Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold104
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: 327367
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 3 of 3
Found at i:256828 original size:60 final size:60
Alignment explanation
Indices: 256695--257862 Score: 1758
Period size: 61 Copynumber: 19.2 Consensus size: 60
256685 TAGCCATTCC
* *
256695 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
*
256756 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTCT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
256816 AGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
256876 AGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
*
256937 AGTCCTCAAAGAGCAGGACGTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
256997 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTC--CTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* *
257061 AGTCCTCAAAGAGCAAGACGC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
257120 AGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257181 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257241 AGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * *
257302 AGTCCTCAAAGAGTAGGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
257362 AGTCCTCAAAGAGCAGGATGCCTTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257423 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTGT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
257483 AGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257544 AGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
257604 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACTCAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * * * * *
257665 AGTCCTCAAAAAGCAGGAC-ATATTTTTCTTTCAAAGCCGACACAAGTTGGTGGCACCCTCT
1 AGTCCTCAAAGAGCAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * * *
257726 AGTCCTCAAGGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACATGTTGGTGGCA-CTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * * *
257785 CCAGTCCTCAAAGAGTAGGACGCCTTTT-CTTTTCAAAGACCACACTAGTTAGTGGCACTTTT
1 --AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
257847 CAGTCCTCAAAGAGCA
1 -AGTCCTCAAAGAGCA
257863 TGGCACACTT
Statistics
Matches: 1025, Mismatches: 61, Indels: 42
0.91 0.05 0.04
Matches are distributed among these distances:
59 27 0.03
60 435 0.42
61 477 0.47
62 62 0.06
63 1 0.00
64 23 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:256940 original size:121 final size:120
Alignment explanation
Indices: 256695--257862 Score: 1783
Period size: 121 Copynumber: 9.6 Consensus size: 120
256685 TAGCCATTCC
* *
256695 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTAGTC
*
256760 CTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTCT
65 CTCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
256816 AGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
*
256880 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
65 CTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
*
256937 AGTCCTCAAAGAGCAGGACGTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTAGTC
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
257001 CTCAAAGAGCAGGACGCCTTTTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
65 CTCAAAGAGCAGGACGCCTTTTTC-T-TTT-AAAGCCCACACAAGTTGGTGGCA-CCTTT
* *
257061 AGTCCTCAAAGAGCAAGACGC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
257125 TCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
66 TCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257181 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
*
257246 TCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
66 TCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * *
257302 AGTCCTCAAAGAGTAGGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
* *
257367 TCAAAGAGCAGGATGCCTTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACCTTT
66 TCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257423 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTGTAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
257488 TCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
66 TCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
257544 AGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
* * *
257609 TCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACTCAAGTTGGTGGCACCCTTT
66 TCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * * * * *
257665 AGTCCTCAAAAAGCAGGAC-ATATTTTTCTTTCAAAGCCGACACAAGTTGGTGGCACCCTCTAGT
1 AGTCCTCAAAGAGCAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTAGT
* * * *
257729 CCTCAAGGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACATGTTGGTGGCA-CTTT
64 CCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * * *
257785 CCAGTCCTCAAAGAGTAGGACGCCTTTT-CTTTTCAAAGACCACACTAGTTAGTGGCACTTTTCA
1 --AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT-A
257849 GTCCTCAAAGAGCA
62 GTCCTCAAAGAGCA
257863 TGGCACACTT
Statistics
Matches: 970, Mismatches: 57, Indels: 39
0.91 0.05 0.04
Matches are distributed among these distances:
120 135 0.14
121 550 0.57
122 202 0.21
123 34 0.04
124 49 0.05
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (120 bp):
AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
TCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:257932 original size:40 final size:40
Alignment explanation
Indices: 257849--257992 Score: 128
Period size: 42 Copynumber: 3.4 Consensus size: 40
257839 GCACTTTTCA
257849 GTCCTCAAAGAGCATGG-CACACTTCTTTCCCTTCTTCTCTCTTTT
1 GTCCTCAAAGAGCA-GGACACACTTCTTT-CC--C-T-TCTCTTTT
257894 GTCCTCAAAGAGCAGGACACACTTCTTTCCCTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCTTTCCCTTCTCTTTT
* * * * * * *
257934 GTCCTTAAAGAACATGACGCACTTTATTTTCCTTTTTCTTTT
1 GTCCTCAAAGAGCAGGACACAC-TT-CTTTCCCTTCTCTTTT
* *
257976 GTCCTTAGAGAGCAGGA
1 GTCCTCAAAGAGCAGGA
257993 AGTATTTCGT
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
40 26 0.30
41 3 0.03
42 28 0.33
44 4 0.05
45 25 0.29
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (40 bp):
GTCCTCAAAGAGCAGGACACACTTCTTTCCCTTCTCTTTT
Found at i:258830 original size:27 final size:27
Alignment explanation
Indices: 258778--258961 Score: 181
Period size: 27 Copynumber: 6.2 Consensus size: 27
258768 ACACGGAATG
*
258778 ATGGGCATGGAATAAAAAAAATGAAGGC
1 ATGGGCATGGAAT-AAAAAATTGAAGGC
258806 ATGGGCATGGAATAAAAAATTGAAGGC
1 ATGGGCATGGAATAAAAAATTGAAGGC
*
258833 ATGGAGTGATGGGCATGGAATAAAAAAATGAAGGC
1 --------ATGGGCATGGAATAAAAAATTGAAGGC
258868 ATGGGCATGGAATAAAAAATTGAAGGC
1 ATGGGCATGGAATAAAAAATTGAAGGC
258895 ATGGAGTGATGGGCATGGAATAAAAAA-TGAAGGC
1 --------ATGGGCATGGAATAAAAAATTGAAGGC
258929 ATGGGCATGGAATAAAAAAATTGAAGGC
1 ATGGGCATGGAAT-AAAAAATTGAAGGC
258957 ATGGG
1 ATGGG
258962 ATGATGGGCT
Statistics
Matches: 135, Mismatches: 3, Indels: 36
0.78 0.02 0.21
Matches are distributed among these distances:
26 13 0.10
27 45 0.33
28 25 0.19
34 7 0.05
35 45 0.33
ACGTcount: A:0.44, C:0.07, G:0.32, T:0.17
Consensus pattern (27 bp):
ATGGGCATGGAATAAAAAATTGAAGGC
Found at i:258852 original size:35 final size:35
Alignment explanation
Indices: 258806--258932 Score: 182
Period size: 35 Copynumber: 3.9 Consensus size: 35
258796 AAATGAAGGC
258806 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
1 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
*
258841 ATGGGCATGGAATAAAAAAATGAAGGC--------
1 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
258868 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
1 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
258903 ATGGGCATGGAATAAAAAA-TGAAGGCATGG
1 ATGGGCATGGAATAAAAAATTGAAGGCATGG
258933 GCATGGAATA
Statistics
Matches: 82, Mismatches: 2, Indels: 17
0.81 0.02 0.17
Matches are distributed among these distances:
27 26 0.32
34 11 0.13
35 45 0.55
ACGTcount: A:0.43, C:0.06, G:0.33, T:0.18
Consensus pattern (35 bp):
ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
Found at i:258875 original size:62 final size:62
Alignment explanation
Indices: 258776--258970 Score: 349
Period size: 62 Copynumber: 3.1 Consensus size: 62
258766 AAACACGGAA
258776 TGATGGGCATGGAATAAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
1 TGATGGGCATGGAAT-AAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
258839 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
258901 TGATGGGCATGGAAT-AAAAAATGAAGGCATGGGCATGGAATAAAAAAATTGAAGGCATGG-G
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAAT-AAAAAATTGAAGGCATGGAG
258962 ATGATGGGC
1 -TGATGGGC
258971 TCAAGGATGT
Statistics
Matches: 130, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
61 27 0.21
62 88 0.68
63 15 0.12
ACGTcount: A:0.43, C:0.07, G:0.33, T:0.18
Consensus pattern (62 bp):
TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
Found at i:258932 original size:26 final size:28
Alignment explanation
Indices: 258903--258961 Score: 104
Period size: 26 Copynumber: 2.2 Consensus size: 28
258893 GCATGGAGTG
258903 ATGGGCATGGAAT-AAAAAA-TGAAGGC
1 ATGGGCATGGAATAAAAAAATTGAAGGC
258929 ATGGGCATGGAATAAAAAAATTGAAGGC
1 ATGGGCATGGAATAAAAAAATTGAAGGC
258957 ATGGG
1 ATGGG
258962 ATGATGGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 13 0.42
27 6 0.19
28 12 0.39
ACGTcount: A:0.44, C:0.07, G:0.32, T:0.17
Consensus pattern (28 bp):
ATGGGCATGGAATAAAAAAATTGAAGGC
Found at i:259838 original size:53 final size:50
Alignment explanation
Indices: 259730--259854 Score: 146
Period size: 53 Copynumber: 2.4 Consensus size: 50
259720 AATTGCTCGT
*
259730 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCCTTT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-CTTC
* **
259781 AATCGAGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTAATTT-TTCAC
1 AATC--GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCTT--C
259834 AATCGGGGATACTCCAACCCC
1 AATCGGGGATACTCCAACCCC
259855 ATTATTGTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
51 23 0.35
52 4 0.06
53 38 0.58
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (50 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTTC
Found at i:260010 original size:79 final size:79
Alignment explanation
Indices: 259784--260091 Score: 449
Period size: 79 Copynumber: 3.9 Consensus size: 79
259774 TTCCTTTAAT
* *
259784 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
*
259849 AACCCCATTATTGT-
66 AACCCCGTTATT-TC
* * * *
259863 TGAGGGGATACTCCAA-CCCGGTTTTATCTCTAAAATATTAATTTTTCACAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
259927 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* * *
259941 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCAGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
260006 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* * * * **
260020 CGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTGCATAATCCGGGATACTTT
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
260085 AACCCCG
66 AACCCCG
260092 ATTTTATTTT
Statistics
Matches: 211, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
77 1 0.00
78 73 0.35
79 137 0.65
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (79 bp):
CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
AACCCCGTTATTTC
Found at i:261169 original size:19 final size:18
Alignment explanation
Indices: 261145--261242 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 18
261135 TAGCTTACAT
261145 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAA-TTA
261164 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
*
261177 TGTATCGATACAACACTTA
1 TGTATCGATACAA-AATTA
*
261196 AGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
*
261209 TGTATCGATACAACATTTTA
1 TGTATCGATACAA-A-ATTA
261229 TGTATCGATACAAA
1 TGTATCGATACAAA
261243 TTGTTGAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 26
0.66 0.05 0.28
Matches are distributed among these distances:
13 21 0.34
14 2 0.03
16 1 0.02
18 1 0.02
19 23 0.38
20 13 0.21
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAAATTA
Found at i:261181 original size:32 final size:32
Alignment explanation
Indices: 261140--261240 Score: 157
Period size: 32 Copynumber: 3.1 Consensus size: 32
261130 GGCAGTAGCT
261140 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
* *
261172 TACATTGTATCGATACAACACTTAAGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
**
261204 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAA-AACTTATGTATCGA
261237 TACA
1 TACA
261241 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 48 0.77
33 14 0.23
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:261182 original size:13 final size:13
Alignment explanation
Indices: 261164--261220 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
261154 ACAAAACTTA
261164 TGTATCGATACAT
1 TGTATCGATACAT
261177 TGTATCGATACAACACT
1 TGTATCGAT---ACA-T
261194 TAAGTATCGATACAT
1 T--GTATCGATACAT
261209 TGTATCGATACA
1 TGTATCGATACA
261221 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 20 0.53
15 2 0.05
16 6 0.16
17 2 0.05
19 8 0.21
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262342 original size:49 final size:49
Alignment explanation
Indices: 262017--262893 Score: 1109
Period size: 49 Copynumber: 18.1 Consensus size: 49
262007 CTTAGGAATG
* *
262017 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262066 TTAAAGATGACAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
262118 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
262170 TT----A--AAGGTGCCAATGTGCTGAATCAAGGCCAGCGACATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262213 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * * *
262263 TT---G--G-AGTTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262306 TTAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * * * *
262355 TT---G--G-AGTTGCCAATGTACTTATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262398 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262447 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262499 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
262548 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262597 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
262646 TTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
262698 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
262747 TTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
262799 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
262842 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
262891 TTA
1 TTA
262894 GAAGGGTTGC
Statistics
Matches: 727, Mismatches: 64, Indels: 74
0.84 0.07 0.09
Matches are distributed among these distances:
43 144 0.20
44 2 0.00
46 4 0.01
47 1 0.00
48 5 0.01
49 312 0.43
50 37 0.05
52 222 0.31
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
Found at i:262538 original size:101 final size:101
Alignment explanation
Indices: 262375--262893 Score: 846
Period size: 101 Copynumber: 5.3 Consensus size: 101
262365 CAATGTACTT
* *
262375 ATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
*
262440 ATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
66 ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
262476 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
*
262541 ATTGGACTTAAAGATG---ATGGTGCCAATATGCTG
66 ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
*
262574 ATTCAAGGCCAGCAATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
* *
262639 ATTGGACTTAAAGATGACAAAGGCGCCAATATGCTA
66 ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
262675 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
262740 ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
66 ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
* * *
262776 ATTCAAGGCCAGCGATATTGGACTT--A-A--A-GGTGCCAATGTGCTGATTCAAGGCCAGCTAC
1 ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
262835 ATTGGACTTAAAGAT---AAAGGTGCCAATATGCTG
66 ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
* *
262868 ATTCAAGGCCAGTGATATTGGGCTTA
1 ATTCAAGGCCAGCGATATTGGACTTA
262894 GAAGGGTTGC
Statistics
Matches: 398, Mismatches: 16, Indels: 16
0.93 0.04 0.04
Matches are distributed among these distances:
92 41 0.10
95 43 0.11
96 1 0.00
98 96 0.24
99 1 0.00
101 216 0.54
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (101 bp):
ATTCAAGGCCAGCGATATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
ATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
Found at i:262946 original size:33 final size:33
Alignment explanation
Indices: 262893--263128 Score: 311
Period size: 33 Copynumber: 7.2 Consensus size: 33
262883 TATTGGGCTT
*
262893 AGAAGGGTTGCCACCGACTTGTATGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
262926 AGAATGGTTACCACCTACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
262959 AG-AGGGTTGCCACCGACTTGAGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
262990 AGAAGGGTTGCCACCGACTTGTATGGGCTTCAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
263023 AAGAA-GGTTGCCACAGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
263056 AGAAGGGTTGCCATCGACTTGTGTGGGCTTGAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
263089 AAGAA-GGTTGCCACTGACTTGTGTGGGCTTTA-
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
263121 AAAAGGGT
1 AGAAGGGT
263129 GAAAGATGCC
Statistics
Matches: 176, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.03
32 56 0.32
33 106 0.60
34 8 0.05
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:263088 original size:97 final size:96
Alignment explanation
Indices: 262886--263118 Score: 335
Period size: 97 Copynumber: 2.4 Consensus size: 96
262876 CCAGTGATAT
* **
262886 TGGGCTT-AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAGAATGGTTACCACCTACTTGTGT
1 TGGGCTTGAGAAGGGTTGCCACCGACTTGTATGGGCTTCAGAGAATGGTTACCACAGACTTGTGT
262950 GGGCTTTAGAGAGGGTTGCCACCGACTTGAG
66 GGGCTTTAGAGAGGGTTGCCACCGACTTGAG
*
262981 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTATGGGCTTCAGAAGAA-GGTTGCCACAGACTTGT
1 TGGGC-TTGAGAAGGGTTGCCACCGACTTGTATGGGCTTCAG-AGAATGGTTACCACAGACTTGT
* *
263045 GTGGGCTTTAGAGAAGGGTTGCCATCGACTTGTG
64 GTGGGCTTTAGAG-AGGGTTGCCACCGACTTGAG
* *
263079 TGGGCTTGAGAAGAAGGTTGCCACTGACTTGTGTGGGCTT
1 TGGGCTTGAGAAG--GGTTGCCACCGACTTGTATGGGCTT
263119 TAAAAAGGGT
Statistics
Matches: 124, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
95 5 0.04
96 2 0.02
97 67 0.54
98 27 0.22
99 23 0.19
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (96 bp):
TGGGCTTGAGAAGGGTTGCCACCGACTTGTATGGGCTTCAGAGAATGGTTACCACAGACTTGTGT
GGGCTTTAGAGAGGGTTGCCACCGACTTGAG
Found at i:263174 original size:35 final size:33
Alignment explanation
Indices: 263130--263258 Score: 116
Period size: 34 Copynumber: 3.8 Consensus size: 33
263120 AAAAAGGGTG
*
263130 AAAGATGCCACGAAGTTGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGAAGTTGTGGACTTTAAAA-GAA
* *
263163 CAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 -AAAG-GTGCCACGAAGTTGTGGACTTT-AAAAGAA
* * * * *
263199 TAAGGTGCGAAGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGAAGTTGTGGACTTT-AAAAGAA
**
263233 AAAGGTGCCACGAAGTCATGGACTTT
1 AAAGGTGCCACGAAGTTGTGGACTTT
263259 GGAAAGAGAT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
34 50 0.64
35 19 0.24
36 5 0.06
37 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGAAGTTGTGGACTTTAAAAGAA
Found at i:263217 original size:34 final size:34
Alignment explanation
Indices: 263143--263240 Score: 117
Period size: 34 Copynumber: 2.9 Consensus size: 34
263133 GATGCCACGA
* * * *
263143 AGTTGTGGAC-TTAAAAGGAACAAAGAGTGCCACGG
1 AGTTGTGGGCTTTAAAAAGAA-AAAG-GTGCGAAGG
* *
263178 AGTTGTGGGCTTTGAAAAGAATAAGGTGCGAAGG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCGAAGG
263212 AGTTGTGGGCTTTAAAAAGAAAAAGGTGC
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGC
263241 CACGAAGTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 34 0.63
35 12 0.22
36 8 0.15
ACGTcount: A:0.36, C:0.09, G:0.34, T:0.21
Consensus pattern (34 bp):
AGTTGTGGGCTTTAAAAAGAAAAAGGTGCGAAGG
Found at i:263272 original size:30 final size:31
Alignment explanation
Indices: 263238--263361 Score: 98
Period size: 30 Copynumber: 4.0 Consensus size: 31
263228 AAGAAAAAGG
263238 TGCCAC-GAAGTCATGGACTTTGGAAAGAGA
1 TGCCACTGAAGTCATGGACTTTGGAAAGAGA
** *
263268 TGCCACTGAA-TTGTGGACTTTGAGACA-AGA
1 TGCCACTGAAGTCATGGACTTTG-GAAAGAGA
* **
263298 TGCCACT-AAGTCGTGGACATTAAGAAGAGAAGA
1 TGCCACTGAAGTCATGGAC-TTTGGAA-AG-AGA
*
263331 TGCCACTG-AGTCATGGGCTTT-GAGAAGAGA
1 TGCCACTGAAGTCATGGACTTTGGA-AAGAGA
263361 T
1 T
263362 TTGAAGAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
29 2 0.03
30 39 0.52
31 13 0.17
32 3 0.04
33 18 0.24
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (31 bp):
TGCCACTGAAGTCATGGACTTTGGAAAGAGA
Found at i:263334 original size:33 final size:33
Alignment explanation
Indices: 263294--263360 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
263284 ACTTTGAGAC
*
263294 AAGATGCCACTAAGTCGTGGACATTAAGAAGAG
1 AAGATGCCACTAAGTCATGGACATTAAGAAGAG
* * * *
263327 AAGATGCCACTGAGTCATGGGCTTTGAGAAGAG
1 AAGATGCCACTAAGTCATGGACATTAAGAAGAG
263360 A
1 A
263361 TTTGAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (33 bp):
AAGATGCCACTAAGTCATGGACATTAAGAAGAG
Found at i:263487 original size:16 final size:17
Alignment explanation
Indices: 263456--263493 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
263446 GATGCAAATA
* *
263456 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
263473 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
263489 ATGAT
1 ATGAT
263494 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:264355 original size:17 final size:16
Alignment explanation
Indices: 264315--264367 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
264305 CTTTCTTCTT
*
264315 TTTTTTG-TTTGTTTG
1 TTTTTTGTTTTGTTTC
*
264330 TTTCTTT-TTTT-TTCC
1 TTT-TTTGTTTTGTTTC
264345 TTTTTTGTTTTGTTTC
1 TTTTTTGTTTTGTTTC
264361 TTTTTTG
1 TTTTTTG
264368 GAAAAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 3 0.10
15 12 0.39
16 16 0.52
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (16 bp):
TTTTTTGTTTTGTTTC
Found at i:264363 original size:27 final size:24
Alignment explanation
Indices: 264306--264366 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 24
264296 GGGTTTTTCC
*
264306 TTTCTTCTTTTTTTTGTTTGTTTG
1 TTTCTTTTTTTTTTTGTTTGTTTG
*
264330 TTTCTTTTTTTTTCCTTTTTTGTTTTG
1 TTTCTTTTTTTTT--TTGTTTG-TTTG
264357 TTTCTTTTTT
1 TTTCTTTTTT
264367 GGAAAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 12 0.38
26 6 0.19
27 14 0.44
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (24 bp):
TTTCTTTTTTTTTTTGTTTGTTTG
Found at i:264621 original size:12 final size:12
Alignment explanation
Indices: 264604--264644 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
264594 CCTTTGCACC
264604 TTTTTTTTGTGT
1 TTTTTTTTGTGT
264616 TTTTTTTTGTTTTGT
1 TTTTTTTTG---TGT
264631 TTTTTTTTGTGT
1 TTTTTTTTGTGT
264643 TT
1 TT
264645 ACTTTTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 14 0.54
15 12 0.46
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGTGT
Found at i:264622 original size:15 final size:15
Alignment explanation
Indices: 264604--264640 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
264594 CCTTTGCACC
*
264604 TTTTTT-TTGTGTTT
1 TTTTTTGTTTTGTTT
264618 TTTTTTGTTTTGTTT
1 TTTTTTGTTTTGTTT
264633 TTTTTTGT
1 TTTTTTGT
264641 GTTTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (15 bp):
TTTTTTGTTTTGTTT
Found at i:269368 original size:27 final size:27
Alignment explanation
Indices: 269330--269396 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
269320 GGTTGAAAAC
269330 GGGGTTGGAGTGTCCCCTCGGAAGAAT
1 GGGGTTGGAGTGTCCCCTCGGAAGAAT
269357 GGGGTTGGAGTGTCCCCTCGGAAGAAT
1 GGGGTTGGAGTGTCCCCTCGGAAGAAT
269384 GGGGTTGGAGTGT
1 GGGGTTGGAGTGT
269397 GTCCGATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.16, C:0.15, G:0.45, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCGGAAGAAT
Found at i:269749 original size:38 final size:38
Alignment explanation
Indices: 269698--269775 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
269688 AAGGTAACTC
269698 AATGGGGGTCGATCTAAAAATATTCCAAAAATCCAGAA
1 AATGGGGGTCGATCTAAAAATATTCCAAAAATCCAGAA
269736 AATGGGGGTCGATCTAAAAATATTCCAAAAATCCAGAA
1 AATGGGGGTCGATCTAAAAATATTCCAAAAATCCAGAA
269774 AA
1 AA
269776 ATCCCTTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (38 bp):
AATGGGGGTCGATCTAAAAATATTCCAAAAATCCAGAA
Found at i:271641 original size:52 final size:52
Alignment explanation
Indices: 271563--271743 Score: 344
Period size: 52 Copynumber: 3.5 Consensus size: 52
271553 CGAAATATGA
*
271563 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
271615 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
271667 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
271719 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
271744 AAGATCAGTG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:271770 original size:13 final size:13
Alignment explanation
Indices: 271752--271776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271742 CAAAGATCAG
271752 TGTATCGATACAA
1 TGTATCGATACAA
271765 TGTATCGATACA
1 TGTATCGATACA
271777 TTTTCTTGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:271823 original size:19 final size:18
Alignment explanation
Indices: 271799--271896 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
271789 TAGCTTACAT
271799 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAA-TTA
271818 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
*
271831 TGTATCGATACAACACTTA
1 TGTATCGATACAA-AATTA
271850 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
*
271863 TGTATCGATACAACATTTTA
1 TGTATCGATACAA-A-ATTA
271883 TGTATCGATACAAA
1 TGTATCGATACAAA
271897 TCGTTGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 26
0.68 0.03 0.28
Matches are distributed among these distances:
13 22 0.35
14 2 0.03
16 1 0.02
18 1 0.02
19 24 0.38
20 13 0.21
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAAATTA
Found at i:271835 original size:32 final size:32
Alignment explanation
Indices: 271794--271894 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
271784 GGCAGTAGCT
271794 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
271826 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
**
271858 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAA-AACTTATGTATCGA
271891 TACA
1 TACA
271895 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:271836 original size:13 final size:13
Alignment explanation
Indices: 271818--271874 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
271808 ACAAAACTTA
271818 TGTATCGATACAT
1 TGTATCGATACAT
271831 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
271849 ATGTATCGATACAT
1 -TGTATCGATACAT
271863 TGTATCGATACA
1 TGTATCGATACA
271875 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:274926 original size:20 final size:20
Alignment explanation
Indices: 274901--274972 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
274891 AAAACCTAGA
*
274901 TGTATCAATACAATGTTCTT
1 TGTATCGATACAATGTTCTT
*
274921 TGTATCGATACAATGTTTTT
1 TGTATCGATACAATGTTCTT
274941 TGTATCGATACAATGTTCTT
1 TGTATCGATACAATGTTCTT
*
274961 TGTATTGATACA
1 TGTATCGATACA
274973 TTGTATTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (20 bp):
TGTATCGATACAATGTTCTT
Found at i:274978 original size:13 final size:13
Alignment explanation
Indices: 274960--274999 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
274950 ACAATGTTCT
274960 TTGTATTGATACA
1 TTGTATTGATACA
274973 TTGTATTGATACA
1 TTGTATTGATACA
*
274986 ATGTATTGATACA
1 TTGTATTGATACA
274999 T
1 T
275000 GGGTTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:277559 original size:32 final size:32
Alignment explanation
Indices: 277516--277593 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
277506 AGATTATGCT
*
277516 TTGTATCGATACATTCTATCAATACATGTTCA
1 TTGTATCGATACATTCTATCAATACATCTTCA
* *
277548 TTGTATTGATACATTGTATCAATACATCTTCA
1 TTGTATCGATACATTCTATCAATACATCTTCA
277580 TTGTATCGATACAT
1 TTGTATCGATACAT
277594 GCACTATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (32 bp):
TTGTATCGATACATTCTATCAATACATCTTCA
Found at i:283758 original size:52 final size:52
Alignment explanation
Indices: 283688--283808 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
283678 GAAAATTTAT
*
283688 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
283740 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
283792 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
283809 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:283821 original size:52 final size:51
Alignment explanation
Indices: 283688--283828 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
283678 GAAAATTTAT
283688 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
283740 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
283792 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
283829 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:283835 original size:13 final size:13
Alignment explanation
Indices: 283817--283841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
283807 CAAAGATCAG
283817 TGTATCGATACAA
1 TGTATCGATACAA
283830 TGTATCGATACA
1 TGTATCGATACA
283842 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:284847 original size:67 final size:67
Alignment explanation
Indices: 284730--284856 Score: 191
Period size: 67 Copynumber: 1.9 Consensus size: 67
284720 TTTTTAGAGA
* * *
284730 TGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAA
1 TGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGAGAAA
284795 AG
66 AG
* * * *
284797 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAAGATG
1 TGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
284857 CCAATATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (67 bp):
TGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGAGAAA
AG
Found at i:284858 original size:49 final size:49
Alignment explanation
Indices: 284802--285765 Score: 1354
Period size: 49 Copynumber: 20.0 Consensus size: 49
284792 AAAAGTGATA
* * * *
284802 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
284851 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * *
284897 --G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
284943 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * *
284989 --G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285035 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * *
285084 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285133 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285182 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * *
285228 --G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285274 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * *
285323 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
285372 AAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * * *
285421 AAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285470 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * *
285519 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285568 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * *
285617 AAGGTGCCAATGTGCTGAGTT-AAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGA-TTCAAGGCCAGCGATATTGGACTTAAAGATG
*
285666 AAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * *
285715 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
285764 AA
1 AA
285766 AAAGGCCAGC
Statistics
Matches: 808, Mismatches: 87, Indels: 40
0.86 0.09 0.04
Matches are distributed among these distances:
43 102 0.13
44 9 0.01
45 3 0.00
46 6 0.01
47 3 0.00
48 11 0.01
49 672 0.83
50 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:285832 original size:33 final size:34
Alignment explanation
Indices: 285793--285857 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
285783 GGCTTAGAGG
285793 GGTTGCCACCGACTTGCGTGGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGCGTGGGCTTTAGGAAGAA
*
285826 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGCGTGGGCTTTAGGAAG
285858 GGAGAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.17, C:0.20, G:0.37, T:0.26
Consensus pattern (34 bp):
GGTTGCCACCGACTTGCGTGGGCTTTAGGAAGAA
Found at i:286078 original size:160 final size:155
Alignment explanation
Indices: 285894--286281 Score: 523
Period size: 160 Copynumber: 2.4 Consensus size: 155
285884 CTTAAAAGGG
285894 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
*
285959 AGA-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAG
65 AGAGGTGCCACGGAGTCGTGGGCTTT-AAAGG-AAAA-GGTGCCACGGAGTTATGGACTTA-AAG
* *
286023 -GAAAGAGAGTGCCACAGAGTTGTGGGCTTTT
126 AGAAA-AAAGTGCCACAGAATTGTGGGC-TTT
*
286054 AAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--
* *
286119 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAA
63 --A-AAG-AGGTGCCACGGAGTCGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTATGGACTTAA
*
286184 AGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
124 AGA-GAAAAAAGTGCCACAGAATTGTGGGCTTT
* * *
286217 -AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAA-AAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
286280 GA
66 GA
286282 AAAAATGCTA
Statistics
Matches: 207, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
154 1 0.00
155 3 0.01
160 86 0.42
161 6 0.03
162 26 0.13
163 6 0.03
164 41 0.20
165 11 0.05
166 6 0.03
167 21 0.10
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (155 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
GAGGTGCCACGGAGTCGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTATGGACTTAAAGAGAAA
AAAGTGCCACAGAATTGTGGGCTTT
Found at i:286117 original size:194 final size:192
Alignment explanation
Indices: 285862--286279 Score: 548
Period size: 194 Copynumber: 2.1 Consensus size: 192
285852 AGGAAGGGAG
*
285862 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
285925 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA-G-A-GTGCCACGGAGTCGTGGGCTTTAAA
64 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAGGTGCCACGGAGTCGTGGAC-TTAAA
* *
285987 -AGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAGAGAGTGCCACAGAGTTGTGGGCT
128 GAGGAAAAA-AGTGCCACGGAATTATGGGCTT--AA--AAAG-G-GTGCCACAGAGTTGTGGGC-
286051 TTTAAA-A
185 TTTAAAGA
*
286058 AAAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
286121 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAG
66 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGG--AAGGTGCCACGGAGTCGTGGACTTAAAG
* * * *
286186 ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGA
129 AGGAAAAAAGTGCCACGGAATTATGGGCTTAAAAAGGGTGCCACAGAGTTGTGGGCTTTAAA-GA
286251 AAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAA-GTGCCACGGAGTTGTGGGCTTTGAA
286280 GAAAAAATGC
Statistics
Matches: 201, Mismatches: 10, Indels: 24
0.86 0.04 0.10
Matches are distributed among these distances:
191 6 0.03
192 18 0.09
193 5 0.02
194 88 0.44
195 24 0.12
196 7 0.03
197 4 0.02
198 25 0.12
199 24 0.12
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (192 bp):
AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAGAG
GAAAAAAGTGCCACGGAATTATGGGCTTAAAAAGGGTGCCACAGAGTTGTGGGCTTTAAAGA
Found at i:286357 original size:32 final size:32
Alignment explanation
Indices: 285862--286432 Score: 422
Period size: 34 Copynumber: 17.8 Consensus size: 32
285852 AGGAAGGGAG
* *
285862 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAA--GAA
285896 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTT--AAAGAA
* *
285931 GAAGGTGCCACGGAGTTGTGGGCTTTAAAG--
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
*
285961 --AG-TGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAA-GAA
* *
285992 AAAGGGTGCCACGGAGTTATGGGC-TTAGAAGGAA
1 AAA-GATGCCACGGAGTTGTGGGCTTTA-AA-GAA
* * *
286026 AGAGAGTGCCACAGAGTTGTGGGCTTTTAA-AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAGAA
286058 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT--AAAGAA
* *
286091 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT--AAAGAA
* * *
286125 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
* *
286157 AAAGGTGCCACGGAGTTGTGGAC-TTAAAGATGA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGA--A
* *
286190 AAAAAGTGCCACGGAATTGTGGGCTTT----AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAGAA
* * *
286219 AAGGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
* *
286251 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
* ** * * * * *
286283 AAA-ATGCTATTGAGTCGTGGACCTT-GAGAC
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
* * *
286313 AAA-ATGCCACTGAGTCGTGGACTTTAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
* * * * *
286344 AAAGATGCCACTGAGTCGTGGACTTT-GAG-C
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
* * * *
286374 AGAGATTGCCACTGAGTCGTGGACTTTAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAGAA
* * *
286407 AAAGATGCCACTGAGTCGTGGACTTT
1 AAAGATGCCACGGAGTTGTGGGCTTT
286433 GAGCAGAGAT
Statistics
Matches: 453, Mismatches: 53, Indels: 64
0.79 0.09 0.11
Matches are distributed among these distances:
27 20 0.04
28 25 0.06
29 4 0.01
30 49 0.11
31 51 0.11
32 115 0.25
33 16 0.04
34 125 0.28
35 45 0.10
37 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.22
Consensus pattern (32 bp):
AAAGATGCCACGGAGTTGTGGGCTTTAAAGAA
Found at i:286387 original size:31 final size:31
Alignment explanation
Indices: 286251--286463 Score: 227
Period size: 31 Copynumber: 6.8 Consensus size: 31
286241 CTTTAAAGGA
* * * *
286251 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGA-
1 AAAGATGCCACTGAGTCGTGGACTTTG-AGAC
* * * *
286282 AAAAATGCTATTGAGTCGTGGACCTTGAGAC
1 AAAGATGCCACTGAGTCGTGGACTTTGAGAC
* *
286313 AAA-ATGCCACTGAGTCGTGGACTTTAAAGAA
1 AAAGATGCCACTGAGTCGTGGACTTT-GAGAC
286344 AAAGATGCCACTGAGTCGTGGACTTTGAG-C
1 AAAGATGCCACTGAGTCGTGGACTTTGAGAC
* * *
286374 AGAGATTGCCACTGAGTCGTGGACTTTAAAGAA
1 AAAGA-TGCCACTGAGTCGTGGACTTT-GAGAC
286407 AAAGATGCCACTGAGTCGTGGACTTTGAG-C
1 AAAGATGCCACTGAGTCGTGGACTTTGAGAC
*
286437 AGAGATTGCCACTGAGTCGTGGACTTT
1 AAAGA-TGCCACTGAGTCGTGGACTTT
286464 TTTTTTTTTT
Statistics
Matches: 153, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
30 30 0.20
31 74 0.48
32 45 0.29
33 4 0.03
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (31 bp):
AAAGATGCCACTGAGTCGTGGACTTTGAGAC
Found at i:286396 original size:63 final size:63
Alignment explanation
Indices: 286256--286463 Score: 314
Period size: 63 Copynumber: 3.3 Consensus size: 63
286246 AAGGAAAAGG
* * * * * * * *
286256 TGCCACGGAGTTGTGGGCTTTGAAGAAAAA-ATGCTATTGAGTCGTGGACCTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
286317 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGAT
286380 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGAT
286443 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
286464 TTTTTTTTTT
Statistics
Matches: 136, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
61 28 0.21
62 23 0.17
63 85 0.62
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGAT
Found at i:294800 original size:52 final size:52
Alignment explanation
Indices: 294730--294850 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
294720 GAAAATTTAT
*
294730 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
294782 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
294834 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
294851 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:294863 original size:52 final size:51
Alignment explanation
Indices: 294730--294870 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
294720 GAAAATTTAT
294730 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
294782 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
294834 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
294871 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:294877 original size:13 final size:13
Alignment explanation
Indices: 294859--294883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
294849 CAAAGATCAG
294859 TGTATCGATACAA
1 TGTATCGATACAA
294872 TGTATCGATACA
1 TGTATCGATACA
294884 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:294966 original size:13 final size:13
Alignment explanation
Indices: 294948--294972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
294938 CAAAAAAATA
294948 TGTATCGATACAT
1 TGTATCGATACAT
294961 TGTATCGATACA
1 TGTATCGATACA
294973 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:294968 original size:33 final size:33
Alignment explanation
Indices: 294926--294992 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
294916 AGTAGCTTAA
294926 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
294959 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
294992 A
1 A
294993 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:298738 original size:34 final size:34
Alignment explanation
Indices: 298690--298892 Score: 307
Period size: 34 Copynumber: 6.0 Consensus size: 34
298680 AAATATTTTA
* * * *
298690 CTCACCTAACACATTACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
* * * * *
298724 TTCACCAAATACATTACCTAGCACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
298758 CTTACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
298792 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
298826 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
298860 CTCACCAAATACATTACCTAACACACCTAACAT
1 CTCACCAAATACATCACCTAACACACCTAACAT
298893 GCTTCAGGTA
Statistics
Matches: 156, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 156 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.24
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAACATT
Found at i:298810 original size:25 final size:25
Alignment explanation
Indices: 298781--298882 Score: 71
Period size: 25 Copynumber: 4.4 Consensus size: 25
298771 TCACCTAACA
298781 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
298806 CACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
298828 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
298849 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
298874 TACCTAACA
1 CACCTAACA
298883 CACCTAACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 26
0.64 0.07 0.29
Matches are distributed among these distances:
20 1 0.02
21 11 0.19
22 15 0.26
23 7 0.12
24 3 0.05
25 21 0.36
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:303855 original size:34 final size:34
Alignment explanation
Indices: 303802--303981 Score: 288
Period size: 34 Copynumber: 5.3 Consensus size: 34
303792 AAATATTTTA
* * * *
303802 CTCACCTAACACATTACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
303836 TTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
303870 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
303904 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
* *
303938 CTCACCAAATACATTACCTAACACACCTAACATG
1 CTCACCAAATACATCACCTAACACACCTAACATT
303972 CTTCACCAAA
1 C-TCACCAAA
303982 CACACTTAAC
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
34 129 0.94
35 8 0.06
ACGTcount: A:0.41, C:0.37, G:0.01, T:0.22
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAACATT
Found at i:303888 original size:25 final size:25
Alignment explanation
Indices: 303859--303960 Score: 71
Period size: 25 Copynumber: 4.4 Consensus size: 25
303849 TCACCTAACA
303859 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
303884 CACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
303906 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
303927 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
303952 TACCTAACA
1 CACCTAACA
303961 CACCTAACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 26
0.64 0.07 0.29
Matches are distributed among these distances:
20 1 0.02
21 11 0.19
22 15 0.26
23 7 0.12
24 3 0.05
25 21 0.36
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:307266 original size:79 final size:78
Alignment explanation
Indices: 307082--307267 Score: 178
Period size: 79 Copynumber: 2.3 Consensus size: 78
307072 ATATTTCCCG
* * *
307082 ATGAGAAATTTAATATTTT-GGAGATAATAACGGGGTTGGAGGATCCCCTTGAAAATAACAGGGT
1 ATGAGAAA-TCAATATTTTGGGA-ATAA-AACGGGATTGGAGGATCCCCTCGAAAATAACAGGGT
* **
307146 TGGAGTATCCCCGGTT
63 CGGAGTATCCCCAATT
* * * * * * * * *
307162 GTGAAAAATCGATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCCTCGGACATAACGGGGTC
1 ATGAGAAATCAAT-ATTTTGGGAATAAAA-CGGGATTGGAGGATCCCCTCGAAAATAACAGGGTC
307226 GGAGTATCCCCAATT
64 GGAGTATCCCCAATT
307241 ATGAGAAATCAATATTTTGGGAATAAA
1 ATGAGAAATCAATATTTTGGGAATAAA
307268 GCTGAGGTTG
Statistics
Matches: 82, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
78 3 0.04
79 70 0.85
80 9 0.11
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (78 bp):
ATGAGAAATCAATATTTTGGGAATAAAACGGGATTGGAGGATCCCCTCGAAAATAACAGGGTCGG
AGTATCCCCAATT
Found at i:307329 original size:52 final size:50
Alignment explanation
Indices: 307273--307866 Score: 306
Period size: 51 Copynumber: 11.4 Consensus size: 50
307263 ATAAAGCTGA
307273 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGG
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTGGTGTTTTGAA-ATAAAACCGG
* ** *
307325 GGTTGGAGTATCCCCGACTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTT-GAAATAAAACCGG
* * * * * *
307376 GGTTGGATTATCCCCGATTATGAGAAATCAAT-AT-TTTTGAAATAAAGCCGA
1 GGTTGGAGTATCCCCGATTAAG-GAAA--ATTGGTGTTTTGAAATAAAACCGG
* ** * * *** * *
307427 GGTTGGAGTATCCCTTCGGAGGTAACGG--GGTTGGAGTATCTCCGATGAAATAACGA
1 GGTTGGAGTATCCC--C-GA-TTAA-GGAAAATTGGTGT-TTTGAAAT-AAA-ACCGG
* ** * *
307483 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTG-TTTT-GAAATAAAACCGG
* *
307535 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAATCGG
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTGGTGTTTTGAA-ATAAAACCGG
* ** *
307587 GGTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTT-GAAATAAAACCGG
* * *** * **
307638 GGTTGGAGTATCCTCGATT-ATGAGAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTAAGGA-AAATTGGTGTTTT-GAAATAAAACCGG
* ** * ***** * *
307689 GGTTGGAGTATCCCC--TCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGATTA-AGG-AA---AATTGGTGT-TTTGAAAT-AAA-ACCGG
* ** * *
307745 GGTT-GAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATC-G
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTG-TTTT-GAAATAAAACCGG
*
307795 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTGGTGTTTTG-AAATAAAACCGG
**
307847 GGTTGGAACATCCCCGATTA
1 GGTTGGAGTATCCCCGATTA
307867 TGAACAATTG
Statistics
Matches: 401, Mismatches: 102, Indels: 79
0.69 0.18 0.14
Matches are distributed among these distances:
49 1 0.00
50 6 0.01
51 181 0.45
52 122 0.30
53 29 0.07
54 16 0.04
55 21 0.05
56 24 0.06
57 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTTGAAATAAAACCGG
Found at i:307371 original size:51 final size:51
Alignment explanation
Indices: 307219--307703 Score: 306
Period size: 51 Copynumber: 9.4 Consensus size: 51
307209 TCGGACATAA
* * * * * * * *
307219 CGGGGTCGGAGTATCCCCAATTAT-GAGAAATCAATATTTTGGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAGAAATAAAAC
* * * *
307270 TGAGGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT-GAAGATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTAGAA-ATAAAAC
* *
307322 CGGGGTTGGAGTATCCCCGACTGTGGAAAATTAGTGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAAC
* * * * * *
307373 CGGGGTTGGATTATCCCCGATTAT-GAGAAATCAATATTTTTGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAGAAATAAAAC
* * * ** * **
307424 CGAGGTTGGAGTATCCCTTCGGAGGTAACGG--GGTTGGAGTATCTCCGATGAAAT--AA-
1 CGGGGTTGGAGTATCCC--C-GA--TTATGGAAAATT--AGTGT-T-TTA-GAAATAAAAC
* * * * * * *
307480 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTG-TTTTAGAAATAAAAC
* * * *
307532 CGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT-GAAGATAAAAT
1 CGGGGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTAGAA-ATAAAAC
* *
307584 CGGGGTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAAC
* * * * * **
307635 CGGGGTTGGAGTATCCTCGATTAT-GAGAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAGAAATAAAAC
307686 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
307704 TCAGAGGTAA
Statistics
Matches: 337, Mismatches: 71, Indels: 52
0.73 0.15 0.11
Matches are distributed among these distances:
49 5 0.01
50 4 0.01
51 184 0.55
52 92 0.27
53 18 0.05
54 4 0.01
56 22 0.07
57 3 0.01
59 5 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:307500 original size:28 final size:28
Alignment explanation
Indices: 307424--307500 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
307414 GAAATAAAGC
**
307424 CGAGGTTGGAGTATCCCTTCG--GAGGTAA
1 CGAGGTTGGAGTAT-CC-TCGATGAAATAA
*
307452 CGGGGTTGGAGTAT-CTCCGATGAAATAA
1 CGAGGTTGGAGTATCCT-CGATGAAATAA
307480 CGAGGTTGGAGTATCCTCGAT
1 CGAGGTTGGAGTATCCTCGAT
307501 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
28 35 0.85
29 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCTCGATGAAATAA
Found at i:307580 original size:262 final size:260
Alignment explanation
Indices: 307274--307863 Score: 1036
Period size: 262 Copynumber: 2.3 Consensus size: 260
307264 TAAAGCTGAG
307274 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGGGGTTGGAGTATCCC
*
307339 CGACTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGATTATCCCCGATTATGAGAAAT
66 CGACTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAAT
* * * *
307404 CAATATTTTTGAAATAAAGCCGAGGTTGGAGTATCCCTTCGGAGGTAACGGGGTTGGAGTATCTC
131 CAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCCCCTCAGAGGTAACGGGGTTGGAGTATCCC
307469 CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCG
196 CGATGAAATAACGAGGTT-GAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATC-
307534 GA
259 GA
*
307536 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGGGGTTGGAGTATCCC
* * *
307601 TGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCTCGATTATGAGAAAT
66 CGACTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAAT
* *
307666 CAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCAGAGGTAACGGGGTTGGAGTATCCC
131 CAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCCCCTCAGAGGTAACGGGGTTGGAGTATCCC
307731 CGATGAAATAACGAGGTTGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGA
196 CGATGAAATAACGAGGTTGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGA
* **
307796 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAACATCCC
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGGGGTTGGAGTATCCC
307861 CGA
66 CGA
307864 TTATGAACAA
Statistics
Matches: 312, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
260 65 0.21
261 45 0.14
262 202 0.65
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (260 bp):
GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGGGGTTGGAGTATCCC
CGACTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAAT
CAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCCCCTCAGAGGTAACGGGGTTGGAGTATCCC
CGATGAAATAACGAGGTTGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGA
Found at i:307742 original size:28 final size:28
Alignment explanation
Indices: 307686--307761 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
307676 GAAATAAAGT
* **
307686 CGGGGTTGGAGTATCCCCTCA-GAGGTAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
307714 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
307742 CGAGGTT-GAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
307762 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.31
28 29 0.69
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:310225 original size:13 final size:13
Alignment explanation
Indices: 310207--310232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
310197 ACATAGATCG
310207 ATGTATCGATACA
1 ATGTATCGATACA
310220 ATGTATCGATACA
1 ATGTATCGATACA
310233 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:310243 original size:21 final size:21
Alignment explanation
Indices: 310219--310260 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
310209 GTATCGATAC
310219 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
310240 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
310261 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:310309 original size:19 final size:18
Alignment explanation
Indices: 310285--310347 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
310275 AGCGATACAT
310285 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
310304 TGTATCGAT----ACGT-
1 TGTATCGATACAAACTTA
310317 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
310336 TGTATCGATACA
1 TGTATCGATACA
310348 TTTACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.25
14 3 0.08
18 3 0.08
19 21 0.58
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:310320 original size:32 final size:32
Alignment explanation
Indices: 310277--310349 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
310267 AGCTTCGTAG
310277 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
310309 CGATACGTTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
310341 CGATACATT
1 CGATACATT
310350 TACGGTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:311796 original size:52 final size:52
Alignment explanation
Indices: 311711--311843 Score: 169
Period size: 52 Copynumber: 2.6 Consensus size: 52
311701 AATTACTTGT
* * * * * ** *
311711 ATGTATGGATACATTGAATAATGTATCGATACAT-TTAGGTTAAAAACTTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATAAT-GGTCAAAAACCCAAA
*
311763 ATTTATCGATACAATGAAAAATGTATCGATACATAATGGTCAAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATAATGGTCAAAAACCCAAA
311815 ATGTATCGATACAATGAAAAATGTATCGA
1 ATGTATCGATACAATGAAAAATGTATCGA
311844 ATAAGTGTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
52 69 0.99
53 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATAATGGTCAAAAACCCAAA
Found at i:312087 original size:16 final size:16
Alignment explanation
Indices: 312066--312098 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
312056 CGATACATGC
*
312066 CTGAAATGTATTGATA
1 CTGAAATGTATTAATA
312082 CTGAAATGTATTAATA
1 CTGAAATGTATTAATA
312098 C
1 C
312099 ATGTAAGCTC
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:0.09, G:0.15, T:0.36
Consensus pattern (16 bp):
CTGAAATGTATTAATA
Found at i:312851 original size:13 final size:13
Alignment explanation
Indices: 312833--312858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312823 CGTTGGGTTT
312833 AATGTATCGATAC
1 AATGTATCGATAC
312846 AATGTATCGATAC
1 AATGTATCGATAC
312859 TAAGTGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:312934 original size:19 final size:17
Alignment explanation
Indices: 312883--312937 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 17
312873 TACTGCTAGT
*
312883 TTCATGTATCGATACAA
1 TTCATGTATCGATACTA
312900 TTCAATGTGCATCGATACTA
1 TTC-ATGT--ATCGATACTA
312920 TGATCATGTATCGATACT
1 T--TCATGTATCGATACT
312938 TTCTAGGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 9 0.28
20 10 0.31
21 4 0.12
22 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (17 bp):
TTCATGTATCGATACTA
Found at i:313046 original size:22 final size:20
Alignment explanation
Indices: 313016--313056 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
313006 ACTTTTGATT
*
313016 ATTTTTACTTGAAAACATATG
1 ATTTTTACTT-AAAAAATATG
313037 ATTTATTACTTAAAAAATAT
1 ATTT-TTACTTAAAAAATAT
313057 TTATACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTTTTACTTAAAAAATATG
Found at i:313051 original size:21 final size:18
Alignment explanation
Indices: 313015--313066 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
313005 TACTTTTGAT
313015 TATTT-TTACTTGAAAACATA
1 TATTTATTACTT-AAAA-A-A
313035 TGATTTATTACTTAAAAAA
1 T-ATTTATTACTTAAAAAA
313054 TATTTA-TACTTAA
1 TATTTATTACTTAA
313067 CTCTAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.23
18 5 0.17
19 2 0.07
20 2 0.07
21 8 0.27
22 6 0.20
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (18 bp):
TATTTATTACTTAAAAAA
Found at i:315608 original size:13 final size:13
Alignment explanation
Indices: 315590--315614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315580 AATAGTGCCC
315590 ATGTATCGATACA
1 ATGTATCGATACA
315603 ATGTATCGATAC
1 ATGTATCGATAC
315615 TAAGAACACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:320348 original size:19 final size:20
Alignment explanation
Indices: 320302--320356 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
320292 TTGCTAGTTT
320302 CATGTATCGATACAATTCAA
1 CATGTATCGATACAATTCAA
** *
320322 TGTGTATCGATACTATT-AA
1 CATGTATCGATACAATTCAA
*
320341 CATGTATCAATACAAT
1 CATGTATCGATACAAT
320357 GTATCGATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACAATTCAA
Found at i:326818 original size:20 final size:20
Alignment explanation
Indices: 326793--326843 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
326783 AATTAAAATG
*
326793 TATCGATACATG-GGACATTA
1 TATCGATACATGAAGA-ATTA
*
326813 TATCGATACATGAAGAATTG
1 TATCGATACATGAAGAATTA
326833 TATCGATACAT
1 TATCGATACAT
326844 TATGCCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACATGAAGAATTA
Done.