Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008773.1 Hibiscus syriacus cultivar Beakdansim tig00111881_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: 1239499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:577897 original size:104 final size:104
Alignment explanation
Indices: 577588--577897 Score: 369
Period size: 103 Copynumber: 3.0 Consensus size: 104
577578 CGTTTAAGGC
* * *
577588 AATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACCAATTTTGAAT
1 AATTTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAAT
* *
577653 TTGTTTCACTT-AAA-AAACA-AAATCTCACTTGAAATTGT
66 TTGTTT-ACTTGAAACAAA-ATTAATCTCACTTGAGATTGT
** *
577691 AATTTCCTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAGTTTCGAAT
1 AATTTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAAT
* * *
577756 TTGCTTCACATGAAACACAATTAATCTCACTTGAGATTGT
66 TTG-TTTACTTGAAACAAAATTAATCTCACTTGAGATTGT
** * * * *
577796 TGTTTATTTCAAAACAAATTTCGTCTCACTTGAGACATTTTCCCTCAT-A-ATACAAATTTCAAA
1 AATTTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCT-TTGAGATACAAATTTCGAA
* *
577859 ATTGTTGTACTTGAAACAAAATTAATATCACTTGAGATT
65 TTTGTT-TACTTGAAACAAAATTAATCTCACTTGAGATT
577898 TTCAAAGATG
Statistics
Matches: 178, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
103 69 0.39
104 49 0.28
105 59 0.33
106 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (104 bp):
AATTTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAAT
TTGTTTACTTGAAACAAAATTAATCTCACTTGAGATTGT
Found at i:578156 original size:30 final size:29
Alignment explanation
Indices: 578064--578167 Score: 124
Period size: 29 Copynumber: 3.6 Consensus size: 29
578054 TCTTAAGACA
*
578064 GTTTCTTTTGAAAC--AAATCTATTGAGAAT
1 GTTTCTTTTGAAACAAAAATCT-TTGAG-TT
* * *
578093 GTTCCTTTTG-AATAAAAATATTTGAGTT
1 GTTTCTTTTGAAACAAAAATCTTTGAGTT
578121 GTTTCTTTTGAAACAAAAATCTTTGAGTCT
1 GTTTCTTTTGAAACAAAAATCTTTGAGT-T
578151 GTTTCTTTTGAAACAAA
1 GTTTCTTTTGAAACAAA
578168 GTTTTATCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.19
29 29 0.45
30 23 0.36
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (29 bp):
GTTTCTTTTGAAACAAAAATCTTTGAGTT
Found at i:578205 original size:62 final size:61
Alignment explanation
Indices: 578135--578289 Score: 240
Period size: 62 Copynumber: 2.5 Consensus size: 61
578125 CTTTTGAAAC
* *
578135 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTATCTCTTTTGAGGCAATTTCGTG
1 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTATCTCTCTTGAGACAATTTCGTG
* * *
578196 AAAAAATCTTTGAGTCTATTTCTTTTGAAGCAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
1 -AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTATCTCTCTTGAGACAATTTCGTG
*
578258 AAAAATCTTTGAGT-TGTTTCTTTTGGAACAAA
1 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAA
578290 AAAAAAATAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
60 15 0.18
61 14 0.16
62 56 0.66
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (61 bp):
AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTATCTCTCTTGAGACAATTTCGTG
Found at i:578312 original size:106 final size:110
Alignment explanation
Indices: 578196--578391 Score: 294
Period size: 106 Copynumber: 1.8 Consensus size: 110
578186 CAATTTCGTG
* * *
578196 AAAAAATCTTTGAGTCTATTTCTTTTGAAGCAAAGTTTTGTCTCTCTTGAGACA-ATT-TCGTG-
1 AAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGATTCTCGTGA
578258 AA-AAATCTTTGAGT-TGTTTCTTTTGGAACAAAAAAAAAATAAAA
66 AATAAATCTTTGAGTATG-TTCTTTTGGAACAAAAAAAAAATAAAA
* * *
578302 AAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 AAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGATTCTCGTGA
578367 AATAAATCTTTGAGTATGTTCTTTT
66 AATAAATCTTTGAGTATGTTCTTTT
578392 CAAAAATATT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
106 50 0.63
107 2 0.03
108 4 0.05
109 2 0.03
110 19 0.24
111 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (110 bp):
AAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGATTCTCGTGA
AATAAATCTTTGAGTATGTTCTTTTGGAACAAAAAAAAAATAAAA
Found at i:578620 original size:30 final size:29
Alignment explanation
Indices: 578586--578649 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
578576 ATTTTGTCTC
* * *
578586 TTGAGACAATTTCTTTTTAGAAAAAAATCT
1 TTGAGACAACTCCTTTTGA-AAAAAAATCT
* *
578616 TTGAGTCTACTCCTTTTGAAAAAAAATCT
1 TTGAGACAACTCCTTTTGAAAAAAAATCT
578645 TTGAG
1 TTGAG
578650 TTTGTTTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (29 bp):
TTGAGACAACTCCTTTTGAAAAAAAATCT
Found at i:578807 original size:243 final size:239
Alignment explanation
Indices: 578307--578850 Score: 794
Period size: 243 Copynumber: 2.3 Consensus size: 239
578297 TAAAAAAAAA
* * *
578307 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTC-TCTTGAAATA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTG--TCTCTTGAGACAATTTCTTTTTGAAAAA
* * * *
578371 AATCTTTGAGTATGTTCTTTTCAAAAATATTTGAGTTTATTTCTCTTAACAAAATCATCTTTGAA
64 AATCTTTGAGTATCTCCTTTTAAAAAATATTTGAGTTTATTTCTATTAACAAAATCATCTTTGAA
578436 TATATTTCTTTAAAAACAAATTTTGTCTCTCTTGAGACATTTCCTAAAGAAAAACCAACCTTTGA
129 TATATTTCTTTAAAAACAAATTTTGTCTCTCTTGAGACATTTCCTAAAGAAAAACCAACCTTTGA
578501 GATTGTTTCCTTTGAAACAAATTTCATCTCACTTAAGACGTAACCC
194 GATTGTTTCCTTTGAAACAAATTTCATCTCACTTAAGACGTAACCC
578547 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACAATTTCTTTTTAGAAAAAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACAATTTCTTTTT-GAAAAAA
* * *
578612 ATCTTTGAGTCTACTCCTTTTGAAAAAAAATCTTTGAGTTTGTTTCTATTAACAAAATCATCTTT
65 ATCTTTGAGTAT-CTCCTTTT---AAAAAATATTTGAGTTTATTTCTATTAACAAAATCATCTTT
* * * *
578677 GAGTCTATTTCTTTAAAAACAAATTTTGTCTCTCTTGAGATAGTTT-CTAATA-AAAAA-TAACC
126 GAATATATTTCTTTAAAAACAAATTTTGTCTCTCTTGAGACA-TTTCCTAA-AGAAAAACCAACC
* *
578739 TTTGAGATTGTTTCCTTTGAAACAAATTTCGTCTCACTTAAGACGTAATCC
189 TTTGAGATTGTTTCCTTTGAAACAAATTTCATCTCACTTAAGACGTAACCC
**
578790 ATCTTTGAG-CATGTTTCTTTGGAAACAAAATTTTGTCTCTCAAGACAATTTC-TTTTGAAAA
1 ATCTTTGAGTC-TGTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACAATTTCTTTTTGAAAA
578851 TACCCACCTT
Statistics
Matches: 277, Mismatches: 18, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
238 16 0.06
239 3 0.01
240 52 0.19
241 11 0.04
242 5 0.02
243 101 0.36
244 85 0.31
245 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (239 bp):
ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACAATTTCTTTTTGAAAAAAA
TCTTTGAGTATCTCCTTTTAAAAAATATTTGAGTTTATTTCTATTAACAAAATCATCTTTGAATA
TATTTCTTTAAAAACAAATTTTGTCTCTCTTGAGACATTTCCTAAAGAAAAACCAACCTTTGAGA
TTGTTTCCTTTGAAACAAATTTCATCTCACTTAAGACGTAACCC
Found at i:578865 original size:119 final size:117
Alignment explanation
Indices: 578307--578850 Score: 351
Period size: 119 Copynumber: 4.5 Consensus size: 117
578297 TAAAAAAAAA
* * *
578307 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTC--GAGACAATTTCTTTTGAAAAAA
* * * * * * **
578372 ATCTTTGAG-TATG-TTCTTTTCAAA-AATATTTGAGT-TTATTTCTCTTA-ACAAAAT-C
64 ACCTTTGAGAT-TGTTTCCTTTGAAACAA-ATTT-CGTCTCA---CT-TAAGACGTAATCC
* * * ** ***
578427 ATCTTTGAATATATTTCTTTAAAAAC-AAATTTTGTCTCTCTTGAGAC-ATTTCCTAAAGAAAAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTC--GAGACAATTT-CTTTTGAAAAA
* *
578490 CCAACCTTTGAGATTGTTTCCTTTGAAACAAATTTCATCTCACTTAAGACGTAACCC
63 --AACCTTTGAGATTGTTTCCTTTGAAACAAATTTCGTCTCACTTAAGACGTAATCC
*
578547 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACAATTTCTTTTTAGAAAAAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAATTTC-TTTT-GAAAAAA
* ** * * * ** * **
578612 ATCTTTGAG-TCT-ACTCCTTTTGAAAAAAAATCTTTGAGTTTGTTTCTATTA-ACAAAAT-C
64 ACCTTTGAGAT-TGTTTCC-TTTG-AAACAAA--TTT-CG--TCTCACT-TAAGACGTAATCC
* ** * * ** *
578671 ATCTTTGAGTCTATTTCTTTAAAAAC-AAATTTTGTCTCTCTTGAGATAGTTTCTAATAAAAAAT
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTC--GAGACAATTTCTTTTGAAAAA-
578735 AACCTTTGAGATTGTTTCCTTTGAAACAAATTTCGTCTCACTTAAGACGTAATCC
63 AACCTTTGAGATTGTTTCCTTTGAAACAAATTTCGTCTCACTTAAGACGTAATCC
*
578790 ATCTTTGAG-CATGTTTCTTTGGAAACAAAATTTTGTCTCTCAAGACAATTTCTTTTGAAAA
1 ATCTTTGAGTC-TGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAATTTCTTTTGAAAA
578851 TACCCACCTT
Statistics
Matches: 322, Mismatches: 71, Indels: 64
0.70 0.16 0.14
Matches are distributed among these distances:
117 2 0.01
118 33 0.10
119 76 0.24
120 69 0.21
121 34 0.11
122 19 0.06
123 26 0.08
124 40 0.12
125 21 0.07
126 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (117 bp):
ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAATTTCTTTTGAAAAAAAC
CTTTGAGATTGTTTCCTTTGAAACAAATTTCGTCTCACTTAAGACGTAATCC
Found at i:578938 original size:31 final size:31
Alignment explanation
Indices: 578903--578962 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
578893 CCTTGAGGCA
578903 GTTTCTCTAGAAATACAA-AATCTTTGAGTTT
1 GTTTCTCTAGAAATA-AACAATCTTTGAGTTT
* *
578934 GTTTCTCTTGAAATAAACCATCTTTGAGT
1 GTTTCTCTAGAAATAAACAATCTTTGAGT
578963 CGTTTCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (31 bp):
GTTTCTCTAGAAATAAACAATCTTTGAGTTT
Found at i:579065 original size:69 final size:65
Alignment explanation
Indices: 578987--579115 Score: 159
Period size: 65 Copynumber: 1.9 Consensus size: 65
578977 CGAATTTTGA
**
578987 CTCTTGAGACTTTTTCTCTTAAAACAAGATCATCATTGAGTCTGTTTCTGTGGAAACAAAATTTT
1 CTCTTGAGACAGTTTCT-TT-AAACAA-A-CATCATTGAGTCTGTTTCTGTGGAAACAAAATTTT
579052 GTCT
62 GTCT
** * * *
579056 CTCTTGAGACAGTTTCTTTTGAGAAACATCTTTGAGTCTGTTTCTTTGGAAACAAAATTT
1 CTCTTGAGACAGTTTCTTTAAACAAACATCATTGAGTCTGTTTCTGTGGAAACAAAATTT
579116 ACCATCTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 32 0.60
66 1 0.02
67 3 0.06
68 2 0.04
69 15 0.28
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (65 bp):
CTCTTGAGACAGTTTCTTTAAACAAACATCATTGAGTCTGTTTCTGTGGAAACAAAATTTTGTCT
Found at i:579302 original size:202 final size:196
Alignment explanation
Indices: 578922--579313 Score: 472
Period size: 202 Copynumber: 2.0 Consensus size: 196
578912 GAAATACAAA
* * * * *
578922 ATCTTTGAGTTTGTTTCTCTTGAAATAAACCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTGA
1 ATCTTTAAGTTTGTTTCCCTTGAAACAAACCATCTTTGAGTCGTTTCCCTTAAAACAAATTTTGA
* **
578987 CTCTTGAGACTTTTTCTCTTAAAACAAGATCATCATTGAGTCTGTTTCTGTGGAAACAAAATTTT
66 CTCTTGAGACGTTTTCTCTTAAAAC-AGATCATCATTGAGTCTGTTTCCCTGGAAACAAAATTTT
* *
579052 GTCTCTCTTGAGACAGTTTCTTTTGAGAAACATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTA
130 GTCTCTCTTGAGACAGTTGCTTTTGAAAAACATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTA
579117 CC
195 CC
*
579119 ATCTTTAAGTTTGTTTCCCTTGAAACACAACAAACATCTTTGAGATTGTTTCCCTTAAAAACAAA
1 ATCTTTAAGTTTGTTTCCCTTGAAACA-AAC---CATCTTTGAG-TCGTTTCCCTT-AAAACAAA
* *
579184 TTTTGTCTCGCTTGAGACAGTTTTCT-TT-AAAC-G-TCATCTTTGAGTC-GTTTCCCTGGAAAC
60 TTTTGACT--CTTGAGAC-GTTTTCTCTTAAAACAGATCATCATTGAGTCTGTTTCCCTGGAAAC
* * * *
579244 -GAGTTTTGTCTCTTTTGAGACAGTTGCTTTTGAAACACATCATCTTTGAGTCTGTTTCTTTTGA
122 AAAATTTTGTCTCTCTTGAGACAGTTGCTTTTGAAA-A-A-CATCTTTGAGTCTGTTTCTTTGGA
579308 AACAAA
184 AACAAA
579314 TCTTTGAGTC
Statistics
Matches: 166, Mismatches: 17, Indels: 19
0.82 0.08 0.09
Matches are distributed among these distances:
197 24 0.14
198 3 0.02
199 30 0.18
200 13 0.08
201 23 0.14
202 40 0.24
203 13 0.08
204 4 0.02
205 10 0.06
206 6 0.04
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (196 bp):
ATCTTTAAGTTTGTTTCCCTTGAAACAAACCATCTTTGAGTCGTTTCCCTTAAAACAAATTTTGA
CTCTTGAGACGTTTTCTCTTAAAACAGATCATCATTGAGTCTGTTTCCCTGGAAACAAAATTTTG
TCTCTCTTGAGACAGTTGCTTTTGAAAAACATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTAC
C
Found at i:579328 original size:28 final size:30
Alignment explanation
Indices: 579270--579338 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 30
579260 GAGACAGTTG
*
579270 CTTTTGAAACACATCATCTTTGAGTCTGTTT
1 CTTTTGAAACACA-CATCTTTGAGTCGGTTT
579301 CTTTTGAAACA-A-ATCTTTGAGTCGGTTT
1 CTTTTGAAACACACATCTTTGAGTCGGTTT
*
579329 CTCTTGAAAC
1 CTTTTGAAAC
579339 CATAATCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 24 0.67
30 1 0.03
31 11 0.31
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (30 bp):
CTTTTGAAACACACATCTTTGAGTCGGTTT
Found at i:579559 original size:40 final size:40
Alignment explanation
Indices: 579495--579689 Score: 119
Period size: 40 Copynumber: 4.6 Consensus size: 40
579485 TGGCCTGTCG
* *
579495 TCCTCATCACGT-AGAAACCATGTCATCACCTGACCAGAAC
1 TCCTCATCACGTAAG-AGCCGTGTCATCACCTGACCAGAAC
* *
579535 TCTTCATCACGTAAGAGCCGTGTCA--ACCTGATAACCAG-TC
1 TCCTCATCACGTAAGAGCCGTGTCATCACCTG---ACCAGAAC
* * *
579575 GTCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCCAAGAAC
1 -TCCTCATCACGTAAGAGCCGTGTCATCA--CCT---GA---CC-AGAAC
* * * * *
579625 TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATC
1 TCCTCATCACGTAAGAGCCGTGTCATCACCTGACCAGAAC
*
579665 TCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAAGAGCCGTGTCA
579690 CCCTTAGACG
Statistics
Matches: 119, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
38 5 0.04
40 46 0.39
41 30 0.25
43 1 0.01
44 2 0.02
45 4 0.03
47 3 0.03
48 3 0.03
49 24 0.20
50 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAAGAGCCGTGTCATCACCTGACCAGAAC
Found at i:579731 original size:43 final size:40
Alignment explanation
Indices: 579624--579737 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 40
579614 TGGCCAAGAA
*
579624 CTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGAT
1 CTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGAC
* * * *
579664 CTCCTCATCACGTAGGAGCCGTGTCA-CCCTTAGACGACCAGAC
1 CTCTTCATCACGTATGAGCAGTGTCATCCCCT----GACCAGAC
** *
579707 CTCTTCATTGCGTATGAGCAGTGTCGTCCCC
1 CTCTTCATCACGTATGAGCAGTGTCATCCCC
579738 ACCAACAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
39 4 0.07
40 23 0.40
43 27 0.47
44 3 0.05
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (40 bp):
CTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGAC
Found at i:579895 original size:3 final size:3
Alignment explanation
Indices: 579887--579935 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
579877 TCTTTTTTAA
** *
579887 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
579934 TA
1 TA
579936 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:586683 original size:19 final size:19
Alignment explanation
Indices: 586659--586720 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
586649 TGCATTGGAC
586659 TATGAACTTGAAAATAAGT
1 TATGAACTTGAAAATAAGT
586678 TATGAA-TCTG-AAATAAGT
1 TATGAACT-TGAAAATAAGT
*
586696 TATGAGAC-TGAAAACAAGT
1 TATGA-ACTTGAAAATAAGT
586715 TATGAA
1 TATGAA
586721 TCTGAGTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 17 0.45
19 21 0.55
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (19 bp):
TATGAACTTGAAAATAAGT
Found at i:586693 original size:18 final size:18
Alignment explanation
Indices: 586670--586725 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
586660 ATGAACTTGA
586670 AAATAAGTTATGAATCTG
1 AAATAAGTTATGAATCTG
586688 AAATAAGTTATGAGA-CTG
1 AAATAAGTTATGA-ATCTG
*
586706 AAAACAAGTTATGAATCTG
1 -AAATAAGTTATGAATCTG
586725 A
1 A
586726 GTATGAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 18 0.53
19 16 0.47
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (18 bp):
AAATAAGTTATGAATCTG
Found at i:586725 original size:19 final size:19
Alignment explanation
Indices: 586667--586725 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
586657 ACTATGAACT
586667 TGAAAATAAGTTATGAATC
1 TGAAAATAAGTTATGAATC
586686 TG-AAATAAGTTATGAGA-C
1 TGAAAATAAGTTATGA-ATC
*
586704 TGAAAACAAGTTATGAATC
1 TGAAAATAAGTTATGAATC
586723 TGA
1 TGA
586726 GTATGAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 17 0.47
19 19 0.53
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.29
Consensus pattern (19 bp):
TGAAAATAAGTTATGAATC
Found at i:586776 original size:19 final size:19
Alignment explanation
Indices: 586736--586787 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
586726 GTATGAGTTT
* *
586736 TGAAATGTGAAAATGGATA
1 TGAAATGTGAAAATGAAAA
586755 TGAAA-GTGAAAGATGAAAA
1 TGAAATGTGAAA-ATGAAAA
* *
586774 TGAGATATGAAAAT
1 TGAAATGTGAAAAT
586788 TCTATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 6 0.22
19 16 0.59
20 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (19 bp):
TGAAATGTGAAAATGAAAA
Found at i:586783 original size:13 final size:13
Alignment explanation
Indices: 586743--586787 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
586733 TTTTGAAATG
586743 TGAAAATG-GATA
1 TGAAAATGAGATA
* * *
586755 TGAAAGTGAAAGA
1 TGAAAATGAGATA
586768 TGAAAATGAGATA
1 TGAAAATGAGATA
586781 TGAAAAT
1 TGAAAAT
586788 TCTATATTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (13 bp):
TGAAAATGAGATA
Found at i:590504 original size:22 final size:20
Alignment explanation
Indices: 590468--590511 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 20
590458 AATCGTGCAT
590468 TCATCATCATTCCATCTCAA
1 TCATCATCATTCCATCTCAA
590488 TCATCATCAAATTCCATCTCAA
1 TCATCATC--ATTCCATCTCAA
590510 TC
1 TC
590512 CTAATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (20 bp):
TCATCATCATTCCATCTCAA
Found at i:592256 original size:20 final size:20
Alignment explanation
Indices: 592228--592269 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
592218 GATCTTTAAA
*
592228 TATAGTAGTACCAATACTGC
1 TATAATAGTACCAATACTGC
* *
592248 TATAATAGTATCGATACTGC
1 TATAATAGTACCAATACTGC
592268 TA
1 TA
592270 GTTGTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
TATAATAGTACCAATACTGC
Found at i:592700 original size:53 final size:53
Alignment explanation
Indices: 592631--592740 Score: 166
Period size: 53 Copynumber: 2.1 Consensus size: 53
592621 TAATGAAGTA
* * *
592631 GTACCACTACTGATGAGTCAGTACCGATACTGTCAAAACATAATGCTAAAATG
1 GTACCAATACTGATGAGGCAGTACCGATACTGTCAAAACAGAATGCTAAAATG
* * *
592684 GTACCAATACTTATGAGGCAGTACCGATATTGTCAAAACAGAATGTTAAAATG
1 GTACCAATACTGATGAGGCAGTACCGATACTGTCAAAACAGAATGCTAAAATG
592737 GTAC
1 GTAC
592741 ATATATCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (53 bp):
GTACCAATACTGATGAGGCAGTACCGATACTGTCAAAACAGAATGCTAAAATG
Found at i:593321 original size:69 final size:68
Alignment explanation
Indices: 593219--593355 Score: 265
Period size: 69 Copynumber: 2.0 Consensus size: 68
593209 ATGAATGGAC
593219 TTGTGTCAAGTTCAAATTGACTCGAATTCTTAATGATTTGAAGTGATCTATTTAAAACATGACTC
1 TTGTGTCAAGTTCAAATTGACTCGAATTCTTAATGATTTGAAGTGATCTATTTAAAACATGACTC
593284 AAA
66 AAA
593287 TTGTGTCAAGTTCAAATTTGACTCGAATTCTTAATGATTTGAAGTGATCTATTTAAAACATGACT
1 TTGTGTCAAGTTCAAA-TTGACTCGAATTCTTAATGATTTGAAGTGATCTATTTAAAACATGACT
593352 CAAA
65 CAAA
593356 AAGCTTACGA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 16 0.24
69 52 0.76
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (68 bp):
TTGTGTCAAGTTCAAATTGACTCGAATTCTTAATGATTTGAAGTGATCTATTTAAAACATGACTC
AAA
Found at i:594623 original size:21 final size:21
Alignment explanation
Indices: 594607--594744 Score: 258
Period size: 21 Copynumber: 6.6 Consensus size: 21
594597 GCATTGCATT
*
594607 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
594628 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
594649 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
594670 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
594691 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
594712 TCGCGTTGTGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
594733 TCGCGTTGCGAT
1 TCGCGTTGCGAT
594745 TTTCCAGTTC
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 114 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:594786 original size:22 final size:22
Alignment explanation
Indices: 594761--594819 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 22
594751 GTTCGCGTTG
594761 CGATAGTCTACAGTTGTCATTA
1 CGATAGTCTACAGTTGTCATTA
** * * *
594783 CGATTTTCTA-A-AT-TCGTTG
1 CGATAGTCTACAGTTGTCATTA
594802 CGATAGTCTACAGTTGTC
1 CGATAGTCTACAGTTGTC
594820 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 6
0.65 0.20 0.15
Matches are distributed among these distances:
19 12 0.46
20 2 0.08
21 2 0.08
22 10 0.38
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (22 bp):
CGATAGTCTACAGTTGTCATTA
Found at i:594801 original size:41 final size:41
Alignment explanation
Indices: 594756--594845 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
594746 TTCCAGTTCG
*
594756 CGTTGCGATAGTCTACAGTTGTCATTACGATTTTCTAAATT
1 CGTTGCGATAGTCTACAGTTGTCATTACGATTTTCCAAATT
* *
594797 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCATTACGATTTTCCAAATT
594838 CGTTGCGA
1 CGTTGCGA
594846 AAATCGCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCATTACGATTTTCCAAATT
Found at i:594811 original size:19 final size:19
Alignment explanation
Indices: 594789--594845 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
594779 ATTACGATTT
594789 TCTAAATTCGTTGCGATAG
1 TCTAAATTCGTTGCGATAG
* **
594808 TCTACAGTTGTCGTTGCGATTT
1 TCTA-A-AT-TCGTTGCGATAG
*
594830 TCCAAATTCGTTGCGA
1 TCTAAATTCGTTGCGA
594846 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 13 0.43
20 2 0.07
21 2 0.07
22 13 0.43
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (19 bp):
TCTAAATTCGTTGCGATAG
Found at i:594824 original size:22 final size:22
Alignment explanation
Indices: 594756--594827 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
594746 TTCCAGTTCG
594756 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * ** *
594778 CATTACGATTTTCTA-A-AT-T
1 CGTTGCGATAGTCTACAGTTGT
594797 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
594819 CGTTGCGAT
1 CGTTGCGAT
594828 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:595696 original size:22 final size:22
Alignment explanation
Indices: 595664--595759 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
595654 CTTTTTTTTA
595664 ACTATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* *
595686 ACTTTCGCAACAACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
**
595708 ACTATCGCAACGA-ATTTG-A-
1 ACTATCGCAACGACAACTGTAG
** *
595727 AAAATCGCAACGAC-ATTGTAG
1 ACTATCGCAACGACAACTGTAG
595748 ACTATCGCAACG
1 ACTATCGCAACG
595760 CGAAATGGAA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 14 0.23
20 2 0.03
21 13 0.22
22 31 0.52
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:595772 original size:41 final size:41
Alignment explanation
Indices: 595727--595887 Score: 263
Period size: 41 Copynumber: 3.9 Consensus size: 41
595717 ACGAATTTGA
*
595727 AAAATCGCAACGAC-ATTGT-AGACTATCGCAACGCGAAATGG
1 AAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATGG
*
595768 AAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
595809 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
*
595850 AAAATCGCAAAGCGATTTTCAACTATCGCAACGCGAAA
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
595888 GCAACGCGAA
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
40 1 0.01
41 112 0.98
42 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
Found at i:595776 original size:20 final size:20
Alignment explanation
Indices: 595751--595864 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
595741 ATTGTAGACT
595751 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
595771 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
595792 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
595812 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
595833 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
595853 ATCGCAAAGCGA
1 ATCGCAACGCGA
595865 TTTTCAACTA
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 40 0.58
21 29 0.42
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:595797 original size:21 final size:21
Alignment explanation
Indices: 595771--595885 Score: 108
Period size: 21 Copynumber: 5.6 Consensus size: 21
595761 GAAATGGAAA
*
595771 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
595792 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
595812 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
595833 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
595853 ATCGCAAAGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
595874 ATCGCAACGCGA
1 ATCGCAACGCGA
595886 AAGCAACGCG
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 29 0.42
21 40 0.58
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:598153 original size:15 final size:15
Alignment explanation
Indices: 598133--598161 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
598123 AATAATTTTG
598133 ATAGCCGCCCATGTC
1 ATAGCCGCCCATGTC
598148 ATAGCCGCCCATGT
1 ATAGCCGCCCATGT
598162 TTGTTTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (15 bp):
ATAGCCGCCCATGTC
Found at i:602709 original size:15 final size:15
Alignment explanation
Indices: 602689--602717 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
602679 AATAATTTTG
602689 ATAGCCGCCCATGTC
1 ATAGCCGCCCATGTC
602704 ATAGCCGCCCATGT
1 ATAGCCGCCCATGT
602718 TTTGTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (15 bp):
ATAGCCGCCCATGTC
Found at i:604011 original size:14 final size:14
Alignment explanation
Indices: 603992--604025 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
603982 TCAATTAAAT
603992 TGTTTTAGGGATTG
1 TGTTTTAGGGATTG
604006 TGTTTTAGGGATTG
1 TGTTTTAGGGATTG
604020 TGTTTT
1 TGTTTT
604026 GAAATGAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (14 bp):
TGTTTTAGGGATTG
Found at i:607487 original size:37 final size:38
Alignment explanation
Indices: 607359--607543 Score: 258
Period size: 39 Copynumber: 5.0 Consensus size: 38
607349 ATAGATAATT
*
607359 TTTTTAAATA-TTAATCT-ATTATTTTAGACTTGAATA
1 TTTTTAAATATTTAACCTAATTATTTTAGACTTGAATA
607395 TATTTTAAATATTTAACCTAATTATTTTAGACTTGATATA
1 T-TTTTAAATATTTAACCTAATTATTTTAGACTTGA-ATA
*
607435 TTTTTAAATATTTAACCTAATTA-TTTAGATTTGAATA
1 TTTTTAAATATTTAACCTAATTATTTTAGACTTGAATA
*
607472 TTTTTAAATAGTTAACCTAATTATTTTAGAC-T--ATA
1 TTTTTAAATATTTAACCTAATTATTTTAGACTTGAATA
*
607507 -TTTTAAATATTTAACCTAATTATTTTAGTCCTTGAAT
1 TTTTTAAATATTTAACCTAATTATTTTAG-ACTTGAAT
607544 GTTATTACTA
Statistics
Matches: 134, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
34 27 0.20
35 4 0.03
36 2 0.01
37 35 0.26
38 24 0.18
39 38 0.28
40 4 0.03
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (38 bp):
TTTTTAAATATTTAACCTAATTATTTTAGACTTGAATA
Found at i:607487 original size:76 final size:73
Alignment explanation
Indices: 607359--607531 Score: 246
Period size: 76 Copynumber: 2.4 Consensus size: 73
607349 ATAGATAATT
* *
607359 TTTTTAAATA-TTAATCT-ATTATTTTAGACTTGAATATATTTTAAATATTTAACCTAATTATTT
1 TTTTTAAATATTTAACCTAATTA-TTTAGACTTGAATATATTTTAAATAGTTAACCTAATTATTT
607422 TAGACTTGATATA
65 TAGAC----TATA
*
607435 TTTTTAAATATTTAACCTAATTATTTAGATTTGAATAT-TTTTAAATAGTTAACCTAATTATTTT
1 TTTTTAAATATTTAACCTAATTATTTAGACTTGAATATATTTTAAATAGTTAACCTAATTATTTT
607499 AGACTATA
66 AGACTATA
607507 -TTTTAAATATTTAACCTAATTATTT
1 TTTTTAAATATTTAACCTAATTATTT
607532 TAGTCCTTGA
Statistics
Matches: 92, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
71 25 0.27
72 4 0.04
76 39 0.42
77 20 0.22
78 4 0.04
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (73 bp):
TTTTTAAATATTTAACCTAATTATTTAGACTTGAATATATTTTAAATAGTTAACCTAATTATTTT
AGACTATA
Found at i:611286 original size:27 final size:27
Alignment explanation
Indices: 611252--611305 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
611242 AAAGAGTATG
611252 CTTGCAAATCGATCGAAAAGAGGAAGT
1 CTTGCAAATCGATCGAAAAGAGGAAGT
*
611279 CTTGCAAATCGATCGCAAAGAGGAAGT
1 CTTGCAAATCGATCGAAAAGAGGAAGT
611306 TATTAACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.19
Consensus pattern (27 bp):
CTTGCAAATCGATCGAAAAGAGGAAGT
Found at i:619188 original size:43 final size:46
Alignment explanation
Indices: 619113--619216 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 46
619103 ATAACTAATG
* * *
619113 AATAAAATAATAATAAACTAAACATGTCTTAA-C-TC-TAATTCCT
1 AATAAAATAATAATAAACTAAAAATATCTTAACCACCTTAATTCCT
*
619156 AATAAAATAATAAT-AACTAAATAATATTTTAACCCAACCTTAATTCCT
1 AATAAAATAATAATAAACTAAA-AATATCTTAA-CC-ACCTTAATTCCT
619204 AATAAAATAATAA
1 AATAAAATAATAA
619217 ATCTAATCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 7 0.14
43 21 0.41
45 1 0.02
47 1 0.02
48 21 0.41
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (46 bp):
AATAAAATAATAATAAACTAAAAATATCTTAACCACCTTAATTCCT
Found at i:622231 original size:25 final size:22
Alignment explanation
Indices: 622202--622248 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
622192 ATTTTAACCC
622202 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
622227 AATCTAATCCTAAAAGATAATA
1 AATCTAATCCTAAAAAATAATA
622249 CATCATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 3 0.14
25 4 0.19
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:625853 original size:31 final size:31
Alignment explanation
Indices: 625818--625878 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
625808 GTTTCAAAAA
* **
625818 TAACAAATTGGTCACTAATGTTATCTATTTG
1 TAACAAATCGGTCACTAACATTATCTATTTG
625849 TAACAAATCGGTCACTAACATTATCTATTT
1 TAACAAATCGGTCACTAACATTATCTATTT
625879 AGAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (31 bp):
TAACAAATCGGTCACTAACATTATCTATTTG
Found at i:627273 original size:2 final size:2
Alignment explanation
Indices: 627268--627520 Score: 103
Period size: 2 Copynumber: 124.5 Consensus size: 2
627258 TATATGAACC
* * * * *
627268 AT AT AT AT GT AT AA ACT AT AT AGT TT AT AT AT AA AA AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * *
627312 -T AT AT AT AT AA ACT AT AT AT AA AA ACT AT AT AGT TT AT AT TT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT
* *
627354 AT AT -T AT -T AT AT ACT AT AT AT AA ACT AT AT AT AT -T AT GT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
627395 AA ACT AT AT AGT GT AT AT AT AA AGT AT AT AT AT -T AT AT AT AT
1 AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * *
627437 AA ACT AT GT AT AT AA ACT AT AT AGT TT AT AT TT AT -T AT AT -T
1 AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
627478 AT AT ACT AT AT AT AA AT -T AT AT AT AT -T AT GT AT AA AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
627518 AT A
1 AT A
627521 GTTTATTAAT
Statistics
Matches: 185, Mismatches: 42, Indels: 48
0.67 0.15 0.17
Matches are distributed among these distances:
1 10 0.05
2 159 0.86
3 16 0.09
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:627316 original size:9 final size:9
Alignment explanation
Indices: 627304--627511 Score: 79
Period size: 9 Copynumber: 23.8 Consensus size: 9
627294 ATATATAAAA
627304 ATATATATT
1 ATATATATT
627313 ATATATA-T
1 ATATATATT
*
627321 AAACTATA-T
1 ATA-TATATT
* * *
627330 ATAAAAACT
1 ATATATATT
*
627339 ATATA-GTT
1 ATATATATT
627347 -TATAT-TT
1 ATATATATT
627354 ATAT-TATT
1 ATATATATT
627362 ATATACTA-T
1 ATATA-TATT
* *
627371 ATATAAACT
1 ATATATATT
627380 ATATATATT
1 ATATATATT
* *
627389 ATGTATA-A
1 ATATATATT
627397 ACTATATAGTGT
1 A-TATATA-T-T
*
627409 ATATATAAAGT
1 ATATAT--ATT
627420 ATATATATT
1 ATATATATT
627429 ATATATA-T
1 ATATATATT
627437 A-A-ACTATGT
1 ATATA-TAT-T
* *
627446 ATATAAACT
1 ATATATATT
*
627455 ATATA-GTT
1 ATATATATT
627463 -TATAT-TT
1 ATATATATT
627470 AT-TATATT
1 ATATATATT
627478 ATATACTA-T
1 ATATA-TATT
*
627487 ATATAAATT
1 ATATATATT
627496 ATATATATT
1 ATATATATT
*
627505 ATGTATA
1 ATATATA
627512 AATTATATAG
Statistics
Matches: 151, Mismatches: 23, Indels: 50
0.67 0.10 0.22
Matches are distributed among these distances:
6 1 0.01
7 19 0.13
8 26 0.17
9 84 0.56
10 6 0.04
11 13 0.09
12 1 0.01
13 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (9 bp):
ATATATATT
Found at i:627318 original size:11 final size:11
Alignment explanation
Indices: 627304--627612 Score: 95
Period size: 11 Copynumber: 27.7 Consensus size: 11
627294 ATATATAAAA
627304 ATATATATTAT
1 ATATATATTAT
*
627315 ATATATA-AACT
1 ATATATATTA-T
* *
627326 ATATATA-AAA
1 ATATATATTAT
627336 ACTATATAGTTTAT
1 A-TATATA--TTAT
*
627350 ATTTATATTAT
1 ATATATATTAT
*
627361 -TATATACTAT
1 ATATATATTAT
* *
627371 ATATAAACTAT
1 ATATATATTAT
627382 ATATATTATGTAT
1 ATATA-TAT-TAT
*
627395 AAACTATA-TAGT
1 ATA-TATATTA-T
* *
627407 GTATATATAAAGT
1 ATATATAT-TA-T
627420 ATATATATTAT
1 ATATATATTAT
*
627431 ATATATA-AACT
1 ATATATATTA-T
* *
627442 ATGTATA-TAA
1 ATATATATTAT
627452 ACTATATAGTT-T
1 A-TATATA-TTAT
*
627464 ATATTTATTAT
1 ATATATATTAT
*
627475 ATTATATACTAT
1 A-TATATATTAT
*
627487 ATATA-AAT-T
1 ATATATATTAT
627496 ATATATATTAT
1 ATATATATTAT
* *
627507 GTATAAATTAT
1 ATATATATTAT
*
627518 ATAGTTTATTA-
1 ATA-TATATTAT
* *
627529 ATATAAACTAT
1 ATATATATTAT
* **
627540 ATATAAACAAT
1 ATATATATTAT
*
627551 ATAGTTTATTA-
1 ATA-TATATTAT
*
627562 ATATAAATTAT
1 ATATATATTAT
627573 ATATGA-ATTAT
1 ATAT-ATATTAT
* *
627584 ATTTA-AATAT
1 ATATATATTAT
* *
627594 ATACATCTTAT
1 ATATATATTAT
*
627605 ATTTATAT
1 ATATATAT
627613 CAACAACAAT
Statistics
Matches: 221, Mismatches: 51, Indels: 52
0.68 0.16 0.16
Matches are distributed among these distances:
9 6 0.03
10 35 0.16
11 130 0.59
12 23 0.10
13 23 0.10
14 4 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (11 bp):
ATATATATTAT
Found at i:627328 original size:13 final size:13
Alignment explanation
Indices: 627312--627459 Score: 83
Period size: 13 Copynumber: 11.5 Consensus size: 13
627302 AAATATATAT
627312 TATATATATAAAC
1 TATATATATAAAC
*
627325 TATATATAAAAAC
1 TATATATATAAAC
* *
627338 TATATAGTTTATA-
1 TATATA-TATAAAC
* *
627351 TTTATATTATTATA-
1 TATATA-TA-TAAAC
627365 TACTATATATAAAC
1 TA-TATATATAAAC
* **
627379 TATATATATTATG
1 TATATATATAAAC
* * *
627392 TATAAACTATATAG
1 TATATA-TATAAAC
* *
627406 TGTATATATAAAG
1 TATATATATAAAC
627419 TATATATAT----
1 TATATATATAAAC
627428 TATATATATAAAC
1 TATATATATAAAC
*
627441 TATGTATATAAAC
1 TATATATATAAAC
627454 TATATA
1 TATATA
627460 GTTTATATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
9 9 0.09
13 71 0.68
14 20 0.19
15 4 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:627463 original size:116 final size:115
Alignment explanation
Indices: 627252--627544 Score: 441
Period size: 116 Copynumber: 2.5 Consensus size: 115
627242 ATATAAACTA
* * *
627252 ATACTATATATGAAC--CATATA-TATGTATAAACTATATAGTTTATATATAAAAATATATATTA
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATATATAAATATATATATTA
627314 TATATATAAACTATATATAAAAACTATATAGTTTATATTTA-TATTATTAT
66 TATATATAAACTATATATAAAAACTATATAGTTTATATTTATTA-TATTAT
*
627364 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAAGTATATATATT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATATATAAA-TATATATATT
* *
627429 ATATATATAAACTATGTATATAAACTATATAGTTTATATTTATTATATTAT
65 ATATATATAAACTATATATAAAAACTATATAGTTTATATTTATTATATTAT
* *
627480 ATACTATATATAAATTATATATATTATGTATAAATTATATAGTTTATTAATATAAACTATATATA
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTA-T-ATATAAA-TATATATA
627545 AACAATATAG
Statistics
Matches: 164, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
112 14 0.09
114 5 0.03
115 29 0.18
116 98 0.60
117 3 0.02
118 15 0.09
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (115 bp):
ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATATATAAATATATATATTA
TATATATAAACTATATATAAAAACTATATAGTTTATATTTATTATATTAT
Found at i:627606 original size:116 final size:116
Alignment explanation
Indices: 627252--627606 Score: 363
Period size: 116 Copynumber: 3.1 Consensus size: 116
627242 ATATAAACTA
* * * * *
627252 ATACTATATATGAAC--CATATA-TATGTATAAACTATATAGTTTATATATAAA-AATATATATT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAACTATATATATA
* * * * *
627313 ATATATATAAACTATATATAAAAACTATATAGTTTATATTT-ATATTATTAT
66 ACATATATAAACTATGTATATAAACTATATAGATTATATTTAATA-TATTAC
* *
627364 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAAGTATATATATT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAACTATATATATA
* * * *
627429 ATATATATAAACTATGTATATAAACTATATAGTTTATATTTATTATATTAT
66 ACATATATAAACTATGTATATAAACTATATAGATTATATTTAATATATTAC
* * *
627480 ATACTATATATAAATTATATATATTATGTATAAATTATATAGTTTATTAATATAAACTATATATA
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTA-T-ATATAAACTATATATA
*** *
627545 -AACA-ATATAGTTTAT-TAATATAAATTATATATGAATTATATTTAA-ATATATAC
64 TAACATATATAAACTATGT-ATATAAACTATATA-G-ATTATATTTAATATAT-TAC
627598 AT-CT-TATAT
1 ATACTATATAT
627607 TTATATCAAC
Statistics
Matches: 212, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
112 14 0.07
114 5 0.02
115 30 0.14
116 123 0.58
117 12 0.06
118 28 0.13
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (116 bp):
ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAACTATATATATA
ACATATATAAACTATGTATATAAACTATATAGATTATATTTAATATATTAC
Found at i:627628 original size:9 final size:9
Alignment explanation
Indices: 627614--627645 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
627604 TATTTATATC
627614 AACAACAAT
1 AACAACAAT
627623 AACAACAAT
1 AACAACAAT
627632 AACAACAAT
1 AACAACAAT
627641 AACAA
1 AACAA
627646 AACCCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.22, G:0.00, T:0.09
Consensus pattern (9 bp):
AACAACAAT
Found at i:627977 original size:28 final size:28
Alignment explanation
Indices: 627933--628666 Score: 156
Period size: 27 Copynumber: 26.2 Consensus size: 28
627923 TTATATAGTT
*
627933 TATATAGTTTAAATATAAAGTATATAAG
1 TATATAGTATAAATATAAAGTATATAAG
*
627961 TATATA-TATAAACTATAAATTATAT-A-
1 TATATAGTATAAA-TATAAAGTATATAAG
* * *
627987 TATATA-TACATATATAATAATATA-AAG
1 TATATAGTATAAATATAA-AGTATATAAG
* *
628014 TATA-ATTATAAAAACTAAAGTATATAAG
1 TATATAGTATAAATA-TAAAGTATATAAG
*
628042 TATATA--AGT--ATATAAAGT-T-TTAG
1 TATATAGTA-TAAATATAAAGTATATAAG
* * * *
628065 TACAAAGTATAAATACATA-TATAATAA-
1 TATATAGTATAAATATAAAGTAT-ATAAG
* * *
628092 TATAAAGTATAAGTAT--ATTATATATA-
1 TATATAGTATAAATATAAAGTATATA-AG
* *
628118 TATATA-TATATATATAAAG--TATAAT
1 TATATAGTATAAATATAAAGTATATAAG
* *
628143 TATAAAG-ACTAAAGTATATAAGCATATAA-
1 TATATAGTA-TAAA-TATA-AAGTATATAAG
* * *
628172 TATAAAGTCTATAAGTATATAA-TATA-AAA
1 TATATAG--TATAAATATA-AAGTATATAAG
628201 TATATAAGTATTAAATATAAAGTATATATATG
1 TATAT-AGTA-TAAATATAAAGTATATA-A-G
628233 TATATA--AT-AATATAAAGTATATATA-
1 TATATAGTATAAATATAAAGTATATA-AG
* *
628258 TACATATAACGTATAAGTATGAA-TATATATA-
1 T--ATAT-A-GTATAAATATAAAGTATATA-AG
**
628289 TATATA-TATAAA-AGTTTTAGTATA-AAG
1 TATATAGTATAAATA--TAAAGTATATAAG
* * * *
628316 TATATA-TATATATATAATAATATAAAAT
1 TATATAGTATAAATATAA-AGTATATAAG
*
628344 TCAGTATATTATATAATTATAAAG-ACTA-AAG
1 T-A-TATAGTATA-AA-TATAAAGTA-TATAAG
*
628375 TATATAAGCATATAATATAAA-TATAAATAAG
1 TATAT-AGTATA-AATATAAAGTAT--ATAAG
* *
628406 TATA-A--ATATATA-AAAATATATAAG
1 TATATAGTATAAATATAAAGTATATAAG
628430 TATAATA-TATATATATATATAA-TATATATA-
1 TAT-ATAGTATA-A-ATATA-AAGTATATA-AG
* ****
628460 TATATA-TATATATACTTTTTTATATAAG
1 TATATAGTATAAATA-TAAAGTATATAAG
*
628488 TATATA-TATATAATATATA-TAATATATA-
1 TATATAGTATA-AATATAAAGT-ATATA-AG
* *
628516 TATATA-TATATATATATA-TATATATA-
1 TATATAGTATAAATATAAAGTATATA-AG
* *
628542 TATATA-TATATATATATACGTATATAAG
1 TATATAGTATAAATATA-AAGTATATAAG
*
628570 TATATAAGTATAAGTATATAAGTATTAAATATAAG
1 TATAT-AGTATAA--ATATAA--AGT--ATATAAG
* *
628605 TATATAAATATTAAATATAAAGTACATAAG
1 TATAT-AGTA-TAAATATAAAGTATATAAG
*
628635 TATATA-TA-AACTATAAAGTATATATA-
1 TATATAGTATAAATATAAAGTATATA-AG
628661 TATATA
1 TATATA
628667 CAATATATAT
Statistics
Matches: 551, Mismatches: 65, Indels: 182
0.69 0.08 0.23
Matches are distributed among these distances:
23 7 0.01
24 11 0.02
25 40 0.07
26 94 0.17
27 100 0.18
28 98 0.18
29 59 0.11
30 53 0.10
31 35 0.06
32 23 0.04
33 6 0.01
34 6 0.01
35 16 0.03
36 3 0.01
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.39
Consensus pattern (28 bp):
TATATAGTATAAATATAAAGTATATAAG
Found at i:628009 original size:16 final size:16
Alignment explanation
Indices: 627942--628677 Score: 105
Period size: 18 Copynumber: 43.1 Consensus size: 16
627932 TTATATAGTT
627942 TAAATATA-AAGT-ATA
1 TAAATATATAA-TAATA
*
627957 TAAGTATATATATAAACTA
1 TAAATATATA-AT-AA-TA
627976 TAAAT-TATATATATATA
1 TAAATATATA-ATA-ATA
*
627993 TACATATATAATAATA
1 TAAATATATAATAATA
* *
628009 TAAAGTATAATTATAAAAA
1 TAAA-TAT-ATAAT-AATA
628028 CTAAAGTATATAAGT-ATA
1 -TAAA-TATATAA-TAATA
* * *
628046 TAAGTATATAA-AGTT
1 TAAATATATAATAATA
* * * *
628061 TTAGTACA-AAGTATAAA
1 TAAATATATAA-TA-ATA
*
628078 TACATATATAATAATA
1 TAAATATATAATAATA
*
628094 TAAAGTATAAGTATATTATA
1 TAAA-TAT-A-TA-ATAATA
*
628114 TATATATATATATATATA
1 TAAATATATA-ATA-ATA
* *
628132 TAAAGTATAATTATAAAGA
1 TAAA-TAT-ATAAT-AATA
**
628151 CTAAAGTATATAAGCATA
1 -TAAA-TATATAATAATA
*
628169 T-AATATA-AAGT-CTA
1 TAAATATATAA-TAATA
*
628183 TAAGTATATAAT-ATA
1 TAAATATATAATAATA
628198 -AAATATATAAGT-AT-
1 TAAATATATAA-TAATA
628212 TAAATATA-AAGTATATA
1 TAAATATATAA-TA-ATA
**
628229 TATGTATATAATAATA
1 TAAATATATAATAATA
628245 TAAAGTATATATATACATA
1 TAAA-TATATA-ATA-ATA
628264 TAACGTATAAGTATGAATATATA
1 TAA---AT-A-TAT-AATA-ATA
*
628287 TATATATATATAA-AAGTT
1 TA-A-ATATATAATAA-TA
* *
628305 TTAGTATA-AAGTATATA
1 TAAATATATAA-TA-ATA
*
628322 TATATATATAATAATA
1 TAAATATATAATAATA
*
628338 TAAA-ATTCAGTATATTATA
1 TAAATA-T-A-TA-ATAATA
* * *
628357 TAATTATA-AAGACTA
1 TAAATATATAATAATA
*
628372 -AAGTATATAAGCATATAATA
1 TAAATATAT-A--A--TAATA
628392 TAAATATA-AATAAGTA
1 TAAATATATAATAA-TA
*
628408 TAAATATATAAAAATA
1 TAAATATATAATAATA
*
628424 TATAA-GTATAAT-ATA
1 TA-AATATATAATAATA
*
628439 TATATATAT-ATAATA
1 TAAATATATAATAATA
*
628454 TATATATATATATATATA
1 TAAATATATA-ATA-ATA
** * *
628472 TACTTTTTTATATAAGTA
1 TAAATATATA-ATAA-TA
*
628490 TATATATATAAT-ATA
1 TAAATATATAATAATA
628505 TATAATATAT-ATATATA
1 TA-AATATATAATA-ATA
*
628522 TATATATATATATATATA
1 TAAATATATA-ATA-ATA
*
628540 TATATATATATATATATA
1 TAAATATATA-ATA-ATA
**
628558 TACGTATATAAGT-ATA
1 TAAATATATAA-TAATA
*
628574 TAAGTATAAGTATATAAGTA
1 TAAATAT-A-TA-ATAA-TA
*
628594 TTAAATATA-AGT-ATA
1 -TAAATATATAATAATA
628609 TAAATAT-T-A-AATA
1 TAAATATATAATAATA
*
628622 TAAAGTACATAAGTATATA
1 TAAA-TATATAA-TA-ATA
628641 TAAACTATA-AAGTATATA
1 TAAA-TATATAA-TA-ATA
* *
628659 TATATATACAATATATA
1 TAAATATATAATA-ATA
628676 TA
1 TA
628678 TAATTTATAT
Statistics
Matches: 545, Mismatches: 84, Indels: 182
0.67 0.10 0.22
Matches are distributed among these distances:
13 7 0.01
14 38 0.07
15 74 0.14
16 88 0.16
17 91 0.17
18 120 0.22
19 57 0.10
20 38 0.07
21 14 0.03
22 5 0.01
23 11 0.02
24 2 0.00
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (16 bp):
TAAATATATAATAATA
Found at i:628009 original size:24 final size:22
Alignment explanation
Indices: 627956--628010 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
627946 TATAAAGTAT
627956 ATAAGTATATATATAAACTATAA
1 ATAA-TATATATATAAACTATAA
* *
627979 ATTATATATATATATACATATATA
1 ATAATATATATATAAAC-TATA-A
628003 ATAATATA
1 ATAATATA
628011 AAGTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 7 0.26
24 8 0.30
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATATATATATAAACTATAA
Found at i:628044 original size:8 final size:8
Alignment explanation
Indices: 628031--628640 Score: 147
Period size: 8 Copynumber: 80.1 Consensus size: 8
628021 ATAAAAACTA
628031 AAGTATAT
1 AAGTATAT
628039 AAGTATAT
1 AAGTATAT
628047 AAGTATAT
1 AAGTATAT
628055 AAAGT-T-T
1 -AAGTATAT
* *
628062 TAGTACA-
1 AAGTATAT
628069 AAGTATAAAT
1 AAGTAT--AT
628079 ACA-TATAT
1 A-AGTATAT
628087 AA-TAATAT
1 AAGT-ATAT
628095 AA--AGTAT
1 AAGTA-TAT
628102 AAGTATAT
1 AAGTATAT
*
628110 TA-TATAT
1 AAGTATAT
628117 ATA-TATAT
1 A-AGTATAT
628125 ATA-TATAT
1 A-AGTATAT
628133 AA--AGTAT
1 AAGTA-TAT
*
628140 AATTATA-
1 AAGTATAT
628147 AAG-ACTA-
1 AAGTA-TAT
628154 AAGTATAT
1 AAGTATAT
*
628162 AAGCATAT
1 AAGTATAT
628170 AA-TATA-
1 AAGTATAT
*
628176 AAGTCTAT
1 AAGTATAT
628184 AAGTATAT
1 AAGTATAT
628192 AA-TATA-
1 AAGTATAT
*
628198 AAATATAT
1 AAGTATAT
628206 AAGTAT-T
1 AAGTATAT
*
628213 AAATATA-
1 AAGTATAT
628220 AAGTATAT
1 AAGTATAT
628228 ATATGTATAT
1 A-A-GTATAT
628238 AA-TAATAT
1 AAGT-ATAT
628246 AAAGTATAT
1 -AAGTATAT
628255 ATA-TACATAT
1 A-AGT--ATAT
628265 AACG--TAT
1 AA-GTATAT
*
628272 AAGTAT-G
1 AAGTATAT
628279 AA-TATAT
1 AAGTATAT
628286 -A-TATAT
1 AAGTATAT
*
628292 ATA-TATAA
1 A-AGTATAT
628300 AAGT-T-T
1 AAGTATAT
*
628306 TAGTATA-
1 AAGTATAT
628313 AAGTATAT
1 AAGTATAT
628321 -A-TATAT
1 AAGTATAT
628327 -A-TATAAT
1 AAGTAT-AT
*
628334 AA-TATAA
1 AAGTATAT
*
628341 AATTCAGTAT
1 AAGT-A-TAT
*
628351 -ATTATAT
1 AAGTATAT
*
628358 AATTATA-
1 AAGTATAT
628365 AAG-ACTA-
1 AAGTA-TAT
628372 AAGTATAT
1 AAGTATAT
*
628380 AAGCATAT
1 AAGTATAT
628388 AA-TATA-
1 AAGTATAT
628394 AA-TATAAAT
1 AAGTAT--AT
628403 AAGTATA-
1 AAGTATAT
628410 AA-TATAT
1 AAGTATAT
*
628417 AAAAATATAT
1 --AAGTATAT
628427 AAGTATA-
1 AAGTATAT
628434 ATA-TATAT
1 A-AGTATAT
628442 ATA-TATAT
1 A-AGTATAT
628450 AA-TATAT
1 AAGTATAT
628457 ATA-TATAT
1 A-AGTATAT
628465 ATA-TATAT
1 A-AGTATAT
**
628473 ACTTTTTTATAT
1 A----AGTATAT
628485 AAGTATAT
1 AAGTATAT
628493 -A-TATAT
1 AAGTATAT
628499 AA-TATAT
1 AAGTATAT
*
628506 ATAATATAT
1 A-AGTATAT
628515 -A-TATAT
1 AAGTATAT
628521 -A-TATAT
1 AAGTATAT
628527 ATA-TATAT
1 A-AGTATAT
628535 ATA-TATAT
1 A-AGTATAT
628543 ATA-TATAT
1 A-AGTATAT
628551 ATA-TATAT
1 A-AGTATAT
*
628559 ACGTATAT
1 AAGTATAT
628567 AAGTATAT
1 AAGTATAT
628575 AAG--TAT
1 AAGTATAT
628581 AAGTATAT
1 AAGTATAT
628589 AAGTAT-T
1 AAGTATAT
628596 AA--ATAT
1 AAGTATAT
628602 AAGTATAT
1 AAGTATAT
*
628610 AAATAT-T
1 AAGTATAT
*
628617 AAATATA-
1 AAGTATAT
*
628624 AAGTACAT
1 AAGTATAT
628632 AAGTATAT
1 AAGTATAT
628640 A
1 A
628641 TAAACTATAA
Statistics
Matches: 487, Mismatches: 35, Indels: 160
0.71 0.05 0.23
Matches are distributed among these distances:
5 2 0.00
6 67 0.14
7 134 0.28
8 219 0.45
9 30 0.06
10 27 0.06
11 2 0.00
12 6 0.01
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.39
Consensus pattern (8 bp):
AAGTATAT
Found at i:628117 original size:2 final size:2
Alignment explanation
Indices: 628105--629357 Score: 269
Period size: 2 Copynumber: 636.0 Consensus size: 2
628095 AAAGTATAAG
*
628105 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA AA GTA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * *
628145 TA AA GA CTA AA GTA TA TA -A GCA TA TA -A TA TA AA GTC TA TA -A
1 TA TA TA -TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * *
628186 GTA TA TA -A TA TA -A AA TA TA TA -A GTA T- TA AA TA TA AA GTA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * *
628225 TA TA TA TG TA TA TA -A TA -A TA TA AA GTA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
** *
628266 -A CG TA TA -A GTA TGA -A TA TA TA TA TA TA TA TA TA -A AA GT-
1 TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
628304 TT TA GTA TA AA GTA TA TA TA TA TA TA TA -A TA -A TA TA -A AA T-
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
628344 TCA GTA TA T- TA TA TA -A T- TA TA AA GA CTA AA GTA TA TA -A GCA
1 T-A -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA -TA
* * * * *
628385 TA TA -A TA TA AA TA TA AA TA -A GTA TA AA TA TA TA AA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
628426 TA -A GTA TA -A TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
628466 TA TA TA TA CT- TT TT TA TA TA -A GTA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
628507 TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
**
628548 TA TA TA TA TA TA CG TA TA TA -A GTA TA TA -A GTA TA -A GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
* * * *
628588 TA -A GTA T- TA AA TA TA -A GTA TA TA AA TA T- TA AA TA TA AA GTA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
628629 CA TA -A GTA TA TA TA AA CTA TA AA GTA TA TA TA TA TA TA CA -A
1 TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
628670 TA TA TA TA TA -A TT TA TA T- TA TA TA CT- TA TA TA CTT TA GTC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA
* * * *
628710 TT TA TA -A T- TA TGC TC TA TA TA TA -A TA TA CT- TA TA CTT TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
628749 TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TA TT TA -A TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* ** * *
628789 TA TA CTT TA TA T- TA T- TA TA TA CG TG TG TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
628830 CT- TT TA -A TT TA TC T- TA T- TA TA TA TG TA TA TA TA CTT TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* ** * * * *
628870 CTA AA GC TT TA TA TA TA TA TA TA CA CTT TA TA GTT TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * *
628913 TA CT- TA TA TA CTT TA TA TT TA TA TA CT- TA TA TT TA -A TA CT-
1 TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
628953 TA TA TA T- TT TA TA T- TA TA TA CT- TA TA TA CTT TA GTC TT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA
* * *
628993 TA -A T- TA TA -A TT TT TA TA TA TA TA -A TA TA CT- TG TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* *
629031 TA CTT TA TA T- TA T- TA TA TA TA TA CTT TA TA T- TA T- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
629071 TG TA TA TA TA CTT TA TA CTA -A AA CTT TA TA TA AA TA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* **
629113 TA TA TA TA TA TA TA CT- TA TA CTT TA TA GG T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
629155 TA TA CT- TG TA CT- TG TA CTT TA TA TG TA TA TA TA T- TT TA TA
1 TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
629195 TT TA TA T- TA TA TA CT- TA TA TA CTT TA GTC TT TA TA -A T- TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA
** * * *
629234 TA TA TA CG TA TA -A TA TA TT TA TA CT- TA TA CTT TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* *
629275 TA TA TA T- TA TA CTT TA TA CTA -A AA CTA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
*
629316 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
629358 CTTATAATGT
Statistics
Matches: 917, Mismatches: 169, Indels: 330
0.65 0.12 0.23
Matches are distributed among these distances:
1 92 0.10
2 752 0.82
3 72 0.08
4 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:628161 original size:29 final size:30
Alignment explanation
Indices: 628128--628193 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
628118 TATATATATA
628128 TATATAAAG-TATAATTATAAAGACTA-AAG
1 TATATAAAGATATAA-TATAAAGACTATAAG
*
628157 TATAT-AAGCATATAATATAAAGTCTATAAG
1 TATATAAAG-ATATAATATAAAGACTATAAG
628187 TATATAA
1 TATATAA
628194 TATAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.09
29 15 0.47
30 13 0.41
31 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (30 bp):
TATATAAAGATATAATATAAAGACTATAAG
Found at i:628292 original size:33 final size:35
Alignment explanation
Indices: 628069--628415 Score: 138
Period size: 35 Copynumber: 10.2 Consensus size: 35
628059 TTTTAGTACA
*
628069 AAGTATAAA-TACATATATAATA-ATAT-AAAGTAT
1 AAGTATAAAGTATATATAT-ATACATATAAAAGTAT
*
628102 AAGTATATTATA-TATATATATATATATATATAAAGTAT
1 AAGTATA--A-AGTATATATATATACATATA-AAAGTAT
* * *
628140 AATTATAAAG-ACTAAAGTATATAAGCATATAATA-TA-
1 AAGTATAAAGTA-TATA-TATAT-A-CATATAAAAGTAT
* * *
628176 AAGTCTATAAGTATATA-ATATAAAATATATAAGTATT
1 AAGTATA-AAGTATATATATAT-ACATATAAAAGTA-T
* *
628213 AAATATAAAGTATATATATGT--ATAT---A--AT
1 AAGTATAAAGTATATATATATACATATAAAAGTAT
*
628241 AA-TATAAAG--TATATATATACATAT-AACGTAT
1 AAGTATAAAGTATATATATATACATATAAAAGTAT
* * *
628272 AAGTATGAA-TATATATATATATATATAAAAGTTT
1 AAGTATAAAGTATATATATATACATATAAAAGTAT
*
628306 TAGTATAAAGTATATATATAT--ATATAATAA-TAT
1 AAGTATAAAGTATATATATATACATATAA-AAGTAT
* ** *
628339 AA-AATTCAGTATAT-TATATA-ATTATAAAGACTA-
1 AAGTATAAAGTATATATATATACA-TATAAA-AGTAT
* *
628372 AAGTATATAAGCATATA-ATATAAATATAAATAAGTAT
1 AAGTATA-AAGTATATATATATACATAT-AA-AAGTAT
*
628409 AAATATA
1 AAGTATA
628416 TAAAAATATA
Statistics
Matches: 241, Mismatches: 33, Indels: 76
0.69 0.09 0.22
Matches are distributed among these distances:
25 8 0.03
27 11 0.05
28 3 0.01
29 1 0.00
31 10 0.04
32 16 0.07
33 38 0.16
34 28 0.12
35 39 0.16
36 37 0.15
37 28 0.12
38 17 0.07
39 5 0.02
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (35 bp):
AAGTATAAAGTATATATATATACATATAAAAGTAT
Found at i:628622 original size:13 final size:14
Alignment explanation
Indices: 627942--628664 Score: 117
Period size: 14 Copynumber: 51.6 Consensus size: 14
627932 TTATATAGTT
627942 TAAATATAAAGTATA
1 TAAATAT-AAGTATA
*
627957 TAAGTAT-A-TATA
1 TAAATATAAGTATA
*
627969 TAAACTATAAAT-TA
1 TAAA-TATAAGTATA
*
627983 TATATAT-A-TATA
1 TAAATATAAGTATA
* *
627995 CATATATAA-TAATA
1 TAAATATAAGT-ATA
*
628009 TAAAGTATAATTATA
1 TAAA-TATAAGTATA
*
628024 AAAACTA-AAGTATA
1 TAAA-TATAAGTATA
628038 TAAGTATATAAGTATA
1 TAA--ATATAAGTATA
* * *
628054 TAAAGTTTTAGTACA
1 TAAA-TATAAGTATA
*
628069 -AAGTATAA--ATA
1 TAAATATAAGTATA
* *
628080 CATATATAA-TAATA
1 TAAATATAAGT-ATA
628094 TAAAGTATAAGTATA
1 TAAA-TATAAGTATA
*
628109 T-TATAT-A-TATA
1 TAAATATAAGTATA
*
628120 TATATAT-A-TATA
1 TAAATATAAGTATA
628132 TAAAGTATAA-T-TA
1 TAAA-TATAAGTATA
*
628145 TAAAGACTAAAGTATA
1 TAAATA-T-AAGTATA
628161 TAAGCATATAA-TATA
1 TAA--ATATAAGTATA
*
628176 -AAGTCTATAAGTATA
1 TAA--ATATAAGTATA
628191 T-AATATAA--A-A
1 TAAATATAAGTATA
628201 T--ATATAAGTAT-
1 TAAATATAAGTATA
628212 TAAATATAAAGTATA
1 TAAATAT-AAGTATA
628227 TATATGTATATAA-TAATA
1 TA-A---ATATAAGT-ATA
628245 TAAAGTAT-A-TATA
1 TAAA-TATAAGTATA
*
628258 TACATATAACG--TA
1 TAAATATAA-GTATA
*
628271 TAAGTATGAA-TATA
1 TAAATAT-AAGTATA
*
628285 TATATAT-A-TATA
1 TAAATATAAGTATA
* *
628297 TAAAAGTTTTAGTATA
1 T-AAA-TATAAGTATA
*
628313 -AAGTAT-A-TATA
1 TAAATATAAGTATA
*
628324 TATATATAA-TAATA
1 TAAATATAAGT-ATA
*
628338 TAAA-ATTCAGTATA
1 TAAATA-TAAGTATA
*
628352 T-TATATAA-T-TA
1 TAAATATAAGTATA
*
628363 TAAAGACTAAAGTATA
1 TAAATA-T-AAGTATA
628379 TAAGCATAT-A--ATA
1 TAA--ATATAAGTATA
*
628392 TAAATATAAATAAGTA
1 TAAATATAAGT-A-TA
628408 TAAATAT-A-TA-A
1 TAAATATAAGTATA
*
628419 AAATATATAAGTATAA
1 TAA-ATATAAGTAT-A
*
628435 TATATATATA-TATA
1 TAAATATA-AGTATA
628449 TAATATATATA-TATA
1 TAA-ATATA-AGTATA
* * *
628464 TATATATATACT-TT
1 TAAATATA-AGTATA
**
628478 TTTATATAAGTATA
1 TAAATATAAGTATA
*
628492 TATATATAA-TATA
1 TAAATATAAGTATA
628505 TATAATATATA-TATA
1 TA-AATATA-AGTATA
628520 TATATATATATA-TATA
1 TA-A-ATATA-AGTATA
628536 TATATATATATA-TATA
1 TA-A-ATATA-AGTATA
* *
628552 TATATATACGTATA
1 TAAATATAAGTATA
628566 TAAGTATATAAGTATA
1 TAA--ATATAAGTATA
*
628582 -AGTATATAAGTAT-
1 TA-AATATAAGTATA
628595 TAAATATAAGTATA
1 TAAATATAAGTATA
628609 TAAATATTAA--ATA
1 TAAATA-TAAGTATA
628622 TAAAGTACATAAGTATATA
1 TAAA-T--ATAAG--TATA
628641 TAAACTATAAAGTATA
1 TAAA-TAT-AAGTATA
*
628657 TATATATA
1 TAAATATA
628665 TACAATATAT
Statistics
Matches: 547, Mismatches: 65, Indels: 193
0.68 0.08 0.24
Matches are distributed among these distances:
9 6 0.01
10 2 0.00
11 25 0.05
12 59 0.11
13 92 0.17
14 142 0.26
15 100 0.18
16 89 0.16
17 6 0.01
18 14 0.03
19 12 0.02
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (14 bp):
TAAATATAAGTATA
Found at i:628698 original size:13 final size:14
Alignment explanation
Indices: 628655--629357 Score: 143
Period size: 13 Copynumber: 50.6 Consensus size: 14
628645 CTATAAAGTA
628655 TATATATATATAC-
1 TATATATATATACT
* *
628668 AATATATATATAAT
1 TATATATATATACT
628682 T-TATATTATATACT
1 TATATA-TATATACT
*
628696 TATATACTTTAGT-CT
1 TATATA-TATA-TACT
*
628711 T-TATA-ATTATGCT
1 TATATATA-TATACT
628724 CTATATATAATATACT
1 -TATATAT-ATATACT
* *
628740 TATACTTTATATTATT
1 TATA-TATATA-TACT
628756 ATATATGTATATATACT
1 -TATA--TATATATACT
*
628773 T-TATATTTAATACT
1 TATATATAT-ATACT
*
628787 TATATACTTTATA-T
1 TATATA-TATATACT
**
628801 TAT-TATATACGTGTGT
1 TATATATATA--T-ACT
628817 ATATATATATATACT
1 -TATATATATATACT
* *
628832 TTTA-ATTTAT-CT
1 TATATATATATACT
*
628844 TAT-TATATAT-GT
1 TATATATATATACT
*
628856 ATATATACTTTATAC-
1 -TATATA-TATATACT
* ** *
628871 TAAAGCTTTATA--
1 TATATATATATACT
*
628883 TATATATATACACT
1 TATATATATATACT
*
628897 T-TATAGTTTATA--
1 TATATA-TATATACT
628909 TATATACTTATATACTT
1 TATATA--TATATAC-T
*
628926 TATATTTATATACT
1 TATATATATATACT
*
628940 TATATTTA-ATACT
1 TATATATATATACT
*
628953 TATATATTTTATA-T
1 TATATA-TATATACT
628967 TATATACTTATATACT
1 TATATA--TATATACT
* * *
628983 T-TAGTCTTTATAAT
1 TATA-TATATATACT
* *
628997 TATA-ATTTTTA--
1 TATATATATATACT
629008 TATATATAATATACTT
1 TATATAT-ATATAC-T
*
629024 GTACTTATACTTTATA-T
1 -TA--TATA-TATATACT
629041 TATTATATATATACT
1 TA-TATATATATACT
629056 T-TATAT-TATTA-T
1 TATATATATA-TACT
*
629068 ATATGTATATATACT
1 -TATATATATATACT
*
629083 T-TATACTA-AAACT
1 TATATA-TATATACT
*
629096 T-TATATAAATA--
1 TATATATATATACT
629107 TATATATATATA--
1 TATATATATATACT
629119 TATATATACTTATACT
1 TATATATA--TATACT
629135 T-TATAGGT-TATA--
1 TATATA--TATATACT
629147 TATATATATATACT
1 TATATATATATACT
* * *
629161 TGTA-CT-TGTACT
1 TATATATATATACT
*
629173 T-TATATGTATA--
1 TATATATATATACT
* *
629184 TATAT-TTTATATT
1 TATATATATATACT
629197 TATAT-TATATACT
1 TATATATATATACT
*
629210 TATATACTTTAGT-CTT
1 TATATA-TATA-TAC-T
629226 TATAATTATATATACGT
1 TAT-A-TATATATAC-T
*
629243 ATAATATATTTATACT
1 -T-ATATATATATACT
* *
629259 TATACTTTATAT-TT
1 TATA-TATATATACT
629273 TATATATATTATACT
1 TATATATA-TATACT
*
629288 T-TATACTA-AAAC-
1 TATATA-TATATACT
629300 TATATATATATA--
1 TATATATATATACT
629312 TATATATATATA--
1 TATATATATATACT
*
629324 TATATATATATACA
1 TATATATATATACT
629338 TATATATATATA--
1 TATATATATATACT
629350 TATATATA
1 TATATATA
629358 CTTATAATGT
Statistics
Matches: 524, Mismatches: 74, Indels: 185
0.67 0.09 0.24
Matches are distributed among these distances:
11 14 0.03
12 96 0.18
13 123 0.23
14 118 0.23
15 83 0.16
16 30 0.06
17 34 0.06
18 15 0.03
19 10 0.02
20 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (14 bp):
TATATATATATACT
Found at i:628784 original size:49 final size:47
Alignment explanation
Indices: 628727--629360 Score: 172
Period size: 47 Copynumber: 13.4 Consensus size: 47
628717 TTATGCTCTA
*
628727 TATATAATATACTTATACTTTATATTATTATATATGTATATATACTT
1 TATATTATATACTTATACTTTATATTATTATATATGTATATATACTT
* * *
628774 TATATT-TAATACTTATATACTTTATATTATTATATACGTGTGTATA---
1 TATATTAT-ATAC-T-TATACTTTATATTATTATATATGTATATATACTT
* * *
628820 TATA-TATATACTTTTAATTTATCTTATTATATATGTATATATACTT
1 TATATTATATACTTATACTTTATATTATTATATATGTATATATACTT
* * *
628866 TATACTA-A-AGCTTTATA-TATATATATACACTT-TATA-GT-T-TATA-TA
1 TATATTATATA-C-TTATACT-T-TATAT-TA-TTATATATGTATATATACTT
* * *
628911 TATACTTATATACTTTATA-TTTATA-TACTTATATTTAATACTTATATATTT
1 TATA-TTATATAC-TTATACTTTATATTA-TTATATAT-GTA--TATATACTT
* * * * *
628962 TATATTATATACTTATATACTTTAGTCTTTATAATTATAATTTTTATATA-TA
1 TATATTATATAC-T-TATACTTTA-T-ATTATTA-TAT-ATGTATATATACTT
* * * *
629014 TA-ATATACTTGTACTTATACTTTATATTATTATATATATACTTTATATTAT
1 TATAT-TA--TATACTTATACTTTATATTATTATATATGTA-TATATACT-T
* * ** *
629065 TATA-TATGTA-TATATACTTTATACTAAAACTTTATATAAATATATATA-TA
1 TATATTATATACT-TATACTTTATA-T--TA--TTATATATGTATATATACTT
**
629115 TATATATATATACTTATACTTTATA--GGT-TATA--TATATATA---
1 TATAT-TATATACTTATACTTTATATTATTATATATGTATATATACTT
* * *
629155 TATACT-TGTACTTGTACTTTATATGTA-TATATAT-T-T-TATA-TT
1 TATATTATATACTTATACTTTATAT-TATTATATATGTATATATACTT
*
629197 TATATTATATACTTATATACTTTAGT-CT-TTATA-AT-TATATATACGTAT
1 TATATTATATAC-T-TATACTTTA-TATTATTATATATGTATATATAC-T-T
629245 AATATATT-TATACTTATACTTTATATT-TTATATA--TAT-TATACTT
1 --TATATTATATACTTATACTTTATATTATTATATATGTATATATACTT
* * * *
629289 TATACTA-AAACTATATA-TATATATATATATATATATATATATATATACATA
1 TATATTATATACT-TATACT-T-TATAT-TAT-TATATATGTATATATAC-TT
629340 TATATATATATA-TATATACTT
1 TATAT-TATATACT-TATACTT
629361 ATAATGTATT
Statistics
Matches: 451, Mismatches: 53, Indels: 161
0.68 0.08 0.24
Matches are distributed among these distances:
38 15 0.03
39 1 0.00
40 9 0.02
41 5 0.01
42 24 0.05
43 41 0.09
44 21 0.05
45 30 0.07
46 29 0.06
47 52 0.12
48 29 0.06
49 51 0.11
50 39 0.09
51 21 0.05
52 49 0.11
53 22 0.05
54 6 0.01
55 6 0.01
56 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (47 bp):
TATATTATATACTTATACTTTATATTATTATATATGTATATATACTT
Found at i:628823 original size:130 final size:124
Alignment explanation
Indices: 628682--629343 Score: 384
Period size: 130 Copynumber: 5.2 Consensus size: 124
628672 TATATATAAT
* *
628682 TTATATTATATACTTATATACTTTAGTCTTTATAATTATGCTCTATATATAATATACTTATACTT
1 TTATA-TATATACTTATATACTTTAGTCTTTATAATTAT-ATCTATATATATTATACTTATACTT
*
628747 TATATTATTATATATGTATATATACTTTATATTTAATACTTATATACTTTATATTATTATATA
64 TATATTATTATATATATAT-TATACTTTATATTT-ATACTTATATACTTTATATTATTATATA
* * * * *
628810 CGTGTGTATATATA--TATATACTTTTAAT-TTATCTTATTATATATGTATATATACTTTATAC-
1 --T-TATATATATACTTATATAC-TTTAGTCTT-T-ATAAT-TATATCTATATATA--TTATACT
* * * *
628871 TAAAGCTTTATA-TA-TATATATACACTTTATAGTTTATATATATACTTATATACTTTATA-T-T
57 TATA-CTTTATATTATTATATATATA--TTATACTTTATATTTATACTTATATACTTTATATTAT
628932 TATATA
119 TATATA
* * * * * * *
628938 CTTATATTTAATACTTATATATTTTA-TATTATATACTTATATACTTTAGTCT-TTATAATTATA
1 -TTATATAT-ATACTTATATACTTTAGTCTT-TATAATTATAT-CTATA-TATATTATACTTAT-
* * *
629001 ATTTTTATATATATAATATACTTGTACTTATACTTTATA-TTATTA-TATATATACTTTATATTA
60 A-CTTTATAT-TATTATATA--TATA-TTATACTTTATATTTA-TACT-TATATACTTTATATTA
629064 TTATATA
118 TTATATA
* * ** *
629071 -TGTATATATACTT-TATAC-TAAAACTTTATATAAATATATATATATATATATATATACTTATA
1 TTATATATATACTTATATACTTTAGTC-TT-TAT-AAT-TATATCTATATATAT-TATACTTATA
* * * * *
629133 CTTTATAGGTTA-TATATATATA-TATAC-TTGTACTTGTACTT-TATA-TGTATATATATTTTA
61 CTTTATA--TTATTATATATATATTATACTTTATATTTATACTTATATACTTTATAT-TATTATA
629193 TA
123 TA
629195 TTTATATTATATACTTATATACTTTAGTCTTTATAATTATATATACGTATAATATATTTATACTT
1 -TTATA-TATATACTTATATACTTTAGTCTTTATAA-T-TATAT-C-TAT-ATATA-TTATACTT
* * * *
629260 ATACTTTATA-T-TT-TATATATATTATACTTTATACTAAAAC-TATATA-TATATATATATATA
58 ATACTTTATATTATTATATATATATTATACTTTATATTTATACTTATATACTTTATAT-TAT-TA
629320 TATA
121 TATA
*
629324 TATATATATATACATATATA
1 T-TATATATATACTTATATA
629344 TATATATATA
Statistics
Matches: 417, Mismatches: 61, Indels: 110
0.71 0.10 0.19
Matches are distributed among these distances:
123 6 0.01
124 12 0.03
125 12 0.03
126 33 0.08
127 45 0.11
128 74 0.18
129 34 0.08
130 100 0.24
131 64 0.15
132 30 0.07
133 7 0.02
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (124 bp):
TTATATATATACTTATATACTTTAGTCTTTATAATTATATCTATATATATTATACTTATACTTTA
TATTATTATATATATATTATACTTTATATTTATACTTATATACTTTATATTATTATATA
Found at i:628907 original size:158 final size:148
Alignment explanation
Indices: 628725--629204 Score: 353
Period size: 138 Copynumber: 3.2 Consensus size: 148
628715 AATTATGCTC
628725 TATATATA-ATAT-AC-TTATACTTTATATTATTATATATGTATATATACTTTATATTTAATACT
1 TATATATATATATAACTTTATACTTTATATTATTATATATGTATATATACTTTATATTTAATACT
628787 TATATACTTTATATTATTATATACGTGTGTATATA-TATATA-TACTTT-TAATT-T-ATCTTAT
66 TATATA-TTT-TA-TATTATATAC---T-TATATACT-T-TAGT-CTTTATAATTATAAT-TT-T
*
628847 TATATATGTATATATACTTTATAC-TAAAGCTT
119 TATATATATA-ATATAC-TTATACTTAAA-CTT
* *
628879 TATATATATATATACACTTTATAGTTTATATATATACTTATATACTTTATATTTATA-TACTTAT
1 TATATATATATATA-ACTTTATA-CTT-TATAT-TA-TTATATA-TGTATA--TATACT--TTAT
628943 ATTTAATACTTATATATTTTATATTATATACTTATATACTTTAGTCTTTATAATTATAATTTTTA
56 ATTTAATACTTATATATTTTATATTATATACTTATATACTTTAGTCTTTATAATTATAATTTTTA
* *
629008 TATATATAATATACTTGTACTTATACTT
121 TATATATAATATACTTATACTTAAACTT
* * *
629036 TATAT-TAT-TAT-A-TATATACTTTATATTATTATATATGTATATATACTTTATA-CTAAAACT
1 TATATATATATATAACTTTATACTTTATATTATTATATATGTATATATACTTTATATTTAATACT
** * * ** *
629096 T-TATA-TAAATA-TATATA-TATATATA-TATA-TAC-TTATACTTTATAGGTTATATATATAT
66 TATATATTTTATATTATATACT-TATATACTTTAGT-CTTTATA-ATTATAATTTTTATATATAT
* **
629154 -ATATACTTGTACTTGTACTT
128 AATATACTTATACTTAAACTT
* *
629174 TATATGTATATAT-ATTTTATA-TTTATATTAT
1 TATATATATATATAACTTTATACTTTATATTAT
629205 ATACTTATAT
Statistics
Matches: 281, Mismatches: 19, Indels: 66
0.77 0.05 0.18
Matches are distributed among these distances:
138 30 0.11
139 24 0.09
140 26 0.09
141 9 0.03
142 4 0.01
143 7 0.02
144 5 0.02
145 4 0.01
146 1 0.00
147 5 0.02
148 7 0.02
149 2 0.01
150 5 0.02
151 2 0.01
152 5 0.02
153 1 0.00
154 8 0.03
155 7 0.02
156 3 0.01
157 15 0.05
158 20 0.07
159 25 0.09
160 10 0.04
161 4 0.01
162 7 0.02
163 15 0.05
164 3 0.01
165 7 0.02
166 20 0.07
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (148 bp):
TATATATATATATAACTTTATACTTTATATTATTATATATGTATATATACTTTATATTTAATACT
TATATATTTTATATTATATACTTATATACTTTAGTCTTTATAATTATAATTTTTATATATATAAT
ATACTTATACTTAAACTT
Found at i:629100 original size:218 final size:227
Alignment explanation
Indices: 628816--629359 Score: 570
Period size: 218 Copynumber: 2.4 Consensus size: 227
628806 TATACGTGTG
* * * *
628816 TATA-TATATATATACTTTTAATTTATCTTATTATATATGTATATATACTTTATACTAAAGCTTT
1 TATATTATATATATA-TTATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTT
* * *
628880 ATATATATATATACACTTTATAGTTTATATA-TATACTTATATA-CTT-TATAT-T-TATATACT
65 ATATAAATATATACA-TATATA-TATATATACTATACTT-TATAGCTTATATATATATATATACT
628940 TATA-TT-TA-ATA-CT-TATATATTTTATATTATATACTTATATACTT-TAGT-CTTTA-TAAT
127 TATACTTGTATATATCTATATATATTTTATATT-TATA-TTATATACTTATA-TACTTTAGTAAT
* *
628997 TATAATTTTTATATA-TATAATATACTTGTACTTATACTT
189 TATAA-TTATATATACTATAATATACTTATACTTATACTT
629036 TATATTAT-TATATA-TATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTTA
1 TATATTATATATATATTATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTTA
* * *
629099 TATAAATATATATATATATATATATATACTTATACTTTATAGGTTATATATATATATATACTTGT
66 TATAAATATATACATATATATATATATAC-TATACTTTATAGCTTATATATATATATATACTTAT
* **
629164 ACTTGTACTTTATATGTATATATATTTTATATTTATATTATATACTTATATACTTTAGTCTTTAT
130 ACTTGTA---TATATCTATATATATTTTATATTTATATTATATACTTATATACTTTAGTAATTAT
*
629229 AATTATATATACGTATAATATATTTATACTTATACTT
192 AATTATATATAC-TATAATATACTTATACTTATACTT
* * ** * * * *
629266 TATATTTTATATATATTATACTTTATACTAAAACTATATATATATATA-TATATA-TATATA-TA
1 TATATTATATATATATTATACTTTATATTATTA-TATATGTATATATACTTTATACTA-AAACTT
* * *
629328 TATATATACATATATATATATATATATATACT
64 TATATAAATATATACATATATATATATATACT
629360 TATAATGTAT
Statistics
Matches: 274, Mismatches: 26, Indels: 38
0.81 0.08 0.11
Matches are distributed among these distances:
216 7 0.03
217 9 0.03
218 66 0.24
219 5 0.02
220 11 0.04
221 14 0.05
222 2 0.01
223 2 0.01
227 14 0.05
228 20 0.07
229 22 0.08
230 30 0.11
231 38 0.14
232 21 0.08
233 13 0.05
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (227 bp):
TATATTATATATATATTATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTTA
TATAAATATATACATATATATATATATACTATACTTTATAGCTTATATATATATATATACTTATA
CTTGTATATATCTATATATATTTTATATTTATATTATATACTTATATACTTTAGTAATTATAATT
ATATATACTATAATATACTTATACTTATACTT
Found at i:629147 original size:30 final size:30
Alignment explanation
Indices: 629113--629357 Score: 142
Period size: 29 Copynumber: 8.3 Consensus size: 30
629103 AATATATATA
*
629113 TATATATATATATACTTATACTTTATAGGTT
1 TATATATATATATACTTATACTTTATA-CTT
* *
629144 ATATATATATATATACTTGTAC-TTGTACTT
1 -TATATATATATATACTTATACTTTATACTT
* *
629174 TATATGTATATATATTTTATA-TTTATA--T
1 TATATATATATATA-CTTATACTTTATACTT
*
629202 TATATACT-TATATACTT-TAGTCTTTATAATT
1 TATATA-TATATATACTTATA--CTTTATACTT
*
629233 ATATATACGTATAATATATTTATAC-TTATACTT
1 -TATATA--TAT-ATATACTTATACTTTATACTT
*
629266 TATATTTTATATATA-TTATACTTTATAC-T
1 TATA-TATATATATACTTATACTTTATACTT
* * * *
629295 AAAACTATATATATA--TATA-TATATA-TA
1 TATA-TATATATATACTTATACTTTATACTT
* * *
629322 TATATATATATATACATATA-TATATA-TA
1 TATATATATATATACTTATACTTTATACTT
629350 TATATATA
1 TATATATA
629358 CTTATAATGT
Statistics
Matches: 174, Mismatches: 21, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
26 12 0.07
27 9 0.05
28 36 0.21
29 38 0.22
30 21 0.12
31 8 0.05
32 30 0.17
33 9 0.05
34 2 0.01
35 7 0.04
36 2 0.01
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (30 bp):
TATATATATATATACTTATACTTTATACTT
Found at i:629439 original size:2 final size:2
Alignment explanation
Indices: 629432--629476 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
629422 TAACATTCAT
629432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
629473 TA TA
1 TA TA
629477 ATTGTTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:629804 original size:24 final size:24
Alignment explanation
Indices: 629775--629820 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
629765 TTTAGTCCAT
629775 TTTTAT-ATTAATATCAACTTCACA
1 TTTTATAATTAAT-TCAACTTCACA
*
629799 TTTTATAATTAATTCAATTTCA
1 TTTTATAATTAATTCAACTTCA
629821 TCACTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATAATTAATTCAACTTCACA
Found at i:629930 original size:3 final size:3
Alignment explanation
Indices: 629922--629950 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
629912 TATAAAGTGT
629922 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
629951 AACCCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:630144 original size:20 final size:20
Alignment explanation
Indices: 630103--630153 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
630093 AAATAAATAA
630103 ATTATATATACATGCATCAT
1 ATTATATATACATGCATCAT
* *
630123 ATTATCATA-ACATTCATTAT
1 ATTAT-ATATACATGCATCAT
630143 ATATATATATA
1 AT-TATATATA
630154 TATATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTATATATACATGCATCAT
Found at i:630493 original size:24 final size:24
Alignment explanation
Indices: 630448--630493 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
630438 TCAGTCCATT
**
630448 TTTTATATTAATTTTATCTTCACA
1 TTTTATATTAATTCAATCTTCACA
630472 TTTTATAATTAATTCAAT-TTCA
1 TTTTAT-ATTAATTCAATCTTCA
630494 TCCCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATATTAATTCAATCTTCACA
Found at i:630639 original size:22 final size:23
Alignment explanation
Indices: 630570--630834 Score: 176
Period size: 22 Copynumber: 12.2 Consensus size: 23
630560 TGGTACTTTA
* *
630570 TATACATATATAAACTA-TAAAG
1 TATATATATATAAAGTATTAAAG
* * * *
630592 TATACATGTAT-ATGTATGTATA-
1 TATATATATATAAAGTAT-TAAAG
630614 TATATATATATAAAGTA-TAAAG
1 TATATATATATAAAGTATTAAAG
*
630636 TATATA-ATAAAAAGTATTAAAG
1 TATATATATATAAAGTATTAAAG
*
630658 TATATA-ATATAAAGTAAT-AAG
1 TATATATATATAAAGTATTAAAG
* * **
630679 TGTTTGGATAT-AAGTATTAAAG
1 TATATATATATAAAGTATTAAAG
*
630701 TATATAAATAT-AAGTATTAAA-
1 TATATATATATAAAGTATTAAAG
* *
630722 TATAAAGTATAT-AAGTACTAAAG
1 TATATA-TATATAAAGTATTAAAG
* *
630745 TATATA-ATATAAAGTTTTAAAC
1 TATATATATATAAAGTATTAAAG
630767 TATATA-ATAT-AAGTATTAAA-
1 TATATATATATAAAGTATTAAAG
*
630787 TATAAAT-TATTAAAGTATATAAA-
1 TATATATATA-TAAAGTAT-TAAAG
630810 TATA-AGTAT-TAAA-TA-TAAAG
1 TATATA-TATATAAAGTATTAAAG
630830 TATAT
1 TATAT
630835 TAATTATCAT
Statistics
Matches: 197, Mismatches: 28, Indels: 37
0.75 0.11 0.14
Matches are distributed among these distances:
19 4 0.02
20 11 0.06
21 48 0.24
22 112 0.57
23 21 0.11
24 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (23 bp):
TATATATATATAAAGTATTAAAG
Found at i:630700 original size:65 final size:64
Alignment explanation
Indices: 630614--630834 Score: 208
Period size: 65 Copynumber: 3.4 Consensus size: 64
630604 TGTATGTATA
*
630614 TATATATATATAAAGTA-TAAAGTATATAATAAAAAGTATTAAAGTATATAA-TATAAAGTAATA
1 TATATA-ATATAAAGTATTAAAGTATATAATAATAAGTATTAAA-TATA-AAGTATAAAGTAATA
630677 AG
63 AG
* * * *
630679 TGTTTGGATAT-AAGTATTAAAGTATATAA-ATATAAGTATTAAATATAAAGTATATAAGTACTA
1 TATAT-AATATAAAGTATTAAAGTATATAATA-ATAAGTATTAAATATAAAGTATA-AAGTAAT-
630742 AAG
62 AAG
* * *
630745 TATATAATATAAAGTTTTAAACTATATAAT-ATAAGTATTAAATATAAATTATTAAAGTATATAA
1 TATATAATATAAAGTATTAAAGTATATAATAATAAGTATTAAATATAAAGTA-TAAAGTA-ATAA
630809 -
64 G
630809 -ATATAAGTATTAAA-TA-TAAAGTATAT
1 TATATAA-TA-TAAAGTATTAAAGTATAT
630835 TAATTATCAT
Statistics
Matches: 130, Mismatches: 14, Indels: 26
0.76 0.08 0.15
Matches are distributed among these distances:
63 17 0.13
64 17 0.13
65 71 0.55
66 25 0.19
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (64 bp):
TATATAATATAAAGTATTAAAGTATATAATAATAAGTATTAAATATAAAGTATAAAGTAATAAG
Found at i:630738 original size:87 final size:86
Alignment explanation
Indices: 630613--630834 Score: 226
Period size: 87 Copynumber: 2.6 Consensus size: 86
630603 ATGTATGTAT
* *
630613 ATATATATATATAAAGTA-TAAAGTATATAA-TA-AAAAGTATTAAAGTATATAATATAAAGTAA
1 ATATATAAATATAAAGTATTAAA-TATA-AAGTATATAAGTA-TAAAGTATATAATATAAAGTAA
* * * *
630675 T-AAGTGTTTGGATATAAGTATTAA
63 TAAACTATAT-AATATAAGTATTAA
**
630699 AGTATATAAATAT-AAGTATTAAATATAAAGTATATAAGTACTAAAGTATATAATATAAAGTTTT
1 A-TATATAAATATAAAGTATTAAATATAAAGTATATAAGTA-TAAAGTATATAATATAAAGTAAT
630763 AAACTATATAATATAAGTATTAA
64 AAACTATATAATATAAGTATTAA
* *
630786 ATATA-AATTATTAAAGTATATAAATAT-AAGTAT-TAAATATAAAGTATAT
1 ATATATAAATA-TAAAGTAT-TAAATATAAAGTATATAAGTATAAAGTATAT
630835 TAATTATCAT
Statistics
Matches: 117, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
85 16 0.14
86 22 0.19
87 67 0.57
88 12 0.10
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (86 bp):
ATATATAAATATAAAGTATTAAATATAAAGTATATAAGTATAAAGTATATAATATAAAGTAATAA
ACTATATAATATAAGTATTAA
Found at i:630856 original size:21 final size:21
Alignment explanation
Indices: 630830--630918 Score: 62
Period size: 21 Copynumber: 4.4 Consensus size: 21
630820 AAATATAAAG
630830 TATATTAATTATCATAATTAA
1 TATATTAATTATCATAATTAA
* *
630851 TATATTAAGTAT-AT--TTAT
1 TATATTAATTATCATAATTAA
*
630869 TA-ATTTAATTATCATAACTAA
1 TATA-TTAATTATCATAATTAA
* * *
630890 TAT-TTTATTATAATATTTAA
1 TATATTAATTATCATAATTAA
* *
630910 AAAATTAAT
1 TATATTAAT
630919 CATATTAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 1 0.02
18 12 0.24
19 2 0.04
20 16 0.32
21 19 0.38
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
TATATTAATTATCATAATTAA
Found at i:631038 original size:16 final size:16
Alignment explanation
Indices: 630990--631045 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
630980 TTTCATCAAT
*
630990 GGTAATATATAAG-TCA
1 GGTAA-ATATCAGATCA
*
631006 GGTAAATGTCA-AGTCA
1 GGTAAATATCAGA-TCA
631022 GGTAAATATCAGATCA
1 GGTAAATATCAGATCA
*
631038 GGTCAATA
1 GGTAAATA
631046 ACAAGTCGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 28 0.85
17 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (16 bp):
GGTAAATATCAGATCA
Found at i:631081 original size:32 final size:32
Alignment explanation
Indices: 631045--631118 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
631035 TCAGGTCAAT
*
631045 AACAAGTCGGA-TCATTTACAGGCCAGGTTGAA
1 AACAAGTCGGATTCA-TAACAGGCCAGGTTGAA
* * *
631077 AACAAGTCAGATTCATAACATGTCAGGTTGAA
1 AACAAGTCGGATTCATAACAGGCCAGGTTGAA
*
631109 AACAGGTCGG
1 AACAAGTCGG
631119 GTAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 32 0.91
33 3 0.09
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (32 bp):
AACAAGTCGGATTCATAACAGGCCAGGTTGAA
Found at i:631112 original size:16 final size:16
Alignment explanation
Indices: 631068--631112 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
631058 ATTTACAGGC
631068 CAGGTTGAAAACAAGT
1 CAGGTTGAAAACAAGT
* * * *
631084 CAGATTCATAACATGT
1 CAGGTTGAAAACAAGT
631100 CAGGTTGAAAACA
1 CAGGTTGAAAACA
631113 GGTCGGGTAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (16 bp):
CAGGTTGAAAACAAGT
Found at i:638946 original size:30 final size:29
Alignment explanation
Indices: 638890--638967 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
638880 TTTGTAATTT
* * * *
638890 TTCCAAAATTATATTTTGGTCCCTAAACC
1 TTCCAAATTTATAATTTGATCACTAAACC
*
638919 TTCCAAAGTTTATAATTTGATCACTAAACT
1 TTCCAAA-TTTATAATTTGATCACTAAACC
638949 TTACCAAATTTATAATTTG
1 TT-CCAAATTTATAATTTG
638968 GTCATTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.17
30 30 0.71
31 5 0.12
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (29 bp):
TTCCAAATTTATAATTTGATCACTAAACC
Found at i:642448 original size:18 final size:18
Alignment explanation
Indices: 642425--642465 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
642415 TCGAATCGGT
*
642425 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCATTGAC
642443 CCGACCCGACCCATTGAC
1 CCGACCCGACCCATTGAC
642461 CCGAC
1 CCGAC
642466 TTGTGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (18 bp):
CCGACCCGACCCATTGAC
Found at i:646305 original size:43 final size:43
Alignment explanation
Indices: 646257--646520 Score: 191
Period size: 43 Copynumber: 6.1 Consensus size: 43
646247 CTAAAAATAG
646257 CGCCGCTAA-AGGTGTTGATGTTTAGCGGCGTTTTCTTCACAAA
1 CGCCGC-AATAGGTGTTGATGTTTAGCGGCGTTTTCTTCACAAA
* * * ** *
646300 CGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTGC-AGAAAAA
1 CGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTT-CTTCACAAA
* * * * * **
646343 TGCCGCAATAGGTGTTGATATTTAACGGCATTTGGC-AAACAAA
1 CGCCGCAATAGGTGTTGATGTTTAGCGGCGTTT-TCTTCACAAA
** * *
646386 TACCGCAATATGTGTTAATGTTTAGCGGCGTTTTCTTCACAAA
1 CGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTCTTCACAAA
* * * * *
646429 CGCTGCAATAGATGTTGATTTTTA-CTGACGTTTT-TCCTACAAA
1 CGCCGCAATAGGTGTTGATGTTTAGC-GGCGTTTTCTTC-ACAAA
* * *
646472 CGCCGCAATATGTATTGA-GATTTAGCGGCGTTTT-TATCAAAAA
1 CGCCGCAATAGGTGTTGATG-TTTAGCGGCGTTTTCT-TCACAAA
646515 CGCCGC
1 CGCCGC
646521 TAAATGTATG
Statistics
Matches: 173, Mismatches: 39, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
42 6 0.03
43 164 0.95
44 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (43 bp):
CGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTCTTCACAAA
Found at i:646516 original size:86 final size:87
Alignment explanation
Indices: 646295--646520 Score: 212
Period size: 86 Copynumber: 2.6 Consensus size: 87
646285 CGTTTTCTTC
* * * * * *
646295 ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTGC-A-GAAAAATGCCGCAATAGGTGT
1 ACAAACGCCGCAATATGTATTGAGATTTAGCGGCGTTTT-CTATCAAAAACGCCGCAATAGATGT
*
646358 TGATATTTAACGGCATTTGGCAA
65 TGATATTTAACGACATTTGGCAA
** * * * *
646381 ACAAATACCGCAATATGTGTTAATG-TTTAGCGGCGTTTTCT-TCACAAACGCTGCAATAGATGT
1 ACAAACGCCGCAATATGTATTGA-GATTTAGCGGCGTTTTCTATCAAAAACGCCGCAATAGATGT
* * ** **
646444 TGAT-TTTTACTGACGTTTTTCCT
65 TGATATTTAAC-GACATTTGGCAA
646467 ACAAACGCCGCAATATGTATTGAGATTTAGCGGCGTTTT-TATCAAAAACGCCGC
1 ACAAACGCCGCAATATGTATTGAGATTTAGCGGCGTTTTCTATCAAAAACGCCGC
646521 TAAATGTATG
Statistics
Matches: 109, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
85 8 0.07
86 101 0.93
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (87 bp):
ACAAACGCCGCAATATGTATTGAGATTTAGCGGCGTTTTCTATCAAAAACGCCGCAATAGATGTT
GATATTTAACGACATTTGGCAA
Found at i:646877 original size:21 final size:21
Alignment explanation
Indices: 646853--646929 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
646843 TTATATATTA
646853 CTTCTCTCTGTGCTGCCAATG
1 CTTCTCTCTGTGCTGCCAATG
**
646874 CTTCTCTCTGTGCTGCCGTTG
1 CTTCTCTCTGTGCTGCCAATG
* *
646895 CCTCTCTCTGTGCTGCCACTG
1 CTTCTCTCTGTGCTGCCAATG
*
646916 CTTCTCTCTCTGCT
1 CTTCTCTCTGTGCT
646930 TCCGCTGCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.04, C:0.38, G:0.18, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTGTGCTGCCAATG
Found at i:646937 original size:21 final size:21
Alignment explanation
Indices: 646853--646971 Score: 105
Period size: 21 Copynumber: 5.7 Consensus size: 21
646843 TTATATATTA
* **
646853 CTTCTCTCTGTGCTGCCAATG
1 CTTCTCTCTCTGCTGCCGCTG
* *
646874 CTTCTCTCTGTGCTGCCGTTG
1 CTTCTCTCTCTGCTGCCGCTG
* * *
646895 CCTCTCTCTGTGCTGCCACTG
1 CTTCTCTCTCTGCTGCCGCTG
*
646916 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
* ** *
646937 CTGCTCTAACTGCTTCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
646958 -TTGCTCTCTCTGCT
1 CTT-CTCTCTCTGCT
646972 TCCCTTGCTT
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 1 0.01
21 81 0.99
ACGTcount: A:0.04, C:0.38, G:0.18, T:0.39
Consensus pattern (21 bp):
CTTCTCTCTCTGCTGCCGCTG
Found at i:657523 original size:30 final size:29
Alignment explanation
Indices: 657439--657594 Score: 82
Period size: 30 Copynumber: 5.0 Consensus size: 29
657429 ATGCATGTTG
*
657439 TATTATTTATACATATATTTAACAGATTT
1 TATTATTTATACATATATTTAATAGATTT
* * * * * *
657468 TCTAATTGGATTCGGATTTCTTTTAATATGATTT
1 TATTATT-TATAC--ATAT-ATTTAATA-GATTT
657502 TATTATTTATACATATATTTAATA-ATTT
1 TATTATTTATACATATATTTAATAGATTT
* ** * *
657530 T-TCTAATTGGATTTGGATTTCATTTAATATTATTT
1 TAT-T-ATT---TATACATAT-ATTTAATA-GATTT
657565 TATTATTTATACATATATTTAATAGATTT
1 TATTATTTATACATATATTTAATAGATTT
657594 T
1 T
657595 CTAATTGGAT
Statistics
Matches: 91, Mismatches: 22, Indels: 28
0.65 0.16 0.20
Matches are distributed among these distances:
27 1 0.01
28 6 0.07
29 13 0.14
30 18 0.20
31 8 0.09
32 8 0.09
33 17 0.19
34 13 0.14
35 6 0.07
36 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.07, T:0.55
Consensus pattern (29 bp):
TATTATTTATACATATATTTAATAGATTT
Found at i:657538 original size:63 final size:63
Alignment explanation
Indices: 657439--657612 Score: 296
Period size: 63 Copynumber: 2.8 Consensus size: 63
657429 ATGCATGTTG
* * *
657439 TATTATTTATACATATATTTAACAGATTTTCTAATTGGATTCGGATTTCTTTTAATATGATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTTGGATTTCATTTAATATGATTT
*
657502 TATTATTTATACATATATTTAATA-ATTTTTCTAATTGGATTTGGATTTCATTTAATATTATTT
1 TATTATTTATACATATATTTAATAGA-TTTTCTAATTGGATTTGGATTTCATTTAATATGATTT
657565 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTTGGATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTTGGATTT
657613 GGATTTCATT
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
62 1 0.01
63 103 0.98
64 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.55
Consensus pattern (63 bp):
TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTTGGATTTCATTTAATATGATTT
Found at i:658355 original size:54 final size:54
Alignment explanation
Indices: 658272--658375 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
658262 AAAGTAATCA
* *
658272 TTAAGCCATAAATGAATGTTTCAAGCGTATGGTATTCTATATATGTATATTACT
1 TTAAGCCATAAATGAATGTTTCAAACGTATGGTATTCTATATATATATATTACT
658326 TTAAGCCATAAATGAATGTTTCAAACGTATGGTATTCTATATATATATAT
1 TTAAGCCATAAATGAATGTTTCAAACGTATGGTATTCTATATATATATAT
658376 ATATATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (54 bp):
TTAAGCCATAAATGAATGTTTCAAACGTATGGTATTCTATATATATATATTACT
Found at i:661031 original size:6 final size:6
Alignment explanation
Indices: 661020--661046 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
661010 AATTAAAAAT
661020 TATCTA TATCTA TATCTA TATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TAT
661047 TTATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:665442 original size:24 final size:24
Alignment explanation
Indices: 665415--665514 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
665405 GATATAAAAA
* *
665415 ATCAAAACATAATTCAGATCAAAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
665439 ATCAGAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
*
665463 ATCAAAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
665487 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
665511 ATCA
1 ATCA
665515 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 55 0.95
25 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:665514 original size:48 final size:48
Alignment explanation
Indices: 665413--665514 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 48
665403 GAGATATAAA
* * ** *
665413 AAATCAAAACATAATTCAGATCAAATATCAGAACAGAATCCAGGTTAG
1 AAATCAAAACAGAATTCAGATCAAATATCAAAACAGAATCCAAATCAG
* * * * *
665461 GAATCAAAACAGATTTCAGATCAGATGTCAAAACAGAATTCAAATCAG
1 AAATCAAAACAGAATTCAGATCAAATATCAAAACAGAATCCAAATCAG
665509 AAATCA
1 AAATCA
665515 GATAAAATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
AAATCAAAACAGAATTCAGATCAAATATCAAAACAGAATCCAAATCAG
Found at i:671292 original size:2 final size:2
Alignment explanation
Indices: 671285--671310 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
671275 TATGCTACTG
671285 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
671311 CATTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:677081 original size:15 final size:13
Alignment explanation
Indices: 677053--677078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
677043 AAAGTTTGAT
677053 TGATTTTTTTAAA
1 TGATTTTTTTAAA
677066 TGATTTTTTTAAA
1 TGATTTTTTTAAA
677079 AATAAAATAA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TGATTTTTTTAAA
Found at i:679530 original size:46 final size:45
Alignment explanation
Indices: 679468--679558 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
679458 TTGAAAAAGC
* *
679468 CTGAGTGCATCGATGCATAGTCTTATGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGT-ATATGCATCGATGCATAAAATGCA
* * *
679514 CTGAGTGCATCGATGCATGGTATGTGTATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTATATGCATCGATGCATAAAATGCA
679559 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 20 0.50
46 20 0.50
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (45 bp):
CTGAGTGCATCGATGCATAGTATATGCATCGATGCATAAAATGCA
Found at i:685762 original size:17 final size:17
Alignment explanation
Indices: 685740--685779 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
685730 AATTTCTAAT
*
685740 TTTTGGTACCCAAATCC
1 TTTTGGTACCCAAACCC
685757 TTTTGGTACCCAAACCC
1 TTTTGGTACCCAAACCC
685774 TTTTGG
1 TTTTGG
685780 GTCCATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (17 bp):
TTTTGGTACCCAAACCC
Found at i:686936 original size:592 final size:591
Alignment explanation
Indices: 685805--686992 Score: 2198
Period size: 592 Copynumber: 2.0 Consensus size: 591
685795 TTTCTAAAAT
685805 CCTTG-TCCCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTTA
1 CCTTGTTCCCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTTA
*
685869 GGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAGCT
66 GGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAACT
*
685934 TCTAAAACTTTTCTTAATAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCAA
131 TCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCAA
*
685999 CCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATGATCATCATGAACTTTTGAAAGT
196 CCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGACGATCATCATGAACTTTTGAAAGT
686064 AAGTTATGCAAATCAGTATTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTCTTTGATCTT
261 AAGTTATGCAAATCAGTATTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTCTTTGATCTT
*
686129 ACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTTGTTTTTCAATTTTAAAATATCAT
326 ACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTCGTTTTTCAATTTTAAAATATCAT
* *
686194 TTTTGTATTTTGAAAACAGAGTCTTATAATCTGAAGCCAACCCATTATAATCCTCTAATAACTCA
391 TTTTGTATTTTAAAAACAGAGTCTTATAATCCGAAGCCAACCCATTATAATCCTCTAATAACTCA
*
686259 TCATAAGATAATTCATCCAAATCGAATGAGTTGGAGGTTACCTTAGAATCTTCCCCGATAGCCAT
456 TCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCCCCGATAGCCAT
686324 CAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCTA
521 CAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCTA
686389 CATGAG
586 CATGAG
*
686395 CCTTGTTCTCCCTTTGGTATCCATTTATGAAGGACATCTTTATCTTTAGTAGTAATGAATTCTTT
1 CCTTGTTC-CCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTT
* *
686460 AGGAACCCATATACTCTTAATAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAAC
65 AGGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAAC
686525 TTCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
130 TTCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
686590 ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGACGATCATCATGAACTTTTGAAAG
195 ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGACGATCATCATGAACTTTTGAAAG
686655 TAAGTTATGCAAATCAGTATTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTCTTTGATCT
260 TAAGTTATGCAAATCAGTATTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTCTTTGATCT
* * *
686720 TACTTTCAAGCTCATTGTTGGTCTTGGATATAAGACTATTTTCGTTTTTCAATTTTGAAATATCA
325 TACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTCGTTTTTCAATTTTAAAATATCA
*
686785 TTTTTGTATTTTAAAAATAGAGTCTTATAATCCGAAGCCAACCCATTATAATCCTCTAATAACTC
390 TTTTTGTATTTTAAAAACAGAGTCTTATAATCCGAAGCCAACCCATTATAATCCTCTAATAACTC
*
686850 ATCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCTCCGATAGCCA
455 ATCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCCCCGATAGCCA
* *
686915 TCAAGCACAAGTTTGCAACTTCTTGTTTCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCT
520 TCAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCT
*
686980 ATATGAG
585 ACATGAG
686987 CCTTGT
1 CCTTGT
686993 GCTTCTTTTT
Statistics
Matches: 578, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
590 5 0.01
591 2 0.00
592 571 0.99
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (591 bp):
CCTTGTTCCCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTTA
GGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAACT
TCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCAA
CCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGACGATCATCATGAACTTTTGAAAGT
AAGTTATGCAAATCAGTATTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTCTTTGATCTT
ACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTCGTTTTTCAATTTTAAAATATCAT
TTTTGTATTTTAAAAACAGAGTCTTATAATCCGAAGCCAACCCATTATAATCCTCTAATAACTCA
TCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCCCCGATAGCCAT
CAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCTA
CATGAG
Found at i:688845 original size:46 final size:46
Alignment explanation
Indices: 688782--688873 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
688772 TTGAAAAAGC
* * *
688782 CTGAGTGCATCGATGCAT-AGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGAATCGATGCATGAGT-ATGTGCATCGATGCATAAAATGCA
*
688828 CTGAGTGAATCGATGCATGGGTATGTGCATCGATGCATAAAATGCA
1 CTGAGTGAATCGATGCATGAGTATGTGCATCGATGCATAAAATGCA
688874 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 39 0.95
47 2 0.05
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGAATCGATGCATGAGTATGTGCATCGATGCATAAAATGCA
Found at i:688921 original size:20 final size:20
Alignment explanation
Indices: 688893--688930 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
688883 CAAGAAATTA
688893 ATTGATGCATCGGTGCATGG
1 ATTGATGCATCGGTGCATGG
*
688913 ATTGGTGCATCGGTGCAT
1 ATTGATGCATCGGTGCAT
688931 ACCCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGGTGCATGG
Found at i:696782 original size:18 final size:18
Alignment explanation
Indices: 696759--696794 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
696749 AATAATTTAT
* *
696759 ATTTATTTCAAACTAATA
1 ATTTATTTAAAACAAATA
696777 ATTTATTTAAAACAAATA
1 ATTTATTTAAAACAAATA
696795 TTTGAATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTATTTAAAACAAATA
Found at i:699796 original size:2 final size:2
Alignment explanation
Indices: 699789--699857 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
699779 CTAGAAATCA
699789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699831 AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699858 CAAGATACTA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:703960 original size:24 final size:24
Alignment explanation
Indices: 703928--703976 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
703918 CCCACTCATG
703928 CATGAATGATAGATCTTAACCCTA
1 CATGAATGATAGATCTTAACCCTA
*
703952 CATGAATGATAGATCTTAAGCCTA
1 CATGAATGATAGATCTTAACCCTA
703976 C
1 C
703977 GATTAGGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (24 bp):
CATGAATGATAGATCTTAACCCTA
Found at i:706650 original size:24 final size:24
Alignment explanation
Indices: 706618--706665 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
706608 AATTCGATGC
706618 CCCCTTAG-CCCCTCTTTTTGACTT
1 CCCCTTAGCCCCCT-TTTTTGACTT
706642 CCCCTTAGCCCCCTTTTTTGACTT
1 CCCCTTAGCCCCCTTTTTTGACTT
706666 TTCTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.08, C:0.42, G:0.08, T:0.42
Consensus pattern (24 bp):
CCCCTTAGCCCCCTTTTTTGACTT
Found at i:717485 original size:20 final size:20
Alignment explanation
Indices: 717448--717486 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
717438 AGATTGAGTG
* * *
717448 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
717468 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
717487 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:717707 original size:20 final size:21
Alignment explanation
Indices: 717661--717721 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
717651 TTCCCCTGTG
717661 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
717684 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
717704 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
717722 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:718729 original size:183 final size:183
Alignment explanation
Indices: 718421--718787 Score: 689
Period size: 183 Copynumber: 2.0 Consensus size: 183
718411 ATTTGCATCC
* *
718421 TCCATAATCCGCATCAGAAAAAGCATGCAAGCTAAAGCTAGAGTCTCTAGGATACCAAAGTCCTA
1 TCCATAATCCGCATCACAAAAAGCATGCAAGCTAAAGCTAAAGTCTCTAGGATACCAAAGTCCTA
*
718486 AACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATTCCTTATGA
66 AACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATTCCTTAGGA
*
718551 CATGATTGAAATCTAACACATAAGCAAACACTAAACATAATGTCCGGTCTACT
131 CATGATTGAAATCTAACACATAAGCAAACACTAAACATAATATCCGGTCTACT
718604 TCCATAATCCGCATCACAAAAAGCATGCAAGCTAAAGCTAAAGTCTCTAGGATACCAAAGTCCTA
1 TCCATAATCCGCATCACAAAAAGCATGCAAGCTAAAGCTAAAGTCTCTAGGATACCAAAGTCCTA
718669 AACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATTCCTTAGGA
66 AACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATTCCTTAGGA
*
718734 CATGATTGAAATCTAGCACATAAGCAAACACTAAACATAATATCCGGTCTACT
131 CATGATTGAAATCTAACACATAAGCAAACACTAAACATAATATCCGGTCTACT
718787 T
1 T
718788 GCAGTTAGAT
Statistics
Matches: 179, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (183 bp):
TCCATAATCCGCATCACAAAAAGCATGCAAGCTAAAGCTAAAGTCTCTAGGATACCAAAGTCCTA
AACTAGGAGTGTCCTTAAGGTATCTAAAGATTCTCTTAACAGCTAGTAAATGTGATTCCTTAGGA
CATGATTGAAATCTAACACATAAGCAAACACTAAACATAATATCCGGTCTACT
Found at i:727206 original size:24 final size:24
Alignment explanation
Indices: 727169--727217 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
727159 GAATTCGGTA
727169 TCCCCTTAACCCCTCTTATTGACT
1 TCCCCTTAACCCCTCTTATTGACT
** *
727193 TCCCCTTAGGCCCTCTTTTTGACT
1 TCCCCTTAACCCCTCTTATTGACT
727217 T
1 T
727218 TTCTAACACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.39, G:0.08, T:0.41
Consensus pattern (24 bp):
TCCCCTTAACCCCTCTTATTGACT
Found at i:727943 original size:3 final size:3
Alignment explanation
Indices: 727937--728013 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
727927 TTCATTTGAA
* * * * *
727937 TAT TAT T-T ATAT TAT TAT TAT AAT TAT AAT AAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
727982 TAT TAT TA- TAT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
728014 AAAATAATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.05
3 59 0.89
4 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:728844 original size:39 final size:39
Alignment explanation
Indices: 728800--728886 Score: 174
Period size: 39 Copynumber: 2.2 Consensus size: 39
728790 AGGGAAATTA
728800 AGAGAGAAGGGGAGAGAGCTTCTTCTTCTCTCATTTTTG
1 AGAGAGAAGGGGAGAGAGCTTCTTCTTCTCTCATTTTTG
728839 AGAGAGAAGGGGAGAGAGCTTCTTCTTCTCTCATTTTTG
1 AGAGAGAAGGGGAGAGAGCTTCTTCTTCTCTCATTTTTG
728878 AGAGAGAAG
1 AGAGAGAAG
728887 AAGAAGAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (39 bp):
AGAGAGAAGGGGAGAGAGCTTCTTCTTCTCTCATTTTTG
Found at i:729778 original size:21 final size:23
Alignment explanation
Indices: 729751--729803 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
729741 GATATTTCTA
*
729751 AATAAATAAATATTTAT-ATTAT
1 AATAAATAAATAATTATAATTAT
*
729773 -ATAAATATATAATTATAATTAT
1 AATAAATAAATAATTATAATTAT
729795 AATAAATAA
1 AATAAATAA
729804 TAGGATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 14 0.54
22 5 0.19
23 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAATAAATAATTATAATTAT
Found at i:729822 original size:24 final size:22
Alignment explanation
Indices: 729749--729822 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 22
729739 CTGATATTTC
* *
729749 TAAATAAATAAATATTTAT-AT
1 TAAATAAATATATAATTATAAT
*
729770 TATATAAATATATAATTATAAT
1 TAAATAAATATATAATTATAAT
729792 TATAATAAATA-ATAGGATTATAAAT
1 TA-AATAAATATATA--ATTAT-AAT
729817 TAAATA
1 TAAATA
729823 TATTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.36
22 7 0.16
23 7 0.16
24 9 0.20
25 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
TAAATAAATATATAATTATAAT
Found at i:731736 original size:12 final size:12
Alignment explanation
Indices: 731719--731743 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
731709 TTTCAGATCG
731719 TTTGTAGAAAGC
1 TTTGTAGAAAGC
731731 TTTGTAGAAAGC
1 TTTGTAGAAAGC
731743 T
1 T
731744 AGGAGGTGGA
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TTTGTAGAAAGC
Found at i:733621 original size:15 final size:15
Alignment explanation
Indices: 733601--733632 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
733591 GATCAATACC
733601 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
733616 TTTTGCATACATTCA
1 TTTTGCATACATGCA
733631 TT
1 TT
733633 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:741038 original size:6 final size:6
Alignment explanation
Indices: 740967--741052 Score: 70
Period size: 7 Copynumber: 13.8 Consensus size: 6
740957 TGCTTGAAGA
*
740967 AAAAATG AAAAA- AAAGAAG AAGAAG -AAAAG AAAAAG AAAAAATG AAAAA-
1 AAAAA-G AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG -AAAAA-G AAAAAG
* *
741016 AAAAAG AAGAAG AAAAAAG AAAAAA AAGAAAG AAAAA
1 AAAAAG AAAAAG -AAAAAG AAAAAG AA-AAAG AAAAA
741053 AGAGGGGGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
5 12 0.18
6 25 0.38
7 27 0.42
8 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:741040 original size:33 final size:36
Alignment explanation
Indices: 740963--741055 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 36
740953 ATTATGCTTG
740963 AAGAAAAAATGAAAAAAAAGAAGAAGAAGAAAAGAAA
1 AAGAAAAAATGAAAAAAAA-AAGAAGAAGAAAAGAAA
*
741000 AAGAAAAAATGAAAAAAAAAAGAAGAAGAAAA-AAG
1 AAGAAAAAATGAAAAAAAAAAGAAGAAGAAAAGAAA
*
741035 AA-AAAAAA-GAAAGAAAAAAGA
1 AAGAAAAAATGAAAAAAAAAAGA
741056 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 12 0.22
34 6 0.11
35 4 0.07
36 13 0.24
37 19 0.35
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (36 bp):
AAGAAAAAATGAAAAAAAAAAGAAGAAGAAAAGAAA
Found at i:741420 original size:20 final size:22
Alignment explanation
Indices: 741384--741423 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
741374 TATTTATTAA
741384 TAAATTCTAAGTTTATTTTCTC
1 TAAATTCTAAGTTTATTTTCTC
741406 TAAATTC-AA-TTTATTTTC
1 TAAATTCTAAGTTTATTTTC
741424 GAAAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (22 bp):
TAAATTCTAAGTTTATTTTCTC
Found at i:742885 original size:23 final size:22
Alignment explanation
Indices: 742843--742888 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
742833 GTTCATAATG
*
742843 AGAAGAACTCATCTGAAGAAGA
1 AGAAGAACTCATATGAAGAAGA
742865 AGAAGAACTTCATAATG-AGAAGA
1 AGAAGAAC-TCAT-ATGAAGAAGA
742888 A
1 A
742889 CTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 11 0.52
24 2 0.10
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (22 bp):
AGAAGAACTCATATGAAGAAGA
Found at i:743039 original size:112 final size:112
Alignment explanation
Indices: 742600--743031 Score: 729
Period size: 112 Copynumber: 3.9 Consensus size: 112
742590 ATCAACATTT
*
742600 TCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
1 TCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
* * * * *
742665 CTTGTTTAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAACATTT
66 CTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTG
* *
742712 TCGGTTAGAGTTCATAATGAGACGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
1 TCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
*
742777 CTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGTAGTG
66 CTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTG
*
742824 TCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAACTTCATAATGAGAAGAA
1 TCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
*
742889 CTTGTTCAACTTTTTTCTTAAATTCATCACTCGGTGGATCAGCAGTG
66 CTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTG
* * *
742936 CCAGTTAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAA
1 TCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
*
743001 CTTGTTCAACATTTTGCTTAAATTCATCACT
66 CTTGTTCAACTTTTTGCTTAAATTCATCACT
743032 TGATGGATTC
Statistics
Matches: 300, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 300 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (112 bp):
TCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTG
Found at i:743335 original size:3 final size:3
Alignment explanation
Indices: 743329--743405 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
743319 TTCATTTGAA
* * * * *
743329 TAT TAT T-T ATAT TAT TAT TAT AAT TAT AAT AAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
743374 TA- TAT ATAT TAT TA- TAT ATAT TAT TAT TAT TA
1 TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TA
743406 AAAAATAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.08
3 52 0.81
4 7 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:743850 original size:19 final size:19
Alignment explanation
Indices: 743812--743851 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
743802 CCCTGCAAAC
* *
743812 AAAAAAACAGAGAGGGGAG
1 AAAAAAACAGAGAAGAGAG
*
743831 AAAAAAATAGAGAAGAGAG
1 AAAAAAACAGAGAAGAGAG
743850 AA
1 AA
743852 GAAAGAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.30, T:0.03
Consensus pattern (19 bp):
AAAAAAACAGAGAAGAGAG
Found at i:746258 original size:20 final size:20
Alignment explanation
Indices: 746230--746268 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
746220 GATGATACCC
746230 CAATCTAATTTACCCCATTT
1 CAATCTAATTTACCCCATTT
* *
746250 CAATTTAATTTACCTCATT
1 CAATCTAATTTACCCCATT
746269 CGCAAACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.44
Consensus pattern (20 bp):
CAATCTAATTTACCCCATTT
Found at i:759715 original size:20 final size:20
Alignment explanation
Indices: 759692--759743 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
759682 AACGCGATCC
759692 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
759712 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
759732 CCAAAATCGCAA
1 CCAGAATCGCAA
759744 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:759882 original size:60 final size:60
Alignment explanation
Indices: 759799--759991 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
759789 GATTTTCCAT
* ** * *
759799 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
759859 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* ** *
759919 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
759980 AATCGCAACGCG
1 AATCGCAACGCG
759992 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:759893 original size:20 final size:20
Alignment explanation
Indices: 759799--759991 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
759789 GATTTTCCAT
* ** *
759799 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
759819 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
759839 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
759859 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
759879 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
759899 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
759919 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
759939 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
*
759960 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
759980 AATCGCAACGCG
1 AATCGCAACGCG
759992 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:760413 original size:33 final size:33
Alignment explanation
Indices: 760374--760444 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
760364 TTCACTTAGA
*
760374 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
760407 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
760440 TTTCA
1 TTTCA
760445 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:760584 original size:14 final size:14
Alignment explanation
Indices: 760565--760619 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
760555 AGAATGACTG
760565 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
760579 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
760598 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
760612 TCGCAACG
1 TCGCAACG
760620 CGAAACCAAA
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:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Done.