Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008339.1 Hibiscus syriacus cultivar Beakdansim tig00111061_pilon, 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: 1048908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:172347 original size:24 final size:23
Alignment explanation
Indices: 172285--172348 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
172275 ATAATATGTA
* *
172285 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
172308 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
172332 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
172349 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:172734 original size:40 final size:39
Alignment explanation
Indices: 172669--172744 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
172659 TGGTTATCTA
* * *
172669 GGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
* *
172708 GGGGATGACACGACTCATACGTGATGAAGAGTTCTGG
1 GGGG-TGACACGACTCATACGCGATGAAGAGATCTGG
172745 CCATCTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
Found at i:172808 original size:134 final size:134
Alignment explanation
Indices: 172536--172890 Score: 471
Period size: 134 Copynumber: 2.6 Consensus size: 134
172526 GTCGTCTAAA
* * * * * **
172536 GGTGACAAGGTTCCTACATGATGAGGAAATATGGTCGAGGGATGACACTTCTCATACGTGATGAA
1 GGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGGGGATGACACGACTCATACGTGATGAA
* *
172601 GAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTAT
66 GAGTTC-TGGCCATCTTTAGGAAGGGCGATAACTCGGTTCCTACGCGATGAGGACGGCTAGTTAT
172666 CTAGG
130 CTAGG
* *
172671 GGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAA
1 GGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGGGGATGACACGACTCATACGTGATGAA
* *
172736 GAGTTCTGGCCATCTTTAGGAAGGGCGATAACAT-GGTTCCTACGTGATGAGGACGTCTAGTTAT
66 GAGTTCTGGCCATCTTTAGGAAGGGCGATAAC-TCGGTTCCTACGCGATGAGGACGGCTAGTTAT
172800 CTAGG
130 CTAGG
* * * * * * * *
172805 GGTGACACGACTCCTACGTGATGAGGAGATTTGATCAGGAGATGACACGATTCCTACGTGATGAG
1 GGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGGGGATGACACGACTCATACGTGATGAA
*
172870 GACG-GCTGGCCATCTTTAGGA
66 GA-GTTCTGGCCATCTTTAGGA
172891 GTTATGATTT
Statistics
Matches: 195, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
134 131 0.67
135 64 0.33
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (134 bp):
GGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGGGGATGACACGACTCATACGTGATGAA
GAGTTCTGGCCATCTTTAGGAAGGGCGATAACTCGGTTCCTACGCGATGAGGACGGCTAGTTATC
TAGG
Found at i:172990 original size:31 final size:28
Alignment explanation
Indices: 172898--172993 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
172888 GGAGTTATGA
* * *
172898 TTTCAAGAGAAACCGATTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
172926 TTTCAAAAGAAACAGACTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
172954 TTTCAAGAA-AAACA-AGCTCAAAGATAATGTG
1 TTTCAA-AAGAAACAGA-CTCAAAGAT--T-TG
172985 TTTCAAAAG
1 TTTCAAAAG
172994 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 45 0.76
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTG
Found at i:173626 original size:64 final size:62
Alignment explanation
Indices: 173376--173639 Score: 159
Period size: 62 Copynumber: 4.3 Consensus size: 62
173366 GTATCTTAGT
* * * *
173376 GAGACAAAATTTTATTTCCAAAGAAACAGACTC--AGATTTTTCTTCAAAAGAAACTGTTTTAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTC-TC-AAAGAAACTGTCTCAA
* * ** * ** ** *
173438 GGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGA-TGATCGGAAACAAA---T-TCAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTCAA
**
173495 TGATG-GTAAATTTTGTTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTCGA
1 -GA-GACAAAATTTTG-TTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTC-A
173559 GA
62 -A
* * * * * * * * *
173561 GAAACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTAAAGACATTGTCAT-AA
1 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTC-TCAA
*
173623 GAGACAAAACTTTGTTT
1 GAGACAAAATTTTGTTT
173640 TTCAGAAAAT
Statistics
Matches: 151, Mismatches: 37, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
57 3 0.02
58 8 0.05
59 24 0.16
60 9 0.06
61 6 0.04
62 42 0.28
63 5 0.03
64 41 0.27
65 12 0.08
66 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (62 bp):
GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTCAA
Found at i:173731 original size:285 final size:287
Alignment explanation
Indices: 173194--173765 Score: 1103
Period size: 285 Copynumber: 2.0 Consensus size: 287
173184 TTGTTTCAAG
173194 GGAAACAAATTCAATGATGGTAAATTTTGTTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAA
1 GGAAACAAATTCAATGATGGTAAATTTTGTTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAA
173259 GAAACTGTCTCGAGAGAAACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTTAAA
66 GAAACTGTCTCGAGAGAAACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTTAAA
173324 AAACATTGTCATAAGAGACAAAACTTTGTTTTTCAGAAAATTGTATCTTAGTGAGACAAAATTTT
131 AAACATTGTCATAAGAGACAAAACTTTGTTTTTCAGAAAATTGTATCTTAGTGAGACAAAATTTT
173389 ATTTCCAAAGAAACAGACTCAGATTTTTCTTCAAAAGAAACTGTTTTAAGGGATAAAACCTTGTT
196 ATTTCCAAAGAAACAGACTCAGATTTTTCTTCAAAAGAAACTGTTTTAAGGGATAAAACCTTGTT
173454 TCCAGAGAAACAAACTCAAAGATGATC
261 TCCAGAGAAACAAACTCAAAGATGATC
173481 GGAAACAAATTCAATGATGGTAAATTTTGTTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAA
1 GGAAACAAATTCAATGATGGTAAATTTTGTTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAA
173546 GAAACTGTCTCGAGAGAAACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGA-TTTTTTTT-AA
66 GAAACTGTCTCGAGAGAAACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTTAAA
*
173609 AGACATTGTCATAAGAGACAAAACTTTGTTTTTCAGAAAATTGTATCTTAGTGAGACAAAATTTT
131 AAACATTGTCATAAGAGACAAAACTTTGTTTTTCAGAAAATTGTATCTTAGTGAGACAAAATTTT
* *
173674 GTTTCCAAAGAAACAGACTCAGATTTTTCTTCAAAAGAAATTGTTTTAAGGGATAAAACCTTGTT
196 ATTTCCAAAGAAACAGACTCAGATTTTTCTTCAAAAGAAACTGTTTTAAGGGATAAAACCTTGTT
173739 TCCAGAGAAACAAACTCAAAGATGATC
261 TCCAGAGAAACAAACTCAAAGATGATC
173766 TTGTTTTAAG
Statistics
Matches: 282, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
285 156 0.55
286 8 0.03
287 118 0.42
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (287 bp):
GGAAACAAATTCAATGATGGTAAATTTTGTTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAA
GAAACTGTCTCGAGAGAAACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTTAAA
AAACATTGTCATAAGAGACAAAACTTTGTTTTTCAGAAAATTGTATCTTAGTGAGACAAAATTTT
ATTTCCAAAGAAACAGACTCAGATTTTTCTTCAAAAGAAACTGTTTTAAGGGATAAAACCTTGTT
TCCAGAGAAACAAACTCAAAGATGATC
Found at i:173919 original size:40 final size:40
Alignment explanation
Indices: 173875--173954 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
173865 GTTTTAATAG
173875 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
173915 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
173955 CGAGAGACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (40 bp):
AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
Found at i:174040 original size:65 final size:64
Alignment explanation
Indices: 173936--174061 Score: 180
Period size: 65 Copynumber: 2.0 Consensus size: 64
173926 AAGGTGGGTA
* * * *
173936 TTTTCAAAAGAAGTTGTCTCGAGAGACAAAATTTTGTTTCAAAGGAAATAAACTCAAAGATTTT
1 TTTTCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
* * *
174000 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTC-TCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
174062 GGATCACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
64 17 0.31
65 37 0.69
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:174112 original size:119 final size:121
Alignment explanation
Indices: 173958--174182 Score: 271
Period size: 120 Copynumber: 1.9 Consensus size: 121
173948 GTTGTCTCGA
* * * *
173958 GAGACAAAATTTTGTTTCAAAGGAAATAAACTC-AAAGATT-TTTTTTCAAAAGAAATTGTCTTT
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAAG-TTAGTTTTTCAAAAGAAACTGTC-TC
*
174021 AAGAGATA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
64 AAGAGAGACAACA-TTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
* * * **
174078 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAAAGTTAGTTTTTCATTAGAAACTGTCTCAA
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAAGTTAGTTTTTCAAAAGAAACTGTCTCAA
** *
174142 GAGAGACAACATTTGTTTTTAAAGAAATAGACTCAAAGATG
66 GAGAGACAACATTTGTTTCAAAAGAAACAGACTCAAAGATG
174183 ATTTTGTTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
119 30 0.34
120 57 0.65
121 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (121 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAAGTTAGTTTTTCAAAAGAAACTGTCTCAA
GAGAGACAACATTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
Found at i:174370 original size:30 final size:31
Alignment explanation
Indices: 174336--174541 Score: 108
Period size: 30 Copynumber: 6.4 Consensus size: 31
174326 AGAGACAAAA
*
174336 TTTTGTTTCCAAAGAAA-CAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAATCAGACTCAAAGAT
**
174366 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--ATC-----AGACTCAAAGAT
*
174403 TTTTGTTTCCAAAGAAA-CAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAATCAGACTCAAAGAT
**
174433 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--ATC-----AGACTCAAAGAT
* *
174470 TTTTGTTTCCAAAGAAACCA-ACTCAAAGAT
1 TTTTGTTTCAAAAGAAATCAGACTCAAAGAT
174500 TTTTGTTTCAAAAGAAA-CA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAATCAGA-CTCAAAGAT
*
174530 TTTT-TTACAAAA
1 TTTTGTTTCAAAA
174542 TTGTCTCAAG
Statistics
Matches: 138, Mismatches: 15, Indels: 47
0.69 0.08 0.23
Matches are distributed among these distances:
28 12 0.09
29 13 0.09
30 55 0.40
31 4 0.03
33 3 0.02
34 5 0.04
36 4 0.03
37 26 0.19
38 2 0.01
39 14 0.10
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (31 bp):
TTTTGTTTCAAAAGAAATCAGACTCAAAGAT
Found at i:174394 original size:67 final size:67
Alignment explanation
Indices: 174283--174516 Score: 420
Period size: 67 Copynumber: 3.5 Consensus size: 67
174273 TCATTTTAAG
* *
174283 AGAAACAGATTCAAAGA-TTTT-TTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
174346 AA
66 AA
174348 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
174413 AA
66 AA
174415 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
174480 AA
66 AA
174482 AGAAACCA-ACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAA-CAGACTCAAAGATTTTTGTTTCAAAAGAAA
174517 CAATCTCAAA
Statistics
Matches: 164, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
65 16 0.10
66 4 0.02
67 142 0.87
68 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:174417 original size:37 final size:37
Alignment explanation
Indices: 174366--174486 Score: 125
Period size: 37 Copynumber: 3.5 Consensus size: 37
174356 ACTCAAAGAT
174366 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
* **
174403 TTTTGTTTCCAAAG-AA--A-C-----AGACTCAAAGA
1 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A
174432 TTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 -TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
*
174470 TTTTGTTTCCAAAGAAA
1 TTTTGTTTCAAAAGAAA
174487 CCAACTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
28 7 0.11
29 1 0.02
30 13 0.20
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 29 0.44
38 1 0.02
39 7 0.11
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (37 bp):
TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
Found at i:174598 original size:52 final size:53
Alignment explanation
Indices: 174521--174623 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
174511 AAGAAACAAT
*
174521 CTCAAAGATTTTTTTACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
174574 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
174624 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 40 0.83
53 8 0.17
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:174649 original size:30 final size:29
Alignment explanation
Indices: 174620--174801 Score: 169
Period size: 27 Copynumber: 6.4 Consensus size: 29
174610 AAAACTTTGT
* * * *
174620 TTCAAAATAAATAGACTCAAAGATTTTTGT
1 TTCAAAAGAAACAAACTCAAAGATTTTT-A
** *
174650 TTCAAACTAAAC-AACTCAAAAATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
174678 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
174707 TTCAAAAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
174734 TTCAAGAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
174761 TTCAAGAGGAACAAACTCAAAGATTTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
174789 TCCTCAAAAGAAA
1 T--TCAAAAGAAA
174802 TTGTCTTTAA
Statistics
Matches: 134, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
27 49 0.37
28 18 0.13
29 49 0.37
30 18 0.13
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:174674 original size:29 final size:30
Alignment explanation
Indices: 174615--174734 Score: 93
Period size: 29 Copynumber: 4.1 Consensus size: 30
174605 GAGACAAAAC
* *
174615 TTTGTTTCAAAATAAATAGACTCAAAGATT
1 TTTGTTTCAAAATAAACAGACTCAAAAATT
*
174645 TTTGTTTCAAACTAAACA-ACTCAAAAATT
1 TTTGTTTCAAAATAAACAGACTCAAAAATT
* ** * * *
174674 TTT-ATTCAAAAGGAACAAACTCCAAGATT
1 TTTGTTTCAAAATAAACAGACTCAAAAATT
* ** * *
174703 TTT-ATTCAAAAGGAACAAACTCAAAGATT
1 TTTGTTTCAAAATAAACAGACTCAAAAATT
174732 TTT
1 TTT
174735 TCAAGAGGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 10 0.13
29 53 0.67
30 16 0.20
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (30 bp):
TTTGTTTCAAAATAAACAGACTCAAAAATT
Found at i:174745 original size:27 final size:27
Alignment explanation
Indices: 174662--174790 Score: 186
Period size: 27 Copynumber: 4.6 Consensus size: 27
174652 CAAACTAAAC
*
174662 AACTCAAAAATTTTTATTCAAAAGGAACA
1 AACTCAAAGA-TTTT-TTCAAAAGGAACA
*
174691 AACTCCAAGATTTTTATTCAAAAGGAACA
1 AACTCAAAGA-TTTT-TTCAAAAGGAACA
*
174720 AACTCAAAGATTTTTTCAAGAGGAACA
1 AACTCAAAGATTTTTTCAAAAGGAACA
*
174747 AACTCAAAGATTTTTTCAAGAGGAACA
1 AACTCAAAGATTTTTTCAAAAGGAACA
174774 AACTCAAAGATTTTTTC
1 AACTCAAAGATTTTTTC
174791 CTCAAAAGAA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
27 56 0.58
28 4 0.04
29 36 0.38
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (27 bp):
AACTCAAAGATTTTTTCAAAAGGAACA
Found at i:174762 original size:29 final size:29
Alignment explanation
Indices: 174634--174798 Score: 187
Period size: 29 Copynumber: 5.8 Consensus size: 29
174624 AAATAAATAG
***
174634 ACTCAAAGATTTTTGTTTCAAACTAAAC-A
1 ACTCAAAGATTTTT-TTTCAAAAGGAACAA
* *
174663 ACTCAAAAATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
* *
174692 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
*
174721 ACTCAAAGA--TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
*
174748 ACTCAAAGA--TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTTCAAAAGGAACAA
*
174775 ACTCAAAGATTTTTTCCTCAAAAG
1 ACTCAAAGATTTTTT-TTCAAAAG
174799 AAATTGTCTT
Statistics
Matches: 120, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
27 52 0.43
28 9 0.08
29 53 0.44
30 6 0.05
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.29
Consensus pattern (29 bp):
ACTCAAAGATTTTTTTTCAAAAGGAACAA
Found at i:174787 original size:54 final size:56
Alignment explanation
Indices: 174634--174790 Score: 194
Period size: 54 Copynumber: 2.8 Consensus size: 56
174624 AAATAAATAG
* *** *
174634 ACTCAAAGATTTTTGTTTCAAACTAAAC-AACTCAAAAATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-ATTCAAAAGGAACAAACTCAAAGA-TTTT-TTCAAAAGGAACAA
* *
174692 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGGAACAA
*
174748 ACTCAAAGA-TTTT-TTCAAGAGGAACAAACTCAAAGATTTTTTC
1 ACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTC
174791 CTCAAAAGAA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
54 29 0.33
55 4 0.04
56 21 0.24
57 13 0.15
58 22 0.25
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (56 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:175152 original size:36 final size:36
Alignment explanation
Indices: 175041--175159 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
175031 AGAAAATGAT
* * * *
175041 GTCTCAAGCGAAACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAAC
** **
175075 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
175111 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
175146 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
175160 TTAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 18 0.26
35 12 0.18
36 38 0.56
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:175169 original size:36 final size:36
Alignment explanation
Indices: 175075--175171 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 36
175065 TTAAGATATA
** * **
175075 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAACTTTGTTTTTAGAGAAAAC
*
175111 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAACTTTGTTTTTAGAGAAAAC
* **
175146 GATCTCAAGTGAGATTAACTTTGTTT
1 G-TCTCAAGCGAGACAAACTTTGTTT
175172 AATGTGAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 7 0.14
36 44 0.86
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAACTTTGTTTTTAGAGAAAAC
Found at i:175228 original size:102 final size:104
Alignment explanation
Indices: 175111--175343 Score: 296
Period size: 105 Copynumber: 2.2 Consensus size: 104
175101 TAGAGAAATT
* *
175111 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AG-AA-AACGATCTCAA-GTGAGATTAACTTTGTTT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACAATCT-AAGGTGAGATTAACTTTGTTT
* *
175172 A-ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 ATA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
175213 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAACAATCTAAGGTGAGATTAACTTTGTTTA
* * *
175278 TAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 TAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
175318 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
175344 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.18
103 2 0.02
104 4 0.04
105 81 0.71
106 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (104 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACAATCTAAGGTGAGATTAACTTTGTTTAT
AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:177040 original size:12 final size:11
Alignment explanation
Indices: 177012--177049 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
177002 CCTCTTTTTG
*
177012 TTCTTTGCTTT
1 TTCTTTGATTT
177023 TTCTTTGATTT
1 TTCTTTGATTT
177034 TTGCTTTGATTT
1 TT-CTTTGATTT
177046 TTCT
1 TTCT
177050 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:177053 original size:13 final size:12
Alignment explanation
Indices: 177007--177054 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
176997 TTTGTCCTCT
177007 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
177019 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
177031 TTTTTGCTTTGA
1 TTTTTTCTTTGA
177043 TTTTTCTCTTTG
1 TTTTT-TCTTTG
177055 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:177066 original size:20 final size:20
Alignment explanation
Indices: 177037--177074 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
177027 TTGATTTTTG
177037 CTTTGATTTTTCTCTTTGCT
1 CTTTGATTTTTCTCTTTGCT
* *
177057 CTTTGTTTTTTTTCTTTG
1 CTTTGATTTTTCTCTTTG
177075 GTTTGATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.16, G:0.11, T:0.71
Consensus pattern (20 bp):
CTTTGATTTTTCTCTTTGCT
Found at i:180777 original size:16 final size:16
Alignment explanation
Indices: 180756--180792 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
180746 GTATTGGATT
180756 GCAATACTTCGACCAA
1 GCAATACTTCGACCAA
*
180772 GCAATACTTCGATCAA
1 GCAATACTTCGACCAA
180788 GCAAT
1 GCAAT
180793 GCTTTCCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.22
Consensus pattern (16 bp):
GCAATACTTCGACCAA
Found at i:181001 original size:4 final size:4
Alignment explanation
Indices: 180992--181019 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
180982 GTCCTTTATG
180992 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
181020 GAGATCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:182280 original size:16 final size:16
Alignment explanation
Indices: 182261--182293 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
182251 CGAATGGATC
182261 TCGGTTCTTTTTTTCT
1 TCGGTTCTTTTTTTCT
182277 TCGGTTCTTTTTTTCT
1 TCGGTTCTTTTTTTCT
182293 T
1 T
182294 TTATTGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.12, T:0.70
Consensus pattern (16 bp):
TCGGTTCTTTTTTTCT
Found at i:182781 original size:3 final size:3
Alignment explanation
Indices: 182768--182829 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
182758 ATAATATGTA
** *
182768 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
182812 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
182830 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:182830 original size:24 final size:23
Alignment explanation
Indices: 182768--182831 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
182758 ATAATATGTA
* *
182768 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
182791 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
182815 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
182832 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:190947 original size:23 final size:23
Alignment explanation
Indices: 190913--190968 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
190903 TACAAAGGGG
190913 ACAAGATGTTAATATCAGGAGTT
1 ACAAGATGTTAATATCAGGAGTT
*
190936 ACAATGAT-TTAATTTCAGGAGTT
1 ACAA-GATGTTAATATCAGGAGTT
*
190959 ACGAGA-GTTA
1 ACAAGATGTTA
190969 TAATAGCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 21 0.72
24 3 0.10
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (23 bp):
ACAAGATGTTAATATCAGGAGTT
Found at i:207918 original size:21 final size:21
Alignment explanation
Indices: 207892--207938 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
207882 AAGATATTTG
207892 TGAAAAGAATGGCATAATTCA
1 TGAAAAGAATGGCATAATTCA
207913 TGAAAAGAATGGCATAATTCA
1 TGAAAAGAATGGCATAATTCA
207934 TGAAA
1 TGAAA
207939 CTTCAGCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (21 bp):
TGAAAAGAATGGCATAATTCA
Found at i:210534 original size:17 final size:17
Alignment explanation
Indices: 210525--210573 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
210515 GTCAACGGTC
*
210525 CGGTCGGGTCGGGTTAA
1 CGGTCGGGTCGGGTCAA
*
210542 CGGTCGGGTCTGGTCAA
1 CGGTCGGGTCGGGTCAA
210559 CGGTCGGGTCGGGTC
1 CGGTCGGGTCGGGTC
210574 GGGTCGGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.08, C:0.22, G:0.47, T:0.22
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:210602 original size:19 final size:18
Alignment explanation
Indices: 210575--210653 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 18
210565 GGTCGGGTCG
*
210575 GGTCGGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
210593 GGATCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
*
210612 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
* *
210632 GGTCAAACAGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
210651 GGT
1 GGT
210654 TGAAAATCGG
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.10
19 37 0.74
20 8 0.16
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:210632 original size:29 final size:31
Alignment explanation
Indices: 210600--210675 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
210590 ACCGGATCAG
210600 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
210629 ACCGGTCAAACAGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
* *
210659 ATCGGTTAAACCGGTTC
1 ACCGGTCAAACCGGTTC
210676 CCAGCAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 13 0.32
31 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:217844 original size:17 final size:17
Alignment explanation
Indices: 217835--217883 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
217825 GTCAACGGTC
217835 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
217852 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
217869 CGGTCGGGTCGGGTC
1 CGGTCGGGTCGGGTC
217884 GGACCGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.08, C:0.24, G:0.49, T:0.18
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:217849 original size:22 final size:22
Alignment explanation
Indices: 217824--217885 Score: 80
Period size: 17 Copynumber: 3.0 Consensus size: 22
217814 GAAAGTCAAC
217824 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
217846 GGTCAA-----CGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
*
217863 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
217885 G
1 G
217886 ACCGGTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 17 0.50
22 17 0.50
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCCGGTCGGGTCG
Found at i:217917 original size:10 final size:10
Alignment explanation
Indices: 217886--217960 Score: 59
Period size: 9 Copynumber: 7.7 Consensus size: 10
217876 GTCGGGTCGG
217886 ACCGG-TCAA
1 ACCGGTTCAA
* *
217895 ACCAGTTCGA
1 ACCGGTTCAA
*
217905 ACCGGTTGAA
1 ACCGGTTCAA
217915 ACCGG-TCAA
1 ACCGGTTCAA
217924 ACCGG-TCAGA
1 ACCGGTTCA-A
* *
217934 ACTGGTTGAAA
1 ACCGGTT-CAA
217945 ACCGGTT-AA
1 ACCGGTTCAA
217954 ACCGGTT
1 ACCGGTT
217961 TCCAGCAGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
9 24 0.45
10 20 0.38
11 8 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:217935 original size:29 final size:29
Alignment explanation
Indices: 217886--217959 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
217876 GTCGGGTCGG
*
217886 ACCGGTCAAACCAGTTCGAACCGGTTG-AA
1 ACCGGTCAAACC-GGTCGAACCGGTTGAAA
*
217915 ACCGGTCAAACCGGTCAGAACTGGTTGAAA
1 ACCGGTCAAACCGGTC-GAACCGGTTGAAA
*
217945 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
217960 TTCCAGCAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.08
29 21 0.52
30 16 0.40
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.18
Consensus pattern (29 bp):
ACCGGTCAAACCGGTCGAACCGGTTGAAA
Found at i:224990 original size:17 final size:16
Alignment explanation
Indices: 224966--225009 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
224956 TACTTGATAA
*
224966 AATTAAATATTAATTT
1 AATTAAATATTAAATT
224982 AACTTAAATATTAAATT
1 AA-TTAAATATTAAATT
224999 AATTAAA-ATTA
1 AATTAAATATTA
225010 TATAACTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 7 0.27
17 15 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAAATATTAAATT
Found at i:228281 original size:23 final size:23
Alignment explanation
Indices: 228263--228323 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
228253 CTCATATAAA
*
228263 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
228286 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
228309 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
228324 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:228510 original size:103 final size:103
Alignment explanation
Indices: 228339--228556 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
228329 TAATGTCCAT
228339 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
228404 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
228442 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
228507 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
228545 AAGGACCACATA
1 AAGGACCACATA
228557 GACCCTCGAC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:233347 original size:23 final size:23
Alignment explanation
Indices: 233321--233381 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
233311 CTCATATAAA
*
233321 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
233344 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
233367 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
233382 TATAACAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:233568 original size:103 final size:103
Alignment explanation
Indices: 233397--233614 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
233387 CAATGTCCAT
* *
233397 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACAA
* *
233462 GACTTCACACATGTTCCAAAGAATACATATATGTCACG
66 GACTTCACACATGTTCCAAAAAATACATATATCTCACG
233500 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACAA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACAA
*
233565 GACTTCACACATGTTCCAAAAAATACATATATCTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATCTCACG
233603 AAGGACCACATA
1 AAGGACCACATA
233615 AACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACAA
GACTTCACACATGTTCCAAAAAATACATATATCTCACG
Found at i:235298 original size:23 final size:23
Alignment explanation
Indices: 235272--235324 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
235262 AATACACCAA
* *
235272 AGTGCTACATAGAATTGCACCGT
1 AGTGCCACATAGAATTACACCGT
* * *
235295 AGTGCCGCGTAGAATTACACTGT
1 AGTGCCACATAGAATTACACCGT
235318 AGTGCCA
1 AGTGCCA
235325 TATAATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (23 bp):
AGTGCCACATAGAATTACACCGT
Found at i:235471 original size:103 final size:103
Alignment explanation
Indices: 235340--235557 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
235330 TAATGTCCAT
235340 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
235405 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
235443 AAGGGCCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
235508 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
235546 AAGGACCACATA
1 AAGGACCACATA
235558 GACCCTTGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:245680 original size:25 final size:25
Alignment explanation
Indices: 245650--245697 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
245640 TCTCCACCTA
**
245650 AATAAAAAAATTTGTTAATAATTTT
1 AATAAAAAAAACTGTTAATAATTTT
245675 AATAAAAAAAACTGTTAATAATT
1 AATAAAAAAAACTGTTAATAATT
245698 CACAAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
AATAAAAAAAACTGTTAATAATTTT
Found at i:249080 original size:18 final size:16
Alignment explanation
Indices: 249049--249094 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
249039 CAAACCAATT
249049 AAAAATTA--AAAAAG
1 AAAAATTATGAAAAAG
249063 AAAAAATTATGTAAAAAG
1 -AAAAATTATG-AAAAAG
*
249081 ATAAATTATGAAAA
1 AAAAATTATGAAAA
249095 TCAAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.30
16 4 0.15
17 9 0.33
18 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAAATTATGAAAAAG
Found at i:249755 original size:22 final size:23
Alignment explanation
Indices: 249727--249783 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
249717 ATTTTTTAAC
249727 ATAATGAAAATA-TC-CTAAATAA
1 ATAATGAAAATATTCAC-AAATAA
249749 ATAATGAAAAGTATTCACAAATAA
1 ATAATGAAAA-TATTCACAAATAA
*
249773 TTAAT-AAAATA
1 ATAATGAAAATA
249784 GTTAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 12 0.39
23 6 0.19
24 12 0.39
25 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (23 bp):
ATAATGAAAATATTCACAAATAA
Found at i:259380 original size:128 final size:131
Alignment explanation
Indices: 259243--259489 Score: 392
Period size: 130 Copynumber: 1.9 Consensus size: 131
259233 ATTTTATATA
*
259243 ATCAATTTGGTCCT-AATTAAATAAAATTTAAT-AATTAATCATTTAATTAGGATATGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
* * *
259306 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTA-CCACCTAATTATTTATATATGC
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCCACCTAATTATTTATATATGC
259370 T
131 T
*
259371 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
* * * *
259436 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCCACCTAATTA
259490 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
128 14 0.13
129 18 0.17
130 65 0.61
131 10 0.09
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (131 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCCACCTAATTATTTATATATGC
T
Found at i:259518 original size:130 final size:127
Alignment explanation
Indices: 259257--259519 Score: 278
Period size: 130 Copynumber: 2.0 Consensus size: 127
259247 ATTTGGTCCT
* *
259257 AATTAAATAAAATTTAATAATTAATCATTTAATTAGGATATGACATGTGTTAGCACATGATCATG
1 AATTAAATAAAATTTAATAATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCATG
* * *** * * * **
259322 ACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCTA
66 ACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAA--TAGAACTA
*
259386 AATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCAT
1 AATTAAATAAAATTTAAT-AATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCAT
* * * * * *
259451 GATATGTGTTATTGGTGACACATGTCACCCTCCTAATTAGAAGAAAATTAAGTTA-CAA-AGAAG
65 GACACGTGTCATTGGTGACACATGTCA-CCACCTAATT--AAGAAAA-TAAGCTATCAATAGAAC
259514 TA
126 TA
259516 AATT
1 AATT
259520 TGGGTCTTGG
Statistics
Matches: 110, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
129 18 0.16
130 72 0.65
131 9 0.08
133 6 0.05
134 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (127 bp):
AATTAAATAAAATTTAATAATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCATG
ACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAATAGAACTA
Found at i:260116 original size:20 final size:20
Alignment explanation
Indices: 260091--260130 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
260081 TATTACCTTA
260091 AATTGAAGTATTTTAGAATT
1 AATTGAAGTATTTTAGAATT
260111 AATTGAAGTATTTTAGAATT
1 AATTGAAGTATTTTAGAATT
260131 TAGGGTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
AATTGAAGTATTTTAGAATT
Found at i:260175 original size:33 final size:34
Alignment explanation
Indices: 260102--260181 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
260092 ATTGAAGTAT
* *
260102 TTTAGAATTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAATTGAAGTACTTTAGAATTTAGGG
* * *
260136 TTTAGAATAAATTGAATTACTTTGGAA-TTGGGG
1 TTTAGAATAAATTGAAGTACTTTAGAATTTAGGG
260169 TTTAGAATGAAAT
1 TTTAGAAT-AAAT
260182 GATGACTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 13 0.32
34 27 0.68
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.41
Consensus pattern (34 bp):
TTTAGAATAAATTGAAGTACTTTAGAATTTAGGG
Found at i:260366 original size:29 final size:29
Alignment explanation
Indices: 260314--260371 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
260304 GCAAACATAA
* *
260314 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
260343 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
260372 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:264742 original size:114 final size:115
Alignment explanation
Indices: 264619--264826 Score: 319
Period size: 114 Copynumber: 1.8 Consensus size: 115
264609 TTTCCTTAAC
* * * **
264619 ATATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACACCTCTTTCTTTTG
1 ATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAACTCTTTCCTTCA
*
264684 ATATT-AAAAAATAAATAAAAAATAAAAAAAATTATTTTAATATAGTAAG
66 ATATTAAAAAAATAAATAAAAAACAAAAAAAATTATTTTAATATAGTAAG
* * *
264733 ATATTTATTTATTTAAAAATATTAGAAAAGGGCTTCTAGTTGTTTTAAGACAACTCTTTCCTTCA
1 ATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAACTCTTTCCTTCA
*
264798 ATATTAAAAAAATAAATAAATAACAAAAA
66 ATATTAAAAAAATAAATAAAAAACAAAAA
264827 CATAATAAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 62 0.75
115 21 0.25
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (115 bp):
ATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAACTCTTTCCTTCA
ATATTAAAAAAATAAATAAAAAACAAAAAAAATTATTTTAATATAGTAAG
Found at i:266234 original size:3 final size:3
Alignment explanation
Indices: 266226--266261 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
266216 ATATTTATTA
*
266226 AAT AAT AAT AAT AAC AAT -AT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
266262 GAATGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:266247 original size:17 final size:17
Alignment explanation
Indices: 266227--266261 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
266217 TATTTATTAA
266227 ATAATAATAATAACAAT
1 ATAATAATAATAACAAT
*
266244 ATAATAATAATAATAAT
1 ATAATAATAATAACAAT
266261 A
1 A
266262 GAATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAATAATAATAACAAT
Found at i:266515 original size:76 final size:76
Alignment explanation
Indices: 266386--267099 Score: 1302
Period size: 76 Copynumber: 9.4 Consensus size: 76
266376 GAAATATTGA
* * *
266386 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
266451 AGGCTTTTTGG
66 AGGCTTTTTGG
*
266462 AAGCATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
266527 AAGCTTTTTGG
66 AGGCTTTTTGG
* *
266538 AAACATCATGCACTGTAGAACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
266603 AGGCTTTTTGG
66 AGGCTTTTTGG
*
266614 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
266679 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
266690 AAACATCATGCACTGTAGGACTTAGAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
266755 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
266766 AAACATCATACACTATAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
266831 AGGATTTTTGG
66 AGGCTTTTTGG
*
266842 AAACATCATGCACTGTAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
266907 AGGCTTTTTGG
66 AGGCTTTTTGG
266918 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
266983 AGGCTTTTTGG
66 AGGCTTTTTGG
266994 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
267059 AGGCTTTTTGG
66 AGGCTTTTTGG
267070 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
267100 TGGGAAATAG
Statistics
Matches: 613, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 613 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:267802 original size:22 final size:22
Alignment explanation
Indices: 267777--267853 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
267767 AATAAAGCTT
*
267777 TCATCTTTGAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
267799 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
267821 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
267843 TCATCTTTGAA
1 TCATCTTTGAA
267854 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:277573 original size:28 final size:32
Alignment explanation
Indices: 277507--277575 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 32
277497 TGAAAATAAA
277507 ATGAAACATTAATAAAATAATATATATAAATATT
1 ATGAAA-A-TAATAAAATAATATATATAAATATT
277541 ATGAAAATAAT-AAAT-ATATATATAAAT-TT
1 ATGAAAATAATAAAATAATATATATAAATATT
277570 -TGAAAA
1 ATGAAAA
277576 GAAACAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
28 6 0.17
29 2 0.06
30 12 0.34
31 4 0.11
32 4 0.11
33 1 0.03
34 6 0.17
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (32 bp):
ATGAAAATAATAAAATAATATATATAAATATT
Found at i:279783 original size:3 final size:3
Alignment explanation
Indices: 279775--279809 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
279765 ATATTTATTA
279775 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
279810 TAATGTCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:283492 original size:30 final size:31
Alignment explanation
Indices: 283415--283494 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
283405 ACTGTTTAGC
* * **
283415 CCTTTAACTTTTTGTTTTTGCTATTTTTTGT
1 CCTTTAACTTTATGTTTTTACTATTTTTAAT
*
283446 TCTTTAACTTTATGTTTTTACTA-TTTTAAT
1 CCTTTAACTTTATGTTTTTACTATTTTTAAT
* *
283476 CCTTTAAGTTTCTGTTTTT
1 CCTTTAACTTTATGTTTTT
283495 GTTGTTTTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 21 0.51
31 20 0.49
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.65
Consensus pattern (31 bp):
CCTTTAACTTTATGTTTTTACTATTTTTAAT
Found at i:285798 original size:20 final size:20
Alignment explanation
Indices: 285773--285820 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
285763 TTCACAACCA
285773 AAGTCACATACATCAATCAC
1 AAGTCACATACATCAATCAC
285793 AAGTCACATACATCAATCAC
1 AAGTCACATACATCAATCAC
285813 AAGTCACA
1 AAGTCACA
285821 ATATTACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.19
Consensus pattern (20 bp):
AAGTCACATACATCAATCAC
Found at i:286433 original size:30 final size:30
Alignment explanation
Indices: 286397--286458 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
286387 TGACTAAGGC
286397 AGTTATTTGAAAACCGTCCAAATGAAAGTA
1 AGTTATTTGAAAACCGTCCAAATGAAAGTA
286427 AGTTATTTGAAAACCGTCCAAATGAAAGTA
1 AGTTATTTGAAAACCGTCCAAATGAAAGTA
286457 AG
1 AG
286459 AACCCAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (30 bp):
AGTTATTTGAAAACCGTCCAAATGAAAGTA
Found at i:287675 original size:22 final size:22
Alignment explanation
Indices: 287650--287702 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
287640 TTCCAGTTCG
*
287650 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTAT
287672 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTTAT
287694 CGTTGCGAT
1 CGTTGCGAT
287703 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTAT
Found at i:288348 original size:6 final size:6
Alignment explanation
Indices: 288337--288381 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
288327 GTCCGTCTCG
288337 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
288382 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:288523 original size:21 final size:21
Alignment explanation
Indices: 288480--288552 Score: 119
Period size: 21 Copynumber: 3.4 Consensus size: 21
288470 AATTTGGAAA
* *
288480 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGAC-ATTGTACACT
288502 ATCGCAACGACATTGTACACT
1 ATCGCAACGACATTGTACACT
288523 ATCGCAACGACATTGTACACT
1 ATCGCAACGACATTGTACACT
288544 ATCGCAACG
1 ATCGCAACG
288553 CGAAATGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 38 0.78
22 11 0.22
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (21 bp):
ATCGCAACGACATTGTACACT
Found at i:288635 original size:20 final size:20
Alignment explanation
Indices: 288587--288717 Score: 118
Period size: 20 Copynumber: 6.5 Consensus size: 20
288577 TTCAACTATA
288587 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
***
288607 GCGTTGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
* * ** *
288627 ACAACGCGATATTCAACTATC
1 GCAACGCGAAATGGAA-AATC
288648 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
* ** ** *
288668 GCAATGCGATTTTCAACTATC
1 GCAACGCGAAATGGAA-AATC
288689 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
288709 GCAACGCGA
1 GCAACGCGA
288718 TTTTCAACTA
Statistics
Matches: 81, Mismatches: 28, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
20 52 0.64
21 29 0.36
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAATGGAAAATC
Found at i:288652 original size:21 final size:21
Alignment explanation
Indices: 288628--288759 Score: 135
Period size: 21 Copynumber: 6.4 Consensus size: 21
288618 TGGAAAATCA
288628 CAACGCGATATTCAACTATCG
1 CAACGCGATATTCAACTATCG
* ** *
288649 CAACGCGAAATGGAA-AATCG
1 CAACGCGATATTCAACTATCG
* *
288669 CAATGCGATTTTCAACTATCG
1 CAACGCGATATTCAACTATCG
* ** *
288690 CAACGCGAAATGGAA-AATCG
1 CAACGCGATATTCAACTATCG
*
288710 CAACGCGATTTTCAACTATCG
1 CAACGCGATATTCAACTATCG
288731 CAACGCGAT-TTCTAACTATCG
1 CAACGCGATATTC-AACTATCG
288752 CAACGCGA
1 CAACGCGA
288760 ATTTGCGATA
Statistics
Matches: 87, Mismatches: 21, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
20 32 0.37
21 55 0.63
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
CAACGCGATATTCAACTATCG
Found at i:288657 original size:41 final size:41
Alignment explanation
Indices: 288612--288738 Score: 227
Period size: 41 Copynumber: 3.1 Consensus size: 41
288602 AAATCGCGTT
* *
288612 GCGAAATGGAAAATCACAACGCGATATTCAACTATCGCAAC
1 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
*
288653 GCGAAATGGAAAATCGCAATGCGATTTTCAACTATCGCAAC
1 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
288694 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
1 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
288735 GCGA
1 GCGA
288739 TTTCTAACTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
Found at i:288676 original size:61 final size:60
Alignment explanation
Indices: 288544--288676 Score: 194
Period size: 61 Copynumber: 2.2 Consensus size: 60
288534 ATTGTACACT
* * * *
288544 ATCGCAACGCGAAATGGAAAATTAAACGTGATTTTCAACTATAGCAACGCGAAATGGAAA
1 ATCGCAATGCGAAATGGAAAATCAAACGCGATATTCAACTATAGCAACGCGAAATGGAAA
** *
288604 ATCGCGTTGCGAAATGGAAAATCACAACGCGATATTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAATGCGAAATGGAAAATCA-AACGCGATATTCAACTATAGCAACGCGAAATGGAAA
288665 ATCGCAATGCGA
1 ATCGCAATGCGA
288677 TTTTCAACTA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
60 20 0.32
61 43 0.68
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.19
Consensus pattern (60 bp):
ATCGCAATGCGAAATGGAAAATCAAACGCGATATTCAACTATAGCAACGCGAAATGGAAA
Found at i:290670 original size:21 final size:20
Alignment explanation
Indices: 290595--290701 Score: 62
Period size: 21 Copynumber: 5.3 Consensus size: 20
290585 TAATGTTGAT
290595 ATAATA-TTTTAATATCATTTTA
1 ATAATATTTTTAATAT-A--TTA
* * *
290617 ATAAAAATGTTAAT-TATTA
1 ATAATATTTTTAATATATTA
**
290636 A-AATATTTAAAATATATTA
1 ATAATATTTTTAATATATTA
290655 ATTAATATTTTTAATAT-TATA
1 A-TAATATTTTTAATATAT-TA
* *
290676 ATAATATATTTAGTTATATT-
1 ATAATATTTTTA-ATATATTA
290696 ATAATA
1 ATAATA
290702 ATATATGATA
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
18 7 0.10
19 10 0.15
20 17 0.25
21 20 0.30
22 7 0.10
23 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAATATTTTTAATATATTA
Found at i:290682 original size:20 final size:22
Alignment explanation
Indices: 290638--290707 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
290628 AATTATTAAA
*
290638 ATATTTAAAATA-TATTAATTAAT
1 ATATTTATAATATTA-TAA-TAAT
290661 AT-TTT-TAATATTATAATAAT
1 ATATTTATAATATTATAATAAT
*
290681 ATATTTAGTTATATTATAATAAT
1 ATATTTA-TAATATTATAATAAT
290704 ATAT
1 ATAT
290708 GATATTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 6 0.15
21 10 0.24
22 5 0.12
23 20 0.49
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATTTATAATATTATAATAAT
Found at i:290715 original size:23 final size:23
Alignment explanation
Indices: 290668--290718 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
290658 AATATTTTTA
*
290668 ATATTATAATAATATATTTAGTT
1 ATATTATAATAATATATATAGTT
290691 ATATTATAATAATATATGATA-TT
1 ATATTATAATAATATAT-ATAGTT
290714 ATATT
1 ATATT
290719 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATTATAATAATATATATAGTT
Found at i:291221 original size:16 final size:15
Alignment explanation
Indices: 291200--291229 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
291190 TATTTTAATG
291200 ATAATATTGACATAAC
1 ATAATATTGA-ATAAC
291216 ATAATATTGAATAA
1 ATAATATTGAATAA
291230 TTATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
ATAATATTGAATAAC
Found at i:291266 original size:17 final size:16
Alignment explanation
Indices: 291240--291317 Score: 58
Period size: 16 Copynumber: 5.0 Consensus size: 16
291230 TTATTATATA
291240 TTTTATTAATAATATTAT
1 TTTTA-TAATAA-ATTAT
291258 TTTTATAATAAA-TAT
1 TTTTATAATAAATTAT
**
291273 CTTTT-T-ATATTTTAT
1 -TTTTATAATAAATTAT
* *
291288 ATTTATAATAAATAAT
1 TTTTATAATAAATTAT
291304 TTTTA-AA-AAATTAT
1 TTTTATAATAAATTAT
291318 CAATTAACGA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
14 12 0.25
15 10 0.21
16 15 0.31
17 6 0.12
18 5 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTATAATAAATTAT
Found at i:291271 original size:18 final size:16
Alignment explanation
Indices: 291234--291281 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
291224 GAATAATTAT
291234 TATATATTTTATTAATAA
1 TATAT-TTTTA-TAATAA
291252 TATTATTTTTATAATAAA
1 TA-TATTTTTATAAT-AA
*
291270 TATCTTTTTATA
1 TATATTTTTATA
291282 TTTTATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.48
18 11 0.41
19 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTTTATAATAA
Found at i:291571 original size:7 final size:7
Alignment explanation
Indices: 291555--291591 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
291545 TCACACTCGC
*
291555 CCTTCAT
1 CCTTCCT
291562 CCTTCCT
1 CCTTCCT
291569 CCTTCCT
1 CCTTCCT
291576 CCTTCCT
1 CCTTCCT
291583 CCTTTCCT
1 CC-TTCCT
291591 C
1 C
291592 TCTCTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.03, C:0.54, G:0.00, T:0.43
Consensus pattern (7 bp):
CCTTCCT
Found at i:291949 original size:30 final size:30
Alignment explanation
Indices: 291912--292000 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
291902 CCCAGTTTCA
*
291912 ACCCCTCCACCTAGC-TCTCCTCCTCCAGCC
1 ACCCCTCCACCT-GCTTCTCCCCCTCCAGCC
* * *
291942 ACTCCTCCGCCTGCTTCTCCCCCTCCCGCC
1 ACCCCTCCACCTGCTTCTCCCCCTCCAGCC
* * *
291972 ACCCCACCACCTTCTTCTCCCCCACCAGC
1 ACCCCTCCACCTGCTTCTCCCCCTCCAGC
292001 ATCTCCCCCT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 2 0.04
30 46 0.96
ACGTcount: A:0.11, C:0.62, G:0.07, T:0.20
Consensus pattern (30 bp):
ACCCCTCCACCTGCTTCTCCCCCTCCAGCC
Found at i:292042 original size:30 final size:30
Alignment explanation
Indices: 291988--292060 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
291978 CCACCTTCTT
* * * *
291988 CTCCCCCACCAGCATCTCCCCCTCCCGCTA
1 CTCCACCACCTGCAACTCCCCCTCCAGCTA
*
292018 CTCCACCACCTGCAACTCCTCCTCCAGCTA
1 CTCCACCACCTGCAACTCCCCCTCCAGCTA
* *
292048 CCCCACCGCCTGC
1 CTCCACCACCTGC
292061 TCCCTTGGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.15, C:0.60, G:0.08, T:0.16
Consensus pattern (30 bp):
CTCCACCACCTGCAACTCCCCCTCCAGCTA
Found at i:292045 original size:45 final size:45
Alignment explanation
Indices: 291942--292045 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
291932 TCCTCCAGCC
* * * * *
291942 ACTCCTCCGCCTGCTTCTCCCCCTCCCGCCACCCCACCACCTTCT
1 ACTCCTCCACCAGCATCTCCCCCTCCCGCCACCCCACCACCTGCA
* * * *
291987 TCTCCCCCACCAGCATCTCCCCCTCCCGCTACTCCACCACCTGCA
1 ACTCCTCCACCAGCATCTCCCCCTCCCGCCACCCCACCACCTGCA
*
292032 ACTCCTCCTCCAGC
1 ACTCCTCCACCAGC
292046 TACCCCACCG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.12, C:0.61, G:0.07, T:0.20
Consensus pattern (45 bp):
ACTCCTCCACCAGCATCTCCCCCTCCCGCCACCCCACCACCTGCA
Found at i:294721 original size:54 final size:54
Alignment explanation
Indices: 294655--294940 Score: 416
Period size: 54 Copynumber: 5.3 Consensus size: 54
294645 TTCGTTACGA
* * * * *
294655 TGCACACGTAGTGCCTATACGGTCATTCATAAACATATTATGAATTCCGTGAAT
1 TGCACACTTAGTGCCTAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
294709 TGCACACTTAGTG-CTGAAATGGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCT-AAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
294763 TGCACACTTAGTGCCGAAACGG-TATTCATCAGCATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCTAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
294816 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAAT
1 TGCACACTTAGTGCCTAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
294870 TGCACACTTAGTG-CTGAAACGGTTATTCATCAACATATGATGAATTCCATGAGT
1 TGCACACTTAGTGCCT-AAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
294924 TGCGCACTTAGTGCCTA
1 TGCACACTTAGTGCCTA
294941 TTTGGTAATC
Statistics
Matches: 211, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
53 55 0.26
54 153 0.73
55 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (54 bp):
TGCACACTTAGTGCCTAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:294810 original size:107 final size:107
Alignment explanation
Indices: 294655--294938 Score: 433
Period size: 107 Copynumber: 2.6 Consensus size: 107
294645 TTCGTTACGA
* * * * *
294655 TGCACACGTAGTGCCTATACGGTCATTCATAAACATATTATGAATTCCGTGAATTGCACACTTAG
1 TGCACACTTAGTGCCGAAACGGT-ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAG
* *
294720 TGCTGAAATGGTTATTCATCAACATATGATGAATTCCGTGAAT
65 TGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
294763 TGCACACTTAGTGCCGAAACGGTATTCATCAGCATATGATGAATTCCGTGAATTGCACACTTAGT
1 TGCACACTTAGTGCCGAAACGGTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGT
*
294828 GCCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAAT
66 GCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * * *
294870 TGCACACTTAGTGCTGAAACGGTTATTCATCAACATATGATGAATTCCATGAGTTGCGCACTTAG
1 TGCACACTTAGTGCCGAAACGG-TATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAG
294935 TGCC
65 TGCC
294939 TATTTGGTAA
Statistics
Matches: 161, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
107 99 0.61
108 62 0.39
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (107 bp):
TGCACACTTAGTGCCGAAACGGTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGT
GCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:294913 original size:26 final size:26
Alignment explanation
Indices: 294831--294913 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
294821 ACTTAGTGCC
294831 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
* * * * *
294857 GAATTCTGTGAATTGCA-C-ACTTAGTGCT
1 GAA-ACGGT-TATT-CATCAACATA-TGAT
294885 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
294911 GAA
1 GAA
294914 TTCCATGAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
25 2 0.05
26 13 0.32
27 14 0.34
28 10 0.24
29 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (26 bp):
GAAACGGTTATTCATCAACATATGAT
Found at i:295395 original size:20 final size:20
Alignment explanation
Indices: 295349--295401 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
295339 TCTGTTAACA
*
295349 ATGGTATCGATACCTTCCTC
1 ATGGTATCGATACCTCCCTC
* *
295369 ATAGTATCGATACCTCCCTT
1 ATGGTATCGATACCTCCCTC
*
295389 TTGGTATCGATAC
1 ATGGTATCGATAC
295402 TACTTGCATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGGTATCGATACCTCCCTC
Found at i:296670 original size:65 final size:64
Alignment explanation
Indices: 296529--296684 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 64
296519 TACACTAGAG
* * * * *
296529 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAGAGCCAGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGCTCT
* * ** *
296593 GTGTATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGTATCGATGCATGACT-
1 GTGCATCGGTACACAAAATGCATTCGATGTTTC-AAAGAGCCAAGAGTGCATCGATGCATG-CTC
296657 T
64 T
296658 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
296685 AATAGGTGTG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 29 0.37
65 49 0.62
66 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGCTCT
Found at i:303141 original size:20 final size:21
Alignment explanation
Indices: 303102--303141 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
303092 GAAGCTTTAA
* *
303102 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
303123 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
303142 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:303542 original size:43 final size:43
Alignment explanation
Indices: 303484--303567 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
303474 GAGCCTTGTG
303484 TTTTTTCTTCGATTAACCATTCTTCTTTAATTGTGGGCAATGT
1 TTTTTTCTTCGATTAACCATTCTTCTTTAATTGTGGGCAATGT
303527 TTTTTTCTTCGATTAACCATTCTTCTTTAATTGTGGGCAAT
1 TTTTTTCTTCGATTAACCATTCTTCTTTAATTGTGGGCAAT
303568 CCTATTTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (43 bp):
TTTTTTCTTCGATTAACCATTCTTCTTTAATTGTGGGCAATGT
Found at i:305328 original size:19 final size:19
Alignment explanation
Indices: 305304--305348 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
305294 AATGCCAGGA
305304 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTCT
*
305323 GTGCATCGATGCATGTTCT
1 GTGCATCGATGCATGGTCT
305342 GTGCATC
1 GTGCATC
305349 AGTACACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGGTCT
Found at i:305411 original size:19 final size:19
Alignment explanation
Indices: 305387--305433 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
305377 AATATTCAAG
305387 AGTGCATCGATGCAT-GACT
1 AGTGCATCGATGCATAG-CT
305406 AGTGCATCGATGCATAGCT
1 AGTGCATCGATGCATAGCT
*
305425 TGTGCATCG
1 AGTGCATCG
305434 GTACACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 25 0.96
20 1 0.04
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGCATAGCT
Found at i:305413 original size:84 final size:83
Alignment explanation
Indices: 305280--305449 Score: 236
Period size: 84 Copynumber: 2.0 Consensus size: 83
305270 CACTAATTAT
* * * *
305280 ATTCGATGTTTTAAAATGCCAGGAGTGCATCGATGCATGGTCTGTGCATCGATGCAT-GTTCTGT
1 ATTCGATGTTTCAAAATGCCAAGAGTGCATCGATGCATGGACTGTGCATCGATGCATAGCT-TGT
305344 GCATCAGTACACAAAATGC
65 GCATCAGTACACAAAATGC
**
305363 ATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCAT-GACTAGTGCATCGATGCATAGCTTG
1 ATTCGATGTTTCAAAAT-GCCAAGAGTGCATCGATGCATGGACT-GTGCATCGATGCATAGCTTG
*
305427 TGCATCGGTACACAAAATGC
64 TGCATCAGTACACAAAATGC
305447 ATT
1 ATT
305450 TGAAATGGGT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
83 19 0.25
84 56 0.73
85 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (83 bp):
ATTCGATGTTTCAAAATGCCAAGAGTGCATCGATGCATGGACTGTGCATCGATGCATAGCTTGTG
CATCAGTACACAAAATGC
Found at i:308700 original size:14 final size:15
Alignment explanation
Indices: 308678--308706 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
308668 TTTATATATA
308678 TTATCTTATTTATTT
1 TTATCTTATTTATTT
308693 TTAT-TTATTTATTT
1 TTATCTTATTTATTT
308707 AAATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATCTTATTTATTT
Found at i:309522 original size:13 final size:14
Alignment explanation
Indices: 309506--309558 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
309496 GTGTCATTTA
309506 TTTATTTATC-TAT
1 TTTATTTATCATAT
*
309519 TTTATTTGTCATAT
1 TTTATTTATCATAT
* *
309533 TATATTTGATAATAT
1 TTTATTT-ATCATAT
*
309548 TATATTTATCA
1 TTTATTTATCA
309559 GAGAGCGGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 9 0.27
14 12 0.36
15 12 0.36
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (14 bp):
TTTATTTATCATAT
Found at i:309549 original size:15 final size:14
Alignment explanation
Indices: 309516--309554 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
309506 TTTATTTATC
* *
309516 TATTTTATTTGTCA
1 TATTATATTTGTAA
309530 TATTATATTTGATAA
1 TATTATATTTG-TAA
309545 TATTATATTT
1 TATTATATTT
309555 ATCAGAGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (14 bp):
TATTATATTTGTAA
Found at i:322345 original size:21 final size:22
Alignment explanation
Indices: 322319--322381 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
322309 TTTGGTGCAG
322319 AGGGAATCGATACCCCTTGA-A
1 AGGGAATCGATACCCCTTGACA
* * ***
322340 AGGGAACCGATTCCCCCACACA
1 AGGGAATCGATACCCCTTGACA
*
322362 GGGGAATCGATACCCCTTGA
1 AGGGAATCGATACCCCTTGA
322382 GGGTTCTGGT
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (22 bp):
AGGGAATCGATACCCCTTGACA
Found at i:323957 original size:18 final size:19
Alignment explanation
Indices: 323929--323964 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
323919 GATGAACCAC
323929 AGCACGAGGAACAAGCACG
1 AGCACGAGGAACAAGCACG
323948 AGCA-GAGGAACAAGCAC
1 AGCACGAGGAACAAGCAC
323965 ATCCAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00
Consensus pattern (19 bp):
AGCACGAGGAACAAGCACG
Found at i:324284 original size:16 final size:16
Alignment explanation
Indices: 324263--324294 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
324253 AGGGGGAGTA
324263 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
324279 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
324295 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTCAAACTTGATTT
Found at i:325465 original size:23 final size:25
Alignment explanation
Indices: 325435--325489 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
325425 ATAGGAAAAC
325435 ATTTTAA-TATTTAAAAAA-A-TAAA
1 ATTTTAATTA-TTAAAAAATATTAAA
325458 ATTTTAATTATTAAAAAATATTAAA
1 ATTTTAATTATTAAAAAATATTAAA
*
325483 AATTTAA
1 ATTTTAA
325490 AATACAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 15 0.54
24 3 0.11
25 10 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTTAATTATTAAAAAATATTAAA
Found at i:334562 original size:492 final size:495
Alignment explanation
Indices: 333630--334617 Score: 1937
Period size: 492 Copynumber: 2.0 Consensus size: 495
333620 TTCATTTAAA
333630 ATTTTGACCGTTTGAATAGGGGGTTTTGAAACCTTTAAGGGGGTTTCGAAACATGTAGGCCACAT
1 ATTTTGACCGTTTGAATAGGGGGTTTTGAAACCTTTAAGGGGGTTTCGAAACATGTAGGCCACAT
333695 TTAGACTTTGTCTTAGGGGTTTCGAAATCAAACCCAAAATTGTCTGTTTCACCTTTTTAAAAACT
66 TTAGACTTTGTCTTAGGGGTTTCGAAATCAAACCCAAAATTGTCTGTTTCACCTTTTTAAAAACT
333760 TAATAACTTTGAATTATTTTTCTAATGTTTGAACAAATTCAATTTGGTCCAAAAACAATTTTGCC
131 TAATAACTTTGAATTATTTTTCTAATGTTTGAACAAATTCAATTTGGTCCAAAAACAATTTTGCC
333825 CTTATTTATTATATCAAAATATTAGTTCTACAATCTCCCCCTTTTTTATATAACAAAACCTTTGA
196 CTTATTTATTATATCAAAATATTAGTTCTACAATCTCCCCCTTTTTTATATAACAAAACCTTTGA
333890 AAAATAGTTTTTGGTAAAAGCCCTTCATATCAATACATTTAATGAAAAAGATAATTATTTGGAAA
261 AAAATAGTTTTTGGTAAAAGCCCTTCATATCAATACATTTAATGAAAAAGATAATTATTTGGAAA
*
333955 ATATTAAAGCTCCCTCTTTATCATTCTTGAAATTGAAATTTTCAAACTCACACTTCTTCTCCTTT
326 ATATTAAAGCTCCCTCTTTATCATTCTTGAAATTGAAATTTTCAAACTCACACTTCTCCTCCTTT
*
334020 TTGTTATATAAAAAATAATTCATACTTTTAAGGTACAAAATAACAATGGAGAGTAACTAGTAATT
391 TTGTTATATAAAAAATAATTCATACTTTTAAGGTACAAAATAAAAATGGAGAGTAACTAGTAATT
334085 TTAACATTAAAATCATTTGGAAAATCAAAAACTCTCTCTC
456 TTAACATTAAAATCATTTGGAAAATCAAAAACTCTCTCTC
334125 ATTTTGACCGTTTGAATAGGGGGTTTTGAAACCTTTAAGGGGGTTTCGAAACATGTAGGCCACAT
1 ATTTTGACCGTTTGAATAGGGGGTTTTGAAACCTTTAAGGGGGTTTCGAAACATGTAGGCCACAT
334190 TTAGACTTTGTCTTAGGGGTTTCGAAATCAAACCC-AAATTGTCTG-TTCACCTTTTTAAAAACT
66 TTAGACTTTGTCTTAGGGGTTTCGAAATCAAACCCAAAATTGTCTGTTTCACCTTTTTAAAAACT
334253 TAATAACTTTGAATTA-TTTTCTAATGTTTGAACAAATTCAATTTGGTCCAAAAACAATTTTGCC
131 TAATAACTTTGAATTATTTTTCTAATGTTTGAACAAATTCAATTTGGTCCAAAAACAATTTTGCC
334317 CTTATTTATTATATCAAAATATTAGTTCTACAATCTCCCCCTTTTTTATATAACAAAACCTTTGA
196 CTTATTTATTATATCAAAATATTAGTTCTACAATCTCCCCCTTTTTTATATAACAAAACCTTTGA
334382 AAAATAGTTTTTGGTAAAAGCCCTTCATATCAATACATTTAATGAAAAAGATAATTATTTGGAAA
261 AAAATAGTTTTTGGTAAAAGCCCTTCATATCAATACATTTAATGAAAAAGATAATTATTTGGAAA
334447 ATATTAAAGCTCCCTCTTTATCATTCTTGAAATTGAAATTTTCAAACTCACACTTCTCCTCCTTT
326 ATATTAAAGCTCCCTCTTTATCATTCTTGAAATTGAAATTTTCAAACTCACACTTCTCCTCCTTT
334512 TTGTTATATAAAAAATAATTCATACTTTTAAGGTACAAAATAAAAATGGAGAGTAACTAGTAATT
391 TTGTTATATAAAAAATAATTCATACTTTTAAGGTACAAAATAAAAATGGAGAGTAACTAGTAATT
334577 TTAACATTAAAATCATTTGGAAAATCAAAAACTCTCTCTC
456 TTAACATTAAAATCATTTGGAAAATCAAAAACTCTCTCTC
334617 A
1 A
334618 ACAAGTGCAT
Statistics
Matches: 491, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
492 347 0.71
493 34 0.07
494 10 0.02
495 100 0.20
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (495 bp):
ATTTTGACCGTTTGAATAGGGGGTTTTGAAACCTTTAAGGGGGTTTCGAAACATGTAGGCCACAT
TTAGACTTTGTCTTAGGGGTTTCGAAATCAAACCCAAAATTGTCTGTTTCACCTTTTTAAAAACT
TAATAACTTTGAATTATTTTTCTAATGTTTGAACAAATTCAATTTGGTCCAAAAACAATTTTGCC
CTTATTTATTATATCAAAATATTAGTTCTACAATCTCCCCCTTTTTTATATAACAAAACCTTTGA
AAAATAGTTTTTGGTAAAAGCCCTTCATATCAATACATTTAATGAAAAAGATAATTATTTGGAAA
ATATTAAAGCTCCCTCTTTATCATTCTTGAAATTGAAATTTTCAAACTCACACTTCTCCTCCTTT
TTGTTATATAAAAAATAATTCATACTTTTAAGGTACAAAATAAAAATGGAGAGTAACTAGTAATT
TTAACATTAAAATCATTTGGAAAATCAAAAACTCTCTCTC
Found at i:337939 original size:13 final size:12
Alignment explanation
Indices: 337921--337962 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
337911 TAAATCTCAG
337921 ATGACACGTATTT
1 ATGACAC-TATTT
337934 ATGACAC-ATTT
1 ATGACACTATTT
*
337945 ATGACGCTCATTT
1 ATGACACT-ATTT
337958 ATGAC
1 ATGAC
337963 GCGCATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.38
13 16 0.62
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (12 bp):
ATGACACTATTT
Found at i:337963 original size:13 final size:13
Alignment explanation
Indices: 337940--337969 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
337930 ATTTATGACA
*
337940 CATTTATGACGCT
1 CATTTATGACGCG
337953 CATTTATGACGCG
1 CATTTATGACGCG
337966 CATT
1 CATT
337970 GAACGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (13 bp):
CATTTATGACGCG
Found at i:342022 original size:21 final size:20
Alignment explanation
Indices: 341936--342093 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
341926 AAATGACCAA
**
341936 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
341955 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
341975 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
341995 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
342016 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
342037 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
342057 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
342078 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
342094 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:342084 original size:20 final size:20
Alignment explanation
Indices: 342060--342289 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
342050 CGATTTTCCA
** *
342060 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
342080 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
342100 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
342120 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
342140 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
342160 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
342180 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
342200 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
342220 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
342240 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
342260 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
342280 AAATCACAAC
1 AAATCGCAAC
342290 ACTGAAATTT
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:343010 original size:24 final size:24
Alignment explanation
Indices: 342971--343017 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
342961 AAATTTGGTC
342971 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
342995 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
343018 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:343209 original size:12 final size:12
Alignment explanation
Indices: 343192--343216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
343182 ATATAATCCT
343192 GAAGAAGAAAAA
1 GAAGAAGAAAAA
343204 GAAGAAGAAAAA
1 GAAGAAGAAAAA
343216 G
1 G
343217 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:345587 original size:19 final size:19
Alignment explanation
Indices: 345547--345644 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
345537 GATTCTCTCG
345547 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
345567 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
345586 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
345600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
345619 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
345638 TTGCGAT
1 TTGCGAT
345645 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:345641 original size:52 final size:53
Alignment explanation
Indices: 345528--345644 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
345518 GAAATGAAAA
345528 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
345581 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
345633 TCGCATTGCGAT
1 TCGCATTGCGAT
345645 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:345740 original size:14 final size:14
Alignment explanation
Indices: 345721--345775 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
345711 CGGAAATGAA
345721 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
345735 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
345754 AATCGCAACGAGAG
1 AATCGCAACGAGAG
345768 AATCGCAA
1 AATCGCAA
345776 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:345755 original size:33 final size:33
Alignment explanation
Indices: 345703--345794 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
345693 CCATTACATT
345703 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
*
345737 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
345770 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
345795 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.86
34 8 0.14
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:345759 original size:19 final size:19
Alignment explanation
Indices: 345703--345851 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
345693 CCATTACATT
345703 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
345723 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
345737 TCGCAACGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
345756 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
345770 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
345789 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
345808 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
*
345822 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
345841 TCGCATTGCGA
1 TCGCAATGCGA
345852 TTCTCCCATT
Statistics
Matches: 106, Mismatches: 8, Indels: 31
0.73 0.06 0.21
Matches are distributed among these distances:
14 30 0.28
15 3 0.03
16 6 0.06
17 5 0.05
18 4 0.04
19 52 0.49
20 6 0.06
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:345851 original size:52 final size:52
Alignment explanation
Indices: 345735--345851 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
345725 GCAACGAGAG
*
345735 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
345787 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
345839 AATCGCATTGCGA
1 AATCGCAATGCGA
345852 TTCTCCCATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:345897 original size:19 final size:19
Alignment explanation
Indices: 345858--345976 Score: 176
Period size: 19 Copynumber: 6.5 Consensus size: 19
345848 GCGATTCTCC
345858 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
*
345878 CATTGCGATTTTCATTCCG
1 CATTGCGATTTTCATTTCG
345897 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
345916 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
345932 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
345949 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
345968 CATTGCGAT
1 CATTGCGAT
345977 AGTCAATTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 7 0.08
19 54 0.60
20 16 0.18
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:345941 original size:33 final size:33
Alignment explanation
Indices: 345841--345958 Score: 155
Period size: 33 Copynumber: 3.4 Consensus size: 33
345831 GAAATTAAAA
* *
345841 TCGCATTGCGATTCTCCCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
345874 TCCGCATTGCGATTTTCATTCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTCTC--T-CG--TTGCGATTTTCATT
345913 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
345946 TCGCATTGCGATT
1 TCGCATTGCGATT
345959 TTCATTTCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
33 28 0.37
34 14 0.19
35 2 0.03
36 1 0.01
37 1 0.01
38 14 0.19
39 15 0.20
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:345945 original size:72 final size:71
Alignment explanation
Indices: 345841--345976 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 71
345831 GAAATTAAAA
345841 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTCCGCATTGCGAT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTCCGCATTGCGAT
345906 TTTCATT
65 TTTCATT
* * *
345913 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCGCATTGCGATTTTCATTCCGCATTGCGAT
345977 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
71 29 0.48
72 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (71 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCGCATTGCGATTTTCATTCCGCATTGCGATT
TTCATT
Found at i:346116 original size:14 final size:14
Alignment explanation
Indices: 346083--346118 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
346073 CATCAATTAC
346083 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
346097 AC-AATCATCTTTT
1 ACAAATCAACTTTT
346110 ACAAATCAA
1 ACAAATCAA
346119 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:348049 original size:19 final size:18
Alignment explanation
Indices: 348009--348143 Score: 97
Period size: 19 Copynumber: 7.6 Consensus size: 18
347999 TAGTTTACTT
*
348009 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
348029 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
348048 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
348067 TCGCAA--CG-AA-AGAA
1 TCGCAACGCGAAACAAAA
*
348081 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
348100 TCGCAA--CG-AA-AGAA
1 TCGCAACGCGAAACAAAA
*
348114 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
348133 TCGCAATGCGA
1 TCGCAACGCGA
348144 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
14 18 0.19
16 8 0.08
17 8 0.08
19 49 0.51
20 12 0.12
21 1 0.01
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:348083 original size:33 final size:33
Alignment explanation
Indices: 348046--348138 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
348036 GCGAAACCAA
348046 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* **
348079 AATCGCAATGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
348112 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
348139 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:348084 original size:14 final size:14
Alignment explanation
Indices: 348065--348121 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
348055 GCGAAATGAA
348065 AATCGCAACGAAAG
1 AATCGCAACGAAAG
*
348079 AATCGCAATGCGAAACCAA
1 AATCGCAA--CG-AA--AG
348098 AATCGCAACGAAAG
1 AATCGCAACGAAAG
348112 AATCGCAACG
1 AATCGCAACG
348122 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 19 0.53
16 4 0.11
17 4 0.11
19 9 0.25
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:348135 original size:52 final size:54
Alignment explanation
Indices: 348009--348143 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 54
347999 TAGTTTACTT
* *
348009 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG-AAA
348067 TCGCAA-CGAAA-G--AATCGCAATGCGAAACCAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
348114 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAATGCGA
348144 TTTTGGTTTC
Statistics
Matches: 70, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
47 8 0.11
49 6 0.09
50 6 0.09
52 39 0.56
56 5 0.07
58 6 0.09
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:348161 original size:19 final size:19
Alignment explanation
Indices: 348139--348267 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
348129 AAAATCGCAA
348139 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
348158 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
348172 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
348191 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
348205 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
348224 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
348243 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
348263 TGCGA
1 TGCGA
348268 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:348181 original size:33 final size:33
Alignment explanation
Indices: 348139--348230 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
348129 AAAATCGCAA
348139 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
348172 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
348205 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
348231 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Done.