGACCCGAA
153968 --ACCCGAA
1 TGACCCGAA
153975 TGACCCG-A
1 TGACCCGAA
*
153983 -GACCCGTA
1 TGACCCGAA
153991 TGACCC
1 TGACCC
153997 AAAACTCGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
7 18 0.41
8 2 0.05
9 24 0.55
ACGTcount: A:0.32, C:0.38, G:0.19, T:0.11
Consensus pattern (9 bp):
TGACCCGAA
Found at i:153948 original size:16 final size:16
Alignment explanation
Indices: 153936--154014 Score: 95
Period size: 16 Copynumber: 4.9 Consensus size: 16
153926 CGAACCCGTG
*
153936 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
*
153952 ACCCAAATGACCCGAA
1 ACCCGAATGACCCGAA
*
153968 ACCCGAATGACCCGAG
1 ACCCGAATGACCCGAA
* *
153984 ACCCGTATGACCCAAA
1 ACCCGAATGACCCGAA
* *
154000 ACTCGAATAACCCGA
1 ACCCGAATGACCCGA
154015 GAAATTAACC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.37, C:0.37, G:0.16, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:154148 original size:21 final size:21
Alignment explanation
Indices: 154123--154169 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
154113 TACAATTTAT
154123 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
154144 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
154165 ATTAT
1 ATTAT
154170 AAATTGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:154665 original size:32 final size:30
Alignment explanation
Indices: 154629--154712 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 30
154619 AACCCGCCCA
154629 ACCCGAAACCCGGTAGACCCGAGACCCGAATG
1 ACCCGAAACCC-G-AGACCCGAGACCCGAATG
* *
154661 ACCCGGAACCCGAATGACCCGAGACTCGAATG
1 ACCCGAAACCCG-A-GACCCGAGACCCGAATG
*
154693 ACCCGAGACCCGAGACCCGA
1 ACCCGAAACCCGAGACCCGA
154713 ATAACCCGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 7 0.15
31 3 0.07
32 36 0.78
ACGTcount: A:0.31, C:0.38, G:0.25, T:0.06
Consensus pattern (30 bp):
ACCCGAAACCCGAGACCCGAGACCCGAATG
Found at i:154713 original size:23 final size:22
Alignment explanation
Indices: 154677--154725 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
154667 AACCCGAATG
* *
154677 ACCCGAGACTCGAATGACCCGA
1 ACCCGAGACCCGAATAACCCGA
154699 GACCCGAGACCCGAATAACCCGA
1 -ACCCGAGACCCGAATAACCCGA
154722 ACCC
1 ACCC
154726 AGATGACCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.33, C:0.41, G:0.20, T:0.06
Consensus pattern (22 bp):
ACCCGAGACCCGAATAACCCGA
Found at i:154721 original size:16 final size:16
Alignment explanation
Indices: 154644--154705 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
154634 AAACCCGGTA
154644 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
154660 GACCCG-GAACCCGAAT
1 GACCCGAG-ACCCGAAT
*
154676 GACCCGAGACTCGAAT
1 GACCCGAGACCCGAAT
154692 GACCCGAGACCCGA
1 GACCCGAGACCCGA
154706 GACCCGAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.02
16 40 0.95
17 1 0.02
ACGTcount: A:0.31, C:0.37, G:0.26, T:0.06
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:159490 original size:7 final size:7
Alignment explanation
Indices: 159478--159506 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
159468 AATATCAGGG
159478 TGGGCAT
1 TGGGCAT
159485 TGGGCAT
1 TGGGCAT
159492 TGGGCAT
1 TGGGCAT
159499 TGGGCAT
1 TGGGCAT
159506 T
1 T
159507 TCTGATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.41, T:0.31
Consensus pattern (7 bp):
TGGGCAT
Found at i:161314 original size:20 final size:20
Alignment explanation
Indices: 161289--161330 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
161279 TTATTGACTT
161289 AACCGCACGTACACAACACC
1 AACCGCACGTACACAACACC
161309 AACCGCACGTACACAACACC
1 AACCGCACGTACACAACACC
161329 AA
1 AA
161331 GAGGTTCCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.43, G:0.10, T:0.05
Consensus pattern (20 bp):
AACCGCACGTACACAACACC
Found at i:162167 original size:85 final size:87
Alignment explanation
Indices: 162004--162178 Score: 318
Period size: 85 Copynumber: 2.0 Consensus size: 87
161994 AAACCCAACC
*
162004 TGCCGCTCACCCTCACATTCTCACTCCTCCTCCTTCTTCTTCTTCTATTAAACAAAACCTAATAT
1 TGCCGCTCACCCTCACATTCTCACTCATCCTCCTTC-TCTTCTTCTATTAAACAAAACCTAATAT
162069 TTTCCCCAAATCCCAATTCGGCT
65 TTTCCCCAAATCCCAATTCGGCT
162092 TGCCGCTCACCCTCACATTCTCACTCATCCTCC-TC-CTTCTTCTATTAAACAAAACCTAATATT
1 TGCCGCTCACCCTCACATTCTCACTCATCCTCCTTCTCTTCTTCTATTAAACAAAACCTAATATT
162155 TTCCCCAAATCCCAATTCGGCT
66 TTCCCCAAATCCCAATTCGGCT
162177 TG
1 TG
162179 GATCTCGTCA
Statistics
Matches: 86, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
85 52 0.60
87 2 0.02
88 32 0.37
ACGTcount: A:0.23, C:0.38, G:0.05, T:0.33
Consensus pattern (87 bp):
TGCCGCTCACCCTCACATTCTCACTCATCCTCCTTCTCTTCTTCTATTAAACAAAACCTAATATT
TTCCCCAAATCCCAATTCGGCT
Found at i:162580 original size:29 final size:29
Alignment explanation
Indices: 162538--162596 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
162528 TAATTCATTC
162538 TATGTAATGTTTCTGAATATTATGTTGTT
1 TATGTAATGTTTCTGAATATTATGTTGTT
162567 TATGTAATGTTTCTGAATATTATGTTGTT
1 TATGTAATGTTTCTGAATATTATGTTGTT
162596 T
1 T
162597 CTGAAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.17, T:0.56
Consensus pattern (29 bp):
TATGTAATGTTTCTGAATATTATGTTGTT
Found at i:162836 original size:33 final size:33
Alignment explanation
Indices: 162790--162869 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
162780 CGGGTATATG
*
162790 TAGGGTTC-GGGTACCCTGAAATTTTATAGGGT
1 TAGGGTACAGGGTACCCTGAAATTTTATAGGGT
162822 TAGGGTACAGGGTACCCTGAAATTTTATAGGGT
1 TAGGGTACAGGGTACCCTGAAATTTTATAGGGT
162855 TAGGGTACA-GGTACC
1 TAGGGTACAGGGTACC
162870 GTCATTTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 13 0.28
33 33 0.72
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (33 bp):
TAGGGTACAGGGTACCCTGAAATTTTATAGGGT
Found at i:163727 original size:14 final size:15
Alignment explanation
Indices: 163708--163740 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
163698 TATGCTCATC
*
163708 TCTTTTTTTTCTT-T
1 TCTTTTCTTTCTTGT
163722 TCTTTTCTTTCTTGT
1 TCTTTTCTTTCTTGT
163737 TCTT
1 TCTT
163741 CTTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (15 bp):
TCTTTTCTTTCTTGT
Found at i:164795 original size:28 final size:28
Alignment explanation
Indices: 164763--164834 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
164753 CTGCTTACAT
164763 AAAACTGTAATTGTTTTTGTAGAAAAAG
1 AAAACTGTAATTGTTTTTGTAGAAAAAG
164791 AAAACTGTAATTGTTTTTGTAGAAAAAG
1 AAAACTGTAATTGTTTTTGTAGAAAAAG
164819 AAAACTGTAATTGTTT
1 AAAACTGTAATTGTTT
164835 ATTCTTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (28 bp):
AAAACTGTAATTGTTTTTGTAGAAAAAG
Found at i:165672 original size:3 final size:3
Alignment explanation
Indices: 165666--165707 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
165656 TTAAAATAAA
165666 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
165708 TAATTCTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:169748 original size:14 final size:14
Alignment explanation
Indices: 169729--169769 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
169719 CACTTTGGCC
169729 TTCTTTTCCTTTTT
1 TTCTTTTCCTTTTT
169743 TTC-TTTCTCTTTTT
1 TTCTTTTC-CTTTTT
169757 TT-TTTTCCGTTTT
1 TTCTTTTCC-TTTT
169770 ATTTATTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (14 bp):
TTCTTTTCCTTTTT
Found at i:170627 original size:43 final size:45
Alignment explanation
Indices: 170579--170666 Score: 153
Period size: 43 Copynumber: 2.0 Consensus size: 45
170569 TCGAAATGTC
170579 ATATTTTTAATCCTAGATGT-AAAAAT-AAAAAAAATATTTAATT
1 ATATTTTTAATCCTAGATGTGAAAAATAAAAAAAAATATTTAATT
*
170622 ATATTTTTAATCCTAGATGTGAAAATTAAAAAAAAATATTTAATT
1 ATATTTTTAATCCTAGATGTGAAAAATAAAAAAAAATATTTAATT
170667 TAATATGGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
43 20 0.48
44 5 0.12
45 17 0.40
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.40
Consensus pattern (45 bp):
ATATTTTTAATCCTAGATGTGAAAAATAAAAAAAAATATTTAATT
Found at i:170815 original size:12 final size:12
Alignment explanation
Indices: 170798--170836 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
170788 GTACAGATAT
170798 CGGATATATCGA
1 CGGATATATCGA
170810 CGGATATATCGA
1 CGGATATATCGA
170822 -GG-TAT-T-GA
1 CGGATATATCGA
170830 CGGATAT
1 CGGATAT
170837 TTAATTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.08
9 3 0.12
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:174009 original size:1 final size:1
Alignment explanation
Indices: 174003--174029 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
173993 TCTTTTCCTC
174003 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
174030 GACCAGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:179432 original size:15 final size:15
Alignment explanation
Indices: 179412--179450 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
179402 GTGATAGCTG
179412 AGCTAATGAGGTAGC
1 AGCTAATGAGGTAGC
* **
179427 AGCTAAGGATTTAGC
1 AGCTAATGAGGTAGC
179442 AGCTAATGA
1 AGCTAATGA
179451 TCCATTAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (15 bp):
AGCTAATGAGGTAGC
Found at i:181849 original size:25 final size:26
Alignment explanation
Indices: 181821--181871 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
181811 CAGAATGATT
181821 GAAA-AAAACAGAGGACTTTCCAGGG
1 GAAACAAAACAGAGGACTTTCCAGGG
* *
181846 GAAACAGAACAGAGGATTTTCCAGGG
1 GAAACAAAACAGAGGACTTTCCAGGG
181872 TCTAAACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (26 bp):
GAAACAAAACAGAGGACTTTCCAGGG
Found at i:183578 original size:60 final size:60
Alignment explanation
Indices: 183514--183637 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 60
183504 CTGAAAAGAT
* * * *
183514 TCAATTTAGGGCTCATGCTTTTAATTTGGTTAAAT-GAGACCCTAATGTATGCGAAAATGC
1 TCAATTTAGGACTCATACTTTTAATTTGGTTAAATAG-GACCCTAACGTATACGAAAATGC
* * *
183574 TCAATTTAGGACTCGTACTTTTAATTTGGTTAAATAGGATCCTAGCGTATACGAAAATGC
1 TCAATTTAGGACTCATACTTTTAATTTGGTTAAATAGGACCCTAACGTATACGAAAATGC
183634 TCAA
1 TCAA
183638 ATAAGAACCC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 55 0.98
61 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (60 bp):
TCAATTTAGGACTCATACTTTTAATTTGGTTAAATAGGACCCTAACGTATACGAAAATGC
Found at i:183839 original size:60 final size:60
Alignment explanation
Indices: 183695--183827 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 60
183685 AAGTCCATAT
** * * * * *
183695 TTGAGCATTTGAGCATACGTTAAGGTCCTATTTAACCAAATTCAAAGCATGAGCCCTAAA
1 TTGAGCATTTTCGCATACATTAGGGCCCTATTTAACCAAATTAAAAGCATAAGCCCTAAA
*
183755 TTGAGCATTTTCGCATACATTAGGGCCCTATTTTACCAAATTAAAAGCATAAGCCCTAAA
1 TTGAGCATTTTCGCATACATTAGGGCCCTATTTAACCAAATTAAAAGCATAAGCCCTAAA
183815 TTGAGCATTTTCG
1 TTGAGCATTTTCG
183828 TATATGTTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (60 bp):
TTGAGCATTTTCGCATACATTAGGGCCCTATTTAACCAAATTAAAAGCATAAGCCCTAAA
Found at i:185709 original size:23 final size:23
Alignment explanation
Indices: 185679--185724 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
185669 ATGACATCAA
185679 ATTTCTTTGTTTACATTATATAT
1 ATTTCTTTGTTTACATTATATAT
185702 ATTTCTTTGTTTACATTATATAT
1 ATTTCTTTGTTTACATTATATAT
185725 CGTTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.61
Consensus pattern (23 bp):
ATTTCTTTGTTTACATTATATAT
Found at i:194621 original size:35 final size:33
Alignment explanation
Indices: 194582--194715 Score: 122
Period size: 35 Copynumber: 4.1 Consensus size: 33
194572 TTAAGTCGAT
194582 CTTAATTACCCTGAATTAAGCTAACTACTGACTCA
1 CTTAATTACCCTGAATTAAG-T-ACTACTGACTCA
194617 CTTAATTACCCTGAA-T---TA-T--TGAACT-A
1 CTTAATTACCCTGAATTAAGTACTACTG-ACTCA
* *
194643 CTTAATTACCCTGAATTAAATTGATTACTGACTCA
1 CTTAATTACCCTGAATT-AAGT-ACTACTGACTCA
*
194678 CTTAATTACCCTGAATTAAGTTACTCATTGACTCA
1 CTTAATTACCCTGAATTAAG-TACT-ACTGACTCA
194713 CTT
1 CTT
194716 TTACTCATTG
Statistics
Matches: 83, Mismatches: 3, Indels: 26
0.74 0.03 0.23
Matches are distributed among these distances:
26 18 0.22
27 4 0.05
28 1 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 1 0.01
33 1 0.01
34 8 0.10
35 47 0.57
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (33 bp):
CTTAATTACCCTGAATTAAGTACTACTGACTCA
Found at i:202875 original size:13 final size:13
Alignment explanation
Indices: 202857--202881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202847 GAGTTTTTTT
202857 CTTAAACGATCAA
1 CTTAAACGATCAA
202870 CTTAAACGATCA
1 CTTAAACGATCA
202882 TTTACGTCCT
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:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
CTTAAACGATCAA
Found at i:205429 original size:12 final size:12
Alignment explanation
Indices: 205414--205452 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
205404 CTGATGACGA
205414 TGATGAGGATAG
1 TGATGAGGATAG
205426 TGATGAGGATAG
1 TGATGAGGATAG
205438 TGATGAGGATAG
1 TGATGAGGATAG
205450 TGA
1 TGA
205453 AGGCGAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (12 bp):
TGATGAGGATAG
Found at i:205499 original size:3 final size:3
Alignment explanation
Indices: 205493--205581 Score: 108
Period size: 3 Copynumber: 29.7 Consensus size: 3
205483 AGAAGACGAC
* * *
205493 GAT GAT GAT GAT GAT GAT GAT GTT GAT GAAT -AT GAT TAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G-AT GAT GAT GAT GAT GAT
* * *
205538 GAA GAT GAA GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
205582 GAACCAAGAT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 68 0.94
4 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:206350 original size:1 final size:1
Alignment explanation
Indices: 206344--206372 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
206334 TCTTTGGGTG
206344 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
206373 AGGGGGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:211448 original size:32 final size:32
Alignment explanation
Indices: 211407--211468 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
211397 GCAGGCTGGT
211407 CCTAAACTTTTTATGAGCAAAAGGAAAAAATA
1 CCTAAACTTTTTATGAGCAAAAGGAAAAAATA
211439 CCTAAACTTTTTATGAGCAAAAGGAAAAAA
1 CCTAAACTTTTTATGAGCAAAAGGAAAAAA
211469 AAAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (32 bp):
CCTAAACTTTTTATGAGCAAAAGGAAAAAATA
Found at i:211717 original size:33 final size:33
Alignment explanation
Indices: 211675--211756 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
211665 TTTTTACACT
* *
211675 GAGCCTCCCCACTAGGACGGCTCTG-TCACGGTG
1 GAGCCTCCCCACTAGGACGGCTCAGCT-ACGGCG
*
211708 GAGCCTCCCCACTAGAACGGCTCAGCTACGGCG
1 GAGCCTCCCCACTAGGACGGCTCAGCTACGGCG
*
211741 GAGCCGCCCCACTAGG
1 GAGCCTCCCCACTAGG
211757 GTGGCTAGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 42 0.98
34 1 0.02
ACGTcount: A:0.18, C:0.39, G:0.29, T:0.13
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTCAGCTACGGCG
Found at i:211859 original size:33 final size:33
Alignment explanation
Indices: 211809--211882 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
211799 AAAATAGCTG
211809 AGCCGCCCCAGGAGGGCGGCCTG-CCCATGGTGA
1 AGCCGCCCCAGGAGGGCGGCCTGACCCATGGT-A
* *
211842 AGTCGCCCCAGTG-GGGCGGCTTGACCCATGGTA
1 AGCCGCCCCAG-GAGGGCGGCCTGACCCATGGTA
211875 AGCCGCCC
1 AGCCGCCC
211883 TCCTGGGGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 27 0.75
34 9 0.25
ACGTcount: A:0.15, C:0.36, G:0.36, T:0.12
Consensus pattern (33 bp):
AGCCGCCCCAGGAGGGCGGCCTGACCCATGGTA
Found at i:211890 original size:33 final size:33
Alignment explanation
Indices: 211809--211894 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
211799 AAAATAGCTG
*
211809 AGCCGCCCCA-GGAGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCACTG-GGGCGGCCTGCCCATGGTGA
* * *
211842 AGTCGCCCCAGTGGGGCGGCTTGACCCATGGT-A
1 AGCCGCCCCACTGGGGCGGCCTG-CCCATGGTGA
211875 AGCCGCCCTC-CTGGGGCGGC
1 AGCCGCCC-CACTGGGGCGGC
211895 ACAGGTCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 35 0.78
34 10 0.22
ACGTcount: A:0.13, C:0.36, G:0.38, T:0.13
Consensus pattern (33 bp):
AGCCGCCCCACTGGGGCGGCCTGCCCATGGTGA
Found at i:212450 original size:26 final size:26
Alignment explanation
Indices: 212421--212472 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
212411 GCTTCGCTTG
*
212421 CCTTCTCATCTCTCTACCATAAAGCC
1 CCTTCTCATCTCTCGACCATAAAGCC
*
212447 CCTTCTCATCTTTCGACCATAAAGCC
1 CCTTCTCATCTCTCGACCATAAAGCC
212473 GAGAAGAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.06, T:0.31
Consensus pattern (26 bp):
CCTTCTCATCTCTCGACCATAAAGCC
Found at i:217941 original size:21 final size:21
Alignment explanation
Indices: 217915--217964 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
217905 TCATCAGAAT
217915 GATGATGCAAGCCAAAAGGAA
1 GATGATGCAAGCCAAAAGGAA
*
217936 GATGATGCAAGCCACAAGGAA
1 GATGATGCAAGCCAAAAGGAA
217957 GATGATGC
1 GATGATGC
217965 TGCTAATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.30, T:0.12
Consensus pattern (21 bp):
GATGATGCAAGCCAAAAGGAA
Found at i:231915 original size:16 final size:16
Alignment explanation
Indices: 231894--231926 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
231884 ACTAAGCCAC
231894 AAACTCTCCAATCGTA
1 AAACTCTCCAATCGTA
*
231910 AAACTCTCTAATCGTA
1 AAACTCTCCAATCGTA
231926 A
1 A
231927 GTAGTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (16 bp):
AAACTCTCCAATCGTA
Found at i:232148 original size:31 final size:31
Alignment explanation
Indices: 232110--232192 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 31
232100 ACAACTCTTG
232110 ATTCATGAATAATCACAATATATATTAATTA
1 ATTCATGAATAATCACAATATATATTAATTA
*
232141 ATTCATGAATAATCAC---AT-TATTAATTG
1 ATTCATGAATAATCACAATATATATTAATTA
* *
232168 ATTTAGGAATAATCACATATATATA
1 ATTCATGAATAATCACA-ATATATA
232193 CTACATATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 22 0.50
28 2 0.05
31 18 0.41
32 2 0.05
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (31 bp):
ATTCATGAATAATCACAATATATATTAATTA
Found at i:238804 original size:31 final size:33
Alignment explanation
Indices: 238743--238805 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
238733 CCCAAGAGGG
238743 CGGCATACCGTGGCTCATGCCAACCCCCTGGGA
1 CGGCATACCGTGGCTCATGCCAACCCCCTGGGA
* *
238776 CGGCATACCGTGG-TCGTGCC-GCCCCCTGGG
1 CGGCATACCGTGGCTCATGCCAACCCCCTGGG
238806 GGGGCGCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.32
32 6 0.21
33 13 0.46
ACGTcount: A:0.13, C:0.40, G:0.32, T:0.16
Consensus pattern (33 bp):
CGGCATACCGTGGCTCATGCCAACCCCCTGGGA
Found at i:240401 original size:214 final size:210
Alignment explanation
Indices: 239999--240417 Score: 572
Period size: 214 Copynumber: 2.0 Consensus size: 210
239989 ATTTTTTATC
* * * * *
239999 CACATATCCGATTGAAGTTATTGAAGCGGCAGTTAAAAGGTTATTGCATGATTTAGGACTTTCAT
1 CACATATCCGATTAAAGTTATTCAAGCGGCAGTTAAAAGGTTACTGAATGATTTACGACTTTCAT
*
240064 GAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGC
66 GAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGC
* * * * *
240129 TTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGTCCCTCATATTTTT
131 TTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTT
240194 CTACTTTATACTACT
196 CTACTTTATACTACT
* * * *
240209 CACATGTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGAATGATTTACGACTTTCAT
1 CACATATCCGATTAAAGTTATTCAAGCGGCAGTTAAAAGGTTACTGAATGATTTACGACTTTCAT
* *
240274 GAAGAACCCGAAAG-TTAATTTGAT-TCACGAGTTTCATGAAAGGTTCGCTTGAAAAGGGAATTT
66 GAAGAACCCGAAAGCTAAATTTGATCT-ACGAGTTTCATG-AAGG---G-TTCAAAAGGGAATTT
* * * *
240337 TTATGTTTCAAGATATCCATTAAGATATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCAT
125 TTATGCTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCAT
*
240402 ACTTTTCTATTTTATA
190 ACTTTTCTACTTTATA
240418 TTTTATGCTA
Statistics
Matches: 181, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
208 1 0.01
209 21 0.12
210 73 0.40
213 1 0.01
214 85 0.47
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (210 bp):
CACATATCCGATTAAAGTTATTCAAGCGGCAGTTAAAAGGTTACTGAATGATTTACGACTTTCAT
GAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGC
TTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTT
CTACTTTATACTACT
Found at i:240937 original size:21 final size:22
Alignment explanation
Indices: 240891--240937 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
240881 CAGGTCTCTC
*
240891 ATTCTCATTCTCTCCTTTTTTT
1 ATTCTCATGCTCTCCTTTTTTT
240913 -TTCTCA-GCTCT-CTTTTCTTT
1 ATTCTCATGCTCTCCTTTT-TTT
240933 ATTCT
1 ATTCT
240938 TCCAATTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTCTCATGCTCTCCTTTTTTT
Found at i:241725 original size:12 final size:13
Alignment explanation
Indices: 241700--241732 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
241690 GGTTGTTTTC
*
241700 TTTTTTCTATCTT
1 TTTTTTCTAACTT
241713 TTTTTTC-AACTT
1 TTTTTTCTAACTT
241725 TTTTTTCT
1 TTTTTTCT
241733 TTTTGTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCTAACTT
Found at i:245055 original size:28 final size:28
Alignment explanation
Indices: 245018--245076 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
245008 TGGTAAATTC
245018 AAAATCAAAGATGTTAGAGATCTAGTCA
1 AAAATCAAAGATGTTAGAGATCTAGTCA
245046 AAAATCAAAGATGTTAGAGATCTAGTCA
1 AAAATCAAAGATGTTAGAGATCTAGTCA
245074 AAA
1 AAA
245077 TGGCTCAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAATCAAAGATGTTAGAGATCTAGTCA
Found at i:246180 original size:1 final size:1
Alignment explanation
Indices: 246174--246207 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
246164 TCGGTTCAAG
*
246174 TTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
246208 AAATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:270006 original size:27 final size:27
Alignment explanation
Indices: 269951--270008 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
269941 TTTGCTACTC
* * ** *
269951 AACTTTTCCTACTCCTTTACATTATCA
1 AACTGTTCCTACTCCTTAACAACACCA
269978 AACTGTTCCTACTCCTTAACAACACCA
1 AACTGTTCCTACTCCTTAACAACACCA
270005 AACT
1 AACT
270009 ACACCAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACACCA
Found at i:271063 original size:2 final size:2
Alignment explanation
Indices: 271051--271081 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
271041 AAACTAGGAA
271051 AT AT CAT 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
271082 TGCCTACCCC
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:273449 original size:2 final size:2
Alignment explanation
Indices: 273437--273472 Score: 54
Period size: 2 Copynumber: 17.0 Consensus size: 2
273427 TAATCACATC
273437 AT AT AT CAT AT AT AT CAT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
273473 TAAAACTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 28 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:273451 original size:9 final size:8
Alignment explanation
Indices: 273437--273472 Score: 54
Period size: 9 Copynumber: 4.2 Consensus size: 8
273427 TAATCACATC
273437 ATATATCAT
1 ATATAT-AT
273446 ATATATCAT
1 ATATAT-AT
273455 ATATATAT
1 ATATATAT
273463 ATATATAT
1 ATATATAT
273471 AT
1 AT
273473 TAAAACTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (8 bp):
ATATATAT
Done.