Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 11 of 202
Found at i:3657684 original size:5 final size:5
Alignment explanation
Indices: 3657674--3657699 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3657664 TGAGCATTTG
3657674 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
3657700 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:3658204 original size:19 final size:19
Alignment explanation
Indices: 3658171--3658218 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3658161 TAAACAATTC
3658171 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
3658188 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
3658207 AATAATATAAAT
1 AATAATATAAAT
3658219 CGTATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:3658570 original size:9 final size:9
Alignment explanation
Indices: 3658556--3658592 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3658546 TATAGTTTGA
3658556 TATTCGAAT
1 TATTCGAAT
3658565 TATTCGAAT
1 TATTCGAAT
*
3658574 TATTCGAGT
1 TATTCGAAT
3658583 TATTCGAAT
1 TATTCGAAT
3658592 T
1 T
3658593 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3665548 original size:19 final size:20
Alignment explanation
Indices: 3665511--3665550 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3665501 TCTTTTCGCA
* *
3665511 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
3665531 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
3665550 T
1 T
3665551 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:3669755 original size:44 final size:44
Alignment explanation
Indices: 3669707--3670468 Score: 264
Period size: 44 Copynumber: 17.3 Consensus size: 44
3669697 ATTGGCGTGA
* * *
3669707 AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGTAGTAGTAG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* ** * * * *
3669751 AGTAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCT-AGG-CAGCAGTGG
* * *
3669796 AGTACATTGAAG-CTAGTA-AT-TCTATCTCCCTAGGCAGCAGTGG
1 AGTAGATTGAAGATTA-CAGATCT-TATCTCCCTAGGCAGCAGTGG
* * *
3669839 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* * ** * * * * *
3669883 AGCAGA-TCAAGGATGGCGGATTTTACCTCCCTGAGGTTA-TAGTGG
1 AGTAGATTGAA-GATTACAGATCTTATCTCCCT-AGG-CAGCAGTGG
* * * * *
3669928 AGTACATTGAAGCCATTA-A-TTC-TATCTCCATGGGCAACAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* ** *
3669971 AATAGATTGAAGA-TACCAGATCTTGCCTTCCT--GCATTGACAGTGG
1 AGTAGATTGAAGATTA-CAGATCTTATCTCCCTAGGCA--G-CAGTGG
** **** * * *
3670016 A-TCAGATCAAAGATGGTGGATTTTACCTCCCTAAGGTTA-CAGTGG
1 AGT-AGATTGAAGATTACAGATCTTATCTCCCT-AGG-CAGCAGTGG
* * * * *
3670061 AGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAGCAGTGA
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* * **
3670104 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* * ** * * *
3670148 AGCAGATCGAAGATGGC-GAATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAG-ATCTTATCTCCCT-AGG-CAGCAGTGG
* * * * *
3670193 AGTACATTGAAG---CCAGTATTTTTATCTCCCTGGGTAGCAGTGG
1 AGTAGATTGAAGATTACAG-A-TCTTATCTCCCTAGGCAGCAGTGG
* * * *
3670236 AATAGATTGGAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* * * * * *
3670280 AGCAGATCGAAGATGACAGATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCT-AGG-CAGCAGTGG
* * * * * *
3670325 AGTACATTGAAGCCAGTA-A-TTC-TATCTCCATGGGCAACAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* * *
3670368 AATAGATTGAAGATTACAGGTCTTATCTCCCTAGGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGCAGTGG
* ** * * *
3670412 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCT-AGG-CAGCAGTGG
*
3670457 AGTATATTGAAG
1 AGTAGATTGAAG
3670469 CTAGTAATTC
Statistics
Matches: 512, Mismatches: 152, Indels: 107
0.66 0.20 0.14
Matches are distributed among these distances:
40 2 0.00
41 7 0.01
42 13 0.03
43 102 0.20
44 243 0.47
45 124 0.24
46 14 0.03
47 5 0.01
48 1 0.00
49 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
AGTAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGCAGTGG
Found at i:3669851 original size:132 final size:132
Alignment explanation
Indices: 3669709--3670512 Score: 1166
Period size: 132 Copynumber: 6.1 Consensus size: 132
3669699 TGGCGTGAAG
* * * *
3669709 TAGATTGAAGATTACAGATCTTATCTCCCTAGGTAGTAGTAGAGTAGATCGAAGATGGCGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
* *
3669774 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCTAGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
3669839 AA
131 AA
3669841 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGGATGGCGGATT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GATGGCGGATT
* * * *
3669905 TTACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCATTAATTCTATCTCCATGGGCAACAGTG
65 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTG
3669970 GAA
130 GAA
** * * * * *
3669973 TAGATTGAAGA-TACCAGATCTTGCCTTCCT--GCATTGACAGTGGATCAGATCAAAGATGGTGG
1 TAGATTGAAGATTA-CAGATCTTATCTCCCTAAGCA--G-TAGTGGAGCAGATCGAAGATGGCGG
*
3670035 ATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
62 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
*
3670100 GTGAAA
127 GTGGAA
* *
3670106 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
* * *
3670171 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTATTTTTATCTCCCTGGGTAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
3670236 AA
131 AA
* * *
3670238 TAGATTGGAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
* *
3670303 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
3670368 AA
131 AA
* * * *
3670370 TAGATTGAAGATTACAGGTCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
* * * * * *
3670435 TACCTCCCTGAGGTTACAGTGGAGTATATTGAAGCTAGTAATTCTATCTCTCTAGTCGGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
3670500 AA
131 AA
* *
3670502 TCGATCGAAGA
1 TAGATTGAAGA
3670513 AAGCAGATCT
Statistics
Matches: 602, Mismatches: 61, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
130 3 0.00
131 4 0.01
132 480 0.80
133 108 0.18
134 4 0.01
135 3 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
AA
Found at i:3670117 original size:265 final size:263
Alignment explanation
Indices: 3669709--3670484 Score: 1144
Period size: 265 Copynumber: 2.9 Consensus size: 263
3669699 TGGCGTGAAG
* * * * *
3669709 TAGATTGAAGATTACAGATCTTATCTCCCTAGGTAGTAGTAGAGTAGATCGAAGATGGCGGATTT
1 TAGATTGAAGATTACAGATCTTACCTCCCTA-GCAGCAGTGGAGCAGATCGAAGATGGCGGATTT
* *
3669774 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCTAGGCAGCAGTGG
65 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
3669839 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGGATGGCGGA
130 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GATGGCGGA
* *
3669903 TTTTACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCATTAATTCTATCTCCATGGGCAACAG
194 TTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATGGGCAACAG
3669968 TGGAA
259 TGGAA
* * * * *
3669973 TAGATTGAAGA-TACCAGATCTTGCCTTCCT-GCATTGACAGTGGATCAGATCAAAGATGGTGGA
1 TAGATTGAAGATTA-CAGATCTTACCTCCCTAGCA--G-CAGTGGAGCAGATCGAAGATGGCGGA
*
3670036 TTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAG
62 TTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAG
* *
3670101 TGAAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCG
127 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCG
* * * * * *
3670166 AATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTATTTTTATCTCCCTGGGTAGC
192 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATGGGCAAC
3670231 AGTGGAA
257 AGTGGAA
* * * * *
3670238 TAGATTGGAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTT
1 TAGATTGAAGATTACAGATCTTACCTCCCT-AGCAGCAGTGGAGCAGATCGAAGATGGCGGATTT
* *
3670303 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATGGGCAACAGTGG
65 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
* * * *
3670368 AATAGATTGAAGATTACAGGTCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGGCAGAT
130 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGAT
* *
3670433 TTTACCTCCCTGAGGTTACAGTGGAGTATATTGAAGCTAGTAATTCTATCTC
195 TTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTC
3670485 TCTAGTCGGC
Statistics
Matches: 457, Mismatches: 47, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
262 2 0.00
263 2 0.00
264 216 0.47
265 230 0.50
266 4 0.01
267 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (263 bp):
TAGATTGAAGATTACAGATCTTACCTCCCTAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTT
ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
ATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATT
TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATGGGCAACAGTG
GAA
Found at i:3670567 original size:44 final size:44
Alignment explanation
Indices: 3670504--3670617 Score: 183
Period size: 44 Copynumber: 2.6 Consensus size: 44
3670494 CAGTGGAATC
3670504 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTA
* *
3670548 GATCGAAGAAAGTAGATCTTGTATTCATGTATTGGCATGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTA
* * *
3670592 GATCAAAGAGAGCAAATCTTGTCTTC
1 GATCGAAGAAAGCAGATCTTGTCTTC
3670618 CCATACTGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (44 bp):
GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTA
Found at i:3672198 original size:21 final size:21
Alignment explanation
Indices: 3672157--3672198 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3672147 ATTTTCTCCC
* **
3672157 ATTATTTATTATTATTGTTAT
1 ATTATTTATTATCATCATTAT
3672178 ATTATTTATTATCATCATTAT
1 ATTATTTATTATCATCATTAT
3672199 TTTTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATTTATTATCATCATTAT
Found at i:3672396 original size:2 final size:2
Alignment explanation
Indices: 3672391--3672423 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3672381 TATATACGTG
3672391 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 T
3672424 TTTCACATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3709231 original size:57 final size:57
Alignment explanation
Indices: 3709168--3709285 Score: 227
Period size: 57 Copynumber: 2.1 Consensus size: 57
3709158 GAGCTTTCGA
*
3709168 TTGGTGCAAATAGTGCAAGCAAAAAAGGTCATACATGATACAACAATTTTAGTAATT
1 TTGGTGCAAATAGTGCAAGCAAAAAAGGTCATACATGATACAACAATTTTAGTAACT
3709225 TTGGTGCAAATAGTGCAAGCAAAAAAGGTCATACATGATACAACAATTTTAGTAACT
1 TTGGTGCAAATAGTGCAAGCAAAAAAGGTCATACATGATACAACAATTTTAGTAACT
3709282 TTGG
1 TTGG
3709286 GTGTAGTTTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (57 bp):
TTGGTGCAAATAGTGCAAGCAAAAAAGGTCATACATGATACAACAATTTTAGTAACT
Found at i:3720122 original size:14 final size:14
Alignment explanation
Indices: 3720092--3720133 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3720082 GTTTCTTAAA
* *
3720092 ATTTTAAAAAT-AC
1 ATTTAAAAAATAAT
3720105 ATTTAAAAAATAAT
1 ATTTAAAAAATAAT
*
3720119 ATTTAAATAATAAT
1 ATTTAAAAAATAAT
3720133 A
1 A
3720134 AAATAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTAAAAAATAAT
Found at i:3722664 original size:5 final size:6
Alignment explanation
Indices: 3722647--3722673 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3722637 AACAAGGTAC
3722647 TGTTTT TGTTTT TGTTTT TGTTTT TGT
1 TGTTTT TGTTTT TGTTTT TGTTTT TGT
3722674 AAAAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (6 bp):
TGTTTT
Found at i:3734133 original size:43 final size:43
Alignment explanation
Indices: 3734063--3734165 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
3734053 ACACACCAAC
* * *
3734063 CTGGCAC-CACAA-TGCATCATCAGATAAACTAAAGCAGATAAA
1 CTGGCACACA-AAGTGCATAATCAAATAAACTAAAGCAAATAAA
* * *
3734105 CTGGCACACAAAGTGCATAATCAAATAAACTGAAGTAAATATA
1 CTGGCACACAAAGTGCATAATCAAATAAACTAAAGCAAATAAA
*
3734148 CTGGCACACGAAGTGCAT
1 CTGGCACACAAAGTGCAT
3734166 CATCGTACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 9 0.17
43 43 0.83
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (43 bp):
CTGGCACACAAAGTGCATAATCAAATAAACTAAAGCAAATAAA
Found at i:3734181 original size:43 final size:43
Alignment explanation
Indices: 3734104--3734190 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
3734094 AAGCAGATAA
*
3734104 ACTGGCACACAAAGTGCATAATCAAATAAACTG-AAGTAAATAT
1 ACTGGCACACAAAGTGCATAATCAAACAAACTGAAAG-AAATAT
* * ** *
3734147 ACTGGCACACGAAGTGCATCATCGTACAAGCTGAAAGAAATAT
1 ACTGGCACACAAAGTGCATAATCAAACAAACTGAAAGAAATAT
3734190 A
1 A
3734191 TTGACTCATG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 34 0.92
44 3 0.08
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (43 bp):
ACTGGCACACAAAGTGCATAATCAAACAAACTGAAAGAAATAT
Found at i:3734367 original size:49 final size:49
Alignment explanation
Indices: 3734306--3734435 Score: 217
Period size: 49 Copynumber: 2.7 Consensus size: 49
3734296 CACTTTTTCT
3734306 ATTTGA-TATTGATTAGAATAAGGTGTTTCAACCTTACTACATTGCTTCC
1 ATTTGACT-TTGATTAGAATAAGGTGTTTCAACCTTACTACATTGCTTCC
* *
3734355 ATTTGACTTTGATTAGAATAAGGTGTTTCAACCTTACTACATTGTTTCT
1 ATTTGACTTTGATTAGAATAAGGTGTTTCAACCTTACTACATTGCTTCC
*
3734404 ATTTGACTTTGATTAGAATAAGGTTTTTCAAC
1 ATTTGACTTTGATTAGAATAAGGTGTTTCAAC
3734436 ATATAAATAG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
49 76 0.99
50 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (49 bp):
ATTTGACTTTGATTAGAATAAGGTGTTTCAACCTTACTACATTGCTTCC
Found at i:3739492 original size:15 final size:17
Alignment explanation
Indices: 3739465--3739498 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3739455 CCTAGTTTTA
3739465 CATTTTTGTAAA-TCGT
1 CATTTTTGTAAATTCGT
3739481 CATTTTTG-AAATTCGT
1 CATTTTTGTAAATTCGT
3739497 CA
1 CA
3739499 GTTGGATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (17 bp):
CATTTTTGTAAATTCGT
Found at i:3743020 original size:9 final size:10
Alignment explanation
Indices: 3743001--3743032 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3742991 AAAATATTTT
3743001 AAAA-TTAAA
1 AAAACTTAAA
3743010 AAAACTTAAA
1 AAAACTTAAA
3743020 AAAACTTAAA
1 AAAACTTAAA
3743030 AAA
1 AAA
3743033 GTATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAACTTAAA
Found at i:3743032 original size:51 final size:47
Alignment explanation
Indices: 3742968--3743106 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 47
3742958 AAATTAAAAC
3742968 AAAAATTAAAAAAAGTATTTTAAAAAATATTTTAAAATTAAAAAAACTT
1 AAAAATT-AAAAAAGTATTTTAAAAAATATTTTAAAATTAAAAAAA-TT
* *
3743017 AAAAAAACTTAAAAAAGTATTTTAAAAAA-GTTTTAAAATTTAAAAAATT
1 --AAAAA-TTAAAAAAGTATTTTAAAAAATATTTTAAAATTAAAAAAATT
*
3743066 --AAA--AAAAAAGTATTTT-AAAAGTATTTTAAAATTAAAAAAAT
1 AAAAATTAAAAAAGTATTTTAAAAAATATTTTAAAATTAAAAAAAT
3743107 AATAAATAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
41 4 0.05
42 30 0.37
45 3 0.04
49 2 0.02
50 16 0.20
51 24 0.30
52 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (47 bp):
AAAAATTAAAAAAGTATTTTAAAAAATATTTTAAAATTAAAAAAATT
Found at i:3743085 original size:11 final size:11
Alignment explanation
Indices: 3743071--3743096 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3743061 AAATTAAAAA
3743071 AAAAGTATTTT
1 AAAAGTATTTT
3743082 AAAAGTATTTT
1 AAAAGTATTTT
3743093 AAAA
1 AAAA
3743097 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3748246 original size:23 final size:22
Alignment explanation
Indices: 3748203--3748251 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
3748193 CGGATTGAAA
*
3748203 TTTAATTATAATTTTTTATTATAT
1 TTTAATTATAA-TTTTCATTAT-T
3748227 TTTAATTTATAA-TTTCATTATT
1 TTTAA-TTATAATTTTCATTATT
3748249 TTT
1 TTT
3748252 GAATGGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 5 0.22
25 6 0.26
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTAATTATAATTTTCATTATT
Found at i:3749090 original size:45 final size:45
Alignment explanation
Indices: 3749037--3749132 Score: 167
Period size: 45 Copynumber: 2.1 Consensus size: 45
3749027 ATTCAAATAT
3749037 ATTATTTT-AGATTATCTTAACATCAATCAGTGTTAAATTTAGTTA
1 ATTATTTTAAG-TTATCTTAACATCAATCAGTGTTAAATTTAGTTA
3749082 ATTATTTTAAGTTATCTTAACATCAATCAGTGTTAAATTTAGTTA
1 ATTATTTTAAGTTATCTTAACATCAATCAGTGTTAAATTTAGTTA
*
3749127 AGTATT
1 ATTATT
3749133 GTACTATCTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.47
Consensus pattern (45 bp):
ATTATTTTAAGTTATCTTAACATCAATCAGTGTTAAATTTAGTTA
Found at i:3756728 original size:18 final size:18
Alignment explanation
Indices: 3756705--3756741 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3756695 GAACCACAGT
3756705 ATGGAAATTCCTCTGGTC
1 ATGGAAATTCCTCTGGTC
3756723 ATGGAAATTCCTCTGGTC
1 ATGGAAATTCCTCTGGTC
3756741 A
1 A
3756742 CGATCAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (18 bp):
ATGGAAATTCCTCTGGTC
Found at i:3763434 original size:27 final size:27
Alignment explanation
Indices: 3763404--3763468 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
3763394 CTCACTCGAG
*
3763404 GCTATAATACTACAACCATTCAGGAGT
1 GCTATAATACTACAACCATTCAAGAGT
* * *
3763431 GCTATAGTACGACAACCATTTAAGAGT
1 GCTATAATACTACAACCATTCAAGAGT
* *
3763458 GTTATGATACT
1 GCTATAATACT
3763469 TGTAATGGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (27 bp):
GCTATAATACTACAACCATTCAAGAGT
Found at i:3768231 original size:42 final size:42
Alignment explanation
Indices: 3768179--3768277 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
3768169 GATCTTGGTA
* ***
3768179 TCGCACACTTAGTGCTCGTTATTCGACATCGTCATTTTTGTT
1 TCGCACACTTAGTGCTCGTTATTCAACATCGTCATTTGAATT
3768221 TCGCACACTTAGTGCTCGTTATTCAACATCGTCATTTGAATT
1 TCGCACACTTAGTGCTCGTTATTCAACATCGTCATTTGAATT
3768263 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
3768278 CATTCGTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCTCGTTATTCAACATCGTCATTTGAATT
Found at i:3769195 original size:27 final size:27
Alignment explanation
Indices: 3769165--3769230 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
3769155 CTCACTCGAG
*
3769165 GCTATAATACTACAACCATTCAGGAGT
1 GCTATAATACTACAACCATTCAAGAGT
* * *
3769192 GCTATAGTACGACAACCATTTAAGAGT
1 GCTATAATACTACAACCATTCAAGAGT
* *
3769219 GTTATGATACTA
1 GCTATAATACTA
3769231 ATTAATGACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (27 bp):
GCTATAATACTACAACCATTCAAGAGT
Found at i:3785918 original size:22 final size:21
Alignment explanation
Indices: 3785864--3785920 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
3785854 AAAATTATAC
*
3785864 TTAAAATAGTATTTTTAAAAAAA
1 TTAAAA-A-TATTATTAAAAAAA
*
3785887 TT-AAAA-ATTATTATAAAAA
1 TTAAAAATATTATTAAAAAAA
3785906 TTAAAACATATTATT
1 TTAAAA-ATATTATT
3785921 TATTGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 2 0.07
22 9 0.31
23 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAATATTATTAAAAAAA
Found at i:3787076 original size:18 final size:18
Alignment explanation
Indices: 3787053--3787095 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3787043 TATTTAAAAA
3787053 AATAAA-AAAATTATATTT
1 AATAAATAAAATTAT-TTT
*
3787071 AATAAATATAATTATTTT
1 AATAAATAAAATTATTTT
*
3787089 CATAAAT
1 AATAAAT
3787096 GATGTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAAATAAAATTATTTT
Found at i:3789492 original size:19 final size:21
Alignment explanation
Indices: 3789454--3789506 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
3789444 TAAAATATAA
*
3789454 ATTTTAAATTTTTTATAAA-T
1 ATTTTAAATTTTTGATAAATT
3789474 ATTTTAAATTTTTGA-AAATT
1 ATTTTAAATTTTTGATAAATT
3789494 ATTTT-AATTTTTG
1 ATTTTAAATTTTTG
3789507 TTGTGAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
ATTTTAAATTTTTGATAAATT
Found at i:3791431 original size:32 final size:33
Alignment explanation
Indices: 3791392--3791454 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3791382 TATACCAAAC
*
3791392 AATAAATAATA-TTT-AAGAATCTTTTTATCTAA
1 AATAAATAATATTTTAAAG-ATATTTTTATCTAA
*
3791424 AATAAATATTATTTTAAAGATATTTTTATCT
1 AATAAATAATATTTTAAAGATATTTTTATCT
3791455 TTTAGGCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 10 0.37
33 14 0.52
34 3 0.11
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (33 bp):
AATAAATAATATTTTAAAGATATTTTTATCTAA
Found at i:3791479 original size:17 final size:18
Alignment explanation
Indices: 3791447--3791480 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3791437 TTAAAGATAT
3791447 TTTTATCTTTTAGGCCCC
1 TTTTATCTTTTAGGCCCC
*
3791465 TTTTAT-TTTTGGGCCC
1 TTTTATCTTTTAGGCCC
3791481 TGGGCGGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.53
Consensus pattern (18 bp):
TTTTATCTTTTAGGCCCC
Found at i:3806323 original size:26 final size:26
Alignment explanation
Indices: 3806286--3806335 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3806276 TAAACTTGTA
*
3806286 CAATTTGCTGCTGCTGGTCTTTTGAC
1 CAATTTGCTGCTGCTGGTCCTTTGAC
* *
3806312 CAATTTGTTGCTGTTGGTCCTTTG
1 CAATTTGCTGCTGCTGGTCCTTTG
3806336 TTGCAATGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (26 bp):
CAATTTGCTGCTGCTGGTCCTTTGAC
Found at i:3810824 original size:26 final size:26
Alignment explanation
Indices: 3810781--3810830 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3810771 TAAACTTGTA
*
3810781 CAATTTGCTGCTGCTGGTCTTTTGAC
1 CAATTTGCTGCTGCTGGTCCTTTGAC
* * *
3810807 CAATTTGTTGTTGTTGGTCCTTTG
1 CAATTTGCTGCTGCTGGTCCTTTG
3810831 TTGCAATGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (26 bp):
CAATTTGCTGCTGCTGGTCCTTTGAC
Found at i:3814294 original size:7 final size:7
Alignment explanation
Indices: 3814279--3814308 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3814269 CCCTTATCAT
*
3814279 CACCATG
1 CACCTTG
3814286 CACCTTG
1 CACCTTG
3814293 CACCTTG
1 CACCTTG
3814300 CACCTTG
1 CACCTTG
3814307 CA
1 CA
3814309 GAGAAAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.20, C:0.43, G:0.13, T:0.23
Consensus pattern (7 bp):
CACCTTG
Found at i:3821552 original size:190 final size:190
Alignment explanation
Indices: 3821229--3821614 Score: 754
Period size: 190 Copynumber: 2.0 Consensus size: 190
3821219 ATAACCAAGA
3821229 AAAACACATTTAATGTATCTCGGTTCCAATTTTCCATTATCGACATGAGTATACGTAGGACACCC
1 AAAACACATTTAATGTATCTCGGTTCCAATTTTCCATTATCGACATGAGTATACGTAGGACACCC
* *
3821294 AAAGATCTTTAAATCAGAATAGTCTGCAGGATTACCAGACCATACCTCTTGTGGAGTCTTTTTCT
66 AAAGATCTTTAAATCAGAATAGTCAGCAAGATTACCAGACCATACCTCTTGTGGAGTCTTTTTCT
3821359 CAATGGCAACGGATGGAGATCGATTAATCAAAAAACATACAATAGAGGCTGCTTTGGCCC
131 CAATGGCAACGGATGGAGATCGATTAATCAAAAAACATACAATAGAGGCTGCTTTGGCCC
3821419 AAAACACATTTAATGTATCTCGGTTCCAATTTTCCATTATCGACATGAGTATACGTAGGACACCC
1 AAAACACATTTAATGTATCTCGGTTCCAATTTTCCATTATCGACATGAGTATACGTAGGACACCC
3821484 AAAGATCTTTAAATCAGAATAGTCAGCAAGATTACCAGACCATACCTCTTGTGGAGTCTTTTTCT
66 AAAGATCTTTAAATCAGAATAGTCAGCAAGATTACCAGACCATACCTCTTGTGGAGTCTTTTTCT
3821549 CAATGGCAACGGATGGAGATCGATTAATCAAAAAACATACAATAGAGGCTGCTTTGGCCC
131 CAATGGCAACGGATGGAGATCGATTAATCAAAAAACATACAATAGAGGCTGCTTTGGCCC
3821609 AAAACA
1 AAAACA
3821615 ACTTCGGTAA
Statistics
Matches: 194, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 194 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (190 bp):
AAAACACATTTAATGTATCTCGGTTCCAATTTTCCATTATCGACATGAGTATACGTAGGACACCC
AAAGATCTTTAAATCAGAATAGTCAGCAAGATTACCAGACCATACCTCTTGTGGAGTCTTTTTCT
CAATGGCAACGGATGGAGATCGATTAATCAAAAAACATACAATAGAGGCTGCTTTGGCCC
Found at i:3834427 original size:17 final size:17
Alignment explanation
Indices: 3834407--3834440 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3834397 TAAGAGATTA
3834407 TAAATAAAAATAAACAT
1 TAAATAAAAATAAACAT
* *
3834424 TAAATCAAAATATACAT
1 TAAATAAAAATAAACAT
3834441 ACATCGTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAATAAAAATAAACAT
Found at i:3835003 original size:7 final size:7
Alignment explanation
Indices: 3834993--3835018 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3834983 AAGGGAATTA
3834993 GGGGATT
1 GGGGATT
3835000 GGGGATT
1 GGGGATT
3835007 GGGGATT
1 GGGGATT
3835014 GGGGA
1 GGGGA
3835019 GGGGAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.62, T:0.23
Consensus pattern (7 bp):
GGGGATT
Found at i:3835663 original size:14 final size:14
Alignment explanation
Indices: 3835646--3835692 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3835636 GAAGAGAATG
3835646 AAAAATAAAGAAAA
1 AAAAATAAAGAAAA
* **
3835660 AAAAAGAAAGTTAA
1 AAAAATAAAGAAAA
*
3835674 AAAAATAAA-ACAA
1 AAAAATAAAGAAAA
3835687 AAAAAT
1 AAAAAT
3835693 TAAATTGCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAAATAAAGAAAA
Found at i:3837895 original size:27 final size:26
Alignment explanation
Indices: 3837810--3837895 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
3837800 TCTTAAAAAG
* *
3837810 AAAAAAAACTTAAATACCAAATTAAA
1 AAAAAAAATTTAAATAACAAATTAAA
* * *
3837836 AAATATCAAATTTTAATAACAAATTAGAT
1 AAA-A-AAAATTTAAATAACAAATTA-AA
*
3837865 AAAAGAAATTTAAATAACAAATTAAA
1 AAAAAAAATTTAAATAACAAATTAAA
3837891 AAAAA
1 AAAAA
3837896 TTTAATATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 8 0.17
27 19 0.40
28 17 0.35
29 4 0.08
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (26 bp):
AAAAAAAATTTAAATAACAAATTAAA
Found at i:3849363 original size:16 final size:16
Alignment explanation
Indices: 3849342--3849378 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3849332 TTGGTTCGCT
*
3849342 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
3849358 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
3849374 GTAAT
1 GTAAT
3849379 AGTATTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:3849683 original size:120 final size:121
Alignment explanation
Indices: 3849547--3849836 Score: 514
Period size: 120 Copynumber: 2.4 Consensus size: 121
3849537 TTAATCATAT
*
3849547 TTTAACATTATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATA-
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATAT
*
3849611 TAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
3849667 TTTAACATAATTATTATGAAATATAATTTAA-AAAATATATATAATTTAATAAAATTCTTAATAT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATAT
3849731 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
3849787 TTTAAAATAATTATTATTAAATATAATTTAAT-AAAAATATATAATTTAAT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAAT
3849837 CTAAAGTTTG
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 31 0.19
120 130 0.81
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (121 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:3855513 original size:8 final size:9
Alignment explanation
Indices: 3855495--3855524 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3855485 ATAGTTTGTA
3855495 TTTCTTTTT
1 TTTCTTTTT
3855504 TTTCTTTTT
1 TTTCTTTTT
3855513 TTTCTTTTT
1 TTTCTTTTT
3855522 TTT
1 TTT
3855525 TTATATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:3862672 original size:15 final size:15
Alignment explanation
Indices: 3862648--3862681 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3862638 ACTAACAATT
*
3862648 CACATGTATACAGTA
1 CACATATATACAGTA
*
3862663 CACATATATACAGTT
1 CACATATATACAGTA
3862678 CACA
1 CACA
3862682 GAACACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (15 bp):
CACATATATACAGTA
Found at i:3866455 original size:27 final size:28
Alignment explanation
Indices: 3866425--3866477 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3866415 GCAAAATCAT
3866425 TATACTGTT-TATA-TAGTTAAATAATCC
1 TATACT-TTGTATATTAGTTAAATAATCC
*
3866452 TATACTTTGTCTATTAGTTAAATAAT
1 TATACTTTGTATATTAGTTAAATAAT
3866478 TGGTCCATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 9 0.39
28 12 0.52
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (28 bp):
TATACTTTGTATATTAGTTAAATAATCC
Found at i:3871406 original size:3 final size:3
Alignment explanation
Indices: 3871398--3871438 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3871388 AATGAGTAAG
3871398 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3871439 AACTCACAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3886883 original size:100 final size:100
Alignment explanation
Indices: 3886766--3886966 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
3886756 TATATTATCA
3886766 TTGTAAAATTATTTTTTAATTTATATTAAATAAATATTATTTTAATGTCTTGATGTAGGCATTAT
1 TTGTAAAATTATTTTTTAATTTATATTAAATAAATATTATTTTAATGTCTTGATGTAGGCATTAT
3886831 TTCTGAAAATATATGAAAAGTAAGGAAGTTGGTTT
66 TTCTGAAAATATATGAAAAGTAAGGAAGTTGGTTT
3886866 TTGTAAAATTATTTTTTAATTTATATTAAATAAATATTATTTTAATGTCTTGATGTAGGCATTAT
1 TTGTAAAATTATTTTTTAATTTATATTAAATAAATATTATTTTAATGTCTTGATGTAGGCATTAT
3886931 TTCTGAAAATATATGAAAAGTAAGGAAGTTGGTTT
66 TTCTGAAAATATATGAAAAGTAAGGAAGTTGGTTT
3886966 T
1 T
3886967 CTCTGTAAAT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (100 bp):
TTGTAAAATTATTTTTTAATTTATATTAAATAAATATTATTTTAATGTCTTGATGTAGGCATTAT
TTCTGAAAATATATGAAAAGTAAGGAAGTTGGTTT
Found at i:3889310 original size:15 final size:15
Alignment explanation
Indices: 3889290--3889319 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3889280 ATATAGGCAT
*
3889290 TTAATTTTTTCTAAA
1 TTAATTATTTCTAAA
3889305 TTAATTATTTCTAAA
1 TTAATTATTTCTAAA
3889320 AATATATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTATTTCTAAA
Found at i:3923358 original size:22 final size:20
Alignment explanation
Indices: 3923326--3923367 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3923316 AAAGAAAAGT
*
3923326 AAAAAAAAAAACTTTGATGG
1 AAAAAAAAAAACGTTGATGG
3923346 AAAAAATAGAAAACGTTGATGG
1 AAAAAA-A-AAAACGTTGATGG
3923368 CTAAAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (20 bp):
AAAAAAAAAAACGTTGATGG
Found at i:3923630 original size:21 final size:21
Alignment explanation
Indices: 3923583--3923637 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3923573 ACTGCTATTT
* *
3923583 CTAATCTCACTGCTACAATAC
1 CTAATCTCACCGCTACAATAA
* * *
3923604 CCAATCTCACCGCTATAGTAA
1 CTAATCTCACCGCTACAATAA
3923625 CTAATCTCACCGC
1 CTAATCTCACCGC
3923638 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.36, G:0.07, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAATAA
Found at i:3923928 original size:19 final size:18
Alignment explanation
Indices: 3923900--3923941 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
3923890 TTCAAAATAT
*
3923900 AAAAATTTAACAACTATA
1 AAAAATTTAAAAACTATA
*
3923918 AAAAATATTAAAAATTATA
1 AAAAAT-TTAAAAACTATA
3923937 AAAAA
1 AAAAA
3923942 AACTGGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATTTAAAAACTATA
Found at i:3925649 original size:158 final size:150
Alignment explanation
Indices: 3925273--3925661 Score: 571
Period size: 158 Copynumber: 2.5 Consensus size: 150
3925263 GGAAAAATCC
*
3925273 AAAAAAGCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
1 AAAAAATCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
*** * * *
3925338 CTGAGCTAGACGGGCCGGTTGATCTAGAATGTGTAAATTCTTTTACAAATTCAAAACTAATTGTT
66 CTGAGCTAGACGGGCTAATTGATCTACAATGTGTAAATTCTTTTACAAATTAAAAACTAATAGTT
3925403 TCCAGTTACTTGGAAAAAGT
131 TCCAGTTACTTGGAAAAAGT
* *
3925423 TAAAGATCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
1 AAAAAATCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
* *
3925488 CTGAGCTAGACGGGCTAATTGATCTCCATTGTGTAAGATTATAAACTTCTTACAAATTTAAAAAC
66 CTGAGCTAGACGGGCTAATTGATCTACAATGTGTAA-A-T-T---CTT-TTACAAA-TTAAAAAC
* *
3925553 TAATAGTTTCCAGTTCCTTGGAAAATGT
123 TAATAGTTTCCAGTTACTTGGAAAAAGT
**
3925581 AAAAAATCTTCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
1 AAAAAATCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
3925646 CTGAGCTAGACGGGCT
66 CTGAGCTAGACGGGCT
3925662 TCTTGTCGCG
Statistics
Matches: 214, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
150 92 0.43
151 1 0.00
152 1 0.00
153 1 0.00
156 3 0.01
157 7 0.03
158 109 0.51
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (150 bp):
AAAAAATCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTCTACCGA
CTGAGCTAGACGGGCTAATTGATCTACAATGTGTAAATTCTTTTACAAATTAAAAACTAATAGTT
TCCAGTTACTTGGAAAAAGT
Found at i:3928481 original size:21 final size:21
Alignment explanation
Indices: 3928433--3928517 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 21
3928423 CTTTGCCGAC
*
3928433 CAGGCACTTTATGTGTTGTATTT
1 CAGGCACTTTATGTGTCGTA--T
3928456 CAGGCACTTTATGTGTCGTAT
1 CAGGCACTTTATGTGTCGTAT
** *
3928477 CAGGCA-TCTCGTGTGTCGTTT
1 CAGGCACT-TTATGTGTCGTAT
3928498 CAGGCAC-TTATGTGTCGTAT
1 CAGGCACTTTATGTGTCGTAT
3928518 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.21
21 23 0.43
23 19 0.36
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (21 bp):
CAGGCACTTTATGTGTCGTAT
Found at i:3929630 original size:18 final size:18
Alignment explanation
Indices: 3929607--3929642 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3929597 AAGTTTACAT
* *
3929607 TATATTATATTATTTTTA
1 TATATTAAATAATTTTTA
3929625 TATATTAAATAATTTTTA
1 TATATTAAATAATTTTTA
3929643 ACACACTAAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTAAATAATTTTTA
Found at i:3942110 original size:2 final size:2
Alignment explanation
Indices: 3942105--3942132 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3942095 TATATTTGAA
3942105 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
3942133 TTACATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3942426 original size:9 final size:9
Alignment explanation
Indices: 3942412--3942481 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
3942402 TGGAATTATA
3942412 AAAAAATAT
1 AAAAAATAT
3942421 AAAAAA-AT
1 AAAAAATAT
*
3942429 AAAAATTAT
1 AAAAAATAT
3942438 AAAAATTATTAT
1 AAAAA--A-TAT
*
3942450 AAATTAAT-T
1 AAA-AAATAT
*
3942459 AAAAATTAT
1 AAAAAATAT
3942468 AAAAAATTAT
1 AAAAAA-TAT
3942478 AAAA
1 AAAA
3942482 TGATTTACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 9 0.19
9 23 0.48
10 8 0.17
11 1 0.02
12 6 0.12
13 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAAATAT
Found at i:3942442 original size:10 final size:10
Alignment explanation
Indices: 3942405--3942481 Score: 81
Period size: 10 Copynumber: 8.0 Consensus size: 10
3942395 TACATTATGG
3942405 AATTATAAAA
1 AATTATAAAA
*
3942415 AAATATAAAA
1 AATTATAAAA
3942425 AA--AT-AAA
1 AATTATAAAA
3942432 AATTAT-AAA
1 AATTATAAAA
* *
3942441 AATTATTATA
1 AATTATAAAA
*
3942451 AATTAATTAAA
1 AATT-ATAAAA
3942462 AATTATAAAA
1 AATTATAAAA
3942472 AATTATAAAA
1 AATTATAAAA
3942482 TGATTTACTA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 11 0.19
10 32 0.54
11 9 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTATAAAA
Found at i:3942461 original size:21 final size:21
Alignment explanation
Indices: 3942405--3942476 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
3942395 TACATTATGG
*
3942405 AATTATAAAAAAAT-A-TAAA
1 AATTATAAAAAATTAATTAAA
*
3942424 AA-AAT-AAAAATT-A-TAAA
1 AATTATAAAAAATTAATTAAA
* *
3942441 AATTATTATAAATTAATTAAA
1 AATTATAAAAAATTAATTAAA
3942462 AATTATAAAAAATTA
1 AATTATAAAAAATTA
3942477 TAAAATGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.30
18 4 0.09
19 8 0.19
20 1 0.02
21 17 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTATAAAAAATTAATTAAA
Found at i:3949506 original size:8 final size:8
Alignment explanation
Indices: 3949493--3949613 Score: 66
Period size: 8 Copynumber: 14.2 Consensus size: 8
3949483 GTCACCCTTC
3949493 TTTTATTT
1 TTTTATTT
3949501 TTTTA-TT
1 TTTTATTT
*
3949508 TTTTACTT
1 TTTTATTT
3949516 TTTTATTAACT
1 TTTTATT---T
*
3949527 TTTGTCTCTT
1 TTT-TAT-TT
*
3949537 TCTTTAAATT
1 T-TTT-ATTT
*
3949547 TTTTCTTT
1 TTTTATTT
**
3949555 TTTTAAGT
1 TTTTATTT
*
3949563 TTTTATTA
1 TTTTATTT
*
3949571 TTTT-TTA
1 TTTTATTT
3949578 TTTTATTT
1 TTTTATTT
3949586 TGTTTATTT
1 T-TTTATTT
*
3949595 ATTTATTT
1 TTTTATTT
3949603 ATTTTATTT
1 -TTTTATTT
3949612 TT
1 TT
3949614 ATTAATTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
7 14 0.16
8 41 0.47
9 17 0.20
10 6 0.07
11 6 0.07
12 2 0.02
13 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTATTT
Found at i:3949517 original size:15 final size:15
Alignment explanation
Indices: 3949493--3949522 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3949483 GTCACCCTTC
*
3949493 TTTTATTTTTTTATT
1 TTTTACTTTTTTATT
3949508 TTTTACTTTTTTATT
1 TTTTACTTTTTTATT
3949523 AACTTTTGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTACTTTTTTATT
Found at i:3949543 original size:19 final size:17
Alignment explanation
Indices: 3949533--3949566 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3949523 AACTTTTGTC
3949533 TCTTTCTTTAAATTTTT
1 TCTTTCTTTAAATTTTT
* *
3949550 TCTTTTTTTAAGTTTTT
1 TCTTTCTTTAAATTTTT
3949567 ATTATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTCTTTAAATTTTT
Found at i:3949590 original size:26 final size:25
Alignment explanation
Indices: 3949564--3949612 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
3949554 TTTTTAAGTT
3949564 TTTA-TTATTTTTTATTTTATTTTG
1 TTTATTTATTTTTTATTTTATTTTG
3949588 TTTATTTATTTATTTATTTTATTTT
1 TTTATTTATTT-TTTATTTTATTTT
3949613 TATTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.17
25 6 0.26
26 13 0.57
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTATTTATTTTTTATTTTATTTTG
Found at i:3949701 original size:20 final size:20
Alignment explanation
Indices: 3949657--3949701 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3949647 AATGTTTTAT
*
3949657 AATATATTTTTAAATATTAA
1 AATATATTTTAAAATATTAA
*
3949677 TATATATTTTAATAATA-TAA
1 AATATATTTTAA-AATATTAA
3949697 AATAT
1 AATAT
3949702 TTAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATATTTTAAAATATTAA
Found at i:3950115 original size:13 final size:13
Alignment explanation
Indices: 3950069--3950116 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3950059 TAATTAAAAA
*
3950069 TAAAAATATTTGT
1 TAAAAATATTTAT
3950082 TAAAAATAAATTTATT
1 TAAAAAT--ATTTA-T
*
3950098 TAAAAATATATAT
1 TAAAAATATTTAT
3950111 TAAAAA
1 TAAAAA
3950117 GTAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 14 0.47
14 4 0.13
15 4 0.13
16 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAT
Found at i:3950193 original size:7 final size:7
Alignment explanation
Indices: 3950181--3950249 Score: 102
Period size: 7 Copynumber: 9.7 Consensus size: 7
3950171 ATGCCAGTAA
3950181 AAATATT
1 AAATATT
3950188 AAATATT
1 AAATATT
3950195 AAATATT
1 AAATATT
3950202 AAATATT
1 AAATATT
3950209 AAATATT
1 AAATATT
3950216 AAATATT
1 AAATATT
* **
3950223 ATATAAA
1 AAATATT
3950230 AAATATT
1 AAATATT
3950237 AAATAATT
1 AAAT-ATT
3950245 AAATA
1 AAATA
3950250 AAAAAATCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
7 48 0.87
8 7 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:3950660 original size:20 final size:20
Alignment explanation
Indices: 3950637--3950701 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
3950627 ATAATTTTTT
3950637 AATTTTAGTACACATTTATA
1 AATTTTAGTACACATTTATA
* * *
3950657 AATTTATA-TATTA-ATTTTTT
1 AATTT-TAGTA-CACATTTATA
*
3950677 AATTTTAGTACACATTCATA
1 AATTTTAGTACACATTTATA
3950697 AATTT
1 AATTT
3950702 ATGTACTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (20 bp):
AATTTTAGTACACATTTATA
Found at i:3950672 original size:40 final size:41
Alignment explanation
Indices: 3950628--3950712 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 41
3950618 GTGTTGGTTA
*
3950628 TAATTTTTTAATTTTAGTACACATTTATAAATTTATATA-T
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
*
3950668 TAATTTTTTAATTTTAGTACACATTCATAAATTTATGTACT
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
3950709 TAAT
1 TAAT
3950713 ATATATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (41 bp):
TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
Found at i:3950723 original size:40 final size:40
Alignment explanation
Indices: 3950636--3950723 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
3950626 TATAATTTTT
* * *
3950636 TAATTTTAGTACACATTTATAAATTTATATATTAATTTTT
1 TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
*
3950676 TAATTTTAGTACACATTCATAAATTTATGTACTTAA-TATA
1 TAATTTTAGTACACATTCATAAATTTATATA-TTAATTATA
*
3950716 TATTTTTA
1 TAATTTTA
3950724 ATAGATAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (40 bp):
TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
Found at i:3950899 original size:71 final size:72
Alignment explanation
Indices: 3950782--3950928 Score: 215
Period size: 71 Copynumber: 2.1 Consensus size: 72
3950772 AAACTTAGAG
* * * * * *
3950782 AAATTAAATATATTAAAAAAATGTTATGTATAGCCAATTTTAAAATTTTAATATATTTAATATAT
1 AAATTAAATATATTAAAAAAATATTAAGTATAACCAATATTAAAATTATAATATATTCAATATAT
3950847 TTTTAAA
66 TTTTAAA
*
3950854 AAATTAAATATATT-AAAAAATATTAAGTATAACTAATATTAAAATTATAATATATTCAATATAT
1 AAATTAAATATATTAAAAAAATATTAAGTATAACCAATATTAAAATTATAATATATTCAATATAT
*
3950918 TTTTTAA
66 TTTTAAA
3950925 AAAT
1 AAAT
3950929 ATATTTTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 53 0.79
72 14 0.21
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (72 bp):
AAATTAAATATATTAAAAAAATATTAAGTATAACCAATATTAAAATTATAATATATTCAATATAT
TTTTAAA
Found at i:3951077 original size:6 final size:6
Alignment explanation
Indices: 3951068--3951126 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
3951058 AATTAATAAT
* * *
3951068 TAAAAA T-AAAA T-AAAA TAAAAA TAAATAAA TAAAGA TAAAGA CAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA T-AA-AAA TAAAAA TAAAAA TAAAAA
3951116 TAAAAA -AAAAA
1 TAAAAA TAAAAA
3951127 GTCAGAGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
5 15 0.33
6 23 0.50
7 4 0.09
8 4 0.09
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (6 bp):
TAAAAA
Found at i:3951096 original size:30 final size:32
Alignment explanation
Indices: 3951056--3951121 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
3951046 TAAGTTTTTT
* * *
3951056 AAAATTAATAATTAAAAATAAA-A-TAAAATA
1 AAAATAAATAAATAAAAATAAAGACAAAAATA
*
3951086 AAAATAAATAAATAAAGATAAAGACAAAAATA
1 AAAATAAATAAATAAAAATAAAGACAAAAATA
3951118 AAAA
1 AAAA
3951122 AAAAAGTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.63
31 1 0.03
32 10 0.33
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.20
Consensus pattern (32 bp):
AAAATAAATAAATAAAAATAAAGACAAAAATA
Found at i:3951402 original size:19 final size:19
Alignment explanation
Indices: 3951378--3951448 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
3951368 TTAAATATTA
3951378 TTAAAAATATATTTAATAT
1 TTAAAAATATATTTAATAT
**
3951397 TTAAAAATA-A-AAAATAAT
1 TTAAAAATATATTTAAT-AT
*
3951415 TTCAAAAATATATATTTAAAAT
1 TT--AAAA-ATATATTTAATAT
3951437 TTAAAAATATAT
1 TTAAAAATATAT
3951449 ATTTGAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 15 0.37
20 8 0.20
21 3 0.07
22 5 0.12
23 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAATATATTTAATAT
Found at i:3951444 original size:21 final size:21
Alignment explanation
Indices: 3951380--3951458 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
3951370 AAATATTATT
*
3951380 AAAA-ATATATTTAATATTTA
1 AAAATATATATTTAAAATTTA
*
3951400 AAAATA-A-A--AAATAATTTCA
1 AAAATATATATTTAA-AATTT-A
3951419 AAAATATATATTTAAAATTTA
1 AAAATATATATTTAAAATTTA
*
3951440 AAAATATATATTTGAAATT
1 AAAATATATATTTAAAATT
3951459 ATTTTATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
17 2 0.04
18 4 0.08
19 8 0.17
20 6 0.12
21 21 0.44
22 5 0.10
23 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
AAAATATATATTTAAAATTTA
Found at i:3951489 original size:14 final size:14
Alignment explanation
Indices: 3951470--3951544 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
3951460 TTTTATTTTG
*
3951470 TTTAAAAATATATT
1 TTTAAAAATATAAT
3951484 TTTAAAAATAT-A-
1 TTTAAAAATATAAT
* *
3951496 TTT-AAAATTTAAAA
1 TTTAAAAATAT-AAT
3951510 TTTAGAAAAT-TAAT
1 TTTA-AAAATATAAT
* *
3951524 TTCAAAAATATATT
1 TTTAAAAATATAAT
3951538 TTTAAAA
1 TTTAAAA
3951545 TTTATAAGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 6 0.12
12 3 0.06
13 6 0.12
14 28 0.57
15 1 0.02
16 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
TTTAAAAATATAAT
Found at i:3951566 original size:35 final size:33
Alignment explanation
Indices: 3951503--3951600 Score: 119
Period size: 35 Copynumber: 2.8 Consensus size: 33
3951493 ATATTTAAAA
*
3951503 TTTAAAATTTAGAAAATTAATTTCAAAAATAT-ATT
1 TTTAAAATTTA-AAAA-TAATTT-AAAAATATAATG
3951538 TTTAAAATTTATAAGACATAATTTAAAAA-ATAATG
1 TTTAAAATTTA-AA-A-ATAATTTAAAAATATAATG
3951573 TTTAAAATTTAAAAATAATTTAAAAATA
1 TTTAAAATTTAAAAATAATTTAAAAATA
3951601 ATATATATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
32 12 0.21
33 2 0.04
34 4 0.07
35 31 0.54
36 7 0.12
37 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (33 bp):
TTTAAAATTTAAAAATAATTTAAAAATATAATG
Found at i:3951748 original size:19 final size:18
Alignment explanation
Indices: 3951721--3951762 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3951711 AAAAAGAGAA
3951721 AAAAATTAA-AGAAAAAGAC
1 AAAAATTAATA-AAAAAG-C
*
3951740 AAAAGTTAATAAAAAAGC
1 AAAAATTAATAAAAAAGC
3951758 AAAAA
1 AAAAA
3951763 AAAAAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 14 0.70
20 1 0.05
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAAATTAATAAAAAAGC
Found at i:3952611 original size:18 final size:19
Alignment explanation
Indices: 3952576--3952614 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3952566 ACAAAACAAA
3952576 AATCATGAAAAATGTGGAC
1 AATCATGAAAAATGTGGAC
*
3952595 AATCATG-AAACTGTGGAC
1 AATCATGAAAAATGTGGAC
3952613 AA
1 AA
3952615 AATCACGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (19 bp):
AATCATGAAAAATGTGGAC
Found at i:3953266 original size:3 final size:3
Alignment explanation
Indices: 3953258--3953293 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3953248 ATTCATTTCA
*
3953258 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3953294 TTAACTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3957084 original size:17 final size:17
Alignment explanation
Indices: 3957059--3957222 Score: 109
Period size: 17 Copynumber: 9.2 Consensus size: 17
3957049 CGTGATTTTT
3957059 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* *
3957076 TTTTCAAAACACCGAAAT
1 TTTTGAAAACA-CGAAAA
*
3957094 TTTTG-AAACACGGAAAT
1 TTTTGAAAACAC-GAAAA
* *
3957111 TTTTAGAAAATCACGAGGAT
1 TTTT-GAAAA-CACGA-AAA
*
3957131 TTTTG-AAACACGAAATTT
1 TTTTGAAAACACGAAA--A
** *
3957149 TTTTTTAAACACGAGAAT
1 TTTTGAAAACACGA-AAA
* *
3957167 TTTTGAAAACATGAAACT
1 TTTTGAAAACACGAAA-A
*
3957185 TTTTG-AAACACGAGAA
1 TTTTGAAAACACGAAAA
3957201 TTTTGAAAACACGAAAAA
1 TTTTGAAAACACG-AAAA
3957219 TTTT
1 TTTT
3957223 CCAATTTTAT
Statistics
Matches: 121, Mismatches: 13, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.06
17 46 0.38
18 43 0.36
19 14 0.12
20 11 0.09
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:3957097 original size:36 final size:35
Alignment explanation
Indices: 3957058--3957222 Score: 167
Period size: 34 Copynumber: 4.7 Consensus size: 35
3957048 ACGTGATTTT
*
3957058 TTTTTGAAAACACGAAAATTTTCAAAACACCGA-AA
1 TTTTTGAAAACACGAAAATTTTTAAAACA-CGAGAA
* *
3957093 TTTTTG-AAACACGGAAATTTTTAGAAAATCACGAGGA
1 TTTTTGAAAACACGAAAATTTTT--AAAA-CACGAGAA
* *
3957130 TTTTTG-AAACACGAAATTTTTTTTTAAACACGAGAA
1 TTTTTGAAAACACGAAA--ATTTTTAAAACACGAGAA
* * *
3957166 TTTTTGAAAACATGAAACTTTTTGAAACACGAGAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAGAA
*
3957201 -TTTTGAAAACACGAAAAATTTT
1 TTTTTGAAAACACGAAAATTTTT
3957223 CCAATTTTAT
Statistics
Matches: 110, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
34 33 0.30
35 22 0.20
36 20 0.18
37 30 0.27
39 5 0.05
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACGAGAA
Found at i:3957152 original size:19 final size:20
Alignment explanation
Indices: 3957130--3957170 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3957120 ATCACGAGGA
3957130 TTTTTGAAACACGA-AATTT
1 TTTTTGAAACACGAGAATTT
*
3957149 TTTTTTAAACACGAGAATTT
1 TTTTTGAAACACGAGAATTT
3957169 TT
1 TT
3957171 GAAAACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTTTGAAACACGAGAATTT
Found at i:3957205 original size:34 final size:35
Alignment explanation
Indices: 3957058--3957216 Score: 157
Period size: 37 Copynumber: 4.5 Consensus size: 35
3957048 ACGTGATTTT
* **
3957058 TTTTTGAAAACACGAAAATTTTCAAAACACCGA-AA
1 TTTTTGAAAACACGAAACTTTTTGAAACA-CGAGAA
*
3957093 TTTTTG-AAACACGGAAA-TTTTTAGAAAATCACGAGGA
1 TTTTTGAAAACAC-GAAACTTTTT-G-AAA-CACGAGAA
* *
3957130 TTTTTG-AAACACGAAATTTTTTTTTAAACACGAGAA
1 TTTTTGAAAACACGAAA--CTTTTTGAAACACGAGAA
*
3957166 TTTTTGAAAACATGAAACTTTTTGAAACACGAGAA
1 TTTTTGAAAACACGAAACTTTTTGAAACACGAGAA
3957201 -TTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
3957217 AATTTTCCAA
Statistics
Matches: 106, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
34 25 0.24
35 26 0.25
36 23 0.22
37 27 0.25
39 5 0.05
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAAACTTTTTGAAACACGAGAA
Found at i:3957352 original size:21 final size:20
Alignment explanation
Indices: 3957326--3957367 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
3957316 CGTTACCTTA
3957326 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
3957347 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
3957367 T
1 T
3957368 CAAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:3957539 original size:5 final size:5
Alignment explanation
Indices: 3957529--3957563 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
3957519 TAAAATTATT
3957529 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
3957564 ATATATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:3957544 original size:20 final size:20
Alignment explanation
Indices: 3957519--3957579 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3957509 CTTTATTTAT
*
3957519 TAAAATTATTTAAAATAAAA
1 TAAAATTATATAAAATAAAA
* *
3957539 TAAAATAAAATAAAATAAAA
1 TAAAATTATATAAAATAAAA
*
3957559 TAAAAATATATAAATATAAAA
1 TAAAATTATATAAA-ATAAAA
3957580 AATATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 28 0.82
21 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAATTATATAAAATAAAA
Found at i:3957571 original size:15 final size:15
Alignment explanation
Indices: 3957538--3957588 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
3957528 TTAAAATAAA
*
3957538 ATAAAAT-AAAATAAA
1 ATAAAATAAAAAT-AT
3957553 ATAAAATAAAAATAT
1 ATAAAATAAAAATAT
3957568 ATAAATATAAAAA-AT
1 ATAAA-ATAAAAATAT
3957583 ATAAAA
1 ATAAAA
3957589 ATGTATGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 12 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAATAAAAATAT
Found at i:3957734 original size:9 final size:9
Alignment explanation
Indices: 3957722--3957841 Score: 98
Period size: 9 Copynumber: 12.7 Consensus size: 9
3957712 ATTGAACCTC
3957722 TTTTTT-TT
1 TTTTTTCTT
* *
3957730 CTTTTTCTC
1 TTTTTTCTT
3957739 TTTTTTCTT
1 TTTTTTCTT
3957748 TTTTTTCTCT
1 TTTTTTCT-T
3957758 TTTTTCTCTTT
1 TTTTT-TC-TT
*
3957769 TCTCTTTTCTC
1 T-T-TTTTCTT
3957780 TTTTTTCTT
1 TTTTTTCTT
* *
3957789 TTTTCTGTT
1 TTTTTTCTT
3957798 TTCTTTTCTT
1 TT-TTTTCTT
*
3957808 TTTCTTCTT
1 TTTTTTCTT
3957817 TTTTTTCTCT
1 TTTTTTCT-T
**
3957827 CCTTTTCTT
1 TTTTTTCTT
3957836 TTTTTT
1 TTTTTT
3957842 TTGCTGGGCT
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
8 5 0.06
9 49 0.56
10 21 0.24
11 6 0.07
12 4 0.05
13 3 0.03
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:3957742 original size:7 final size:7
Alignment explanation
Indices: 3957726--3957838 Score: 89
Period size: 7 Copynumber: 16.6 Consensus size: 7
3957716 AACCTCTTTT
3957726 TTTTCT-
1 TTTTCTC
3957732 TTTTCTC
1 TTTTCTC
*
3957739 TTTTTTC
1 TTTTCTC
3957746 TTTT-T-
1 TTTTCTC
*
3957751 TTTCTCTT
1 TTT-TCTC
3957759 TTTTCTC
1 TTTTCTC
3957766 TTTTCTC
1 TTTTCTC
3957773 TTTTCTC
1 TTTTCTC
*
3957780 TTTTTTC
1 TTTTCTC
*
3957787 TTTTTTC
1 TTTTCTC
3957794 TGTTT-TC
1 T-TTTCTC
3957801 TTTTCT-
1 TTTTCTC
3957807 TTTTCTTC
1 TTTTC-TC
3957815 TTTT-T-
1 TTTTCTC
3957820 TTTCTCTCC
1 TTT-TCT-C
3957829 TTTTCT-
1 TTTTCTC
3957835 TTTT
1 TTTT
3957839 TTTTTGCTGG
Statistics
Matches: 92, Mismatches: 3, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
5 6 0.07
6 22 0.24
7 48 0.52
8 13 0.14
9 3 0.03
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (7 bp):
TTTTCTC
Found at i:3957749 original size:14 final size:14
Alignment explanation
Indices: 3957724--3957818 Score: 99
Period size: 14 Copynumber: 6.8 Consensus size: 14
3957714 TGAACCTCTT
3957724 TTTTTTCTTTTTCTC
1 TTTTTTC-TTTTCTC
3957739 TTTTTTCTTTT-T-
1 TTTTTTCTTTTCTC
3957751 TTTCTCTT-TTTTCTC
1 TTT-T-TTCTTTTCTC
*
3957766 TTTTCTCTTTTCTC
1 TTTTTTCTTTTCTC
*
3957780 TTTTTTCTTTTTTC
1 TTTTTTCTTTTCTC
*
3957794 TGTTTTCTTTTCT-
1 TTTTTTCTTTTCTC
3957807 TTTTCTTCTTTT
1 TTTT-TTCTTTT
3957819 TTTTCTCTCC
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.04
13 10 0.15
14 45 0.66
15 10 0.15
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTTCTC
Found at i:3957831 original size:23 final size:23
Alignment explanation
Indices: 3957720--3957843 Score: 91
Period size: 24 Copynumber: 5.4 Consensus size: 23
3957710 GAATTGAACC
* *
3957720 TCTTTTTTTTCTTTTTCTCTTTT-T
1 TCTTTTTTTTC-TCTCCT-TTTTCT
3957744 TCTTTTTTTTCTCT--TTTTTC-
1 TCTTTTTTTTCTCTCCTTTTTCT
*
3957764 TCTTTTCTCTTT-TCTCTTTTTTCT
1 TCTTTT-T-TTTCTCTCCTTTTTCT
* * *
3957788 TTTTTCTGTTTTCTTTTCTTTTTCT
1 TCTTT-T-TTTTCTCTCCTTTTTCT
3957813 TCTTTTTTTTCTCTCC-TTTTCT
1 TCTTTTTTTTCTCTCCTTTTTCT
3957835 T-TTTTTTTT
1 TCTTTTTTTT
3957844 GCTGGGCTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
20 10 0.12
21 13 0.16
22 10 0.12
23 16 0.19
24 19 0.23
25 15 0.18
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (23 bp):
TCTTTTTTTTCTCTCCTTTTTCT
Found at i:3958101 original size:14 final size:14
Alignment explanation
Indices: 3958079--3958108 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3958069 GTCGGACTAA
3958079 TCAGACGGGTCGGG
1 TCAGACGGGTCGGG
*
3958093 TCAGTCGGGTCGGG
1 TCAGACGGGTCGGG
3958107 TC
1 TC
3958109 GACCCGACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.23, G:0.47, T:0.20
Consensus pattern (14 bp):
TCAGACGGGTCGGG
Found at i:3958555 original size:30 final size:30
Alignment explanation
Indices: 3958502--3958644 Score: 177
Period size: 30 Copynumber: 4.9 Consensus size: 30
3958492 GCCGAAACAA
*
3958502 AATTTTGAGAAAG-TTAGGGGTCAAAATGT
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
*
3958531 AATTTTAAGAAAGTTTACGGGTCAAAATGT
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
* * * *
3958561 AA-TTTAA-AAATTTTAAGGGTTAAAATGC
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
*
3958589 AATTTTGAGAAAGTTTAGGGGTCAAAATGT
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
*
3958619 AATTTT-AGAAAATTTTAGGGGTCAAA
1 AATTTTAAG-AAAGTTTAGGGGTCAAA
3958645 GTGCAAAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
28 19 0.19
29 23 0.23
30 56 0.57
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.34
Consensus pattern (30 bp):
AATTTTAAGAAAGTTTAGGGGTCAAAATGT
Found at i:3958594 original size:58 final size:60
Alignment explanation
Indices: 3958519--3958650 Score: 196
Period size: 58 Copynumber: 2.2 Consensus size: 60
3958509 AGAAAGTTAG
*
3958519 GGGTCAAAATGTAATTTTAAGAAAGTTTACGGGTCAAAATGTAA-TTTA-AAAATTTTAA
1 GGGTCAAAATGCAATTTTAAGAAAGTTTACGGGTCAAAATGTAATTTTAGAAAATTTTAA
* * * *
3958577 GGGTTAAAATGCAATTTTGAGAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAATTTTAG
1 GGGTCAAAATGCAATTTTAAGAAAGTTTACGGGTCAAAATGTAATTTTAGAAAATTTTAA
*
3958637 GGGTCAAAGTGCAA
1 GGGTCAAAATGCAA
3958651 AAAAATTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 40 0.62
59 4 0.06
60 21 0.32
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
GGGTCAAAATGCAATTTTAAGAAAGTTTACGGGTCAAAATGTAATTTTAGAAAATTTTAA
Found at i:3959035 original size:76 final size:75
Alignment explanation
Indices: 3958817--3959445 Score: 899
Period size: 76 Copynumber: 8.3 Consensus size: 75
3958807 CTTTTTATTC
* * * * * * * *
3958817 GAAAAGCAGAAA-TCAAGAATAGCTCGGCGTGCGACTCAAAGCTCAACTCACCTCTCGAAATATG
1 GAAAAACAGAAATTTAA-AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
3958881 AGTTGATTTTT
65 AGTTGATTTTT
* * * * * *
3958892 GAAAAACAAAAATTTAAAAGAAATACCTCAGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAGT
1 GAAAAACAGAAATTT---A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
3958956 ATGAGTTGATTTTTT
62 ATGAGTTGA-TTTTT
* *
3958971 GAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGACTCAACTCACCTATCGCAATATGA
1 GAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
3959036 GTTGATTTTTT
66 GTTGA-TTTTT
3959047 GAAAAACAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
1 GAAAAACAGAAATTT-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
3959112 AGTTGATTTTT
65 AGTTGATTTTT
*
3959123 GAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 G-AAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
3959188 AGTTGATTTTT
65 AGTTGATTTTT
3959199 GAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAAT
1 GAAAAACAGAAATTT---A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
3959262 ATGAGTTGATTTTT
62 ATGAGTTGATTTTT
3959276 GAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
1 G-AAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
3959341 AGTTGATTTTT
65 AGTTGATTTTT
* *
3959352 GAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCAAGACTCAACTCACCTCTCGCAATATG
1 G-AAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
3959417 AGTTGATTTTT
65 AGTTGATTTTT
* *
3959428 G-AAAATAGAAATTGAAAA
1 GAAAAACAGAAATTTAAAA
3959446 ATATTTCTTG
Statistics
Matches: 508, Mismatches: 30, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
74 29 0.06
75 40 0.08
76 238 0.47
77 110 0.22
78 44 0.09
79 46 0.09
80 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (75 bp):
GAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTT
Found at i:3959131 original size:153 final size:154
Alignment explanation
Indices: 3958834--3959432 Score: 937
Period size: 153 Copynumber: 3.9 Consensus size: 154
3958824 AGAAATCAAG
* * * * * *
3958834 AATAGCTCGGCGTGCGACTCAAAGCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAAAC
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
* * * * * *
3958899 AAAAATTTAAAAGAAATACCTCAGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAGTATGAGTT
66 AGAAATTT-AAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
3958963 GATTTTTTG-AAAAACAGAAATTTAA
130 GA-TTTTTGAAAAAACAGAAATTTAA
* *
3958988 AATACCTCAGCGTGCGACCCGAGACTCAACTCACCTATCGCAATATGAGTTGATTTTTTGAAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAA
3959053 CAGAAATTT-AA-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
65 CAGAAATTTAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
3959116 GATTTTTGAAAAAACAGAAATTTAA
130 GATTTTTGAAAAAACAGAAATTTAA
*
3959141 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
3959206 AGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
66 AGAAATTT-AAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
3959269 GATTTTTGAAAAAACAGAAATTTAA
130 GATTTTTGAAAAAACAGAAATTTAA
3959294 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAA
* *
3959359 CAGAAATTT--A-AAATACCTCAGCGTGCGACCCAAGACTCAACTCACCTCTCGCAATATGAGTT
65 CAGAAATTTAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
3959421 GATTTTTGAAAA
130 GATTTTTGAAAA
3959433 TAGAAATTGA
Statistics
Matches: 416, Mismatches: 20, Indels: 20
0.91 0.04 0.04
Matches are distributed among these distances:
150 14 0.03
151 1 0.00
152 87 0.21
153 220 0.53
154 61 0.15
155 33 0.08
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (154 bp):
AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
AGAAATTTAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAAACAGAAATTTAA
Found at i:3959281 original size:229 final size:230
Alignment explanation
Indices: 3958817--3959446 Score: 920
Period size: 229 Copynumber: 2.7 Consensus size: 230
3958807 CTTTTTATTC
* * * * * * * * *
3958817 GAAAAGCAGAAA-TCAAGAATAGCTCGGCGTGCGACTCAAAGCTCAACTCACCTCTCGAAATATG
1 GAAAAACAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
* * * *
3958881 AGTTGATTTTTG-AAAAACAAAAATTTAAAAGAAATACCTCAGCATGTG-TCCGAGGCTCAACTC
66 AGTTGATTTTTGAAAAAACAGAAATTT---A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTC
* *
3958944 ACTTCTCGCAGTATGAGTTGATTTTTTGAAAAACAGAAATTT---AAAATACCTCAGCGTGCGAC
127 ACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAAAAAATACCTCAGCGT-CGAC
3959006 CCGAGACTCAACTCACCTATCGCAATATGAGTTGATTTTTT
190 CCGAGACTCAACTCACCTATCGCAATATGAGTTGATTTTTT
3959047 GAAAAACAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
1 GAAAAACAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
3959112 AGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCT
66 AGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCT
*
3959177 CTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-GACCCGAG
131 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAA-AAATACCTCAGCGTCGACCCGAG
* *
3959241 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
195 ACTCAACTCACCTATCGCAATATGAGTTGATTTTTT
3959276 GAAAAAACAGAAATTT-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 G-AAAAACAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATAT
* *
3959340 GAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCAAGACTCAACTCACC
65 GAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACC
* *
3959405 TCTCGCAATATGAGTTGATTTTTG-AAAATAGAAATTGAAAAA
130 TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAA
3959447 TATTTCTTGA
Statistics
Matches: 370, Mismatches: 22, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
227 1 0.00
228 50 0.14
229 174 0.47
230 61 0.16
231 57 0.15
232 27 0.07
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (230 bp):
GAAAAACAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAAAATACCTCAGCGTCGACCCGAGA
CTCAACTCACCTATCGCAATATGAGTTGATTTTTT
Found at i:3966374 original size:17 final size:17
Alignment explanation
Indices: 3966352--3966598 Score: 160
Period size: 17 Copynumber: 14.1 Consensus size: 17
3966342 CGTGATCCGA
3966352 TTAAAACACGAGAATTT
1 TTAAAACACGAGAATTT
3966369 TTAAAACACGAGAATTT
1 TTAAAACACGAGAATTT
** * ***
3966386 TGGAAACACAATTTTTT
1 TTAAAACACGAGAATTT
* *
3966403 TTAAAAAAACGAAAATTT
1 TT-AAAACACGAGAATTT
* * *
3966421 ATGAAACACGAGATTTTTT
1 TTAAAACACGAGA--ATTT
*
3966440 TTAAAACACGAAAATTT
1 TTAAAACACGAGAATTT
*
3966457 TCAAAACACCGA-AATTT
1 TTAAAACA-CGAGAATTT
*
3966474 TTGAAACACG-GAAATTT
1 TTAAAACACGAG-AATTT
*
3966491 TTAGAAAATCACGAGGATTT
1 TT--AAAA-CACGAGAATTT
* *
3966511 TTGAAACACGA-ATTTTT
1 TTAAAACACGAGA-ATTT
*
3966528 TTTAAACACGAGAATTT
1 TTAAAACACGAGAATTT
*
3966545 TTGAAAACATGA-AACTTT
1 TT-AAAACACGAGAA-TTT
* *
3966563 TTGAAACACGGGAATTT
1 TTAAAACACGAGAATTT
* *
3966580 TGAAAACACGAAAATTT
1 TTAAAACACGAGAATTT
3966597 TT
1 TT
3966599 CCAATTTTAT
Statistics
Matches: 173, Mismatches: 42, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
16 2 0.01
17 113 0.65
18 31 0.18
19 16 0.09
20 10 0.06
21 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.32
Consensus pattern (17 bp):
TTAAAACACGAGAATTT
Found at i:3966427 original size:35 final size:36
Alignment explanation
Indices: 3966366--3966597 Score: 128
Period size: 35 Copynumber: 6.6 Consensus size: 36
3966356 AACACGAGAA
*
3966366 TTTTTAAAACACGAGAATTTTGGAAACAC-A-ATTT
1 TTTTTAAAACACGAAAATTTTGGAAACACGAGATTT
*
3966400 TTTTTAAAAAAACGAAAATTTAT-GAAACACGAGATTT
1 TTTTT-AAAACACGAAAATTT-TGGAAACACGAGATTT
** *
3966437 TTTTTAAAACACGAAAATTTTCAAAACACCGA-A--A
1 TTTTTAAAACACGAAAATTTTGGAAACA-CGAGATTT
* * *
3966471 TTTTTGAAACACGGAAATTTTTAGAAAATCACGAGGA---
1 TTTTTAAAACAC-GAAAATTTT-GGAAA-CACGA-GATTT
* ** ** *
3966508 TTTTTGAAACACGAATTTTTTTTAAACACGAGA-AT
1 TTTTTAAAACACGAAAATTTTGGAAACACGAGATTT
* * * * * *
3966543 TTTTGAAAACATGAAACTTTTTGAAACACGGGA--A
1 TTTTTAAAACACGAAAATTTTGGAAACACGAGATTT
*
3966577 TTTTGAAAACACGAAAATTTT
1 TTTTTAAAACACGAAAATTTT
3966598 TCCAATTTTA
Statistics
Matches: 164, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
33 2 0.01
34 40 0.24
35 58 0.35
36 37 0.23
37 26 0.16
38 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (36 bp):
TTTTTAAAACACGAAAATTTTGGAAACACGAGATTT
Found at i:3966464 original size:36 final size:35
Alignment explanation
Indices: 3966352--3966475 Score: 121
Period size: 35 Copynumber: 3.5 Consensus size: 35
3966342 CGTGATCCGA
* *
3966352 TTAAAACACGAGA--ATTTTTAAAACACGAGAATT
1 TTAAAACACGAGATTTTTTTTAAAACACGAAAATT
* *
3966385 TTGGAAACAC-A-ATTTTTTTTAAAAAAACGAAAATT
1 TT-AAAACACGAGATTTTTTTT-AAAACACGAAAATT
*
3966420 TATGAAACACGAGATTTTTTTTAAAACACGAAAATT
1 T-TAAAACACGAGATTTTTTTTAAAACACGAAAATT
*
3966456 TTCAAAACACCGAAATTTTT
1 TT-AAAACA-CGAGATTTTT
3966476 GAAACACGGA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
32 1 0.01
33 3 0.04
34 11 0.15
35 21 0.28
36 21 0.28
37 18 0.24
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (35 bp):
TTAAAACACGAGATTTTTTTTAAAACACGAAAATT
Found at i:3966728 original size:21 final size:20
Alignment explanation
Indices: 3966702--3966743 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
3966692 CGTTACCTTA
3966702 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
3966723 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
3966743 T
1 T
3966744 CAAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:3966916 original size:5 final size:5
Alignment explanation
Indices: 3966906--3966943 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
3966896 TAAAATTATT
3966906 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TTAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -TAAAA TA
3966944 TATAAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:3967111 original size:9 final size:9
Alignment explanation
Indices: 3967097--3967168 Score: 62
Period size: 9 Copynumber: 8.1 Consensus size: 9
3967087 GAATTGAACC
3967097 TCTTTTTTT
1 TCTTTTTTT
3967106 TC--TTTTT
1 TCTTTTTTT
*
3967113 T-TTTTTTC
1 TCTTTTTTT
*
3967121 TCTTTTTTC
1 TCTTTTTTT
3967130 TCTTTTTTCT
1 TCTTTTTT-T
3967140 T-TTTTCTTT
1 TCTTTT-TTT
*
3967149 TCTTTTTCT
1 TCTTTTTTT
3967158 TCTTTATTTT
1 TCTTT-TTTT
3967168 T
1 T
3967169 TTCTCTCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 6 0.12
8 5 0.10
9 30 0.58
10 11 0.21
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:3967136 original size:25 final size:25
Alignment explanation
Indices: 3967096--3967191 Score: 108
Period size: 25 Copynumber: 3.9 Consensus size: 25
3967086 CGAATTGAAC
3967096 CTCTTTTTTTTC-TTTTTTTTTTTT
1 CTCTTTTTTTTCTTTTTTTTTTTTT
* *
3967120 CTCTTTTTTCTCTTTTTTCTTTTTT
1 CTCTTTTTTTTCTTTTTTTTTTTTT
*
3967145 CT-TTTCTTTTTCTTCTTTATTTTTTT
1 CTCTTT-TTTTTCTT-TTTTTTTTTTT
**
3967171 CTC-TCATTTTCTTTTTTTTTT
1 CTCTTTTTTTTCTTTTTTTTTT
3967192 GCTGGGCTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
24 21 0.35
25 27 0.45
26 12 0.20
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (25 bp):
CTCTTTTTTTTCTTTTTTTTTTTTT
Found at i:3967143 original size:30 final size:31
Alignment explanation
Indices: 3967101--3967186 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 31
3967091 TGAACCTCTT
*
3967101 TTTTTTCTTTTTTTTTTTTCTCTTTT-TTCTC
1 TTTTTTCTTTTTTTCTTTTCT-TTTTCTTCTC
3967132 TTTTTTC-TTTTTTCTTTTCTTTTTCTTCT-
1 TTTTTTCTTTTTTTCTTTTCTTTTTCTTCTC
* *
3967161 TTATTTT-TTTCTCTCATTTTCTTTTT
1 TT-TTTTCTTTTTTTC-TTTTCTTTTT
3967187 TTTTTGCTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.12
30 25 0.52
31 17 0.35
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (31 bp):
TTTTTTCTTTTTTTCTTTTCTTTTTCTTCTC
Found at i:3967170 original size:43 final size:42
Alignment explanation
Indices: 3967099--3967191 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
3967089 ATTGAACCTC
* * * *
3967099 TTTTTTTTCTTTTTTTTTTTTCTCTTTTTTCTCT-TTTTTCTT
1 TTTTTTTTCTTTTTCTTCTTT-ACTTTTTTCTCTCATTTTCTT
*
3967141 TTTTCTTTTCTTTTTCTTCTTTATTTTTTTCTCTCATTTTCTT
1 TTTT-TTTTCTTTTTCTTCTTTACTTTTTTCTCTCATTTTCTT
3967184 TTTTTTTT
1 TTTTTTTT
3967192 GCTGGGCTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
42 18 0.41
43 26 0.59
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (42 bp):
TTTTTTTTCTTTTTCTTCTTTACTTTTTTCTCTCATTTTCTT
Found at i:3967188 original size:21 final size:20
Alignment explanation
Indices: 3967099--3967191 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 20
3967089 ATTGAACCTC
* *
3967099 TTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTCTCTTTTTTCTT
3967119 TCTCTTTTTTCTCTTTTTTCTT
1 T-T-TTTTTTCTCTTTTTTCTT
3967141 TTTTCTTTTCT-TTTTCTTCTT
1 TTTT-TTTTCTCTTTT-TTCTT
*
3967162 TATTTTTTTCTCTCATTTTCTT
1 T-TTTTTTTCTCT-TTTTTCTT
3967184 TTTTTTTT
1 TTTTTTTT
3967192 GCTGGGCTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
20 7 0.11
21 27 0.43
22 27 0.43
23 2 0.03
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTTTCTCTTTTTTCTT
Found at i:3967377 original size:25 final size:25
Alignment explanation
Indices: 3967331--3967378 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3967321 TACGGGCTGT
* ** *
3967331 TTTTTTTTGTTTCTTTTTTTTTTAC
1 TTTTTTTTGCTTAATTTCTTTTTAC
3967356 TTTTTTTTGCTTAATTTCTTTTT
1 TTTTTTTTGCTTAATTTCTTTTT
3967379 TTTTTTGGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTTTTGCTTAATTTCTTTTTAC
Found at i:3967377 original size:26 final size:25
Alignment explanation
Indices: 3967331--3967379 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3967321 TACGGGCTGT
** *
3967331 TTTTTTTTGTTTCTTTTTTTTTTAC
1 TTTTTTTTGTTAATTTCTTTTTTAC
3967356 TTTTTTTTGCTTAATTTCTTTTTT
1 TTTTTTTTG-TTAATTTCTTTTTT
3967380 TTTTTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (25 bp):
TTTTTTTTGTTAATTTCTTTTTTAC
Found at i:3967384 original size:25 final size:23
Alignment explanation
Indices: 3967330--3967384 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
3967320 CTACGGGCTG
**
3967330 TTTTTTTTTGTTTCTTTTTTTTT
1 TTTTTTTTTGTTAATTTTTTTTT
*
3967353 TACTTTTTTTTGCTTAATTTCTTTTT
1 T--TTTTTTTTG-TTAATTTTTTTTT
3967379 TTTTTT
1 TTTTTT
3967385 GGATTGGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 5 0.19
25 9 0.35
26 11 0.42
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.84
Consensus pattern (23 bp):
TTTTTTTTTGTTAATTTTTTTTT
Found at i:3967502 original size:20 final size:20
Alignment explanation
Indices: 3967477--3967538 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
3967467 TATAATAATT
*
3967477 TTCTTT-TTTCTCTTTTTTCC
1 TTCTTTCTTTCTCTTTCTT-C
*
3967497 TTCTTTCTTTTTCTTTCTTC
1 TTCTTTCTTTCTCTTTCTTC
3967517 TTC-TTC-TTC-C-TTCTTC
1 TTCTTTCTTTCTCTTTCTTC
3967533 TTCTTT
1 TTCTTT
3967539 TCTTCTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.24
17 3 0.08
18 2 0.05
19 3 0.08
20 10 0.27
21 10 0.27
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TTCTTTCTTTCTCTTTCTTC
Found at i:3967507 original size:13 final size:15
Alignment explanation
Indices: 3967487--3967545 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 15
3967477 TTCTTTTTTC
3967487 TCTT-TTTTCCTTC-
1 TCTTCTTTTCCTTCT
*
3967500 T-TTCTTTTTCTTTCT
1 TCTTC-TTTTCCTTCT
3967515 TCTTCTTCTTCCTTCT
1 TCTTCTT-TTCCTTCT
3967531 TCTTCTTTT-CTTCT
1 TCTTCTTTTCCTTCT
3967545 T
1 T
3967546 TTGGAAACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 2 0.05
13 1 0.03
14 14 0.36
15 5 0.13
16 17 0.44
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTCTTTTCCTTCT
Found at i:3967510 original size:30 final size:30
Alignment explanation
Indices: 3967475--3967531 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3967465 ACTATAATAA
* *
3967475 TTTTCTTTTTTC-TCTTTTTTCCTTCTTTCT
1 TTTTCTTTCTTCTTC-TTCTTCCTTCTTTCT
3967505 TTTTCTTTCTTCTTCTTCTTCCTTCTT
1 TTTTCTTTCTTCTTCTTCTTCCTTCTT
3967532 CTTCTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTTCTTTCTTCTTCTTCTTCCTTCTTTCT
Found at i:3967519 original size:3 final size:3
Alignment explanation
Indices: 3967496--3967545 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
3967486 CTCTTTTTTC
*
3967496 CTT CTTT CTT TTT CTTT CTT CTT CTT CTT CCTT CTT CTT CTT -TT CTT
1 CTT C-TT CTT CTT C-TT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT
3967543 CTT
1 CTT
3967546 TTGGAAACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:3967687 original size:20 final size:21
Alignment explanation
Indices: 3967628--3967690 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3967618 CCGTCGGAGG
*
3967628 CTCTTCTCTTCTTCTCCTTTCTC
1 CTCTTCT-TT-TTCTCCTTTTTC
* *
3967651 CTC-TATTTCTCTCCTTTTTC
1 CTCTTCTTTTTCTCCTTTTTC
*
3967671 CTCTTCTTTTTCTCTTTTTT
1 CTCTTCTTTTTCTCCTTTTT
3967691 GCAAGTTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.39
21 15 0.45
22 2 0.06
23 3 0.09
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (21 bp):
CTCTTCTTTTTCTCCTTTTTC
Found at i:3967961 original size:30 final size:30
Alignment explanation
Indices: 3967925--3968069 Score: 177
Period size: 30 Copynumber: 4.9 Consensus size: 30
3967915 GCCGAAACAA
*
3967925 AATTTTGAGAAAGTTTAGGGGTCAAAATGT
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
**
3967955 AATTTTGGGAAAGTTTAGGGGTCAAAATGT
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
* * ** *
3967985 AA-TTTAAAAAAATTTAGGGGTTGAAATGG
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
*
3968014 AATTTTAAGAAAGTTTAGGGGTCAAAATGC
1 AATTTTAAGAAAGTTTAGGGGTCAAAATGT
*
3968044 AATTTT-AGAAAATTTTAGGGGTCAAA
1 AATTTTAAG-AAAGTTTAGGGGTCAAA
3968070 GTGCAAAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 24 0.24
30 75 0.76
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (30 bp):
AATTTTAAGAAAGTTTAGGGGTCAAAATGT
Found at i:3968012 original size:59 final size:60
Alignment explanation
Indices: 3967938--3968069 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 60
3967928 TTTGAGAAAG
* ** *
3967938 TTTAGGGGTCAAAATGTAATTTTGGGAAAGTTTAGGGGTCAAAATGTAA-TTTAAAAAAA
1 TTTAGGGGTCAAAATGGAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAAAAAAA
** * *
3967997 TTTAGGGGTTGAAATGGAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAT
1 TTTAGGGGTCAAAATGGAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAAAAAAA
3968057 TTTAGGGGTCAAA
1 TTTAGGGGTCAAA
3968070 GTGCAAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 43 0.69
60 19 0.31
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (60 bp):
TTTAGGGGTCAAAATGGAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAAAAAAA
Found at i:3969664 original size:25 final size:25
Alignment explanation
Indices: 3969604--3969674 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
3969594 CACACGACAA
* *
3969604 CTCTTATGAGCATCCCGATATTTGG
1 CTCTTATGAGCTTCCCAATATTTGG
* *
3969629 CTCTCACGAGCTTCCCAAT-TTATGG
1 CTCTTATGAGCTTCCCAATATT-TGG
*
3969654 CTCTTATGAGCTTCCTAATAT
1 CTCTTATGAGCTTCCCAATAT
3969675 ACAGCTTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.05
25 34 0.92
26 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCAATATTTGG
Found at i:3969713 original size:25 final size:25
Alignment explanation
Indices: 3969685--3969751 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
3969675 ACAGCTTGAT
3969685 TGAGCTTCCTGTTATACAACTCACA
1 TGAGCTTCCTGTTATACAACTCACA
** ** *
3969710 TGAGCTTCCCATTATATGACTCAGA
1 TGAGCTTCCTGTTATACAACTCACA
*
3969735 AGAGCTTCCTGTT-TACA
1 TGAGCTTCCTGTTATACA
3969752 TGCTCGTATG
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
24 2 0.06
25 30 0.94
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (25 bp):
TGAGCTTCCTGTTATACAACTCACA
Found at i:3974274 original size:21 final size:21
Alignment explanation
Indices: 3974248--3974292 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3974238 TCCAACAACC
3974248 TATGTATTTCTCTTATCTTCA
1 TATGTATTTCTCTTATCTTCA
*
3974269 TATGTATTTCTCTTATCTTTA
1 TATGTATTTCTCTTATCTTCA
3974290 TAT
1 TAT
3974293 AACAAACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.60
Consensus pattern (21 bp):
TATGTATTTCTCTTATCTTCA
Found at i:3978743 original size:5 final size:5
Alignment explanation
Indices: 3978733--3978771 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
3978723 TAAACGTATG
3978733 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
3978772 ATGTTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:3985242 original size:22 final size:21
Alignment explanation
Indices: 3985200--3985243 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3985190 GAAAAGGGAG
*
3985200 ATTTTTATTTTTTATTATTTT
1 ATTTTTATTTTTTACTATTTT
* *
3985221 ATTTTTCTTCTTTTACTGTTTT
1 ATTTTTATT-TTTTACTATTTT
3985243 A
1 A
3985244 AAGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (21 bp):
ATTTTTATTTTTTACTATTTT
Done.