Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold388
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: 417701
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:173547 original size:13 final size:13
Alignment explanation
Indices: 173529--173554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
173519 ACAAAGATCC
173529 ATGTATCGATACA
1 ATGTATCGATACA
173542 ATGTATCGATACA
1 ATGTATCGATACA
173555 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:174183 original size:65 final size:65
Alignment explanation
Indices: 173960--174186 Score: 215
Period size: 65 Copynumber: 3.5 Consensus size: 65
173950 GGTGTCTACA
* * *
173960 TCAACTAAAGGGTGACCAGGACGAAACCTAAGT-GGAAAAGAGTTGACTAGGGCAAAACTAAGAA
1 TCAACT-AAGGGTGACTAGGATGAAACCTAAGTCAGAAAAG-GTTGACTAGGGCAAAACTAA-AA
174024 AAG
63 AAG
* * * * ** * * *
174027 TCAATTAAGAGTGACTAGGATGAAAACTTAAGTCA-AAAGGGTAAACTAGGGCAAAATTAGAATA
1 TCAACTAAGGGTGACTAGGATG-AAACCTAAGTCAGAAAAGGTTGACTAGGGCAAAACTAAAAAA
174091 G
65 G
* ** * ** * *
174092 TCAACTAAGGGTGACTATGAAAAAACCTAAGTCAGAAAAGGTTGACCAGAACAAAACCAAAACAG
1 TCAACTAAGGGTGACTAGGATGAAACCTAAGTCAGAAAAGGTTGACTAGGGCAAAACTAAAAAAG
*
174157 TCAACTAAGGGTAACTAGGATGAAACCTAA
1 TCAACTAAGGGTGACTAGGATGAAACCTAA
174187 AAGTTTGATT
Statistics
Matches: 125, Mismatches: 32, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
64 11 0.09
65 67 0.54
66 29 0.23
67 18 0.14
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (65 bp):
TCAACTAAGGGTGACTAGGATGAAACCTAAGTCAGAAAAGGTTGACTAGGGCAAAACTAAAAAAG
Found at i:177498 original size:21 final size:20
Alignment explanation
Indices: 177442--177499 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
177432 AATCTTTTTG
* *
177442 AAAAGAAAGTTAATGAATTAG
1 AAAAGAAA-ATAATGAATTAC
*
177463 AAAAGAAGATAAATGAATTAC
1 AAAAGAAAAT-AATGAATTAC
*
177484 AAGATGAAAATAATGA
1 AA-AAGAAAATAATGA
177500 GTTAACTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 23 0.77
22 6 0.20
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAAGAAAATAATGAATTAC
Found at i:181664 original size:35 final size:34
Alignment explanation
Indices: 181613--181678 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
181603 CAAGTAATTG
*
181613 AGAGATTCTATCTTAGCCTTTGTAAAAGATAGGAC
1 AGAGATTCTATCTTAGCCTTCG-AAAAGATAGGAC
*
181648 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
1 AGAGATTCTATCTTAGCCTTCGAAAAGATAG
181679 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (34 bp):
AGAGATTCTATCTTAGCCTTCGAAAAGATAGGAC
Found at i:186994 original size:153 final size:153
Alignment explanation
Indices: 186836--187131 Score: 592
Period size: 153 Copynumber: 1.9 Consensus size: 153
186826 AAATTTTTAA
186836 TATTAAAAATTTATGATGAATGTTTTTATTCATATACATGAAAAATTGATAATAAATATTATTCT
1 TATTAAAAATTTATGATGAATGTTTTTATTCATATACATGAAAAATTGATAATAAATATTATTCT
186901 TAAATCTCTCAACCATTGAAAAAATTAAAGATTTTTAGTGATATTTTTCAAAAAATTTCTTGAGG
66 TAAATCTCTCAACCATTGAAAAAATTAAAGATTTTTAGTGATATTTTTCAAAAAATTTCTTGAGG
186966 AATAATTTAATGATGAATGTTTT
131 AATAATTTAATGATGAATGTTTT
186989 TATTAAAAATTTATGATGAATGTTTTTATTCATATACATGAAAAATTGATAATAAATATTATTCT
1 TATTAAAAATTTATGATGAATGTTTTTATTCATATACATGAAAAATTGATAATAAATATTATTCT
187054 TAAATCTCTCAACCATTGAAAAAATTAAAGATTTTTAGTGATATTTTTCAAAAAATTTCTTGAGG
66 TAAATCTCTCAACCATTGAAAAAATTAAAGATTTTTAGTGATATTTTTCAAAAAATTTCTTGAGG
187119 AATAATTTAATGA
131 AATAATTTAATGA
187132 ATTTCATTAA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 143 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (153 bp):
TATTAAAAATTTATGATGAATGTTTTTATTCATATACATGAAAAATTGATAATAAATATTATTCT
TAAATCTCTCAACCATTGAAAAAATTAAAGATTTTTAGTGATATTTTTCAAAAAATTTCTTGAGG
AATAATTTAATGATGAATGTTTT
Found at i:195801 original size:22 final size:24
Alignment explanation
Indices: 195770--195823 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
195760 TTTGTGAAAA
* *
195770 TATTAAATAATTA-AAAAT-TATT
1 TATTATATAATAATAAAATATATT
195792 TATTATATAATAATAAAATATATT
1 TATTATATAATAATAAAATATATT
*
195816 GATTATAT
1 TATTATAT
195824 TATTCTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 11 0.41
23 5 0.19
24 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TATTATATAATAATAAAATATATT
Found at i:201563 original size:6 final size:6
Alignment explanation
Indices: 201552--201588 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
201542 TAAATTTTTT
201552 ATTTAA ATTTAA A-TTAA A-TTAA ATTTAAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA AT
201589 AATTACTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:202681 original size:2 final size:2
Alignment explanation
Indices: 202674--202703 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
202664 CTAGCTTTTA
202674 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
202704 TCATATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203257 original size:20 final size:20
Alignment explanation
Indices: 203232--203275 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
203222 AGTGTTTCTG
203232 TAACAAGTACAGAAATTATC
1 TAACAAGTACAGAAATTATC
203252 TAACAAGTACAGAAATTATC
1 TAACAAGTACAGAAATTATC
203272 TAAC
1 TAAC
203276 CGGCATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (20 bp):
TAACAAGTACAGAAATTATC
Found at i:207199 original size:12 final size:13
Alignment explanation
Indices: 207165--207200 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
207155 AGACCTATGT
207165 AAAA-CATCAGAA
1 AAAATCATCAGAA
207177 AAAATCATCAGAA
1 AAAATCATCAGAA
207190 AAAATC-TCAGA
1 AAAATCATCAGA
207201 CCTAGTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.61, C:0.17, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAATCATCAGAA
Found at i:209045 original size:25 final size:25
Alignment explanation
Indices: 209017--209067 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
209007 TAGTTAAAGA
209017 TTTAAAATTAGAGATTCAATGAGAG
1 TTTAAAATTAGAGATTCAATGAGAG
209042 TTTAAAATTAGAGATTCAATGAGAG
1 TTTAAAATTAGAGATTCAATGAGAG
209067 T
1 T
209068 CATTCTGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (25 bp):
TTTAAAATTAGAGATTCAATGAGAG
Found at i:210086 original size:13 final size:13
Alignment explanation
Indices: 210068--210157 Score: 72
Period size: 13 Copynumber: 6.0 Consensus size: 13
210058 AATTTTTTTG
210068 TGTATCGATACAT
1 TGTATCGATACAT
210081 TGTATCGATACATACTT
1 TGTATCGATAC--A--T
210098 GCTGTATCGATACAT
1 --TGTATCGATACAT
210113 TGTATCGATACATACTT
1 TGTATCGATAC--A--T
210130 GCTGTATCGATACAT
1 --TGTATCGATACAT
210145 TGTATCGATACAT
1 TGTATCGATACAT
210158 ACTTGCTGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 35 0.54
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:210105 original size:19 final size:19
Alignment explanation
Indices: 210081--210175 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
210071 ATCGATACAT
210081 TGTATCGATACATACTTGC
1 TGTATCGATACATACTTGC
210100 TGTATCGATAC--A--T--
1 TGTATCGATACATACTTGC
210113 TGTATCGATACATACTTGC
1 TGTATCGATACATACTTGC
210132 TGTATCGATAC--A--T--
1 TGTATCGATACATACTTGC
210145 TGTATCGATACATACTTGC
1 TGTATCGATACATACTTGC
210164 TGTATCGATACA
1 TGTATCGATACA
210176 AGTTTGGCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 34 0.53
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATACTTGC
Found at i:210109 original size:32 final size:32
Alignment explanation
Indices: 210068--210175 Score: 216
Period size: 32 Copynumber: 3.4 Consensus size: 32
210058 AATTTTTTTG
210068 TGTATCGATACATTGTATCGATACATACTTGC
1 TGTATCGATACATTGTATCGATACATACTTGC
210100 TGTATCGATACATTGTATCGATACATACTTGC
1 TGTATCGATACATTGTATCGATACATACTTGC
210132 TGTATCGATACATTGTATCGATACATACTTGC
1 TGTATCGATACATTGTATCGATACATACTTGC
210164 TGTATCGATACA
1 TGTATCGATACA
210176 AGTTTGGCTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACATACTTGC
Found at i:212570 original size:21 final size:21
Alignment explanation
Indices: 212546--212592 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
212536 TTTGATGCTG
212546 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
212566 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
212587 ATTTTG
1 ATTTTG
212593 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:214798 original size:15 final size:15
Alignment explanation
Indices: 214778--214808 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
214768 ATTTCGTTTG
*
214778 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
214793 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
214808 G
1 G
214809 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:218888 original size:13 final size:13
Alignment explanation
Indices: 218870--218895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
218860 AATTTTTTTG
218870 TGTATCGATACAT
1 TGTATCGATACAT
218883 TGTATCGATACAT
1 TGTATCGATACAT
218896 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:221676 original size:32 final size:32
Alignment explanation
Indices: 221605--221676 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
221595 TTTGAGCAGG
* *
221605 TTTGGGTTTGGGTTCGTTCGGGTTCGAGCTCA
1 TTTGGGTTTGGCTTCGTTCGGGTTCAAGCTCA
* * **
221637 TTCGGGTTTAGGCTT-GTTCGGGTTTAAGCTTT
1 TTTGGGTTT-GGCTTCGTTCGGGTTCAAGCTCA
221669 TTTGGGTT
1 TTTGGGTT
221677 CGAGCTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.07, C:0.12, G:0.35, T:0.46
Consensus pattern (32 bp):
TTTGGGTTTGGCTTCGTTCGGGTTCAAGCTCA
Found at i:221693 original size:16 final size:16
Alignment explanation
Indices: 221621--221718 Score: 74
Period size: 16 Copynumber: 6.1 Consensus size: 16
221611 TTTGGGTTCG
**
221621 TTCGGGTTCGAGCTCA
1 TTCGGGTTCGAGCTTT
* *
221637 TTCGGGTT-TAGGCTTG
1 TTCGGGTTCGA-GCTTT
**
221653 TTCGGGTTTAAGCTTT
1 TTCGGGTTCGAGCTTT
*
221669 TTTGGGTTCGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
221685 TTCGAGTTCG-GACTTA
1 TTCGGGTTCGAG-CTTT
*
221701 TTCGGGTTCGAACTTT
1 TTCGGGTTCGAGCTTT
221717 TT
1 TT
221719 TGAGGTTGGG
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
15 2 0.03
16 61 0.95
17 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (16 bp):
TTCGGGTTCGAGCTTT
Found at i:221717 original size:32 final size:32
Alignment explanation
Indices: 221672--221740 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
221662 AAGCTTTTTT
*
221672 GGGTTCGAGCTTTTTCGA-GTTCGGACTTATTC
1 GGGTTCGAACTTTTTCGAGGTT-GGACTTATTC
* **
221704 GGGTTCGAACTTTTTTGAGGTTGGGTTTATTC
1 GGGTTCGAACTTTTTCGAGGTTGGACTTATTC
221736 GGGTT
1 GGGTT
221741 TGGTTCGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 29 0.91
33 3 0.09
ACGTcount: A:0.12, C:0.13, G:0.32, T:0.43
Consensus pattern (32 bp):
GGGTTCGAACTTTTTCGAGGTTGGACTTATTC
Found at i:221883 original size:18 final size:17
Alignment explanation
Indices: 221856--221889 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
221846 AAAAAATAAA
221856 TTAATAAATTATTATTT
1 TTAATAAATTATTATTT
*
221873 TTAAGTAAATTTTTATT
1 TTAA-TAAATTATTATT
221890 ATACTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAATAAATTATTATTT
Found at i:221935 original size:17 final size:18
Alignment explanation
Indices: 221915--221960 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
221905 TAATATATTT
221915 AATTATTTATTTAT-TAA
1 AATTATTTATTTATATAA
221932 AATTTATATT-TTTATATAA
1 AA-TTAT-TTATTTATATAA
221951 AATTAATTTA
1 AATT-ATTTA
221961 CAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATTTATTTATATAA
Found at i:223140 original size:16 final size:16
Alignment explanation
Indices: 223119--223159 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
223109 TGAGTCAATA
*
223119 TCGGGTTTGAGTTCTC
1 TCGGGTTCGAGTTCTC
*
223135 TCGGGTTCGAGTTCTT
1 TCGGGTTCGAGTTCTC
223151 TCGGGTTCG
1 TCGGGTTCG
223160 GATTTTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.20, G:0.34, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGAGTTCTC
Found at i:223205 original size:16 final size:16
Alignment explanation
Indices: 223119--223217 Score: 51
Period size: 16 Copynumber: 6.2 Consensus size: 16
223109 TGAGTCAATA
*
223119 TCGGGTTTGAG-TTCTC
1 TCGGGTTCGAGCTT-TC
*
223135 TCGGGTTCGAG-TTCTT
1 TCGGGTTCGAGCTT-TC
*
223151 TCGGGTTCG-GATTTTC
1 TCGGGTTCGAG-CTTTC
* * * * *
223167 TTGAGTTTGGGCTGTC
1 TCGGGTTCGAGCTTTC
*
223183 TCAGGTTCGAGCTTTC
1 TCGGGTTCGAGCTTTC
* *
223199 TCGGGTTCAAGCTATC
1 TCGGGTTCGAGCTTTC
223215 TCG
1 TCG
223218 AGTTTGAGTT
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
15 1 0.02
16 59 0.94
17 3 0.05
ACGTcount: A:0.09, C:0.20, G:0.30, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGAGCTTTC
Found at i:230563 original size:33 final size:32
Alignment explanation
Indices: 230521--230583 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
230511 CACCTAGATG
*
230521 TATCGATACATCATGCTTTGTATCAATACATTA
1 TATCGATACATCAT-CATTGTATCAATACATTA
* *
230554 TATCGATACATGATCATTGTATCGATACAT
1 TATCGATACATCATCATTGTATCAATACAT
230584 GGACAATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (32 bp):
TATCGATACATCATCATTGTATCAATACATTA
Found at i:230576 original size:19 final size:18
Alignment explanation
Indices: 230548--230605 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
230538 TTGTATCAAT
*
230548 ACATTATATCGATACATG
1 ACATTGTATCGATACATG
230566 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
230586 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
230605 A
1 A
230606 AACTGGTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 17 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:230594 original size:20 final size:20
Alignment explanation
Indices: 230549--230604 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
230539 TGTATCAATA
*
230549 CATTATATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
230568 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
230587 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
230605 AAACTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:230677 original size:33 final size:33
Alignment explanation
Indices: 230631--230732 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
230621 CCCTATCACT
*
230631 ATTTGTATTGATACATGGTATAATATATCGATAC
1 ATTT-TATCGATACATGGTATAATATATCGATAC
**
230665 ATTTTATCGATACATGGTATAATGCATCGATAC
1 ATTTTATCGATACATGGTATAATATATCGATAC
*
230698 ATTGTATCGATACAT--TATGAATTATATCGATAC
1 ATTTTATCGATACATGGTAT-AA-TATATCGATAC
230731 AT
1 AT
230733 GGCTACGAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
31 3 0.05
32 2 0.03
33 51 0.85
34 4 0.07
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
ATTTTATCGATACATGGTATAATATATCGATAC
Found at i:231026 original size:33 final size:33
Alignment explanation
Indices: 230981--231080 Score: 141
Period size: 33 Copynumber: 3.0 Consensus size: 33
230971 CTATCACTAC
230981 TTGTATCGATACATGGTATAATATATCGATACA
1 TTGTATCGATACATGGTATAATATATCGATACA
* **
231014 TTTTATCGATACATGGTATAATGCATCGATACA
1 TTGTATCGATACATGGTATAATATATCGATACA
231047 TTGTATCGATACAT--TATGAATTATATCGATACA
1 TTGTATCGATACATGGTAT-AA-TATATCGATACA
231080 T
1 T
231081 GGCTACGAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
31 3 0.05
32 2 0.03
33 54 0.92
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGGTATAATATATCGATACA
Found at i:237511 original size:32 final size:33
Alignment explanation
Indices: 237470--237553 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
237460 TTTGTCCAGG
*
237470 ACAGTGATGTATCGATACATG-AATAGTGATGA
1 ACAGTGATGTATCGATACATGAAACAGTGATGA
237502 ACAGTGATGTATCGATACATGAAACAGTGATGA
1 ACAGTGATGTATCGATACATGAAACAGTGATGA
*
237535 ATAGTGATGTATCGATACA
1 ACAGTGATGTATCGATACA
237554 CCAGCGGCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 21 0.43
33 28 0.57
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (33 bp):
ACAGTGATGTATCGATACATGAAACAGTGATGA
Found at i:242232 original size:20 final size:22
Alignment explanation
Indices: 242195--242235 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
242185 TTACAAATTT
*
242195 CATTGTTTTTTACTTCAAAATA
1 CATTGTTTTTTACATCAAAATA
242217 CATTG-TTTTT-CATCAAAAT
1 CATTGTTTTTTACATCAAAAT
242236 CACTAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.49
Consensus pattern (22 bp):
CATTGTTTTTTACATCAAAATA
Found at i:244338 original size:13 final size:13
Alignment explanation
Indices: 244320--244346 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
244310 ATATCATGCT
244320 TTGTATCGATACA
1 TTGTATCGATACA
244333 TTGTATCGATACA
1 TTGTATCGATACA
244346 T
1 T
244347 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:244355 original size:19 final size:18
Alignment explanation
Indices: 244330--244387 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
244320 TTGTATCGAT
244330 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
244348 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
244368 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
244387 A
1 A
244388 AACTGGCAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:244361 original size:32 final size:33
Alignment explanation
Indices: 244301--244365 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
244291 CACACCCAGA
* *
244301 TGTATCGATATATCATGCTTTGTATCGATACAT
1 TGTATCGATACATCATGCATTGTATCGATACAT
*
244334 TGTATCGATACATGAT-CATTGTATCGATACAT
1 TGTATCGATACATCATGCATTGTATCGATACAT
244366 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATCATGCATTGTATCGATACAT
Found at i:244376 original size:20 final size:20
Alignment explanation
Indices: 244331--244386 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
244321 TGTATCGATA
244331 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
244350 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
244369 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
244387 AAACTGGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:244441 original size:20 final size:20
Alignment explanation
Indices: 244416--244453 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
244406 TATCACTGTT
244416 TGTATCAATACATGGTATAA
1 TGTATCAATACATGGTATAA
* *
244436 TGTATCGATACATTGTAT
1 TGTATCAATACATGGTAT
244454 TGATACATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCAATACATGGTATAA
Found at i:249019 original size:13 final size:13
Alignment explanation
Indices: 249001--249027 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
248991 ACATTATGCT
249001 TTGTATCGATACA
1 TTGTATCGATACA
249014 TTGTATCGATACA
1 TTGTATCGATACA
249027 T
1 T
249028 GTTCACTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:249061 original size:20 final size:19
Alignment explanation
Indices: 249011--249147 Score: 73
Period size: 20 Copynumber: 6.9 Consensus size: 19
249001 TTGTATCGAT
*
249011 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* * *
249030 TCACTATATCGATACATGG
1 ACATTGTATCGATACATGG
249049 ACAATTGTATCGATACAT-G
1 AC-ATTGTATCGATACATGG
* * * * *
249068 AGATTGGCAGTAGCTACCCTAT-C
1 ACATT-GTA-TCGATA--C-ATGG
249091 ACTATTTGTATCGATACATGGG
1 AC-A-TTGTATCGATACAT-GG
*
249113 ACAATGTATCGATACAT-G
1 ACATTGTATCGATACATGG
*
249131 AAATTGTATCGATACAT
1 ACATTGTATCGATACAT
249148 TGCTTGTAAC
Statistics
Matches: 88, Mismatches: 20, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
18 19 0.22
19 20 0.23
20 32 0.36
21 2 0.02
22 3 0.03
23 7 0.08
24 3 0.03
25 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:249140 original size:18 final size:20
Alignment explanation
Indices: 249096--249147 Score: 74
Period size: 18 Copynumber: 2.7 Consensus size: 20
249086 CTATCACTAT
249096 TTGTATCGATACATGGGACAA
1 TTGTATCGATACAT-GGACAA
249117 -TGTATCGATACAT-GA-AA
1 TTGTATCGATACATGGACAA
249134 TTGTATCGATACAT
1 TTGTATCGATACAT
249148 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.50
20 13 0.43
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:250288 original size:97 final size:97
Alignment explanation
Indices: 250122--250317 Score: 392
Period size: 97 Copynumber: 2.0 Consensus size: 97
250112 TTGTTTATCC
250122 AAGCAAATGATTATGAGGTATGGAAGATTATTGTAAATGGACCTCGTATTCCCGTCGATAGCACT
1 AAGCAAATGATTATGAGGTATGGAAGATTATTGTAAATGGACCTCGTATTCCCGTCGATAGCACT
250187 GCCGTACCTAAAAGAGAAGAAGATTGGGATGA
66 GCCGTACCTAAAAGAGAAGAAGATTGGGATGA
250219 AAGCAAATGATTATGAGGTATGGAAGATTATTGTAAATGGACCTCGTATTCCCGTCGATAGCACT
1 AAGCAAATGATTATGAGGTATGGAAGATTATTGTAAATGGACCTCGTATTCCCGTCGATAGCACT
250284 GCCGTACCTAAAAGAGAAGAAGATTGGGATGA
66 GCCGTACCTAAAAGAGAAGAAGATTGGGATGA
250316 AA
1 AA
250318 ACGACACGAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (97 bp):
AAGCAAATGATTATGAGGTATGGAAGATTATTGTAAATGGACCTCGTATTCCCGTCGATAGCACT
GCCGTACCTAAAAGAGAAGAAGATTGGGATGA
Found at i:254978 original size:21 final size:21
Alignment explanation
Indices: 254949--254990 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
254939 AAAAAAAAAT
*
254949 TTATCCAAATGTATCGATACA
1 TTATACAAATGTATCGATACA
254970 TTATACAAATGTATCGATACA
1 TTATACAAATGTATCGATACA
254991 AGGTCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
TTATACAAATGTATCGATACA
Found at i:255109 original size:13 final size:13
Alignment explanation
Indices: 255091--255116 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
255081 CATTTTTCTG
255091 TGTATCGATACAT
1 TGTATCGATACAT
255104 TGTATCGATACAT
1 TGTATCGATACAT
255117 CTATTCTTTG
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:255134 original size:34 final size:33
Alignment explanation
Indices: 255072--255137 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
255062 CCAAGGAAAC
*
255072 GTATCGATACATTTTTCTGTGTATCGATACATT
1 GTATCGATACATTATTCTGTGTATCGATACATT
*
255105 GTATCGATACATCTATTCTTTGTATCGATACAT
1 GTATCGATACAT-TATTCTGTGTATCGATACAT
255138 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (33 bp):
GTATCGATACATTATTCTGTGTATCGATACATT
Found at i:257538 original size:51 final size:52
Alignment explanation
Indices: 257482--257864 Score: 219
Period size: 51 Copynumber: 7.3 Consensus size: 52
257472 AATTCTTCGC
* * *
257482 AATCGGGGATATTCTC-ACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTAT
1 AATCGGGGATACTC-CAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-AT
257533 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAT
* * * * *** * ** ** * *
257585 AATCGAGGATACTCCAAC-CTCG-TTGTCTCATCGGGGATAGTCCAACCCCGTTACCT
1 AATCGGGGATACTCCAACTC-CGATTTTAT-TTC-CAAAAACACCAA---TTTTTCAT
**** * ** * * *** *
257641 CCGAGGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAT
* * * * *
257692 AATCGGGGATACTCCAAC-CTCGGTTTTATTT-CTAAAACACTAATTTTGCAC
1 AATCGGGGATACTCCAACTC-CGATTTTATTTCCAAAAACACCAATTTTTCAT
* * * *
257743 AATCGGGGATACTCCAA-TCCCGGTTTTATTTTC-AAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAATTTTTC-AT
* *
257795 AATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAT
*
257847 AATCGAGGATACTCCAAC
1 AATCGGGGATACTCCAAC
257865 CTTGTTATTT
Statistics
Matches: 251, Mismatches: 62, Indels: 37
0.72 0.18 0.11
Matches are distributed among these distances:
50 2 0.01
51 113 0.45
52 82 0.33
53 27 0.11
54 3 0.01
55 2 0.01
56 19 0.08
57 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAT
Found at i:257622 original size:28 final size:28
Alignment explanation
Indices: 257586--257662 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
257576 ATTTTTCATA
* * **
257586 ATCGAGGATACTCCAACCTCGTTGTCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
*
257614 ATCGGGGATAGTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
257642 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
257663 GCTTTATTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:257945 original size:262 final size:261
Alignment explanation
Indices: 257481--257972 Score: 824
Period size: 262 Copynumber: 1.9 Consensus size: 261
257471 CAATTCTTCG
* * * *
257481 CAATCGGGGATATTCTCACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCTCAATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACT
* *
257546 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCATAATCGAGGATACTCCAACCTCGTTGT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
* *
257611 CTCATCGGGGATAGTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
131 CTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
257676 AATATTGATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTGC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTGC
257741 A
261 A
* *
257742 CAATCGGGGATACTC-CAATCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATA
1 CAATCGGGGATACTCTCAAT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGAGGATA
*
257806 CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTTGTT
64 CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTT
* *
257871 ATTTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATATTCCAACCCCGGCTTTATTCCC
129 ATCTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCC
* *
257936 AAAATATTGATTTCTCATAATTGGGGATAGTCCAACC
194 AAAATATTGATTTCTCATAATCGGGGATACTCCAACC
257973 CCGTTATTTC
Statistics
Matches: 214, Mismatches: 15, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
260 3 0.01
261 40 0.19
262 171 0.80
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (261 bp):
CAATCGGGGATACTCTCAATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
CTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTGC
A
Found at i:259714 original size:13 final size:13
Alignment explanation
Indices: 259696--259724 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
259686 ACAACATTCC
259696 TTGTATCGATACA
1 TTGTATCGATACA
259709 TTGTATCGATACA
1 TTGTATCGATACA
259722 TTG
1 TTG
259725 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:261522 original size:66 final size:66
Alignment explanation
Indices: 261432--261575 Score: 274
Period size: 66 Copynumber: 2.2 Consensus size: 66
261422 TGTATAGACA
261432 AAATTTTT-T-TTTCTCGATCTTATTTTTTCTATGACAAAAGGGGGAGAAGATATTGAAAATAAA
1 AAATTTTTATATTTCTCGATCTTATTTTTTCTATGACAAAAGGGGGAGAAGATATTGAAAATAAA
261495 T
66 T
261496 AAATTTTTATATTTCTCGATCTTATTTTTTCTATGACAAAAGGGGGAGAAGATATTGAAAATAAA
1 AAATTTTTATATTTCTCGATCTTATTTTTTCTATGACAAAAGGGGGAGAAGATATTGAAAATAAA
261561 T
66 T
261562 AAATTTTTATATTT
1 AAATTTTTATATTT
261576 GATTAAGGGG
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
64 8 0.10
65 1 0.01
66 69 0.88
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (66 bp):
AAATTTTTATATTTCTCGATCTTATTTTTTCTATGACAAAAGGGGGAGAAGATATTGAAAATAAA
T
Found at i:262268 original size:20 final size:19
Alignment explanation
Indices: 262220--262276 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
262210 TTATATCGAT
*
262220 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
262239 TCACTGTATCGATACATGG
1 ACATTGTATCGATACATGG
262258 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
262277 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:262344 original size:13 final size:13
Alignment explanation
Indices: 262326--262351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
262316 CACGGGACAA
262326 TGTATCGATACAT
1 TGTATCGATACAT
262339 TGTATCGATACAT
1 TGTATCGATACAT
262352 GAGGAAATTG
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262369 original size:34 final size:33
Alignment explanation
Indices: 262305--262373 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 33
262295 CTATCACTAT
262305 TTGTATCGATACACGGGACAATGTATCGATACA
1 TTGTATCGATACACGGGACAATGTATCGATACA
*
262338 TTGTATCGATACATGAGGA-AATTGTATCGATACA
1 TTGTATCGATACACG-GGACAA-TGTATCGATACA
262372 TT
1 TT
262374 ACTTATAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACGGGACAATGTATCGATACA
Found at i:264472 original size:13 final size:13
Alignment explanation
Indices: 264454--264480 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
264444 ATAGTAACCC
264454 ATGTATCGATACA
1 ATGTATCGATACA
264467 ATGTATCGATACA
1 ATGTATCGATACA
264480 A
1 A
264481 GGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:268212 original size:13 final size:13
Alignment explanation
Indices: 268194--268218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
268184 ACACAAAGTA
268194 TGTATCGATACAT
1 TGTATCGATACAT
268207 TGTATCGATACA
1 TGTATCGATACA
268219 CCAAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:268215 original size:32 final size:33
Alignment explanation
Indices: 268174--268241 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
268164 GTAGCCAAAC
**
268174 TTGTATCGATACA-CAAAGTATGTATCGATACA
1 TTGTATCGATACACCAAAAAATGTATCGATACA
268206 TTGTATCGATACACCAAAAAATGTATCGATACA
1 TTGTATCGATACACCAAAAAATGTATCGATACA
268239 TTG
1 TTG
268242 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACACCAAAAAATGTATCGATACA
Found at i:270283 original size:19 final size:19
Alignment explanation
Indices: 270240--270283 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
270230 ATTTAAAACA
*
270240 TAAAAAGACAATCACAAAT
1 TAAAAAGACAATAACAAAT
*
270259 TTAAAAGA-AGATAACAAAT
1 TAAAAAGACA-ATAACAAAT
270278 TAAAAA
1 TAAAAA
270284 TTGTTGCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.66, C:0.09, G:0.07, T:0.18
Consensus pattern (19 bp):
TAAAAAGACAATAACAAAT
Found at i:274422 original size:13 final size:13
Alignment explanation
Indices: 274404--274442 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
274394 ACATCATTCT
*
274404 TTGTATCGATATA
1 TTGTATCGATACA
274417 TTGTATCGATACA
1 TTGTATCGATACA
*
274430 CTGTATCGATACA
1 TTGTATCGATACA
274443 AGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:274591 original size:21 final size:21
Alignment explanation
Indices: 274567--274615 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
274557 AAATCTTTTG
274567 CAAAATT-CTT-GTTTTTCACTT
1 CAAAATTACTTCGTTTTTCA--T
274588 C-AAATTACTTCGTTTTTCAT
1 CAAAATTACTTCGTTTTTCAT
274608 CAAAATTA
1 CAAAATTA
274616 GTTTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.28
21 10 0.40
22 8 0.32
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (21 bp):
CAAAATTACTTCGTTTTTCAT
Found at i:274610 original size:20 final size:19
Alignment explanation
Indices: 274569--274611 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
274559 ATCTTTTGCA
274569 AAATTCTTGTTTTTCACTTC
1 AAATTCTTGTTTTTCAC-TC
274589 AAATTACTTCGTTTTTCA-TC
1 AAATT-CTT-GTTTTTCACTC
274609 AAA
1 AAA
274612 ATTAGTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (19 bp):
AAATTCTTGTTTTTCACTC
Found at i:274925 original size:21 final size:20
Alignment explanation
Indices: 274888--274930 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
274878 GCAGCACCCA
* *
274888 CCAGGTCGCGACTGGCACTC
1 CCAGGTCGCAACGGGCACTC
*
274908 CCAGGTCGCAACCGGGCAGTC
1 CCAGGTCGCAA-CGGGCACTC
274929 CC
1 CC
274931 CACACTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.16, C:0.42, G:0.30, T:0.12
Consensus pattern (20 bp):
CCAGGTCGCAACGGGCACTC
Found at i:276839 original size:13 final size:13
Alignment explanation
Indices: 276821--276846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
276811 TACAGCAAAT
276821 ATGTATCGATACA
1 ATGTATCGATACA
276834 ATGTATCGATACA
1 ATGTATCGATACA
276847 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:276844 original size:32 final size:33
Alignment explanation
Indices: 276803--276866 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
276793 TAGCCAAACT
*
276803 TGTATCGATACAGC-AAATA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAAATTGTATCGATACAA
276835 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
276867 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 16 0.55
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:282991 original size:20 final size:20
Alignment explanation
Indices: 282966--283040 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
282956 TCCAAAATGC
282966 ATCGATACATGTTTCTATGT
1 ATCGATACATGTTTCTATGT
* *
282986 ATCGATACATCTGGAAATTCAATGT
1 ATCGATACA--T-G--TTTCTATGT
* *
283011 ATCGATACATTTTTCTTTGT
1 ATCGATACATGTTTCTATGT
283031 ATCGATACAT
1 ATCGATACAT
283041 TGTATCGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 25 0.57
22 1 0.02
23 2 0.05
25 16 0.36
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (20 bp):
ATCGATACATGTTTCTATGT
Found at i:283045 original size:13 final size:13
Alignment explanation
Indices: 283027--283065 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
283017 ACATTTTTCT
283027 TTGTATCGATACA
1 TTGTATCGATACA
283040 TTGTATCGATACA
1 TTGTATCGATACA
283053 TTGTATCGATACA
1 TTGTATCGATACA
283066 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:285641 original size:13 final size:13
Alignment explanation
Indices: 285623--285648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
285613 TACAGCAAAT
285623 ATGTATCGATACA
1 ATGTATCGATACA
285636 ATGTATCGATACA
1 ATGTATCGATACA
285649 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:285646 original size:32 final size:33
Alignment explanation
Indices: 285605--285668 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
285595 TAGCCAAACT
*
285605 TGTATCGATACAGC-AAATA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAAATTGTATCGATACAA
285637 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
285669 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 16 0.55
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:287383 original size:13 final size:13
Alignment explanation
Indices: 287365--287390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
287355 CAATTTTTTG
287365 TGTATCGATACAT
1 TGTATCGATACAT
287378 TGTATCGATACAT
1 TGTATCGATACAT
287391 ACTTTGGTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:287401 original size:33 final size:33
Alignment explanation
Indices: 287345--287409 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
287335 TACAAGCCAA
* * *
287345 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCAATACAT
287378 TGTATCGATAC-ATACTTTGGTGTATCAATACA
1 TGTATCGATACAAT-CTTTGGTGTATCAATACA
287410 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCAATACAT
Found at i:289966 original size:13 final size:13
Alignment explanation
Indices: 289948--289986 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
289938 ATAATCCCCC
289948 TGTATCGATACAA
1 TGTATCGATACAA
289961 TGTATCGATACAA
1 TGTATCGATACAA
289974 TGTATCGATACAA
1 TGTATCGATACAA
289987 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:293687 original size:13 final size:13
Alignment explanation
Indices: 293669--293694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293659 CAATTTTTTG
293669 TGTATCGATACAT
1 TGTATCGATACAT
293682 TGTATCGATACAT
1 TGTATCGATACAT
293695 ACTTTGGTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:293691 original size:33 final size:33
Alignment explanation
Indices: 293649--293713 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
293639 TACAAGCCAA
* *
293649 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
293682 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
293714 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:294487 original size:32 final size:33
Alignment explanation
Indices: 294443--294510 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
294433 GTAGCCAAAC
** *
294443 TTGTATAGATACA-CAAAGTATGTATCGATACA
1 TTGTATAGATACACCAAAAAATGTATCAATACA
294475 TTGTATCA-ATACACCAAAAAATGTATCAATACA
1 TTGTAT-AGATACACCAAAAAATGTATCAATACA
294508 TTG
1 TTG
294511 CCTTGTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (33 bp):
TTGTATAGATACACCAAAAAATGTATCAATACA
Found at i:297349 original size:20 final size:20
Alignment explanation
Indices: 297304--297355 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
297294 GTAGCCAAAC
**
297304 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
297324 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
297343 TTGTATCGATACA
1 TTGTATCGATACA
297356 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:299699 original size:18 final size:18
Alignment explanation
Indices: 299678--299715 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
299668 ATAAAAATGG
299678 TGTAGGATATAATGCCTT
1 TGTAGGATATAATGCCTT
299696 TGTAGGATATAATGCCTT
1 TGTAGGATATAATGCCTT
299714 TG
1 TG
299716 AAAAATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (18 bp):
TGTAGGATATAATGCCTT
Found at i:303531 original size:13 final size:13
Alignment explanation
Indices: 303513--303538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303503 ACATTTTTCT
303513 TTGTATCGATACA
1 TTGTATCGATACA
303526 TTGTATCGATACA
1 TTGTATCGATACA
303539 GGGGGATTAT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:306118 original size:32 final size:33
Alignment explanation
Indices: 306075--306138 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
306065 TAGCCAAACT
* **
306075 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCAATACACCAAAAATTGTATCGATACAA
306107 TGTATCAATACACCAAAAATTGTATCGATACA
1 TGTATCAATACACCAAAAATTGTATCGATACA
306139 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACCAAAAATTGTATCGATACAA
Found at i:307807 original size:32 final size:34
Alignment explanation
Indices: 307758--307848 Score: 100
Period size: 36 Copynumber: 2.7 Consensus size: 34
307748 CAACACTATC
*
307758 TTTC-AAGGCTAAAATAGAAACCTC-C-CTATC-T
1 TTTCAAAGGCTAAGATAG-AACCTCTCTCTATCTT
**
307789 TTTCACGGGCTAAGATAGAACCTTTCTCTCTATCTT
1 TTTCAAAGGCTAAGATAGAACC--TCTCTCTATCTT
307825 TTTCAAAGGCTAAGATAGAACCTC
1 TTTCAAAGGCTAAGATAGAACCTC
307849 ACAATCACTT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 8 0.16
32 10 0.20
33 2 0.04
34 3 0.06
35 5 0.10
36 21 0.43
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAACCTCTCTCTATCTT
Found at i:308399 original size:32 final size:32
Alignment explanation
Indices: 308316--308440 Score: 135
Period size: 32 Copynumber: 3.8 Consensus size: 32
308306 ACAATATATT
* * *
308316 AATACATGAACAGTTATGAACAGT-AGTGAATTGT
1 AATACATGAACAGTGATGAACAGTGA-TGTA-T-C
* * *
308350 GATACATAAACAATGATGAACAGTGATGTATC
1 AATACATGAACAGTGATGAACAGTGATGTATC
* *
308382 GATACATGAATAGTGATGAACAGTGATGTATC
1 AATACATGAACAGTGATGAACAGTGATGTATC
*
308414 AATACATGAACAGTGATGAATAGTGAT
1 AATACATGAACAGTGATGAACAGTGAT
308441 TAGTTTTATG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 53 0.68
33 1 0.01
34 23 0.29
35 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (32 bp):
AATACATGAACAGTGATGAACAGTGATGTATC
Found at i:308466 original size:13 final size:13
Alignment explanation
Indices: 308448--308472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308438 GATTAGTTTT
308448 ATGTATCGATACA
1 ATGTATCGATACA
308461 ATGTATCGATAC
1 ATGTATCGATAC
308473 TAAGAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:309285 original size:19 final size:20
Alignment explanation
Indices: 309248--309285 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
309238 TCCTGTAGCT
309248 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
309268 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
309286 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:312413 original size:20 final size:19
Alignment explanation
Indices: 312373--312424 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
312363 TAATGCTTTA
* *
312373 TATCGATACATGTTCATTG
1 TATCGATACATGATAATTG
312392 TATCGATACATGCATAATTG
1 TATCGATACATG-ATAATTG
312412 TATCGATACATGA
1 TATCGATACATGA
312425 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (19 bp):
TATCGATACATGATAATTG
Found at i:312491 original size:13 final size:13
Alignment explanation
Indices: 312473--312497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312463 CTTGGCACAT
312473 TGTATCGATACAA
1 TGTATCGATACAA
312486 TGTATCGATACA
1 TGTATCGATACA
312498 TAACAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:318646 original size:11 final size:10
Alignment explanation
Indices: 318612--318644 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
318602 AATCAAATTG
318612 AAAAG-AAAA
1 AAAAGAAAAA
*
318621 AAATGAAAAA
1 AAAAGAAAAA
318631 AAAAGAAAAA
1 AAAAGAAAAA
318641 AAAA
1 AAAA
318645 AGGATGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:318781 original size:20 final size:19
Alignment explanation
Indices: 318756--318795 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
318746 GGAACATGGA
318756 AAGAAAAAAGAAAAAAAATG
1 AAGAAAAAA-AAAAAAAATG
* *
318776 AAGAAAGAAAAAAAAGATG
1 AAGAAAAAAAAAAAAAATG
318795 A
1 A
318796 TGGACGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAGAAAAAAAAAAAAAATG
Found at i:323359 original size:22 final size:21
Alignment explanation
Indices: 323334--323381 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
323324 ATGAGCCCTA
* * *
323334 TTGTATACATTTGTTTATATTT
1 TTGTATAAATTT-TGTATATCT
323356 TTGTTATAAATTTTGTATATCT
1 TTG-TATAAATTTTGTATATCT
323378 TTGT
1 TTGT
323382 TTGATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 13 0.59
23 8 0.36
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.62
Consensus pattern (21 bp):
TTGTATAAATTTTGTATATCT
Found at i:337530 original size:1 final size:1
Alignment explanation
Indices: 337526--337565 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
337516 CATCCTCCAC
* * *
337526 AAAAAAAAAAAAAACAAAAACAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
337566 GGGTCCGGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:337545 original size:16 final size:16
Alignment explanation
Indices: 337526--337565 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
337516 CATCCTCCAC
337526 AAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAACA
*
337542 AAAACAAAAAAAAACA
1 AAAAAAAAAAAAAACA
337558 AAAAAAAA
1 AAAAAAAA
337566 GGGTCCGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAACA
Found at i:337548 original size:21 final size:20
Alignment explanation
Indices: 337524--337565 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
337514 GGCATCCTCC
337524 ACAAAAAAAAAAAAAACAAAA
1 ACAAAAAAAAAAAAAA-AAAA
337545 ACAAAAAAAAACAAAAAAAAA
1 ACAAAAAAAAA-AAAAAAAAA
337566 GGGTCCGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (20 bp):
ACAAAAAAAAAAAAAAAAAA
Found at i:338985 original size:29 final size:30
Alignment explanation
Indices: 338946--339241 Score: 169
Period size: 30 Copynumber: 9.7 Consensus size: 30
338936 TCACCCTTCA
* *
338946 AAAGTCCACAAGTCAGTGGC-TTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAATCTTTTTC
* *
338975 AAAGCCCACAAGTCAGTGGCATTTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-ATCTTTTTC
*
339006 AAAAGCCCACAAGTCAGTGGCAA-C--CTTC
1 -AAAGCCCACAAGTCAGTGGCAATCTTTTTC
* **
339034 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAATCTTTTTC
* * *
339064 GAAGCCCACAAGTCGGTGGC-ATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAATCTTTTTC
* * * *
339093 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAATCTTTTTC
* * * *
339123 TTTTGTAAGCTCACAACTCTA-TGGCACTCTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCAATCTTTTTC
* * * *
339158 TTTTTAAGCCCACAAGTTAGTGGC-ACCCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCAATCTTTTTC
* * *
339191 AAAAGCCCATAAGTCAGTGGCAA-C-CTTTA
1 -AAAGCCCACAAGTCAGTGGCAATCTTTTTC
*
339220 AAAGCCCACAAGTCAGTAGCAA
1 AAAGCCCACAAGTCAGTGGCAA
339242 CCTTCAAAAG
Statistics
Matches: 213, Mismatches: 39, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
27 20 0.09
28 24 0.11
29 44 0.21
30 45 0.21
31 9 0.04
32 21 0.10
33 7 0.03
34 18 0.08
35 25 0.12
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCAATCTTTTTC
Found at i:339054 original size:59 final size:59
Alignment explanation
Indices: 338942--339122 Score: 177
Period size: 59 Copynumber: 3.1 Consensus size: 59
338932 TTCCTCACCC
* ** * * ***
338942 TTCAAAAGTCCACAAGTCAGTGGCTTCTTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAAATCAGTGGCA-CCCTTT
339003 TTCAAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCTTT
* * * * * * * *
339061 TTC-GAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTCTT-CAAAGCCCACAAATCAGTGGCACCCTTT
339120 TTC
1 TTC
339123 TTTTGTAAGC
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
57 20 0.20
58 8 0.08
59 50 0.49
61 24 0.24
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCTTT
Found at i:339172 original size:34 final size:35
Alignment explanation
Indices: 339098--339189 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
339088 TTTCCAAAGT
**
339098 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTATGGCACTCTTTTTCTTTTGTAAGC
*
339133 TCACAACTCTATGGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTATGGCACTCTTTTTCTTTTGTAAGC
* *
339167 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTA-TGGCACTCTTTT
339190 CAAAAGCCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 2 0.04
34 22 0.44
35 26 0.52
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (35 bp):
CCACAACTCTATGGCACTCTTTTTCTTTTGTAAGC
Found at i:339197 original size:30 final size:29
Alignment explanation
Indices: 339163--339260 Score: 128
Period size: 28 Copynumber: 3.4 Consensus size: 29
339153 TTTTCTTTTT
* *
339163 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
*
339193 AAGCCCATAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
339221 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
339249 AAGCACACAAGT
1 AAGCCCACAAGT
339261 TGATGCAAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.03
28 36 0.59
29 3 0.05
30 20 0.33
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:339375 original size:48 final size:47
Alignment explanation
Indices: 339306--339487 Score: 207
Period size: 48 Copynumber: 4.0 Consensus size: 47
339296 GGCGTCTCCT
*
339306 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CC
* * *
339354 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC--C
* * *
339403 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA----CC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCC
* *
339446 TTTAAGTCCAATGTCGCTGGCCTTGAATCA-C--ATTGGCACCTT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
339488 TATCTTCGAG
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
40 7 0.06
42 1 0.01
43 28 0.24
45 1 0.01
47 1 0.01
48 42 0.36
49 36 0.31
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (47 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCC
Found at i:339470 original size:43 final size:40
Alignment explanation
Indices: 339403--339489 Score: 129
Period size: 43 Copynumber: 2.1 Consensus size: 40
339393 CACCTTCATA
339403 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATGTAGCTGACCTTGAAT---CACATTGGCACC
* *
339446 TTTAAGTCCAATGTCGCTGGCCTTGAATCACATTGGCACC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCACATTGGCACC
339486 TTTA
1 TTTA
339490 TCTTCGAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
40 16 0.38
43 26 0.62
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (40 bp):
TTTAAGTCCAATGTAGCTGACCTTGAATCACATTGGCACC
Found at i:340272 original size:13 final size:13
Alignment explanation
Indices: 340254--340278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340244 CATAAAGTAT
340254 TGTATCGATACAA
1 TGTATCGATACAA
340267 TGTATCGATACA
1 TGTATCGATACA
340279 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:340276 original size:33 final size:33
Alignment explanation
Indices: 340234--340300 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
340224 TTCAATGATT
340234 TGTATCGATACATAAAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
*** *
340267 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
340300 T
1 T
340301 TCAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTATTGTATCGATACAA
Found at i:340359 original size:13 final size:13
Alignment explanation
Indices: 340341--340366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340331 ATCACTTAAA
340341 TGTATCGATACAT
1 TGTATCGATACAT
340354 TGTATCGATACAT
1 TGTATCGATACAT
340367 GCAGGCAAAT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:340432 original size:52 final size:52
Alignment explanation
Indices: 340354--340482 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
340344 ATCGATACAT
* *
340354 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
340406 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
340458 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
340483 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:344282 original size:18 final size:18
Alignment explanation
Indices: 344261--344301 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
344251 TTCTCTAAAT
* *
344261 AAAAAATAAAAAAGA-GA
1 AAAAAAGAAAAAACATGA
344278 AAAAAAGAAAAAACATGA
1 AAAAAAGAAAAAACATGA
344296 AAAAAA
1 AAAAAA
344302 AGATGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAAGAAAAAACATGA
Found at i:352181 original size:108 final size:111
Alignment explanation
Indices: 352027--352259 Score: 436
Period size: 108 Copynumber: 2.1 Consensus size: 111
352017 TAATTTGATG
352027 AAAAATCATAAATCCATGCTAATCTTTATTGATCGAGGTTAACATAAATTTAGCTTGGGGAGGAT
1 AAAAATCATAAATCCATGCTAATCTTTATTGATCGAGGTTAACATAAATTTAGCTTGGGGAGGAT
352092 TTTC-AA-ATATATATGCATAAAACAAGCAAATATGTTAATAAT-A
66 TTTCAAATATATATATGCATAAAACAAGCAAATATGTTAATAATAA
352135 AAAAATCATAAATCCATGCTAATCTTTATTGATCGAGGTTAACATAAATTTAGCTTGGGGAGGAT
1 AAAAATCATAAATCCATGCTAATCTTTATTGATCGAGGTTAACATAAATTTAGCTTGGGGAGGAT
352200 TTTCAAATATATATATGCATAAAACAAGCAAATATGTTAATAATAA
66 TTTCAAATATATATATGCATAAAACAAGCAAATATGTTAATAATAA
*
352246 AAAAATCAAAAATC
1 AAAAATCATAAATC
352260 AAATGCAAAC
Statistics
Matches: 121, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
108 69 0.57
109 2 0.02
110 36 0.30
111 14 0.12
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (111 bp):
AAAAATCATAAATCCATGCTAATCTTTATTGATCGAGGTTAACATAAATTTAGCTTGGGGAGGAT
TTTCAAATATATATATGCATAAAACAAGCAAATATGTTAATAATAA
Found at i:352664 original size:89 final size:91
Alignment explanation
Indices: 352563--352738 Score: 284
Period size: 92 Copynumber: 1.9 Consensus size: 91
352553 CCCAGGCCAC
**
352563 TCCATTTTCTTTTTTTTCTTTCATCTTCTTCTTC-T-TTACTTCTTCTTCCTTCTTTCTTACCAA
1 TCCATTTTCTTTTTTTTCTTTCATCTTCTTCTTCTTATTACTTCTTCTTCCTTCTTTCACACCAA
*
352626 TAACCACCCATACCTAGACCAACCAT
66 TAACCACCCATAACTAGACCAACCAT
* *
352652 TCCATTTTCTTTTTTTTCTTTCATCTTCTTCTTCTTCATTCCTTTTTCTTCCTTCTTTCACACCA
1 TCCATTTTCTTTTTTTTCTTTCATCTTCTTCTTCTT-ATTACTTCTTCTTCCTTCTTTCACACCA
352717 ATAACCACCCATAACTAGACCA
65 ATAACCACCCATAACTAGACCA
352739 TGACAGGAGA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 34 0.43
90 1 0.01
92 44 0.56
ACGTcount: A:0.18, C:0.32, G:0.01, T:0.48
Consensus pattern (91 bp):
TCCATTTTCTTTTTTTTCTTTCATCTTCTTCTTCTTATTACTTCTTCTTCCTTCTTTCACACCAA
TAACCACCCATAACTAGACCAACCAT
Found at i:353394 original size:17 final size:18
Alignment explanation
Indices: 353372--353405 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
353362 CCACTCATTC
353372 TTTTTTTTGT-TTTTTTA
1 TTTTTTTTGTATTTTTTA
353389 TTTTTTTTGTATTTTTT
1 TTTTTTTTGTATTTTTT
353406 CAATTAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (18 bp):
TTTTTTTTGTATTTTTTA
Found at i:354465 original size:19 final size:19
Alignment explanation
Indices: 354441--354491 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
354431 TTTCAACGAT
*
354441 TTGTATCAATACATAAGTG
1 TTGTATCGATACATAAGTG
*
354460 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
354479 TTGTATCGATACA
1 TTGTATCGATACA
354492 ATATAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:354623 original size:52 final size:52
Alignment explanation
Indices: 354567--354688 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
354557 TACTGATCTT
354567 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
* *
354619 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
*
354671 TGTATCGATACAAGCAGG
1 TGTATCGATACATGCAGG
354689 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
Found at i:360563 original size:49 final size:49
Alignment explanation
Indices: 360186--360945 Score: 763
Period size: 43 Copynumber: 16.1 Consensus size: 49
360176 CTTAGGAATG
* *
360186 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
** **
360235 TTAAAGATGACAAAGACGCCAATATGCTGATTCAAGGCCAGGGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
360287 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCTAG-TGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGAC
* *
360339 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * *
360391 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
360434 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAG-TGATATTAGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGAC
* * *
360484 TT----A-G-AGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * *
360527 TTAAAGATGATGGTGCCAATATGCTGATTAAAGGCCAGCGATATTAGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
360576 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAATGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
360619 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
360668 TT----A--AAGGTGCCAATGCT-CTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAAT-ATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
360711 TTTAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
360760 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
360803 TTAAA-AAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
360851 TT----A--AAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
360894 TTAAAGATGAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
360943 TTA
1 TTA
360946 GAAAGGTTGC
Statistics
Matches: 604, Mismatches: 62, Indels: 90
0.80 0.08 0.12
Matches are distributed among these distances:
43 222 0.37
44 3 0.00
45 5 0.01
46 1 0.00
47 4 0.01
48 44 0.07
49 155 0.26
50 35 0.06
52 135 0.22
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
Found at i:360576 original size:92 final size:92
Alignment explanation
Indices: 360298--360945 Score: 1005
Period size: 92 Copynumber: 7.0 Consensus size: 92
360288 TAAAGATGAC
* * * * *
360298 AAAGGCGCCAATATGCTGATTCAAGGCTAG-TGATATTGGACTTAAAGATGACAAAGGCGCCAAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCT-ACATTGGACTTAAAGATG---AAGGTGCCAAT
360362 ATGCTGATTCAAGGCCAGCGATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
360393 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATGAAGGTGCCAATATG
* *
360458 CTGATTCAAGGCCAGTGATATTAGACTT
65 CTGATTCAAGGCCAGCGATATTGGACTT
* * *
360486 AGAGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
360551 TGATTAAAGGCCAGCGATATTAGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
360578 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAATGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
360643 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
360670 AAAGGTGCCAATGCT-CTGATTCAAGGCCAGCTACATTGGACTTTAAGATGAAGGTGCCAATATG
1 AAAGGTGCCAATG-TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
*
360734 CTGATTCAAGGCCAGCGATATTGGGCTT
65 CTGATTCAAGGCCAGCGATATTGGACTT
*
360762 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
360826 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
360853 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
360918 TGATCCAAGGCCAGCGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
360945 A
1 A
360946 GAAAGGTTGC
Statistics
Matches: 511, Mismatches: 37, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
91 88 0.17
92 302 0.59
93 78 0.15
95 36 0.07
96 7 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:360707 original size:184 final size:184
Alignment explanation
Indices: 360195--360945 Score: 1060
Period size: 184 Copynumber: 4.0 Consensus size: 184
360185 GTTAAAGATG
* **
360195 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGACGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGCCAATAT
** * *
360260 GCTGATTCAAGGCCAGGGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGC
63 GCTGATTCAAGGCCAGCTATATTGGAC-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGC
* * *
360325 TAG-TGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGG
119 CAGCT-ACATTGGACTTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
360389 ACTTA
180 ACTTA
* *
360394 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATGC
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGAAGGTGCCAATATGC
* * *
360459 TGATTCAAGGCCAG-TGATATTAGACTTAGAGTTGCCAATGTGCTGATTCAAGGCCAGCTACATT
65 TGATTCAAGGCCAGCT-ATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
* * *
360523 GGACTTAAAGATGATGGTGCCAATATGCTGATTAAAGGCCAGCGATATTAGACTTA
129 GGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
* *
360579 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAATGGACTTAAAGATGAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCT
360644 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGCT-CTGATTCAAGGCCAGCTACATTG
66 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATG-TGCTGATTCAAGGCCAGCTACATTG
* *
360708 GACTTTAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
130 GACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
* *
360763 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AAGAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCT
*
360827 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGG
66 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
* *
360892 ACTTAAAGATGAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGGCTTA
131 ACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
360946 GAAAGGTTGC
Statistics
Matches: 512, Mismatches: 34, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
182 1 0.00
183 132 0.26
184 173 0.34
185 80 0.16
188 42 0.08
189 1 0.00
191 1 0.00
196 1 0.00
197 34 0.07
199 40 0.08
200 7 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (184 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
ACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
Found at i:360857 original size:22 final size:21
Alignment explanation
Indices: 360832--360899 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
360822 ATGCTGATTC
360832 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
360854 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
360875 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
360897 AAG
1 AAG
360900 ATGAAGGTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:360984 original size:33 final size:33
Alignment explanation
Indices: 360945--361041 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
360935 TATTGGGCTT
360945 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
360978 AGAAAGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
361010 AGAAGGGTTACCACCAACTTGTGTGGGCTTTA
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
361042 AAAAGGGTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.48
33 31 0.52
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (33 bp):
AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:361081 original size:34 final size:33
Alignment explanation
Indices: 361051--361784 Score: 473
Period size: 32 Copynumber: 22.8 Consensus size: 33
361041 AAAAAGGGTG
*
361051 AAAGATGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
361084 CAAGGTGCCATGAAGTTGTGGACTTTAAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* * **
361119 AAAGAGTGCCATGGAGTTGTGGGCTTTGAA--AA
1 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
361151 GAAGGTGCCACGGAGTCGTGGACTTAAAAGTAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
361184 CAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGA
1 AAAGATGCCACGGAGTTGTGGAC-TTAAAA-GGAA
*
361219 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
361253 AAAGAGTGCCACGGAGTTGCGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGAA
* *
361288 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
*
361321 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
*
361353 ---G-TGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
*
361382 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
361414 ---G-TGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
361443 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGAA
* *
361478 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
** * ** *
361511 AAA-ATGCCATTGAGTCGTGGACTT-TGA-GAC
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
361541 AAA-ATGCCACTGAGTCGTGGACTTTAAA-GAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * ** *
361572 AAGGATGCCACTGAGTCGTGGACTT-TGA-GAC
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
** * **
361603 AAA-ATGCCACTAAGTCGTGGACTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* ** * ** *
361634 AAGGATGCCACTAAGTCGTGGACTTTGAA--AC
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* ** **
361665 AAA-ATGCCACTGAGTCATGGACTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * **
361696 AAGGATGCCACTGAGTCGTGGACTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * **
361728 AAGGATGCCACTGAGTCGTGGACTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
361760 AAGGATGCCACTGAGTCGTGGACTT
1 AAAGATGCCACGGAGTTGTGGACTT
361785 TGAGCAGAGA
Statistics
Matches: 591, Mismatches: 79, Indels: 63
0.81 0.11 0.09
Matches are distributed among these distances:
27 49 0.08
29 2 0.00
30 68 0.12
31 41 0.07
32 154 0.26
33 65 0.11
34 131 0.22
35 48 0.08
36 33 0.06
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:361350 original size:27 final size:27
Alignment explanation
Indices: 361320--361439 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 27
361310 CTTAGAAGGA
*
361320 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
*
361347 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
*
361374 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
*
361408 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
361435 AAAAG
1 AAAAG
361440 GAAAAAGAGT
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
27 55 0.69
34 25 0.31
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:361386 original size:61 final size:61
Alignment explanation
Indices: 361286--361513 Score: 366
Period size: 61 Copynumber: 3.6 Consensus size: 61
361276 CTTTAAAAAG
*
361286 AAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
361347 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
361408 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
361470 AAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAA
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAA
361514 ATGCCATTGA
Statistics
Matches: 156, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
61 117 0.75
62 2 0.01
63 5 0.03
68 32 0.21
ACGTcount: A:0.34, C:0.12, G:0.35, T:0.19
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:361485 original size:190 final size:195
Alignment explanation
Indices: 361051--361597 Score: 638
Period size: 190 Copynumber: 2.8 Consensus size: 195
361041 AAAAAGGGTG
* * * * * *
361051 AAAGA-TGCCACGAAGTTGTGGAC-TTAAAAGGAACAAGGTGCCATGAAGTTGTGGACTTTAAAA
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT-AGA
*
361114 AGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAA
63 AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG-AGGTGCCACGGAGTCGTGGACTTAAA
* * *
361179 AGTAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGACT
127 AGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA--GG---AGAGTGCCACGGAGTTGTGGACT
*
361244 TAGAAGGAA
187 TAAAAGGAA
*
361253 AAAGAGTGCCACGGAGTTGCGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCAC-GAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAG
* *
361318 GAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAG-GGTGCCACGGAGTTGTGGACTTAGAAGG
65 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAGGTGCCACGGAGTCGTGGACTTAAAAGG
*
361380 AAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-G-G-GTGCCACGGAGTTGTGGACTTAAAAGG
130 AAAAAG-GTGCCACGGAGTTGTGGACTTTAAAAGGAGAGTGCCACGGAGTTGTGGACTTAAAAGG
361441 AA
194 AA
361443 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCAC-GAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAG
** * * * * *
361508 GAAAAA-A-TGCCATTGAGTCGTGGACTTTGAGACAA-A-ATGCCACTGAGTCGTGGACTTTAAA
65 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA-A-AAGAGGTGCCACGGAGTCGTGGACTTAAAA
* *
361569 -G-AAAAGGATGCCACTGAGTCGTGGACTTT
128 GGAAAAAGG-TGCCACGGAGTTGTGGACTTT
361598 GAGACAAAAT
Statistics
Matches: 305, Mismatches: 29, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
188 15 0.05
189 23 0.08
190 101 0.33
191 22 0.07
192 2 0.01
195 1 0.00
198 36 0.12
199 17 0.06
200 5 0.02
201 2 0.01
202 35 0.11
203 16 0.05
204 30 0.10
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (195 bp):
AAAGAGTGCCACGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGG
AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAGGTGCCACGGAGTCGTGGACTTAAAAGGA
AAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:361531 original size:32 final size:31
Alignment explanation
Indices: 361473--361914 Score: 484
Period size: 32 Copynumber: 14.2 Consensus size: 31
361463 GGGCTTTAAA
* * * *
361473 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAG
1 AAGAAAAA-ATGCCACTGAGTCGTGGACTTTG
*
361505 AAGGAAAAAATGCCATTGAGTCGTGGACTTTG
1 AA-GAAAAAATGCCACTGAGTCGTGGACTTTG
* *
361537 -AGACAAAATGCCACTGAGTCGTGGACTTTA
1 AAGAAAAAATGCCACTGAGTCGTGGACTTTG
*
361567 AAGAAAAGGATGCCACTGAGTCGTGGACTTTG
1 AAGAAAA-AATGCCACTGAGTCGTGGACTTTG
* *
361599 -AGACAAAATGCCACTAAGTCGTGGACTTTG
1 AAGAAAAAATGCCACTGAGTCGTGGACTTTG
* *
361629 AAGAAAAGGATGCCACTAAGTCGTGGACTTTG
1 AAGAAAA-AATGCCACTGAGTCGTGGACTTTG
* *
361661 AA-ACAAAATGCCACTGAGTCATGGACTTTG
1 AAGAAAAAATGCCACTGAGTCGTGGACTTTG
*
361691 AAGAAAAGGATGCCACTGAGTCGTGGACTTTG
1 AAGAAAA-AATGCCACTGAGTCGTGGACTTTG
*
361723 AAGAAAAGGATGCCACTGAGTCGTGGACTTTG
1 AAGAAAA-AATGCCACTGAGTCGTGGACTTTG
*
361755 AAGAAAAGGATGCCACTGAGTCGTGGACTTTG
1 AAGAAAA-AATGCCACTGAGTCGTGGACTTTG
* * *
361787 -AGCAGAGATTGCCACTGAGTCGTGGACTTTG
1 AAG-AAAAAATGCCACTGAGTCGTGGACTTTG
* * *
361818 ATGAAAAGGATGCCACTAAGTCGTGGACTTTG
1 AAGAAAA-AATGCCACTGAGTCGTGGACTTTG
* * * *
361850 -AGACAAAATGCCATTGAGTCATGGGCTTT-
1 AAGAAAAAATGCCACTGAGTCGTGGACTTTG
* *
361879 AAGAAGAGATTGCCACTGAGTCGTGGACTTT-
1 AAGAA-AAAATGCCACTGAGTCGTGGACTTTG
361910 AAGAA
1 AAGAA
361915 GGTATTTGAC
Statistics
Matches: 352, Mismatches: 46, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
30 92 0.26
31 77 0.22
32 177 0.50
33 6 0.02
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.23
Consensus pattern (31 bp):
AAGAAAAAATGCCACTGAGTCGTGGACTTTG
Found at i:361580 original size:62 final size:62
Alignment explanation
Indices: 361483--361909 Score: 603
Period size: 62 Copynumber: 6.9 Consensus size: 62
361473 AAGAAAAAGG
* * * * *
361483 TGCCACGGAGTTGTGGACTTAGAAGGAAAA-AATGCCATTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAA-GAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAA
*
361545 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAA
* * *
361607 TGCCACTAAGTCGTGGACTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTTGAAACAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAA
*
361669 TGCCACTGAGTCATGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAAGA-AAAGGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTG-AGACAAA--A
*
361733 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
* *
361796 TGCCACTGAGTCGTGGACTTTGATGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAA
* * * *
361858 TGCCATTGAGTCATGGGCTTT-AAGAAGA-GATTGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA-TGCCACTGAGTCGTGGACTTT
361910 AAGAAGGTAT
Statistics
Matches: 331, Mismatches: 25, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
60 2 0.01
61 30 0.09
62 181 0.55
63 60 0.18
64 57 0.17
65 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:368812 original size:52 final size:52
Alignment explanation
Indices: 368734--368852 Score: 220
Period size: 52 Copynumber: 2.3 Consensus size: 52
368724 AAGTTGTCTA
*
368734 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTG
1 CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTG
*
368786 CATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTG
1 CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTG
368838 CATGTATCGATACAT
1 CATGTATCGATACAT
368853 AGATCAGTGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTG
Found at i:368864 original size:52 final size:51
Alignment explanation
Indices: 368734--368871 Score: 206
Period size: 52 Copynumber: 2.6 Consensus size: 51
368724 AAGTTGTCTA
368734 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTG
1 CATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCCTG
* *
368786 CATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTG
1 CATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCCTG
*
368838 CATGTATCGATACA-TAGATCAGTGTATAGATACA
1 CATGTATCGATACATTA-AT-AGTGTATCGATACA
368872 ATGTATCGAT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
50 1 0.01
51 2 0.03
52 76 0.96
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
CATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGCCTG
Found at i:368964 original size:13 final size:13
Alignment explanation
Indices: 368946--368970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
368936 ACAAAACTTA
368946 TGTATCGATACAT
1 TGTATCGATACAT
368959 TGTATCGATACA
1 TGTATCGATACA
368971 AATCGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:373009 original size:26 final size:28
Alignment explanation
Indices: 372954--373021 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
372944 GTTCTTTTCC
*
372954 AAAAAAAAGAAACAAAACAAAATAGGAAA
1 AAAAAAAAGAAACAAAACAAAACA-GAAA
*
372983 AAAAAAGAAGAAAC-AAAC-AAACAAAAA
1 AAAAAA-AAGAAACAAAACAAAACAGAAA
373010 AAAAAAAAGAAA
1 AAAAAAAAGAAA
373022 GGAAAAACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 6 0.17
27 9 0.25
28 4 0.11
29 10 0.28
30 7 0.19
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.01
Consensus pattern (28 bp):
AAAAAAAAGAAACAAAACAAAACAGAAA
Found at i:374064 original size:32 final size:32
Alignment explanation
Indices: 373959--374212 Score: 199
Period size: 32 Copynumber: 8.2 Consensus size: 32
373949 GTCAAATACC
*
373959 TTCTT-AAAGTCCACGACTCAGTGGCAATC-TC
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTTT
* *
373990 TTC-TCAACGCCCACGACTCAGTGGCAT-TTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
*
374020 GTC-TCAAAGTCCACGACTCAGT-GCAATCTTT
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTTT
374051 TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
* **
374083 TGTCTT-AAAGTCCACGACTTAGTGGCATCCAT
1 T-TCTTCAAAGTCCACGACTCAGTGGCATCTTT
* * * * **
374115 TTCTGCAAAGTCTACAACTCCGTGGCA-C-CC
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
* * *
374145 TT-TT--AAGCCCACAACTCTGTGGCACTCTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCA-TCTTT
* * * *
374175 TTCTTTCTAAGTCCACAACTCTGTGGCACCTTT
1 TTC-TTCAAAGTCCACGACTCAGTGGCATCTTT
374208 TTCTT
1 TTCTT
374213 TTTAAGGCCT
Statistics
Matches: 183, Mismatches: 25, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
27 17 0.09
29 4 0.02
30 29 0.16
31 30 0.16
32 71 0.39
33 13 0.07
34 19 0.10
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (32 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
Found at i:374166 original size:27 final size:27
Alignment explanation
Indices: 374128--374303 Score: 109
Period size: 34 Copynumber: 5.8 Consensus size: 27
374118 TGCAAAGTCT
*
374128 ACAACTCCGTGGCACCCTTTTAAGCCC
1 ACAACTCTGTGGCACCCTTTTAAGCCC
*
374155 ACAACTCTGTGGCACTCTTTTTCTTTCTAAGTCC
1 ACAACTCTGTGGCAC-C-----CTTT-TAAGCCC
*
374189 ACAACTCTGTGGCACCTTTTTCTTTTTAAGGCCT
1 ACAACTCTGTGGCACC-----C-TTTTAA-GCCC
* *
374223 ACAACCCTGTGGCATCCTGTTCCTTTTAAGTCC
1 ACAACTCTGTGGCA--C----CCTTTTAAGCCC
*
374256 ACAACTCCGTGGCACCCTTTTAAGCCC
1 ACAACTCTGTGGCACCCTTTTAAGCCC
*
374283 ACAACTCTGTGGCACTCTTTT
1 ACAACTCTGTGGCACCCTTTT
374304 CCCCTTTTAA
Statistics
Matches: 122, Mismatches: 12, Indels: 30
0.74 0.07 0.18
Matches are distributed among these distances:
27 44 0.36
28 1 0.01
31 1 0.01
33 28 0.23
34 45 0.37
35 1 0.01
36 1 0.01
40 1 0.01
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.34
Consensus pattern (27 bp):
ACAACTCTGTGGCACCCTTTTAAGCCC
Done.